--- /dev/null
+\section{File List}
+Here is a list of all documented files with brief descriptions\-:\begin{DoxyCompactList}
+\item\contentsline{section}{{\bfseries mainpage.\-h} }{\pageref{mainpage_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{2Dfold_8h}{2\-Dfold.\-h} }{\pageref{2Dfold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{2Dpfold_8h}{2\-Dpfold.\-h} }{\pageref{2Dpfold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries ali\-\_\-plex.\-h} }{\pageref{ali__plex_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{alifold_8h}{alifold.\-h} \\*Compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments }{\pageref{alifold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries aln\-\_\-util.\-h} }{\pageref{aln__util_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{cofold_8h}{cofold.\-h} \\*M\-F\-E version of cofolding routines }{\pageref{cofold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{convert__epars_8h}{convert\-\_\-epars.\-h} \\*Functions and definitions for energy parameter file format conversion }{\pageref{convert__epars_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h} \\*All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here }{\pageref{data__structures_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{dist__vars_8h}{dist\-\_\-vars.\-h} \\*Global variables for Distance-\/\-Package }{\pageref{dist__vars_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{duplex_8h}{duplex.\-h} \\*Duplex folding function declarations.. }{\pageref{duplex_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{edit__cost_8h}{edit\-\_\-cost.\-h} \\*Global variables for Edit Costs included by treedist.\-c and stringdist.\-c }{\pageref{edit__cost_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{energy__const_8h}{energy\-\_\-const.\-h} }{\pageref{energy__const_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries energy\-\_\-par.\-h} }{\pageref{energy__par_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{findpath_8h}{findpath.\-h} \\*Compute direct refolding paths between two secondary structures }{\pageref{findpath_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{fold_8h}{fold.\-h} \\*M\-F\-E calculations and energy evaluations for single R\-N\-A sequences }{\pageref{fold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{fold__vars_8h}{fold\-\_\-vars.\-h} \\*Here all all declarations of the global variables used throughout R\-N\-Alib }{\pageref{fold__vars_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{gquad_8h}{gquad.\-h} \\*Various functions related to G-\/quadruplex computations }{\pageref{gquad_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{inverse_8h}{inverse.\-h} \\*Inverse folding routines }{\pageref{inverse_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{Lfold_8h}{Lfold.\-h} \\*Predicting local M\-F\-E structures of large sequences }{\pageref{Lfold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} \\*Energy evaluation for M\-F\-E and partition function calculations }{\pageref{loop__energies_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{LPfold_8h}{L\-Pfold.\-h} \\*Function declarations of partition function variants of the Lfold algorithm }{\pageref{LPfold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{MEA_8h}{M\-E\-A.\-h} \\*Computes a M\-E\-A (maximum expected accuracy) structure }{\pageref{MEA_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{mm_8h}{mm.\-h} \\*Several Maximum Matching implementations }{\pageref{mm_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries move\-\_\-set.\-h} }{\pageref{move__set_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{naview_8h}{naview.\-h} }{\pageref{naview_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries pair\-\_\-mat.\-h} }{\pageref{pair__mat_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{params_8h}{params.\-h} }{\pageref{params_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{part__func_8h}{part\-\_\-func.\-h} \\*Partition function of single R\-N\-A sequences }{\pageref{part__func_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{part__func__co_8h}{part\-\_\-func\-\_\-co.\-h} \\*Partition function for two R\-N\-A sequences }{\pageref{part__func__co_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{part__func__up_8h}{part\-\_\-func\-\_\-up.\-h} \\*Partition Function Cofolding as stepwise process }{\pageref{part__func__up_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries P\-Kplex.\-h} }{\pageref{PKplex_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries plex.\-h} }{\pageref{plex_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{plot__layouts_8h}{plot\-\_\-layouts.\-h} \\*Secondary structure plot layout algorithms }{\pageref{plot__layouts_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries Profile\-Aln.\-h} }{\pageref{ProfileAln_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{profiledist_8h}{profiledist.\-h} }{\pageref{profiledist_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h} \\*Various functions for plotting R\-N\-A secondary structures, dot-\/plots and other visualizations }{\pageref{PS__dot_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{read__epars_8h}{read\-\_\-epars.\-h} }{\pageref{read__epars_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries ribo.\-h} }{\pageref{ribo_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{RNAstruct_8h}{R\-N\-Astruct.\-h} \\*Parsing and Coarse Graining of Structures }{\pageref{RNAstruct_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries snofold.\-h} }{\pageref{snofold_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries snoop.\-h} }{\pageref{snoop_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{stringdist_8h}{stringdist.\-h} \\*Functions for String Alignment }{\pageref{stringdist_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{subopt_8h}{subopt.\-h} \\*R\-N\-Asubopt and density of states declarations }{\pageref{subopt_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries svm\-\_\-utils.\-h} }{\pageref{svm__utils_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{treedist_8h}{treedist.\-h} \\*Functions for \hyperlink{structTree}{Tree} Edit Distances }{\pageref{treedist_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{utils_8h}{utils.\-h} \\*Various utility-\/ and helper-\/functions used throughout the Vienna R\-N\-A package }{\pageref{utils_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/\hyperlink{1_88_84__epars_8h}{1.\-8.\-4\-\_\-epars.\-h} \\*Free energy parameters for parameter file conversion }{\pageref{1_88_84__epars_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/\hyperlink{1_88_84__intloops_8h}{1.\-8.\-4\-\_\-intloops.\-h} \\*Free energy parameters for interior loop contributions needed by the parameter file conversion functions }{\pageref{1_88_84__intloops_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl11.\-h} }{\pageref{intl11_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl11d\-H.\-h} }{\pageref{intl11dH_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl21.\-h} }{\pageref{intl21_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl21d\-H.\-h} }{\pageref{intl21dH_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl22.\-h} }{\pageref{intl22_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl22d\-H.\-h} }{\pageref{intl22dH_8h}}{}
+\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries list.\-h} }{\pageref{list_8h}}{}
+\end{DoxyCompactList}
git://source.jalview.org / jabaws.git / blobdiff