--- /dev/null
+\batchmode
+\documentclass{book}
+\usepackage[a4paper,top=2.5cm,bottom=2.5cm,left=2.5cm,right=2.5cm]{geometry}
+\usepackage{makeidx}
+\usepackage{natbib}
+\usepackage{graphicx}
+\usepackage{multicol}
+\usepackage{float}
+\usepackage{listings}
+\usepackage{color}
+\usepackage{ifthen}
+\usepackage[table]{xcolor}
+\usepackage{textcomp}
+\usepackage{alltt}
+\usepackage{ifpdf}
+\ifpdf
+\usepackage[pdftex,
+ pagebackref=true,
+ colorlinks=true,
+ linkcolor=blue,
+ unicode
+ ]{hyperref}
+\else
+\usepackage[ps2pdf,
+ pagebackref=true,
+ colorlinks=true,
+ linkcolor=blue,
+ unicode
+ ]{hyperref}
+\usepackage{pspicture}
+\fi
+\usepackage[utf8]{inputenc}
+\usepackage{mathptmx}
+\usepackage[scaled=.90]{helvet}
+\usepackage{courier}
+\usepackage{sectsty}
+\usepackage{amssymb}
+\usepackage[titles]{tocloft}
+\usepackage{doxygen}
+\lstset{language=C++,inputencoding=utf8,basicstyle=\footnotesize,breaklines=true,breakatwhitespace=true,tabsize=2,numbers=left }
+\makeindex
+\setcounter{tocdepth}{3}
+\renewcommand{\footrulewidth}{0.4pt}
+\renewcommand{\familydefault}{\sfdefault}
+\hfuzz=15pt
+\setlength{\emergencystretch}{15pt}
+\hbadness=750
+\tolerance=750
+\begin{document}
+\hypersetup{pageanchor=false,citecolor=blue}
+\begin{titlepage}
+\vspace*{7cm}
+\begin{center}
+{\Large R\-N\-Alib-\/2.1.2 }\\
+\vspace*{1cm}
+{\large Generated by Doxygen 1.8.3.1}\\
+\vspace*{0.5cm}
+{\small Thu Sep 5 2013 11:51:49}\\
+\end{center}
+\end{titlepage}
+\clearemptydoublepage
+\pagenumbering{roman}
+\tableofcontents
+\clearemptydoublepage
+\pagenumbering{arabic}
+\hypersetup{pageanchor=true,citecolor=blue}
+\chapter{Vienna\-R\-N\-A Package core -\/ R\-N\-Alib}
+\label{index}\hypertarget{index}{}\input{index}
+\chapter{Parsing and Comparing -\/ Functions to Manipulate Structures}
+\label{mp_parse}
+\hypertarget{mp_parse}{}
+\input{mp_parse}
+\chapter{Utilities -\/ Odds and Ends}
+\label{mp_utils}
+\hypertarget{mp_utils}{}
+\input{mp_utils}
+\chapter{Example -\/ A Small Example Program}
+\label{mp_example}
+\hypertarget{mp_example}{}
+\input{mp_example}
+\chapter{Deprecated List}
+\label{deprecated}
+\hypertarget{deprecated}{}
+\input{deprecated}
+\chapter{Module Index}
+\input{modules}
+\chapter{Data Structure Index}
+\input{annotated}
+\chapter{File Index}
+\input{files}
+\chapter{Module Documentation}
+\input{group__folding__routines}
+\include{group__mfe__fold}
+\include{group__pf__fold}
+\include{group__mea__fold}
+\include{group__centroid__fold}
+\include{group__subopt__fold}
+\include{group__subopt__zuker}
+\include{group__subopt__wuchty}
+\include{group__subopt__stochbt}
+\include{group__cofold}
+\include{group__mfe__cofold}
+\include{group__pf__cofold}
+\include{group__up__cofold}
+\include{group__consensus__fold}
+\include{group__consensus__mfe__fold}
+\include{group__consensus__pf__fold}
+\include{group__consensus__stochbt}
+\include{group__local__fold}
+\include{group__local__mfe__fold}
+\include{group__local__pf__fold}
+\include{group__local__consensus__fold}
+\include{group__energy__parameters}
+\include{group__energy__parameters__rw}
+\include{group__energy__parameters__convert}
+\include{group__eval}
+\include{group__inverse__fold}
+\include{group__class__fold}
+\include{group__kl__neighborhood}
+\include{group__kl__neighborhood__mfe}
+\include{group__kl__neighborhood__pf}
+\include{group__kl__neighborhood__stochbt}
+\include{group__dos}
+\include{group__parse}
+\chapter{Data Structure Documentation}
+\input{structbondT}
+\input{structbondTEn}
+\input{structcofoldF}
+\input{structConcEnt}
+\input{structconstrain}
+\input{structCOORDINATE}
+\input{structcpair}
+\input{structduplexT}
+\input{structdupVar}
+\input{structfolden}
+\input{structinteract}
+\input{structintermediate__t}
+\input{structINTERVAL}
+\input{structLIST}
+\input{structLST__BUCKET}
+\input{structmodel__detailsT}
+\input{structmove__t}
+\input{structPAIR}
+\input{structpair__info}
+\input{structpairpro}
+\input{structparamT}
+\input{structpath__t}
+\input{structpf__paramT}
+\input{structplist}
+\input{structPostorder__list}
+\input{structpu__contrib}
+\input{structpu__out}
+\input{structsect}
+\input{structsnoopT}
+\input{structSOLUTION}
+\input{structstruct__en}
+\input{structsvm__model}
+\input{structswString}
+\input{structTree}
+\input{structTwoDfold__solution}
+\input{structTwoDfold__vars}
+\input{structTwoDpfold__solution}
+\input{structTwoDpfold__vars}
+\chapter{File Documentation}
+\input{2Dfold_8h}
+\input{2Dpfold_8h}
+\input{alifold_8h}
+\input{cofold_8h}
+\input{convert__epars_8h}
+\input{data__structures_8h}
+\input{dist__vars_8h}
+\input{duplex_8h}
+\input{edit__cost_8h}
+\input{energy__const_8h}
+\input{findpath_8h}
+\input{fold_8h}
+\input{fold__vars_8h}
+\input{gquad_8h}
+\input{inverse_8h}
+\input{Lfold_8h}
+\input{loop__energies_8h}
+\input{LPfold_8h}
+\input{MEA_8h}
+\input{mm_8h}
+\input{naview_8h}
+\input{params_8h}
+\input{part__func_8h}
+\input{part__func__co_8h}
+\input{part__func__up_8h}
+\input{plot__layouts_8h}
+\input{profiledist_8h}
+\input{PS__dot_8h}
+\input{read__epars_8h}
+\input{RNAstruct_8h}
+\input{stringdist_8h}
+\input{subopt_8h}
+\input{treedist_8h}
+\input{utils_8h}
+\input{1_88_84__epars_8h}
+\input{1_88_84__intloops_8h}
+\newpage \bibliographystyle{plain}
+\bibliography{viennarna}
+\addcontentsline{toc}{part}{Index}
+\printindex
+\end{document}
git://source.jalview.org / jabaws.git / blobdiff