thesis.tex

\documentclass[nocenter,twoside,a4paper,12pt,crosshair,upper,bold,final]{thesis}

% === Tex ======================================================================

\input{tex/packages}
\input{tex/colors}
\input{tex/fonts}
\input{tex/macros}
\input{tex/theorem}
\input{tex/cv}

% === Tikz =====================================================================

\usetikzlibrary{arrows,snakes,backgrounds,decorations,patterns,matrix,shapes,fit,calc,shadows,plotmarks,mindmap,trees,positioning}

%\input{tikz/tikz}
\input{tikz/string}
\input{tikz/dp}
\input{tikz/tree}
\input{tikz/transcript}
\input{tikz/tabular}

% --- Commands ---

\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}             

% === Layout ========================================================================

\chapapp{\chaptername}

% --- Style ---

\pagestyle{myheadings}

% --- Margins ---

\setlength{\textheight}{225mm}
\setlength{\textwidth}{145mm}
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\setlength{\evensidemargin}{10mm}
\setlength{\topmargin}{0mm}
\setlength{\exampleindent}{0mm}

\reversemarginpar % Notes on the inside margin

%\setlength{\marginparsep}{2mm}
%\setlength{\marginparwidth}{20mm}
%\renewcommand{\baselinestretch}{1.2} % Zeilenabstand

% --- Fractions ---

\renewcommand{\floatpagefraction}{.99}%tex-buch sagt: werte muessen
%kleiner als 1 sein, tatsache, jetzt geht es.
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% --- Itemize/Enumerate spacing ---

%\setlist{nolistsep}
%\setlist{noitemsep}
%\setlist{noitemskip}
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\let\olditemize\itemize
\renewcommand{\itemize}{
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% --- Title page fonts ---

\titlefont{\Huge\bfseries}
\authorfont{\Large}
\departmentfont{\Large}
\institutionfont{\Large}

% --- Caption fonts ---

\captionheaderfont{\sl\bfseries}
\captionbodyfont{\sl}
\pagenumberfont{\small\bf}
\renewcommand{\tableshortname}{Table}
\renewcommand{\figureshortname}{Figure}

% --- Italic font ---

\renewcommand{\itdefault}{sl}

% --- Index ---

\makeindex
%\citeindextrue	% References in the index


\graphicspath{{figures/}{plots/}}


% === Document =========================================================================

\begin{document} 

\selectlanguage{english}

\frontmatter

% === Cover Page ========================================================================

\title{Approximate string matching \\for high-throughput sequencing} % Insert return with: \\[.5ex]
%\subtitle{Working Title}

\selectlanguage{ngerman}
\translator{\large Dissertation zur Erlangung des Grades eines\\Doktors der Naturwissenschaften (Dr. rer. nat.)}
\author{Enrico Siragusa}
\department{
    \begin{center}
        \includegraphics[scale=0.3]{Siegel_blau_RGB}
    \end{center}
    \vspace{0.5cm}
    \vfill
{\textrm{am }}Fachbereich Mathematik und Informatik}
\institution{der Freien Universit{\"a}t Berlin}
\selectlanguage{english}


% === Dedication Page ===================================================================

%\ifthenelse{\boolean{noskeleton}}{}{\dedication{f\"ur XXX}}


% === Disputation Page ==================================================================

\lowertitleback{
\selectlanguage{ngerman}
Datum des Disputation: \emph{\textbf{08.07.2015}}\\[1ex]
Gutachter:\\
\emph{\textbf{Prof. Dr. Knut Reinert}, Freie Universit"at Berlin, Deutschland}\\
\emph{\textbf{Prof. Dr. Raffaele Giancarlo}, Universit\`a degli Studi di Palermo, Italien}\\
\selectlanguage{english}
}
\date{Berlin 2015}

\maketitle
\clearemptydoublepage

% Initialize page counter.
\setcounter{page}{5}


% === Abstract =========================================================================

\include{scripts/abstract_en}
\include{scripts/abstract_de}
\clearemptydoublepage

% === Acknowledgments ==================================================================

\include{scripts/acknowledgments}
\clearemptydoublepage

% === Quote ============================================================================

%{
%	\centering
%	\null\vspace{\stretch{1}}
%	\begin{quotation}
%		\it ``...''
%	\end{quotation}
%	\flushright
%	\citet{Vyverman2012}
%	\vspace{\stretch{2}}\null
%	\par
%}
%\clearemptydoublepage

% === Table of Contents ================================================================

\setcounter{secnumdepth}{2}
\setcounter{tocdepth}{2}

{\small \tableofcontents}
\clearemptydoublepage

\mainmatter

% === Introduction =====================================================================

\include{scripts/introduction}
\clearemptydoublepage

% === Approximate String Matching ======================================================

\part{Approximate string matching}
\label{part:asm}

\include{scripts/asm_background}
\clearemptydoublepage

\include{scripts/asm_indexed}
\clearemptydoublepage

\include{scripts/asm_filtering}
\clearemptydoublepage

% === Read Mapping =====================================================================

\part{Read mapping}
\label{part:rm}

\include{scripts/rm_background}
\clearemptydoublepage

\include{scripts/rm_masai}
\clearemptydoublepage

\include{scripts/rm_yara}
\clearemptydoublepage

% === Conclusion --=====================================================================

\include{scripts/conclusion}
\clearemptydoublepage

% === Appendix =========================================================================

\appendix

%\include{scripts/appendix_related}
\clearemptydoublepage
\include{scripts/appendix_param}

% === Curriculum Vitae ==================================================================

\include{scripts/appendix_cv}
\clearemptydoublepage

% === Declaration =======================================================================

\include{scripts/appendix_declaration}
\clearemptydoublepage

% === Bibiliography ==========================================================================

\bibliographystyle{natbib}
\addcontentsline{toc}{chapter}{Bibliography}
\bibliography{thesis}
\clearemptydoublepage

% === Lists ==================================================================================

\listoffigures
\clearemptydoublepage
\listoftables
\clearemptydoublepage
%\listofalgorithms
%\clearemptydoublepage

%\markboth{List of Notations \hfill}{List of Notations \hfill}
%\listofnotations
%\markboth{}{}

\clearemptydoublepage
\raggedright
\addcontentsline{toc}{chapter}{Index}
\printindex

\end{document}