cornell.cls

%%
%% This is file `cornell.cls',
%% generated with the docstrip utility.
%%
%% The original source files were:
%%
%% cornell.dtx  (with options: `class')
%% 
%% IMPORTANT NOTICE:
%% 
%% For the copyright see the source file.
%% 
%% Any modified versions of this file must be renamed
%% with new filenames distinct from cornell.cls.
%% 
%% For distribution of the original source see the terms
%% for copying and modification in the file cornell.dtx.
%% 
%% This generated file may be distributed as long as the
%% original source files, as listed above, are part of the
%% same distribution. (The sources need not necessarily be
%% in the same archive or directory.)
%% Document class `cornell' to use with LaTeX 2e.
%% Based on `crnlphd' class.  The following is from the file `crnlphd.dtx':
%%   Based loosely on old cuphdthesis style file.
%%   Found to give good results, according to the thesis secretary.
%%   File: crnlphd.dtx Copyright (C) 1994 Sergio Gelato
%%   Made available without any warranty, express or implied.
%%
%% $Id: cornell.dtx,v 1.11 2008/04/17 16:56:31 andru Exp $
%% \CharacterTable
%%  {Upper-case    \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
%%   Lower-case    \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
%%   Digits        \0\1\2\3\4\5\6\7\8\9
%%   Exclamation   \!     Double quote  \"     Hash (number) \#
%%   Dollar        \$     Percent       \%     Ampersand     \&
%%   Acute accent  \'     Left paren    \(     Right paren   \)
%%   Asterisk      \*     Plus          \+     Comma         \,
%%   Minus         \-     Point         \.     Solidus       \/
%%   Colon         \:     Semicolon     \;     Less than     \<
%%   Equals        \=     Greater than  \>     Question mark \?
%%   Commercial at \@     Left bracket  \[     Backslash     \\
%%   Right bracket \]     Circumflex    \^     Underscore    \_
%%   Grave accent  \`     Left brace    \{     Vertical bar  \|
%%   Right brace   \}     Tilde         \~}
%%
\NeedsTeXFormat{LaTeX2e}[1995/12/01]
\ProvidesClass{cornell}
[2008/4/17 v2.9
  Cornell University thesis class]
\newif\ifphd
\DeclareOption{phd}{\phdtrue}
\DeclareOption{master}{\phdfalse}
\ExecuteOptions{phd}
\newif\ifcornellheadings
\newif\ifhalfcornellheadings
\newif\ifsmallerheadings
\DeclareOption{latexheadings}{\cornellheadingsfalse \halfcornellheadingsfalse}
\DeclareOption{cornellheadings}{\cornellheadingstrue \halfcornellheadingsfalse}
\DeclareOption{halfcornellheadings}{\halfcornellheadingstrue \cornellheadingsfalse}
\DeclareOption{normalsizeheadings}{\smallerheadingsfalse}
\DeclareOption{smallerheadings}{\smallerheadingstrue}
\ExecuteOptions{cornellheadings}
\ExecuteOptions{smallerheadings}
\DeclareOption{10pt}{%
 \iffinal%
  \OptionNotUsed%
  \ClassWarningNoLine{cornell}{Font size 10pt not allowed; using 12pt}%
 \else%
  \PassOptionsToClass{10pt}{report}%
 \fi%
}
\DeclareOption{11pt}{%
 \final%
  \OptionNotUsed%
  \ClassWarningNoLine{cornell}{Font size 11pt not allowed; using 12pt}%
 \else%
  \PassOptionsToClass{11pt}{report}%
 \fi
}
\newcommand{\prelim@contents}[1]{}
\DeclareOption{tocprelim}{%
  \renewcommand{\prelim@contents}[1]{\addcontentsline{toc}{section}{#1}}
}
\DeclareOption{draft}{%
  \let\ifdraft\iftrue%
  \let\iffinal\iffalse%
  \PassOptionsToClass{final}{report}%
}
\DeclareOption{final}{%
  \let\ifdraft\iffalse%
  \let\iffinal\iftrue%
  \PassOptionsToClass{final}{report}%
}
\DeclareOption{semifinal}{%
  \let\ifdraft\iffalse%
  \let\iffinal\iftrue%
  \PassOptionsToClass{draft}{report}%
}
\DeclareOption*{%
  \PassOptionsToClass{\CurrentOption}{report}%
}
\ExecuteOptions{final}
\ProcessOptions

\iffinal\LoadClass[12pt]{report}[1994/06/01]\else\LoadClass{report}[1994/06/01]\fi
\newif\ifpdf
\ifx\pdfoutput\undefined
\else
  \ifx\pdfoutput\relax
  \else
    \ifcase\pdfoutput
    \else
      \pdftrue
    \fi
  \fi
\fi
\ifpdf
  \setlength{\pdfpagewidth}{8.5in}
  \setlength{\pdfpageheight}{11in}
\fi
\ifcornellheadings
  \def\@makechapterhead#1{%
    \begin{center}%
      \MakeUppercase{\@chapapp\space \thechapter} \\
      \MakeUppercase{\bfseries #1}
    \end{center}%
    }
  \def\@makeschapterhead#1{%
    \begin{center}%
      \MakeUppercase{\bfseries #1}
    \end{center}%
    }
\fi
\ifhalfcornellheadings
  \def\@makeschapterhead#1{%
    \begin{center}%
      \MakeUppercase{\bfseries #1}
    \end{center}%
    }
  \def\@makechapterhead#1{%
    \vspace*{50\p@}%
    {\parindent \z@ \raggedright \normalfont
      \ifnum \c@secnumdepth >\m@ne
          \huge\bfseries \@chapapp\space \thechapter
          \par\nobreak
          \vskip 20\p@
      \fi
      \interlinepenalty\@M
      \singlespacing \Huge \bfseries #1\par\nobreak
      \vskip 40\p@
    }}
  \ifsmallerheadings
    \def\@makechapterhead#1{%
      {\parindent \z@ \raggedright \normalfont
        \ifnum \c@secnumdepth >\m@ne
            \LARGE\bfseries \@chapapp\space \thechapter
            \par\nobreak
        \fi
        \interlinepenalty\@M
        \singlespacing \LARGE \bfseries #1\par\nobreak
      }}
  \fi
\fi

\ifsmallerheadings
\renewcommand\section{\@startsection {section}{1}{\z@}%
                                   {-3.5ex \@plus -1ex \@minus -.2ex}%
                                   {2.3ex \@plus.2ex}%
                                   {\normalfont\large\bfseries}}
\fi

\renewcommand{\footnotesize}{\normalsize}
\renewcommand{\@makefntext}[1]{%
  \parindent 1em%
  \noindent
  \footnotespacing
  \hbox to 1.8em{\hss\@makefnmark}#1
  \par\normalspacing
}
\renewcommand{\defaultscriptratio}{.75}
\renewcommand{\defaultscriptscriptratio}{.6}
\setlength\headsep{25\p@}
\if@twocolumn
\else
  \setlength\topmargin{-0.4in}
  \setlength\headheight{0.16667in}
  \setlength\headsep{0.33333in}
  \setlength\textheight{8.8in}
  \setlength\footskip{0.5in}
  \setlength\oddsidemargin{.6in}
  \setlength\evensidemargin{.6in}
  \setlength\textwidth{5.80in}
  \setlength\marginparsep{0.1in}
  \setlength\marginparwidth{0.8in}
\fi
\if@compatibility
  \setlength\topmargin{0\p@}
\else
\fi
\newcommand{\ps@cornell}{%
\def\@oddhead{}
\def\@oddfoot{\hfil\thepage\hfil}%
\def\@evenhead{}%
\def\@evenfoot{\@oddfoot}%
\def\chaptermark##1{}%
\def\sectionmark##1{}%
}
\newcommand{\ps@oldcornell}{%
\def\@oddhead{{\slshape\rightmark}\hfil\thepage}%
\def\@oddfoot{}%
\def\@evenhead{\thepage\hfil{\slshape\leftmark}}%
\def\@evenfoot{}%
\def\chaptermark##1{}%
\def\sectionmark##1{}%
}
\newcommand{\ps@cornellc}{%
\def\@oddhead{\hfil\thepage\hfil}%
\def\@oddfoot{}%
\def\@evenhead{\@oddhead}%
\def\@evenfoot{}%
\def\chaptermark##1{}%
\def\sectionmark##1{}%
}
\raggedbottom
\renewcommand{\contentsname}{Table of Contents}
\renewcommand{\l@figure}{\@dottedtocline{1}{1.5em}{2.6em}}
\let\l@table\l@figure

\newcommand{\@titlesize}{\fontsize{18}{24}\selectfont}
\newcommand{\@subtitlesize}{\fontsize{12}{24}\selectfont}
\newcommand{\@authorsize}{\normalsize\doublespacing} % No Pharaoh he.
\newcommand{\@conferralmonth}{January}
\newcommand{\@conferralyear}{1995}

\newcommand{\titlesize}[1]{\renewcommand{\@titlesize}{#1}}
\newcommand{\subtitlesize}[1]{\renewcommand{\@subtitlesize}{#1}}
\newcommand{\authorsize}[1]{\renewcommand{\@authorsize}{#1}}
\newcommand{\conferraldate}[2]{%
  \renewcommand{\@conferralmonth}{#1}
  \renewcommand{\@conferralyear}{#2}
}
\newcommand{\@degreefield}{Master of Science}
\newcommand{\degreefield}[1]{\renewcommand{\@degreefield}{#1}}

\renewcommand{\maketitle}{%
  \begin{titlepage}%
    \realsinglespacing
    \begin{center}%
      \hrule height 0.5in width 0pt % force vertical space at top
      \@titlesize \expandafter\uppercase\expandafter{\@title} \\
        \@authorsize
      by \\
      \@author \\
    \end{center}
    \vfill
    \begin{center}
      \@subtitlesize
      A \ifphd Dissertation \else Thesis \fi \\
       Presented to the Faculty of the Louis V. Gerstner Jr., \\
      Graduate School of Biomedical Sciences,\\
      Memorial Sloan Kettering Cancer Center \\
      in Partial Fulfillment of the Requirements for the Degree of \\
      \ifphd Doctor of Philosophy \else \@degreefield \fi
    \end{center}
    \vfill
    \begin{center}
    \@authorsize
    	New York, NY \\
          \@conferralmonth\ \@conferralyear
    \end{center}
    \vfill
    \@authorsize
    \realsinglespacing
	\noindent\begin{tabular}{ll}
	\makebox[3in]{\hrulefill} & \makebox[2in]{\hrulefill}\\
	John D. Chodera, PhD & Date\\
	Dissertation Mentor  & \\
	\end{tabular}                                       
    \vspace{0.25in}
  \end{titlepage}
}

\renewenvironment{titlepage}{%
  \typeout{Title page}
  \pagestyle{empty}
  \doublespacing
}{%
  \normalspacing\clearpage
}


\newenvironment{copyrightpage}{%
  \typeout{Copyleft page}
  \pagestyle{empty}
  \null\vfill
  \begin{center}
}{%
  \end{center}
  \vfill\null
  \newpage
  \clearpage%
}

\newcommand{\makecopyright}{%
  \begin{copyrightpage}
  \copyright\ \@copyrightyear{} \@copyrightholder \\
  ALL RIGHTS RESERVED
  \end{copyrightpage}%
}
\newcommand{\@copyrightholder}{\@author}
\newcommand{\@copyrightyear}{\@conferralyear}

\newcommand{\copyrightholder}[1]{\renewcommand{\@copyrightholder}{#1}}
\newcommand{\copyrightyear}[1]{\renewcommand{\@copyrightyear}{#1}}

\newcommand{\makepublicdomain}{%
  \begin{copyrightpage}
  This document is in the public domain.
  \end{copyrightpage}%
}


\newlength{\@abhdskip}%
\renewenvironment{abstract}{
  \typeout{Abstract}
  \setlength{\@abhdskip}{.6in}
  \addtolength{\@abhdskip}{-\topmargin}
  \addtolength{\@abhdskip}{-\headheight}
  \addtolength{\@abhdskip}{-\headsep}
  \addtolength{\@abhdskip}{-\baselineskip}
  \begin{center}%
    \vspace*{\@abhdskip}%
    \ifphd%
    \normalsize \bfseries\selectfont
      ABSTRACT
    \else
      \normalsize \bfseries\selectfont
      ABSTRACT
    \fi%
    \vspace{0.5\baselineskip}
  \end{center}%
  \pagestyle{plain}
  \pagenumbering{roman}
  \setcounter{page}{4}
  
}{%
  \clearpage
}

\newcommand{\@abstracttitle}{\@title}
\newcommand{\abstracttitle}[1]{\renewcommand{\@abstracttitle}{#1}}


\newenvironment{biosketch}{%
  \typeout{Vita}
  \pagestyle{plain}
    \pagenumbering{roman}
  \setcounter{page}{6}
  \prelim@contents{Biographical Sketch}
  \chapter*{Biographical Sketch}
}{%
  \clearpage
}

\newenvironment{dedication}{%
  \prelim@contents{Dedication}
  \null\vfill
  \begin{center}
}{
  \end{center}
  \vfill\null
    \pagenumbering{roman}
  \setcounter{page}{3}
  \clearpage
}

\newenvironment{acknowledgements}{%
  \prelim@contents{Acknowledgements}
  \chapter*{Acknowledgements}
}{%
  \cleardoublepage
}

\newcommand{\contentspage}{%
  \listspacing{toc}
  \label{toc}
  \prelim@contents{\contentsname}
  \tableofcontents
  \normalspacing
  \clearpage
}

\newcommand{\tablelistpage}{%
  \listspacing{tab}
  \label{lot}
  \prelim@contents{\listtablename}
  \listoftables
  \normalspacing
  \clearpage
}

\newcommand{\figurelistpage}{%
  \listspacing{fig}
  \label{lof}
  \prelim@contents{\listfigurename}
  \listoffigures
  \normalspacing
  \clearpage
}
\newcommand{\abbrlist}{%
  \listspacing{abbr}
  \prelim@contents{List of Abbreviations}
  \chapter*{List of Abbreviations}
}

\newcommand{\symlist}{%
  \listspacing{sym}
  \prelim@contents{List of Symbols}
  \chapter*{List of Symbols}
}

\newcommand{\preface}{%
  \listspacing{pref}
  \prelim@contents{Preface}
  \chapter*{Preface}
}

\renewcommand\normalsize{%
   \@setfontsize\normalsize\@xiipt{12}%
   \abovedisplayskip 12\p@ \@plus3\p@ \@minus7\p@
   \abovedisplayshortskip \z@ \@plus3\p@
   \belowdisplayshortskip 6.5\p@ \@plus3.5\p@ \@minus3\p@
   \def\@listi{\leftmargin\leftmargini
               \parsep 5\p@  \@plus2.5\p@ \@minus\p@
               \topsep 10\p@ \@plus4\p@   \@minus6\p@
               \itemsep \z@  \@plus2.5\p@ \@minus\p@}%
   \belowdisplayskip \abovedisplayskip
}
\renewcommand\small{%
   \@setfontsize\small\@xipt{11}%
   \abovedisplayskip 11\p@ \@plus3\p@ \@minus6\p@
   \abovedisplayshortskip \z@ \@plus3\p@
   \belowdisplayshortskip 6.5\p@ \@plus3.5\p@ \@minus3\p@
   \def\@listi{\leftmargin\leftmargini
               \topsep 9\p@ \@plus3\p@ \@minus5\p@
               \parsep 4.5\p@ \@plus2\p@ \@minus\p@
               \itemsep \z@  \@plus2\p@ \@minus\p@}%
   \belowdisplayskip \abovedisplayskip
}
\renewcommand\footnotesize{%
   \@setfontsize\footnotesize\@xpt\@xpt
   \abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
   \abovedisplayshortskip \z@ \@plus3\p@
   \belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
   \def\@listi{\leftmargin\leftmargini
               \topsep 6\p@ \@plus2\p@ \@minus2\p@
               \parsep 3\p@ \@plus2\p@ \@minus\p@
               \itemsep \parsep}%
   \belowdisplayskip \abovedisplayskip
}

\newcommand{\realsinglespacing}{%
  \let\CS=\@currsize\renewcommand{\baselinestretch}{1.0}\CS}
\newcommand{\singlespacing}{%
  \let\CS=\@currsize\renewcommand{\baselinestretch}{1.208333}\CS}
\newcommand{\singlespacingplus}{%
  \let\CS=\@currsize\renewcommand{\baselinestretch}{1.5}\CS}
\newcommand{\doublespacing}{%
  \let\CS=\@currsize\renewcommand{\baselinestretch}{2}\CS}
\newcommand{\realdoublespacing}{%
  \let\CS=\@currsize\renewcommand{\baselinestretch}{2}\CS}
\newcommand{\normalspacing}{\doublespacing}
\newcommand{\footnotespacing}{\singlespacing}
\newcommand{\listspacing}[1]{\singlespacing} % extra arg is extensibility hook
\newcommand{\changespacing}[2]{%
  \renewcommand{#1}{%
    \let\CS=\@currsize\renewcommand{\baselinestretch}{#2}\CS}%
}
\ifdraft\changespacing{\normalspacing}{1}\fi
\newcommand{\changenormalspacing}[1]{\renewcommand{\normalspacing}{#1}}
\normalspacing

\def \@floatboxreset {%
        \reset@font
        \normalsize
        \singlespacing
        \@setminipage
}

\RequirePackage{graphicx,xcolor}
\definecolor{eLifeDarkBlue}{HTML}{273B81}
\definecolor{eLifeLightBlue}{HTML}{0A9DD9}
\definecolor{eLifeMediumGrey}{HTML}{6D6E70}
\definecolor{eLifeLightGrey}{HTML}{929497}

%\RequirePackage{natbib} % author last names
\RequirePackage[square,numbers,sort&compress]{natbib}
\RequirePackage{xpatch}
\renewcommand{\bibfont}{\small}
% modifed from https://github.com/gbhutani/vancouver_authoryear_bibstyle/
\IfFileExists{vancouver-elife.bst}
  {\bibliographystyle{vancouver-elife}}
  {\PackageWarning{elife}{vancouver-elife.bst not found; falling back to apalike bibliography style.}\bibliographystyle{apalike}}
% Make author in citation italic
\renewcommand{\NAT@nmfmt}[1]{{\bfseries\itshape\color{eLifeMediumGrey} #1}}

% ...as well as the year
\xpatchcmd{\NAT@citex}
{\@citea\NAT@hyper@{\NAT@nmfmt{\NAT@nm}\NAT@date}}
{\@citea\NAT@hyper@{\NAT@nmfmt{\NAT@nm}\NAT@nmfmt{\NAT@date}}}
{}{\PackageWarning{eLife}{Failed to patch year format in citation}}

\xpatchcmd{\NAT@citex}
{\else\unskip\NAT@spacechar\NAT@hyper@{\NAT@date}}
{\else\unskip\NAT@spacechar\NAT@hyper@{\NAT@nmfmt{\NAT@date}}}
{}{\PackageWarning{eLife}{Failed to patch year format in citation}}

\xpatchcmd{\NAT@citex}
{\hyper@natlinkbreak{\NAT@aysep\NAT@spacechar}{\@citeb\@extra@b@citeb}\NAT@date}
{\hyper@natlinkbreak{\NAT@nmfmt{\NAT@aysep\NAT@spacechar}}{\@citeb\@extra@b@citeb}\NAT@nmfmt{\NAT@date}}
{}{\PackageWarning{eLife}{Failed to patch year format in citation}}

\xpatchcmd{\NAT@citex}
{\@citea\NAT@hyper@{\NAT@date}}
{\@citea\NAT@hyper@{\NAT@nmfmt{\NAT@date}}}
{}{\PackageWarning{eLife}{Failed to patch year format in citation}}

\xpatchcmd{\NAT@citex}
{{\@citeb\@extra@b@citeb}\NAT@date}
{{\@citeb\@extra@b@citeb}\NAT@nmfmt{\NAT@date}}
{}{\PackageWarning{eLife}{Failed to patch year format in citation}}



\RequirePackage[colorlinks=true,allcolors=black,citecolor=eLifeLightBlue,linkcolor=eLifeLightBlue,urlcolor=eLifeLightBlue]{hyperref}
\urlstyle{sf}

\RequirePackage[small,labelfont=small,textfont=small]{caption}

\renewcommand{\equationautorefname}{Eq.}
\newcommand{\FIG}[1]{\autoref{fig:#1}}
\newcommand{\TABLE}[1]{\autoref{tab:#1}}
\newcommand{\EQ}[1]{\autoref{eq:#1}}
\newcommand{\BOX}[1]{\autoref{box:#1}}
\let\oldautoref\autoref
\renewcommand{\autoref}[1]{\emph{\textbf{\oldautoref{#1}}}}
\endinput
%%
%% End of file `cornell.cls'.