# Table of Contents - [LocARNA-2.0.0: Main Page](#locarna-2-0-0-main-page) - [LocARNA-2.0.0: exparna_p](#locarna-2-0-0-exparna-p) - [LocARNA-2.0.0: sparse](#locarna-2-0-0-sparse) - [LocARNA-2.0.0: mlocarna](#locarna-2-0-0-mlocarna) - [LocARNA-2.0.0: locarnate](#locarna-2-0-0-locarnate) - [LocARNA-2.0.0: locarna_p](#locarna-2-0-0-locarna-p) - [LocARNA-2.0.0: locarna](#locarna-2-0-0-locarna) - [LocARNA-2.0.0: Related Pages](#locarna-2-0-0-related-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [Page not found · GitHub Pages](#page-not-found-github-pages) - [LocARNA-2.0.0: Class Members](#locarna-2-0-0-class-members) - [LocARNA-2.0.0: Class Members - Functions](#locarna-2-0-0-class-members-functions) - [LocARNA-2.0.0: Class Members - Enumerations](#locarna-2-0-0-class-members-enumerations) - [LocARNA-2.0.0: Class Members - Related Functions](#locarna-2-0-0-class-members-related-functions) - [LocARNA-2.0.0: Class Members - Variables](#locarna-2-0-0-class-members-variables) - [LocARNA-2.0.0: Class Members - Typedefs](#locarna-2-0-0-class-members-typedefs) - [LocARNA-2.0.0: File Members](#locarna-2-0-0-file-members) - [LocARNA-2.0.0: File Members](#locarna-2-0-0-file-members) - [LocARNA-2.0.0: File Members](#locarna-2-0-0-file-members) - [LocARNA-2.0.0: ChangeLog](#locarna-2-0-0-changelog) - [LocARNA-2.0.0: Class Hierarchy](#locarna-2-0-0-class-hierarchy) - [LocARNA-2.0.0: File List](#locarna-2-0-0-file-list) - [LocARNA-2.0.0: Class Index](#locarna-2-0-0-class-index) - [LocARNA-2.0.0: Class List](#locarna-2-0-0-class-list) - [LocARNA-2.0.0: LocARNA::MultipleAlignment::AliColumn Class Reference](#locarna-2-0-0-locarna-multiplealignment-alicolumn-class-reference) - [LocARNA-2.0.0: Class Hierarchy](#locarna-2-0-0-class-hierarchy) - [LocARNA-2.0.0: src Directory Reference](#locarna-2-0-0-src-directory-reference) - [LocARNA-2.0.0: src/LocARNA/quadmath.hh Source File](#locarna-2-0-0-src-locarna-quadmath-hh-source-file) - [LocARNA-2.0.0: src/Utils Directory Reference](#locarna-2-0-0-src-utils-directory-reference) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Graph Legend](#locarna-2-0-0-graph-legend) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - [LocARNA-2.0.0: Member List](#locarna-2-0-0-member-list) - 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usage](https://s-will.github.io/LocARNA#autotoc_md1) * [More on features and alignment variants](https://s-will.github.io/LocARNA#autotoc_md2) * [Installation](https://s-will.github.io/LocARNA#autotoc_md4) * [Installation from Conda package (recommended)](https://s-will.github.io/LocARNA#autotoc_md5) * [Alternative installation from source](https://s-will.github.io/LocARNA#autotoc_md6) * [Installation from source distribution](https://s-will.github.io/LocARNA#autotoc_md7) * [Installation from the git repository](https://s-will.github.io/LocARNA#autotoc_md8) * [Usage](https://s-will.github.io/LocARNA#autotoc_md10) * [Web server](https://s-will.github.io/LocARNA#autotoc_md12) * [Contact](https://s-will.github.io/LocARNA#autotoc_md14) * [References](https://s-will.github.io/LocARNA#autotoc_md16) LocARNA: Alignment of RNAs ========================== The LocARNA package provides several tools for the structural analysis of RNA. LocARNA's main functionality is to align a set of a priori unaligned RNAs sequences and at the same time predict their common structure. In this way, LocARNA performs simultaneous alignment and folding in the spirit of the classical Sankoff algorithm, but implements strategies to perform this computationally challenging task efficiently and comparably fast. Due to the central ability to simultaneously assess sequence similarity and the similarity of predicted structure, LocARNA is recommends itself for the analysis of RNAs in the twilight zone (around or below 60% sequence identity), where alignments based on only sequence similarity are unreliable. Thus, it could be sometimes easier and typically faster to align highly similar RNAs using pure sequence alignment tools; similarily, RNAs with existing trusted alignments can be more efficiently analyzed based on specialized tools like RNAalifold, R-scape, or Infernal. ### Example of standard usage Most of the package's functionality is accessible via the command-line tool [`mlocarna`](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html) through its various options. In the simplest case, we provide the input sequences in a fasta file. $ mlocarna archaea.fa yields text output and writes results (and intermediary results) to disk; here to folder `archaea.out`. As main result, it produces the alignment of the seven short RNA sequences in [`archaea.fa`](https://raw.githubusercontent.com/s-will/LocARNA/master/Data/Examples/archaea.fa) together with a consensus structure: ![](https://raw.githubusercontent.com/s-will/LocARNA/master/Data/Examples/archaea-aln.png) The graphical RNAalifold-generated output shows the aligned RNAs (with gaps), the consensus structure as dot-bracket string on top, and the column similarities by bars at the bottom. In the way of alifold, columns are color-coded to visualize compensatory and incompatible mutations at predicted base pairs. ### More on features and alignment variants LocARNA distinguishes itself from many other Sankoff-style multiple alignment programs by its high performance (strongly improved in the 2.x line) and low memory complexity, high accuracy, and a broad set of features. As unique features, it offers structure-local alignment, flexible structure constraints and anchor constraints, specialized realignment modes for refining existing alignments, and provides efficient computation of reliabilities in sequence-structure alignment. The package offers a robust core of features and is used as experimental platform for new RNA alignment related methods. Multiple alignment can be performed in one of several different ways: * progressive alignment using sequence-structure alignment of profiles * progressive alignment after consistency transformation using T-Coffee * progressive alignment using probabilistic consistency transformation and sequence-structure profile alignments, optionally followed by iterative refinement. Besides of global alignment, LocARNA supports two kinds of locality. Local alignment as it is known from sequence alignment, identifies and aligns the best matching subsequences. This form of locality is called sequence local to distinguish it from structural locality. When performing structure local alignment, LocARNA identifies and aligns the best matching substructures in the RNAs. The sequences of those substructures can be discontinuous on the sequence level, but remain connected via structural bonds. Alignment Reliabilities (LocARNA-P). In this special, probabilistic mode of operation LocARNA supports the efficient computation of match probabilities, probabilistic consistency transformation for more accurate multiple alignment, and generates reliability profiles of multiple alignments. * * * Installation ------------ The software can be installed on recent Linux or MacOSX systems; Windows is untested but should be supported via WSL. ### Installation from Conda package (recommended) On Mac/Linux, LocARNA is installed most easily via Conda from a pre-compiled package. For this purpose, install Conda and run from the command line: conda install -c conda-forge -c bioconda locarna ### Alternative installation from source Installing from source requires a C++ compiler (GNU C++, Clang, ...) and Autotools. Moreover, it depends on the Vienna RNA package. #### Installation from source distribution Obtain the tar.gz source distribution, e.g. from Github [https://github.com/s-will/LocARNA/releases](https://github.com/s-will/LocARNA/releases) Then, build and install like tar xzf locarna-xxx.tar.gz cd locarna-xxx ./configure --prefix=/usr/local make make install Is Vienna RNA installed in a non-standard location, this has to be specified by configure option \``--with-vrna=path-to-vrna`. Installing from source furthermore allows testing via make check and building documentation locally by make doxygen-doc Building documentation requires additional tools: doxygen, pod2markdown and pandoc. #### Installation from the git repository Installing from repository is possible after cloning and setting up the autotools suite. This is most easily achieved by running autoreconf -i in the cloned repository. Then, the installation essentially works like installing from source distribution. Note that, we will however require additional tools to build the documentation: help2man, pod2man. * * * Usage ----- For instructions on the use of the tools, please see the documentation / man pages of the single tools * [mlocarna](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html) — for multiple alignment of RNAs. This program supports most of the functionality of the package via a high level interface. * [locarna](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html) — for pairwise alignment * [locarna\_p](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html) — for pairwise computation of alignment partition function and (sequence and structure) match probabilities * [sparse](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html) — for structurally stronger sparsified pairwise alignment For additional functionality and special purposes, see * [exparna\_p](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html) — for generating exact matches from the ensembles of two RNAs * [locarnate](https://s-will.github.io/LocARNA/md_src_Utils_locarnate.html) — for multiple alignment of RNAs via T-Coffee. This script offers multiple alignment of RNAs that is performed by sequence-structurally aligning all pairs of RNAs and then using T-Coffee to construct a common multiple alignment out of all pairwise ones. * * * Web server ---------- The core functionality of the package is accessible through a web interface at [http://rna.informatik.uni-freiburg.de](http://rna.informatik.uni-freiburg.de/) * * * Contact ------- Main author and contact: Sebastian Will sebastian.will (at) polytechnique.edu * * * References ---------- * Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology, 3 no. 4 pp. e65, 2007. doi:10.1371/journal.pcbi.0030065 * Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18 no. 5 pp. 900-914, 2012. doi:10.1261/rna.029041.111 * Sebastian Will, Michael Yu, and Bonnie Berger. Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. Genome Research, no. 23 pp. 1018-1027, 2013. doi:10.1101/gr.137091.111 * Sebastian Will, Christina Otto, Milad Miladi, Mathias Mohl, and Rolf Backofen. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 31(15):2489–2496, 2015. doi:10.1093/bioinformatics/btv185 --- # LocARNA-2.0.0: exparna_p LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * 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accuracy trade off:](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md114) * [Output:](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md115) * [Suboptimal traceback:](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md116) * [Constraints:](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md117) * [Miscellaneous:](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md118) * [Input files:](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md119) * [AVAILABILITY](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md120) * [REFERENCES](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md121) * [EXAMPLES](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md122) * [AUTHOR](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md123) * [REPORTING BUGS](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md124) * [COPYRIGHT](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md125) * [SEE ALSO](https://s-will.github.io/LocARNA/md__build_Doc_man_exparna_p.html#autotoc_md126) exparna\_p ========== NAME ==== exparna\_p - manual page for exparna\_p (LocARNA 2.0.0) DESCRIPTION =========== exparna\_p: fast exact structure local matching of RNAs. USAGE: exparna\_p \[options\] exparna\_p performs pairwise matching and folding, i.e. it determines exactly matching local favourable sub-structures that can be simulataneously formed in the input RNAs. Input ----- Input consists of two sequences or alignments, which are specified in fasta, clustal, stockholm, or LocARNA pp format. Optionally, one can specify structure and anchor constraints in these input files. Output ------ The program enumerates exactly matching local substructures (exact pattern matches = EPMs) and optionally chains them. It returns lists of chained and unchained matches, visualizations of the results and anchor constraints for alignment. OPTIONS ======= **\-h**, **–help** : Help **\-V**, **–version** : Version info **\-v**, **–verbose** : Verbose **\-q**, **–quiet** : Quiet Scoring parameters: ------------------- **–no-stacking** : Do not use stacking terms (otherwise needs stacking probs by RNAfold **\-p2**) **–alpha\_1=**(1) : Multiplier for sequential score **–alpha\_2=**(5) : Multiplier for structural score **–alpha\_3=**(5) : Multiplier for stacking score, 0 means no stacking contribution **–struct-mismatch-score=**(**\-10**) : Score for a structural mismatch (nucleotide mismatch in an arcmatch) Heuristics for speed accuracy trade off: ---------------------------------------- **\-p**, **–min-prob=**(0.01) : Minimal probability **–max-bps-length-ratio=**(0.0) : Maximal ratio of #base pairs divided by sequence length (default: no effect) **–max-uil-length-ratio=**(0.0) : Maximal ratio of #unpaired bases in loops divided by sequence length (default: no effect) **–max-bpil-length-ratio=**(0.0) : Maximal ratio of #base pairs in loops divided by loop length (default: no effect) **\-D**, **–max-diff-am=**(30) : Maximal difference for sizes of matched arcs **\-d**, **–max-diff=**(**\-1**) : Maximal difference for alignment traces **–max-diff-at-am=**(**\-1**) : Maximal difference for alignment traces, only at arc match positions **–prob\_unpaired\_in\_loop\_threshold=**(0.01) : Threshold for prob\_unpaired\_in\_\\ loop **–prob\_basepair\_in\_loop\_threshold=**(0.01) : Threshold for prob\_basepair\_in\_\\ loop Output: ------- **\-p**, **–out-min-prob=**(0.0005) : Minimal probability for output (min-prob overrides if smaller) **–output-ps** : Output best EPM chain as colored postscript **\-a**, **–PS\_fileA=**() : Postscript output file for sequence A **\-b**, **–PS\_fileB=**() : Postscript output file for sequence B **\-o**, **–output-locarna=**() : Fasta file with anchor constraints for locarna **–output-anchor-pp=**() : PP files \_A.pp and \_B.pp, merging input PPs and anchor constraints from chaining **–output-clustal=**() : Write file with chain as alignment in clustalw format **–output-epm-list=**() : A list of all found epms **–output-chained-epm-list=**() : A list of all EPMs that are present in the chain **–inexact-struct-match** : Allow inexact structure matches **–add-filter** : Apply an additional filter to enumerate only EPMs that are maximally extended (only inexact) **–no-chaining** : Do not use the chaining algorithm to find best overall chain Suboptimal traceback: --------------------- **–subopt** : Use the suboptimal traceback **–diff-to-opt-score=**(**\-1**) : Threshold for suboptimal traceback **–min-score=**(90) : Minimal score of a traced EPM **–number-of-EPMs=**(100) : Maximal number of EPMs for the suboptimal traceback Constraints: ------------ **–noLP** : use **–noLP** option for folding **–maxBPspan=**(**\-1**) : Limit maximum base pair span (default=off) **–relaxed-anchors** : Relax anchor constraints (default=off) Miscellaneous: -------------- **–stopwatch** : Print run time information. Input files: ------------ > The two input files and specify the input sequences in various, automatically detected formats. Accepted formats are: Fasta, Clustal, Stockholm LocARNA PP, ViennaRNA postscript dotplot. Unless in-loop > > probabilities are provided (only possible in LocARNA PP), base pair : probabilities are computed by partition function folding. Clustal, Stockholm, and PP input can contain constraints. AVAILABILITY ============ The latest LocARNA package release is available online at at Github [https://github.com/s-will/LocARNA](https://github.com/s-will/LocARNA) and [http://www.bioinf.uni-freiburg.de/Software/LocARNA/](http://www.bioinf.uni-freiburg.de/Software/LocARNA/) REFERENCES ========== Christina Otto, Mathias Mohl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, and Sebastian Will. ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinformatics, 15:404, 2014. doi:10.1186/s12859-014-0404-0 EXAMPLES ======== Essentially exparna\_p is called in the same way as locarna and the other pairwise alignemnt tools of the package. Please refer to their documentation. Note that exparna is usually called with single sequences rather than alignments. AUTHOR ====== This man page is written and maintained by Sebastian Will it is part of the LocARNA package. The exparna\_p tool and the library classes for strong ensemble-based sparsification were written by Christina Otto. REPORTING BUGS ============== Report bugs to . COPYRIGHT ========= Copyright 2005- Christina Otto, Sebastian Will. The LocARNA package is released under GNU Public License v3.0 SEE ALSO ======== The LocARNA PP 2.0 format is described online at [http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/](http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/) --- # LocARNA-2.0.0: sparse LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * 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![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) ### Table of Contents * [sparse](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md69) * [NAME](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md70) * [DESCRIPTION](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md71) * [Input, Constraints, and Output](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md72) * [OPTIONS](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md73) * [Scoring parameters:](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md74) * [Partition function representation (for sequence envelopes):](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md75) * [Controlling\_output:](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md76) * [Heuristics for speed accuracy trade off:](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md77) * [MEA score:](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md78) * [Constraints:](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md79) * [Input files:](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md80) * [AVAILABILITY](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md81) * [COPYING (LICENSE)](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md82) * [REFERENCES](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md83) * [AUTHOR](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md84) * [REPORTING BUGS](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md85) * [SEE ALSO](https://s-will.github.io/LocARNA/md__build_Doc_man_sparse.html#autotoc_md86) sparse ====== NAME ==== sparse - manual page for sparse (LocARNA 2.0.0) DESCRIPTION =========== sparse - fast pairwise fast alignment of RNAs. USAGE: sparse \[options\] sparse is an even faster, stronger sparsified pairwise alignment algorithm than locarna. Like locarna, it performs fast simultaneous folding and alignment based on two RNA sequences (or alignments). In addition to the filtering of considered base pairs by their probabilities, it filters by conditional probabilities of bases and base pairs in their enclosing loops. Input, Constraints, and Output ------------------------------ The usage, input, constraints-specifications and output are analogous to locarna; please refer to the help or man page of locarna for explanations and examples. OPTIONS ======= **\-h**, **–help** : Print this help. **–galaxy-xml** : Print galaxy xml wrapper. **\-V**, **–version** : Print only version string. **\-v**, **–verbose** : Be verbose. Prints input parameters, sequences and size information. **\-q**, **–quiet** : Be quiet. Scoring parameters: ------------------- **\-i**, **–indel=**(**\-150**) : Indel score. Score contribution of each single base insertion or deletion. Indel opening score and indel score define the affine scoring of gaps. **\-i**, **–indel-loop=**(**\-300**) : Score for insertions and deletions of loops per base **–indel-opening=**(**\-750**) : Indel opening score. Score contribution of opening an insertion or deletion, i.e. score for a consecutive run of deletions or insertions. Indel opening score and indel score define the affine scoring of gaps. **–indel-opening-loop=**(**\-900**) : Opening score for insertions and deletions of loops **–ribosum-file=**(RIBOSUM85\_60) : File specifying the Ribosum base and base-pair similarities. \[default: use RIBOSUM85\_60 without requiring a Ribosum file.\] **–use-ribosum=**(true) : Use ribosum scores for scoring base matches and base pair matches; note that tau=0 suppresses any effect on the latter. **\-m**, **–match=**(50) : Set score contribution of a base match (unless ribosum scoring). **\-M**, **–mismatch=**(0) : Set score contribution of a base mismatch (unless ribosum scoring). **–unpaired-penalty=**(0) : Penalty for unpaired bases **\-s**, **–struct-weight=**(200) : Maximal weight of 1/2 arc match. Balances structure vs. sequence score contributions. **\-e**, **–exp-prob=** : Expected base pair probability. Used as background probability for base pair scoring \[default: calculated from sequence length\]. **\-t**, **–tau=**(100) : Tau factor. Factor for contribution of sequence similarity in an arc match (in percent). tau=0 does not penalize any sequence information including compensatory mutations at arc matches, while tau=100 scores sequence similarity at ends of base matches (if a scoring matrix like ribosum is used, this adds the contributions for base pair match from the matrix). \[default tau=0!\] **\-E**, **–exclusion=**(0) : Score contribution per exclusion in structure local alignment. Set to zero for unrestricted structure locality. **–stacking** : Use stacking terms (requires stack-probs by RNAfold **\-p2**) **–new-stacking** : Use new stacking terms (requires stack-probs by RNAfold **\-p2**) Partition function representation (for sequence envelopes): ----------------------------------------------------------- **–extended-pf** : Use extended precision for the computation of sequence envelopes. This enables handling significantly larger instances. \[default\] **–quad-pf** : Use quad precision for partition function values. Even more precision than extended pf, but usually much slower (overrides extended-pf). Controlling\_output: -------------------- **\-w**, **–width=**(120) : Width of alignment output. **–clustal=** : Write alignment in ClustalW (aln) format to given file. **–stockholm=** : Write alignment Stockholm format to given file. **–pp=** : Write alignment in PP format to given file. **–alifold-consensus-dp** : Compute consensus dot plot by alifold (warning: this may fail for long sequences). **–consensus-structure=**(alifold) : Type of consensus structures written to screen and stockholm output \[alifold|mea|none\] (default: none). **–consensus-gamma=**(1.0) : Base pair weight for mea consensus computation. For MEA, base pairs are scored by their pair probability times 2 gamma; unpaired bases, by their unpaired probability. **\-L**, **–local-output** : Output only local sub-alignment (to std out). **–local-file-output** : Write only local sub-alignment to output files. **\-P**, **–pos-output** : Output only local sub-alignment positions. **–write-structure** : Write guidance structure in output. **–special-gap-symbols** : Special distinct gap symbols for loop gaps or gaps caused by sparsification **–stopwatch** : Print run time informations. Heuristics for speed accuracy trade off: ---------------------------------------- **\-p**, **–min-prob=**(0.001) : Minimal probability. Only base pairs of at least this probability are taken into account. **–prob-unpaired-in-loop-threshold=**(0.00005) : Threshold for prob\_unpaired\_in\_loop **–prob-basepair-in-loop-threshold=**(0.0001) : Threshold for prob\_basepair\_in\_loop **–max-bps-length-ratio=**(0.0) : Maximal ratio of #base pairs divided by sequence length. This serves as a second filter on the "significant" base pairs. \[default: 0.0 = no effect\]. **–max-uil-length-ratio=**(0.0) : Maximal ratio of #unpaired bases in loops divided by sequence length (def: no effect) **–max-bpil-length-ratio=**(0.0) : Maximal ratio of #base pairs in loops divided by loop length (def: no effect) **\-D**, **–max-diff-am=**(**\-1**) : Maximal difference for sizes of matched arcs. \[-1=off\] **\-d**, **–max-diff=**(**\-1**) : Maximal difference for positions of alignment traces (and aligned bases). \[-1=off\] **–max-diff-at-am=**(**\-1**) : Maximal difference for positions of alignment traces at arc match ends. \[-1=off\] **–max-diff-aln=**() : Maximal difference relative to given alignment (file in clustalw format) **–max-diff-pw-aln=**() : Maximal difference relative to given alignment (string, delim=AMPERSAND) **–max-diff-relax** : Relax deviation constraints in multiple aligmnent **–min-trace-probability=**(1e-5) : Minimal sequence alignment probability of potential traces (probability-based sequence alignment envelope) \[default=1e-4\]. MEA score: ---------- **–mea-alignment** : Perform maximum expected accuracy alignment (instead of using the default similarity scoring). **–match-prob-method=**(0) : Select method for computing sequence-based base match probablities (to be used for mea-type alignment scores). Methods: 1=probcons-style from HMM, 2=probalign-style from PFs, 3=from PFs, local **–probcons-file=** : Read parameters for probcons-like calculation of match probabilities from probcons parameter file. **–temperature-alipf=**(300) : Temperature for the \*/sequence\* alignment/ partition functions used by the probcons-like sequence-based match/trace probability computation (this temperature is different from the \\'physical\\' temperature of RNA folding!). **–pf-struct-weight=**(200) : Structure weight in PF computations (for the computation of sequence-based match probabilties from partition functions). **–mea-gapcost** : Use gap cost in mea alignment **–mea-alpha=**(0) : Weight alpha for MEA **–mea-beta=**(200) : Weight beta for MEA **–mea-gamma=**(100) : Weight gamma for MEA **–probability-scale=**(10000) : Scale for probabilities/resolution of mea score **–write-match-probs=** : Write match probs to file (don\\'t align!). **–read-match-probs=** : Read match probabilities from file. **–write-arcmatch-scores=** : Write arcmatch scores (don\\'t align!) **–read-arcmatch-scores=** : Read arcmatch scores. **–read-arcmatch-probs=** : Read arcmatch probabilities (weighted by factor mea\_beta/100) Constraints: ------------ **–noLP** : Disallow lonely pairs in prediction and alignment. **–maxBPspan=**(**\-1**) : Limit maximum base pair span \[default=off\]. **–relaxed-anchors** : Use relaxed semantics of anchor constraints \[default=strict semantics\]. Input files: ------------ > The tool is called with two input files and , which specify the two input sequences or input alignments. Different input formats (Fasta, Clustal, Stockholm, LocARNA PP, ViennaRNA postscript dotplots) are accepted and automatically recognized (by file content); the two input files can be in different formats. Extended variants of the Clustal and Stockholm formats enable specifying anchor and structure constraints. AVAILABILITY ============ The latest LocARNA package release is available online at at Github [https://github.com/s-will/LocARNA](https://github.com/s-will/LocARNA) and [http://www.bioinf.uni-freiburg.de/Software/LocARNA/](http://www.bioinf.uni-freiburg.de/Software/LocARNA/) COPYING (LICENSE) ================= Copyright 2005- Milad Miladi, Sebastian Will, Christina Otto. The LocARNA package is released under GNU Public License v3.0 REFERENCES ========== Sebastian Will, Christina Otto, Milad Miladi, Mathias M??hl, and Rolf Backofen. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics 31 (15): 2489-2496, 2015. doi:10.1093/bioinformatics/btv185 AUTHOR ====== This man page is written and maintained by Sebastian Will it is part of the LocARNA package. The sparse tool and sparse alignment algorithm is written by Milad Miladi. Library classes for strong ensemble-based sparsification are written by Christina Otto. REPORTING BUGS ============== Report bugs to . SEE ALSO ======== The LocARNA PP 2.0 format is described online at [http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/](http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/) --- # LocARNA-2.0.0: mlocarna LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * 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![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) ### Table of Contents * [mlocarna](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md17) * [NAME](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md18) * [SYNOPSIS](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md19) * [DESCRIPTION](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md20) * [OPTIONS](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md21) * [Load configurations from file](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md22) * [Major alignment modes](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md23) * [Controlling Output](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md24) * [Locality](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md25) * [Pairwise alignment and scoring](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md26) * [Alignment heuristics](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md27) * [Low-level selection of pairwise alignment tools and options](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md28) * [Controlling the guide tree construction](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md29) * [Controlling multiple alignment construction](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md30) * [Further options for probabilistic mode](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md31) * [Miscallaneous modes of operation](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md32) * [Constraints](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md33) * [Rna folding (RNAfold/RNAplfold)](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md34) * [Multithreading](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md35) * [Getting Help](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md36) * [EXAMPLES](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md37) * [Calling mlocarna](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md38) * [Use of constraints](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md39) * [Realignment](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md40) * [AUTHORS](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md41) * [ONLINE INFORMATION](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md42) * [REFERENCES](https://s-will.github.io/LocARNA/md_src_Utils_mlocarna.html#autotoc_md43) mlocarna ======== NAME ==== **MLocARNA** - multiple alignment of RNA SYNOPSIS ======== mlocarna \[options\] DESCRIPTION =========== **MLocarna** computes a multiple sequence-structure alignment of RNA sequences. The structure of these sequences does not have to be known but is inferred based in simultaneous alignment and folding. Generally, mlocarna takes multiple sequences as input, given in a fasta file. The fasta file can be extended to specify structure and anchor constraints that respectively control the possible foldings and possible alignments. The main outcome is a multiple alignment together with a consensus structure. Technically, mlocarna works as front end to the pairwise alignment tools locarna, locarna\_p, and sparse (and even carna), which are employed to construct the multiple alignment progressively. Going beyond the basic progressive alignment scheme, Mlocarna implements probabilistic consistency transformation and iterative alignment, which are available in probabilistic mode. Moreover, the LocARNA package provides an alternative multiple alignment tool "locarnate", which generates alignments based on T-Coffee using (non-probabilistic) consistency transformation. OPTIONS ======= Load configurations from file ----------------------------- * **–configure**\=file Load a parameter set from a configuration file of options and option value pairs. This enables specifying (sets of) default parameters for mlocarna, which can still be modified by other options to mlocarna. Command line arguments always take precedence over this configuration. Options are specified as single entries per line; option value pairs, like option: value. Whitespace and '#'-prefixed comments are ignored. Major alignment modes --------------------- By default, mlocarna performs progressive alignment, where the progressive alignment steps are computed by the pairwise aligner locarna based on sequences and dot plots (RNAfold -p); subsequently, partial alignmetns and their consensus dot plots. * **–probabilistic** In probabilistic mode, mlocarna scores alignments using match probabilities that are computed by a partition function approach \[tech. details: the probability computation is implemented in locarna\_p; the probability-based scoring is performed by locarna in mea mode\]. This enables mlocarna to consistency-transform the probabilities (option –consistency-transform) and to compute reliabilities. The tool reliability-profile.pl is provided to visualize reliability profiles. Reliabilities can also be used for iterating the alignment with reliably aligned base pairs as structural constraints (option –it-reliable-structure). * **–sparse** Apply the sparsified alignment algorithm SPARSE for all pairwise alignments (instead of the default pairwise aligner locarna). SPARSE supports stronger sparsification for faster alignment computation and increases the structure prediction capabilities over locarna. Controlling Output ------------------ * **–tgtdir** Target directory. All output files are written to this directory. Per default the target directory is generated from the input filename by replacing suffix fa by (or appending) out. * **\-v, –verbose** Turn on verbose ouput. Shows progress of computation of all-2-all pairwise alignments for guide tree computation; shows intermediary alignments during the progressive alignment computation. * **–moreverbose** Be even more verbose: additionally shows parameters for the pairwise aligner; moreover, the calls and output of the RNA base pair probability computations as well as the pairwise aligner during progressive alignment. * **\-q, –quiet** Be quiet. * **–keep-sequence-order** Preserve sequence order of the input in the final alignment. Affects output to stdout and results/result.aln. * **–stockholm** Write STOCKHOLM files of all final and intermediate alignments (in addition to CLUSTALW files). * **–consensus-structure** Type of consensus structures written to stockholm output (and screen in verbose modes) \[alifold|mea|none\] (default: none). This includes intermediate alignments of the progressive multiple alignment. If not explicitly specified othwise, the option alifold-consensus-dp implicitly sets this to alifold. Note that the alifold consenus of the final alignment is computed and printed, regardless of this option. * **\-w, –width**\=columns (120) Output width for sequences in clustal-like and stockholm output; note that the clustalw standard format requires 60 or less. * **–write-structure** Write guidance structure in output to stdout. This provides some insight into the influence of structure into the generated pairwise alignments. The guidance structure shows the base pairs 'predicted' by each pairwise locarna (or sparse) alignment. These structures should not be mistaken as predicted consensus structures of multiple alignments. Consensus structures can be more adequately derived from the multiple alignment. For this reason, mlocarna reports the consensus structure by RNAalifold. Locality -------- * **–free-endgaps** Allow free endgaps. (Corresponds to pairwise locarna option –free-endgaps "++++".) * **–free-endgaps-3** Allow free endgaps 3'. * **–free-endgaps-5** Allow free endgaps 5'. * **–sequ-local**\=bool (false) Turns on/off sequence locality \[def=off\]. Sequence locality refers to the usual form of local alignment. If on, mlocarna bases all calculations on local pairwise alignments, which determin the best alignments of subsequences (disregarding dissimilar starts and ends). Note that truely local structure alignments as well as local multiple alignments are still a matter of research; so don't expect perfect results in all instances. * **–struct-local**\=bool (false) Turns on/off structure locality \[def=off\]. Structural locality enables skipping entire substructures in alignments. In pairwise alignments, this allows one exclusion of some subsequence in each loop; thus, guaranteeing that the (structure locally) aligned parts of the sequences are always connected w.r.t. the predicted structure but not necessarily consecutive in the sequence. Structure locality does not imply sequence locality, but rather the two concepts are orthogonal. * **–penalized**\=score Variant of sequence local alignment (cf. –sequ-local), where the specified penalty score is subtracted for each base in the local alignment. \[Experimental\] Pairwise alignment and scoring ------------------------------ * **–indel=score** (-150) Score of each single base insertion or deletion. * **–indel-opening**\=score (-750) Score of opening an insertion or deletion, i.e. score for a consecutive run of deletions or insertions. Indel opening score and indel score define the affine scoring of gaps. * **\-m, –match**\=score (50) Score of a base match (unless ribosum-based scoring) * **\-M, –mismatch**\=score (0) Score of a base mismatch (unless ribosum-based scoring) * **–use-ribosum**\=bool (true) Use ribosum scores for scoring base matches and base pair matches; note that tau=0 suppresses any effect on the latter. * **–ribosum-file**\=file File specifying the Ribosum base and base-pair similarities. \[default: use RIBOSUM85\_60 without requiring a Ribosum file.\] * **\-s, –struct-weight**\=score (200) Maximum weight of one predicted arc, aka base pair. Note that this means that the maximum weight of an arc match is twice as high. The maximum weight is assigned to base pairs with (almost) probability 1 in the dot plot; less probable base pairs receive gradually degrading scores. The struct-weight factor balances the score contribution from structure to the score contribution from base similarity scores (e.g. ribosum scores). * **\-e, –exp-prob**\=prob Expected probability of a base pair. * **\-t, –tau**\=factor (0) Tau factor in percent. The tau factor controls the contribution of sequence-dependent scores to the score of arc matches. * **\-E, –exclusion**\= (0) Weight of an exclusion, i.e. an ommitted subsequence in a loop, which applies only to structural local alignment. * **–stacking** Use stacking terms. In this case, stacked arcs are scored based on conditional probabilities (conditioned by their stacked inner arc) rather than unconditioned base pair probabilities. \[Experimental\] * **–new-stacking** Use new stacking terms; cf. –stacking. These terms directly award bonuses to stacking. \[Experimental\] Alignment heuristics -------------------- Several parameters are available to speed up the pairwise alignment computations heuristically. Choosing these parameters reasonably is necessary to achieve good trade-off between speed and accuracy, especially for large alignment instances. * **\-p, –min-prob**\=probability (0.001) Minimum base pair / arc probability. Arc with lower probability in the input RNA structure ensembles are ignored. * **\-P, –tree-min-prob**\=probability Minimal prob for constructing guide tree. This probability can be set separately for the all-2-all comparison for constructing the guide tree and the progressive/iterative alignment steps. * **–max-bps-length-ratio**\=factor (0.0) Maximal ratio of the number of base pairs divided by sequence length (default: no effect) * **\-D, –max-diff-am**\=difference Maximal difference for lengths of matched arcs. Two arcs that have a higher difference of their lengths are ignored. This speeds up the alignment, since less arc comparisons (i.e. less DP matrices) have to be computed. \[def: off/-1\] * **\-d, –max-diff**\=difference Maximal difference of the positions of any two bases that are considered to be aligned. Bases with higher difference are generally not aligned. This allows banding of the DP matrices and thus can result in high speed ups. Note that the semantic changes in the context of a reference alignment specified with max-diff-aln. Then, the difference to the reference alignment is restricted. \[def: off/-1\] * **–max-diff-at-am**\=difference Same restriction as max-diff but only at the ends of arcs in arc matches. \[def: off/-1\] * **–min-trace-probability**\=probability Minimal sequence alignment probability of potential traces (probability-based sequence alignment envelope) \[default=1e-4, moderate filter\]. * **–max-diff-aln**\=file Computes "realignment" in the environment of the given reference alignment (file in clustalw format) by constraining the maximum difference to this reference (controlled by –max-diff). The input sequences (and their names) have to be identical to these alignment sequences; however the alignment is allowed to contain extra sequences, which are ignored. In combination with option –realign, the reference alignment is taken from the (main) input file. In this case, the 'file' argument should be '.', but is ignored (with warning) otherwise. * **–max-diff-relax** Relax deviation constraints (cf. –max-diff-aln) in multiple aligmnent. This option is useful if the default strategy for realignment fails. * **\-a, –min-am-prob**\=probability (0.001) Minimum arc-match probability (filters output of locarna-p) * **\-b, –min-bm-prob**\=probability (0.001) Minimum base-match probability (filters output of locarna-p) Low-level selection of pairwise alignment tools and options ----------------------------------------------------------- * **–pw-aligner** Utilize the given tool for computing pairwise alignments (def=locarna). * **–pw-aligner-p**\=tool Utilize the given tool for computing partition function pairwise alignments (def=locarna\_p). * **–pw-aligner-options** Additional option string for the pairwise alignment tool (def=""). * **–pw-aligner-p-options** Additional option string for the partition function pairwise alignment tool (def=""). Controlling the guide tree construction --------------------------------------- * **–treefile**\=file File with guide tree in NEWICK format. The given tree is used as guide tree for the progressive alignment. This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree. * **–similarity-matrix**\=file File with similarity matrix. The similarities in the matrix are used to construct the guide tree for the progressive alignment. This saves the calculation of pairwise all-vs-all similarities. * **–score-lists** Construct the guide tree from pairwise scores in files scores\* in the subdirectory scores of the target directory. The scores are typically precomputed, possibly in a distributed way, using –compute-pairwise-scores. * **–compute-pairwise-scores**\=k/N Compute only the pairwise alignments for the guide tree construction. Write scores to the file $tgtdir/scores/scores-$k and terminate. By computing only the k-th fraction of N parts, the option supports distributing the computation of the alignments. Before computing the pairwise scores, the dot plot files should be precomputed using –only-dps. (see also: –score-lists) * **–graphkernel** Use the graphkernel for constructing the guide tree. * **–svmsgdnspdk**\=program Specify the svmsgdnspdk program (potentially including path). Default: use "svmsgdnspdk" in path. * **–fasta2shrep**\=program Program "fasta2shrep" for generating graphs from the input sequences for use with the graph kernel guide tree generation (potentially including path). Default: use "fasta2shrep\\\_gspan.pl" in path. * **–fasta2shrep-options**\=argument-string Command line arguments for fasta2shrep. Default: "-wins 200 -shift 50 \\-stack -t 3 -M 3". Controlling multiple alignment construction ------------------------------------------- * **–alifold-consensus-dp** Employs **RNAalifold -p** for generating consensus dotplot after each progressive alignment step. This replaces the default consensus dotplot computation, which averages over the input dot plots. This method should be used with care in combination with structural constraints, since it ignores them for all but the pairwise alignments of single sequences. Furthermore, note that it does not support **–stacking** or **–new-stacking**. * **–max-alignment-size**\=size Limit the maximum number of sequences that are aligned together by progressive alignment. This can be used to save unnecessary computations, when producing a clustering of the input RNAs rather than constructing a single multiple alignment. \[default: no limit\]. * **–local-progressive** Align only the subalignment of locally aligned subsequences in subsequent steps of the progressive multiple alignment. Note: this is only effective if local alignment is turned on. (Default for sequence local alignment; turn off by **–global-progressive**) * **–global-progressive** Use alignments including "locality gaps" in subsequent steps of the progressive multiple alignment. Note: this is only effective if local alignment is turned on. (Opposite of **–local-progressive**) * **–consistency-transformation** Apply probabilistic consistency transformation (only possible in probabilistic mode). * **–iterate** Refine iteratively after progressive alignment. Currently, iterative refinement optimizes the SCI or RELIABILITY (not the locarna score)! Iterative refinement realigns all binary splits along the guide tree. * **–iterations**\=number Refine iteratively for given number of iterations (or stop at convergence). * **–it-reliable-structure**\=number Iterate alignment times with reliable structure. This works only in probabilistic mode, when reliabilities can be computed. Further options for probabilistic mode -------------------------------------- * **–pf-only-basematch-probs** Use only base match probabilities (no base pair match probabilities). * **–extended-pf** Use extended precision for partition function values. This increases run-time and space (less than 2x), however enables handling significantly larger instances. * **–quad-pf** Use quad precision for partition function values. Even more precision than extended pf, but usually much slower (overrides extended-pf). * **–pf-scale= Scale of partition function; use for avoiding overflow in larger instances. * **–fast-mea** Compute base match probabilities using Gotoh PF-algorithm. * **–mea-alpha** Weight of unpaired probabilities in fast mea mode. * **–mea-beta** Weight of base pair match contribution in probabilistic mode. * **–mea-gamma** Reserved parameter for fast-mea mode. * **–mea-gapcost** Turn on gap penalties in probabilistic/mea mode (default: off). * **–write-probs** / **–no-write-probs** Write / don't write probabilities (of base matches and arc matches) to the target directory. Override by single options –(no-)write-bm-probs and –(no-)write-am-probs is possible. Use this to make the probability files available for post-processing. (default: don't write). * **–write-bm-probs** / **–no-write-bm-probs** Don't write / Write base match probabilities to files in target dir (default: don't write). * **–write-am-probs** / **–no-write-am-probs** Don't write / Write arc match probabilities to files in target dir (default: don't write). Miscallaneous modes of operation -------------------------------- * **–realign** Realignment mode. In this mode, the input must be in clustal format and is interpreted as alignment of the input sequences; the sequences are obtained by removing all gap symbols. Moreover, the given alignment is set as reference alignment for –max-diff-aln. Structure and anchor constraints can be specified as consensus constraints in the input; constraints are specified as 'alignment strings' with names 'A1', 'S', or 'FS' for anchor, structure, or fixed structure constraints, respectively. Characters in the 'A1' anchor specification other than '-' and '.' constrain the aligned residues in the respective column to remain aligned (blanks are disallowed; annotations 'A2', 'A3', ... are ignored). The consensus structure constraint is equivalent to constraining each single sequence by the projection of the consensus constraint to the sequence (removing all base pairs with at least one gapped end). * **–dp-cache**\=directory Use directory as cache for dot plot or pp files (useful for avoiding multiple computation). * **–only-dps** Compute only the pair probability files / dot plots, don't align (useful for filling the dp-cache). * **–evaluate**\=file Evaluate the given multiple alignment (clustalw aln format, or use --eval-fasta). This requires that probailities are already computed (mlocarna –probabilistic) and present in the target directory (–tgtdir). * **–eval-fasta** Assume that alignment for evaluation (cf. –evaluate) is in fasta format. Constraints ----------- * **–anchor-constraints= Read anchor constraints from bed format specification. Anchor constraints in four-column bed format specify positions of named anchor regions per sequence. The 'contig' names have to correspond to the fasta input sequence names. Anchor names must be unique per sequence and regions of the same name for different sequences must have the same length. This constrains the alignment to align all regions of the same name. The specification of anchors via this option removes all anchor definitions that may be given directly in the fasta input file! * **–ignore-constraints** Ignore all constraints (anchor and structure constraints) even if given. Rna folding (RNAfold/RNAplfold) ------------------------------- * **–noLP** / **–LP** Disallow/Allow lonely pairs (default: Disallow). * **–maxBPspan** Limit maximum span of base pairs (default off). * **–relaxed-anchors** Relax semantics of anchor constraints (default off, meaning 'strict' semantics). For lexicographically ordered anchors, where each sequence is annotated with exactly the same names, both semantics are equivalent; thus, in this common case, the subtle differences can be ignored. In strict semantics, anchor names must be ordered lexicographically and can only be aligned in this order. In relaxed semantics, the only requirement is that equal anchor names are matched. Consequently, anchor names that don't occur in all sequences could be overwritten (if two names are assigned to the same position) or even introduce inconsistencies. * **–plfold-span=span** Use RNAplfold with span. * **–plfold-winsize=ws** Use RNAplfold with window of size ws (default=2\*span). * **–rnafold-parameter= Parameter file for RNAfold (RNAfold's -P option) * **–rnafold-temperature= Temperature for RNAfold (RNAfold's -T option) * **–skip-pp** Skip computation of pair probs if the probabilities are already existing. Non-existing ones are still computed. * **–no-bpp-precomputation** Switch off precomputation of base pair probabilties. Overwrite potentially existing input files. (compare skip-pp). For use with special pairwise aligners (e.g. locarna\_n) that recompute the base pair probabilities at each invokation. * **–in-loop-probabilities** Turn on precomputation of in loop probabilties. For use with special pairwise aligners (e.g. locarna\_n) that use such probabilities. Multithreading -------------- * **–threads, –cpus**\=number Use the given number of threads for computing pair probabilities and all-2-all alignments in parallel (multicore/processor support). Be aware: mlocarna seems not to scale well for more than a few threads (often only 2 or 3). Using more threads is often detrimental, since it strongly increases memory consumption due to the current perl threading implementation. This unfortunate behavior seems hard to improve without major rewrite of the software. Getting Help ------------ * **–help** Brief help message * **–man** Full documentation The sequences are given in input file in mfasta format. All results are written to a target directory . If the file tree is given, contained tree (in NEWICK-tree format) is used as guide tree for the progressive alignment. The final results are collected in /results. The final multiple alignment is /results/result.aln. EXAMPLES ======== Calling mlocarna ---------------- \[Note that the LocARNA distribution provides files of the following and other examples in Data/Examples.\] Sequences are typically given in plain fasta format like example.fa ---------------------------------------- >fruA CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG >fdhA CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG >vhuU AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU ---------------------------------------- To align these sequences, simply call mlocarna example.fa Usually, it makes sense to set additional options; this is either done on the command line or via configuration files. A reasonable small configuration for global alignment of large instances would be short-example.cfg ---------------------------------------- max-diff-am: 25 max-diff: 60 min-prob: 0.01 plfold-span: 100 indel: -50 indel-open: -750 threads: 8 # <- adapt to your hardware alifold-consensus-dp ---------------------------------------- To use it, call mlocarna --config short-example.cfg example.fa which is equivalent to mlocarna --max-diff-am 25 --max-diff 60 --min-prob 0.01 \\ --indel -50 --indel-open -750 \\ --plfold-span 100 --threads 8 --alifold-consensus-dp \\ example.fa For probabilistic alignment with consistency transformation, call mlocarna --probabilistic --consistency-transform example.fa In both cases, mlocarna writes the main results to stdout and more detailed results to the target directory example.out. The results directory is overwritten if it exists already. To avoid this, one can specify the target directory (–tgtdir). Use of constraints ------------------ Mlocarna supports structure constraints for folding and anchor constraints for alignment. Both types of constraints can be specified in extension of the standard fasta format via 'constraint lines'. Fasta-ish input with constraints looks like this example-w-constraints.fa ---------------------------------------- >A GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA ..((.(....xxxxxx...................))).xxx #S ..........000000.......................111 #1 ..........123456.......................123 #2 >B ACGGAGGGAAAGCAAGCCUUCUGCGACA .(((....xxxxxx.......))).xxx #S ........000000...........111 #1 ........123456...........123 #2 ---------------------------------------- The same anchor constraints (like by the lines tagged #1, #2) can alternatively be specified in bed format by the entries example-anchors.bed ---------------------------------------- A 10 16 first\_box B 8 14 first\_box A 39 42 ACA-box B 25 28 ACA-box ---------------------------------------- where anchor regions (boxes) have arbitrary but matching names and contig/sequence names correspond to the sequence names of the fasta(-like) input. Given, e.g. example-wo-anchors.fa ---------------------------------------- >A GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA ..((.(....xxxxxx...................))).xxx #S >B ACGGAGGGAAAGCAAGCCUUCUGCGACA .(((....xxxxxx.......))).xxx #S ---------------------------------------- one calls mlocarna --anchor-constraints example-anchors.bed example-wo-anchors.fa Realignment ----------- In realignment mode (option –realign), mlocarna is called with an input alignment in clustal format, e.g. mlocarna --realign example-realign.aln This allows to define constraints as 'consensus constraints' in the input, e.g. example-realign.aln ---------------------------------------- CLUSTAL W fruA --CCUCGAGGGGAACCCGAA-------------AGGGACCCGAGAGG-- vhuU AGCUCACAACCGAACCCAUU-------------UGGGAGGUUGUGAGCU fdhA CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG #A1 ..\*...........CCC.............................5.. #S ((((((.((((...(((.................))).)))).)))))) ---------------------------------------- Note that anchor names are arbitrary and the consensus structure is 'projected' to the single sequences. Moreover, the input alignment can be used as reference for fast limited realignment, e.g. call to realign in distance 5 of the reference alignment: mlocarna --realign example-realign.aln --max-diff 5 --max-diff-aln . AUTHORS ======= Sebastian Will Christina Otto (ExpaRNA-P, sparsification classes for ExpaRNA-P and SPARSE) Milad Miladi (SPARSE) ONLINE INFORMATION ================== For download and online information, see [https://github.com/s-will/LocARNA](https://github.com/s-will/LocARNA) and [http://www.bioinf.uni-freiburg.de/Software/LocARNA](http://www.bioinf.uni-freiburg.de/Software/LocARNA) . Latest releases are available as source code on Github at [https://github.com/s-will/LocARNA/releases](https://github.com/s-will/LocARNA/releases) . REFERENCES ========== Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology, 3 no. 4 pp. e65, 2007. doi:10.1371/journal.pcbi.0030065 Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18 no. 5 pp. 900-914, 2012. doi:10.1261/rna.029041.111 Sebastian Will, Michael Yu, and Bonnie Berger. Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. Genome Research, no. 23 pp. 1018-1027, 2013. doi:10.1101/gr.137091.111 --- # LocARNA-2.0.0: locarnate LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * 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pairwise aligners and TCoffee as a multiple alignment tool AUTHORS ======= Niklas Meinzer <[meinz.nosp@m.ern@.nosp@m.infor.nosp@m.mati.nosp@m.k.uni.nosp@m.\-fre.nosp@m.iburg.nosp@m..de](https://s-will.github.io/LocARNA/md_src_Utils_locarnate.html#) OPTIONS ======= * **–pairwise\_parameters** parameters for the pairwise alignment step * **–tcoffee\_params** parameters for tcoffee * **–pp\_calculator\_params** parameters for locarna\_rnafold\_pp * **–output** path to output folder * **–library-only** if given only a t-coffee library will be written without actual computation * **–library-name** the file name of the produced t-coffee library (default: "input.lib") * **–additional-libraries** a comma separated list of paths to t-coffee library files that should be given to t-coffee in addition to the one generated during this run * **–pairwise\_aligner** which pairwise aligner to use (default: locarna) * **–scaling\_factor** each edge from each EPM gets the same weight (exparnap only!) * **–help** display this help message and exit --- # LocARNA-2.0.0: locarna_p LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * 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 [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) ### Table of Contents * [locarna\_p](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md87) * [NAME](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md88) * [DESCRIPTION](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md89) * [Input and Constraints](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md90) * [Output](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md91) * [OPTIONS](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md92) * [Scoring parameters:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md93) * [Partition function representation:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md94) * [Output:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md95) * [Heuristics for speed accuracy trade off:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md96) * [Computed probabilities:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md97) * [Constraints:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md98) * [Input files:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md99) * [DISCLAIMER](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md100) * [AVAILABILITY](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md101) * [COPYING (LICENSE)](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md102) * [REFERENCES](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md103) * [EXAMPLES](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md104) * [AUTHOR](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md105) * [REPORTING BUGS](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna_p.html#autotoc_md106) locarna\_p ========== NAME ==== locarna\_p - manual page for locarna\_p (LocARNA 2.0.0) DESCRIPTION =========== locarna\_p - pairwise partition function of RNA alignments. Computes base and base pair match probabilities from alignment partitition functions. USAGE: locarna\_p \[options\] locarna\_p computes sequence and structure match probabilities from partition functions of locarna pairwise alignments, i.e. from fast simultaneous folding and alignment based on two RNA sequences (or alignments). Input and Constraints --------------------- Please see the documentation of locarna for inputs and the possible constraints specifications. Output ------ Probabilities of base and base pair matches can be written to files. (The total partition function is reported to standard out.) OPTIONS ======= **\-h**, **–help** : Print this help. **\-V**, **–version** : Print only version string. **\-v**, **–verbose** : Be verbose. Prints input parameters, sequences and size information. **\-q**, **–quiet** : Be quiet. Scoring parameters: ------------------- **\-i**, **–indel=**(**\-150**) : Indel score. Score contribution of each single base insertion or deletion. Indel opening score and indel score define the affine scoring of gaps. **–indel-opening=**(**\-750**) : Indel opening score. Score contribution of opening an insertion or deletion, i.e. score for a consecutive run of deletions or insertions. Indel opening score and indel score define the affine scoring of gaps. **–ribosum-file=**(RIBOSUM85\_60) : File specifying the Ribosum base and base-pair similarities. \[default: use RIBOSUM85\_60 without requiring a Ribosum file.\] **–use-ribosum=**(true) : Use ribosum scores for scoring base matches and base pair matches; note that tau=0 suppresses any effect on the latter. **\-m**, **–match=**(50) : Set score contribution of a base match (unless ribosum scoring). **\-M**, **–mismatch=**(0) : Set score contribution of a base mismatch (unless ribosum scoring). **\-s**, **–struct-weight=**(200) : Maximal weight of 1/2 arc match. Balances structure vs. sequence score contributions. **\-e**, **–exp-prob=** : Expected base pair probability. Used as background probability for base pair scoring \[default: calculated from sequence length\]. **\-t**, **–tau=**(50) : Tau factor. Factor for contribution of sequence similarity in an arc match (in percent). tau=0 does not penalize any sequence information including compensatory mutations at arc matches, while tau=100 scores sequence similarity at ends of base matches (if a scoring matrix like ribosum is used, this adds the contributions for base pair match from the matrix). \[default tau=0!\] **–temperature-alipf=**(300) : Temperature for the \*/sequence\* alignment/ partition functions used by the probcons-like sequence-based match/trace probability computation (this temperature is different from the \\'physical\\' temperature of RNA folding!). Partition function representation: ---------------------------------- **–pf-scale=**(1.0) : Factor for scaling the partition functions. Use in order to avoid overflow. **–extended-pf** : Use extended precision for partition function values. This increases run-time and space (less than 2x), however enables handling significantly larger instances. **–quad-pf** : Use quad precision for partition function values. Even more precision than extended pf, but usually much slower (overrides extended-pf). Output: ------- **–write-arcmatch-probs=** : Write arcmatch probabilities **–write-basematch-probs=** : Write basematch probabilities **\-a**, **–min-am-prob=**(0.001) : Minimal arc match probability. Write probabilities for only the arc matchs of at least this probability. **\-b**, **–min-bm-prob=**(0.001) : Minimal base match probability. Write probabilities for only the base matchs of at least this probability. **–include-am-in-bm** : Include arc match cases in base match probabilities **–stopwatch** : Print run time informations. Heuristics for speed accuracy trade off: ---------------------------------------- **\-p**, **–min-prob=**(0.001) : Minimal probability. Only base pairs of at least this probability are taken into account. **–max-bps-length-ratio=**(0.0) : Maximal ratio of #base pairs divided by sequence length. This serves as a second filter on the "significant" base pairs. \[default: 0.0 = no effect\]. **\-D**, **–max-diff-am=**(**\-1**) : Maximal difference for sizes of matched arcs. \[-1=off\] **\-d**, **–max-diff=**(**\-1**) : Maximal difference for positions of alignment traces (and aligned bases). \[-1=off\] **–max-diff-at-am=**(**\-1**) : Maximal difference for positions of alignment traces at arc match ends. \[-1=off\] **–max-diff-aln=**() : Maximal difference relative to given alignment (file in clustalw format) **–max-diff-pw-aln=**() : Maximal difference relative to given alignment (string, delim=AMPERSAND) **–max-diff-relax** : Relax deviation constraints in multiple aligmnent **–min-trace-probability=**(1e-5) : Minimal sequence alignment probability of potential traces (probability-based sequence alignment envelope) \[default=1e-4\]. Computed probabilities: ----------------------- **–fragment-match-probs=**<"i j k l">() : Requests probabilities for the match of fragments \[i..j\] and \[k..l\]. Accepts a \\';\\' separated list of ranges. Constraints: ------------ **–maxBPspan=**(**\-1**) : Limit maximum base pair span \[default=off\]. **–relaxed-anchors** : Use relaxed semantics of anchor constraints \[default=strict semantics\]. Input files: ------------ > The tool is called with two input files and , which specify the two input sequences or input alignments. Different input formats (Fasta, Clustal, Stockholm, LocARNA PP, ViennaRNA postscript dotplots) are accepted and automatically recognized (by file content); the two input files can be in different formats. Extended variants of the Clustal and Stockholm formats enable specifying anchor and structure constraints. DISCLAIMER ========== locarna\_p is a low level tool; most often this tool is used indirectly, by calling mlocarna with \*\*–probabilistic. Note that the performance of locarna\_p (as well as basically all tools in the LocARNA package) is often significantly improved by the use of suitable application-specific options, deviating from the default settings. AVAILABILITY ============ The latest LocARNA package release is available online at at Github [https://github.com/s-will/LocARNA](https://github.com/s-will/LocARNA) and [http://www.bioinf.uni-freiburg.de/Software/LocARNA/](http://www.bioinf.uni-freiburg.de/Software/LocARNA/) COPYING (LICENSE) ================= Copyright 2005- Sebastian Will. The LocARNA package is released under GNU Public License v3.0 REFERENCES ========== Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18 no. 5 pp. 900-914, 2012. doi: 10.1261/rna.029041.111 EXAMPLES ======== Please see the documentation of locarna for call and input constraint examples. AUTHOR ====== This man page is written and maintained by Sebastian Will it is part of the LocARNA package. First versions of locarna\_p and its aligner class were written by Tejal Joshi. REPORTING BUGS ============== Report bugs to . --- # LocARNA-2.0.0: locarna LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * 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 [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) ### Table of Contents * [locarna](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md44) * [NAME](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md45) * [DESCRIPTION](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md46) * [Input](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md47) * [Constraints](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md48) * [Output](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md49) * [OPTIONS](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md50) * [Scoring parameters:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md51) * [Partition function representation (for sequence envelopes):](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md52) * [Locality:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md53) * [Output:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md54) * [Heuristics for speed accuracy trade off:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md55) * [Special sauce options:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md56) * [MEA score:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md57) * [Constraints:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md58) * [Input files:](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md59) * [DISCLAIMER](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md60) * [REFERENCES](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md61) * [AVAILABILITY](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md62) * [EXAMPLES](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md63) * [Constraint Examples](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md64) * [AUTHOR](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md65) * [REPORTING BUGS](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md66) * [COPYRIGHT](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md67) * [SEE ALSO](https://s-will.github.io/LocARNA/md__build_Doc_man_locarna.html#autotoc_md68) locarna ======= NAME ==== LocARNA - manual page for LocARNA 2.0.0 DESCRIPTION =========== locarna - pairwise (global and local) alignment of RNA. USAGE: locarna \[options\] locarna is the pairwise alignment tool of the LocARNA package, which performs fast simultaneous folding and alignment based on two RNA sequences (or alignments). Input ----- Input consists of two sequences or alignments, which are specified in fasta, clustal, stockholm, or LocARNA pp format. Optionally, structure and anchor constraints can be specified in the input files. If alignments are given in the input, they are aligned without revising the gap structure within the given alignments. Unless specified, base pair probabilities of the input sequences or alignments are predicted using the ViennaRNA package. Optionally, base pair probability information can be passed for one or both input sequences (or alignments) using the input formats LocARNA PP 2.0 or ViennaRNA postscript dotplot format. Constraints ----------- Anchor and structure constraints can be specified in the input files. Anchor constraints for sequences (alignments) are defined by assigning names to sequence positions (alignment columns), respectively. The exact semantics is either strict or relaxed (controled by \*\*–relaxed-anchors). In strict semantics, anchor names have to be sorted lexicographically in the input as well as in the result alignment (in the sense that result columns receive inherit the name from one or both input positions, where conflicts are disallowed). In relaxed semantics, anchors of the same name are forced into the same alignment column. The actual syntax of the constraint specification depends on the file format (see Constraint Examples below). Output ------ The final pairwise alignment is reported in standard and/or variants of the clustal and stockholm format, as well as LocARNA\\'s own pp format. OPTIONS ======= **\-h**, **–help** : Print this help. **–galaxy-xml** : Print galaxy xml wrapper. **\-V**, **–version** : Print only version string. **\-v**, **–verbose** : Be verbose. Prints input parameters, sequences and size information. **\-q**, **–quiet** : Be quiet. Scoring parameters: ------------------- **\-i**, **–indel=**(**\-150**) : Indel score. Score contribution of each single base insertion or deletion. Indel opening score and indel score define the affine scoring of gaps. **–indel-opening=**(**\-750**) : Indel opening score. Score contribution of opening an insertion or deletion, i.e. score for a consecutive run of deletions or insertions. Indel opening score and indel score define the affine scoring of gaps. **–ribosum-file=**(RIBOSUM85\_60) : File specifying the Ribosum base and base-pair similarities. \[default: use RIBOSUM85\_60 without requiring a Ribosum file.\] **–use-ribosum=**(true) : Use ribosum scores for scoring base matches and base pair matches; note that tau=0 suppresses any effect on the latter. **\-m**, **–match=**(50) : Set score contribution of a base match (unless ribosum scoring). **\-M**, **–mismatch=**(0) : Set score contribution of a base mismatch (unless ribosum scoring). **–unpaired-penalty=**(0) : Penalty for unpaired bases **\-s**, **–struct-weight=**(200) : Maximal weight of 1/2 arc match. Balances structure vs. sequence score contributions. **\-e**, **–exp-prob=** : Expected base pair probability. Used as background probability for base pair scoring \[default: calculated from sequence length\]. **\-t**, **–tau=**(50) : Tau factor. Factor for contribution of sequence similarity in an arc match (in percent). tau=0 does not penalize any sequence information including compensatory mutations at arc matches, while tau=100 scores sequence similarity at ends of base matches (if a scoring matrix like ribosum is used, this adds the contributions for base pair match from the matrix). \[default tau=0!\] **\-E**, **–exclusion=**(0) : Score contribution per exclusion in structure local alignment. Set to zero for unrestricted structure locality. **–stacking** : Use stacking terms (requires stack-probs by RNAfold **\-p2**) **–new-stacking** : Use new stacking terms (requires stack-probs by RNAfold **\-p2**) Partition function representation (for sequence envelopes): ----------------------------------------------------------- **–extended-pf** : Use extended precision for the computation of sequence envelopes. This enables handling significantly larger instances. \[default\] **–quad-pf** : Use quad precision for partition function values. Even more precision than extended pf, but usually much slower (overrides extended-pf). Locality: --------- **–struct-local=**(false) : Turn on/off structure locality. Allow exclusions in alignments of connected substructures. **–sequ-local=**(false) : Turn on/off sequence locality. Find best alignment of arbitrary subsequences of the input sequences. **–free-endgaps=**(**\-**\-\*\*–\*\*) : Control where end gaps are allowed for free. String of four +/- symbols, allowing/disallowing free end gaps at the four sequence ends in the order left end of first sequence, right end of first sequence, left end of second sequence, right end of second sequence. For example, "+\*\*-\*\*--" allows free end gaps at the left end of the first alignment string; "\*\*-\*\*-\*\*--" forbids free end gaps \[default\]. **–normalized=**(0) : Perform normalized local alignment with parameter L. This causes locarna to compute the best local alignment according to \\'Score\\' / ( L + \\'length\\' ), where length is the sum of the lengths of the two locally aligned subsequences. Thus, the larger L, the larger the local alignment; the size of value L is in the order of local alignment lengths. Verbose yields info on the iterative optimizations. **–penalized=**(0) : Penalized local alignment with penalty PP Output: ------- **\-w**, **–width=**(120) : Width of alignment output. **–clustal=** : Write alignment in ClustalW (aln) format to given file. **–stockholm=** : Write alignment Stockholm format to given file. **–pp=** : Write alignment in PP format to given file. **–alifold-consensus-dp** : Compute consensus dot plot by alifold (warning: this may fail for long sequences). **–consensus-structure=**(none) : Type of consensus structures written to screen and stockholm output \[alifold|mea|none\] (default: none). **–consensus-gamma=**(1.0) : Base pair weight for mea consensus computation. For MEA, base pairs are scored by their pair probability times 2 gamma; unpaired bases, by their unpaired probability. **\-L**, **–local-output** : Output only local sub-alignment (to std out). **–local-file-output** : Write only local sub-alignment to output files. **\-P**, **–pos-output** : Output only local sub-alignment positions. **–write-structure** : Write guidance structure in output. **–score-components** : Output components of the score (experimental). **–stopwatch** : Print run time informations. Heuristics for speed accuracy trade off: ---------------------------------------- **\-p**, **–min-prob=**(0.001) : Minimal probability. Only base pairs of at least this probability are taken into account. **–max-bps-length-ratio=**(0.0) : Maximal ratio of #base pairs divided by sequence length. This serves as a second filter on the "significant" base pairs. \[default: 0.0 = no effect\]. **\-D**, **–max-diff-am=**(**\-1**) : Maximal difference for sizes of matched arcs. \[-1=off\] **\-d**, **–max-diff=**(**\-1**) : Maximal difference for positions of alignment traces (and aligned bases). \[-1=off\] **–max-diff-at-am=**(**\-1**) : Maximal difference for positions of alignment traces at arc match ends. \[-1=off\] **–max-diff-aln=**() : Maximal difference relative to given alignment (file in clustalw format) **–max-diff-pw-aln=**() : Maximal difference relative to given alignment (string, delim=AMPERSAND) **–max-diff-relax** : Relax deviation constraints in multiple aligmnent **–min-trace-probability=**(1e-4) : Minimal sequence alignment probability of potential traces (probability-based sequence alignment envelope) \[default=1e-4\]. Special sauce options: ---------------------- **–kbest=**(**\-1**) : Enumerate k-best alignments **–better=**(**\-1000000**) : Enumerate alignments better threshold t MEA score: ---------- **–mea-alignment** : Perform maximum expected accuracy alignment (instead of using the default similarity scoring). **–match-prob-method=**(0) : Select method for computing sequence-based base match probablities (to be used for mea-type alignment scores). Methods: 1=probcons-style from HMM, 2=probalign-style from PFs, 3=from PFs, local **–probcons-file=** : Read parameters for probcons-like calculation of match probabilities from probcons parameter file. **–temperature-alipf=**(300) : Temperature for the \*/sequence\* alignment/ partition functions used by the probcons-like sequence-based match/trace probability computation (this temperature is different from the \\'physical\\' temperature of RNA folding!). **–pf-struct-weight=**(200) : Structure weight in PF computations (for the computation of sequence-based match probabilties from partition functions). **–mea-gapcost** : Use gap cost in mea alignment **–mea-alpha=**(0) : Weight alpha for MEA **–mea-beta=**(200) : Weight beta for MEA **–mea-gamma=**(100) : Weight gamma for MEA **–probability-scale=**(10000) : Scale for probabilities/resolution of mea score **–write-match-probs=** : Write match probs to file (don\\'t align!). **–write-trace-probs=** : Write trace probs to file (don\\'t align!). **–read-match-probs=** : Read match probabilities from file. **–write-arcmatch-scores=** : Write arcmatch scores (don\\'t align!) **–read-arcmatch-scores=** : Read arcmatch scores. **–read-arcmatch-probs=** : Read arcmatch probabilities (weighted by factor mea\_beta/100) Constraints: ------------ **–noLP** : Disallow lonely pairs in prediction and alignment. **–maxBPspan=**(**\-1**) : Limit maximum base pair span \[default=off\]. **–relaxed-anchors** : Use relaxed semantics of anchor constraints \[default=strict semantics\]. Input files: ------------ > The tool is called with two input files and , which specify the two input sequences or input alignments. Different input formats (Fasta, Clustal, Stockholm, LocARNA PP, ViennaRNA postscript dotplots) are accepted and automatically recognized (by file content); the two input files can be in different formats. Extended variants of the Clustal and Stockholm formats enable specifying anchor and structure constraints. DISCLAIMER ========== For many purposes, it is more convenient to use the multiple alignment tool mlocarna (even for pairwise alignment). However, certain tasks **–like aligning two specific alignments**– are supported only by the pairwise tool or can be better controlled. Note that the performance of locarna (as well as basically all tools in the LocARNA package) is often significantly improved by the use of suitable application-specific options, deviating from the default settings. REFERENCES ========== If you use locarna please cite us: Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology, 3 no. 4 pp. e65, 2007. doi:10.1371/journal.pcbi.0030065 Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18(5):900???14, 2012. doi:10.1261/rna.029041.111 AVAILABILITY ============ The latest LocARNA package release is available online at at Github [https://github.com/s-will/LocARNA](https://github.com/s-will/LocARNA) and [http://www.bioinf.uni-freiburg.de/Software/LocARNA/](http://www.bioinf.uni-freiburg.de/Software/LocARNA/) EXAMPLES ======== In the simplest case, the tool is called with two sequences in fasta format or two alignments in multiple fasta, clustal or stockholm format like locarna file1.fa file2.fa or locarna file1.aln file2.aln Note that input formats can be mixed like in locarna file1.aln file2.stk Constraint Examples ------------------- Anchor and structure constraints can be specified in extended versions of the Clustal format, in the LocARNA PP 2.0 format, as well as in Stockholm format. Currently, the pairwise alignment tools of the package do not support constraints in fasta-like input. Here is an example of constraints in Clustal format: CLUSTAL W vhuU AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU fruA CC-UCGAGGG-GAACCCGAAA-GGGACCCGAGA-GG #S (<<<<<<<<<......xxxx...............) #A1 .............AAABB.................. #A2 .............12312.................. The syntax (and semantic) of structure constraint strings (prefixed by #S) is the one of RNAfold of the ViennaRNA package. Moreover, fixed structures prefixed by #FS are accepted; fixed structures can contain pseudoknots encodes by different bracket symbols. Anchors are specified by naming columns, where names can consist of several places, in the example each name consists of two characters, such that the names are A1, A2, A3, B1, B2 for the respective columns. Constraints in PP format are specified in the same way; however, in Stockholm format we use different prefixes, such that the example would look like \# STOCKHOLM 1.0 vhuU AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU fruA CC-UCGAGGG-GAACCCGAAA-GGGACCCGAGA-GG #=GC cS (<<<<<<<<<......xxxx...............) #=GC cA1 .............AAABB.................. #=GC cA2 .............12312.................. The prefix for fixed structures is \\'#=GC cFS\\'. AUTHOR ====== This man page is written and maintained by Sebastian Will. It is part of the LocARNA package. REPORTING BUGS ============== Report bugs to . COPYRIGHT ========= Copyright 2005- Sebastian Will. The LocARNA package is released under GNU Public License v3.0 SEE ALSO ======== The LocARNA PP 2.0 format is described online at [http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/](http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/) --- # LocARNA-2.0.0: Related Pages LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * 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[![](data:image/png;base64,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)](https://s-will.github.io/) --- # LocARNA-2.0.0: Class Members LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * 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[v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * 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[y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) Here is a list of all documented class members with links to the class documentation for each member: ### \- a - * a2s() : [LocARNA::McC\_ali\_matrices\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__ali__matrices__t.html#a9f4fa11032876c136b71761aea362624) * add() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a23b1fd97e2a98af7980c8deb06d2b7cc) , [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#af05aa07c1891b4837ad3f4a409eabce3) * add\_am() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a5624b7b1e380ba8a1373f46e1815cd64) * add\_basepairA() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a2b83ad0aa99dc4fc9ea7cc72293d95fd) * add\_basepairB() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#af012bb3518fd7d5773fd8905d39e6e69) * add\_deleted\_basepairA() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#ae5787cf7b8e3e66da463d837969229fd) * add\_deleted\_basepairB() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a3a1ebb55fcc42998bcb1a6fc8ca0e6c7) * addInsideBounds() : [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a9102659544b70aa201797720cacd4192) * addr() : [LocARNA::Matrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html#add3cc22e5d61dcc44b7228e1c4024b7b) , [LocARNA::OMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1OMatrix.html#a12cf9e8fdd75c392d1714a087ecd2f30) , [LocARNA::RMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1RMatrix.html#a8187f2946fc21d9e31bbea4ed4fbf0c7) , [LocARNA::RotMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1RotMatrix.html#ac946bb241fe9be75c49a9c6885d6e210) * AliColumn() : [LocARNA::MultipleAlignment::AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#affdced7f6d2e4a0aab01272fc887f2d9) * align() : [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a49a89aa973f2c3f15f73828bffe41e59) , [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a0b6b6316c6528d5e8b2908f7d147da0b) , [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#acc28fbab6f55103a04eb9bfc734f559f) * align\_D() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a4ab47540b9f2dc0fdc3c1c0c022078e9) , [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a438d7810608b94597850992d9004ea98) , [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#ab107b9615e74df2788ed99efed657c6b) * align\_Dprime() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#ae984d8c87a6089cf2056308c60056ae2) * align\_in\_arcmatch() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#ac58bf0d60b4805d414ea2678d7b4a01b) * align\_inside() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a43572ee7912d91275326c16ecbd6101e) * align\_inside\_arcmatch() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a5d54f5d14a7b225dcd56494b8ae8ebcb) * align\_noex() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a8b23eb45cfd49e7c2a7a6c4ca11f4ae2) * align\_outside() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#af74ba501022f476eb619d8932a32adcf) * align\_outside\_arcmatch() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#ae60f89fed3ea0b2c09bbdab4c2ddc19c) * align\_reverse() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a9030afd20f92fcf9ba920ca4b4f71a77) * align\_top\_level\_free\_endgaps() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#adc8c4d256c2324436b80b1da38b65585) * align\_top\_level\_locally() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#af3a3ee323bfeeb20eee2588d7caf9d12) * Aligner() : [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#ad13a1f7975d5216a520032a9626a34cd) * AlignerImpl() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#aae5cbef5bbb6df326448e595fea44877) * AlignerN() : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#ac40e84b5bb2031c1117c37b8cc10bc2b) * alignerN\_ : [LocARNA::AlignerN::ModifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html#abd94164f7163e194e879c5ca3a955442) , [LocARNA::AlignerN::UnmodifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html#ac0f6ad1397a646b7ef0783fcaea4c5c5) * AlignerNParams() : [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html#ae07a1777f31e8ea49c465b6d12abbd23) * AlignerP() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a7729af044dbd7c7dee9490bfb2690206) * AlignerParams() : [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html#ac3a2305028f9a20ac4c36dd8696da8eb) * AlignerPParams() : [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html#a11c75399342aa5dd05b660686f4daf28) * AlignerRestriction() : [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#ac531674e470d24ae99caa4853d532b70) * alignment : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a30b248141a175e74e69071f4842e0a43) * Alignment() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a1060eb44ae603a4cfc20b88b8ba55c5a) * alignment\_ : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a8e8f787432399eb277b73dc8fe83050e) * alignment\_edges() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a02b13ed0150f3d6b6c420d66b6f7f183) * AlignmentImpl() : [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a3414c6009ebc4e3e94678c7691b51515) * alistrs\_to\_edges() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a3be3c201ee78e251b46d29f316030a04) * alloc\_inside\_matrices() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#aeda7251b4fb3ca6578e89953d7bd4ff7) * alloc\_outside\_matrices() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a104dcb02bbeb1f8e56e2fa138ec40af5) * allow\_left\_1() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a777a0ef8be08358fb9f76527992b2343) * allow\_left\_2() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a201a40ae33b2988653c930d7c5e447bf) * allow\_right\_1() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a814627ca59db8a93f164fee5315baa32) * allow\_right\_2() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#afc97395591bfdd33901380cec1de5323) * allowed\_del() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a6109506dd6c263285167ef75646fca53) * allowed\_del\_unopt() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a264c89d040d67223ccbf60cdd49e50f5) * allowed\_ins() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a9ef126ad9d8a87920537a07aa00506da) * allowed\_ins\_unopt() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a68f467ae5327d5c4a90cddb22dd48db9) * allowed\_match() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a48db6a9f418118a59541643baee61a20) * Alphabet() : [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a054d43bfdd178810c8fd41c57c706720) * alphabet() : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#ac69b30bacd854c6164d0a7ba218bd9e8) * alphabet\_ : [LocARNA::Ribofit](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit.html#aca3c90cb3573f81f5aa900e5ae1ec6b2) * am\_ : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#a4a5327de94a657615f212f34e25e6cce) * am\_begin() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#af1ab8134520eec1e953c5442333478e6) * am\_end() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a02c2ae158c1ae99145fceba16197c3ec) * am\_index() : [LocARNA::ArcMatchesIndexed](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatchesIndexed.html#a159e02ab8bc2631e4b74269f64fd161d) * am\_prob : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a0ce2f3f0d8b40a39e661730b4f54af6d) * anchor\_annotation() : [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a6fe42e6557b1689641a1fe48ef972885) * AnchorConstraints() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#aed43bc58db910402d5410bb41fbd3833) * annotation() : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#ab4b4278a598f75212f0cfb6a63d73af0) * annotation\_string() : [LocARNA::SequenceAnnotation](https://s-will.github.io/LocARNA/classLocARNA_1_1SequenceAnnotation.html#ab20cf106a5228395d89ba25f02a4619f) * AnnoType : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a7fc15eb5eaf65bb5ed461a71f65822c4) * AnnoTypes : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#abe99c4a95017b70c57ea51d707eb9c4b) * append() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#ae4f8126b4ba4a610c52f38167a9361a9) , [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a24b9d075f0d85266dc4004e35a285c3a) * apply\_bpfilter() : [LocARNA::RnaStructure](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaStructure.html#af009192ac34fe9432cff5fb388f2b832) * apply\_unpaired\_penalty() : [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#ae4108b89e68ccd24449be9388ae7785a) * Arc : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a75a92d48c18a48905420d189f48b4f1d) , [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#ab1c57e4434e22825e3fd6da6201d0a03) , [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a446d6d64ab3a3e2da3d85667a5ebd152) , [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a40edbef728a80a8e14f43259f4db0cd0) , [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#ae9af5600aaf10c7c0d93dd104fe32a49) * arc() : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a70dec5d31812206b0cf69c7d455bb9d0) * Arc : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#aea68c47e0f454c9777168854230d8dd3) , [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a6ad0dad9ead808cfcaede23975be67ba) , [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#a45b343536ae79ebbbb5016566eff8f65) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#aefb623785e50a501f418328d451406dc) * arc\_2\_prob() : [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#ab35571543d55b4bdfa163ec7c947e8a6) * arc\_2\_prob\_ali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#a029f3ee761d568c93dfb1e99e3bbf276) * arc\_2\_prob\_noali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#a02238359c99d099ba99a9f4a71694ec8) * arc\_2\_probs\_ : [LocARNA::RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html#af8b07eeccbf607bdcb55128ace3b1629) * arc\_alphabet\_type : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#abcbd68dda243d9a72e38a5e348de797d) * arc\_cutoff\_prob() : [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#ace516878c8b84b1a37422bf97d83f6b4) * arc\_external\_prob() : [LocARNA::ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html#a1cf54158d661f5fc9eb2d32a6de18dbd) , [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#af9d9fe39f1eacfad63a1772a0cb0355d) * arc\_in\_loop\_cutoff\_prob() : [LocARNA::ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html#ae65ee5061337c8b90fc2cd3e914802f2) * arc\_in\_loop\_prob() : [LocARNA::ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html#af8e40b01cc1a0ea8c25c7486566a7e63) , [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#a9619cd7465893ea55af21e1a5fc16e46) * arc\_in\_loop\_prob\_ali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#aa5cf6baf5443c108064798969a8b1eef) * arc\_in\_loop\_prob\_noali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#a5602105a4c64dd69c6c04c7a6d734f83) * arc\_in\_loop\_probs\_ : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#a54626ea6719bf24fd625c22ff42f910f) * arc\_length() : [LocARNA::AlignerN::ModifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html#a5babd949490abd4306e9705966c45a1f) * arc\_matches : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a0bb65484b9aafa17b29440c8e7fe088b) , [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a97b8f42e497a7671d2e6b2de9f84d822) , [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#af74e3f350feaf383e964800945a6fd61) * arc\_matches\_ : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a75c6b37d9a61d83338c9c7816e8b7b8f) , [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#abc9a59d71599c475e530824a977c71de) * arc\_matches\_vec : [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#aa0f4abeae85fdee743bb74159276c378) * arc\_matrix\_t : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ad7a2f18bed6a451fb04d20d96587b40e) * arc\_prob() : [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#aa968626780932b144cbc266b3fa1e272) , [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#a2e44fc59a949fd44e796c0e2cf24e3cb) * arc\_prob\_matrix\_matrix\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#a3788eee11bffcef532983338d3f7bfd5) * arc\_prob\_matrix\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#a4109c8975dbbb34e10934622791356c8) , [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#a149b89b595d4e54dd7414718653571f6) , [LocARNA::RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html#ac89923b11742e931b9b1cd235dfbf133) * arc\_prob\_vector\_matrix\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#ab76ebf1add03db7857f9aef6f40865b7) * arc\_prob\_vector\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#aa21df8ef54f08fc6c63d153521f48a72) * arc\_probs() : [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#a83eb109d5b77744952c8994b726e86de) * arc\_probs\_ : [LocARNA::RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html#a58d767db1dc59c45bbe00bf73ae5c34e) * arc\_stack\_prob() : [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#a0e8434f6377d7e35182013077136efff) * arc\_vec\_t : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a9c7e59c9997ec3d3ffe9a5779a686b54) * arcA() : [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#afa4017bfb7c59a900e960e3ad28b3f6f) * arcB() : [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a09d44c8926060f7af6ffe564cc415742) * arcDel() : [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#a988a06809a975d90df3e32aef1e67671) * ArcIdx : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a7983fd19d56c0a23da3f7403fd898902) , [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a84109e2a2a5dd15a7bfeb50ac25b2fa9) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#a59cf37151e1ee0f108e90465dafcab6e) * ArcIdxVec : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a95c8ff29890405d92e89713308e5e1f3) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#a240c30515348ac362c459f1cdd73cdf1) * ArcMatch() : [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a5e51ea9bf4c2dc5bb90f1c47db09ad86) * arcmatch() : [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#aaa0feea552df2942c0a067d319596020) , [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#a774b061274110b44ee18370a152c47ca) * arcmatch\_prob() : [LocARNA::RibosumFreq](https://s-will.github.io/LocARNA/classLocARNA_1_1RibosumFreq.html#a5b6de1f50999f89f02abcb0cc9685014) * arcmatch\_probs\_ : [LocARNA::RibosumFreq](https://s-will.github.io/LocARNA/classLocARNA_1_1RibosumFreq.html#a379b784726e5d0eb645e6b6b1c93c3df) * arcmatch\_score() : [LocARNA::Ribofit](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit.html#a102a7e25f5c5c4fcc89941d354ac0341) , [LocARNA::Ribofit\_will2014](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit__will2014.html#a18a7e69cf9caf7f01abdb4dfc832a443) , [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#ab97ef919ec235bfe368eb4fb098f6023) * arcmatch\_stacked() : [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#a249ae84385ded673f93f0797d2face99) * ArcMatches() : [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#a33bdb04b2849e29f7e86a0dadd591404) * ArcMatchesIndexed() : [LocARNA::ArcMatchesIndexed](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatchesIndexed.html#ae16628c9bbd2da5010e7e004ed4190ce) * arcname\_alphabet\_ : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#aca9e9bebc63a479cfe3b872a9dc52d26) * arg\_type : [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a53f4637ea5694775161d27a950f56d78) * argname : [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#ab24e7a7169a24c34ebaa58f3ca4ef2e4) * argument : [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a1634a5717a64ed163daff388a88d79ff) * avg\_deviation\_score() : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a5ac74bf3d758f08580383dc2d9050c32) --- # LocARNA-2.0.0: Class Members - Functions LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class 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[b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0))   ### \- a - * a2s() : [LocARNA::McC\_ali\_matrices\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__ali__matrices__t.html#a9f4fa11032876c136b71761aea362624) * add() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a23b1fd97e2a98af7980c8deb06d2b7cc) , [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#af05aa07c1891b4837ad3f4a409eabce3) * add\_am() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a5624b7b1e380ba8a1373f46e1815cd64) * add\_basepairA() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a2b83ad0aa99dc4fc9ea7cc72293d95fd) * add\_basepairB() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#af012bb3518fd7d5773fd8905d39e6e69) * add\_deleted\_basepairA() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#ae5787cf7b8e3e66da463d837969229fd) * add\_deleted\_basepairB() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a3a1ebb55fcc42998bcb1a6fc8ca0e6c7) * addInsideBounds() : [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a9102659544b70aa201797720cacd4192) * addr() : [LocARNA::Matrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html#add3cc22e5d61dcc44b7228e1c4024b7b) , [LocARNA::OMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1OMatrix.html#a12cf9e8fdd75c392d1714a087ecd2f30) , [LocARNA::RMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1RMatrix.html#a8187f2946fc21d9e31bbea4ed4fbf0c7) , [LocARNA::RotMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1RotMatrix.html#ac946bb241fe9be75c49a9c6885d6e210) * AliColumn() : [LocARNA::MultipleAlignment::AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#affdced7f6d2e4a0aab01272fc887f2d9) * align() : [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a49a89aa973f2c3f15f73828bffe41e59) , [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a0b6b6316c6528d5e8b2908f7d147da0b) , [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#acc28fbab6f55103a04eb9bfc734f559f) * align\_D() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a4ab47540b9f2dc0fdc3c1c0c022078e9) , [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a438d7810608b94597850992d9004ea98) , [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#ab107b9615e74df2788ed99efed657c6b) * align\_Dprime() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#ae984d8c87a6089cf2056308c60056ae2) * align\_in\_arcmatch() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#ac58bf0d60b4805d414ea2678d7b4a01b) * align\_inside() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a43572ee7912d91275326c16ecbd6101e) * align\_inside\_arcmatch() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a5d54f5d14a7b225dcd56494b8ae8ebcb) * align\_noex() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a8b23eb45cfd49e7c2a7a6c4ca11f4ae2) * align\_outside() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#af74ba501022f476eb619d8932a32adcf) * align\_outside\_arcmatch() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#ae60f89fed3ea0b2c09bbdab4c2ddc19c) * align\_reverse() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a9030afd20f92fcf9ba920ca4b4f71a77) * align\_top\_level\_free\_endgaps() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#adc8c4d256c2324436b80b1da38b65585) * align\_top\_level\_locally() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#af3a3ee323bfeeb20eee2588d7caf9d12) * Aligner() : [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#ad13a1f7975d5216a520032a9626a34cd) * AlignerImpl() : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#aae5cbef5bbb6df326448e595fea44877) * AlignerN() : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#ac40e84b5bb2031c1117c37b8cc10bc2b) * AlignerNParams() : [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html#ae07a1777f31e8ea49c465b6d12abbd23) * AlignerP() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a22a5b6c70a0cad00a9f410d0dedb7807) * AlignerParams() : [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html#ac3a2305028f9a20ac4c36dd8696da8eb) * AlignerPParams() : [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html#a11c75399342aa5dd05b660686f4daf28) * AlignerRestriction() : [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#ac531674e470d24ae99caa4853d532b70) * Alignment() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a8d307a79dc21e5aa6928a81fb644c271) * alignment\_edges() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a02b13ed0150f3d6b6c420d66b6f7f183) * AlignmentImpl() : [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a3414c6009ebc4e3e94678c7691b51515) * alistrs\_to\_edges() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a3be3c201ee78e251b46d29f316030a04) * alloc\_inside\_matrices() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#aeda7251b4fb3ca6578e89953d7bd4ff7) * alloc\_outside\_matrices() : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a104dcb02bbeb1f8e56e2fa138ec40af5) * allow\_left\_1() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a777a0ef8be08358fb9f76527992b2343) * allow\_left\_2() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a201a40ae33b2988653c930d7c5e447bf) * allow\_right\_1() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a814627ca59db8a93f164fee5315baa32) * allow\_right\_2() : [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#afc97395591bfdd33901380cec1de5323) * allowed\_del() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a6109506dd6c263285167ef75646fca53) * allowed\_del\_unopt() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a264c89d040d67223ccbf60cdd49e50f5) * allowed\_ins() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a9ef126ad9d8a87920537a07aa00506da) * allowed\_ins\_unopt() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a68f467ae5327d5c4a90cddb22dd48db9) * allowed\_match() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a48db6a9f418118a59541643baee61a20) * Alphabet() : [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a249cea02a97e9399eea0bc58b0a586e5) * alphabet() : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#ac69b30bacd854c6164d0a7ba218bd9e8) * am\_begin() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#af1ab8134520eec1e953c5442333478e6) * am\_end() : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a02c2ae158c1ae99145fceba16197c3ec) * am\_index() : [LocARNA::ArcMatchesIndexed](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatchesIndexed.html#a159e02ab8bc2631e4b74269f64fd161d) * anchor\_annotation() : [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a6fe42e6557b1689641a1fe48ef972885) * AnchorConstraints() : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#aed43bc58db910402d5410bb41fbd3833) * annotation() : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#ab4b4278a598f75212f0cfb6a63d73af0) * annotation\_string() : [LocARNA::SequenceAnnotation](https://s-will.github.io/LocARNA/classLocARNA_1_1SequenceAnnotation.html#ab20cf106a5228395d89ba25f02a4619f) * append() : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#ae4f8126b4ba4a610c52f38167a9361a9) , [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a24b9d075f0d85266dc4004e35a285c3a) * apply\_bpfilter() : [LocARNA::RnaStructure](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaStructure.html#af009192ac34fe9432cff5fb388f2b832) * apply\_unpaired\_penalty() : [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#ae4108b89e68ccd24449be9388ae7785a) * arc() : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ac2ccff2cdeda72c023127c5b85168a71) * arc\_2\_prob() : [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#ab35571543d55b4bdfa163ec7c947e8a6) * arc\_2\_prob\_ali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#a029f3ee761d568c93dfb1e99e3bbf276) * arc\_2\_prob\_noali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#a02238359c99d099ba99a9f4a71694ec8) * arc\_cutoff\_prob() : [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#ace516878c8b84b1a37422bf97d83f6b4) * arc\_external\_prob() : [LocARNA::ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html#a1cf54158d661f5fc9eb2d32a6de18dbd) , [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#af9d9fe39f1eacfad63a1772a0cb0355d) * arc\_in\_loop\_cutoff\_prob() : [LocARNA::ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html#ae65ee5061337c8b90fc2cd3e914802f2) * arc\_in\_loop\_prob() : [LocARNA::ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html#af8e40b01cc1a0ea8c25c7486566a7e63) , [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#a9619cd7465893ea55af21e1a5fc16e46) * arc\_in\_loop\_prob\_ali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#aa5cf6baf5443c108064798969a8b1eef) * arc\_in\_loop\_prob\_noali() : [LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html#a5602105a4c64dd69c6c04c7a6d734f83) * arc\_length() : [LocARNA::AlignerN::ModifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html#a5babd949490abd4306e9705966c45a1f) * arc\_matches() : [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#af74e3f350feaf383e964800945a6fd61) * arc\_prob() : [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#aa968626780932b144cbc266b3fa1e272) , [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#a2e44fc59a949fd44e796c0e2cf24e3cb) * arc\_probs() : [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#a83eb109d5b77744952c8994b726e86de) * arc\_stack\_prob() : [LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html#a0e8434f6377d7e35182013077136efff) * arcA() : [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#afa4017bfb7c59a900e960e3ad28b3f6f) * arcB() : [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a09d44c8926060f7af6ffe564cc415742) * arcDel() : [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#a988a06809a975d90df3e32aef1e67671) * ArcMatch() : [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a5e51ea9bf4c2dc5bb90f1c47db09ad86) * arcmatch() : [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#aaa0feea552df2942c0a067d319596020) , [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#af546744efbc6fd22df455aa33c62e2b1) * arcmatch\_prob() : [LocARNA::RibosumFreq](https://s-will.github.io/LocARNA/classLocARNA_1_1RibosumFreq.html#a5b6de1f50999f89f02abcb0cc9685014) * arcmatch\_score() : [LocARNA::Ribofit](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit.html#a102a7e25f5c5c4fcc89941d354ac0341) , [LocARNA::Ribofit\_will2014](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit__will2014.html#a18a7e69cf9caf7f01abdb4dfc832a443) , [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#ab97ef919ec235bfe368eb4fb098f6023) * arcmatch\_stacked() : [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#a249ae84385ded673f93f0797d2face99) * ArcMatches() : [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#a33bdb04b2849e29f7e86a0dadd591404) * ArcMatchesIndexed() : [LocARNA::ArcMatchesIndexed](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatchesIndexed.html#ae16628c9bbd2da5010e7e004ed4190ce) * avg\_deviation\_score() : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a5ac74bf3d758f08580383dc2d9050c32) --- # LocARNA-2.0.0: Class Members - Enumerations LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0))   * AnnoType : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a7fc15eb5eaf65bb5ed461a71f65822c4) * FormatType : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a3cc694a18f204ea3360fda2250e0c327) --- # LocARNA-2.0.0: Class Members - Related Functions LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0))   * max : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#adaf06c3e9eadadfcdd82b8fefd222fa7) * min : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#af617a2b54fbe36cb74cfc741265dbfc3) * operator+ : [LocARNA::FiniteInt](https://s-will.github.io/LocARNA/classLocARNA_1_1FiniteInt.html#a41f42cf2d1dea57002261e5826ed815d) , [LocARNA::InftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1InftyInt.html#a603c29b109fd6ba7e6227d5572235f67) , [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#a7ec4d86c8d9639d830ee7316e6c249d7) * operator- : [LocARNA::FiniteInt](https://s-will.github.io/LocARNA/classLocARNA_1_1FiniteInt.html#ac9eb91403459595dd33af52e9646a1e8) , [LocARNA::InftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1InftyInt.html#a057c98f1682910a7063c2c4d65d8673d) , [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#ad65fbdf034ea4c2979a42fe1c2edd7dc) * operator< : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#a999ac5d0b6e7ae3effb725d7c7604b71) * operator<< : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#ab83cd5f1f1998bd1d5db622db69ed1e1) , [LocARNA::RibosumFreq](https://s-will.github.io/LocARNA/classLocARNA_1_1RibosumFreq.html#ab63d9ad8654fb1140971e87d8213c979) , [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#afa1f37ce64fc6a482688d851b6a60951) * operator<= : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#ad1f6808f8c886f76150741371b4d098a) * operator== : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#a3af524962b828ad6279a148782251791) * operator> : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#a160ba6a47030fbab2efbe88755d93e43) * operator>= : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#ae4604d5115794e25587c34ba7a3ccf66) --- # LocARNA-2.0.0: Class Members - Variables LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0))   ### \- a - * alignerN\_ : [LocARNA::AlignerN::ModifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html#abd94164f7163e194e879c5ca3a955442) , [LocARNA::AlignerN::UnmodifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html#ac0f6ad1397a646b7ef0783fcaea4c5c5) * alignment : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a30b248141a175e74e69071f4842e0a43) * alignment\_ : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a8e8f787432399eb277b73dc8fe83050e) * alphabet\_ : [LocARNA::Ribofit](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit.html#aca3c90cb3573f81f5aa900e5ae1ec6b2) * am\_ : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#a4a5327de94a657615f212f34e25e6cce) * am\_prob : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a0ce2f3f0d8b40a39e661730b4f54af6d) * AnnoTypes : [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#abe99c4a95017b70c57ea51d707eb9c4b) * arc\_2\_probs\_ : [LocARNA::RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html#af8b07eeccbf607bdcb55128ace3b1629) * arc\_in\_loop\_probs\_ : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#a54626ea6719bf24fd625c22ff42f910f) * arc\_matches : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a0bb65484b9aafa17b29440c8e7fe088b) , [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a97b8f42e497a7671d2e6b2de9f84d822) * arc\_matches\_ : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a75c6b37d9a61d83338c9c7816e8b7b8f) , [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#abc9a59d71599c475e530824a977c71de) * arc\_matches\_vec : [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#aa0f4abeae85fdee743bb74159276c378) * arc\_probs\_ : [LocARNA::RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html#a58d767db1dc59c45bbe00bf73ae5c34e) * arcmatch\_probs\_ : [LocARNA::RibosumFreq](https://s-will.github.io/LocARNA/classLocARNA_1_1RibosumFreq.html#a379b784726e5d0eb645e6b6b1c93c3df) * arcname\_alphabet\_ : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#aca9e9bebc63a479cfe3b872a9dc52d26) * arg\_type : [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a53f4637ea5694775161d27a950f56d78) * argname : [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#ab24e7a7169a24c34ebaa58f3ca4ef2e4) * argument : [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a1634a5717a64ed163daff388a88d79ff) --- # LocARNA-2.0.0: Class Members - Typedefs LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0))   ### \- a - * Arc : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a75a92d48c18a48905420d189f48b4f1d) , [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#ab1c57e4434e22825e3fd6da6201d0a03) , [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a446d6d64ab3a3e2da3d85667a5ebd152) , [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a40edbef728a80a8e14f43259f4db0cd0) , [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#ae9af5600aaf10c7c0d93dd104fe32a49) , [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#aea68c47e0f454c9777168854230d8dd3) , [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a6ad0dad9ead808cfcaede23975be67ba) , [LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html#a45b343536ae79ebbbb5016566eff8f65) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#aefb623785e50a501f418328d451406dc) * arc\_alphabet\_type : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#abcbd68dda243d9a72e38a5e348de797d) * arc\_matrix\_t : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ad7a2f18bed6a451fb04d20d96587b40e) * arc\_prob\_matrix\_matrix\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#a3788eee11bffcef532983338d3f7bfd5) * arc\_prob\_matrix\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#a4109c8975dbbb34e10934622791356c8) , [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#a149b89b595d4e54dd7414718653571f6) , [LocARNA::RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html#ac89923b11742e931b9b1cd235dfbf133) * arc\_prob\_vector\_matrix\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#ab76ebf1add03db7857f9aef6f40865b7) * arc\_prob\_vector\_t : [LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html#aa21df8ef54f08fc6c63d153521f48a72) * arc\_vec\_t : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a9c7e59c9997ec3d3ffe9a5779a686b54) * ArcIdx : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a7983fd19d56c0a23da3f7403fd898902) , [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a84109e2a2a5dd15a7bfeb50ac25b2fa9) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#a59cf37151e1ee0f108e90465dafcab6e) * ArcIdxVec : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a95c8ff29890405d92e89713308e5e1f3) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#a240c30515348ac362c459f1cdd73cdf1) ### \- b - * base\_alphabet\_type : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#a447267343e1b0783c2096cfffa126195) * base\_type : [LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html#aa140d1282b74b89cca9a069271e8f7f7) * bp\_t : [LocARNA::RnaStructure](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaStructure.html#ac93fcf2f945edf4933a7e6f87de001de) * bpair\_set\_t : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ab135bd0a3ad6208e4684ee25547f4710) * bpair\_t : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a7b2fdd5f56063b4caddd80bce9bb5312) * bps\_t : [LocARNA::RnaStructure](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaStructure.html#a5939c35823dc94ea575024e9b81d3960) ### \- c - * char\_alphabet\_type : [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#a9b552c5fb2b97dd5c313ebdfac5d5a35) * const\_iterator : [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#aa8dcb0b0136e77e0449ddd9b1f27c77f) , [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a59434ebe06f4a46f3e8c8efd37ee20ed) , [LocARNA::RnaStructure](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaStructure.html#a9a5f2a956660f3ed14afef43c643cedb) , [LocARNA::SparseVectorBase< Derived, ValueType, KeyType >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html#ab0970a4f01b9e6d62252501209de2e77) ### \- e - * edge\_end\_t : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#ab81bbb18f0400395fb7a59f4a0e79831) * edge\_ends\_t : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#abfd0e29df84b4d6c9907e8f66dc4ae5d) * edges\_t : [LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html#a6537d524c8ac35dbf37ed46fd671d2ef) * el\_pat\_vec : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a50c359d46c02dbcf8e0cd03c5d7c6e2a) * elem\_t : [LocARNA::Matrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html#a5f23b2ddb5425203ab51af14de5e66b2) ### \- i - * idx\_type : [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#abe50ab349a68390fb2b0d79119e598f6) * index\_t : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#ac703a1be5b2e20ea458773e84f010b73) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#ae3c053ef29985b80c6800f452111c867) * InfoForPosVec : [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#ae678178de195ac727c37e6fd77c2bc25) * iterator : [LocARNA::MultipleAlignment::AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aabac5c3625192e91d5e7e870d2698321) , [LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html#a65f7b227cc9ffceb91d4b6b13ff43225) ### \- k - * key\_type : [LocARNA::SparseMatrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html#a24849a877bd5d83be443fa01d6cf9b8a) , [LocARNA::SparseVector< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVector.html#aec9de5f96d142fa207c59063a28292fb) , [LocARNA::SparseVectorBase< Derived, ValueType, KeyType >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html#a6c3f5351c8f0e47eaba5614528b9312f) ### \- l - * LeftAdjList : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ac9079f4805720ed799b1702033b0102d) ### \- m - * M\_matrix\_t : [LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html#a5a3171ba8911268bcfb100c7373560f2) , [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#a95493c40b49eee2bee5bbf75a322be78) * map\_type : [LocARNA::SparseMatrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html#a5c670ac1430690fd5f12bf257dbc7e4a) , [LocARNA::SparseVector< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVector.html#aff210b4244d3f4ab054d5bebf05b604b) * matidx\_t : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#af28e3ee6253ec963a63b0bf13228a3c9) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#a6d445d7d1b878fe7e64d1a5ae4466b09) * matpos\_t : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a20d543f43ab10a7b1ba1a97e065bddb9) , [LocARNA::SparseTraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseTraceController.html#ac7111466c6e8fa617f2e5d64c6d7944c) * matrix\_t : [LocARNA::Ribofit](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit.html#a1a6f7c2b0fac5dc550a94c20d1d5b3b9) , [LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html#ab7afc7da4bd79937aa8e603234ed7d14) ### \- n - * name\_t : [LocARNA::SequenceAnnotation](https://s-will.github.io/LocARNA/classLocARNA_1_1SequenceAnnotation.html#a1e9f1f087c98f34130ab252826eab27a) ### \- o - * orderedMapCITER : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#a54f16ba70c3bb842b0d99a168d2da52a) * orderedMapITER : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#a6cf9053032f2a9592e1d34e75d0a6484) * orderedMapTYPE : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#a769230faf78789be38993ad436dd7d8f) ### \- p - * pair\_seqpos\_t : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a0d1ff4403c98eac65a74e8b308077582) , [LocARNA::SparseTraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseTraceController.html#ae561328718a016306ae0e8539e8e2f8b) * PairArcIdx : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a3bfeb70408fee386a3f1a76ddb313edc) * PairArcIdxVec : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a8e3db461eb636beadcfa1a9f1eb46e13) * pat\_vec\_t : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#adea4a66ab5b4a8c99a8db5cd23e08b51) * patListCITER : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#a50cedf394dc720c5c541fad65949394a) * patListITER : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#ae2221bb23c88eee672ccb298ea3aa4d2) * patListTYPE : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#ac35aacb26084ef20b173d0d6ffc24f84) * PatternIdMapTYPE : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#a39d231f7eeacb95e74a1f2891ae63c88) * PFScoreMatrix : [LocARNA::PFScoring< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFScoring.html#a5f955895c1dd9b68fe124398742433b5) * PFScoreVector : [LocARNA::PFScoring< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFScoring.html#a06e926fb75c83e40f7a127971b8fb653) * pos\_pair\_t : [LocARNA::MultipleAlignment::SeqEntry](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1SeqEntry.html#a2a9cb4797dadbe33acb2ac9ea4e204ea) ### \- r - * range\_t : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#ab1e95716b3b67ba175b3fde006364a74) * RightAdjList : [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#af53b42aa4df3eba885888825030227c5) ### \- s - * SelfValuePTR : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#a195f4c19caa4b083ae5f17b1179303fc) * selfValueTYPE : [LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html#a211bff5858f5705be26300fde705ac48) * seq\_pos\_t : [LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html#afdc032c60acb4f6a78d9c451845fb3ed) , [LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html#a5afe8efbd933016c8873af17b80fc847) * SeqEntry : [LocARNA::TraceRange](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceRange.html#a00c41a3281a142d3e8ffbc6c52bcae33) * seqentry\_pair\_t : [LocARNA::TraceRange](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceRange.html#a197238142997c9e481ad2c2b75f92f38) * seqpos\_t : [LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html#a3ff1e5e445df3fea73e5e811f27c03dc) * size\_pair : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a6b59be9e97404d1b2eaa04606c41f47a) * size\_pair\_t : [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a017a315a365581490f4e28a7293651ea) * size\_pair\_type : [LocARNA::Matrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html#aa2a7701150d21c9109bd4342cf4b334f) * size\_type : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#aea38a43aa1969c8c52c85bbb538c8317) , [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a3d536c8e69cd705899715f2d3a0ec49d) , [LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html#a963b1f559058160d988e7104f164bf6b) , [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a7dddafee26151af4aa1edddde1b33979) , [LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html#ad20766e0365dade492c55fb84242f08e) , [LocARNA::ArcMatches::tuple5](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1tuple5.html#a657844e26b6ba1cd1058dd42192df496) , [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ab8c5c60bc5558e934241313485a067e2) , [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a308c0af797440334a28acf5814a8ceb6) , [LocARNA::Matrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html#a5c91124ea55a0e1c215fc246df308e98) , [LocARNA::PFGotoh< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFGotoh.html#a815d3daa4748a226d6b5d9328434f002) , [LocARNA::PFMatchProbs< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFMatchProbs.html#a082c44215c0aeb5aced8b17767438188) , [LocARNA::PFTraceProbs< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFTraceProbs.html#a999f8e493f2ce7610ae467ba988d2f3c) , [LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html#ae2859c2a64b4be526782899146e46630) , [LocARNA::SparseMatrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html#ab6829eff2267629c843528750a024a30) , [LocARNA::SparseVector< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVector.html#a52cf3e1736829a4aa3972d6f89a23009) , [LocARNA::SparseVectorBase< Derived, ValueType, KeyType >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html#a21fa9f2df695db1a34af7a268429c534) * SparsePFScoreMatrix : [LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html#a481d814b6e32fd262c47345bab2959ef) ### \- v - * value\_type : [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a33ea2031beb67814f6fd97a3337355de) , [LocARNA::SparseMatrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html#a513373755a6283aecd2fe80c91a83765) , [LocARNA::SparseVector< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVector.html#a4a655935a1c291315f4132c64857c53d) , [LocARNA::SparseVectorBase< Derived, ValueType, KeyType >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html#a7af08726a20a23def46c8376cfae2e2e) --- # LocARNA-2.0.0: File Members LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) Here is a list of all documented file members with links to the documentation: * clp : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#ab680a1b7a1c7a469cf22b5378bb64a2d) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#ab680a1b7a1c7a469cf22b5378bb64a2d) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#ab680a1b7a1c7a469cf22b5378bb64a2d) * DO\_TRACE : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#a75e253cc9c9f0125f4032a86c087a672) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#a75e253cc9c9f0125f4032a86c087a672) * main() : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#a3c04138a5bfe5d72780bb7e82a18e627) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#a3c04138a5bfe5d72780bb7e82a18e627) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#a3c04138a5bfe5d72780bb7e82a18e627) * my\_options : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#a0a2c750fb10c2ad5846ba36a38e7d71e) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#a0a2c750fb10c2ad5846ba36a38e7d71e) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#a0a2c750fb10c2ad5846ba36a38e7d71e) * run\_and\_report() : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#aa7d8f4067cfbb927f88549681e6ee114) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#aa7d8f4067cfbb927f88549681e6ee114) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#aa7d8f4067cfbb927f88549681e6ee114) * VERSION\_STRING : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#abe479249dbce12521202efc1d72c379d) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#abe479249dbce12521202efc1d72c379d) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#abe479249dbce12521202efc1d72c379d) --- # LocARNA-2.0.0: File Members LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0))   * main() : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#a3c04138a5bfe5d72780bb7e82a18e627) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#a3c04138a5bfe5d72780bb7e82a18e627) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#a3c04138a5bfe5d72780bb7e82a18e627) * run\_and\_report() : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#aa7d8f4067cfbb927f88549681e6ee114) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#aa7d8f4067cfbb927f88549681e6ee114) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#aa7d8f4067cfbb927f88549681e6ee114) --- # LocARNA-2.0.0: File Members LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0))   * clp : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#ab680a1b7a1c7a469cf22b5378bb64a2d) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#ab680a1b7a1c7a469cf22b5378bb64a2d) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#ab680a1b7a1c7a469cf22b5378bb64a2d) * DO\_TRACE : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#a75e253cc9c9f0125f4032a86c087a672) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#a75e253cc9c9f0125f4032a86c087a672) * my\_options : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#a0a2c750fb10c2ad5846ba36a38e7d71e) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#a0a2c750fb10c2ad5846ba36a38e7d71e) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#a0a2c750fb10c2ad5846ba36a38e7d71e) * VERSION\_STRING : [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html#abe479249dbce12521202efc1d72c379d) , [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html#abe479249dbce12521202efc1d72c379d) , [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html#abe479249dbce12521202efc1d72c379d) --- # LocARNA-2.0.0: ChangeLog LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) 2.0.0 ===== Version 2 of LocARNA introduces several improvements that make LocARNA faster and easier to use. Most prominently, it features a novel sequence envelope heuristic in all major alignment modes, which significantly improves over less sophisticated banding heuristics (in terms of speed, robustness, /and/ flexibility). Most directly notable for users, it changes the default parameters to more appropriate settings. In addition to various detailed improvements of the LocARNA tools, there are significant changes under the hood: the C++-code of the LocARNA library was simplified and modernized making use of C++-14 features. These changes make the library easier to use, maintain and extend. The development of version 2 extended over numerous 'release candidates' that not only fixed bugs and stabilized features, but - despite their RC designation - also introduced some new functionality e.g. (for clustering and benchmarking). Comprehensive change log is therefore provided for the sinlge release candidate releases. * * * 2.0.0RC10 ========= Documentation and examples -------------------------- * Improve readme * Update doxygen documentation * Fix: add conda-forge channel in conda install * Add CLUSTAL-header in realign example * Use full names in tRNA\_5 example * use doxygen awesome style * use REAMDE.md as main page in docu * Reformat changelog and include in docu * include man pages from perl scripts and C++ programs * Reformat help output of C++ programs * Activate doxygen pdf docu * Reformatting in mlocarna pod * Update email address * Remove build status Improvements of functionality / usability ----------------------------------------- * Make mlocarna less chatty * mlocarna: Catch empty names in fasta input + modify output in case of duplicate names * mlocarna: Catch missing clustal header in realignment input * turn off warning about unsupported nucleotides * Add benchmark plot script to compare multiple experiments * Add alignments target in benchmark Makefile Fixes ----- * Keep input file in realignment mode as input.aln * Fix pp2dot * Fix reliability output (aligned offsets/name widths) * Fix mlocarna option width in probabilistic mode * Fix dependency in benchmark makefile * Fix behavior of verbose mode / printing of consensus structure * fix and support png/svg output in benchmarking * Fix: use reference type for loop var * Fix bug: quote names in newick trees * Fix buffer size Internal changes: ----------------- * Update configure.ac by autoupdate * Strip -fno-lto from Vienna RNA configured VRNA\_LIBS * doxygen: Turn off autolink support * Require Vienna RNA 2.5.1 * Update tests * * * 2.0.0RC9 ======== MLocarna functionality ---------------------- * The calculation of the guide tree is rewritten; in consequence mlocarna is now more useful for clustering RNAs, since score distances are reported in the tree output (as well as names that correspond to intermediate alignments of subsets of the input sequences in subtrees) * Generally, improved functionality for multiple alignment * better support for 'clustering' use case * distances and inner node labels in newick output * inner node labels correspond to names of intermediary alignments * introduces new perl Tree class with internal full tree representation * supports flexible traversals, filtering, etc * parsing and writing newick format fully supported * handles multi-ary trees * assign meaningful indices to intermediary alignments from most closely related to further apart * changes naming scheme of intermediary alignments in iterative alignment (include round in name) * Perform distance-based upgma for guide tree computation: Calculate distances from locarna scores as distance = max\_score - score * Add option (max-alignment-size) to limit the size of computed multiple alignments * Don't write am and bm probabilities by default; introduce options to control writing. Motivation: probabilities require lots of disk space, which is rarely used for inspection or further processing Introduces new options * –write-probs / –no-write-probs * –write-am-probs / –no-write-am-probs * –write-bm-probs / –no-write-bm-probs All of them default to 'no-write' Documentation improvements -------------------------- * Improve man pages (add dois, slightly edit) * Include disclaimer about the use of many threads in mlocarna man page * Improve documentation of small tools (add missing man page includes) * Add locarna\_mcc man page Fixes ----- * Fix quoting in newick trees * Update script mlocarna\_nnames MLocarna minor or internal changes ---------------------------------- * Refactorize guide tree computation. * Inform user that results were written to target directory * Code cleanup: Cleanup reference variables Cleanup amprobs/bmprobs hash references Cleanup sparse matrix module, return hash refs Change global var opts to hash reference Expand leading tabs Cleanup in MatchProbs module Cleanup threaded/unthreaded modules Cleanup match probability computation. Remove redundant code for sequential computations of already parallelized steps * Avoid unnecessary cloning of hashs; cleanup shared cloning * factorize: introduce name normalizer class Other internal changes ---------------------- * Remove obsolete script to label trees * Update CARNA server related scripts * Slightly simplify make of man pages (require man\_include files) 2.0.0RC8 ======== Bugfixes -------- * Fix bug in sequence trace probability computation, which was potentially critical for large instances (e.g. aligning sequences with ~1000 length difference) * Remove superfluous output of alignments in probabilistic mode Code improvements/Maintenance ----------------------------- * Update travis CI script * Fix initialization order \[FitOnOff\] * Fix missing and superfluous headers \[alphabet.hh/icc\] Experimental Feature -------------------- * experimental extension of boundary prediction by position wise penalties, can use consistency file information \[reliability-profile.pl, locarnap\_fit\] * * * 2.0.0RC7 ======== * Accept empty sequences in input * Re-enable computing consensus structures in mlocarna output and stk-files * Remove perl prototype specs to avoid perl 5.18 incompatibility 2.0.0RC6 ======== * Adjust behavior of locarna and mlocarna for pairwise alignments * do not use alifold in binaries when calculating base pairs for single sequences * use noLP in mlocarna for calculating base pair probabilties /and/ the alignment * increase output precision for probabilities in pp files (reducing rounding issues for the typical cutoff) 2.0.0RC5 (2018-05-08) ===================== * Allow penalized in global alignment 2.0.0RC4 (2018-05-04) ===================== Bugfixes -------- * Fix kbest HIT line * Fix static linking (with gomp) * Remove one extra line after CLUSTAL header (which used to be written by mlocarna) 2.0.0RC3 (2018-04-30) ===================== Bugfixes -------- * Fix kbest alignment (allow and detect empty alignments) * Fix local end output (HIT line) for non-local alignments Features / Improvements ----------------------- * Add stopwatch (for consensus computation) * Introduce parameter –consensus-gamma for mea consensus 'gamma' API --- * Class Alignment handles start and end position for non-local alignments; methods local\_start(), local\_end() of Alignment are replaced by start\_positions(), end\_positions() 2.0.0RC2 (2018-04-16) ===================== Bugfixes -------- * Fix free endgaps bug (negative alignment scores were handled incorrectly) * Fix empty anchor constraint (correctly recognize/report when anchors are specified) Features / Improvements ----------------------- Both improvements were introduced to handle large instances * Improve alifold consensus computation * turn off by default (also speeds up mlocarna) * handle cases where consensus is not/cannot be computed * warn if consensus is not computed / fail if explicitely required (pp) * handle recomputation of consensus if file/screen output differ (local out) * Support sequence envelope computation with extended precision * set the default to extended precision * recognize failing partition function calculation * (for sequence trace and match probabilities) * extend LocARNA's quadmath.hh header and simplify its use * use templates for partition function type * support extended (long double) and quad precision (float128) 2.0.0RC1 (2017-12-13) ===================== Features / functionality ------------------------ * Sequence envelopes for locarna, locarna\_p and sparse; * Compatible to anchors, local alignment, and free endgaps * New parameter: –min-trace-probability (on by default) * Refactor class MatchProbs -> EdgeProbs and sub-classes; improve interface and docu * use sequence envelopes by default * Change default parameters for scoring (new gap cost and tau factor) * Support higher precision floating point arithmetic for locarna-p * pf calculation (long double and quad math) selectable dynamically without recompiling * support extended (long double) and quad precision (quadmath) * Support caching of pp files (–dp-cache) * Support in-package benchmarking (measuring sps, sci, and mcc) Security -------- * Avoid shell evaluation in mlocarna system calls Optimizations and code improvements ----------------------------------- * Modernize and restructure code Transition to C++14 standard: use of unique\_ptr, auto types, range loops, template meta programmin using type\_traits, ... Systematic clean up of the library classes Introduce named arguments; zip and enumerate iterators Improved organization of command line help; reduce redundancies Improve handling of format and annotation types in MultipleAlignment * Optimize inner loop: add sentinels to left and right adjacency lists * Reduce memory footprint of locarna * Anchor constraints restrict trace controller * Refactor computation of input pp files \[mlocarna\] * Use locarna\_rnafold\_pp for constrained folding \[mlocarna\] * Update travis CI test Bugfixes -------- * Fix specifying anchor constraints via bed file \[mlocarna\] allow arbitrary order of entries in bed input * Fix ribofit code (make experimental ribofit scoring usable) * Fix confusion matrix: count\_common\_bps() * * * 1.9.2 (2017-07-04) ================== Improve consensus dotplot computation (avoid accumulation of low probability base pairs) Some cleanup 1.9.2pre4 Fix left and rightmost anchors (fixed local alignment); add unit tests Optimize maximization in innermost loop Add unit and program tests 1.9.2pre3 Make consensus structure / dotplot types independent \[option –consensus-structure alifold (current default) used to also determine the computation of consensus dotplots. The consensus dot plot is now independent (new default: no alifold consensus dot plot).\] fix strict semantics for anchor constraints fix compatibility '–keep-sequence-order' with anchor constraints 1.9.2pre2 mlocarna: write ps files (aln.ps, alirna.ps and if probabilistic, alidot.ps) from alifold call on result alignment to the results output directory; use alifold options –aln –color –mis fix mlocarna: find pw-aligner and pw-aligner-p executables in PATH 1.9.1 (2017-01-22) ================== improve help and man pages for locarna, locarna\_p, sparse; refactor code for help text (string map for help text) write text inserts for man pages, which are autogenerated from help fix bug in reading stockholm anchors remove parameters min\_am\_prob and min\_bm\_prob from locarna and sparse CLIs; they are useful only for locarna\_p introduce strict semantics for anchor constraints and make default (see mlocarna –relaxed-anchors) fix exparna\_p output add mlocarna option to realign; support 'consensus' constraint specifications 1.9.0 (2016-Dec-26) =================== add mlocarna option to load (default) configuration from file add mlocarna option to read anchor constraints from bed-format specification add option –maxBPspan (analogous to ViennaRNA's maxBPspan) activate penalized option for mlocarna update documentation of mlocarna update reliability-profile.pl: suppress too verbose output; improve behavior of subseq option Tests: introduce mlocarna test with comparison to reference results * generate reference results with make gen-test-results add stockholm writing test Bug fixes: catch empty sequence case for alifold fix error message concerning max-diff-aln in mlocarna fix mlocarna bug: write stockholm also in probabilistic mode fix mlocarna error handling when running multithreaded fix doxygen/docu generation 1.8.12 (2016-Dec-1) =================== Add checks: multi-threaded mlocarna, locarnate Fix severe problem with threads in mlocarna, which caused hangs Fix mlocarna with sparse (precomputation of inloop probs) Update VRNA/C11 configuration (adapts automatically; remove –enable-STDC ) Require ViennaRNA >=2.3.1 Improved options help Cleanup some files in the repository and distribution 1.8.11 (2016-Aug-15) ==================== Add configure flag –enable-STDC; set default to C11 (RNAlib compatibility) Fix output order of reliable structures in mlocarna Migrate to new vrna api; fix pf\_scale bug 1.8.10 (2016-Jul-15) ==================== Improve input checking in mlocarna Increase API version to 1.5 Wrap long alifold consensus output in mlocarna Add consensus structure in locarna output, selectable types mea|alifold|none Add optional stockholm output to mlocarna Introduce quiet switch for locarna, locarna\_p, sparse, and exparna\_p Code cleanup in driver programs Handle sequence name clashes by systematic renaming Read stockholm format Factorize common code in locarna, locarna\_p and sparse (MainHelper) Add stockholm support input and output to locarna Fix bug occuring with empty input sequences Call alifold with /best/ parameters (from perl /and/ c++) Fix locarnate (compatibility to current locarna); add unit test 1.8.9 (2016-21-04) ================== improve configuration improve ubuntu packaging fix anchor constraint check in mlocarna fasta input allow ribofit for mea - e.g. for probabilistic; this used to require ribosum 1.8.8 (2016-15-04) ================== adapt to and require ViennaRNA >=2.2.4 fix all static linking link binaries statically to libLocARNA by default; otherwise use –enable-dynamic-binaries fix & clean up code (after cppcheck static analysis) prepare for rpm packaging * * * 2015 ==== 1.8.7 (2015-11-12) ------------------ prepare for Ubuntu packaging fix man pages * update generation (add missing man pages) * fix program names * improve/fix help/man of binaries and locarnate clean exploc\_p (get rid of "in"-mechanism) fix problems in tests (make check) w/o enable-debug remove wrong MultipleAlignment format check remove locarna.pl from distribution (functionally replaced by binary) 1.8.6 (2015-10-31) ------------------ remove unused parameter "width" from locarna\_rnafold\_pp Increase API version to 1.4 Get rid of locarna.hh In clustal(-like) alignment output, adapt formatting to long names Improve libRNA config, in cases where pkg-config does not work: allow compiling without libgomp, if libgomp is unavailable and is not used by libRNA 1.8.5a ------ Fix behavior in case structure constraints + local folding (see 1.8.2) 1.8.5 (2015-10-10) ------------------ allow empty input sequences/alignments and fix related problems fix score of local alignment w/ empty input sequences 1.8.4 (2015-10-6) ----------------- fix potential overwriting of parameters in classes Aligner\*, which was observed only with gcc-5.2 fix bug that crashed printing string options in verbose mode 1.8.3 ----- improve portability for easier installation on recent MacOS X: compile without openmp; handle VRNA w/o pkgconf file fix c++11 warnings; fix incompatibility with libc++ fix incompatibility with clang (now used by MacOS X); fix warnings of clang remove g++ warnings 1.8.2 ----- change semantics w.r.t. constraints + local folding: constraints turn off local folding reformat change log support generating doxygen documentation from distribution by make doxygen-doc penalized alignment experimental galaxy wrapper generation 1.8.1 ----- implement ribofit Bugfix in OMatrix: incorrect address calculation Bugfix: LocARNA crashed while writing the result pp file if alignments of zero length are computed with options local file output and alifold consensus dp (alifold workaround) bugfixes (OMatrix, alifold len 0 bug) implement slide rule and conflict rule for f1 and mcc calculation; also use default minimal base pair length 3 in class ConfusionMatrix; class interface changes slightly * * * 2014 ==== 1.8.0 ----- Remove absolute path dependencies in scripts. This changes the behavior, since paths are not fixed at compile time. For example, the Vienna RNA programs are located via PATH environment variable. Require linking to VRNA. Remove configure options. Disallow renaming of Vienna RNA tools RNAfold, etc.; expect them in path. Always compile SPARSE/ExpaRNA-P. Don't pass mlocarna script through configure anymore. Add option –sparse to mlocarna Add rnafold-temperature option to mlocarna Use rnafold temperature and parameter files for alifold Warn if used with alifold-consensus-dp Add unit tests for mlocarna calls (standard, prob, sparse) Align alifold structure to alignment in mlocarna output Add Example gcvT.fa for SPARSE sparse: –special-gap-symbols option added (default is false) 1.7.17 ------ max-bps/uil/bpil-length-ratio for SPARSE/ExparnaP Second type of stacking terms: new-stacking Add heuristic to restrict maximum number of "significant" base pairs: max-bps-length-ratio Add max-diff restriction at arc match ends: –max-diff-at-am Restructure parameter passing to Aligner\* classes: use "named argument" idiom 1.7.16 ------ ExpaRNA-P rename of tools 1.7.15 ------ Fix bug concerning iterative alignment and alignment evaluation Rename locarna\_X to exparna\_p ExpaRNA-P code "publication ready" 1.7.14 ------ Handle inconsistencies due to anchor constraints in conflict with other constraints/heuristics, e.g. max-diff: 1) accept -inf pairwise similarities for guide tree construction; 2) clear consensus anchor strings with duplicate names * * * 2013 ==== Jan 2013 -------- Fix bug. Quotes in fasta-names caused failure when generating pps via locarna\_rnafold\_pp in mlocarna. (1.7.3.1) Resolve rnalib dependency. New configure option with-sparse is now required to compile with ExpARNA-P and SPARSE functionality. (1.7.5) Mar 2013 -------- Merge in new sparsification related code. Added fasta input check in mlocarna. (1.7.6) Small bug fixes Fix memory leaks Prepare alignment evaluation functionality Code cleanup/refactorizations (1.7.6.9) Introduce configuration header config.h Fix man page dependency problem May/Jun 2013 ------------ Make sure that make check and make distcheck work Split RnaData into RnaData and RnaEnsemble Introduce new version of pp format (2.0) Read/write of inloop probabilities Cleaner separation of reading/writing of alignments/probability data v.s. computation; in particulare remove I/O from Alignment class Cleaner handling of gaps, alignment edges, and gap symbols in I/O New option –stopwatch (in locarna\*) to turn on detailed internal timing Change class Sequence to be a mere interface to MultipleAlignment that allows operator \[\] for column access Make constraints optional part of multiple alignments; make write/readable with the alignment in clustal and pp format Remove options anchorA, anchorB from locarna and locarna\_X Support anchor and structure annotation in MultipleAlignment RnaEnsemble constrains the folding by structure annotation of Multiple Alignment (if given) (Release 1.7.7) Jul 2013 -------- Support precomputing in loop probabilities for SPARSE Fixed reading of PP 2.0 (Release 1.7.8) Sep 2013 -------- LocARNATE: new code, improvements Exparna-P: Suboptimal traceback and improvements Change default behavior of mlocarna for sequence-local alignment: proceed with only-local subalignments; options local-progressive and global-progressive control behavior, where –global-progressive reactivates the previous one. (Release 1.7.9) Oct 2013 -------- Newick bugfix Small modifications for library use (e.g. for carna) (Release 1.7.10) Nov 2013 -------- Improve max-diff heuristic (without reference alignment): make symmetric and always allow sufficiently large deviation (Release 1.7.11) Fix bug in locarna\_rnafold\_pp (reading clustalw from stdin) Fix bug concerning structure constraints Update format conversions in mlocarna to pp 2.0 format Support for fixed structure constraints (directly in C++) (Release 1.7.12) Fix bug that compromised LocARNA-P w/ anchor-constraints in 1.7.12 In-loop support for fixed structure constraints (Release 1.7.13) Bugfix: computation of consensus anchor constraints could fail; now resolve name clashs by selecting lexicographically smaller name. (Release 1.7.13.1) * * * 2012 ==== Jan 2012 -------- fix bugs in reliability plotting and "fitting" (1.6.2.3) New tool locarna-mea for computing the max. expected accuracy structure from a dot plot (1.6.2.4) New features for pp2dot script New script for generating average pp-files In combination, generate nice colored dot plots; used first for the output of the carna server (1.6.3) Mar 2012 -------- Merge with recent Exparna-P/locarna\_X code (1.7) New classes for infinite integers (this is used for scores, which can be -infty, i.e. undefined). The new mechanism automatizes normalization of infinity using the type system and avoids wrong usage by the type system. Consequently, it is more flexible. It avoids a bug in normalized alignment and helps to clean up the Exparna-P code. (1.7.1) Apr/May 2012 ------------ Add reading of score matrix in mlocarna Fix bug in probabilistic mode, which did not allow '#' in sequence names Fix bugs in output of score matrix Fix drawdplin June 2012 --------- Fix bug in trace controller (1.7.2) Add locarna\_n code, alpha status Aug 2012 -------- Fix a bug related to use of trace controller (max-diff) with free endgaps. Fix autodetection of input multiple alignment file format, i.e. FASTA vs. CLUSTAL. Change interface of scoring such that gapA (gapB) depends on only positions in sequence A (B), resp. (1.7.2.1) Major improvements of the RnaData class and its interface Some clean up (1.7.2.5) Some bug fixes, support for graph kernel guide tree (1.7.2.6) Include graph kernel guide tree support in mlocarna (1.7.2.7) Some cleanup, release. Fix bug (missing initialization) in RnaData (1.7.3) * * * 2011 ==== Jan 2011 -------- Alignment in limited deviation to a reference alignment program deviation computes deviation of alignment to reference Deactivate max-diff-aln for –probabilistic/locarna\_p (Version 1.6) Feb 2011 -------- Restructure code library libLocARNA is generated and is used as library by executables Fix name normalization bug in mlocarna.in (Version 1.6.1) Mar 2011 -------- Doxygen compiles without warning and produces useful documentation of the library Vienna RNA library is now required for compilation and will be linked Locarna accepts clustal files as input and then computes base pair probabilities via pf\_fold of the Vienna RNA lib. Currently this is limited to single sequence clustal files. Implement reading of mfasta files (still switched off). Apr 2011 -------- Implement several alignment comparison measures (and use in locarna\_deviation) (EXPERIMENTAL) Make linking to Vienna librna configurable, default=off! Activate by calling ./configure with –enable-librna. New strategy for consensus dot plot generation: employ RNAalifold -p. Enable via mlocarna's option –alifold-consensus-dp Note: the default consensus dot plot computation seems to be flawed! The new tool pp2dot allows to visualize consensus dot plots (by converting pp to Vienna-like dot plot postscript files) and should help to improve the default strategy (otherwise we are going to replace it!) mlocarna accepts via –tree-file a super-tree as guide tree and automatically projects to the taxa in the input. Allow quotation in newick trees (using Text::ParseWords) and use quotations when generating newick trees May 2011 -------- Fix a problem with compiling on case-insensitive file systems (generate locarna.bin instead of locarna executable in src, rename at install) add alifold-consensus-dp option for mlocarna Aug 2011: Add code for 'locarna\_X' ----------------------------------- Sep 2011: Adding Exparna-P code for "in loop" probabilities ----------------------------------------------------------- Oct 2011: pre-release 1.6.2 --------------------------- Nov 2011: --------- Add mlocarna options (pw-aligner and pw-aligner-p) to run specified binaries in place of locarna and locarna\_p. This can be used to plug in compatible programs like carna Bug fix; compilation without linking libRNA was broken. release (1.6.2) Dec 2011 -------- Bug-fixes: treefile regexp, LARGE\_PF name clash mit Vienna package (1.6.2.1) add script to translate to normalized names for mlocarna Add options pw-aligner-options and pw-aligner-p-options, to mlocarna to pass option strings to the pairwise aligner. This is useful in combination with specifying non-standard pairwise alignment programs. Support generation of pp files from dp2.ps and dp.ps files when skipping dot plot computation with –skip-pp (keep name for legacy). This allows the combine user-defined dotplots with anchor constraints from the mfasta input file. Support fixed structures (with pseudoknots) in the fasta input of mlocarna as structure constraint string with tag FS All base pairs in the fix structure receive a probability of 1. (1.6.2.2) * * * 2010 ==== Jan 2010 -------- new tool Utils/reliability-profile.pl generates nice profile plots from mlocarna –probabilistic output directories stacking turned off, unless exp-prob option used (locarna-1.5a) Mar 2010 -------- Add normalized local alignment, proof of concept (locarna-1.5.1) Combine normalized alignment and kbest Introduce option better to enumerate suboptimal solution better than given threshold –kbest and –better can be used together (locarna-1.5.2) Fix build in separate build directory May 2010 -------- Introduce new representation of fasta data Major restructuring/refactorization of mlocarna.in and MLocarna.pm Move many functions of mlocarna.in to packages and introduce several new packages to group functions thematically (locarna-1.5.3) Resolve a bug that made LocARNA handle Ts as unknown characters. LocARNA now automatically transforms Ts to Us in input sequences. The bug did not affect input sequences without Ts. For matchs involving Ts, LocARNA wrongly used an ad-hoc score instead of the ribosum score for matches involving 'U', as one would expect. Oct 2010 -------- Add EdgeController: adds feature to constrain (max-diff-match) alignment relative to a given alignment. Change handling of max-diff-match in case of unequal length: instead of relaxing constraint, change constraint to |i\*(lenB/lenA)-j|<=max-diff Add multiple alignment class to support construction of EdgeController. Nov 2010 -------- Change Copyright to GPL v2 and update README rename max-diff-match to max-diff heuristic. replace EdgeController by TraceController use the max-diff delta ( TraceController ) to restrict alignment of paired and unpaired positions (not only ends of arcs) in Aligner. Semantics is given by restriction of alignment cuts/matrix cells! * * * 2009 ==== Jan 2009 (v1.42) ---------------- iterative alignment using SCI as optimization criterion Feb 2009 (v1.4.4alpha) ---------------------- cleanup mlocarna code cleanup mlocarna output (inclusive output modes -v, –moreverbose) improve reliability computation multi-threaded mlocarna, new option –cpus : use n threads more structure for mlocarna output to file system (distribute files to subdirs) introduce –pf-scale parameter to locarna\_p and mlocarna precompute exp base match similarity and gap cost for partition function => significant speed up of locarna\_p change handling of max\_diff: guarantee at least |lenA-lenB| improve outside algorithm in locarna\_p (reduce sizes of Mrev-matrices) => with prior optimization massive speedup of locarna\_p add probability filtering after cbt further improvement of outside (cheaper computation of certain Mprime entries) iteration with reliable structure as constraints (option –it-reliable-structure) support for non-threaded perl Mar 2009 -------- fix some problems with the option parsing (e.g. now -p=0.1 is correct and -p=a throws an error) fix bug in initialization for structure locality change semantics of constraints in the context of locality: anchor constraints (i,j) now enforce that edge (i,j) is part of the local alignment (for sequence and structure locality) Apr 2009 -------- add missing options to mlocarna, fix bug in locarnate (thanks to Wolfgang) fix bug with sharing/threads in mlocarna (v1.4.6) locarna\_p computes probabilities for matching fragments May 2009 -------- clean manpage of mlocarna Jun 2009 -------- offer large data type "long double" for partition function computation. this is available when configuring through option –enable-large-pf. Use this in case of long alignments, where the partition function exceeds the range of type "double". Although –pf-scale sometimes provides a workaround, for multiple alignment of large sequences it is often the only viable choice. Jul 2009 -------- add free endgaps via option –free-endgaps "----", for locarna gaps at all for ends can be allowed for free independently. For mlocarna, –free-endgaps will allow free end gaps at any end. Sep 2009 -------- fixed serious bugs concerning stacking: due to these bugs, mlocarna did not profit from stacking and locarna could get wrong results with stacking turned on. Change base pair filtering by probability for stacking: ignore stacking probability, filter only by base pair probability. (locarna-1.4.9alpha) * * * 2008 ==== Feb 2008 -------- remove bug in anchor constraints Ribosum-85-60 compiled in changed default parameters to something reasonable Mar 2008 -------- remove bug in rna\_data.cc reading dp.ps, v 1.2.4 Jun 2008 -------- change char \* to std::string in options module (the g++-compiler does not like it anymore :)) Jul 2008 -------- integrate locarnate - a tool for multiple alignment that uses locarna in combination with tcoffee (Version 1.3) Aug 2008 -------- partition function version of locarna (locarna\_p) experimental support for multiple alignment using basematch probabilities and probabilistic consistency transformation (Version 1.3.2) mlocarna can write basematch probabilities for plotting plotting of basematch probs (Utils/plot-bmprobs) mlocarna now correctly accepts input trees in newick-format that are terminated by ";". However, it does not enforce the ";"-termination mlocarna now writes the result.tree in ";"-terminated newick-format use rounding (instead of truncate) in scoring module, when converting from double to score\_t. This fixes some inconsistency between 32/64bit and is the correct thing to do anyway Oct 2008 -------- improve speed up gained from using anchor constraints Nov 2008 (v1.4) --------------- add probabilistic scoring with consistency transformation with structural scoring in progressive alignment steps change options of mlocarna for probabilistic/mea-type alignment * * * 2007 ==== Sept 2007 (1.0alpha) -------------------- refactoring; new classes Scoring, RnaData, ... preparations for better scoring: reading Ribosum-Data, new class Ribosum computing match probabilities in sequence alignment (Gotoh): Implemented methods: pairHMM, partition function, local pf new class MatchProbs improve option parser: introduce sections and section hiding integrate new scoring scheme: maximum expected accuracy significant speed-up due to re-organization of the recursion equations: redefine D to already contain the score contribution of the arcmatch. This reduces these computations by orders of magnitude! Nov 2007 -------- add constraints to pairwise and multiple alignment. This means for locarna: integrate anchor constraints for mlocarna: read and pass structure constraints to RNAfold -p, read and pass sequence constraints to locarna The pp-format is redefined in order to pass constraint information from mlocarna to locarna. New class for representing and calculating with infinite scores changed default sequ-local=on to off increased min\_prob in mlocarna.pl bug fix in computation of consensus probs rewrite noLP add (pseudo)affine gap penalties make mea working change default output width to 120 ribosum scoring for classic score change handling of options in mlocarna mlocarna learns iterative refinement mlocarna learns conistency based transformation Dec 2007 -------- true affine gap cost (implemented using additional vectors E and F) implemented stacking (v\_1\_2alpha) removed bugs in traceback cleaned options include version name in output (v\_1\_2\_1a) add man pages add Ribosum85-60 matrix in distribution avoid writing to global /tmp directory (v\_1\_2\_2a) avoid potential file name conflicts in mlocarna accept duplicate (or not prefix unique) names in mfasta input * * * 2006 ==== Jan 2006: --------- add support for aligning alignments (used for multiple progressive alignment) Aug 2006: --------- Lower memory consumption of locarna. In particular important in case of scanning (target against genome) Add some options/features that are useful for scanning option –kbest option –max-diff-am option –ungappedA option –local-output handling of nucleotide-symbol N for unknown in input Oct 2006 -------- add support for stacking alignment, not finished May 2006 (0.991) ---------------- small changes, rename mlocarna-p to mlocarna * * * 2005 ==== Mai 2005 -------- global alignment June 2005 --------- extension to local alignment (sequence+structure locality), no\_lonely\_pairs option Nov 2005 -------- command line options Dez 2005 -------- recognize and read dot.ps files (in add to formerly used pp-files) --- # LocARNA-2.0.0: Class Hierarchy LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class 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[Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) [Go to the textual class hierarchy](https://s-will.github.io/LocARNA/hierarchy.html) | | | --- | | ![](https://s-will.github.io/LocARNA/inherit_graph_0.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_1.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_2.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_3.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_4.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_5.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_6.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_7.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_8.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_9.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_10.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_11.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_12.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_13.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_14.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_15.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_16.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_17.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_18.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_19.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_20.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_21.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_22.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_23.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_24.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_25.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_26.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_27.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_28.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_29.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_30.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_31.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_32.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_33.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_34.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_35.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_36.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_37.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_38.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_39.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_40.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_41.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_42.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_43.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_44.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_45.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_46.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_47.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_48.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_49.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_50.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_51.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_52.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_53.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_54.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_55.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_56.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_57.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_58.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_59.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_60.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_61.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_62.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_63.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_64.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_65.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_66.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_67.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_68.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_69.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_70.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_71.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_72.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_73.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_74.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_75.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_76.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_77.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_78.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_79.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_80.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_81.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_82.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_83.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_84.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_85.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_86.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_87.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_88.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_89.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_90.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_91.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_92.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_93.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_94.png) | | ![](https://s-will.github.io/LocARNA/inherit_graph_95.png) | --- # LocARNA-2.0.0: File List LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * 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[e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) Here is a list of all documented files with brief descriptions: \[detail level 123\] | | | | --- | --- | | ▼ [src](https://s-will.github.io/LocARNA/dir_68267d1309a1af8e8297ef4c3efbcdba.html) | | | ▼ [LocARNA](https://s-will.github.io/LocARNA/dir_044ab21d82a82dab8ad00551727c905f.html) | | | [](https://s-will.github.io/LocARNA/aligner_8hh_source.html)
**aligner.hh** | | | [](https://s-will.github.io/LocARNA/aligner__impl_8hh_source.html)
**aligner\_impl.hh** | | | [](https://s-will.github.io/LocARNA/aligner__n_8hh_source.html)
**aligner\_n.hh** | | | [](https://s-will.github.io/LocARNA/aligner__p_8hh_source.html)
**aligner\_p.hh** | | | [](https://s-will.github.io/LocARNA/aligner__params_8hh_source.html)
**aligner\_params.hh** | | | [](https://s-will.github.io/LocARNA/aligner__restriction_8hh_source.html)
**aligner\_restriction.hh** | | | [](https://s-will.github.io/LocARNA/alignment_8hh_source.html)
**alignment.hh** | | | [](https://s-will.github.io/LocARNA/alignment__impl_8hh_source.html)
**alignment\_impl.hh** | | | [](https://s-will.github.io/LocARNA/alphabet_8hh_source.html)
**alphabet.hh** | | | [](https://s-will.github.io/LocARNA/anchor__constraints_8hh_source.html)
**anchor\_constraints.hh** | | | [](https://s-will.github.io/LocARNA/arc__matches_8hh_source.html)
**arc\_matches.hh** | | | [](https://s-will.github.io/LocARNA/aux_8hh_source.html)
**aux.hh** | | | [](https://s-will.github.io/LocARNA/base__pair__filter_8hh_source.html)
**base\_pair\_filter.hh** | | | [](https://s-will.github.io/LocARNA/basepairs_8hh_source.html)
**basepairs.hh** | | | [](https://s-will.github.io/LocARNA/confusion__matrix_8hh_source.html)
**confusion\_matrix.hh** | | | [](https://s-will.github.io/LocARNA/discrete__distribution_8hh_source.html)
**discrete\_distribution.hh** | | | [](https://s-will.github.io/LocARNA/edge__probs_8hh_source.html)
**edge\_probs.hh** | | | [](https://s-will.github.io/LocARNA/exact__matcher_8hh_source.html)
**exact\_matcher.hh** | | | [](https://s-will.github.io/LocARNA/ext__rna__data_8hh_source.html)
**ext\_rna\_data.hh** | | | [](https://s-will.github.io/LocARNA/ext__rna__data__impl_8hh_source.html)
**ext\_rna\_data\_impl.hh** | | | [](https://s-will.github.io/LocARNA/fitonoff_8hh_source.html)
**fitonoff.hh** | | | [](https://s-will.github.io/LocARNA/free__endgaps_8hh_source.html)
**free\_endgaps.hh** | | | [](https://s-will.github.io/LocARNA/global__stopwatch_8hh_source.html)
**global\_stopwatch.hh** | | | [](https://s-will.github.io/LocARNA/infty__int_8hh_source.html)
**infty\_int.hh** | | | [](https://s-will.github.io/LocARNA/matrices_8hh_source.html)
**matrices.hh** | | | [](https://s-will.github.io/LocARNA/matrix_8hh_source.html)
**matrix.hh** | | | [](https://s-will.github.io/LocARNA/mcc__matrices_8hh_source.html)
**mcc\_matrices.hh** | | | [](https://s-will.github.io/LocARNA/multiple__alignment_8hh_source.html)
**multiple\_alignment.hh** | | | [](https://s-will.github.io/LocARNA/named__arguments_8hh_source.html)
**named\_arguments.hh** | | | [](https://s-will.github.io/LocARNA/options_8hh_source.html)
[options.hh](https://s-will.github.io/LocARNA/options_8hh.html) | Options – an interface for getopt\_long | | [](https://s-will.github.io/LocARNA/pfold__params_8hh_source.html)
**pfold\_params.hh** | | | [](https://s-will.github.io/LocARNA/quadmath_8hh_source.html)
**quadmath.hh** | | | [](https://s-will.github.io/LocARNA/ribofit_8hh_source.html)
**ribofit.hh** | | | [](https://s-will.github.io/LocARNA/ribosum_8hh_source.html)
**ribosum.hh** | | | [](https://s-will.github.io/LocARNA/rna__data_8hh_source.html)
**rna\_data.hh** | | | [](https://s-will.github.io/LocARNA/rna__data__impl_8hh_source.html)
**rna\_data\_impl.hh** | | | [](https://s-will.github.io/LocARNA/rna__ensemble_8hh_source.html)
**rna\_ensemble.hh** | | | [](https://s-will.github.io/LocARNA/rna__ensemble__impl_8hh_source.html)
**rna\_ensemble\_impl.hh** | | | [](https://s-will.github.io/LocARNA/rna__structure_8hh_source.html)
**rna\_structure.hh** | | | [](https://s-will.github.io/LocARNA/scoring_8hh_source.html)
**scoring.hh** | | | [](https://s-will.github.io/LocARNA/scoring__fwd_8hh_source.html)
**scoring\_fwd.hh** | | | [](https://s-will.github.io/LocARNA/sequence_8hh_source.html)
**sequence.hh** | | | [](https://s-will.github.io/LocARNA/sequence__annotation_8hh_source.html)
**sequence\_annotation.hh** | | | [](https://s-will.github.io/LocARNA/sparse__matrix_8hh_source.html)
**sparse\_matrix.hh** | | | [](https://s-will.github.io/LocARNA/sparse__vector_8hh_source.html)
**sparse\_vector.hh** | | | [](https://s-will.github.io/LocARNA/sparse__vector__base_8hh_source.html)
**sparse\_vector\_base.hh** | | | [](https://s-will.github.io/LocARNA/sparsification__mapper_8hh_source.html)
**sparsification\_mapper.hh** | | | [](https://s-will.github.io/LocARNA/stopwatch_8hh_source.html)
**stopwatch.hh** | | | [](https://s-will.github.io/LocARNA/stral__score_8hh_source.html)
**stral\_score.hh** | | | [](https://s-will.github.io/LocARNA/string1_8hh_source.html)
**string1.hh** | | | [](https://s-will.github.io/LocARNA/trace__controller_8hh_source.html)
**trace\_controller.hh** | | | [](https://s-will.github.io/LocARNA/tuples_8hh_source.html)
**tuples.hh** | | | [](https://s-will.github.io/LocARNA/zip_8hh_source.html)
**zip.hh** | | | [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html) | Defines main function of locarna | | [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html) | Defines main function of locarna\_p | | [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html) | Defines main function of SPARSE | --- # LocARNA-2.0.0: Class Index LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * 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[SequenceAnnotation](https://s-will.github.io/LocARNA/classLocARNA_1_1SequenceAnnotation.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) (LocARNA::BasePairFilter) [SparseMatrix](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [SparseTraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseTraceController.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [SparseVector](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVector.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [SparseVectorBase](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [StopWatch](https://s-will.github.io/LocARNA/classLocARNA_1_1StopWatch.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [StralScore](https://s-will.github.io/LocARNA/classLocARNA_1_1StralScore.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [string1](https://s-will.github.io/LocARNA/classLocARNA_1_1string1.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) T [TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [TraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceController.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [TraceRange](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceRange.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [triple](https://s-will.github.io/LocARNA/classLocARNA_1_1triple.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [ArcMatches::tuple5](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1tuple5.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [tuple\_cat\_type](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [tuple\_cat\_type< std::tuple< Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [type\_subset\_of](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [type\_subset\_of< std::tuple< T, Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_01T_00_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [type\_subset\_of< std::tuple< Ts... >, std::tuple<> >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_4_01_4.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [type\_subset\_of< std::tuple<>, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) U [AlignerImpl::UnmodifiedScoringView](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl_1_1UnmodifiedScoringView.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) [AlignerN::UnmodifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) W [wrong\_format\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1wrong__format__failure.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) Z [Zip](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) ([LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) ) --- # LocARNA-2.0.0: Class List LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_type.html#index_c) * [e](https://s-will.github.io/LocARNA/functions_type.html#index_e) * [i](https://s-will.github.io/LocARNA/functions_type.html#index_i) * [k](https://s-will.github.io/LocARNA/functions_type.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_type.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_type.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_type.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_type.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_type.html#index_p) * [r](https://s-will.github.io/LocARNA/functions_type.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_type.html#index_s) * [v](https://s-will.github.io/LocARNA/functions_type.html#index_v) * [Enumerations](https://s-will.github.io/LocARNA/functions_enum.html) * [Related Functions](https://s-will.github.io/LocARNA/functions_rela.html) * [Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) Here are the classes, structs, unions and interfaces with brief descriptions: \[detail level 1234\] | | | | --- | --- | | ►N[LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) | | | ►N**BasePairFilter** | | | C[Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | Basic class for base pair filters (no filtering) | | C[BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html) | Loop size base pair filter | | C[SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) | Base pair range filter | | C[Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html) | Base pair filter to allow only canonical base pairs | | C[Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html) | | | C[greater\_second](https://s-will.github.io/LocARNA/classLocARNA_1_1greater__second.html) | Implements comparison by member second | | C[Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | Implements locarna alignment algorithm | | C[Matrix](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | Simple 2D matrix class, provides access via operator (int,int) | | ►C[AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html) | Implementation of Aligner | | C[ModifiedScoringView](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl_1_1ModifiedScoringView.html) | Provides a modified view on the scoring | | C[UnmodifiedScoringView](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl_1_1UnmodifiedScoringView.html) | Provides the standard view on the scoring | | ►C[AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html) | Implements SPARSE, next generation alignment algorithm for locarna | | C[ModifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html) | Provides a modified view on the scoring | | C[UnmodifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html) | Provides the standard view on the scoring | | C[AlignerP](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html) | Computes partition function of alignment, arc match and base match probabilities | | C[tuple\_cat\_type](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type.html) | Type of two concattenated tuples | | C[tuple\_cat\_type< std::tuple< Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) | | | C[AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | Parameter for alignment by Aligner | | C[AlignerPParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | Parameters for AlignerP | | C[AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) | Parameters for AlignerN | | C[AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | Restricts range of an alignment in Aligner | | C[EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | End of an alignment edge | | C[AlignmentEdges](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentEdges.html) | | | C[Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html) | Represents a structure-annotated sequence alignment | | C[AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | Implementation of Alignment | | C[Alphabet](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | Specifies an alphabet of static size | | C[AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html) | Represents anchor constraints between two sequences | | C[ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | Represents a match of two base pairs (arc match) | | ►C[ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html) | Maintains the relevant arc matches and their scores | | C[lex\_greater\_left\_ends](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html) | | | C[tuple5](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1tuple5.html) | | | C[ArcMatchesIndexed](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatchesIndexed.html) | Class ArcMatches with additional mapping | | C[check\_score\_t](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t.html) | | | C[check\_score\_t< extended\_pf\_score\_t >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t_3_01extended__pf__score__t_01_4.html) | | | C[failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | Simple exception class that supports a text message | | C[wrong\_format\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1wrong__format__failure.html) | Thrown, when reading data that is not in the supposed format | | C[syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html) | Thrown, when the format is recognized but syntax is incorrect | | C[Delay](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html) | | | C[make\_delay](https://s-will.github.io/LocARNA/classLocARNA_1_1make__delay.html) | | | C[BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) | Represents a base pair | | ►C[BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | Describes sequence and structure ensemble of an RNA | | C[LeftAdjEntry](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs_1_1LeftAdjEntry.html) | Entry in a left adjacency list | | C[RightAdjEntry](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs_1_1RightAdjEntry.html) | Entry in a right adjacency list | | C[ConfusionMatrix](https://s-will.github.io/LocARNA/classLocARNA_1_1ConfusionMatrix.html) | Compare RNA secondary structure by their confusion matrix | | C[DiscreteDistribution](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html) | | | C[EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | Provides probabilities for alignment egdes (match or trace probabilities etc) | | C[MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) | Provide match probabilities | | C[PFGotoh](https://s-will.github.io/LocARNA/classLocARNA_1_1PFGotoh.html) | Provide Gotoh partition functions | | C[TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html) | Provide trace probabilities | | C[PFMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PFMatchProbs.html) | Provide match probabilities calculated by pf approach | | C[PFTraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PFTraceProbs.html) | Provide match probabilities calculated by pf approach | | ►C[PairHMMMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html) | | | C[PairHMMParams](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs_1_1PairHMMParams.html) | Maintains parameter for computing match probabilities | | C[SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | Stores a Pattern in one sequence | | C[PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | Able to manage an EPM, consists of 2 singlepatterns, one in each RNA | | C[PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html) | Manage a set of EPMs (PatternPair) | | C[LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | Computes the best chain of EPMs, the LCS-EPM | | C[SparseTraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseTraceController.html) | Combines the TraceController with the Mapper for both sequences | | C[EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html) | Class for the representation of exact pattern matches (EPM) | | C[ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) | Computes exact pattern matchings (EPM) between two RNA sequences | | C[ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html) | Represent sparsified data of RNA ensemble extended by in loop probabilities | | C[ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html) | Implementation of ExtRnaData | | C[FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | Implements fitting of a two-step function to a number sequence | | C[FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html) | Fitting of a two-step function with position-specific step penalities | | C[FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | Description of free end gaps | | C[TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html) | | | C[InftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1InftyInt.html) | | | C[FiniteInt](https://s-will.github.io/LocARNA/classLocARNA_1_1FiniteInt.html) | | | C[RMatrix](https://s-will.github.io/LocARNA/classLocARNA_1_1RMatrix.html) | Simple matrix class with restriction to a range | | C[OMatrix](https://s-will.github.io/LocARNA/classLocARNA_1_1OMatrix.html) | Simple matrix class with offset | | C[RotMatrix](https://s-will.github.io/LocARNA/classLocARNA_1_1RotMatrix.html) | A matrix class with rotation | | C[McC\_matrices\_base](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__matrices__base.html) | | | C[McC\_matrices\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__matrices__t.html) | McCaskill matrices | | C[McC\_ali\_matrices\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__ali__matrices__t.html) | Alifold-McCaskill matrices | | ►C[MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html) | Represents a multiple alignment | | ►C[AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html) | Read only proxy class representing a column of the alignment | | C[const\_iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn_1_1const__iterator.html) | Const iterator | | C[SeqEntry](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1SeqEntry.html) | A row in a multiple alignment | | C[has\_type](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type.html) | | | C[has\_type< T, std::tuple<> >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type_3_01T_00_01std_1_1tuple_3_4_01_4.html) | | | C[has\_type< T, std::tuple< U, Ts... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type_3_01T_00_01std_1_1tuple_3_01U_00_01Ts_8_8_8_01_4_01_4.html) | | | C[has\_type< T, std::tuple< T, Ts... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type_3_01T_00_01std_1_1tuple_3_01T_00_01Ts_8_8_8_01_4_01_4.html) | | | C[contains](https://s-will.github.io/LocARNA/structLocARNA_1_1contains.html) | | | C[contains< T, std::tuple<> >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains_3_01T_00_01std_1_1tuple_3_4_01_4.html) | | | C[contains< T, std::tuple< U, Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains_3_01T_00_01std_1_1tuple_3_01U_00_01Us_8_8_8_01_4_01_4.html) | | | C[contains< T, std::tuple< T, Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains_3_01T_00_01std_1_1tuple_3_01T_00_01Us_8_8_8_01_4_01_4.html) | | | C[type\_subset\_of](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of.html) | | | C[type\_subset\_of< std::tuple< Ts... >, std::tuple<> >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_4_01_4.html) | | | C[type\_subset\_of< std::tuple<>, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) | | | C[type\_subset\_of< std::tuple< T, Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_01T_00_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) | | | C[NamedArgument](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) | | | C[option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | Definition structure of an option | | ►C[PFoldParams](https://s-will.github.io/LocARNA/classLocARNA_1_1PFoldParams.html) | Parameters for partition folding | | C[args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | C[Ribofit](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit.html) | Family of Ribofit matrices | | C[Ribofit\_will2014](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit__will2014.html) | | | C[Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html) | Represents ribosum similarity matrices | | C[RibosumFreq](https://s-will.github.io/LocARNA/classLocARNA_1_1RibosumFreq.html) | Represents ribosum similarity matrices including raw frequencies | | C[RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html) | Represent sparsified data of RNA ensemble | | ►C[RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html) | Implementation of RnaData | | C[keyvec](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl_1_1keyvec.html) | | | C[RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html) | Represents the raw structure ensemble data for an RNA | | C[RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html) | Implementation of RnaEnsemble | | C[RnaStructure](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaStructure.html) | An RNA secondary structure | | C[ScoringParams](https://s-will.github.io/LocARNA/classLocARNA_1_1ScoringParams.html) | Parameters for scoring | | C[Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html) | Provides methods for the scoring of alignments | | C[PFScoring](https://s-will.github.io/LocARNA/classLocARNA_1_1PFScoring.html) | | | C[Sequence](https://s-will.github.io/LocARNA/classLocARNA_1_1Sequence.html) | "Sequence View" of multiple alignment as array of column vectors | | C[SequenceAnnotation](https://s-will.github.io/LocARNA/classLocARNA_1_1SequenceAnnotation.html) | Annotation of a sequence | | C[SparseMatrix](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) | Represents a sparse 2D matrix | | C[SparseVector](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVector.html) | Represents a sparse vector | | ►C[SparseVectorBase](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html) | Base class template for sparse vector and matrix | | C[element\_proxy](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase_1_1element__proxy.html) | Proxy for element of sparse vector | | ►C[SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html) | Represents the mapping for sparsification | | C[info\_for\_pos](https://s-will.github.io/LocARNA/structLocARNA_1_1SparsificationMapper_1_1info__for__pos.html) | | | C[StopWatch](https://s-will.github.io/LocARNA/classLocARNA_1_1StopWatch.html) | Control a set of named stop watch like timers | | C[StralScore](https://s-will.github.io/LocARNA/classLocARNA_1_1StralScore.html) | Implements the stral-like scoring function | | C[string1](https://s-will.github.io/LocARNA/classLocARNA_1_1string1.html) | A simple 1-based string | | C[TraceRange](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceRange.html) | Represents a range of traces | | C[MatchController](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html) | Abstract class that declares the method is\_valid\_match() | | C[TraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceController.html) | Controls the matrix cells valid for traces | | C[triple](https://s-will.github.io/LocARNA/classLocARNA_1_1triple.html) | Represents a 3-tuple | | C[quadruple](https://s-will.github.io/LocARNA/classLocARNA_1_1quadruple.html) | Represents a 4-tuple | | C[quintuple](https://s-will.github.io/LocARNA/classLocARNA_1_1quintuple.html) | Represents a 5-tuple | | ►C[Zip](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | C[iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip_1_1iterator.html) | | | ►C[ConstIterableSequence](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | | | C[const\_iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence_1_1const__iterator.html) | | | C[Enumerate](https://s-will.github.io/LocARNA/classLocARNA_1_1Enumerate.html) | | | ►N**std** | STL namespace | | C[hash< std::pair< T1, T2 > >](https://s-will.github.io/LocARNA/structstd_1_1hash_3_01std_1_1pair_3_01T1_00_01T2_01_4_01_4.html) | Hash function for pairs | --- # LocARNA-2.0.0: LocARNA::MultipleAlignment::AliColumn Class Reference LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * 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[Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html) * [AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html) read only proxy class representing a column of the alignment [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#details) `#include <[multiple_alignment.hh](https://s-will.github.io/LocARNA/multiple__alignment_8hh_source.html) >` | | | | --- | --- | | Classes
------- | | | class | [const\_iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn_1_1const__iterator.html) | | | const iterator [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn_1_1const__iterator.html#details) | | | | | | | | --- | --- | | Public Types
------------ | | | using | **value\_type** = char | | | | | using | [iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aabac5c3625192e91d5e7e870d2698321)
= [const\_iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn_1_1const__iterator.html) | | | iterator [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aabac5c3625192e91d5e7e870d2698321) | | | | | | | | --- | --- | | Public Member Functions
----------------------- | | | | [AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#affdced7f6d2e4a0aab01272fc887f2d9)
(const [MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html)
&ma, [size\_type](https://s-will.github.io/LocARNA/namespaceLocARNA.html#adc6caff014e7d9621f0aa488846afe0b)
col\_index) | | | Construct from multiple alignment column. [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#affdced7f6d2e4a0aab01272fc887f2d9) | | | | | const char & | [operator\[\]](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a8cf7150f99c7044211394b2f9562c857)
([size\_type](https://s-will.github.io/LocARNA/namespaceLocARNA.html#adc6caff014e7d9621f0aa488846afe0b)
row\_index) const | | | element access [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a8cf7150f99c7044211394b2f9562c857) | | | | | [size\_type](https://s-will.github.io/LocARNA/namespaceLocARNA.html#adc6caff014e7d9621f0aa488846afe0b) | [size](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aeb3b5a26b58ba4689c8b5d0189872277)
() const | | | Size / Number of rows. [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aeb3b5a26b58ba4689c8b5d0189872277) | | | | | bool | [operator==](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a7b9149158c0f949a624b770f84f90d85)
(const [AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html)
&ac) const | | | Test equality. [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a7b9149158c0f949a624b770f84f90d85) | | | | | bool | [operator!=](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a6ba61c341df7f886c71f2aa49fe48bb6)
(const [AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html)
&ac) const | | | Test inequality. [More...](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a6ba61c341df7f886c71f2aa49fe48bb6) | | | | | auto | [begin](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#ae02c84b7dffb9b735fd73463f8d7b584)
() const | | | begin iterator (always const) | | | | | auto | [end](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a7dff63d2f5c32990ccb4413ee943f42c)
() const | | | end iterator (always const) | | | | Detailed Description -------------------- read only proxy class representing a column of the alignment Allow read only access to the symbols in the column by their row index Member Typedef Documentation ---------------------------- [◆](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aabac5c3625192e91d5e7e870d2698321) iterator ------------------------------------------------------------------------------------------------------------------------------------ using [LocARNA::MultipleAlignment::AliColumn::iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aabac5c3625192e91d5e7e870d2698321) = [const\_iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn_1_1const__iterator.html) iterator Note out of laziness (mostly), do not provide a real non-const iterator; however, the type must exist for use with zip/enumerate Constructor & Destructor Documentation -------------------------------------- [◆](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#affdced7f6d2e4a0aab01272fc887f2d9) AliColumn() --------------------------------------------------------------------------------------------------------------------------------------- | | | | | | --- | --- | --- | --- | | LocARNA::MultipleAlignment::AliColumn::AliColumn | ( | const [MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html)
& | _ma_, | | | | [size\_type](https://s-will.github.io/LocARNA/namespaceLocARNA.html#adc6caff014e7d9621f0aa488846afe0b) | _col\_index_ | | | ) | | | inline Construct from multiple alignment column. Parameters | | | | --- | --- | | ma | multiple alignment | | col\_index | column index | Member Function Documentation ----------------------------- [◆](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a6ba61c341df7f886c71f2aa49fe48bb6) operator!=() ---------------------------------------------------------------------------------------------------------------------------------------- | | | | | | | | --- | --- | --- | --- | --- | --- | | bool LocARNA::MultipleAlignment::AliColumn::operator!= | ( | const [AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html)
& | _ac_ | ) | const | inline Test inequality. Parameters | | | | --- | --- | | ac | second alignment column | Returns whether columns are equal [◆](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a7b9149158c0f949a624b770f84f90d85) operator==() ---------------------------------------------------------------------------------------------------------------------------------------- | | | | | | | | --- | --- | --- | --- | --- | --- | | bool LocARNA::MultipleAlignment::AliColumn::operator== | ( | const [AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html)
& | _ac_ | ) | const | inline Test equality. Parameters | | | | --- | --- | | ac | second alignment column | Returns whether columns are equal [◆](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#a8cf7150f99c7044211394b2f9562c857) operator\[\]() ------------------------------------------------------------------------------------------------------------------------------------------ | | | | | | | | --- | --- | --- | --- | --- | --- | | const char& LocARNA::MultipleAlignment::AliColumn::operator\[\] | ( | [size\_type](https://s-will.github.io/LocARNA/namespaceLocARNA.html#adc6caff014e7d9621f0aa488846afe0b) | _row\_index_ | ) | const | inline element access Parameters | | | | --- | --- | | row\_index | 0-based index of alignment row | Returns character at row in the represented column [◆](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html#aeb3b5a26b58ba4689c8b5d0189872277) size() ---------------------------------------------------------------------------------------------------------------------------------- | | | | | | | --- | --- | --- | --- | --- | | [size\_type](https://s-will.github.io/LocARNA/namespaceLocARNA.html#adc6caff014e7d9621f0aa488846afe0b)
LocARNA::MultipleAlignment::AliColumn::size | ( | | ) | const | inline Size / Number of rows. Returns number of rows of the multiple alignment * * * The documentation for this class was generated from the following file: * src/LocARNA/[multiple\_alignment.hh](https://s-will.github.io/LocARNA/multiple__alignment_8hh_source.html) --- # LocARNA-2.0.0: Class Hierarchy LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * 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![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) [Go to the graphical class hierarchy](https://s-will.github.io/LocARNA/inherits.html) This inheritance list is sorted roughly, but not completely, alphabetically: \[detail level 1234\] | | | | --- | --- | | C[LocARNA::MultipleAlignment::AliColumn](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn.html) | Read only proxy class representing a column of the alignment | | C[LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | Implements locarna alignment algorithm | | C[LocARNA::AlignerImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl.html) | Implementation of Aligner | | C[LocARNA::AlignerN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN.html) | Implements SPARSE, next generation alignment algorithm for locarna | | C[LocARNA::AlignerP< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerP.html) | Computes partition function of alignment, arc match and base match probabilities | | ►C[LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | Parameter for alignment by Aligner | | C[LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) | Parameters for AlignerN | | C[LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | Parameters for AlignerP | | C[LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | Restricts range of an alignment in Aligner | | C[LocARNA::Alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Alignment.html) | Represents a structure-annotated sequence alignment | | C[LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | Implementation of Alignment | | C[LocARNA::AnchorConstraints](https://s-will.github.io/LocARNA/classLocARNA_1_1AnchorConstraints.html) | Represents anchor constraints between two sequences | | C[LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | Represents a match of two base pairs (arc match) | | ►C[LocARNA::ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html) | Maintains the relevant arc matches and their scores | | C[LocARNA::ArcMatchesIndexed](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatchesIndexed.html) | Class ArcMatches with additional mapping | | C[LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | ►C**std::array< T >** | STL class | | C[LocARNA::Alphabet< std::string, 16 >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | C[LocARNA::Alphabet< char, 4 >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | C[LocARNA::Alphabet< std::string, 4 >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | C[LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | Specifies an alphabet of static size | | C[LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | Describes sequence and structure ensemble of an RNA | | ►C[LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) | Represents a base pair | | C[LocARNA::BasePairs::LeftAdjEntry](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs_1_1LeftAdjEntry.html) | Entry in a left adjacency list | | C[LocARNA::BasePairs::RightAdjEntry](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs_1_1RightAdjEntry.html) | Entry in a right adjacency list | | C[LocARNA::check\_score\_t< T >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t.html) | | | C[LocARNA::check\_score\_t< extended\_pf\_score\_t >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t_3_01extended__pf__score__t_01_4.html) | | | C[LocARNA::ConfusionMatrix](https://s-will.github.io/LocARNA/classLocARNA_1_1ConfusionMatrix.html) | Compare RNA secondary structure by their confusion matrix | | C[LocARNA::ConstIterableSequence< T >::const\_iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence_1_1const__iterator.html) | | | C[LocARNA::MultipleAlignment::AliColumn::const\_iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1AliColumn_1_1const__iterator.html) | Const iterator | | C[LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | | | C[LocARNA::contains< T, Us >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains.html) | | | ►C[LocARNA::contains< T, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains.html) | | | C[LocARNA::contains< T, std::tuple< U, Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains_3_01T_00_01std_1_1tuple_3_01U_00_01Us_8_8_8_01_4_01_4.html) | | | C[LocARNA::Delay< Value, Function >](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html) | | | C[LocARNA::DiscreteDistribution](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html) | | | C[LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | End of an alignment edge | | ►C[LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | Provides probabilities for alignment egdes (match or trace probabilities etc) | | ►C[LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) | Provide match probabilities | | C[LocARNA::PFMatchProbs< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFMatchProbs.html) | Provide match probabilities calculated by pf approach | | C[LocARNA::PairHMMMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html) | | | ►C[LocARNA::TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html) | Provide trace probabilities | | C[LocARNA::PFTraceProbs< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFTraceProbs.html) | Provide match probabilities calculated by pf approach | | C[LocARNA::SparseVectorBase< Derived, ValueType, KeyType >::element\_proxy](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase_1_1element__proxy.html) | Proxy for element of sparse vector | | C[LocARNA::EPM](https://s-will.github.io/LocARNA/classLocARNA_1_1EPM.html) | Class for the representation of exact pattern matches (EPM) | | C[LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) | Computes exact pattern matchings (EPM) between two RNA sequences | | ►C**std::exception** | STL class | | ►C[LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | Simple exception class that supports a text message | | C[LocARNA::syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html) | Thrown, when the format is recognized but syntax is incorrect | | C[LocARNA::wrong\_format\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1wrong__format__failure.html) | Thrown, when reading data that is not in the supposed format | | C[LocARNA::ExtRnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaDataImpl.html) | Implementation of ExtRnaData | | ►C**std::false\_type** | | | C[LocARNA::contains< T, std::tuple<> >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains_3_01T_00_01std_1_1tuple_3_4_01_4.html) | | | C[LocARNA::has\_type< T, std::tuple<> >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type_3_01T_00_01std_1_1tuple_3_4_01_4.html) | | | C[LocARNA::type\_subset\_of< std::tuple< Ts... >, std::tuple<> >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_4_01_4.html) | | | ►C[LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | Basic class for base pair filters (no filtering) | | C[LocARNA::BasePairFilter::BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html) | Loop size base pair filter | | C[LocARNA::BasePairFilter::Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html) | Base pair filter to allow only canonical base pairs | | C[LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html) | | | C[LocARNA::BasePairFilter::SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) | Base pair range filter | | ►C[LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | Implements fitting of a two-step function to a number sequence | | C[LocARNA::FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html) | Fitting of a two-step function with position-specific step penalities | | C[LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | Description of free end gaps | | C[LocARNA::greater\_second< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1greater__second.html) | Implements comparison by member second | | C[LocARNA::has\_type< T, Tuple >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type.html) | | | ►C[LocARNA::has\_type< T, std::tuple< Ts... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type.html) | | | C[LocARNA::has\_type< T, std::tuple< U, Ts... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type_3_01T_00_01std_1_1tuple_3_01U_00_01Ts_8_8_8_01_4_01_4.html) | | | C[std::hash< std::pair< T1, T2 > >](https://s-will.github.io/LocARNA/structstd_1_1hash_3_01std_1_1pair_3_01T1_00_01T2_01_4_01_4.html) | Hash function for pairs | | C[LocARNA::SparsificationMapper::info\_for\_pos](https://s-will.github.io/LocARNA/structLocARNA_1_1SparsificationMapper_1_1info__for__pos.html) | | | ►C**iparent\_t** | | | C[LocARNA::Zip< T1, T2 >::iterator](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip_1_1iterator.html) | | | C[LocARNA::RnaDataImpl::keyvec< KEY >](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl_1_1keyvec.html) | | | C[LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | Computes the best chain of EPMs, the LCS-EPM | | C[LocARNA::ArcMatches::lex\_greater\_left\_ends](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html) | | | C[LocARNA::make\_delay< Value >](https://s-will.github.io/LocARNA/classLocARNA_1_1make__delay.html) | | | ►C[LocARNA::MatchController](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html) | Abstract class that declares the method is\_valid\_match() | | ►C[LocARNA::TraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceController.html) | Controls the matrix cells valid for traces | | C[LocARNA::SparseTraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseTraceController.html) | Combines the TraceController with the Mapper for both sequences | | C[LocARNA::Matrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | Simple 2D matrix class, provides access via operator (int,int) | | C[LocARNA::Matrix< ArcMatchIdxVec >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | | | C[LocARNA::Matrix< double >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | | | ►C[LocARNA::Matrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | | | C[LocARNA::OMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1OMatrix.html) | Simple matrix class with offset | | C[LocARNA::RMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1RMatrix.html) | Simple matrix class with restriction to a range | | C[LocARNA::RotMatrix< elem\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1RotMatrix.html) | A matrix class with rotation | | C[LocARNA::Matrix< infty\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | | | C[LocARNA::Matrix< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | | | C[LocARNA::Matrix< score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | | | C[LocARNA::Matrix< size\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1Matrix.html) | | | ►C[LocARNA::McC\_matrices\_base](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__matrices__base.html) | | | C[LocARNA::McC\_ali\_matrices\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__ali__matrices__t.html) | Alifold-McCaskill matrices | | C[LocARNA::McC\_matrices\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1McC__matrices__t.html) | McCaskill matrices | | C[LocARNA::AlignerImpl::ModifiedScoringView](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl_1_1ModifiedScoringView.html) | Provides a modified view on the scoring | | C[LocARNA::AlignerN::ModifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html) | Provides a modified view on the scoring | | ►C[LocARNA::MultipleAlignment](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment.html) | Represents a multiple alignment | | C[LocARNA::Sequence](https://s-will.github.io/LocARNA/classLocARNA_1_1Sequence.html) | "Sequence View" of multiple alignment as array of column vectors | | C[LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) | | | C[LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | Definition structure of an option | | ►C**std::pair** | | | ►C[LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | C[LocARNA::Enumerate< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Enumerate.html) | | | C[LocARNA::Zip< T1, T2 >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | ►C[LocARNA::triple< T1, T2, T3 >](https://s-will.github.io/LocARNA/classLocARNA_1_1triple.html) | Represents a 3-tuple | | ►C[LocARNA::quadruple< T1, T2, T3, T4 >](https://s-will.github.io/LocARNA/classLocARNA_1_1quadruple.html) | Represents a 4-tuple | | C[LocARNA::quintuple< T1, T2, T3, T4, T5 >](https://s-will.github.io/LocARNA/classLocARNA_1_1quintuple.html) | Represents a 5-tuple | | C[LocARNA::PairHMMMatchProbs::PairHMMParams](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs_1_1PairHMMParams.html) | Maintains parameter for computing match probabilities | | C[LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | Able to manage an EPM, consists of 2 singlepatterns, one in each RNA | | C[LocARNA::PatternPairMap](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPairMap.html) | Manage a set of EPMs (PatternPair) | | ►C[LocARNA::PFGotoh< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFGotoh.html) | Provide Gotoh partition functions | | C[LocARNA::PFMatchProbs< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFMatchProbs.html) | Provide match probabilities calculated by pf approach | | C[LocARNA::PFTraceProbs< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFTraceProbs.html) | Provide match probabilities calculated by pf approach | | C[LocARNA::PFoldParams](https://s-will.github.io/LocARNA/classLocARNA_1_1PFoldParams.html) | Parameters for partition folding | | ►C[LocARNA::Ribofit](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit.html) | Family of Ribofit matrices | | C[LocARNA::Ribofit\_will2014](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribofit__will2014.html) | | | ►C[LocARNA::Ribosum](https://s-will.github.io/LocARNA/classLocARNA_1_1Ribosum.html) | Represents ribosum similarity matrices | | C[LocARNA::RibosumFreq](https://s-will.github.io/LocARNA/classLocARNA_1_1RibosumFreq.html) | Represents ribosum similarity matrices including raw frequencies | | ►C[LocARNA::RnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaData.html) | Represent sparsified data of RNA ensemble | | C[LocARNA::ExtRnaData](https://s-will.github.io/LocARNA/classLocARNA_1_1ExtRnaData.html) | Represent sparsified data of RNA ensemble extended by in loop probabilities | | C[LocARNA::RnaDataImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaDataImpl.html) | Implementation of RnaData | | C[LocARNA::RnaEnsemble](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsemble.html) | Represents the raw structure ensemble data for an RNA | | C[LocARNA::RnaEnsembleImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaEnsembleImpl.html) | Implementation of RnaEnsemble | | C[LocARNA::RnaStructure](https://s-will.github.io/LocARNA/classLocARNA_1_1RnaStructure.html) | An RNA secondary structure | | ►C[LocARNA::Scoring](https://s-will.github.io/LocARNA/classLocARNA_1_1Scoring.html) | Provides methods for the scoring of alignments | | C[LocARNA::PFScoring< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1PFScoring.html) | | | C[LocARNA::ScoringParams](https://s-will.github.io/LocARNA/classLocARNA_1_1ScoringParams.html) | Parameters for scoring | | C[LocARNA::MultipleAlignment::SeqEntry](https://s-will.github.io/LocARNA/classLocARNA_1_1MultipleAlignment_1_1SeqEntry.html) | A row in a multiple alignment | | C[LocARNA::SequenceAnnotation](https://s-will.github.io/LocARNA/classLocARNA_1_1SequenceAnnotation.html) | Annotation of a sequence | | C[LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | Stores a Pattern in one sequence | | ►C[LocARNA::SparseVectorBase< Derived, ValueType, KeyType >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html) | Base class template for sparse vector and matrix | | C[LocARNA::SparseMatrix< double >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) | | | C[LocARNA::SparseMatrix< arc\_prob\_vector\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) | | | C[LocARNA::SparseMatrix< arc\_prob\_matrix\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) | | | C[LocARNA::SparseMatrix< int >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) | | | C[LocARNA::SparseMatrix< pf\_score\_t >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) | | | ►C[LocARNA::SparseVectorBase< SparseMatrix< T >, T, std::pair< size\_t, size\_t > >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html) | | | C[LocARNA::SparseMatrix< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseMatrix.html) | Represents a sparse 2D matrix | | ►C[LocARNA::SparseVectorBase< SparseVector< T >, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVectorBase.html) | | | C[LocARNA::SparseVector< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1SparseVector.html) | Represents a sparse vector | | C[LocARNA::SparsificationMapper](https://s-will.github.io/LocARNA/classLocARNA_1_1SparsificationMapper.html) | Represents the mapping for sparsification | | C[LocARNA::StopWatch](https://s-will.github.io/LocARNA/classLocARNA_1_1StopWatch.html) | Control a set of named stop watch like timers | | C[LocARNA::StralScore](https://s-will.github.io/LocARNA/classLocARNA_1_1StralScore.html) | Implements the stral-like scoring function | | C[LocARNA::string1](https://s-will.github.io/LocARNA/classLocARNA_1_1string1.html) | A simple 1-based string | | ►C[LocARNA::TaintedInftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1TaintedInftyInt.html) | | | ►C[LocARNA::InftyInt](https://s-will.github.io/LocARNA/classLocARNA_1_1InftyInt.html) | | | C[LocARNA::FiniteInt](https://s-will.github.io/LocARNA/classLocARNA_1_1FiniteInt.html) | | | ►C[LocARNA::TraceRange](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceRange.html) | Represents a range of traces | | C[LocARNA::TraceController](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceController.html) | Controls the matrix cells valid for traces | | ►C**std::true\_type** | | | C[LocARNA::contains< T, std::tuple< T, Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1contains_3_01T_00_01std_1_1tuple_3_01T_00_01Us_8_8_8_01_4_01_4.html) | | | C[LocARNA::has\_type< T, std::tuple< T, Ts... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1has__type_3_01T_00_01std_1_1tuple_3_01T_00_01Ts_8_8_8_01_4_01_4.html) | | | C[LocARNA::type\_subset\_of< std::tuple<>, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) | | | C[LocARNA::ArcMatches::tuple5](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1tuple5.html) | | | C[LocARNA::tuple\_cat\_type< Tuple1, Tuple2 >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type.html) | Type of two concattenated tuples | | C[LocARNA::tuple\_cat\_type< std::tuple< Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) | | | C[LocARNA::type\_subset\_of< Tuple1, Tuple2 >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of.html) | | | C[LocARNA::type\_subset\_of< std::tuple< T, Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1type__subset__of_3_01std_1_1tuple_3_01T_00_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) | | | C[LocARNA::AlignerImpl::UnmodifiedScoringView](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerImpl_1_1UnmodifiedScoringView.html) | Provides the standard view on the scoring | | C[LocARNA::AlignerN::UnmodifiedScoringViewN](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html) | Provides the standard view on the scoring | | ►C**std::vector< T >** | STL class | | C[LocARNA::AlignmentEdges](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentEdges.html) | | --- # LocARNA-2.0.0: src Directory Reference LocARNA-2.0.0 * [Main Page](https://s-will.github.io/LocARNA/index.html) * [Related Pages](https://s-will.github.io/LocARNA/pages.html) * [Classes](https://s-will.github.io/LocARNA/annotated.html) * [Class List](https://s-will.github.io/LocARNA/annotated.html) * [Class Index](https://s-will.github.io/LocARNA/classes.html) * [Class Hierarchy](https://s-will.github.io/LocARNA/inherits.html) * [Class Members](https://s-will.github.io/LocARNA/functions.html) * [All](https://s-will.github.io/LocARNA/functions.html) * [a](https://s-will.github.io/LocARNA/functions.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_w.html#index_w) * [x](https://s-will.github.io/LocARNA/functions_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_~.html#index__7E) * [Functions](https://s-will.github.io/LocARNA/functions_func.html) * [a](https://s-will.github.io/LocARNA/functions_func.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_func_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_func_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_func_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_func_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_func_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_func_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_func_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_func_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_func_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_func_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_func_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_func_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_func_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_func_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_func_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_func_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_func_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_func_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_func_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_func_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_func_v.html#index_v) * [w](https://s-will.github.io/LocARNA/functions_func_w.html#index_w) * [z](https://s-will.github.io/LocARNA/functions_func_z.html#index_z) * [~](https://s-will.github.io/LocARNA/functions_func_~.html#index__7E) * [Variables](https://s-will.github.io/LocARNA/functions_vars.html) * [a](https://s-will.github.io/LocARNA/functions_vars.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_vars_b.html#index_b) * [c](https://s-will.github.io/LocARNA/functions_vars_c.html#index_c) * [d](https://s-will.github.io/LocARNA/functions_vars_d.html#index_d) * [e](https://s-will.github.io/LocARNA/functions_vars_e.html#index_e) * [f](https://s-will.github.io/LocARNA/functions_vars_f.html#index_f) * [g](https://s-will.github.io/LocARNA/functions_vars_g.html#index_g) * [h](https://s-will.github.io/LocARNA/functions_vars_h.html#index_h) * [i](https://s-will.github.io/LocARNA/functions_vars_i.html#index_i) * [j](https://s-will.github.io/LocARNA/functions_vars_j.html#index_j) * [k](https://s-will.github.io/LocARNA/functions_vars_k.html#index_k) * [l](https://s-will.github.io/LocARNA/functions_vars_l.html#index_l) * [m](https://s-will.github.io/LocARNA/functions_vars_m.html#index_m) * [n](https://s-will.github.io/LocARNA/functions_vars_n.html#index_n) * [o](https://s-will.github.io/LocARNA/functions_vars_o.html#index_o) * [p](https://s-will.github.io/LocARNA/functions_vars_p.html#index_p) * [q](https://s-will.github.io/LocARNA/functions_vars_q.html#index_q) * [r](https://s-will.github.io/LocARNA/functions_vars_r.html#index_r) * [s](https://s-will.github.io/LocARNA/functions_vars_s.html#index_s) * [t](https://s-will.github.io/LocARNA/functions_vars_t.html#index_t) * [u](https://s-will.github.io/LocARNA/functions_vars_u.html#index_u) * [v](https://s-will.github.io/LocARNA/functions_vars_v.html#index_v) * [x](https://s-will.github.io/LocARNA/functions_vars_x.html#index_x) * [y](https://s-will.github.io/LocARNA/functions_vars_y.html#index_y) * [z](https://s-will.github.io/LocARNA/functions_vars_z.html#index_z) * [Typedefs](https://s-will.github.io/LocARNA/functions_type.html) * [a](https://s-will.github.io/LocARNA/functions_type.html#index_a) * [b](https://s-will.github.io/LocARNA/functions_type.html#index_b) * 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[Files](https://s-will.github.io/LocARNA/files.html) * [File List](https://s-will.github.io/LocARNA/files.html) * [File Members](https://s-will.github.io/LocARNA/globals.html) * [All](https://s-will.github.io/LocARNA/globals.html) * [Functions](https://s-will.github.io/LocARNA/globals_func.html) * [Variables](https://s-will.github.io/LocARNA/globals_vars.html) * ![](https://s-will.github.io/LocARNA/search/mag_sel.svg)[![](https://s-will.github.io/LocARNA/search/close.svg)](javascript:searchBox.CloseResultsWindow()) [•All](javascript:void(0))  [Classes](javascript:void(0))  [Namespaces](javascript:void(0))  [Files](javascript:void(0))  [Functions](javascript:void(0))  [Variables](javascript:void(0))  [Typedefs](javascript:void(0))  [Enumerations](javascript:void(0))  [Enumerator](javascript:void(0))  [Friends](javascript:void(0))  [Pages](javascript:void(0)) * [src](https://s-will.github.io/LocARNA/dir_68267d1309a1af8e8297ef4c3efbcdba.html) Directory dependency graph for src: ![src](https://s-will.github.io/LocARNA/dir_68267d1309a1af8e8297ef4c3efbcdba_dep.png) | | | | --- | --- | | Directories
----------- | | | directory | [Utils](https://s-will.github.io/LocARNA/dir_a7363e98f9e0bdd87618633653859815.html) | | | | | | | | --- | --- | | Files
----- | | | file | [locarna.cc](https://s-will.github.io/LocARNA/locarna_8cc.html) | | | Defines main function of locarna. | | | | | file | [locarna\_p.cc](https://s-will.github.io/LocARNA/locarna__p_8cc.html) | | | Defines main function of locarna\_p. | | | | | file | [sparse.cc](https://s-will.github.io/LocARNA/sparse_8cc.html) | | | Defines main function of SPARSE. | | | | --- # LocARNA-2.0.0: src/LocARNA/quadmath.hh Source File LocARNA-2.0.0 * [src](https://s-will.github.io/LocARNA/dir_68267d1309a1af8e8297ef4c3efbcdba.html) * [LocARNA](https://s-will.github.io/LocARNA/dir_044ab21d82a82dab8ad00551727c905f.html) 1 #ifndef LOCARNA\_QUADMATH\_HH 2 #define LOCARNA\_QUADMATH\_HH 3  4 // include only if Gnu's float128 is available 5 #if defined( \_GLIBCXX\_USE\_FLOAT128 ) && ! defined(\_\_clang\_\_) 6  10  11 #include 12 #include 13 #include 14 #include 15  18 inline 19 std::ostream & 20 operator << (std::ostream &out, \_\_float128 x) { 21  auto format = "%Qe"; 22  auto n = quadmath\_snprintf(NULL, 0, format, x); 23  auto buf = std::make\_unique(n+1); 24  quadmath\_snprintf(buf.get(), n+1, format, x); 25  return 26  out << buf.get(); 27 } 28  29  30 // We overload the used quadmath functions for \_\_float128, such that we do not need 31 // to rename them elsewhere 32 // 33 // NOTE: the defined functions are the only math functions that we use on 34 // partition functions; 35 // comfortably, since the overloads are required, one gets 'ambigous overload' 36 // compiler errors when using other math functions 37  38 namespace std { 39  41 inline 42 \_\_float128 43 exp(\_\_float128 x) {return expq(x);} 44  45 // @brief quadmath log 46 inline 47 \_\_float128 48 log(\_\_float128 x) {return logq(x);} 49  50 // @brief quadmath isinf 51 inline 52 bool 53 isinf(\_\_float128 x) {return isinfq(x);} 54  55 // @brief quadmath isnan 56 inline 57 bool 58 isnan(\_\_float128 x) {return isnanq(x);} 59  60 } 61  62 #endif 63  64 #endif --- # LocARNA-2.0.0: src/Utils Directory Reference LocARNA-2.0.0 * [src](https://s-will.github.io/LocARNA/dir_68267d1309a1af8e8297ef4c3efbcdba.html) * [Utils](https://s-will.github.io/LocARNA/dir_a7363e98f9e0bdd87618633653859815.html) --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * **std** * [hash< std::pair< T1, T2 > >](https://s-will.github.io/LocARNA/structstd_1_1hash_3_01std_1_1pair_3_01T1_00_01T2_01_4_01_4.html) This is the complete list of members for [std::hash< std::pair< T1, T2 > >](https://s-will.github.io/LocARNA/structstd_1_1hash_3_01std_1_1pair_3_01T1_00_01T2_01_4_01_4.html) , including all inherited members. | | | | | --- | --- | --- | | **operator()**(const std::pair< T1, T2 > &p) const noexcept(noexcept(hash< T1 >()(p.first)) &&noexcept(hash< T2 >()(p.second))) (defined in [std::hash< std::pair< T1, T2 > >](https://s-will.github.io/LocARNA/structstd_1_1hash_3_01std_1_1pair_3_01T1_00_01T2_01_4_01_4.html)
) | [std::hash< std::pair< T1, T2 > >](https://s-will.github.io/LocARNA/structstd_1_1hash_3_01std_1_1pair_3_01T1_00_01T2_01_4_01_4.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [AlignmentEdges](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentEdges.html) This is the complete list of members for [LocARNA::AlignmentEdges](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentEdges.html) , including all inherited members. | | | | | --- | --- | --- | | **edge\_t** typedef (defined in [LocARNA::AlignmentEdges](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentEdges.html)
) | [LocARNA::AlignmentEdges](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentEdges.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [greater\_second](https://s-will.github.io/LocARNA/classLocARNA_1_1greater__second.html) This is the complete list of members for [LocARNA::greater\_second< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1greater__second.html) , including all inherited members. | | | | | --- | --- | --- | | [operator()](https://s-will.github.io/LocARNA/classLocARNA_1_1greater__second.html#a2c73f480ef066d3472ff5c2e2f3aca65)
(const T &a, const T &b) | [LocARNA::greater\_second< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1greater__second.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * **BasePairFilter** * [Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) This is the complete list of members for [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) , including all inherited members. | | | | | --- | --- | --- | | **Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inline | | **operator()**(size\_t i, size\_t j) const (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | | **operator()**(const bp\_t &bp) const (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | | **~Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [check\_score\_t](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t.html) This is the complete list of members for [LocARNA::check\_score\_t< T >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t.html) , including all inherited members. | | | | | --- | --- | --- | | **check\_score\_t**(const CLP &clp) (defined in [LocARNA::check\_score\_t< T >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t.html)
) | [LocARNA::check\_score\_t< T >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [tuple\_cat\_type< std::tuple< Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) This is the complete list of members for [LocARNA::tuple\_cat\_type< std::tuple< Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) , including all inherited members. | | | | | --- | --- | --- | | **type** typedef (defined in [LocARNA::tuple\_cat\_type< std::tuple< Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html)
) | [LocARNA::tuple\_cat\_type< std::tuple< Ts... >, std::tuple< Us... > >](https://s-will.github.io/LocARNA/structLocARNA_1_1tuple__cat__type_3_01std_1_1tuple_3_01Ts_8_8_8_01_4_00_01std_1_1tuple_3_01Us_8_8_8_01_4_01_4.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [DiscreteDistribution](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html) This is the complete list of members for [LocARNA::DiscreteDistribution](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html) , including all inherited members. | | | | | --- | --- | --- | | [DiscreteDistribution](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html#a58da597b6ed6281fe84fb8796fedb477)
(const std::vector< double > &distvec) | [LocARNA::DiscreteDistribution](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html) | inlineexplicit | | [operator()](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html#a52333baa790a318e05eb3cb2c1bb2c57)
(size\_t x) | [LocARNA::DiscreteDistribution](https://s-will.github.io/LocARNA/classLocARNA_1_1DiscreteDistribution.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [check\_score\_t< extended\_pf\_score\_t >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t_3_01extended__pf__score__t_01_4.html) This is the complete list of members for [LocARNA::check\_score\_t< extended\_pf\_score\_t >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t_3_01extended__pf__score__t_01_4.html) , including all inherited members. | | | | | --- | --- | --- | | **check\_score\_t**(const CLP &clp) (defined in [LocARNA::check\_score\_t< extended\_pf\_score\_t >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t_3_01extended__pf__score__t_01_4.html)
) | [LocARNA::check\_score\_t< extended\_pf\_score\_t >](https://s-will.github.io/LocARNA/structLocARNA_1_1check__score__t_3_01extended__pf__score__t_01_4.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * **BasePairFilter** * [Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html) This is the complete list of members for [LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html) , including all inherited members. | | | | | --- | --- | --- | | **Combined**(const Filter &fa, const Filter &fb) (defined in [LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html)
) | [LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html) | inline | | **Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inline | | **operator()**(size\_t i, size\_t j) const (defined in [LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html)
) | [LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html) | inlinevirtual | | **operator()**(const bp\_t &bp) const (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | | **~Combined**() (defined in [LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html)
) | [LocARNA::BasePairFilter::Combined](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Combined.html) | inline | | **~Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [Enumerate](https://s-will.github.io/LocARNA/classLocARNA_1_1Enumerate.html) This is the complete list of members for [LocARNA::Enumerate< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Enumerate.html) , including all inherited members. | | | | | --- | --- | --- | | **begin**() (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | inline | | **end**() (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | inline | | **Enumerate**(T &c) (defined in [LocARNA::Enumerate< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Enumerate.html)
) | [LocARNA::Enumerate< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Enumerate.html) | inline | | **iparent\_t** typedef (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | **iterator1\_t** typedef (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | **iterator2\_t** typedef (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | **parent\_t** typedef (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | **value\_pair\_t** typedef (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | **value\_type1** typedef (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | **value\_type2** typedef (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | | | **Zip**(const ConstIterableSequence<> &c1, T &c2) (defined in [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html)
) | [LocARNA::Zip< const ConstIterableSequence<>, T >](https://s-will.github.io/LocARNA/classLocARNA_1_1Zip.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) This is the complete list of members for [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) , including all inherited members. | | | | | --- | --- | --- | | [getmyId](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html#a232333850ddb8e0d4a7875b419e4207e)
() const | [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | inline | | [getPat](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html#a8a7628acc96151ff0e8724c77d933466)
() const | [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | inline | | [getseqId](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html#ae90b63e068db7a8992df4a349872bc83)
() const | [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | inline | | **SinglePattern**() (defined in [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html)
) | [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | inline | | [SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html#aa972bde99e2ce5c20b2d5583229177bd)
(const std::string &myId\_, const std::string &seqId\_, const intVec &mySinglePattern\_) | [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | inline | | [~SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html#a27de631820388fcae034a3b32b0735e0)
() | [LocARNA::SinglePattern](https://s-will.github.io/LocARNA/classLocARNA_1_1SinglePattern.html) | inlinevirtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) This is the complete list of members for [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) , including all inherited members. | | | | | --- | --- | --- | | [allow\_left\_1](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a777a0ef8be08358fb9f76527992b2343)
() const | [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | inline | | [allow\_left\_2](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a201a40ae33b2988653c930d7c5e447bf)
() const | [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | inline | | [allow\_right\_1](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#a814627ca59db8a93f164fee5315baa32)
() const | [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | inline | | [allow\_right\_2](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#afc97395591bfdd33901380cec1de5323)
() const | [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | inline | | [FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html#ab3a090007d063360034ff945d2c7b28f)
(const std::string &d) | [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | inlineexplicit | | **FreeEndgaps**() (defined in [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html)
) | [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | inline | | **reverse**() const (defined in [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html)
) | [LocARNA::FreeEndgaps](https://s-will.github.io/LocARNA/classLocARNA_1_1FreeEndgaps.html) | inline | --- # LocARNA-2.0.0: Graph Legend LocARNA-2.0.0 This page explains how to interpret the graphs that are generated by doxygen. Consider the following example: /\*! Invisible class because of truncation \*/ class Invisible { }; /\*! Truncated class, inheritance relation is hidden \*/ class Truncated : public Invisible { }; /\* Class not documented with doxygen comments \*/ class Undocumented { }; /\*! Class that is inherited using public inheritance \*/ class PublicBase : public Truncated { }; /\*! A template class \*/ template class Templ { }; /\*! Class that is inherited using protected inheritance \*/ class ProtectedBase { }; /\*! Class that is inherited using private inheritance \*/ class PrivateBase { }; /\*! Class that is used by the Inherited class \*/ class Used { }; /\*! Super class that inherits a number of other classes \*/ class Inherited : public PublicBase, protected ProtectedBase, private PrivateBase, public Undocumented, public Templ { private: Used \*m\_usedClass; }; This will result in the following graph: ![](https://s-will.github.io/LocARNA/graph_legend.png) The boxes in the above graph have the following meaning: * A filled gray box represents the struct or class for which the graph is generated. * A box with a black border denotes a documented struct or class. * A box with a gray border denotes an undocumented struct or class. * A box with a red border denotes a documented struct or class forwhich not all inheritance/containment relations are shown. A graph is truncated if it does not fit within the specified boundaries. The arrows have the following meaning: * A dark blue arrow is used to visualize a public inheritance relation between two classes. * A dark green arrow is used for protected inheritance. * A dark red arrow is used for private inheritance. * A purple dashed arrow is used if a class is contained or used by another class. The arrow is labelled with the variable(s) through which the pointed class or struct is accessible. * A yellow dashed arrow denotes a relation between a template instance and the template class it was instantiated from. The arrow is labelled with the template parameters of the instance. --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * **BasePairFilter** * [BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html) This is the complete list of members for [LocARNA::BasePairFilter::BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html) , including all inherited members. | | | | | --- | --- | --- | | [BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html#a627e88269a5692ac9174521b819bfc72)
(size\_t mls) | [LocARNA::BasePairFilter::BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html) | inlineexplicit | | **Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inline | | [operator()](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html#ad42ab75d72a22b45542d48d373d985d0)
(size\_t i, size\_t j) const | [LocARNA::BasePairFilter::BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html) | inlinevirtual | | **operator()**(const bp\_t &bp) const (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | | [~BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html#ab71bd80513c9aac4682a15234582ec76)
() | [LocARNA::BasePairFilter::BPMinLoopSize](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1BPMinLoopSize.html) | inline | | **~Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) This is the complete list of members for [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) , including all inherited members. | | | | | --- | --- | --- | | [AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html#ac3a2305028f9a20ac4c36dd8696da8eb)
(Args... argpack) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inline | | **AlignerParams**() (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inlineprotected | | **construct**(const ArgTuple &args) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inlineprotected | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(no\_lonely\_pairs, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(struct\_local, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(sequ\_local, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(free\_endgaps, FreeEndgaps, FreeEndgaps("----")) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(DO\_TRACE, bool, true) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(max\_diff\_am, int, -1) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(max\_diff\_at\_am, int, -1) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(stacking, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(constraints, const AnchorConstraints \*, nullptr) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(seqA, const Sequence \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(seqB, const Sequence \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(scoring, const Scoring \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(trace\_controller, const TraceController \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **valid\_args** typedef (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * **BasePairFilter** * [Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html) This is the complete list of members for [LocARNA::BasePairFilter::Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html) , including all inherited members. | | | | | --- | --- | --- | | [Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html#ad246e803be051548fcd559d25f3c7abd)
(const std::string &sequence) | [LocARNA::BasePairFilter::Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html) | inlineexplicit | | **Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inline | | [operator()](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html#af0db7d6d13fca5b132c3f9998603d541)
(size\_t i, size\_t j) const | [LocARNA::BasePairFilter::Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html) | inlinevirtual | | **operator()**(const bp\_t &bp) const (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | | [~Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html#ad23158151f87cbf33abf046349fe3547)
() | [LocARNA::BasePairFilter::Canonical](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Canonical.html) | inline | | **~Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) This is the complete list of members for [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) , including all inherited members. | | | | | --- | --- | --- | | [AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a3414c6009ebc4e3e94678c7691b51515)
(const Sequence &seqA, const Sequence &seqB) | [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | inline | | [edges\_](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#abae96ab434c3ba1292262d86ac258e06) | [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | | | [empty](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a55906d20becca51fa674fded9a18e452)
() const | [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | inline | | [seqA\_](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a096629dc6aa0c0a2b4afad7a7015ec68) | [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | | | [seqB\_](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a9cc81a646bb623fb69055bb2fa59a946) | [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | | | [strA\_](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a042d998dcde218991a42e358efc92402) | [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | | | [strB\_](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html#a7c907d08de20765f7ed85691fd1dc468) | [LocARNA::AlignmentImpl](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignmentImpl.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [Alphabet](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) This is the complete list of members for [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) , including all inherited members. | | | | | --- | --- | --- | | [Alphabet](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a054d43bfdd178810c8fd41c57c706720)
() | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | [Alphabet](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a249cea02a97e9399eea0bc58b0a586e5)
(const std::array< T, N > &a) | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | explicit | | [Alphabet](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#ad09ec236bd7a9b541e489e64fe057a59)
(const std::vector< T > &v) | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | explicit | | [Alphabet](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a1e633ff870d1e5302e9466a7d250e6ba)
(const std::string &s) | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | explicit | | [idx](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a2b1ba30a849cfde9f2ba4277adbfcaa3)
(const value\_type &x) const | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | [in](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a427efeae32d836c5cf619fa606cfd94d)
(const value\_type &x) const | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | **operator=**(const std::array< T, N > &a) (defined in [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html)
) | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | [size\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a3d536c8e69cd705899715f2d3a0ec49d)
typedef | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | | [value\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html#a33ea2031beb67814f6fd97a3337355de)
typedef | [LocARNA::Alphabet< T, N >](https://s-will.github.io/LocARNA/classLocARNA_1_1Alphabet.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) This is the complete list of members for [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) , including all inherited members. | | | | | --- | --- | --- | | [Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a40edbef728a80a8e14f43259f4db0cd0)
typedef | [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | | | [arcA](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#afa4017bfb7c59a900e960e3ad28b3f6f)
() const | [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | inline | | [arcB](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a09d44c8926060f7af6ffe564cc415742)
() const | [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | inline | | [ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a5e51ea9bf4c2dc5bb90f1c47db09ad86)
(const Arc \*arcA, const Arc \*arcB, idx\_type idx) | [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | inline | | [idx](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a75ebe8208c1648d7fc5ce6b9b01bb20e)
() const | [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | inline | | [idx\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#abe50ab349a68390fb2b0d79119e598f6)
typedef | [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | | | [size\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html#a7dddafee26151af4aa1edddde1b33979)
typedef | [LocARNA::ArcMatch](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatch.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) This is the complete list of members for [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) , including all inherited members. | | | | | --- | --- | --- | | [failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#afbb326abd40d3505ce03d9d43aa4904d)
(const std::string &msg) | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | inlineexplicit | | [failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a379e840cc59b71689bc6d2f7f6dfc5f3)
() | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | inlineexplicit | | [what](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a16d1964a4c206e8e40f35ed37b965b12)
() const noexcept | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | virtual | | [~failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a6c4a6907dc24c1fe62050d9d2659c684)
() | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | virtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * **BasePairFilter** * [SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) This is the complete list of members for [LocARNA::BasePairFilter::SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) , including all inherited members. | | | | | --- | --- | --- | | **Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inline | | [operator()](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html#a350e21193dd0fc527d4ef65f4f51d506)
(size\_t i, size\_t j) const | [LocARNA::BasePairFilter::SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) | inlinevirtual | | **operator()**(const bp\_t &bp) const (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | | [SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html#ae6a2f3ce4bd7a7c6667c30b747bd6e6b)
(size\_t lo, size\_t up) | [LocARNA::BasePairFilter::SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) | inline | | **~Filter**() (defined in [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html)
) | [LocARNA::BasePairFilter::Filter](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1Filter.html) | inlinevirtual | | [~SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html#acebffba55b0adf134943c1e9d68bfd56)
() | [LocARNA::BasePairFilter::SpanRange](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairFilter_1_1SpanRange.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) This is the complete list of members for [LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) , including all inherited members. | | | | | --- | --- | --- | | [BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html#aebf6827544ee3702af78d96aacf913e5)
(size\_t idx, size\_t left, size\_t right) | [LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) | inline | | [idx](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html#a3e769a65c46a703fa90e802e72d027ae)
() const | [LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) | inline | | [left](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html#a4f46804d8e0541957a3e64e4a75b76bf)
() const | [LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) | inline | | [right](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html#a18ddf0e8455b98b24322e7727b040fdc)
() const | [LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) | inline | | **~BasePairs\_\_Arc**() (defined in [LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html)
) | [LocARNA::BasePairs\_\_Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs____Arc.html) | virtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) This is the complete list of members for [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) , including all inherited members. | | | | | --- | --- | --- | | [EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html#a6dcbd4897c0216aa495c591d2c29eaf3)
() | [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | inline | | [EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html#a7b170a9599a91288d429fefe5654ea9e)
(pos\_type end) | [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | inline | | [EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html#a1cd155f707729a2143d3b43e25d49b0b)
(Gap end) | [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | inline | | [gap](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html#abc4f687ef5f9035f1890bfbf275798b0)
() const | [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | inline | | [is\_gap](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html#a3ea27ecf895b31264e8d556808a0e174)
() const | [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | inline | | [is\_pos](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html#ace03650315f6ee245133b7ff86ec85f4)
() const | [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | inline | | [operator pos\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html#a3383c2cd37759813f027b39c141ec1fc)
() const | [LocARNA::EdgeEnd](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeEnd.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [wrong\_format\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1wrong__format__failure.html) This is the complete list of members for [LocARNA::wrong\_format\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1wrong__format__failure.html) , including all inherited members. | | | | | --- | --- | --- | | [failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#afbb326abd40d3505ce03d9d43aa4904d)
(const std::string &msg) | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | inlineexplicit | | [failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a379e840cc59b71689bc6d2f7f6dfc5f3)
() | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | inlineexplicit | | [what](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a16d1964a4c206e8e40f35ed37b965b12)
() const noexcept | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | virtual | | **wrong\_format\_failure**() (defined in [LocARNA::wrong\_format\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1wrong__format__failure.html)
) | [LocARNA::wrong\_format\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1wrong__format__failure.html) | inline | | [~failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a6c4a6907dc24c1fe62050d9d2659c684)
() | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | virtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [Delay](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html) This is the complete list of members for [LocARNA::Delay< Value, Function >](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html) , including all inherited members. | | | | | --- | --- | --- | | **Delay**(Function fun) (defined in [LocARNA::Delay< Value, Function >](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html)
) | [LocARNA::Delay< Value, Function >](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html) | inline | | **get**() (defined in [LocARNA::Delay< Value, Function >](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html)
) | [LocARNA::Delay< Value, Function >](https://s-will.github.io/LocARNA/classLocARNA_1_1Delay.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [ConstIterableSequence](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) This is the complete list of members for [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) , including all inherited members. | | | | | --- | --- | --- | | **begin**() const (defined in [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html)
) | [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | inline | | **cbegin**() const (defined in [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html)
) | [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | inline | | **cend**() const (defined in [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html)
) | [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | inline | | **ConstIterableSequence**(value\_type start) (defined in [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html)
) | [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | inline | | **end**() const (defined in [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html)
) | [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | inline | | **iterator** typedef (defined in [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html)
) | [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | | | **value\_type** typedef (defined in [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html)
) | [LocARNA::ConstIterableSequence< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1ConstIterableSequence.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [make\_delay](https://s-will.github.io/LocARNA/classLocARNA_1_1make__delay.html) This is the complete list of members for [LocARNA::make\_delay< Value >](https://s-will.github.io/LocARNA/classLocARNA_1_1make__delay.html) , including all inherited members. | | | | | --- | --- | --- | | **fun**(Function fun\_) (defined in [LocARNA::make\_delay< Value >](https://s-will.github.io/LocARNA/classLocARNA_1_1make__delay.html)
) | [LocARNA::make\_delay< Value >](https://s-will.github.io/LocARNA/classLocARNA_1_1make__delay.html) | inlinestatic | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) This is the complete list of members for [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) , including all inherited members. | | | | | --- | --- | --- | | [AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html#ae07a1777f31e8ea49c465b6d12abbd23)
(Args... argpack) | [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) | inline | | [AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html#ac3a2305028f9a20ac4c36dd8696da8eb)
(Args... argpack) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inline | | **AlignerParams**() (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inlineprotected | | **construct**(const ArgTuple &args) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inlineprotected | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(no\_lonely\_pairs, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(struct\_local, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(sequ\_local, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(free\_endgaps, FreeEndgaps, FreeEndgaps("----")) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(DO\_TRACE, bool, true) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(max\_diff\_am, int, -1) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(max\_diff\_at\_am, int, -1) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(stacking, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(constraints, const AnchorConstraints \*, nullptr) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(sparsification\_mapperA, const SparsificationMapper \*) (defined in [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html)
) | [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(sparsification\_mapperB, const SparsificationMapper \*) (defined in [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html)
) | [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(seqA, const Sequence \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(seqB, const Sequence \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(scoring, const Scoring \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(trace\_controller, const TraceController \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **valid\_args** typedef (defined in [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html)
) | [LocARNA::AlignerNParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerNParams.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) This is the complete list of members for [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) , including all inherited members. | | | | | --- | --- | --- | | [AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#ac531674e470d24ae99caa4853d532b70)
(int startA, int startB, int endA, int endB) | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [endA](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#ad32ec91c870ea69e03995754fcacc266)
() const | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [endB](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#a3b6c12a6cc0f7c16a62c776fa6e58628)
() const | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [set\_endA](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#a73b3941c4ba600914676dcf1822f61d4)
(size\_t p) | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [set\_endB](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#a5baf81836ae82e743567e2792ce1dced)
(size\_t p) | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [set\_startA](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#a1f6dff979266ca98fca6f9917a5c7adf)
(size\_t p) | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [set\_startB](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#a8be24a1a053cdf80c05ef9603c50a4b8)
(size\_t p) | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [startA](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#a1c2c58f1a05afbc50bdb857912b1bb23)
() const | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | | [startB](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html#a2d28ac19fb7a0eae680993458c6f570c)
() const | [LocARNA::AlignerRestriction](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerRestriction.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [AlignerPParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) This is the complete list of members for [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) , including all inherited members. | | | | | --- | --- | --- | | [AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html#ac3a2305028f9a20ac4c36dd8696da8eb)
(Args... argpack) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inline | | **AlignerParams**() (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inlineprotected | | [AlignerPParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html#a11c75399342aa5dd05b660686f4daf28)
(Args... argpack) | [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | inline | | **construct**(const ArgTuple &args) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | inlineprotected | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(min\_am\_prob, double, 0) (defined in [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html)
) | [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(min\_bm\_prob, double, 0) (defined in [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html)
) | [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(pf\_scale, pf\_score\_t, 1.0) (defined in [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html)
) | [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(no\_lonely\_pairs, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(struct\_local, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(sequ\_local, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(free\_endgaps, FreeEndgaps, FreeEndgaps("----")) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(DO\_TRACE, bool, true) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(max\_diff\_am, int, -1) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(max\_diff\_at\_am, int, -1) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(stacking, bool, false) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT\_FEATURE**(constraints, const AnchorConstraints \*, nullptr) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(seqA, const Sequence \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(seqB, const Sequence \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(scoring, const Scoring \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **DEFINE\_NAMED\_ARG\_FEATURE**(trace\_controller, const TraceController \*) (defined in [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html)
) | [LocARNA::AlignerParams](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerParams.html) | | | **pf\_score\_t** typedef (defined in [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html)
) | [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | | | **valid\_args** typedef (defined in [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html)
) | [LocARNA::AlignerPParams< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1AlignerPParams.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) This is the complete list of members for [LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) , including all inherited members. | | | | | --- | --- | --- | | [EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a05a8030272d9978c0244f4f6206d5fcb)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | **EdgeProbs**() (defined in [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html)
) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inlineprotected | | [lenA](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a81ef8ce0ab4345f3738491b9a4550e8e)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [lenB](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a3691f1f1863f752f4ce7e5457369a8a2)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html#a3af43c7d4208ccdda8a626a7747f2c91)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) | inline | | **MatchProbs**() (defined in [LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html)
) | [LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) | inlineprotected | | [prob](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a9cafa8c72decd26680a7ed7880c18846)
(size\_t i, size\_t j) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [probs\_](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a6ff8f54ec7681a3fd380f53d4074c3d6) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#ac2644c906640be93c7f046980b12d38c)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#aa59c4b4cb7bea38d32e2c1d6f67da2ef)
(const std::string &filename, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [size\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a308c0af797440334a28acf5814a8ceb6)
typedef | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | | [write\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a134ba1f851cd5d8f31079a7f0701239c)
(std::ostream &out, double threshold) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html) This is the complete list of members for [LocARNA::syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html) , including all inherited members. | | | | | --- | --- | --- | | [failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#afbb326abd40d3505ce03d9d43aa4904d)
(const std::string &msg) | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | inlineexplicit | | [failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a379e840cc59b71689bc6d2f7f6dfc5f3)
() | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | inlineexplicit | | [syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html#a33832b234f146367334f72a173e2d126)
() | [LocARNA::syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html) | inline | | [syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html#ab34a1834acddb294c43f0a5f4895af41)
(const std::string &msg) | [LocARNA::syntax\_error\_failure](https://s-will.github.io/LocARNA/structLocARNA_1_1syntax__error__failure.html) | inlineexplicit | | [what](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a16d1964a4c206e8e40f35ed37b965b12)
() const noexcept | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | virtual | | [~failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html#a6c4a6907dc24c1fe62050d9d2659c684)
() | [LocARNA::failure](https://s-will.github.io/LocARNA/classLocARNA_1_1failure.html) | virtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) This is the complete list of members for [LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) , including all inherited members. | | | | | --- | --- | --- | | [compute\_arcmatch\_score](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html#a31d23819da5c84898003d8e5f2a60f4f)
() | [LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) | | | [ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html#a5829e1a4fa619bb12af85760c093591d)
(const Sequence &seqA\_, const Sequence &seqB\_, const RnaData &rna\_dataA\_, const RnaData &rna\_dataB\_, const ArcMatches &arc\_matches\_, const SparseTraceController &sparse\_trace\_controller\_, PatternPairMap &foundEPMs\_, int alpha\_1\_, int alpha\_2\_, int alpha\_3\_, score\_t difference\_to\_opt\_score\_, score\_t min\_score\_, long int max\_number\_of\_EPMs\_, bool inexact\_struct\_match\_, score\_t struct\_mismatch\_score\_, bool apply\_filter\_, bool verbose\_) | [LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) | | | [test\_arcmatch\_score](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html#a68e4a77634acdf0c4b9b4dbeb9e3cb99)
() | [LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) | | | [trace\_EPMs](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html#aafb4071296457db83e78696b3c3d7d57)
(bool suboptimal) | [LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) | | | **~ExactMatcher**() (defined in [LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html)
) | [LocARNA::ExactMatcher](https://s-will.github.io/LocARNA/classLocARNA_1_1ExactMatcher.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) This is the complete list of members for [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) , including all inherited members. | | | | | --- | --- | --- | | [anchor\_annotation](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a6fe42e6557b1689641a1fe48ef972885)
() | [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | | | [calculateLCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a4ebcf056f43c6ede4e0ca8b3d061e32f)
(bool quiet) | [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | | | [LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a0fa1f906e3f184d55067486a55c6436a)
(const Sequence &seqA\_, const Sequence &seqB\_, const PatternPairMap &myPatterns, PatternPairMap &myLCSEPM) | [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | inline | | [MapToPS](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#ad4ca9c28458fe59c58c703ac62762e4b)
(const std::string &sequenceA, const std::string &sequenceB, PatternPairMap &myMap, const std::string &file1, const std::string &file2) | [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | | | [output\_clustal](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a75e6867f6007fd408dd55856a58b0c0b)
(const std::string &outfile\_name) | [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | | | [output\_locarna](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a064f90d29b2188e44df99dd714083717)
(const std::string &sequenceA, const std::string &sequenceB, const std::string &outfile) | [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | | | [~LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html#a409abad787c134c29595b57377e1f257)
() | [LocARNA::LCSEPM](https://s-will.github.io/LocARNA/classLocARNA_1_1LCSEPM.html) | virtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html) This is the complete list of members for [LocARNA::TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html) , including all inherited members. | | | | | --- | --- | --- | | [EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a05a8030272d9978c0244f4f6206d5fcb)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | **EdgeProbs**() (defined in [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html)
) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inlineprotected | | [lenA](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a81ef8ce0ab4345f3738491b9a4550e8e)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [lenB](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a3691f1f1863f752f4ce7e5457369a8a2)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [prob](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a9cafa8c72decd26680a7ed7880c18846)
(size\_t i, size\_t j) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [probs\_](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a6ff8f54ec7681a3fd380f53d4074c3d6) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#ac2644c906640be93c7f046980b12d38c)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#aa59c4b4cb7bea38d32e2c1d6f67da2ef)
(const std::string &filename, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [size\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a308c0af797440334a28acf5814a8ceb6)
typedef | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | | [TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html#ab2fa9eace98c6678262f92fe91d233f7)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html) | inline | | **TraceProbs**() (defined in [LocARNA::TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html)
) | [LocARNA::TraceProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1TraceProbs.html) | inlineprotected | | [write\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a134ba1f851cd5d8f31079a7f0701239c)
(std::ostream &out, double threshold) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html) This is the complete list of members for [LocARNA::FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html) , including all inherited members. | | | | | --- | --- | --- | | [best\_once\_on](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a8068a95904e73c3cc4b97d2b67f2c121)
(double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | **delta**(int i) const (defined in [LocARNA::FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html)
) | [LocARNA::FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html) | inlineprotectedvirtual | | **exp\_delta**(int i) const (defined in [LocARNA::FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html)
) | [LocARNA::FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html) | inlineprotectedvirtual | | [FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a427f7f742771c1385d1bffd44d7c15c0)
(numseq\_t &x\_, double delta\_, double beta\_) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | inline | | [FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html#a4d7b3cb098f672c371b5698ff1443569)
(numseq\_t &x\_, numseq\_t &penalties\_, double beta\_) | [LocARNA::FitOnOffVarPenalty](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOffVarPenalty.html) | inline | | [forward](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#ac00514532546e97d2c6a64e77261476b)
(double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [optimize](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a559708be65e10bd42be70bd4d4c06e7b)
(double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [print\_table](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a9825cb248c92cef6fae1ac4f539856f1)
(const std::string &name, const std::vector< bool > &v) const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [print\_table](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#ae7faa64c95825495936dfbb89cecf47e)
(const std::string &name, const std::vector< pf\_t > &v) const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [print\_tables](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#af910fc9c14ffe4964b7e0693fa905066)
() const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [viterbi](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a40ef56acb9380743a3219351687d567e)
(double c0, double c1, bool traceback) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [write\_viterbi\_path](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#ab305dbbd7ee27b7a44d9c2d0a5660fa4)
(std::ostream &out, double c0, double c1) const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [write\_viterbi\_path\_compact](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a9a4aaff7c47e9c9d93d31031f796f54d)
(std::ostream &out, double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [MatchController](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html) This is the complete list of members for [LocARNA::MatchController](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html) , including all inherited members. | | | | | --- | --- | --- | | [is\_valid\_match](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html#ae199ef1985ff10f63e8903727d560816)
(size\_t i, size\_t j) const =0 | [LocARNA::MatchController](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html) | pure virtual | | **~MatchController**() (defined in [LocARNA::MatchController](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html)
) | [LocARNA::MatchController](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchController.html) | virtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [PFoldParams](https://s-will.github.io/LocARNA/classLocARNA_1_1PFoldParams.html) * [args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) This is the complete list of members for [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) , including all inherited members. | | | | | --- | --- | --- | | **DEFINE\_NAMED\_ARG\_DEFAULT**(noLP, bool, false) (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT**(stacking, bool, false) (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT**(dangling, int, 2) (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT**(max\_bp\_span, int, -1) (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT**(ribo, bool, true) (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT**(cv\_fact, double, 0.6) (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | **DEFINE\_NAMED\_ARG\_DEFAULT**(nc\_fact, double, 0.5) (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | | **valid\_args** typedef (defined in [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html)
) | [LocARNA::PFoldParams::args](https://s-will.github.io/LocARNA/structLocARNA_1_1PFoldParams_1_1args.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [ArcMatches](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches.html) * [lex\_greater\_left\_ends](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html) This is the complete list of members for [LocARNA::ArcMatches::lex\_greater\_left\_ends](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html) , including all inherited members. | | | | | --- | --- | --- | | [lex\_greater\_left\_ends](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html#a993ff6e6fe1e94695ebc4ae7ad9ea423)
(const ArcMatches &arc\_matches\_) | [LocARNA::ArcMatches::lex\_greater\_left\_ends](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html) | inlineexplicit | | [operator()](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html#a08c81b1290ecfcf82075570b3d06c975)
(const ArcMatch::idx\_type &i, const ArcMatch::idx\_type &j) const | [LocARNA::ArcMatches::lex\_greater\_left\_ends](https://s-will.github.io/LocARNA/classLocARNA_1_1ArcMatches_1_1lex__greater__left__ends.html) | inline | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) This is the complete list of members for [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) , including all inherited members. | | | | | --- | --- | --- | | [align](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a49a89aa973f2c3f15f73828bffe41e59)
() | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a82feb76f33c60ce8cf3ea78c4a5152c9)
(const Aligner &aligner) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#ad13a1f7975d5216a520032a9626a34cd)
(const AlignerParams &ap) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [evaluate](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a05b9c2bdaeb86a0f78a99b771d0c313a)
() | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [get\_alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a0e8e37bbdca34561fe844c802bc1e03f)
() const | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [get\_restriction](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a9327af44d882c34cf75fc98eb480b670)
() const | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [normalized\_align](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a71636d64db5c202b7c760b13bd57cc9f)
(score\_t L, bool verbose) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [operator=](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a3e7b613301a68d87730f10d104627873)
(const Aligner &aligner) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [optimize\_consensus\_structure](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a6ebbb477f3829e427635d20f149b2dd6)
() | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [penalized\_align](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a3eeaa29cc8cac584553e2360b1484382)
(score\_t position\_penalty) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [set\_alignment](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#ac9b75e39da6e5cfcfd74869af3f13340)
(const Alignment &alignment) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [set\_restriction](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a29bf5f892a492936c33c3a3ffeb6497b)
(const AlignerRestriction &r) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [suboptimal](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#af255b19eda2c3eb3990d9333a03fa092)
(int k, score\_t threshold, bool normalized, score\_t normalized\_L, size\_t output\_width, bool verbose, bool opt\_local\_out, bool opt\_pos\_output, bool opt\_write\_structure) | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [trace](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a509e9439515c04e0921bb3081f2614e4)
() | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | | [~Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html#a7ded09229dd5386c903cc73b4a07e32f)
() | [LocARNA::Aligner](https://s-will.github.io/LocARNA/classLocARNA_1_1Aligner.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) This is the complete list of members for [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) , including all inherited members. | | | | | --- | --- | --- | | [EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a05a8030272d9978c0244f4f6206d5fcb)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | **EdgeProbs**() (defined in [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html)
) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inlineprotected | | [lenA](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a81ef8ce0ab4345f3738491b9a4550e8e)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [lenB](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a3691f1f1863f752f4ce7e5457369a8a2)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [prob](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a9cafa8c72decd26680a7ed7880c18846)
(size\_t i, size\_t j) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [probs\_](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a6ff8f54ec7681a3fd380f53d4074c3d6) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#ac2644c906640be93c7f046980b12d38c)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#aa59c4b4cb7bea38d32e2c1d6f67da2ef)
(const std::string &filename, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [size\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a308c0af797440334a28acf5814a8ceb6)
typedef | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | | [write\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a134ba1f851cd5d8f31079a7f0701239c)
(std::ostream &out, double threshold) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) This is the complete list of members for [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) , including all inherited members. | | | | | --- | --- | --- | | [Arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#aea68c47e0f454c9777168854230d8dd3)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ac2ccff2cdeda72c023127c5b85168a71)
(int i, int j) const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | inline | | [arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a70dec5d31812206b0cf69c7d455bb9d0)
(size\_type idx) const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | inline | | [arc\_matrix\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ad7a2f18bed6a451fb04d20d96587b40e)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [arc\_vec\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a9c7e59c9997ec3d3ffe9a5779a686b54)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#aaa7a66233926250bada88ffd6ccb9de9)
(const RnaData \*rna\_data, double min\_prob) | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a5bb6e1f33a0d752e0833019c38f962b9)
(size\_type len, const bpair\_set\_t &bps) | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [bpair\_set\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ab135bd0a3ad6208e4684ee25547f4710)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [bpair\_t](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a7b2fdd5f56063b4caddd80bce9bb5312)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [exists\_arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#abde524b94ee7c1e4a279277a41ea52e9)
(int i, int j) const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | inline | | [left\_adjlist\_s](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ad03fda423a9766ba916e611b3ac17f11)
(size\_type i) const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | inline | | [LeftAdjList](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ac9079f4805720ed799b1702033b0102d)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [num\_bps](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ad2d3d60374a25f136adbd8c6e304a327)
() const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | inline | | [prob\_min](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a37ce248dec49dce3460182d5e77167c2)
() const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [register\_arc](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a4e0bf29fafd7b1eb84207386f83f1d92)
(int i, int j) | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [right\_adjlist\_s](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a5e0aba814d1975f8e7937b1d9a2bb1d4)
(size\_type i) const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | inline | | [RightAdjList](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#af53b42aa4df3eba885888825030227c5)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [seqlen](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#a215a688ff73fb4d94ab6a896b799b586)
() const | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | | [size\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html#ab8c5c60bc5558e934241313485a067e2)
typedef | [LocARNA::BasePairs](https://s-will.github.io/LocARNA/classLocARNA_1_1BasePairs.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [NamedArgument](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) This is the complete list of members for [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) , including all inherited members. | | | | | --- | --- | --- | | **NamedArgument**() (defined in [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html)
) | [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) | inline | | **NamedArgument**(const value\_type &value) (defined in [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html)
) | [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) | inline | | **NamedArgument**(value\_type &&value) (defined in [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html)
) | [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) | inline | | **value**() const (defined in [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html)
) | [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) | inline | | **value\_type** typedef (defined in [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html)
) | [LocARNA::NamedArgument< T >](https://s-will.github.io/LocARNA/classLocARNA_1_1NamedArgument.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [PairHMMMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html) This is the complete list of members for [LocARNA::PairHMMMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html) , including all inherited members. | | | | | --- | --- | --- | | [EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a05a8030272d9978c0244f4f6206d5fcb)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | **EdgeProbs**() (defined in [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html)
) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inlineprotected | | [lenA](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a81ef8ce0ab4345f3738491b9a4550e8e)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [lenB](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a3691f1f1863f752f4ce7e5457369a8a2)
() const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html#a3af43c7d4208ccdda8a626a7747f2c91)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) | inline | | **MatchProbs**() (defined in [LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html)
) | [LocARNA::MatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1MatchProbs.html) | inlineprotected | | [pairHMM\_probs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html#a8d74f653f09b97997d699c7630ee7dc1)
(const Sequence &seqA, const Sequence &seqB, const PairHMMParams ¶ms) | [LocARNA::PairHMMMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html) | protected | | [PairHMMMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html#a151cdbce96db979bd8040041e7d85bdf)
(const Sequence &seqA, const Sequence &seqB, const PairHMMParams ¶ms) | [LocARNA::PairHMMMatchProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1PairHMMMatchProbs.html) | inline | | [prob](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a9cafa8c72decd26680a7ed7880c18846)
(size\_t i, size\_t j) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | inline | | [probs\_](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a6ff8f54ec7681a3fd380f53d4074c3d6) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#ac2644c906640be93c7f046980b12d38c)
(std::istream &in, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [read\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#aa59c4b4cb7bea38d32e2c1d6f67da2ef)
(const std::string &filename, size\_type lenA, size\_type lenB) | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | protected | | [size\_type](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a308c0af797440334a28acf5814a8ceb6)
typedef | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | | [write\_sparse](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html#a134ba1f851cd5d8f31079a7f0701239c)
(std::ostream &out, double threshold) const | [LocARNA::EdgeProbs](https://s-will.github.io/LocARNA/classLocARNA_1_1EdgeProbs.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) This is the complete list of members for [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) , including all inherited members. | | | | | --- | --- | --- | | [best\_once\_on](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a8068a95904e73c3cc4b97d2b67f2c121)
(double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | **delta**(int i) const (defined in [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html)
) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | inlineprotectedvirtual | | **exp\_delta**(int i) const (defined in [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html)
) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | inlineprotectedvirtual | | [FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a427f7f742771c1385d1bffd44d7c15c0)
(numseq\_t &x\_, double delta\_, double beta\_) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | inline | | [forward](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#ac00514532546e97d2c6a64e77261476b)
(double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [optimize](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a559708be65e10bd42be70bd4d4c06e7b)
(double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [print\_table](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a9825cb248c92cef6fae1ac4f539856f1)
(const std::string &name, const std::vector< bool > &v) const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [print\_table](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#ae7faa64c95825495936dfbb89cecf47e)
(const std::string &name, const std::vector< pf\_t > &v) const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [print\_tables](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#af910fc9c14ffe4964b7e0693fa905066)
() const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [viterbi](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a40ef56acb9380743a3219351687d567e)
(double c0, double c1, bool traceback) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [write\_viterbi\_path](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#ab305dbbd7ee27b7a44d9c2d0a5660fa4)
(std::ostream &out, double c0, double c1) const | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | | [write\_viterbi\_path\_compact](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html#a9a4aaff7c47e9c9d93d31031f796f54d)
(std::ostream &out, double c0, double c1) | [LocARNA::FitOnOff](https://s-will.github.io/LocARNA/classLocARNA_1_1FitOnOff.html) | | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) This is the complete list of members for [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) , including all inherited members. | | | | | --- | --- | --- | | [addInsideBounds](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a9102659544b70aa201797720cacd4192)
(intPPair myPPair) | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | | | [get\_struct](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a60c35198fa490865978da1bb6ab38c39)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getEPMScore](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a8128350e2c64efe4e5b2aebccd0f1b60)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getFirstPat](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#af7f2084617d8a1f24873e67838efcfab)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getId](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#aa61c376f46b63e8d42bdb83e78adb633)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getInsideBounds](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a218774b9d64da2988fb401b839a431e5)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getOutsideBounds](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#ae2f0dc72dbb2e1505c7fbb247bccb1f9)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getScore](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a7843ad7c97803b518e02f84625963f9b)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getSecPat](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a65f33fbd89495b553a5232cd54a6dbf9)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [getSize](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a1472b544d07862abb462b2027bdf4dbb)
() const | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | **PatternPair**() (defined in [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html)
) | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a4eb339fcbb7c0d4c486555ec1de60fab)
(const std::string &myId, const SinglePattern &myFirstPat, const SinglePattern &mySecPat, const std::string &structure\_, int &score\_) | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inline | | [resetBounds](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#ad39d65fe290deb516949b5d340303e5d)
() | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | | | [setEPMScore](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#ac544370accd4251d4dc5072c5494e4d9)
(int myScore) | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | | | [setOutsideBounds](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a3a85b862b81c35a0f5c6fc76601fbd54)
(intPPair myPPair) | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | | | [~PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html#a964a34cff5f368d0092540bc6fc1b5ff)
() | [LocARNA::PatternPair](https://s-will.github.io/LocARNA/classLocARNA_1_1PatternPair.html) | inlinevirtual | --- # LocARNA-2.0.0: Member List LocARNA-2.0.0 * [LocARNA](https://s-will.github.io/LocARNA/namespaceLocARNA.html) * [option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) This is the complete list of members for [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) , including all inherited members. | | | | | --- | --- | --- | | [arg\_type](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a53f4637ea5694775161d27a950f56d78) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | | [argname](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#ab24e7a7169a24c34ebaa58f3ca4ef2e4) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | | [argument](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a1634a5717a64ed163daff388a88d79ff) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | | [deflt](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a5f35723b3908f82229bdb59dae050241) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | | [description](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a9b0e65314e2ac1e6070ba1a062b3558e) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | | [flag](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a8158ce024ed19ff0df48aa9f0f5f93ba) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | | [longname](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#a1854be3ee3b876c379d3e82a0d2b654d) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | | [shortname](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html#ae324344460cdc68f1d816b5c0db78d0f) | [LocARNA::option\_def](https://s-will.github.io/LocARNA/structLocARNA_1_1option__def.html) | | ---