main.tex

%http://www.latextemplates.com/template/masters-doctoral-thesis

\documentclass[11pt, a4paper, oneside]{Thesis}
\graphicspath{{./Figures/}}
\usepackage[square, numbers, comma, sort&compress]{natbib} 
\usepackage{array, booktabs, multirow, longtable}

\usepackage{color}
\definecolor{dkgreen}{rgb}{0,0.6,0}
\definecolor{gray}{rgb}{0.5,0.5,0.5}
\definecolor{mauve}{rgb}{0.58,0,0.82}

\lstset{frame=tb,
  language=Java,
  aboveskip=3mm,
  belowskip=3mm,
  showstringspaces=false,
  columns=flexible,
  basicstyle={\small\ttfamily},
  numbers=none,
  numberstyle=\tiny\color{gray},
  keywordstyle=\color{blue},
  commentstyle=\color{dkgreen},
  stringstyle=\color{mauve},
  breaklines=true,
  breakatwhitespace=true,
  tabsize=3
}

\newcommand{\todo}[1]{\textcolor{red}{(TODO) #1}}
\hypersetup{urlcolor=black, colorlinks=true}
\title{\ttitle} % Defines the thesis title - don't touch this
\begin{document}
\frontmatter
\setstretch{1.3} % Line spacing of 1.3
\fancyhead{} % Clears all page headers and footers
\rhead{\thepage} % Sets the right side header to show the page number
\lhead{} % Clears the left side page header
\pagestyle{fancy} % Finally, use the "fancy" page style to implement the FancyHdr headers



\newcommand{\HRule}{\rule{\linewidth}{0.5mm}} % New command to make the lines in the title page
\hypersetup{pdftitle={\ttitle}}
\hypersetup{pdfsubject=\subjectname}
\hypersetup{pdfauthor=\authornames}
\hypersetup{pdfkeywords=\keywordnames}


%-----------------
%	FIRST PAGES
%-----------------

\input{First_Pages/TitlePage}
\input{First_Pages/Declaration}
\input{First_Pages/Abstract}
\input{First_Pages/Acknowledgements}

%-------------------------------------------
%	LIST OF CONTENTS/FIGURES/TABLES PAGES
%-------------------------------------------

\pagestyle{fancy} % The page style headers have been "empty" all this time, now use the "fancy" headers as defined before to bring them back

\lhead{\emph{Contents}} % Set the left side page header to "Contents"
\tableofcontents % Write out the Table of Contents

\lhead{\emph{List of Figures}} % Set the left side page header to "List of Figures"
\listoffigures % Write out the List of Figures

\lhead{\emph{List of Tables}} % Set the left side page header to "List of Tables"
\listoftables % Write out the List of Tables


%-----------------
%   ABBREVIATIONS
%-----------------

\input{First_Pages/abbreviations}
\input{First_Pages/dedication}

%-----------------
%	CHAPTERS
%-----------------

\mainmatter % Begin numeric (1,2,3...) page numbering
\pagestyle{fancy} % Return the page headers back to the "fancy" style
\input{./Chapters/Chapter1}
\input{./Chapters/Chapter2}
\input{./Chapters/Chapter3}
\input{./Chapters/Chapter4}
\input{./Chapters/Chapter5}
\input{./Chapters/Chapter6}

%-----------------
%	APPENDICES
%-----------------

\addtocontents{toc}{\vspace{2em}} % Add a gap in the Contents, for aesthetics
\appendix
\input{./Appendices/AppendixA}
\input{./Appendices/AppendixB}
\input{./Appendices/AppendixC}
\input{./Appendices/AppendixD}

\addtocontents{toc}{\vspace{2em}} % Add a gap in the Contents, for aesthetics
\backmatter
\label{Bibliography}
\lhead{\emph{Bibliography}}
\bibliographystyle{unsrtnat}
\bibliography{Ref}

\end{document}