\batchmode
-\documentclass{book}
-\usepackage[a4paper,top=2.5cm,bottom=2.5cm,left=2.5cm,right=2.5cm]{geometry}
+\documentclass[a4paper]{book}
\usepackage{makeidx}
-\usepackage{natbib}
\usepackage{graphicx}
\usepackage{multicol}
\usepackage{float}
\usepackage{listings}
\usepackage{color}
-\usepackage{ifthen}
-\usepackage[table]{xcolor}
\usepackage{textcomp}
\usepackage{alltt}
+\usepackage{times}
\usepackage{ifpdf}
\ifpdf
\usepackage[pdftex,
\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}
+\hypersetup{pageanchor=false}
\begin{titlepage}
\vspace*{7cm}
\begin{center}
-{\Large R\-N\-Alib-\/2.1.2 }\\
+{\Large RNAlib-\/2.1.2 }\\
\vspace*{1cm}
-{\large Generated by Doxygen 1.8.3.1}\\
+{\large Generated by Doxygen 1.6.1}\\
\vspace*{0.5cm}
-{\small Thu Sep 5 2013 11:51:49}\\
+{\small Tue Apr 11 12:10:08 2017}\\
\end{center}
\end{titlepage}
\clearemptydoublepage
\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}
+\hypersetup{pageanchor=true}
+\chapter{ViennaRNA Package core -\/ RNAlib}
+\label{index}\hypertarget{index}{}\input{main}
\chapter{Parsing and Comparing -\/ Functions to Manipulate Structures}
\label{mp_parse}
\hypertarget{mp_parse}{}
-\input{mp_parse}
+\include{mp_parse}
\chapter{Utilities -\/ Odds and Ends}
\label{mp_utils}
\hypertarget{mp_utils}{}
-\input{mp_utils}
+\include{mp_utils}
\chapter{Example -\/ A Small Example Program}
\label{mp_example}
\hypertarget{mp_example}{}
-\input{mp_example}
+\include{mp_example}
\chapter{Deprecated List}
\label{deprecated}
\hypertarget{deprecated}{}
-\input{deprecated}
+\include{deprecated}
\chapter{Module Index}
\input{modules}
\chapter{Data Structure Index}
\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}
+\include{structbondTEn}
+\include{structcofoldF}
+\include{structConcEnt}
+\include{structconstrain}
+\include{structCOORDINATE}
+\include{structcpair}
+\include{structduplexT}
+\include{structdupVar}
+\include{structfolden}
+\include{structinteract}
+\include{structintermediate__t}
+\include{structINTERVAL}
+\include{structLIST}
+\include{structLST__BUCKET}
+\include{structmodel__detailsT}
+\include{structmove__t}
+\include{structPAIR}
+\include{structpair__info}
+\include{structpairpro}
+\include{structparamT}
+\include{structpath__t}
+\include{structpf__paramT}
+\include{structplist}
+\include{structPostorder__list}
+\include{structpu__contrib}
+\include{structpu__out}
+\include{structsect}
+\include{structsnoopT}
+\include{structSOLUTION}
+\include{structstruct__en}
+\include{structsvm__model}
+\include{structswString}
+\include{structTree}
+\include{structTwoDfold__solution}
+\include{structTwoDfold__vars}
+\include{structTwoDpfold__solution}
+\include{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}
+\include{2Dpfold_8h}
+\include{alifold_8h}
+\include{cofold_8h}
+\include{convert__epars_8h}
+\include{data__structures_8h}
+\include{dist__vars_8h}
+\include{duplex_8h}
+\include{edit__cost_8h}
+\include{energy__const_8h}
+\include{findpath_8h}
+\include{fold_8h}
+\include{fold__vars_8h}
+\include{gquad_8h}
+\include{inverse_8h}
+\include{Lfold_8h}
+\include{loop__energies_8h}
+\include{LPfold_8h}
+\include{MEA_8h}
+\include{mm_8h}
+\include{naview_8h}
+\include{params_8h}
+\include{part__func_8h}
+\include{part__func__co_8h}
+\include{part__func__up_8h}
+\include{plot__layouts_8h}
+\include{profiledist_8h}
+\include{PS__dot_8h}
+\include{read__epars_8h}
+\include{RNAstruct_8h}
+\include{stringdist_8h}
+\include{subopt_8h}
+\include{treedist_8h}
+\include{utils_8h}
+\include{1_88_84__epars_8h}
+\include{1_88_84__intloops_8h}
\printindex
\end{document}
git://source.jalview.org / jabaws.git / blobdiff