% Copyright (C)  2010-2013  W.Trevor King <wking@tremily.us>
% Permission is granted to copy, distribute, and/or modify this document
% under the terms of the Creative Commons Attribution-ShareAlike License
% Version 3.0.
% 
% You should have revieved a copy of the Creative Commons
% Attribution-ShareAlike License along with this program (COPYING-CC);
% if not, visit
%   http://creativecommons.org/licenses/by-sa/3.0/legalcode

\documentclass[%
  subfig,%
  indenttoc,%
  approvalform,%
  final%
%  draft%
]{drexel-thesis}
% See drexel-thesis.pdf for more options.

%\includeonly{%
%  cantilever/main,%
%  temperature/main%
%  cantilever-calib/main
%}

\author{William Trevor King}
\title{Open source single molecule force spectroscopy}
\DUTmonth{June}
\DUTyear{2013}
\degree{Doctor of Philosophy}
\advisor{Guoliang Yang, Ph.D.}
\advisor{Louis Cruz Cruz, Ph.D.}
\copyrighttext{\copyrighttextCCBYSA}

\input{packages}

\begin{document}

% Work-directory for Asymptote files (no spaces):
\def\asydir{figures/scratch}
\begin{asydef}
// Global Asymptote definitions go here.
//texpreamble("\documentclass{drexel-thesis}");
//usepackage("packages");
defaultpen(fontsize(10));  // match drexel-thesis's default 10pt font size
\end{asydef}


\begin{preamble}

\include{blurb/dedications}
\include{blurb/acknowledgments}

\tableofcontents
\listoftables
\listoffigures

\include{blurb/abstract}

\end{preamble}
\iffinal{}{\linenumbers}

\begin{thesis}
\pdfbookmark[-1]{Mainmatter}{Mainmatter}
\include{introduction/main}
\include{apparatus/main}
\include{sawsim/main}
\include{pyafm/main}
\include{calibcant/main}
\include{hooke/main}
%\include{temperature/main}
%\include{cantilever/main}
\include{salt/main}
\include{future/main}
\end{thesis}

\bibliography{%
  blurb/main,%
  apparatus/main,%
%  sawsim/main,% currently empty
  pyafm/main,%
  calibcant/main,%
  hooke/main,%
  salt/main,%
  future/main,%
  packaging/main,%
  figures/main,%
  root}

\appendix
\include{cantilever-calib/main}
%\include{viscocity/main}

\printnomenclature
% avoid index's second column overlapping the nomenclature space.
\iffinal{}{\pagebreak}
%\printindex

\include{blurb/vita}

\end{document}
