Thesis.tex

%!TEX root = Thesis.tex
%% ----------------------------------------------------------------
%% Author: Alex Schlosser
%%         schlosser@st.cs.uni-saarland.de
%% ---------------------------------------------------------------- 

% Set up the document

\documentclass[a4paper, 12pt]{Thesis}  % Use the "Thesis" style defined in Thesis.cls
\graphicspath{{./Figures/}}  % Location of the graphics files (set up for graphics to be in PDF format)
\setchapterpath{./Chapters/}
\setappendixpath{./Appendices/}

% Include any extra LaTeX packages required
%\usepackage[table,xcdraw]{xcolor}
\usepackage[square, numbers, comma, sort&compress]{natbib}  % Use the "Natbib" style for the references in the Bibliography
\usepackage{verbatim}  % Needed for the "comment" environment to make LaTeX comments
\usepackage{verbatimbox}
\usepackage{array}
\usepackage{rotating}
\usepackage{colortbl}
\usepackage[usenames]{xcolor}
\usepackage{tabularx}
\usepackage{algorithm}
\usepackage{algorithmic}
\usepackage{adjustbox}
\usepackage{multirow}
\usepackage{wrapfig}
\usepackage{framed}
\usepackage{tikz}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{stmaryrd}
\usepackage{framed}
\usepackage{hyperref}
\usepackage{todonotes}
\reversemarginpar
\presetkeys{todonotes}{inline, size=\tiny, prepend, caption={TODO}}{}
\usepackage{listings}
\lstset{language=C,numbers=left}
\usepackage{longtable}
\usepackage{multicol}


%% Specify thesis parameters here
%% ----------------------------------------------------------------
\setboolean  {proposal}{false} % disables all stuff that is not needed for a proposal if set to true
\university  {Saarland University}{http://www.uni-saarland.de/}
\department  {Center for Bioinformatics}{https://zbi-www.bioinf.uni-sb.de/en}
\group       {Algorithms for Computational Genomics}{https://compgen.mpi-inf.mpg.de/}
%\faculty     {}{}
\supervisor  {Prof. Dr. Tobias Marschall}
%\advisor     {Prof. Dr. Olga Kalinina}
\examiner    {Prof. Dr. Tobias Marschall}
\secondexaminer {Prof. Dr. Olga Kalinina}
\degree      {Master of Science}
\thesiskind  {Master Thesis}
\authors     {Fawaz Dabbaghie}
\thesistitle {Superbubble and Bubble Chains Detection in Assembly Graphs}
\date        {\today}
%\subject     {}
%\keywords    {}
%% ----------------------------------------------------------------

% If this is a proposal prepend 'Proposal for a' to thesiskind
\doifproposal{
	\let\thesisnameproposal\thesisname	
	\thesiskind{Proposal for a \thesisnameproposal}
}

\newcommand{\tobias}[1]{\textbf{[Tobias: #1]}}

% Enable git revision parsing (Note: you need to enable shell-excape and pipe support for this feature to work)
%\revision{\input{|"git rev-parse HEAD | cut -c 1-8"}}

\begin{document}
\frontmatter	  % Begin Roman style (i, ii, iii, iv...) page numbering

%% Title Page
%% ----------------------------------------------------------------
\maketitle

%% Declaration Page required for the Thesis, your institution may give you a different text to place here
%% ----------------------------------------------------------------
\doifnotproposal{
\begin{declaration}
%  \begin{center}
%    \bf \large
%    Eidesstattliche Erkl\"{a}rung
%  \end{center}
%  Ich erkl\"{a}re hiermit an Eides Statt,
%  dass ich die vorliegende Arbeit selbstst\"{a}ndig verfasst und keine
%  anderen als die angegebenen Quellen und Hilfsmittel verwendet habe.
%
%  \begin{center}
%    \bf \large
%    Statement in Lieu of an Oath
%  \end{center}
%  I hereby confirm that I have written this thesis on my own and 
%  that I have not used any other media or materials than the ones
%  referred to in this thesis.
%
%  \vfill
%  \begin{center}
%    \bf \large
%    Einverst\"{a}ndniserkl\"{a}rung
%  \end{center}
%  Ich bin damit einverstanden, dass meine (bestandene) Arbeit in beiden 
%  Versionen in die Bibliothek der Informatik aufgenommen und damit 
%  ver\"{o}ffentlicht wird. 
%
%  \begin{center}
%    \bf \large
%    Declaration of Consent
%  \end{center}
%  I agree to make both versions of my thesis (with a passing grade) 
%  accessible to the public by having them added to the library of the
%  Computer Science Department.

  \vfill
  \vfill
  \vfill
  \vfill
  \vfill
  \vfill
  \vfill
  \vfill
  \textbf{Statement}\\
  I hereby confirm that this thesis is my own work and that I have documented all sources used. \\
  Saarbrücken, den \today
  
\end{declaration}
  \cleardoublepage  % Declaration ended, now start a new page
}

%% The Abstract Page
%% ----------------------------------------------------------------
\begin{abstract}
	\input{\chapterpath Abstract}
\end{abstract}

\doifnotproposal{

%% The Acknowledgements page, for thanking everyone
%% ----------------------------------------------------------------
\begin{acknowledgements}

It has been a long journey. However, an exciting one indeed. Many people have accompanied me through this and I hope I do not fail to mention anyone.\\
First and foremost, a big think you to my supervisor Tobias for his continuous support throughout the project, he has been a great mentor, and I am looking forward to our future work together. Second, thanks to Mikko and the many helpful tips and discussions we had throughout the year.\\
Of course, without the support and love of my lovely family I would not have made it this far. Thank you Mom, Dad and Fares.\\
I should not forget all the lovely friends I made in Saarbrücken. Sophian, Anela, Bashak, Rui, Maarten, Saheli, and of course my two best friends here Sandra and Dania.\\
After living for 6 years in Germany, I have met so many amazing people that inspired me to pursue my dreams, and they were there for me in times of need. Thank you all, John, Anna, Robert, Ruben, Sung, Eva, Ursel, George, Dimitra, Tamer, Maria...\ I am sure I forgot some names too :)\\

\end{acknowledgements}
\cleardoublepage
}

%% Table of Contents
%% ----------------------------------------------------------------

\tableofcontents
\clearpage
\doifnotproposal{
	\lhead{\emph{List of Figures}}
	\addtotoc{List of Figures}
	\listoffigures
	\clearpage

  	\lhead{\emph{List of Tables}}
  	  	\addtotoc{List of Tables}
	\listoftables
	\clearpage

}
%% The Dedication page
%% ----------------------------------------------------------------
%\doifnotproposal{
%  \thispagestyle{empty}  % Page style needs to be empty for this page
%  \dedicatory{Dedicated to WHATEVER.}
%}

\mainmatter	  % Begin normal, numeric (1,2,3...) page numbering

%% Chapters
%% ----------------------------------------------------------------
% Include the chapters of the thesis, as separate files (careful of case-sensitivity and spaces in filenames)
% Capitalized chaptertitles generally look better

\loadchapter{Introduction}{Introduction}
\loadchapter{Preliminaries}{Preliminaries}
\loadchapter{Motivation}{Motivation}
\loadchapter{Methods}{Methods}
\loadchapter{Results}{Results}
\loadchapter{Conclusion}{Conclusion}

%% Appendices
%% ----------------------------------------------------------------
\appendix

%\input{./Appendices/Appendix}	% Appendix Title

%\input{./Appendices/AppendixB} % Appendix Title

%\input{./Appendices/AppendixC} % Appendix Title


\backmatter

%% Lists of figures and tables
%% ----------------------------------------------------------------


%% Bibliography
%% ----------------------------------------------------------------
\label{Bibliography}
\addtotoc{Bibliography}
\lhead{\emph{Bibliography}}  % Change the left side page header to "Bibliography"
\bibliographystyle{unsrtnat}  % Use the "unsrtnat" BibTeX style for formatting the Bibliography
\bibliography{Bibliography}  % The references (bibliography) information are stored in the file named "Bibliography.bib"

\beginappendix %Begins the appendix
\loadappendix{Appendix}{Appendix}{appendix}

\end{document}  % The End