main.cls

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Masters/Doctoral Thesis 
% Class File
% Version 1.4 (25/3/16)
%
% This class has been downloaded from:
% http://www.LaTeXTemplates.com
%
% Authors:
% Vel (vel@latextemplates.com)
% Johannes Böttcher
%
% Notes:
% 1) This class file defines the structure and layout of the template file (main.tex).
% 2) It has been written in such a way that under most circumstances you should not need
% to edit it. Updates would be harder. If you do make changes, please change the name of
% the file and add a comment to make your changes more visible.
%
% Class license:
% LPPL v1.3c (http://www.latex-project.org/lppl)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%----------------------------------------------------------------------------------------
%	CLASS DEFINITION AND PARAMETERS
%----------------------------------------------------------------------------------------

\NeedsTeXFormat{LaTeX2e}[1996/12/01]
\newcommand{\classname}{MastersDoctoralThesis}
\ProvidesClass{\classname}[2016/03/25 v1.4 LaTeXTemplates.com]
\providecommand{\baseclass}{book}

\RequirePackage{etoolbox}
\RequirePackage{xparse}
\newbool{nolistspace}
\newbool{chapteroneline}
\newbool{listtoc}
\newbool{toctoc}
\newbool{parskip}
\newbool{hyperrefsupport}
\booltrue{hyperrefsupport}
\newbool{headsepline}

\DeclareOption{nohyperref}{\boolfalse{hyperrefsupport}}
\DeclareOption{nolistspacing}{\booltrue{nolistspace}}
\DeclareOption{liststotoc}{\booltrue{listtoc}}
\DeclareOption{chapterinoneline}{\booltrue{chapteroneline}}
\DeclareOption{toctotoc}{\booltrue{toctoc}}
\DeclareOption{parskip}{\booltrue{parskip}}
\DeclareOption{headsepline}{\booltrue{headsepline}}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{\baseclass}}

\ProcessOptions\relax

\LoadClass{\baseclass}

%----------------------------------------------------------------------------------------
%	CLASS OPTIONS
%----------------------------------------------------------------------------------------

\ifbool{parskip}{\RequirePackage{parskip}} % If the parskip option is passed to the class, require the parskip package 

\newcommand{\abovechapterspace}{\vspace*{50pt}}
\patchcmd{\@makechapterhead}{\vspace*{50\p@}}{\abovechapterspace}{}{}
\patchcmd{\@makeschapterhead}{\vspace*{50\p@}}{\abovechapterspace}{}{}
\newcommand{\autodot}{}
\newcommand{\mdtChapapp}{}
\ifbool{chapteroneline}{%
	\patchcmd{\@makechapterhead}{%
		\if@mainmatter
		\huge\bfseries \@chapapp\space \thechapter
		\par\nobreak
		\vskip 20\p@
		\fi
	}{%
		\if@mainmatter
		\Huge\bfseries \mdtChapapp\thechapter\autodot\enspace
		\fi
	}{}{}
}

\ifbool{listtoc}{% If the liststotoc option has been passed to the class, add the lists to the table of contents
	\patchcmd{\listoftables}{\@starttoc{lot}}{%
		\addchaptertocentry{\listtablename}\@starttoc{lot}}{}{}%
	\patchcmd{\listoffigures}{\@starttoc{lof}}{%
		\addchaptertocentry{\listfigurename}\@starttoc{lof}}{}{}%
}

\ifbool{toctoc}{% If the toctotoc options has been passed to the class, add the table of contents to the table of contents
	\patchcmd{\tableofcontents}{\@starttoc{toc}}{%
		\addchaptertocentry{\contentsname}\@starttoc{toc}}{}{}%
}

\patchcmd{\tableofcontents}{\MakeUppercase}{\MakeMarkcase}{}{}
\patchcmd{\tableofcontents}{\MakeUppercase}{\MakeMarkcase}{}{}
\patchcmd{\listoffigures}{\MakeUppercase}{\MakeMarkcase}{}{}
\patchcmd{\listoffigures}{\MakeUppercase}{\MakeMarkcase}{}{}
\patchcmd{\listoftables}{\MakeUppercase}{\MakeMarkcase}{}{}
\patchcmd{\listoftables}{\MakeUppercase}{\MakeMarkcase}{}{}

% If the option `nolistspacing' is given, the spacing in the different lists is reduced to single spacing. This option is only useful, if the spacing of the document has been changed to onehalfspacing or doublespacing.
\ifbool{nolistspace}{
	\patchcmd{\listoffigures}{%
		\@starttoc{lof}}{%
			\begingroup%
			\singlespace\@starttoc{lof}\endgroup%
		}{}{}%
	\patchcmd{\listoftables}{%
		\@starttoc{lot}}{%
			\begingroup%
			\singlespace\@starttoc{lot}\endgroup%
		}{}{}%
	\patchcmd{\tableofcontents}{%
		\@starttoc{toc}}{%
			\begingroup%
			\singlespace\@starttoc{toc}\endgroup%
		}{}{}%
}{}

% Addchap provides unnumbered chapters with an entry in the table of contents as well as an updated header
\ProvideDocumentCommand{\addchap}{ s o m }{%
	\chapter*{#3}%
	\markboth{}{}%
	\IfBooleanTF{#1}{%
	}{%
		\IfNoValueTF{#2}{%
			\addchaptertocentry{#3}%
			\markboth{\MakeMarkcase{#3}}{\MakeMarkcase{#3}}%
		}{%
			\addchaptertocentry{#2}%
			\markboth{\MakeMarkcase{#2}}{\MakeMarkcase{#2}}%
		}%
	}%
}%

\ProvideDocumentCommand{\addsec}{ s o m }{%
	\section*{#3}%
	\markright{}%
	\IfBooleanTF{#1}{%
	}{%
		\IfNoValueTF{#2}{%
			\addcontentsline{toc}{section}{#3}%
			\markright{\MakeMarkcase{#3}}%%
		}{%
			\addcontentsline{toc}{section}{#2}%
			\markright{\MakeMarkcase{#2}}%
		}%
	}%
}%

%----------------------------------------------------------------------------------------
%	REQUIRED PACKAGES
%----------------------------------------------------------------------------------------

\RequirePackage{babel} % Required for automatically changing names of document elements to languages besides english

\RequirePackage{scrbase} % Required for handling language-dependent names of sections/document elements

\RequirePackage{scrhack} % Loads fixes for various packages

\RequirePackage{setspace} % Required for changing line spacing

\RequirePackage{longtable} % Required for tables that span multiple pages (used in the symbols, abbreviations and physical constants pages)

\RequirePackage{siunitx} % Required for \SI commands

\RequirePackage{graphicx} % Required to include images
\graphicspath{{Figures/}{./}} % Specifies where to look for included images

\RequirePackage{booktabs} % Required for better table rules

\RequirePackage{caption} % Required for customising the captions
\captionsetup{justification=centerlast,font=small,labelfont=sc,margin=50pt}

%----------------------------------------------------------------------------------------

\newcommand{\checktoopen}{% New command to move content to the next page which prints to the next odd page if twosided mode is active  
\if@openright\cleardoublepage\else\clearpage\fi
\ifdef{\phantomsection}{\phantomsection}{}% The \phantomsection command is necessary for hyperref to jump to the correct page
}

\newcommand\bhrule{\typeout{--------------------}}
\newcommand\tttypeout[1]{\bhrule\typeout{\space #1}\bhrule}

\newcommand{\HRule}{\rule{\linewidth}{0.5mm}} % New command to make the lines in the title page
\newcommand{\decoRule}{\rule{.8\textwidth}{.4pt}} % New command for a rule to be used under figures

\renewcommand{\abovechapterspace}{\vspace*{10pt}} % Reduce the whitespace above a chapter heading

\setcounter{tocdepth}{3} % The depth to which the document sections are printed to the table of contents
\providecommand\addchaptertocentry[1]{%
\addcontentsline{toc}{chapter}{#1}%
}

%----------------------------------------------------------------------------------------
%	MARGINS
%----------------------------------------------------------------------------------------

\RequirePackage{geometry}
\geometry{
	headheight=4ex,
	includehead,
	includefoot
}

\raggedbottom

%----------------------------------------------------------------------------------------
%	PENALTIES
%----------------------------------------------------------------------------------------

\doublehyphendemerits=10000 % No consecutive line hyphens
\brokenpenalty=10000 % No broken words across columns/pages
\widowpenalty=9999 % Almost no widows at bottom of page
\clubpenalty=9999 % Almost no orphans at top of page
\interfootnotelinepenalty=9999 % Almost never break footnotes

%----------------------------------------------------------------------------------------
%	HEADERS AND FOOTERS
%----------------------------------------------------------------------------------------

\RequirePackage[markcase=used]{scrlayer-scrpage}
\providepairofpagestyles{thesisSimple}{%
\clearpairofpagestyles%
\automark[chapter]{chapter}
%\ihead{\headmark}% Inner header
\cfoot*{\pagemark}
}
\ifoot{}% Inner footer
\ofoot{}% Outer footer
\pagestyle{thesisSimple}
\providepairofpagestyles[thesisSimple]{thesis}{%
\automark*[section]{}%
}
\providepairofpagestyles[thesisSimple]{review}{%
	\ofoot[\ttitle/\authorname]{\ttitle/\authorname}
	\ifoot[\today]{\today}
}
\pagestyle{thesis}
\ifbool{headsepline}{\KOMAoption{headsepline}{true}}{}
\PreventPackageFromLoading[\ClassError{\classname}{Package `fancyhdr' is
incompatible\MessageBreak with this class}{The pagesyles are defined 
using package `scrlayer-scrpage', please consult the\MessageBreak 
KOMA-script documentation for details.}]{fancyhdr}


\newcommand{\blank@p@gestyle}{empty}
\newcommand{\blankpagestyle}[1]{\def\blank@p@gestyle{#1}}

\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
\hbox{}
\thispagestyle{\blank@p@gestyle}
% \newpage
\if@twocolumn\hbox{}\newpage\fi\fi\fi}

%----------------------------------------------------------------------------------------
%	DEFINE CUSTOM THESIS INFORMATION COMMANDS
%----------------------------------------------------------------------------------------

\def\authorname{}
\def\ttitle{}
\newcommand*{\supervisor}[1]{\def\supname{#1}}
\newcommand*{\thesistitle}[1]{\def\@title{#1}\def\ttitle{#1}}
\newcommand*{\examinerO}[1]{\def\examinerOname{#1}}
\newcommand*{\examinerT}[1]{\def\examinerTname{#1}}
\newcommand*{\examinerTh}[1]{\def\examinerThname{#1}}
\newcommand*{\examinerJr}[1]{\def\examinerJrname{#1}}
\newcommand*{\degree}[1]{\def\degreename{#1}}
\renewcommand*{\author}[1]{\def\authorname{#1}}
\newcommand*{\addresses}[1]{\def\addressname{#1}}
\newcommand*{\university}[1]{\def\univname{#1}}
\newcommand*{\department}[1]{\def\deptname{#1}}
\newcommand*{\group}[1]{\def\groupname{#1}}
\newcommand*{\faculty}[1]{\def\facname{#1}}
\newcommand*{\subject}[1]{\def\subjectname{#1}}
\newcommand*{\keywords}[1]{\def\keywordnames{#1}}

%Commands from RapMap
\newcommand{\rapmap}{\texttt{RapMap}\xspace}
\newcommand{\kallisto}{\texttt{Kallisto}\xspace}
\newcommand{\T}[1]{\texttt{T}\ensuremath{\left[#1\right]}\xspace}
\newcommand{\SA}[1]{\texttt{SA}\ensuremath{\left[#1\right]}\xspace}
\newcommand{\LCP}[2]{\texttt{LCP}\ensuremath{\left(#1, #2)\right)}\xspace}
\newcommand{\LCE}[2]{\texttt{LCE}\ensuremath{\left(#1, #2)\right)}\xspace}

\newcommand{\NIP}[1]{\texttt{NIP}\ensuremath{\left(#1\right)}\xspace}
\newcommand{\loc}[1]{\texttt{loc}\ensuremath{\left(#1\right)}\xspace}
\newcommand{\length}[1]{\ensuremath{\left|#1\right|}\xspace}
\newcommand{\hit}[1]{\texttt{hit}\ensuremath{\left(#1\right)}\xspace}
\newcommand{\hits}[1]{\texttt{hits}\ensuremath{\left(#1\right)}\xspace}
\newcommand{\fjump}[1]{\texttt{jump}\ensuremath{_{\text{f}}\left(#1\right)}\xspace}
\newcommand{\rjump}[1]{\texttt{jump}\ensuremath{_{\text{r}}\left(#1\right)}\xspace} \newcommand{\interval}[2]{\ensuremath{\left[#1,#2\right)}\xspace}

\newcommand{\ival}[1]{\texttt{I}\ensuremath{\left(#1\right)}}
\newcommand{\kmer}{k-mer\xspace}
\newcommand{\kmers}{k-mers\xspace}
\newcommand{\quasiSF}{quasi-Sailfish\xspace}
\newcommand{\note}[1]{\textcolor{red}{#1\xspace}}
\newcommand{\Qm}{Quasi-mapping\xspace}
\newcommand{\qm}{quasi-mapping\xspace}
\newcommand{\STAR}{\texttt{STAR}\xspace}
\newcommand{\bt}{\texttt{Bowtie 2}\xspace}
\newcommand{\MMP}[1][]{\ifthenelse{\equal{#1}{}}{\text{MMP}}{\text{MMP}\ensuremath{_#1}}\xspace}
\newcommand{\denovo}{\textit{de novo}\xspace}
\newcommand{\hsa}{SA\xspace}

%Commands from Alevin
\newcommand{\comment}[1]{\textcolor{red}{#1}\xspace}
\newcommand{\alevin}{\texttt{alevin}\xspace}
\newcommand{\Alevin}{\texttt{Alevin}\xspace}
\newcommand{\salmon}{\texttt{Salmon}\xspace}
\newcommand{\cellr}{\texttt{Cell-Ranger}\xspace}
\newcommand{\naive}{\textit{na\"ive}\xspace}
\newcommand{\scrnaseq}{scRNA-seq\xspace}
\newcommand{\singlecell}{single-cell\xspace}
\newcommand{\dscrnaseq}{\texttt{dscRNA-seq}\xspace}
\newcommand{\kbpipe}{\texttt{kb-pipe}\xspace}
\newcommand{\dropest}{\texttt{dropEst}\xspace}

%Commands from Selective Alignment

\newcommand{\saf}{SAF\xspace}
\newcommand{\cmark}{\ding{51}}%
\newcommand{\xmark}{\ding{55}}%

%Avi's
\newcommand{\reads}{\textit{reads}\xspace}
\newcommand{\ra}{read-alignment\xspace}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%----------------------------------------------------------------------------------------


%----------------------------------------------------------------------------------------
%	DECLARATION PAGE DESIGN
%----------------------------------------------------------------------------------------

\newcommand{\authorshipname}{Declaration of Authorship}
\providecaptionname{american,australian,british,canadian,english,newzealand,UKenglish,USenglish}{\authorshipname}{Declaration of Authorship} % Declaration of Authorship text for English countries
\providecaptionname{german,ngerman,austrian,naustrian}{\authorshipname}{Eidesstattliche Erkl\"arung} % Declaration of Authorship text for Germanic countries

\newenvironment{declaration}{
	\checktoopen
	\tttypeout{\authorshipname}
	\thispagestyle{plain}
	\null\vfil
	{\noindent\huge\bfseries\authorshipname\par\vspace{10pt}}
}{}

%----------------------------------------------------------------------------------------
%	DEDICATION PAGE DESIGN
%----------------------------------------------------------------------------------------

\newcommand\dedicatory[1]{
	\checktoopen
	\tttypeout{Dedicatory}
	\null\vfil
	\thispagestyle{plain}
	\begin{center}{\Large\slshape #1}\end{center}
	\vfil\null
}

%----------------------------------------------------------------------------------------
%	ABSTRACT PAGE DESIGN
%----------------------------------------------------------------------------------------

\newcommand{\byname}{by}
\providecaptionname{german,ngerman,austrian,naustrian}{\byname}{von}
\providecaptionname{american,australian,british,canadian,english,newzealand,UKenglish,USenglish}{\byname}{by}
\newenvironment{abstract}{
	\checktoopen
	\tttypeout{\abstractname}
	\null\vfil
	\thispagestyle{plain}
	\begin{center}
	%{\normalsize \MakeUppercase{\univname} \par} % University name in capitals
	%\bigskip
	{\huge\textit{\abstractname} \par}
	%\bigskip
	% {\normalsize \facname \par} % Faculty name
	% {\normalsize \deptname \par} % Department name
	%\bigskip
	%{\normalsize Preliminary Examination --- Report\par} % Degree name
	%\bigskip
	%{\normalsize\bfseries \@title \par} % Thesis title
	%\medskip
	%{\normalsize \byname{} \authorname \par} % Author name
	%\bigskip
	\end{center}
}
{
  \vfil\vfil\vfil\null
}

%----------------------------------------------------------------------------------------
%	ABBREVIATIONS PAGE DESIGN
%----------------------------------------------------------------------------------------

\newcommand{\abbrevname}{List of Abbreviations}
\providecaptionname{english,british,american}{\abbrevname}{List of Abbreviations}
\providecaptionname{ngerman,german,austrian,naustrian}{\abbrevname}{Abk\"urzungsverzeichnis}
\NewDocumentEnvironment{abbreviations}{ m }{%
	\ifbool{nolistspace}{\begingroup\singlespacing}{}
	\ifbool{listtoc}{\addchap{\abbrevname}}{\addchap*{\abbrevname}}
	\begin{longtable}{#1}
}{%
\end{longtable}
\addtocounter{table}{-1} % Don't count this table as one of the document tables
\ifbool{nolistspace}{\endgroup}{}
}

%----------------------------------------------------------------------------------------
%	PHYSICAL CONSTANTS PAGE DESIGN
%----------------------------------------------------------------------------------------

\newcommand{\constantsname}{Physical Constants}
\providecaptionname{english,british,american}{\constantsname}{Physical Constants}
\providecaptionname{ngerman,german,austrian,naustrian}{\constantsname}{Physikalische Konstanten}

\NewDocumentEnvironment{constants}{ m }{%
	\ifbool{nolistspace}{\begingroup\singlespacing}{}
	\ifbool{listtoc}{\addchap{\constantsname}}{\addchap*{\constantsname}}
	\begin{longtable}{#1}
}{%
\end{longtable}
\addtocounter{table}{-1} % Don't count this table as one of the document tables
\ifbool{nolistspace}{\endgroup}{}
}

%----------------------------------------------------------------------------------------
%	SYMBOLS PAGE DESIGN
%----------------------------------------------------------------------------------------

\newcommand{\symbolsname}{List of Symbols}
\providecaptionname{english,british,american}{\symbolsname}{List of Symbols}
\providecaptionname{ngerman,german,austrian,naustrian}{\symbolsname}{Symbolverzeichnis}

\NewDocumentEnvironment{symbols}{ m }{%
	\ifbool{nolistspace}{\begingroup\singlespacing}{}
	\ifbool{listtoc}{\addchap{\symbolsname}}{\addchap*{\symbolsname}}
	\begin{longtable}{#1}
}{%
\end{longtable}
\addtocounter{table}{-1} % Don't count this table as one of the document tables
\ifbool{nolistspace}{\endgroup}{}
}

%----------------------------------------------------------------------------------------
%	ACKNOWLEDGEMENTS PAGE DESIGN
%----------------------------------------------------------------------------------------

\newcommand{\acknowledgementname}{Acknowledgements}
\providecaptionname{american,australian,british,canadian,english,newzealand,UKenglish,USenglish} {\acknowledgementname}{Acknowledgements} % Acknowledgement text for English countries
\providecaptionname{german,ngerman,austrian,naustrian}{\acknowledgementname}{Danksagung} % Acknowledgement text for Germanic countries

\NewDocumentEnvironment{acknowledgements}{}{%
\checktoopen
\tttypeout{\acknowledgementname}
\thispagestyle{plain}
\begin{center}{\huge\textit{\acknowledgementname}\par}\end{center}
}
{
\vfil\vfil\null
}

%----------------------------------------------------------------------------------------

\ifbool{hyperrefsupport}{% If the nohyperref class option has not been specified
\AfterPackage{biblatex}{ % Load the hyperref package after the biblatex package for compatibility 
\RequirePackage{hyperref} % Required for customising links and the PDF
\hypersetup{pdfpagemode={UseOutlines},
bookmarksopen=true,
bookmarksopenlevel=0,
hypertexnames=false,
colorlinks=true, % Set to false to disable coloring links
citecolor=black, % The color of citations
linkcolor=black, % The color of references to document elements (sections, figures, etc)
urlcolor=black, % The color of hyperlinks (URLs)
pdfstartview={FitV},
unicode,
breaklinks=true,
}

\pdfstringdefDisableCommands{% If there is an explicit linebreak in a section heading (or anything printed to the pdf-bookmarks), it is replaced by a space
   \let\\\space%
}
}
}{%nothing
}

%----------------------------------------------------------------------------------------

\endinput
% lazyLizardTracer