\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,
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            linkcolor=blue
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\fi
\usepackage{doxygen}
\makeindex
\renewcommand{\footrulewidth}{0.4pt}
\newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}}
\setlength\parindent{0pt} % switch of indent 

\renewcommand{\thesubsection}{\arabic{subsection}} % Is needed for the correct toc (since doxygen transforms section to subsection otherwise.

\setcounter{tocdepth}{3}
\setcounter{secnumdepth}{4}

\begin{document}

\begin{titlepage}
\vspace*{7cm}
\begin{center}
{\Large OpenMS Tutorial\\[1ex]\large Version: @CF_OPENMS_PACKAGE_VERSION_FULLSTRING@ }\\
\end{center}
\end{titlepage}

\pagenumbering{arabic}
\tableofcontents
\pagebreak

\input{tutorial}

\end{document}
