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\documentclass[a4paper]{article}
\usepackage{ifthen}
\usepackage{geometry}
\geometry{
includeheadfoot,
margin=2.54cm
}
\usepackage{makeidx}
\usepackage{fancyhdr}
\usepackage{graphicx}
\usepackage{multicol}
\usepackage{float}
\usepackage{alltt}
\usepackage{newtxtext, newtxmath}
% since 1.62 newtxmath defines Bbbk for the small double bold k
% this is also defined in amssymb which is loaded by
% doxygen.sty later. Undefine it here.
% actually newtxmath and amssymb are incompatible. we should choose one!!!
\let\Bbbk\relax
% newtxtext loads textcomp only in newer versions and with differing options between versions
% @commands need to be enclosed by makeatletter and makeatother
\makeatletter
\@ifpackageloaded{textcomp}
{} % do nothing if loaded by the previous package to avoid option clashes
{\usepackage{textcomp}} % otherwise load the package
\makeatother
\ifx\pdfoutput\undefined
\usepackage[ps2pdf,
pagebackref=true,
colorlinks=true,
linkcolor=blue
]{hyperref}
\usepackage{pspicture}
\else
\usepackage[pdftex,
pagebackref=true,
colorlinks=true,
linkcolor=blue
]{hyperref}
\fi
\usepackage{doxygen}
\makeindex
\setcounter{tocdepth}{1}
\renewcommand{\footrulewidth}{0.4pt}
\newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}}
\setlength\parindent{0pt}
\begin{document}
\begin{titlepage}
\vspace*{7cm}
\begin{center}
{\Large TOPP and TOPPView Tutorial\\[1ex]\large Version: @CF_OPENMS_PACKAGE_VERSION_FULLSTRING@ }\\
\end{center}
\end{titlepage}
\pagenumbering{arabic}
\setcounter{tocdepth}{2}
\tableofcontents
\pagebreak
\section{Concepts}
\input{TOPP_concepts}
\pagebreak
\section{TOPPView main interface}
\input{TOPPView_introduction}
\pagebreak
\input{TOPPView_views}
\pagebreak
\input{TOPPView_modes}
\pagebreak
\input{TOPPView_analysis}
\pagebreak
\input{TOPPView_editing}
\pagebreak
\input{TOPPView_hotkeys}
\pagebreak
\section{Calling TOPP tools from TOPPView}
\input{TOPPView_smoothing}
\pagebreak
\input{TOPPView_baseline_reduction}
\pagebreak
\input{TOPPView_peakpicking}
\pagebreak
\input{TOPPView_feature_detection_centroided}
\pagebreak
\section{Using TOPPAS to create and run TOPP pipelines}
\input{TOPPAS_general}
\pagebreak
\input{TOPPAS_interface}
\pagebreak
\input{TOPPAS_examples}
\section{Advanced Users: Tips \& Tricks}
\input{TOPP_advanced}
\pagebreak
\section{Scripting with TOPP}
\input{TOPP_general}
\pagebreak
\input{TOPP_example_handling}
\pagebreak
\input{TOPP_example_signalprocessing}
\pagebreak
\input{TOPP_example_calibration}
\pagebreak
\input{TOPP_example_mapalignment}
\pagebreak
\input{TOPP_example_featuredetection}
\pagebreak
\input{TOPP_example_featuregrouping}
\pagebreak
\input{TOPP_example_id}
\pagebreak
\input{TOPP_example_ppp}
\pagebreak
\input{TOPP_example_convert}
\pagebreak
\input{TOPP_example_qualitycontrol}
\end{document}
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