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% McMaster Masters/Doctoral Thesis
% LaTeX Template
% Version 2.2 (11/23/15)
%
% This template has been downloaded from:
% http://www.LaTeXTemplates.com
% Then subsequently from http://www.overleaf.com
%
% Version 2.0 major modifications by:
% Vel (vel@latextemplates.com)
%
% Original authors:
% Steven Gunn (http://users.ecs.soton.ac.uk/srg/softwaretools/document/templates/)
% Sunil Patel (http://www.sunilpatel.co.uk/thesis-template/)
%
% Modified to McMaster format by Benjamin Furman (contact: https://www.xenben/com; Most up
% to date template at https://github.com/benjaminfurman/McMaster_Thesis_Template,
% occasionally updated on Overleaf template page)
%
% License:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
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%----------------------------------------------------------------------------------------
% DOCUMENT CONFIGURATIONS
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\documentclass[
11pt, % The default document font size, options: 10pt, 11pt, 12pt
oneside, % Two side (alternating margins) for binding by default, uncomment to switch to one side
english, % other languages available
singlespacing, % Single line spacing, alternatives: onehalfspacing or doublespacing
%draft, % Uncomment to enable draft mode (no pictures, no links, overfull hboxes indicated)
%nolistspacing, % If the document is onehalfspacing or doublespacing, uncomment this to set spacing in lists to single
%liststotoc, % Uncomment to add the list of figures/tables/etc to the table of contents
%toctotoc, % Uncomment to add the main table of contents to the table of contents
]{McMasterThesis} % The class file specifying the document structure
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% Import packages here
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\usepackage[utf8]{inputenc} % Required for inputting international characters
\usepackage[T1]{fontenc} % Output font encoding for international characters
\usepackage{lmodern} % could change font type by calling a different package
\usepackage{lastpage} % count pages
\usepackage{siunitx} % for scientific units (micro-liter, etc)
\setcounter{tocdepth}{2} % so that only section and sub sections appear in Table of Contents. Remove or set depth to 3 to include sub-sub-sections
%----------------------------------------------------------------------------------------
% Handling Citations
%----------------------------------------------------------------------------------------
\usepackage[backend=biber, giveninits=true, doi=false, natbib=true, url=false, eprint=false, style=authoryear, sorting=nyt, maxcitenames=2, maxbibnames=99, uniquename=false, uniquelist=false, dashed=false]{biblatex} % can change the maxbibnames to cut long author lists to specified length followed by et al., currently set to 99.
\DeclareFieldFormat[article,inbook,incollection,inproceedings,patent,thesis,unpublished]{title}{#1\isdot} % removes quotes around title
\renewbibmacro*{volume+number+eid}{%
\printfield{volume}%
% \setunit*{\adddot}% DELETED
\printfield{number}%
\setunit{\space}%
\printfield{eid}}
\DeclareFieldFormat[article]{number}{\mkbibparens{#1}}
%\renewcommand*{\newunitpunct}{\space} % remove period after date, but I like it.
\renewbibmacro{in:}{\ifentrytype{article}{}{\printtext{\bibstring{in}\intitlepunct}}} % this remove the "In: Journal Name" from articles in the bibliography, which happens with the ynt
\renewbibmacro*{note+pages}{%
\printfield{note}%
\setunit{,\space}% could add punctuation here for after volume
\printfield{pages}%
\newunit}
\DefineBibliographyStrings{english}{% clears the pp from pages
page = {\ifbibliography{}{\adddot}},
pages = {\ifbibliography{}{\adddot}},
}
\DeclareNameAlias{sortname}{last-first}
\renewcommand*{\nameyeardelim}{\addspace} % remove comma in text between name and date
\addbibresource{Bibliography.bib} % The filename of the bibliography
\usepackage[autostyle=true]{csquotes} % Required to generate language-dependent quotes in the bibliography
% you'll have to play with the citation styles to resemble the standard in your field, or just leave them as is here.
% or, if there is a bst file you like, just get rid of all this biblatex stuff and go back to bibtex.
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% Collect all your header information from the chapters here, things like acronyms, custom commands, necessary packages, etc.
%----------------------------------------------------------------------------------------
\usepackage{parskip} %this will put spaces between paragraphs
\setlength{\parindent}{15pt} % this will create and indent on all but the first paragraph of each section.
% should maybe change to glossaries package
\usepackage{acro}
\DeclareAcronym{est}{
short = EST,
long = expressed sequence tags
}
\DeclareAcronym{Xl}{
short = \textit{X.~laevis},
long = \textit{Xenopus~laevis}
}
\DeclareAcronym{Xg}{
short = \textit{X.~gilli},
long = \textit{Xenopus~gilli}
}
\usepackage{etoolbox}
\preto\chapter{\acresetall} % resets acronyms for each chapter
\usepackage{xspace} %helps spacing with custom commands.
\newcommand{\oddname}{{\sc SoME goOfY LonG ThiNg With an AwkWarD NAme}\xspace}
\usepackage{pgfplotstable} % a much better way to handle tables
\pgfplotsset{compat=1.12}
% \usepackage{float} % if you need to demand figure/table placement, then this will allow you to use [H], which demands a figure placement. Beware, making LaTeX do things it doesn't want may lead to oddities.
%%%%
% LINK COLORS
% You can control the link colors at the end of the McMasterThesis.cls file. There is also a true/false option there to turn off all link colors.
%%%%
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% THESIS INFORMATION
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\thesistitle{Thesis Title} % Your thesis title, print it elsewhere with \ttitle
\supervisor{Dr. Jane \textsc{Smith}} % Your supervisor's name, print it elsewhere with \supname
\examiner{} % Your examiner's name, print it elsewhere with \examname
\degree{Doctor of Philosophy} % Your degree name, print it elsewhere with \degreename
\author{John \textsc{Smith}} % Your name, print it elsewhere with \authorname
\addresses{} % Your address, print it elsewhere with \addressname
\subject{Biological Sciences} % Your subject area, print it elsewhere with \subjectname
\keywords{} % Keywords for your thesis, print it elsewhere with \keywordnames
\university{\href{http://www.mcmaster.ca/}{McMaster University}} % Your university's name and URL, print it elsewhere with \univname
\department{\href{http://www.biology.mcmaster.ca/}{Department of Biology}} % Your department's name and URL, print it elsewhere with \deptname
\group{\href{http://researchgroup.university.com}{Research Group Name}} % Your research group's name and URL, print it elsewhere with \groupname
\faculty{\href{http://www.science.mcmaster.ca/}{Faculty of Science}} % Your faculty's name and URL, print it elsewhere with \facname
% this sets up hyperlinks
\hypersetup{pdftitle=\ttitle} % Set the PDF's title to your title
\hypersetup{pdfauthor=\authorname} % Set the PDF's author to your name
\hypersetup{pdfkeywords=\keywordnames} % Set the PDF's keywords to your keywords
\begin{document}
\frontmatter % Use roman page numbering style (i, ii, iii, iv...) for the pre-content pages
\pagestyle{plain} % Default to the plain heading style until the thesis style is called for the body content
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% Half Title (lay title)
%----------------------------------------------------------------------------------------
%\begin{halftitle} % could not get this environment working
%\vspace*{\fill}
\vspace{6cm}
\begin{center}
A short 60 character title % ideally, but it doesn't seem to matter
\end{center}
%\vspace*{\fill}
\pagenumbering{gobble} % leave this here, McMaster doesn't want this page numbered
%\end{halftitle}
\clearpage
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% TITLE PAGE
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\pagenumbering{gobble}
\begin{center}
\vfill
\textsc{\Large \ttitle} \\
\vfill
By \authorname, \\%% -----> List prior degrees after comma <----
\vfill
{\large \textit{A Thesis Submitted to the School of Graduate Studies in the Partial Fulfillment of the Requirements for the Degree \degreename}}\\
\vfill
{\large \univname\, \copyright\, Copyright by \authorname\, \today}\\[4cm] % replace \today with the submission date
\end{center}
%----------------------------------------------------------------------------------------
% Descriptive note numbered ii
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% Need to add below info
\newpage
\pagenumbering{roman} % leave to turn numbering back on
\setcounter{page}{2} % leave here to make this page numbered ii, a Grad School requirement
\noindent % stops indent on next line
\univname \\
\degreename\, (\the\year) \\
Hamilton, Ontario (\deptname) \\[1.5cm]
TITLE: \ttitle \\
AUTHOR: \authorname\, %list previous degrees
(\univname) \\
SUPERVISOR: \supname\, \\
NUMBER OF PAGES: \pageref{lastoffront}, \pageref{LastPage} % put in iv and number
\clearpage
%----------------------------------------------------------------------------------------
% Lay abstract number iii
%----------------------------------------------------------------------------------------
% not actually included in most theses, though requested by the GSA
% uncomment below lines if you want to include one
%\section*{Lay Abstract}
%\addchaptertocentry{Lay Abstract}
% Type it here
%\clearpage
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% ABSTRACT PAGE
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\section*{\Huge Abstract}
\addchaptertocentry{Abstract}
% Type your abstract here.
An abstract!
\clearpage
%----------------------------------------------------------------------------------------
% ACKNOWLEDGEMENTS
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\begin{acknowledgements}
\addchaptertocentry{\acknowledgementname} % Add the acknowledgments to the table of contents
The acknowledgments and the people to thank go here, don't forget to include your project adviser\ldots
\end{acknowledgements}
%----------------------------------------------------------------------------------------
% LIST OF CONTENTS/FIGURES/TABLES PAGES
%----------------------------------------------------------------------------------------
\tableofcontents % Prints the main table of contents
\listoffigures % Prints the list of figures
\listoftables % Prints the list of tables
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% ABBREVIATIONS
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% many theses don't use this section, as it will be declared at first use and again each chapter. Uncomment these four lines to activate if you want
%\clearpage
%\section*{\Huge Acronyms}
%\addchaptertocentry{Acronyms}
%\printacronyms[name] % name without an option stops the header
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% DECLARATION PAGE
%----------------------------------------------------------------------------------------
\begin{declaration}
\addchaptertocentry{\authorshipname}
\noindent I, \authorname, declare that this thesis titled, \enquote{\ttitle} and the work presented in it are my own. I confirm that:
\begin{itemize}
\item List each chapter
\item and what you have done for it
\end{itemize}
\end{declaration}
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% optional page stuff
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% can do physical constraints and symbols pages, see the original thesis example on overleaf if you want to include them at https://www.overleaf.com/latex/templates/template-for-a-masters-slash-doctoral-thesis/mkzrzktcbzfl#.VlPeicorpE4
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% QUOTATION PAGE
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%\vspace*{0.2\textheight}
%\noindent\enquote{\itshape Thanks to my solid academic training, today I can write hundreds of words on virtually any topic without possessing a shred of information, which is how I got a good job in journalism.}\bigbreak
%\hfill Dave Barry
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% DEDICATION
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% \dedicatory{For/Dedicated to/To my\ldots}
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% The following bit is just here to make sure we end up on a new page and get the total number of roman numeral
\label{lastoffront}
\clearpage
% make sure this command is on the last of your frontmatter pages, i.e. only this command, a \clearpage then \mainmatter
% should be fine without modification
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% THESIS CONTENT - CHAPTERS
%----------------------------------------------------------------------------------------
\mainmatter % Begin numeric (1,2,3...) page numbering
\pagestyle{thesis} % Return the page headers back to the "thesis" style
% Include the chapters of the thesis as separate files from the Chapters folder
\input{Chapters/Chapt1}
\input{Chapters/Chapt2}
% I suggest only compiling one chapter at a time, and comment out the others. That way, the document will typeset faster. When your done with all the chapters, then uncomment them all. Don't worry about the numbering of chapters/figures/etc. LaTeX will take care of that.
%----------------------------------------------------------------------------------------
% THESIS CONTENT - APPENDICES
%----------------------------------------------------------------------------------------
\appendix % Cue to tell LaTeX that the following "chapters" are Appendices
\renewcommand{\thetable}{A\arabic{chapter}.\arabic{table}} % adds an A to table names in appendix (Table A1.1, A1.2...)
\renewcommand{\thefigure}{A\arabic{chapter}.\arabic{figure}} % same for figures
\renewcommand{\thesection}{A\arabic{section}}
% Include the appendices of the thesis as separate files from the Appendices folder
\input{Appendix/Supp_Chap1.tex}
%----------------------------------------------------------------------------------------
% BIBLIOGRAPHY
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\printbibliography[heading=bibintoc]
%----------------------------------------------------------------------------------------
\end{document}
