JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / annotated.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/annotated.tex b/binaries/src/ViennaRNA/doc/latex/annotated.tex
index cb2012c..acef4c9 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/annotated.tex
+++ b/binaries/src/ViennaRNA/doc/latex/annotated.tex
@@ -1,41 +1,41 @@
 \section{Data Structures}
-Here are the data structures with brief descriptions\-:\begin{DoxyCompactList}
-\item\contentsline{section}{\hyperlink{structbondT}{bond\-T} \\*Base pair }{\pageref{structbondT}}{}
-\item\contentsline{section}{\hyperlink{structbondTEn}{bond\-T\-En} \\*Base pair with associated energy }{\pageref{structbondTEn}}{}
-\item\contentsline{section}{\hyperlink{structcofoldF}{cofold\-F} }{\pageref{structcofoldF}}{}
-\item\contentsline{section}{\hyperlink{structConcEnt}{Conc\-Ent} }{\pageref{structConcEnt}}{}
-\item\contentsline{section}{\hyperlink{structconstrain}{constrain} \\*Constraints for cofolding }{\pageref{structconstrain}}{}
-\item\contentsline{section}{\hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E} \\*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} }{\pageref{structCOORDINATE}}{}
-\item\contentsline{section}{\hyperlink{structcpair}{cpair} \\*This datastructure is used as input parameter in functions of P\-S\-\_\-dot.\-c }{\pageref{structcpair}}{}
-\item\contentsline{section}{\hyperlink{structduplexT}{duplex\-T} }{\pageref{structduplexT}}{}
-\item\contentsline{section}{\hyperlink{structdupVar}{dup\-Var} }{\pageref{structdupVar}}{}
+Here are the data structures with brief descriptions:\begin{DoxyCompactList}
+\item\contentsline{section}{\hyperlink{structbondT}{bondT} (Base pair )}{\pageref{structbondT}}{}
+\item\contentsline{section}{\hyperlink{structbondTEn}{bondTEn} (Base pair with associated energy )}{\pageref{structbondTEn}}{}
+\item\contentsline{section}{\hyperlink{structcofoldF}{cofoldF} }{\pageref{structcofoldF}}{}
+\item\contentsline{section}{\hyperlink{structConcEnt}{ConcEnt} }{\pageref{structConcEnt}}{}
+\item\contentsline{section}{\hyperlink{structconstrain}{constrain} (Constraints for cofolding )}{\pageref{structconstrain}}{}
+\item\contentsline{section}{\hyperlink{structCOORDINATE}{COORDINATE} (This is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type \hyperlink{structCOORDINATE}{COORDINATE} )}{\pageref{structCOORDINATE}}{}
+\item\contentsline{section}{\hyperlink{structcpair}{cpair} (This datastructure is used as input parameter in functions of PS\_\-dot.c )}{\pageref{structcpair}}{}
+\item\contentsline{section}{\hyperlink{structduplexT}{duplexT} }{\pageref{structduplexT}}{}
+\item\contentsline{section}{\hyperlink{structdupVar}{dupVar} }{\pageref{structdupVar}}{}
 \item\contentsline{section}{\hyperlink{structfolden}{folden} }{\pageref{structfolden}}{}
 \item\contentsline{section}{\hyperlink{structinteract}{interact} }{\pageref{structinteract}}{}
-\item\contentsline{section}{\hyperlink{structintermediate__t}{intermediate\-\_\-t} }{\pageref{structintermediate__t}}{}
-\item\contentsline{section}{\hyperlink{structINTERVAL}{I\-N\-T\-E\-R\-V\-A\-L} \\*Sequence interval stack element used in subopt.\-c }{\pageref{structINTERVAL}}{}
-\item\contentsline{section}{\hyperlink{structLIST}{L\-I\-S\-T} }{\pageref{structLIST}}{}
-\item\contentsline{section}{\hyperlink{structLST__BUCKET}{L\-S\-T\-\_\-\-B\-U\-C\-K\-E\-T} }{\pageref{structLST__BUCKET}}{}
-\item\contentsline{section}{\hyperlink{structmodel__detailsT}{model\-\_\-details\-T} \\*The data structure that contains the complete model details used throughout the calculations }{\pageref{structmodel__detailsT}}{}
-\item\contentsline{section}{\hyperlink{structmove__t}{move\-\_\-t} }{\pageref{structmove__t}}{}
-\item\contentsline{section}{\hyperlink{structPAIR}{P\-A\-I\-R} \\*Base pair data structure used in subopt.\-c }{\pageref{structPAIR}}{}
-\item\contentsline{section}{\hyperlink{structpair__info}{pair\-\_\-info} \\*A base pair info structure }{\pageref{structpair__info}}{}
+\item\contentsline{section}{\hyperlink{structintermediate__t}{intermediate\_\-t} }{\pageref{structintermediate__t}}{}
+\item\contentsline{section}{\hyperlink{structINTERVAL}{INTERVAL} (Sequence interval stack element used in subopt.c )}{\pageref{structINTERVAL}}{}
+\item\contentsline{section}{\hyperlink{structLIST}{LIST} }{\pageref{structLIST}}{}
+\item\contentsline{section}{\hyperlink{structLST__BUCKET}{LST\_\-BUCKET} }{\pageref{structLST__BUCKET}}{}
+\item\contentsline{section}{\hyperlink{structmodel__detailsT}{model\_\-detailsT} (The data structure that contains the complete model details used throughout the calculations )}{\pageref{structmodel__detailsT}}{}
+\item\contentsline{section}{\hyperlink{structmove__t}{move\_\-t} }{\pageref{structmove__t}}{}
+\item\contentsline{section}{\hyperlink{structPAIR}{PAIR} (Base pair data structure used in subopt.c )}{\pageref{structPAIR}}{}
+\item\contentsline{section}{\hyperlink{structpair__info}{pair\_\-info} (A base pair info structure )}{\pageref{structpair__info}}{}
 \item\contentsline{section}{\hyperlink{structpairpro}{pairpro} }{\pageref{structpairpro}}{}
-\item\contentsline{section}{\hyperlink{structparamT}{param\-T} \\*The datastructure that contains temperature scaled energy parameters }{\pageref{structparamT}}{}
-\item\contentsline{section}{\hyperlink{structpath__t}{path\-\_\-t} }{\pageref{structpath__t}}{}
-\item\contentsline{section}{\hyperlink{structpf__paramT}{pf\-\_\-param\-T} \\*The datastructure that contains temperature scaled Boltzmann weights of the energy parameters }{\pageref{structpf__paramT}}{}
-\item\contentsline{section}{\hyperlink{structplist}{plist} \\*This datastructure is used as input parameter in functions of \hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h} and others }{\pageref{structplist}}{}
-\item\contentsline{section}{\hyperlink{structPostorder__list}{Postorder\-\_\-list} }{\pageref{structPostorder__list}}{}
-\item\contentsline{section}{\hyperlink{structpu__contrib}{pu\-\_\-contrib} \\*Contributions to p\-\_\-u }{\pageref{structpu__contrib}}{}
-\item\contentsline{section}{\hyperlink{structpu__out}{pu\-\_\-out} \\*Collection of all free\-\_\-energy of beeing unpaired values for output }{\pageref{structpu__out}}{}
-\item\contentsline{section}{\hyperlink{structsect}{sect} \\*Stack of partial structures for backtracking }{\pageref{structsect}}{}
-\item\contentsline{section}{\hyperlink{structsnoopT}{snoop\-T} }{\pageref{structsnoopT}}{}
-\item\contentsline{section}{\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} \\*Solution element from subopt.\-c }{\pageref{structSOLUTION}}{}
-\item\contentsline{section}{\hyperlink{structstruct__en}{struct\-\_\-en} }{\pageref{structstruct__en}}{}
-\item\contentsline{section}{\hyperlink{structsvm__model}{svm\-\_\-model} }{\pageref{structsvm__model}}{}
-\item\contentsline{section}{\hyperlink{structswString}{sw\-String} }{\pageref{structswString}}{}
+\item\contentsline{section}{\hyperlink{structparamT}{paramT} (The datastructure that contains temperature scaled energy parameters )}{\pageref{structparamT}}{}
+\item\contentsline{section}{\hyperlink{structpath__t}{path\_\-t} }{\pageref{structpath__t}}{}
+\item\contentsline{section}{\hyperlink{structpf__paramT}{pf\_\-paramT} (The datastructure that contains temperature scaled Boltzmann weights of the energy parameters )}{\pageref{structpf__paramT}}{}
+\item\contentsline{section}{\hyperlink{structplist}{plist} (This datastructure is used as input parameter in functions of \hyperlink{PS__dot_8h}{PS\_\-dot.h} and others )}{\pageref{structplist}}{}
+\item\contentsline{section}{\hyperlink{structPostorder__list}{Postorder\_\-list} }{\pageref{structPostorder__list}}{}
+\item\contentsline{section}{\hyperlink{structpu__contrib}{pu\_\-contrib} (Contributions to p\_\-u )}{\pageref{structpu__contrib}}{}
+\item\contentsline{section}{\hyperlink{structpu__out}{pu\_\-out} (Collection of all free\_\-energy of beeing unpaired values for output )}{\pageref{structpu__out}}{}
+\item\contentsline{section}{\hyperlink{structsect}{sect} (Stack of partial structures for backtracking )}{\pageref{structsect}}{}
+\item\contentsline{section}{\hyperlink{structsnoopT}{snoopT} }{\pageref{structsnoopT}}{}
+\item\contentsline{section}{\hyperlink{structSOLUTION}{SOLUTION} (Solution element from subopt.c )}{\pageref{structSOLUTION}}{}
+\item\contentsline{section}{\hyperlink{structstruct__en}{struct\_\-en} }{\pageref{structstruct__en}}{}
+\item\contentsline{section}{\hyperlink{structsvm__model}{svm\_\-model} }{\pageref{structsvm__model}}{}
+\item\contentsline{section}{\hyperlink{structswString}{swString} }{\pageref{structswString}}{}
 \item\contentsline{section}{\hyperlink{structTree}{Tree} }{\pageref{structTree}}{}
-\item\contentsline{section}{\hyperlink{structTwoDfold__solution}{Two\-Dfold\-\_\-solution} \\*Solution element returned from Two\-Dfold\-List }{\pageref{structTwoDfold__solution}}{}
-\item\contentsline{section}{\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} \\*Variables compound for 2\-Dfold M\-F\-E folding }{\pageref{structTwoDfold__vars}}{}
-\item\contentsline{section}{\hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution} \\*Solution element returned from Two\-Dpfold\-List }{\pageref{structTwoDpfold__solution}}{}
-\item\contentsline{section}{\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} \\*Variables compound for 2\-Dfold partition function folding }{\pageref{structTwoDpfold__vars}}{}
+\item\contentsline{section}{\hyperlink{structTwoDfold__solution}{TwoDfold\_\-solution} (Solution element returned from TwoDfoldList )}{\pageref{structTwoDfold__solution}}{}
+\item\contentsline{section}{\hyperlink{structTwoDfold__vars}{TwoDfold\_\-vars} (Variables compound for 2Dfold MFE folding )}{\pageref{structTwoDfold__vars}}{}
+\item\contentsline{section}{\hyperlink{structTwoDpfold__solution}{TwoDpfold\_\-solution} (Solution element returned from TwoDpfoldList )}{\pageref{structTwoDpfold__solution}}{}
+\item\contentsline{section}{\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} (Variables compound for 2Dfold partition function folding )}{\pageref{structTwoDpfold__vars}}{}
 \end{DoxyCompactList}