
%---------------------------------------------------------
% Header: This file includes all the packages and custom definitions
% we have used in this example thesis.
%----------------------------------------------------------

% Uncomment the following line if, for some reason, you want a PDF 1.4
% document, rather than (at time of writing) PDF 1.5.
% \pdfminorversion=4

\documentclass[12pt,twoside,openright]{report}

% With these lines, when one tried to copy/paste from AR it does The
% Right Things for ligatures.
\input{glyphtounicode}
\pdfgentounicode=1

%---------------------
% START: Packages
%---------------------
\usepackage{textcomp}
\usepackage[latin1]{inputenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage{soul}
\usepackage{listings}
\usepackage{subfig}
\usepackage{verbatim}
\usepackage{alltt}

% There are used in the graphics chapter.
% You can delete the following two lines if you use no tikz/pgf graphics
% in your thesis.
\usepackage{tikz}
\usepackage{pgfplots}

% Load the natbib citation package: set the citations to be numerical
% with square brackets separated by commas.
\usepackage[numbers,square,comma]{natbib}

% Now include the Acadia thesis style
\usepackage{acadia-hon-thesis}

% Load the hyperref package.
% The options tell it to (a) use hyper-links to pages with Roman
% numerals that are different than pages with Arabic numbers, and
% (b) tell Adobe reader to show a page number matching the thesis page
% number (rather than sequentially numbering the PDF pages from 1).
\usepackage[plainpages=false,pdfpagelabels]{hyperref}

% The information in the first three lines here goes into the PDF
% document properties.
% The rest of the lines define options related to hyper-links.
% colorlinks: typeset links in the given colours
%	      (otherwise an ugly box is drawn around the links, although
%	       it is only seen on the screen, not in printed copies)
% A newer option (since May 2011) would be to just use the hidelinks option.
% Note: pdfprintscaling=None should discourage Adobe reader from wanting to
% scale your pages to fit printable area when you print from Adobe reader.
\hypersetup{%
    pdftitle={PUT YOUR THESIS TITLE HERE},
    pdfauthor={PUT YOUR NAME HERE},
    pdfkeywords={PUT ANY KEYWORDS HERE},
    colorlinks = true,
    linkcolor = black,
    anchorcolor = black,
    citecolor = black,
    filecolor = black,
    urlcolor = black,
    pdfprintscaling=None
}


% Load the algorithm/mic packages and use chapter-wise numbering
\usepackage[chapter]{algorithm}
\usepackage{algorithmic}


% JD addition:
% The url package does not, by default, allow breaks at '-'.  Change this
% by adding \do\- to this macro.  If you don't want breaks at '-' in URLs,
% just comment out or delete these lines:
\def\UrlBreaks{\do\.\do\@\do\\\do\/\do\!\do\_\do\|\do\;\do\>\do\]\do\-%
               \do\)\do\,\do\?\do\'\do+\do\=\do\#}%


%---------------------
% END: Packages
%---------------------
%\bibliographystyle{alpha}     % Make citations look like [Smi91], not [12]
\bibliographystyle{plainnat}   % Default boring and almost useless number.

% The depth of the table of contents: change the MAXIMUM depth of
% citations in your table of contents.
\setcounter{tocdepth}{6}

%
% Some definitions of commands used in this thesis
%

% For instance, if you have an acronym you like to use, then define a
% command, it's faster and if the acronym changes you only have to
% change it in one place.
\def\sysacro{SPECIALACRONYM}

% Allow us to change the margins easily and at will
\newenvironment{changemargin}[2]{%
  \begin{list}{}{%
    \setlength{\topsep}{0pt}%
    \setlength{\leftmargin}{#1}%
    \setlength{\rightmargin}{#2}%
    \setlength{\listparindent}{\parindent}%
    \setlength{\itemindent}{\parindent}%
    \setlength{\parsep}{\parskip}%
  }%
  \item[]}{\end{list}}

%setup the default format of listings
\lstset{
    basicstyle=\footnotesize,
    numbers=left,
    xleftmargin=5mm,
    linewidth=\textwidth,
    breaklines,
    frame=tb,
    frameround=fttt
}

% A new definition style
\newtheoremstyle{defstyle}	% name
    {3pt}			% Space above
    {3pt}			% Space below
    {}				% Body font
    {}				% Indent amount
    {\itshape}			% Theorem head font
    {:}				% Punctuation after theorem head
    {.5em}			% Space after theorem head
    {}		% Theorem head spec (can be left empty,meaning 'normal)
\theoremstyle{definition}
\newtheorem{definition}{Definition}[chapter]


% Change comment style for algorithms
\renewcommand{\algorithmiccomment}[1]{/*#1*/}
% Change Require: to Input: for algorithms
\renewcommand{\algorithmicrequire}{\textbf{Input:}}
% Change Ensure: to Output: for algorithms
\renewcommand{\algorithmicensure}{\textbf{Output:}}
