\hypertarget{dir_d72344b28b4f2089ce25682c4e6eba22}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H Directory Reference}
\label{dir_d72344b28b4f2089ce25682c4e6eba22}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H Directory Reference@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H Directory Reference}}
}
Directory dependency graph for H\-:
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\subsection*{Files}
\begin{DoxyCompactItemize}
\item 
file \hyperlink{2Dfold_8h}{2\-Dfold.\-h}
\item 
file \hyperlink{2Dpfold_8h}{2\-Dpfold.\-h}
\item 
file {\bfseries ali\-\_\-plex.\-h}
\item 
file \hyperlink{alifold_8h}{alifold.\-h}
\begin{DoxyCompactList}\small\item\em compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments \end{DoxyCompactList}\item 
file {\bfseries aln\-\_\-util.\-h}
\item 
file \hyperlink{cofold_8h}{cofold.\-h}
\begin{DoxyCompactList}\small\item\em M\-F\-E version of cofolding routines. \end{DoxyCompactList}\item 
file \hyperlink{convert__epars_8h}{convert\-\_\-epars.\-h}
\begin{DoxyCompactList}\small\item\em Functions and definitions for energy parameter file format conversion. \end{DoxyCompactList}\item 
file \hyperlink{data__structures_8h}{data\-\_\-structures.\-h}
\begin{DoxyCompactList}\small\item\em All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here. \end{DoxyCompactList}\item 
file \hyperlink{dist__vars_8h}{dist\-\_\-vars.\-h}
\begin{DoxyCompactList}\small\item\em Global variables for Distance-\/\-Package. \end{DoxyCompactList}\item 
file \hyperlink{duplex_8h}{duplex.\-h}
\begin{DoxyCompactList}\small\item\em Duplex folding function declarations... \end{DoxyCompactList}\item 
file \hyperlink{edit__cost_8h}{edit\-\_\-cost.\-h}
\begin{DoxyCompactList}\small\item\em global variables for Edit Costs included by treedist.\-c and stringdist.\-c \end{DoxyCompactList}\item 
file \hyperlink{energy__const_8h}{energy\-\_\-const.\-h}
\item 
file {\bfseries energy\-\_\-par.\-h}
\item 
file \hyperlink{findpath_8h}{findpath.\-h}
\begin{DoxyCompactList}\small\item\em Compute direct refolding paths between two secondary structures. \end{DoxyCompactList}\item 
file \hyperlink{fold_8h}{fold.\-h}
\begin{DoxyCompactList}\small\item\em M\-F\-E calculations and energy evaluations for single R\-N\-A sequences. \end{DoxyCompactList}\item 
file \hyperlink{fold__vars_8h}{fold\-\_\-vars.\-h}
\begin{DoxyCompactList}\small\item\em Here all all declarations of the global variables used throughout R\-N\-Alib. \end{DoxyCompactList}\item 
file \hyperlink{gquad_8h}{gquad.\-h}
\begin{DoxyCompactList}\small\item\em Various functions related to G-\/quadruplex computations. \end{DoxyCompactList}\item 
file \hyperlink{inverse_8h}{inverse.\-h}
\begin{DoxyCompactList}\small\item\em Inverse folding routines. \end{DoxyCompactList}\item 
file \hyperlink{Lfold_8h}{Lfold.\-h}
\begin{DoxyCompactList}\small\item\em Predicting local M\-F\-E structures of large sequences. \end{DoxyCompactList}\item 
file \hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h}
\begin{DoxyCompactList}\small\item\em Energy evaluation for M\-F\-E and partition function calculations. \end{DoxyCompactList}\item 
file \hyperlink{LPfold_8h}{L\-Pfold.\-h}
\begin{DoxyCompactList}\small\item\em Function declarations of partition function variants of the Lfold algorithm. \end{DoxyCompactList}\item 
file \hyperlink{MEA_8h}{M\-E\-A.\-h}
\begin{DoxyCompactList}\small\item\em Computes a M\-E\-A (maximum expected accuracy) structure. \end{DoxyCompactList}\item 
file \hyperlink{mm_8h}{mm.\-h}
\begin{DoxyCompactList}\small\item\em Several Maximum Matching implementations. \end{DoxyCompactList}\item 
file {\bfseries move\-\_\-set.\-h}
\item 
file \hyperlink{naview_8h}{naview.\-h}
\item 
file {\bfseries pair\-\_\-mat.\-h}
\item 
file \hyperlink{params_8h}{params.\-h}
\item 
file \hyperlink{part__func_8h}{part\-\_\-func.\-h}
\begin{DoxyCompactList}\small\item\em Partition function of single R\-N\-A sequences. \end{DoxyCompactList}\item 
file \hyperlink{part__func__co_8h}{part\-\_\-func\-\_\-co.\-h}
\begin{DoxyCompactList}\small\item\em Partition function for two R\-N\-A sequences. \end{DoxyCompactList}\item 
file \hyperlink{part__func__up_8h}{part\-\_\-func\-\_\-up.\-h}
\begin{DoxyCompactList}\small\item\em Partition Function Cofolding as stepwise process. \end{DoxyCompactList}\item 
file {\bfseries P\-Kplex.\-h}
\item 
file {\bfseries plex.\-h}
\item 
file \hyperlink{plot__layouts_8h}{plot\-\_\-layouts.\-h}
\begin{DoxyCompactList}\small\item\em Secondary structure plot layout algorithms. \end{DoxyCompactList}\item 
file {\bfseries Profile\-Aln.\-h}
\item 
file \hyperlink{profiledist_8h}{profiledist.\-h}
\item 
file \hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h}
\begin{DoxyCompactList}\small\item\em Various functions for plotting R\-N\-A secondary structures, dot-\/plots and other visualizations. \end{DoxyCompactList}\item 
file \hyperlink{read__epars_8h}{read\-\_\-epars.\-h}
\item 
file {\bfseries ribo.\-h}
\item 
file \hyperlink{RNAstruct_8h}{R\-N\-Astruct.\-h}
\begin{DoxyCompactList}\small\item\em Parsing and Coarse Graining of Structures. \end{DoxyCompactList}\item 
file {\bfseries snofold.\-h}
\item 
file {\bfseries snoop.\-h}
\item 
file \hyperlink{stringdist_8h}{stringdist.\-h}
\begin{DoxyCompactList}\small\item\em Functions for String Alignment. \end{DoxyCompactList}\item 
file \hyperlink{subopt_8h}{subopt.\-h}
\begin{DoxyCompactList}\small\item\em R\-N\-Asubopt and density of states declarations. \end{DoxyCompactList}\item 
file {\bfseries svm\-\_\-utils.\-h}
\item 
file \hyperlink{treedist_8h}{treedist.\-h}
\begin{DoxyCompactList}\small\item\em Functions for \hyperlink{structTree}{Tree} Edit Distances. \end{DoxyCompactList}\item 
file \hyperlink{utils_8h}{utils.\-h}
\begin{DoxyCompactList}\small\item\em Various utility-\/ and helper-\/functions used throughout the Vienna R\-N\-A package. \end{DoxyCompactList}\end{DoxyCompactItemize}
