mwe.tex

% This template was originally by R. Jacob Vogelstein
% Updated on March 1, 2010 by Noah J. Cowan
% Updated on May 18, 2014 by Brian Weitzner
% at https://github.com/weitzner/jhu-thesis-template
% Updated on January 29, 2016 by John Muschelli
% at https://github.com/muschellij2/PhD_Thesis
% Updated on April 13, 2016 by Leonardo Collado Torres and
% available at https://github.com/lcolladotor/jhu-thesis-template.
% Forked by John Clayton in December, 2019
% JHU Formatting requirements of Sheridan Libraries may be found at:
% https://www.library.jhu.edu/library-services/
% electronic-theses-dissertations/formatting-requirements/

% The document is based on the standard 12pt LaTeX report class
%\documentclass[12pt,draft]{report}
\documentclass[12pt]{report}

% PDF Creation settings
\pdfcompresslevel=9
\pdfminorversion=5
\pdfobjcompresslevel=2

% Needed to create a PDF/A file
\usepackage[a-1b]{pdfx}

% Incude pdf docs
\usepackage{pdfpages}
% For transferring hyperlinks from PDFs added by pdfpages
\usepackage{pax}

% For dialect-specific hyphenation etc.
\usepackage[american]{babel}

% T1 font encoding
\usepackage[T1]{fontenc}
% Use UTF8 input encoding
\usepackage[utf8]{inputenc}
%\DeclareUnicodeCharacter{00A0}{ }

% Load latin modern, a font with all the characters
\usepackage{lmodern}

% For generating the dummy text in the mwe template
\usepackage{lipsum}

% Provides various text symbols (such as \textdegree) in TS1 encoding.
\usepackage{textcomp}

% provides ul for cv
\usepackage{soul}

% Set the margins according to JHU specifications
\usepackage{geometry}
 \geometry{
   letterpaper,
   left=1.5in,
   right=1.0in,
   top=1.0in,
   bottom=1.0in}

% Spacing options
\usepackage{setspace}

% Typography and fonts
\usepackage[protrusion]{microtype}
% For multiple columns
\usepackage{multicol}
% for proper text wrapping of nucleic acid sequences
\usepackage{seqsplit}

% Fancy verbatim-like environment for code
\usepackage{listings}
\lstset{basicstyle=\footnotesize\ttfamily,
        columns=flexible,
        breaklines=true
}

% Hyperlink handling
\usepackage[pdfa]{hyperref}
\hypersetup{
   linktocpage,
   unicode,
   colorlinks=true,
   citecolor=link,
   filecolor=link,
   linkcolor=link,
   urlcolor=link
}

% Color handling
\usepackage{xcolor}
%\usepackage{color}

% Color for links
\definecolor{link}{rgb}{0.45,0.51,0.67}

%%% Table of Contents %%%
\usepackage[titles]{tocloft}
% Dots for chapters too
\renewcommand{\cftchapleader}{\cftdotfill{\cftdotsep}}

% To add bibliography to the table of contents
\usepackage{tocbibind}

% Set depth of TOC items
\setcounter{tocdepth}{4}

% Set depth of section numbering
\setcounter{secnumdepth}{4}

\usepackage{calc}
% Tweak to TOC to add 'chapter' to chapter name instead of a number only
\renewcommand{\cftchappresnum}{\chaptername\space}
% Set width of box based on longest label name
\setlength{\cftchapnumwidth}{\widthof{\textbf{Appendix~II~}}}

% Stylize chapter headings
%\usepackage{sectsty}
%\chapterfont{\centering}

% Removes 'Chapter #' title while keeping
% it listed in the TOC
\newcommand\chap[1]{%
  \chapter*{#1}%
  \addcontentsline{toc}{chapter}{#1}}

% Removes 'Section #' title while keeping
% it listed in the TOC
\newcommand\sect[1]{%
  \section*{#1}%
  \addcontentsline{toc}{section}{#1}}

% Removes 'Subsection #'title while keeping
% it listed in the TOC
\newcommand\subsect[1]{%
  \subsection*{#1}%
  \addcontentsline{toc}{subsection}{#1}}

% For oligo table
% Changes dot to hyphen in figure references and captions
\renewcommand{\thetable}{\thechapter-\Roman{table}}
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{longtable}
\usepackage{array}
\usepackage{pdflscape}

% Align on numeric decimal in table
%\usepackage{dcolumn}

% Enhanced control over layout of itemize, enumerate, and description
\usepackage{enumitem}

% Graphics Packages
%\usepackage{graphics} 
\usepackage{graphicx}
%\usepackage{float}

% Setup style for figure captions
\usepackage[font=small,
            labelfont=bf,
            labelsep=period,
            font=sf,
            hypcap=true]{caption}

% For captions on the side of figures
\usepackage{ifthen}
\usepackage[rightcaption]{sidecap}

% Individual panel captions
%\usepackage{subfig}

% Options for hyperlinking to floats
\usepackage[all]{hypcap}

% Graphics Path
\graphicspath{{figures/}}

% To change the name of the figures page
\renewcommand{\listfigurename}{Figures}
% To change the default beginning to each line
\renewcommand{\cftfigpresnum}{\bfseries Figure }
% Changes dot to hyphen in figure references and captions
\renewcommand{\thefigure}{\thechapter-\arabic{figure}}
% To change the distance to the start of the figure title
\setlength{\cftfignumwidth}{\widthof{\textbf{Figure~5-10~}}}

% Tikz, for drawing vector graphics
%\usepackage{tikz}
%\usetikzlibrary{positioning}
%\usetikzlibrary{shapes,arrows}

% Enable the glossary
%\makeglossary

% Make appendices
%\usepackage[title,titletoc]{appendix}
\usepackage{appendix}
%\renewcommand{\appendixname}{Appendix}

%%%%%%%%%%%%%%%%%%
% FOR BIBTEX
%%%%%%%%%%%%%%%%%%

% For use with IEEEtran.bst
%\usepackage{cite}
%\usepackage[numbers,square,compress]{natbib}
%\setlength\bibsep{4pt}
% Set bibliography name
%\usepackage{chbibref}
%\renewcommand\bibname{References}

%%%%%%%%%%%%%%%%%%
% FOR BIBLATEX
%%%%%%%%%%%%%%%%%%

\usepackage[
style = nature, 
sorting = none, 
%dashed = false,
%maxbibnames = 99,
backend = biber,
url=false,
isbn=false,
natbib = true
]{biblatex}

% Point to bibfile
\addbibresource{classics.bib}

% If you want to exclude some portions from the bibliography
%\AtEveryBibitem{
%\clearfield{issn}
%\clearfield{note}
%\clearfield{month}
%}

% Change bib font size
\renewcommand{\bibfont}{\small}

%%%%%%%%%%%%%%%%%%
% DOI from Segmentation (needs hyperref)
%%%%%%%%%%%%%%%%%%

%\makeatletter
%\providecommand{\doi}[1]{%
%  \begingroup
%    \let\bibinfo\@secondoftwo
%    \urlstyle{rm}%
%    \href{http://dx.doi.org/#1}{%
%      doi:\discretionary{}{}{}%
%      \nolinkurl{#1}%
%    }%
%  \endgroup
%}
%\makeatother

% Math
%\usepackage{amsmath,amssymb,array}

%\newcommand{\bm}[1]{ \mbox{\boldmath $ #1 $} }
%\newcommand{\bin}[2]{\left(\begin{array}{@{}c@{}} #1 \\ #2
%             \end{array}\right) }
% A math shortcut frequently used by John Muschelli
%\newcommand{\bbeta}{\mbox{\boldmath $\beta$}}

%%%%%%%%%%%
% CONTENT %
%%%%%%%%%%%
%
\begin{document}
% Sets paragraph (and not title) spacing, roughly speaking
\setlength{\parskip}{3pt}
\baselineskip=24pt
%
% front matter page numbering
\pagenumbering{roman}
%
% Add title page
\include{text/01-title}
%
% Setup and add front matter
\pagestyle{plain}
\setcounter{page}{2}
%
% Add abstract
\include{text/02-abstract}
%
% Add readers (JHU style is to include readers with in abstract)
%\include{text/03-committee}
%
% Add preface
%\include{text/04-preface}
%
% Add dedication
\include{text/05-dedication}
%
% Add acknowledgements
\include{text/06-acknowledgements}
%
% To change the name of the contents page
%\renewcommand{\contentsname}{Contents}
%
% Create table of contents
\tableofcontents
%
% Create table list
%\listoftables
%
% Create List of figures
\listoffigures
\clearpage
%
%%% END FRONT MATTER %%%
%
%%%%% MAIN MATTER %%%%%
% Switch page numbering at the end of front matter, before first chapter
\pagenumbering{arabic}
%
%\begin{refsection}[myrefs.bib]
\include{text/07-chapter-1-introduction}
%\printbibliography[title=References]}
%\end{refsection}
%
%\begin{refsection}[myrefs.bib]
\include{text/08-chapter-2}
%\printbibliography[title={References}]
%\end{refsection}
%
%\begin{refsection}[myrefs.bib]
\include{text/09-chapter-3}
%\printbibliography[title={References}]
%\end{refsection}
%
%\begin{refsection}[myrefs.bib]
\include{text/10-chapter-4}
%\printbibliography[title={References}]
%\end{refsection}
%
%\begin{refsection}[myrefs.bib]
\include{text/11-chapter-5-discussion-conclusions}
%\printbibliography[title={References}]
%\end{refsection}
%
%%%%% BACK MATTER %%%%%
%
%%% BIBLATEX BIBLIOGRAPHY %%%
%\footnotesize
\printbibliography[title={References},heading=bibintoc]
%
%%% BIBTEX BIBLIOGRAPHY %%%
%
% Use the IEEEtran.bst style file (bibtex)
%\bibliographystyle{IEEEtran}
%
% Name the bibliography
%\setbibref{References}
% Point to bibfile
%\footnotesize\bibliography{IEEEabrv,classics}
%\bibliography{IEEEabrv,classics}
%
% APPENDICES
\begin{appendices}
% Appendix I
\include{text/12-appendix-i}
% Appendix II
\include{text/13-appendix-ii}
\end{appendices}
%
%%% CV %%%
\include{text/15-my-original-cv}
%
%%% Biographical Sketch %%%
\include{text/16-biographical-sketch}
%
\end{document}