-\hypertarget{data__structures_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.h File Reference}
-\label{data__structures_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.\-h}}
+\hypertarget{data__structures_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\-structures.h File Reference}
+\label{data__structures_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\-structures.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\-structures.h}}
}
-All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here.
-
-
-Include dependency graph for data\-\_\-structures.\-h\-:
-\nopagebreak
+All datastructures and typedefs shared among the Vienna RNA Package can be found here.
+Include dependency graph for data\_\-structures.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=250pt]{data__structures_8h__incl}
+\includegraphics[width=229pt]{data__structures_8h__incl}
\end{center}
\end{figure}
-This graph shows which files directly or indirectly include this file\-:
-\nopagebreak
+This graph shows which files directly or indirectly include this file:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{data__structures_8h__dep__incl}
+\includegraphics[width=420pt]{data__structures_8h__dep__incl}
\end{center}
\end{figure}
\subsection*{Data Structures}
\begin{DoxyCompactItemize}
\item
struct \hyperlink{structplist}{plist}
-\begin{DoxyCompactList}\small\item\em this datastructure is used as input parameter in functions of \hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h} and others \end{DoxyCompactList}\item
+\begin{DoxyCompactList}\small\item\em this datastructure is used as input parameter in functions of \hyperlink{PS__dot_8h}{PS\_\-dot.h} and others \item\end{DoxyCompactList}\item
struct \hyperlink{structcpair}{cpair}
-\begin{DoxyCompactList}\small\item\em this datastructure is used as input parameter in functions of P\-S\-\_\-dot.\-c \end{DoxyCompactList}\item
-struct \hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E}
-\begin{DoxyCompactList}\small\item\em this is a workarround for the S\-W\-I\-G Perl Wrapper R\-N\-A plot function that returns an array of type \hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E} \end{DoxyCompactList}\item
+\begin{DoxyCompactList}\small\item\em this datastructure is used as input parameter in functions of PS\_\-dot.c \item\end{DoxyCompactList}\item
+struct \hyperlink{structCOORDINATE}{COORDINATE}
+\begin{DoxyCompactList}\small\item\em this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type \hyperlink{structCOORDINATE}{COORDINATE} \item\end{DoxyCompactList}\item
struct \hyperlink{structsect}{sect}
-\begin{DoxyCompactList}\small\item\em Stack of partial structures for backtracking. \end{DoxyCompactList}\item
-struct \hyperlink{structbondT}{bond\-T}
-\begin{DoxyCompactList}\small\item\em Base pair. \end{DoxyCompactList}\item
-struct \hyperlink{structbondTEn}{bond\-T\-En}
-\begin{DoxyCompactList}\small\item\em Base pair with associated energy. \end{DoxyCompactList}\item
-struct \hyperlink{structmodel__detailsT}{model\-\_\-details\-T}
-\begin{DoxyCompactList}\small\item\em The data structure that contains the complete model details used throughout the calculations. \end{DoxyCompactList}\item
-struct \hyperlink{structparamT}{param\-T}
-\begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled energy parameters. \end{DoxyCompactList}\item
-struct \hyperlink{structpf__paramT}{pf\-\_\-param\-T}
-\begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled Boltzmann weights of the energy parameters. \end{DoxyCompactList}\item
-struct \hyperlink{structPAIR}{P\-A\-I\-R}
-\begin{DoxyCompactList}\small\item\em Base pair data structure used in subopt.\-c. \end{DoxyCompactList}\item
-struct \hyperlink{structINTERVAL}{I\-N\-T\-E\-R\-V\-A\-L}
-\begin{DoxyCompactList}\small\item\em Sequence interval stack element used in subopt.\-c. \end{DoxyCompactList}\item
-struct \hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N}
-\begin{DoxyCompactList}\small\item\em Solution element from subopt.\-c. \end{DoxyCompactList}\item
-struct \hyperlink{structcofoldF}{cofold\-F}
+\begin{DoxyCompactList}\small\item\em Stack of partial structures for backtracking. \item\end{DoxyCompactList}\item
+struct \hyperlink{structbondT}{bondT}
+\begin{DoxyCompactList}\small\item\em Base pair. \item\end{DoxyCompactList}\item
+struct \hyperlink{structbondTEn}{bondTEn}
+\begin{DoxyCompactList}\small\item\em Base pair with associated energy. \item\end{DoxyCompactList}\item
+struct \hyperlink{structmodel__detailsT}{model\_\-detailsT}
+\begin{DoxyCompactList}\small\item\em The data structure that contains the complete model details used throughout the calculations. \item\end{DoxyCompactList}\item
+struct \hyperlink{structparamT}{paramT}
+\begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled energy parameters. \item\end{DoxyCompactList}\item
+struct \hyperlink{structpf__paramT}{pf\_\-paramT}
+\begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled Boltzmann weights of the energy parameters. \item\end{DoxyCompactList}\item
+struct \hyperlink{structPAIR}{PAIR}
+\begin{DoxyCompactList}\small\item\em Base pair data structure used in subopt.c. \item\end{DoxyCompactList}\item
+struct \hyperlink{structINTERVAL}{INTERVAL}
+\begin{DoxyCompactList}\small\item\em Sequence interval stack element used in subopt.c. \item\end{DoxyCompactList}\item
+struct \hyperlink{structSOLUTION}{SOLUTION}
+\begin{DoxyCompactList}\small\item\em Solution element from subopt.c. \item\end{DoxyCompactList}\item
+struct \hyperlink{structcofoldF}{cofoldF}
\item
-struct \hyperlink{structConcEnt}{Conc\-Ent}
+struct \hyperlink{structConcEnt}{ConcEnt}
\item
struct \hyperlink{structpairpro}{pairpro}
\item
-struct \hyperlink{structpair__info}{pair\-\_\-info}
-\begin{DoxyCompactList}\small\item\em A base pair info structure. \end{DoxyCompactList}\item
-struct \hyperlink{structmove__t}{move\-\_\-t}
+struct \hyperlink{structpair__info}{pair\_\-info}
+\begin{DoxyCompactList}\small\item\em A base pair info structure. \item\end{DoxyCompactList}\item
+struct \hyperlink{structmove__t}{move\_\-t}
\item
-struct \hyperlink{structintermediate__t}{intermediate\-\_\-t}
+struct \hyperlink{structintermediate__t}{intermediate\_\-t}
\item
-struct \hyperlink{structpath__t}{path\-\_\-t}
+struct \hyperlink{structpath__t}{path\_\-t}
\item
-struct \hyperlink{structpu__contrib}{pu\-\_\-contrib}
-\begin{DoxyCompactList}\small\item\em contributions to p\-\_\-u \end{DoxyCompactList}\item
+struct \hyperlink{structpu__contrib}{pu\_\-contrib}
+\begin{DoxyCompactList}\small\item\em contributions to p\_\-u \item\end{DoxyCompactList}\item
struct \hyperlink{structinteract}{interact}
\item
-struct \hyperlink{structpu__out}{pu\-\_\-out}
-\begin{DoxyCompactList}\small\item\em Collection of all free\-\_\-energy of beeing unpaired values for output. \end{DoxyCompactList}\item
+struct \hyperlink{structpu__out}{pu\_\-out}
+\begin{DoxyCompactList}\small\item\em Collection of all free\_\-energy of beeing unpaired values for output. \item\end{DoxyCompactList}\item
struct \hyperlink{structconstrain}{constrain}
-\begin{DoxyCompactList}\small\item\em constraints for cofolding \end{DoxyCompactList}\item
-struct \hyperlink{structduplexT}{duplex\-T}
+\begin{DoxyCompactList}\small\item\em constraints for cofolding \item\end{DoxyCompactList}\item
+struct \hyperlink{structduplexT}{duplexT}
\item
struct \hyperlink{structfolden}{folden}
\item
-struct \hyperlink{structsnoopT}{snoop\-T}
+struct \hyperlink{structsnoopT}{snoopT}
\item
-struct \hyperlink{structdupVar}{dup\-Var}
+struct \hyperlink{structdupVar}{dupVar}
\item
-struct \hyperlink{structTwoDfold__solution}{Two\-Dfold\-\_\-solution}
-\begin{DoxyCompactList}\small\item\em Solution element returned from Two\-Dfold\-List. \end{DoxyCompactList}\item
-struct \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars}
-\begin{DoxyCompactList}\small\item\em Variables compound for 2\-Dfold M\-F\-E folding. \end{DoxyCompactList}\item
-struct \hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution}
-\begin{DoxyCompactList}\small\item\em Solution element returned from Two\-Dpfold\-List. \end{DoxyCompactList}\item
-struct \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars}
-\begin{DoxyCompactList}\small\item\em Variables compound for 2\-Dfold partition function folding. \end{DoxyCompactList}\end{DoxyCompactItemize}
-\subsection*{Macros}
+struct \hyperlink{structTwoDfold__solution}{TwoDfold\_\-solution}
+\begin{DoxyCompactList}\small\item\em Solution element returned from TwoDfoldList. \item\end{DoxyCompactList}\item
+struct \hyperlink{structTwoDfold__vars}{TwoDfold\_\-vars}
+\begin{DoxyCompactList}\small\item\em Variables compound for 2Dfold MFE folding. \item\end{DoxyCompactList}\item
+struct \hyperlink{structTwoDpfold__solution}{TwoDpfold\_\-solution}
+\begin{DoxyCompactList}\small\item\em Solution element returned from TwoDpfoldList. \item\end{DoxyCompactList}\item
+struct \hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars}
+\begin{DoxyCompactList}\small\item\em Variables compound for 2Dfold partition function folding. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Defines}
\begin{DoxyCompactItemize}
\item
-\hypertarget{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{\#define \hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{M\-A\-X\-A\-L\-P\-H\-A}~20}\label{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}
+\hypertarget{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{
+\#define \hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}~20}
+\label{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}
-\begin{DoxyCompactList}\small\item\em Maximal length of alphabet. \end{DoxyCompactList}\item
-\hypertarget{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{\#define \hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{M\-A\-X\-D\-O\-S}~1000}\label{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}
+\begin{DoxyCompactList}\small\item\em Maximal length of alphabet. \item\end{DoxyCompactList}\item
+\hypertarget{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{
+\#define \hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{MAXDOS}~1000}
+\label{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}
-\begin{DoxyCompactList}\small\item\em Maximum density of states discretization for subopt. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\begin{DoxyCompactList}\small\item\em Maximum density of states discretization for subopt. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection{Detailed Description}
-All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here.
\ No newline at end of file
+All datastructures and typedefs shared among the Vienna RNA Package can be found here.
\ No newline at end of file
git://source.jalview.org / jabaws.git / blobdiff