% -*- Mode:TeX -*-

%% IMPORTANT: The official thesis specifications are available at:
%%            http://libraries.mit.edu/archives/thesis-specs/
%%
%%            Please verify your thesis' formatting and copyright
%%            assignment before submission.  If you notice any
%%            discrepancies between these templates and the 
%%            MIT Libraries' specs, please let us know
%%            by e-mailing thesis@mit.edu

%% The documentclass options along with the pagestyle can be used to generate
%% a technical report, a draft copy, or a regular thesis.  You may need to
%% re-specify the pagestyle after you \include  cover.tex.  For more
%% information, see the first few lines of mitthesis.cls. 

%\documentclass[12pt,vi,twoside]{mitthesis}
%%
%%  If you want your thesis copyright to you instead of MIT, use the
%%  ``vi'' option, as above.
%%
%\documentclass[12pt,twoside,leftblank]{mitthesis}
%%
%% If you want blank pages before new chapters to be labelled ``This
%% Page Intentionally Left Blank'', use the ``leftblank'' option, as
%% above. 

\documentclass[12pt,twoside,singlespace,vi]{mitthesis}
%\documentclass[12pt,twoside,vi]{mitthesis}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{mathtools}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage{wasysym}
\usepackage{amssymb}
\usepackage{hyperref}
\usepackage{libertine}
\usepackage{inconsolata}
\usepackage{rotating}
\usepackage{caption}

\usepackage{afterpage}

\afterpage{\clearpage}          %

\usepackage[backend=bibtex,style=alphabetic]{biblatex}
\addbibresource{cortex.bib}

\usepackage{xcolor}
\definecolor{dark-red}{rgb}{0.4,0.15,0.15}
\definecolor{dark-blue}{rgb}{0.15,0.4,0.15}
\definecolor{medium-blue}{rgb}{0.15,0.4,0.4}
\hypersetup{
    colorlinks, linkcolor={dark-red},
    citecolor={dark-blue}, urlcolor={medium-blue}
}


\renewcommand{\thesection}{\arabic{section}}
\renewcommand{\thefigure}{\arabic{figure}}

%%%%% better source code display
\usepackage{minted}

%% dyl fonts

% \usemintedstyle{friendly}
% \usemintedstyle{perldoc}
%\definecolor{bg}{rgb}{0.95,0.95,0.95}
\definecolor{bg}{rgb}{0.625,0,0}
\usemintedstyle{default}
\newcommand{\why}[1]{\\ \par{\footnotesize #1}}
%\setmonofont[Scale=0.9,BoldFont={Inconsolata Bold}]{Inconsolata}

%\usepackage[gray]{xcolor}
\newminted{clojure}{fontsize=\footnotesize}
%\newminted{clojure}{fontsize=\footnotesize,bgcolor=bg}
%\newminted{clojure}{fontsize=\scriptsize}

%\usepackage{lgrind}
\pagestyle{plain}


% Alter some LaTeX defaults for better treatment of figures:
% See p.105 of "TeX Unbound" for suggested values.
% See pp. 199-200 of Lamport's "LaTeX" book for details.
%   General parameters, for ALL pages:
\renewcommand{\topfraction}{0.9}	% max fraction of floats at top
\renewcommand{\bottomfraction}{0.8}	% max fraction of floats at bottom
%   Parameters for TEXT pages (not float pages):
\setcounter{topnumber}{2}
\setcounter{bottomnumber}{2}
\setcounter{totalnumber}{4}     % 2 may work better
\setcounter{dbltopnumber}{2}    % for 2-column pages
\renewcommand{\dbltopfraction}{0.9}	% fit big float above 2-col. text
\renewcommand{\textfraction}{0.07}	% allow minimal text w. figs
%   Parameters for FLOAT pages (not text pages):
\renewcommand{\floatpagefraction}{0.7}	% require fuller float pages
% N.B.: floatpagefraction MUST be less than topfraction !!
\renewcommand{\dblfloatpagefraction}{0.7}	% require fuller float pages
% remember to use [htp] or [htpb] for placement


\begin{document}

\include{cover}
% Some departments (e.g. 5) require an additional signature page.  See
% signature.tex for more information and uncomment the following line if
% applicable.
% \include{signature}
\pagestyle{plain}
\tableofcontents
%\newpage
%\listoffigures
%\newpage
%\listoftables
\include{cortex}
\nocite{*}
%\include{chap2}
\appendix
\begin{singlespace}
%\bibliographystyle{agsm}
%\bibliographystyle{apa}
%\bibliographystyle{plainnat}
\include{user-guide}
\printbibliography
\end{singlespace}
\end{document}

