binaries/src/ViennaRNA/doc/latex/data__structures_8h.tex

   1 \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}
   2 \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}}
   3 }
   4
   5
   6 All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here.
   7
   8
   9 Include dependency graph for data\-\_\-structures.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{data__structures_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 This graph shows which files directly or indirectly include this file\-:
  18 \nopagebreak
  19 \begin{figure}[H]
  20 \begin{center}
  21 \leavevmode
  22 \includegraphics[width=350pt]{data__structures_8h__dep__incl}
  23 \end{center}
  24 \end{figure}
  25 \subsection*{Data Structures}
  26 \begin{DoxyCompactItemize}
  27 \item
  28 struct \hyperlink{structplist}{plist}
  29 \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
  30 struct \hyperlink{structcpair}{cpair}
  31 \begin{DoxyCompactList}\small\item\em this datastructure is used as input parameter in functions of P\-S\-\_\-dot.\-c \end{DoxyCompactList}\item
  32 struct \hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E}
  33 \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
  34 struct \hyperlink{structsect}{sect}
  35 \begin{DoxyCompactList}\small\item\em Stack of partial structures for backtracking. \end{DoxyCompactList}\item
  36 struct \hyperlink{structbondT}{bond\-T}
  37 \begin{DoxyCompactList}\small\item\em Base pair. \end{DoxyCompactList}\item
  38 struct \hyperlink{structbondTEn}{bond\-T\-En}
  39 \begin{DoxyCompactList}\small\item\em Base pair with associated energy. \end{DoxyCompactList}\item
  40 struct \hyperlink{structmodel__detailsT}{model\-\_\-details\-T}
  41 \begin{DoxyCompactList}\small\item\em The data structure that contains the complete model details used throughout the calculations. \end{DoxyCompactList}\item
  42 struct \hyperlink{structparamT}{param\-T}
  43 \begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled energy parameters. \end{DoxyCompactList}\item
  44 struct \hyperlink{structpf__paramT}{pf\-\_\-param\-T}
  45 \begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled Boltzmann weights of the energy parameters. \end{DoxyCompactList}\item
  46 struct \hyperlink{structPAIR}{P\-A\-I\-R}
  47 \begin{DoxyCompactList}\small\item\em Base pair data structure used in subopt.\-c. \end{DoxyCompactList}\item
  48 struct \hyperlink{structINTERVAL}{I\-N\-T\-E\-R\-V\-A\-L}
  49 \begin{DoxyCompactList}\small\item\em Sequence interval stack element used in subopt.\-c. \end{DoxyCompactList}\item
  50 struct \hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N}
  51 \begin{DoxyCompactList}\small\item\em Solution element from subopt.\-c. \end{DoxyCompactList}\item
  52 struct \hyperlink{structcofoldF}{cofold\-F}
  53 \item
  54 struct \hyperlink{structConcEnt}{Conc\-Ent}
  55 \item
  56 struct \hyperlink{structpairpro}{pairpro}
  57 \item
  58 struct \hyperlink{structpair__info}{pair\-\_\-info}
  59 \begin{DoxyCompactList}\small\item\em A base pair info structure. \end{DoxyCompactList}\item
  60 struct \hyperlink{structmove__t}{move\-\_\-t}
  61 \item
  62 struct \hyperlink{structintermediate__t}{intermediate\-\_\-t}
  63 \item
  64 struct \hyperlink{structpath__t}{path\-\_\-t}
  65 \item
  66 struct \hyperlink{structpu__contrib}{pu\-\_\-contrib}
  67 \begin{DoxyCompactList}\small\item\em contributions to p\-\_\-u \end{DoxyCompactList}\item
  68 struct \hyperlink{structinteract}{interact}
  69 \item
  70 struct \hyperlink{structpu__out}{pu\-\_\-out}
  71 \begin{DoxyCompactList}\small\item\em Collection of all free\-\_\-energy of beeing unpaired values for output. \end{DoxyCompactList}\item
  72 struct \hyperlink{structconstrain}{constrain}
  73 \begin{DoxyCompactList}\small\item\em constraints for cofolding \end{DoxyCompactList}\item
  74 struct \hyperlink{structduplexT}{duplex\-T}
  75 \item
  76 struct \hyperlink{structfolden}{folden}
  77 \item
  78 struct \hyperlink{structsnoopT}{snoop\-T}
  79 \item
  80 struct \hyperlink{structdupVar}{dup\-Var}
  81 \item
  82 struct \hyperlink{structTwoDfold__solution}{Two\-Dfold\-\_\-solution}
  83 \begin{DoxyCompactList}\small\item\em Solution element returned from Two\-Dfold\-List. \end{DoxyCompactList}\item
  84 struct \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars}
  85 \begin{DoxyCompactList}\small\item\em Variables compound for 2\-Dfold M\-F\-E folding. \end{DoxyCompactList}\item
  86 struct \hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution}
  87 \begin{DoxyCompactList}\small\item\em Solution element returned from Two\-Dpfold\-List. \end{DoxyCompactList}\item
  88 struct \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars}
  89 \begin{DoxyCompactList}\small\item\em Variables compound for 2\-Dfold partition function folding. \end{DoxyCompactList}\end{DoxyCompactItemize}
  90 \subsection*{Macros}
  91 \begin{DoxyCompactItemize}
  92 \item
  93 \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}
  94
  95 \begin{DoxyCompactList}\small\item\em Maximal length of alphabet. \end{DoxyCompactList}\item
  96 \hypertarget{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{\#define \hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{M\-A\-X\-D\-O\-S}~1000}\label{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}
  97
  98 \begin{DoxyCompactList}\small\item\em Maximum density of states discretization for subopt. \end{DoxyCompactList}\end{DoxyCompactItemize}
  99
 100
 101 \subsection{Detailed Description}
 102 All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here.