Thesis.tex

%Thesis template, last hacked by Eric Spaulding (March 2015)
%This template was built via LaTex => DVI => PDF
%if necessary, you can import the dvi2pdf.tco file
%to get the right build (it's included).

%divpdfm is the dvi=>pdf engine
\documentclass [12 pt,dvipdfm] {report}
\input{macros}
\usepackage[maxfloats=100]{morefloats}
\usepackage{isuthesis}

%numbers produces [1] citations, with corresponding 
%citation numbers next to refs in bibliography
\usepackage[numbers]{natbib} %number format
%\usepackage{natbib} %author year format

%\usepackage[utf8]{inputenc}
%\usepackage[T1]{fontenc}
%\usepackage{textcomp}
%\usepackage{gensymb}

\usepackage{fancybox}% I use it for framing definitions
\usepackage{csvsimple} % used to import csv files into the document as tables
	
\usepackage{xcolor}
%\usepackage{color}

\usepackage{amsmath, amssymb, amscd}%Contains the AMS expanded math symbols library.
\usepackage{graphicx}
\usepackage{rotating}   %allows figures to be rotated
\usepackage{subfig}  %for side-by-side figs
\usepackage{multirow}	%for multirow stuff in tables
\usepackage{nicefrac}	%for slanty 3/4 type fracs

%this handy little package puts bookmarks in your thesis.
%there are a ton of parameters, check it out. (hyperref)
%it hyperlinks all your \ref commands to the object it
%references and adds the bookmarks tab to the pdf file
%as well.  
%comment out to remove
\usepackage[pdftitle={\mytitle}, 
            pdfauthor={\me},
            pdfkeywords={bioinformatics,
             			 computer science,
             			 thesis,
             			 metagenomics},  
            pdfstartview=FitH,   
            pdfpagemode={None}]{hyperref} 	%gives bookmarks in pdf file


\usepackage{listings} %this is for code listings


%define the colors used by listings when doing syntax highlighting
\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{
 captionpos=t,                    % sets the caption-position t -> top, b -> bottom
 aboveskip=\medskipamount,        %above and below skip adds space before or after the listing
 belowskip=\medskipamount,
 %abovecaptionskip=\smallskipamount, 
 %belowcaptionskip=\smallskipamount,
 abovecaptionskip=5px,
 belowcaptionskip=5px,
 mathescape=false,
 backgroundcolor=\color{white},   % choose the background color; you must add \usepackage{color} or \usepackage{xcolor}
 basicstyle=\footnotesize,        % the size of the fonts that are used for the code
 breakatwhitespace=true,         % sets if automatic breaks should only happen at whitespace
 breaklines=true,                 % sets automatic line breaking
 commentstyle=\color{dkgreen},    % comment style
 deletekeywords={...},            % if you want to delete keywords from the given language
 extendedchars=true,              % lets you use non-ASCII characters; for 8-bits encodings only, does not work with UTF-8
 frame=single,	                   % adds a frame around the code
 keepspaces=true,                 % keeps spaces in text, useful for keeping indentation of code (possibly needs columns=flexible)
 keywordstyle=\color{blue},       % keyword style
 language=C++,                 % the language of the code
 numbers=left,                    % where to put the line-numbers; possible values are (none, left, right)
 numbersep=5pt,                   % how far the line-numbers are from the code
 numberstyle=\tiny\color{gray}, % the style that is used for the line-numbers
 rulecolor=\color{black},         % if not set, the frame-color may be changed on line-breaks within not-black text (e.g. comments green here))
 showspaces=false,                % show spaces everywhere adding particular underscores; it overrides 'showstringspaces'
 showstringspaces=false,          % underline spaces within strings only
 showtabs=false,                  % show tabs within strings adding particular underscores
 stepnumber=2,                    % the step between two line-numbers. If it's 1, each line will be numbered
 stringstyle=\color{mauve},     % string literal style
 tabsize=2,	                      % sets default tabsize to 2 spaces
 title=\lstname                   % show the filename of files included with \lstinputlisting; also try caption instead of title
}

\lstnewenvironment{code}[1][]%
{
   \noindent
   \minipage{\linewidth} 
   \vspace{0.5\baselineskip}
   \lstset{basicstyle=\ttfamily\footnotesize,frame=single,#1}}
{\endminipage}

\renewcommand{\lstlistingname}{Code Listing}


% makeatletter block is necessary to get
% listings to stop ignoring the abovecaptionskip setting
\makeatletter
\let\@ORGmakecaption\@makecaption
\long\def\@makecaption#1#2{\@ORGmakecaption{#1}{#2}\vskip\belowcaptionskip\relax}
\makeatother

\renewcommand\floatpagefraction{.9}
\renewcommand\topfraction{.9}
\renewcommand\bottomfraction{.9}
\renewcommand\textfraction{.1}

%any files inside {} below will be compiled, rest
%will not.  separate multiple files with commas
%ex.  
%\includeonly{abstract, acknow, chapter2} will 
%build only those files into .pdf file
%note:  only files inserted via \include{} are
%affected by this.  
%=========== include only ======================
%\includeonly{abstract}
%===============================================

\DeclareGraphicsExtensions{.png,.pdf,.jpg}

%=============== comment this out to eliminate section, subsection numbering
\alternate
%==================================================================


\parindent 12pt
%\bibliographystyle{plainnat} %plainnat is the default thesis format
\bibliographystyle{ieeetran} %only works with [numbers] option of natbib
\renewcommand{\bibname}{BIBLIOGRAPHY}

\setcounter{tocdepth}{3} %include sub sub sections in toc

\begin{document}

%--------------- title section -------------------------
\include{titletocmas}
%-------------------------------------------------------

%--------------- copyright section ---------------------
\include{copyright}
%-------------------------------------------------------

%--------------- abstract, acknowldgements -------------
\include{abstract}
\include{acknowl}
%-------------------------------------------------------

%---------------table of contents ----------------------
\tableofcontents
%-------------------------------------------------------

\renewcommand\lstlistlistingname{CODE LISTINGS}

%--------------- list of figs, tables ------------------
\newpage\phantomsection\specialtocchapt{CODE LISTINGS}
\lstlistoflistings

\newpage\phantomsection\specialtocchapt{LIST OF FIGURES}
\listoffigures

\newpage\phantomsection\specialtocchapt{LIST OF TABLES}
\listoftables     
%-------------------------------------------------------

\newpage

\textheight 8.5in %8.5+.5headsep=9in. This leaves 1 in margin in the thesis body
\pagenumbering{arabic}
\pagestyle{myheadings}


%------------ main body section -----------------------
\include{chapter1}
\include{chapter2}
\include{chapter3}
\include{chapter4}
\include{chapter5}
%-------------------------------------------------------


%------------- appendix section ------------------------
% uncomment this to add appendices to paper
%\input{appendices}
%-------------------------------------------------------

%------------ bibliography section ---------------------
%This will remove "APPENDIX" from the Bibliography title:
\unappendixtitle

%Include bibliograpy in the Table of Contents
\phantomsection\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
\bibliography{references}
%-------------------------------------------------------


\end{document}