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sbmlpkgspec.cls
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sbmlpkgspec.cls
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%% Filename: sbmlpkgspec.cls -*- mode: latex -*-
%% Description: LaTeX style file for SBGN Level 3 package specifications
%% Author(s): Michael Hucka <[email protected]>
%% Organization: California Institute of Technology
%% Date created: 2011-08-11
%%
%% Copyright 2007-2014 California Institute of Technology, Pasadena, CA, USA.
%%
%% This file is free software; you can redistribute it and/or modify it
%% under the terms of the GNU Lesser General Public License as published
%% by the Free Software Foundation; either version 2.1 of the License, or
%% any later version.
%%
%% This library is distributed in the hope that it will be useful, but
%% WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
%% MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
%% documentation provided hereunder is on an "as is" basis, and the
%% California Institute of Technology has no obligations to provide
%% maintenance, support, updates, enhancements or modifications. In no
%% event shall the California Institute of Technology be liable to any
%% party for direct, indirect, special, incidental or consequential
%% damages, including lost profits, arising out of the use of this software
%% and its documentation, even if the California Institute of Technology
%% has been advised of the possibility of such damage. See the
%% GNU Lesser General Public License for more details.
%%
%% You should have received a copy of the GNU Lesser General Public License
%% along with this library; if not, write to the Free Software Foundation,
%% Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
\def\filedate{2017/09/05}
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{sbmlpkgspec}[\filedate\space SBGN Level 3
Package Specification Style]
%% ----------------------------------------------------------------------------
%% Package references and options.
%% ----------------------------------------------------------------------------
%% Keep in mind that hyperref needs to be almost the last package loaded.
\newif\if@draftspec
\DeclareOption{draftspec}{\global\let\if@draftspec\iftrue}
\DeclareOption{finalspec}{\global\let\if@draftspec\iffalse}
\newif\if@notoc
\DeclareOption{toc}{\global\let\if@notoc\iffalse}
\DeclareOption{notoc}{\global\let\if@notoc\iftrue}
\newif\if@twocolumntoc
\DeclareOption{twocolumntoc}{\global\let\if@twocolumntoc\iftrue}
\DeclareOption{singlecolumntoc}{\global\let\if@twocolumntoc\iffalse}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
\ExecuteOptions{toc,twoside}
\ExecuteOptions{singlecolumntoc}
\ProcessOptions
\LoadClass{article}
%% ----------------------------------------------------------------------------
%% Dependencies on other packages.
%% ----------------------------------------------------------------------------
\RequirePackage{lastpage}
\RequirePackage{ifpdf}
\RequirePackage{booktabs}
\RequirePackage{multicol}
\RequirePackage{array}
\RequirePackage[round,sort]{natbib}
\RequirePackage{xspace}
\RequirePackage{scalefnt}
\RequirePackage{pifont}
\RequirePackage[pagewise,mathlines,edtable,right]{lineno}
\RequirePackage{calc}
\RequirePackage{fancyhdr}
\RequirePackage{fancybox}
\RequirePackage{amsmath}
\RequirePackage{amssymb}
\RequirePackage{bbding}
\RequirePackage{wasysym}
\RequirePackage{enumitem}
\RequirePackage{accsupp}
\RequirePackage[T1]{fontenc}
\RequirePackage{suffix}
\RequirePackage{varwidth}
\RequirePackage{etoolbox}
% We use the "optional" package to indicate whether to generate a grayscale
% vs a color version of the document without having to alter the .tex file
% itself. Unfortunately, the "optional" package doesn't offer an "or" type
% switch or a way to set a default, so we have to go through some
% contortions here. Also, it needs *something* in the optional argument
% to RequirePackage or UsePackage, hence the "dummyoption" thing below.
%
% To produce grayscale output without modifying the source file, invoke
% latex with a command of the following form:
%
% pdflatex "\newcommand\UseOption{grayscale}\input{sbml-level-2-version-2}"
\newif\ifgrayscalespec
\global\let\ifgrayscalespec\iffalse
\RequirePackage[dummyoption]{optional}
\opt{grayscale}{\global\let\ifgrayscalespec\iftrue}
% Load varioref only if not generating HTML, because on HTML
% pages it doesn't make sense to use varioref.
% \RequirePackage{html}
% \latexhtml{
%begin{latexonly}
\RequirePackage[american]{varioref}
%end{latexonly}
% }{
% \newcommand{\vref}[1]{\ref{#1}}
% }
% Hyperref, xcolor, graphicx and possibly others have a flag "pdftex"
% that needs to be used if pdflatex is being used. The following puts
% these inside a conditional for that situation.
\ifpdf
% Case: using pdflatex
\RequirePackage[pdftex]{graphicx}
% Options get even more complicated. If we're producing grayscale output,
% we don't want to bother with coloring links, but we still want to load
% hyperref so that its macros are defined (and we don't have to redefine
% everything that uses hyperref). So:
\ifgrayscalespec
\RequirePackage[pdftex,breaklinks=true,colorlinks=false,
bookmarksnumbered=true]{hyperref}
\else
\RequirePackage[pdftex,breaklinks=true,colorlinks=true,
pdfhighlight=/O,linkcolor={sbmlblue},citecolor={sbmlblue},
urlcolor={sbmlblue},anchorcolor={sbmlblue},bookmarksnumbered]{hyperref}
\fi
% Although it may seem like we wouldn't need to load xcolor if
% the grayscale option is given, in fact it doesn't affect anything
% to load this and it avoids having to conditionalize other things.
% (The colors aren't actually invoked if grayscale is being used.)
\RequirePackage[pdftex,rgb,dvipsnames,svgnames,hyperref,table]{xcolor}
\else
% Case: not using pdflatex
\RequirePackage{graphicx}
% Test whether we're being run from latex or latex2html
% \latexhtml{
% For latex.
\RequirePackage[breaklinks]{hyperref}
% }{
% For latex2html.
% \RequirePackage[latex2html,breaklinks]{hyperref}
% }
\RequirePackage[rgb,dvipsnames,svgnames,hyperref,table]{xcolor}
\fi
% Load listings package & set some values.
\RequirePackage{listings}
\lstloadlanguages{bash,csh,XML}
% Load draftwatermark if this document is a draft version.
\if@draftspec
\RequirePackage[firstpage]{draftwatermark}
\SetWatermarkLightness{0.92}
\fi
\RequirePackage{overpic}
% We don't need the rotating package in this file, but there is a strange
% interaction between the rotating package and something else in sbmlpkgclass
% (I don't know what). The effect of the interaction is that sidewaystable
% environment contents are shifted left on the page (or from the perspective
% of the rotated table, shiftted up). The solution is to set \rotFPtop, but
% asking users of sbmlpkgclass to know that they have to do this is too much
% to ask. So, to avoid people experiencing the problem and wasting time
% trying to figure out what's causing it, I decided it's better to preload
% rotating. The problem was first reported to me by Maciej Swat in Aug. 2013
% and I found the solution at http://tex.stackexchange.com/a/47879/8318
\RequirePackage{rotating}
\setlength{\rotFPtop}{0pt plus 1fil}
%% ----------------------------------------------------------------------------
%% Font selection.
%% ----------------------------------------------------------------------------
% This sets up Helvetica for headings and TX Typewriter for the tt font.
% The font scaling is because the default Helvetica size is too big.
\RequirePackage{fourier}
\RequirePackage{helvet}
\ifgrayscalespec
% In the grayscale version of the spec, Helvetica bold is used for class
% names in the text, and the width of the words then is too big unless
% we scale down the font even more compared to the regular case below.
\def\Hv@scale{0.814}
\else
\def\Hv@scale{0.87}
\fi
% The following sets up txtt for the typewriter font.
\renewcommand{\ttdefault}{txtt}
\DeclareMathAlphabet{\mathtt}{T1}{txtt}{m}{n}
\SetMathAlphabet{\mathtt}{bold}{T1}{txtt}{b}{n}
% The next bit is an adaption of code from ot1phv.fd and adapted to the txtt
% fonts. The txtt fonts are just a tad too big, so this tries to rescale
% them down a tiny bit. This isn't completely right because I couldn't
% figure out the right syntax when the DeclareFontShape uses ssub below.
% (Notice how the ones with ssub don't have the \Txtt@@scale factor.)
\def\Txtt@scale{0.97}
\edef\Txtt@@scale{s*[\csname Txtt@scale\endcsname]}%
\DeclareFontFamily{T1}{txtt}{\hyphenchar \font\m@ne}
\DeclareFontShape{T1}{txtt}{m}{n}{ %rebular
<-> \Txtt@@scale txtt%
}{}
\DeclareFontShape{T1}{txtt}{m}{sc}{ %cap & small cap
<-> \Txtt@@scale txttsc%
}{}
\DeclareFontShape{T1}{txtt}{m}{sl}{ %slanted
<-> \Txtt@@scale txttsl%
}{}
\DeclareFontShape{T1}{txtt}{m}{it}{ %italic
<-> ssub * txtt/m/sl%
}{}
\DeclareFontShape{T1}{txtt}{m}{ui}{ %unslanted italic
<-> ssub * txtt/m/sl%
}{}
\DeclareFontShape{T1}{txtt}{b}{n}{ %bold
<-> \Txtt@@scale txbtt%
}{}
\DeclareFontShape{T1}{txtt}{b}{sc}{ %bold cap & small cap
<-> \Txtt@@scale txbttsc%
}{}
\DeclareFontShape{T1}{txtt}{b}{sl}{ %bold slanted
<-> \Txtt@@scale txbttsl%
}{}
\DeclareFontShape{T1}{txtt}{b}{it}{ %bold italic
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{b}{ui}{ %bold unslanted italic
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{bx}{n}{ %bold extended
<-> ssub * txtt/b/n%
}{}
\DeclareFontShape{T1}{txtt}{bx}{sc}{ %bold extended cap & small cap
<-> ssub * txtt/b/sc%
}{}
\DeclareFontShape{T1}{txtt}{bx}{sl}{ %bold extended slanted
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{bx}{it}{ %bold extended italic
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{bx}{ui}{ %bold extended unslanted italic
<-> ssub * txtt/b/sl%
}{}
% Adjustments due to quirks of the combination of fourier and amsmath:
% Make the \big( braces regular height (default is too short):
\delimiterfactor=1000
\delimitershortfall=1pt
%% ----------------------------------------------------------------------------
%% Main code.
%% ----------------------------------------------------------------------------
% Local color definitions.
\definecolor{sbmlblue}{rgb}{0.07,0.50,0.78}
\definecolor{sbmlgray}{gray}{0.7}
\definecolor{sbmlrowgray}{gray}{0.96}
\definecolor{extremelylightgray}{gray}{0.97}
\definecolor{veryverylightgray}{gray}{0.95}
\definecolor{verylightgray}{gray}{0.9}
\definecolor{lightgray}{gray}{0.8}
\definecolor{mediumgray}{gray}{0.5}
\definecolor{darkgray}{gray}{0.3}
\definecolor{almostblack}{gray}{0.23}
\definecolor{lightyellow}{rgb}{0.98,0.94,0.7}
\definecolor{verylightyellow}{rgb}{0.97,0.95,0.85}
\definecolor{darkblue}{rgb}{0.1,0.4,0.55}
\definecolor{mediumgreen}{rgb}{0.1,0.6,0.3}
\definecolor{sbmlnormaltextcolor}{gray}{0.27}
\definecolor{sbmlliteralcolor}{gray}{0}
\definecolor{sbmllinenumbercolor}{gray}{0.75}
\definecolor{sbmlchangedcolor}{rgb}{0.69,0.19,0.376}
% Macros and settings for making consistent font, color, and other
% selections.
%
% If we're outputting grayscale, we don't use the red changed color because
% the result on most printers is text that a hard-to-read light gray color.
\ifgrayscalespec
\colorlet{@sbmlchangedcolor}{sbmlnormaltextcolor}
\else
\colorlet{@sbmlchangedcolor}{sbmlchangedcolor}
\fi
\colorlet{@sectionnumcolor}{sbmlnormaltextcolor}
\colorlet{@literalcolor}{sbmlliteralcolor}
\newcommand{\changed}[1]{%
\protect\colorlet{@currentliteralcolor}{@literalcolor}%
\protect\colorlet{@currentsectionnumcolor}{@sectionnumcolor}%
\protect\colorlet{@literalcolor}{sbmlchangedcolor}%
\protect\colorlet{@sectionnumcolor}{sbmlchangedcolor}%
\textcolor{sbmlchangedcolor}{#1}%
\protect\colorlet{@literalcolor}{@currentliteralcolor}%
\protect\colorlet{@sectionnumcolor}{@currentsectionnumcolor}}
\newenvironment{blockChanged}{%
\colorlet{@currentliteralcolor}{@literalcolor}%
\colorlet{@currentsectionnumcolor}{@sectionnumcolor}%
\colorlet{@literalcolor}{sbmlchangedcolor}%
\colorlet{@sectionnumcolor}{sbmlchangedcolor}%
\color{sbmlchangedcolor}%
}{%
\color{sbmlnormaltextcolor}%
\colorlet{@literalcolor}{@currentliteralcolor}%
\colorlet{@sectionnumcolor}{@currentsectionnumcolor}}
\newcommand{\figureFont}[1]{\textsf{\textbf{#1}}}
\newcommand{\literalFont}[1]{\textcolor{@literalcolor}{\textup{\ttfamily{#1}}}}
\newcommand{\literalFontNC}[1]{\textup{\ttfamily{#1}}}
\newcommand{\tightspacing}{\renewcommand{\baselinestretch}{0.85}}
\newcommand{\regularspacing}{\renewcommand{\baselinestretch}{\normalbaselinestretch}}
\ifgrayscalespec
\newcommand{\defRef}[2]{\textbf{\class{#1}}\xspace}
\newcommand{\absDefRef}[2]{\textbf{\abstractclass{#1}}\xspace}
\else
\newcommand{\defRef}[2]{\class{\hyperref[#2]{#1}}\xspace}
\newcommand{\absDefRef}[2]{\abstractclass{\hyperref[#2]{#1}}\xspace}
\newcommand{\absDefRefUpright}[2]{\abstractclassUpright{\hyperref[#2]{#1}}\xspace}
\fi
\renewcommand{\texttt}[1]{\textcolor{@literalcolor}{\ttfamily #1}}
% Hyperref extras.
\newcommand{\link}[2]{\literalFontNC{\href{#1}{#2}}}
\newcommand{\mailto}[1]{\link{mailto:#1}{#1}}
% 'lineno' package adjustments.
% The BeginAccSupp business causes the line numbers to be ignored for
% copy-paste operations in the PDF output, at least in Acrobat.
\setlength{\linenumbersep}{2.2em}
\renewcommand{\linenumberfont}{\tiny\sffamily}
\renewcommand{\thelinenumber}{%
\BeginAccSupp{ActualText={}}%
\textcolor{sbmllinenumbercolor}{\parbox[b][\height+1.5pt][c]{10pt}{\arabic{linenumber}}}%
\EndAccSupp{}%
}
% 'booktabs' package adjustments:
\setlength{\cmidrulewidth}{0.3 pt}
\setlength{\lightrulewidth}{0.3 pt}
\setlength{\heavyrulewidth}{0.9 pt}
% Fix placement of figures & tables. This keeps latex from shoving big
% floats to the end of a document when they are somewhat big, which it will
% do even if you put [htb] as the argument.
\setcounter{topnumber}{2} % max num of floats at top of page
\setcounter{bottomnumber}{2} % max num of floats at bottom of page
\renewcommand\topfraction{1.0} % fraction that a top float can cover
\renewcommand\bottomfraction{1.0} % fraction a bottom float can cover
\renewcommand\textfraction{0.0} % >5% of a non-float page must be text
\renewcommand\floatpagefraction{0.9} % float page must be 95% full
% Spacing of floats.
\setlength{\intextsep}{20pt plus 4pt minus 0pt}
% Make floats that appear alone on a page appear at the top, rather than
% (as is the LaTeX default) appearing centered vertically on the page.
\setlength{\@fptop}{5pt}
% Margin adjustments. I've tried using vmargin.sty, but it interacts badly
% with page numbers at the bottom of the page, so I've resorted to hardcoding
% the dimensions like this.
\setlength{\marginparwidth}{0.77in}
\setlength{\marginparsep}{4pt}
\setlength{\oddsidemargin}{0 pt}
\setlength{\evensidemargin}{0 pt}
\setlength{\topmargin}{-0.5 in}
\setlength{\voffset}{0 in}
\setlength{\hoffset}{0 in}
\setlength{\textwidth}{6.5 in}
\setlength{\textheight}{8.95 in}
% Playing games with line spacing.
\newcommand{\normalbaselinestretch}{1.04}
\renewcommand{\baselinestretch}{\normalbaselinestretch}
% Set the table of contents depth
\setcounter{tocdepth}{3}
% Title page macros. Severly hacked from originals in LaTeX's article.cls.
\def\packageTitle#1{\title{#1}\gdef\@packageTitle{#1}}
\def\@packageTitle{\@empty}
\def\packageGeneralURL#1{\gdef\@packageGeneralURL{#1}}
\def\packageThisVersionURL#1{\gdef\@packageThisVersionURL{#1}}
\def\@packageThisVersionURL{\@empty}
\def\packageVersion#1{\gdef\@packageVersion{#1}}
\def\@packageVersion{\@empty}
\def\packageVersionDate#1{\gdef\@packageVersionDate{#1}}
\def\@packageVersionDate{\@empty}
\def\frontNotice#1{\gdef\@frontNotice{#1}}
\def\@puttitle{%
\ifx\@packageGeneralURL\undefined
\relax
\else
\vspace*{-1em}
{\large SBGNML Version 0.3 Specification}\\[2em]
\fi
\scalebox{1}[0.9]{%
\fcolorbox{black}{mediumgray}{%
\begin{minipage}{\textwidth - 7pt}%
\vspace*{6pt}%
\centering%
\textcolor{white}{\sffamily\bfseries\huge \ifx\@title\@empty\@packageTitle\else\@title\fi}
\vspace*{4pt}%
\end{minipage}}}}
\def\@putauthorinfo{%
\large
\renewcommand{\arraystretch}{0.95}%
{\begin{tabular}[t]{c}%
\@author
\end{tabular}}}
\def\maketableofcontents{%
\thispagestyle{plain}%
\if@notoc
\else
\begingroup
\small%
% Tighten spacing between lines within an entry.
% This assumes 10 pt font!
\setlength{\baselineskip}{10pt}%
% Now adjust inter-entry spacing.
\addtolength{\parskip}{-1.35 ex}%
\if@twocolumntoc
\setlength{\columnsep}{16pt}%
\begin{multicols}{2}
\fi
\tableofcontents%
\if@twocolumntoc
\end{multicols}
\fi
\normalsize%
\addtolength{\parskip}{1.45 ex}%
\endgroup
\clearpage
\fi%
\linenumbers}
% Need redefine \tableofcontents to counter effects of hacking \section below.
\renewcommand\tableofcontents{%
\@startsection{section}{0}{0pt}{-1.8ex \@plus -1ex \@minus -.2ex}%
{0.8ex}{\normalfont\Large\bfseries\sffamily}*% The star fakes a \section*
\contentsname%
\@mkboth{\MakeUppercase\contentsname}{\MakeUppercase\contentsname}%
\@starttoc{toc}%
}
\renewcommand\maketitle{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 1em\noindent
\hb@[email protected]{%
\hss\@textsuperscript{\normalfont\@thefnmark}}##1}%
\if@twocolumn
\ifnum \col@number=\@ne
\@maketitle
\else
\twocolumn[\@maketitle]%
\fi
\else
\global\@topnum\z@ % Prevents figures from going at top of page.
\@maketitle
\fi
\thispagestyle{empty}\@thanks
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@authoremail\@empty
\global\let\title\relax
\global\let\author\relax
\global\let\date\relax
\global\let\and\relax
}
\newcommand\maketitlepage{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 1em\noindent
\hb@[email protected]{%
\hss\@textsuperscript{\normalfont\@thefnmark}}##1}%
\vskip 2em%
\if@twocolumn
\ifnum \col@number=\@ne
\@maketitle
\else
\twocolumn[\@maketitle]%
\fi
\else
\newpage
\global\@topnum\z@ % Prevents figures from going at top of page.
\@maketitle
\fi
\thispagestyle{empty}\@thanks
\vfill
\centering%
\ifx\@frontNotice\undefined
\relax
\else
{\cornersize{0.25}\color{DarkRed}\ovalbox{\begin{varwidth}{0.9\textwidth}\centering\@frontNotice\end{varwidth}}}%
\fi
\vfill
\ifx\@packageGeneralURL\undefined
\relax
\else
The latest release, past releases, and other materials related to this specification are available at\\
{\small\url{\@packageGeneralURL}}\\[1em]
\emph{This} release of the specification is available at\\
{\small\url{\@packageThisVersionURL}}\\
\vspace*{2em}
\fi
\vfill
\centerline{\includegraphics[width=1in]{\SBGNbadge}}
\clearpage
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@authoremail\@empty
\global\let\title\relax
\global\let\author\relax
\global\let\date\relax
\global\let\and\relax
}
\def\@maketitle{%
\newpage
\null
\begin{center}%
\let \footnote \thanks
\@puttitle
\vskip 1.8em%
{\lineskip .5em%
\@putauthorinfo
}%
\vskip 2em%
{\large\fbox{\@packageVersion}}%
\vskip 1.5em%
{\large\@packageVersionDate}%
\end{center}%
\par%
\vskip 1.5em%
\ifpdf
\hypersetup{pdftitle={\@title}}
\fi%
}
% Including the logo on the front page. We switch which copy of the logo
% file we use, depending on various factors, and we switch which file format
% is used depending on the output we're producing.
\ifgrayscalespec
\newcommand{\@badgebasefile}{sbml-badge-gray}
\else
\newcommand{\@badgebasefile}{sbgn-badge}
\fi
\ifpdf
% Request the JPG format specifically, because the resulting
% quality in the final output is best.
\newcommand{\SBGNbadge}{\@badgebasefile.jpg}%
\else%
\newcommand{\SBGNbadge}{\@badgebasefile.eps}%
\fi
% Graphics adjustments. The path setup is so that the \includegraphics
% in the @puttile definition can find the logo file no matter where the
% document is located (but obviously, it only works for certain path
% combinations -- it's a total hack).
\graphicspath{{./logos/}
{../tex/logos/}
{../project/tex/logos/}
{../../project/tex/logos/}
{../../../project/tex/logos/}
{../../../../project/tex/logos/}}
% Set the page footers.
% Must do this after setting the document title.
\fancyhf{}
\newcommand{\@footchpsection}{\sectionlabel~\nouppercase{\leftmark}}
\newcommand{\@footpage}{Page \thepage\ of \pageref*{LastPage}}
\renewcommand{\footrule}{}
\fancypagestyle{headerandfooter}{%
\renewcommand{\headrulewidth}{0.25pt}
\renewcommand{\headrule}{}
\lhead{}%
\rhead{\color{mediumgray}\small\textsf{\sectionlabel~\nouppercase{\rightmark}}}%
\cfoot{}%
\lfoot{\color{mediumgray}\small\textsf{\@footchpsection}}%
\rfoot{\color{mediumgray}\small\textsf{\@footpage}}%
}
\fancypagestyle{footeronly}{%
\renewcommand{\headrule}{}%
\lhead{}%
\rhead{}%
\lfoot{\color{mediumgray}\small\textsf{\@footchpsection}}%
\rfoot{\color{mediumgray}\small\textsf{\@footpage}}%
}
\fancypagestyle{plain}{%
\renewcommand{\headrule}{}%
\lhead{}%
\rhead{}%
\lfoot{}%
\rfoot{\color{mediumgray}\small\textsf{\@footpage}}%
}
\pagestyle{headerandfooter}
% Definition of paragraph style.
\setlength{\parindent}{0 pt} % Unindented paragraphs, separated ...
\setlength{\parskip}{1.3 ex} % ... by roughly one blank line.
\setlength{\partopsep}{-1ex plus 0.1ex minus -0.2ex}
\setlength{\itemsep}{-0.25ex plus 0.15ex}
% \topsep is supposed to affect list environments like itemize,
% but does nothing there. Instead, it affects environments like tabular.
\setlength{\topsep}{0.3ex plus 0.1ex minus -0.2ex}
\renewcommand{\labelitemi}{\raisebox{0.5pt}{\color{mediumgray}\footnotesize{$\blacksquare$}}}
\renewcommand{\labelitemii}{\raisebox{-1.5pt}{\color{mediumgray}\LARGE$\bullet$}}
\renewcommand{\labelitemiii}{\color{mediumgray}\tiny\DiamondSolid}
\renewcommand{\labelitemiv}{$\diamond$}
% Definition of section heading style.
% The "changed" versions put the numbers in red, to indicate a change
% in section numbers.
\renewcommand\@seccntformat[1]{%
\color{@sectionnumcolor}{\csname the#1\endcsname}\hspace{0.5em}}
\renewcommand{\section}{\@startsection%
{section}{1}{0pt \@plus 1ex}{-3.5ex \@plus -2ex \@minus -.2ex}%
{1.2ex}{\clearpage\thispagestyle{footeronly}%
\hspace*{-24.25pt}\color{sbmlgray}{\rule[1.8em]{6.84in}{0.6em}}\color{sbmlnormaltextcolor}%
\hspace*{-6.84in}\color{sbmlgray}{\rule[-0.8em]{6.84in}{0.1em}}\color{sbmlnormaltextcolor}%
\noindent\normalfont\LARGE\bfseries\sffamily\hspace*{-6.84in}}}
\newcommand{\sectionChanged}[1]{%
\colorlet{@currentsectionnumcolor}{@sectionnumcolor}%
\colorlet{@sectionnumcolor}{sbmlchangedcolor}%
\section{#1}%
\colorlet{@sectionnumcolor}{@currentsectionnumcolor}}
\renewcommand{\subsection}{\@startsection%
{subsection}{2}{0pt}{-1.25ex \@plus 2ex \@minus -.2ex}%
{0.1ex}{\Large\bfseries\sffamily}}
\newcommand{\subsectionChanged}[1]{%
\colorlet{@sectionnumcolor}{sbmlchangedcolor}%
\subsection{#1}%
\colorlet{@sectionnumcolor}{@currentsectionnumcolor}}
\renewcommand{\subsubsection}{\@startsection%
{subsubsection}{3}{0pt}{-1ex \@plus 2ex \@minus -.2ex}%
{0.4ex}{\large\bfseries\sffamily\slshape}}
\newcommand{\subsubsectionChanged}[1]{%
\colorlet{@sectionnumcolor}{sbmlchangedcolor}%
\subsubsection{#1}%
\colorlet{@sectionnumcolor}{@currentsectionnumcolor}}
\renewcommand{\paragraph}{\@startsection%
{paragraph}{4}{0pt}{-0.75ex \@plus 2ex \@minus -.2ex}%
{0.4ex}{\normalsize\bfseries\sffamily\slshape}}
\newcommand{\paragraphChanged}[1]{%
\colorlet{@sectionnumcolor}{sbmlchangedcolor}%
\paragraph{#1}%
\colorlet{@sectionnumcolor}{@currentsectionnumcolor}}
% The References heading needs to be fixed up to account for shift
% we apply to section headings. These defs are modified from article.cls.
\bibliographystyle{apalike}
\renewenvironment{thebibliography}[1]%
{\section*{References}%
\pagestyle{plain}%
\addcontentsline{toc}{section}{\protect\numberline{\refname}}%
\list{\@biblabel{\@arabic\c@enumiv}}%
{\settowidth\labelwidth{\@biblabel{#1}}%
\leftmargin\labelwidth
\advance\leftmargin\labelsep
\@openbib@code
\usecounter{enumiv}%
\let\p@enumiv\@empty
\renewcommand\theenumiv{\@arabic\c@enumiv}}%
\sloppy
\clubpenalty4000
\@clubpenalty \clubpenalty
\widowpenalty4000%
\sfcode`\.\@m}
{\def\@noitemerr
{\@latex@warning{Empty `thebibliography' environment}}%
\endlist}
\newcommand{\sectionspecial}{\@startsection%
{section}{1}{0pt}{-1.8ex \@plus -1ex \@minus -.2ex}%
{0.8ex}{\hspace*{-41.1pt}\colorbox{sbmlgray}{\hspace*{6.99in}}\nopagebreak\\%
\hspace*{-20pt}\normalfont\Large\bfseries\sffamily}}
% The following is a modified version of the macro from article.cls.
% It adjusts the vertical spacing in TOC for section lines.
\renewcommand*\l@section[2]{%
\ifnum \c@tocdepth >\z@
\addpenalty\@secpenalty
\addvspace{0.2ex \@plus\p@}%
\setlength\@tempdima{1.5em}%
\begingroup
\parindent \z@ \rightskip \@pnumwidth
\parfillskip -\@pnumwidth
\leavevmode \bfseries\sffamily
\advance\leftskip\@tempdima
\hskip -\leftskip
#1\nobreak\hfil \nobreak\hb@xt@\@pnumwidth{\hss #2}\par
\endgroup
\fi}
\def\@dottedtocline#1#2#3#4#5{%
\ifnum #1>\c@tocdepth \else
\vskip \z@ \@plus.2\p@
{\if@twocolumntoc\else
\leftskip #2
\fi
\relax \rightskip \@tocrmarg \parfillskip -\rightskip
\if@twocolumntoc\else
\parindent #2
\fi
\relax\@afterindenttrue
\interlinepenalty\@M
\leavevmode
\@tempdima #3\relax
\advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
{\sffamily #4}\nobreak
{\color{mediumgray}
\leaders\hbox{$\m@th
\mkern \@dotsep mu\hbox{.}\mkern \@dotsep
mu$}\hfill
}\nobreak
\hb@xt@\@pnumwidth{\hfil\normalfont\sffamily #5}%
\par}%
\fi}
% The following is modified from natbib.sty, version 1999/05/28 7.0.
% This ensures that the References section gets a TOC entry.
\renewcommand{\bibsection}{%
\addcontentsline{toc}{section}{\protect\textbf{\textsf{\refname}}}%
\section*{\refname}}
% Redefine table & figure to use smaller font, sans serif,
% and to center contents by default.
\renewenvironment{table}[1][] {\@float{table}[#1]\small\sffamily\centering} {\end@float}
\renewenvironment{table*}[1][] {\@dblfloat{table}[#1]\small\sffamily\centering} {\end@dblfloat}
\renewenvironment{figure}[1][] {\@float{figure}[#1]\small\sffamily\centering} {\end@float}
\renewenvironment{figure*}[1][]{\@dblfloat{figure}[#1]\small\sffamily\centering}{\end@dblfloat}
% The following was ripped out of caption.sty, version 1.4b.
% Copyright (C) 1994-95 Harald Axel Sommerfeldt
% The first few lines set up the parameters for the layout created
% by this style file.
\newcommand{\captionsize}{\small}
\newcommand{\captionfont}{\captionsize\sffamily\slshape}
\newcommand{\captionlabelfont}{\captionsize\bfseries\slshape}
\setlength{\abovecaptionskip}{1em}
\newlength{\captionmargin}
\setlength{\captionmargin}{6ex}
\newsavebox{\as@captionbox}
\newlength{\as@captionwidth}
\newcommand{\as@normalcaption}[2]{%
#1 #2\par}
\let\as@caption\as@normalcaption
\newcommand{\as@centercaption}[2]{%
\parbox[t]{\as@captionwidth}{{\centering#1 #2\par}}}
\let\as@shortcaption\as@centercaption
\newcommand{\as@makecaption}[2]{%
\setlength{\leftskip}{\captionmargin}%
\setlength{\rightskip}{\captionmargin}%
\addtolength{\as@captionwidth}{-2\captionmargin}%
\renewcommand{\baselinestretch}{0.9}
\captionfont%
\sbox{\as@captionbox}{{\captionlabelfont #1:} #2}%
\ifdim \wd\as@captionbox >\as@captionwidth
\as@caption{{\captionlabelfont #1:}}{#2}%
\else%
\as@shortcaption{{\captionlabelfont #1:}}{#2}%
\fi}
\renewcommand{\@makecaption}[2]{%
\vskip\abovecaptionskip%
\setlength{\as@captionwidth}{\linewidth}%
\as@makecaption{#1}{#2}%
\vskip\belowcaptionskip}
\ifx\@makerotcaption\undefined
\else
% Adjustment for the "rotating" package.
\renewcommand{\@makerotcaption}[2]{%
\renewcommand{\baselinestretch}{0.9}
\captionfont%
\sbox{\as@captionbox}{{\captionlabelfont #1:} #2}%
\ifdim \wd\as@captionbox > .8\vsize
\rotatebox{90}{%
\setlength{\as@captionwidth}{.8\textheight}%
\begin{minipage}{\as@captionwidth}%
\as@caption{{\captionlabelfont #1:}}{#2}%
\end{minipage}}\par
\else%
\rotatebox{90}{\usebox{\as@captionbox}}%
\fi
\hspace{12pt}}
\fi
\ifx\floatc@plain\undefined
\else
\typeout{\space\space\space\space\space\space\space\space\space
`float' package detected}
\renewcommand\floatc@plain[2]{%
\setlength{\as@captionwidth}{\linewidth}%
\as@makecaption{#1}{#2}}
\ifx\as@ruled\undefined
\else
\renewcommand\floatc@ruled[2]{%
\setlength{\as@captionwidth}{\linewidth}%
\renewcommand{\baselinestretch}{0.9}
\captionfont%
\as@caption{{\captionlabelfont #1:}}{#2}}
\fi
\fi
%
% Additional new commands.
%
% Class and data type formatting macros.
\newcommand{\class}[1]{\figureFont{#1}} % only SBGN UML classes
\newcommand{\abstractclass}[1]{\textsl{\figureFont{#1}}} % abstract classes
\newcommand{\primtype}[1]{\literalFont{#1}} % double, SId, SBOTerm, etc.
\newcommand{\primtypeNC}[1]{\literalFontNC{#1}} % same, but without coloring
\newcommand{\token}[1]{\literalFont{#1}} % everything else
\newcommand{\tokenNC}[1]{\literalFontNC{#1}} % everything else, no color
\newcommand{\val}[1]{``\token{#1}''} % a value in XML
\newcommand{\uri}[1]{``\token{#1}''}
% Macros used for defining validation rules.
% First, preliminary internal macros.
\newcommand{\vSymbol}{\textcolor{red}{$\Box\mkern-14mu\checkmark$}}
\newcommand{\vSymbolName}{checked box\xspace}
\newcommand{\cSymbol}{\textcolor{Goldenrod}{\scalefont{0.9}\ding{115}}}
\newcommand{\cSymbolName}{triangle\xspace}
\newcommand{\mSymbol}{\textcolor{Green}{$\bigstar$}}
\newcommand{\mSymbolName}{star\xspace}
% Spacing adjustments when using the symbols inside regular 'description' env.
% Note: *not* used in \sbmlrule below.
\newcommand{\vsp}{\hspace*{4pt}}
\newcommand{\csp}{\hspace*{6.25pt}}
\newcommand{\msp}{\hspace*{4.9pt}}
% Now the actual user commands for validation rules.
\newcommand{\sbmlrule}[3]{\begin{enumerate}[labelwidth=8em,leftmargin=10em,align=left]
\item[\textbf{\textsf{#1}}~~#2] #3
\end{enumerate}}
\newcommand{\validRule}[2] {\sbmlrule{#1}{\vSymbol}{#2}}
\newcommand{\consistencyRule}[2]{\sbmlrule{#1}{\cSymbol}{#2}}
\newcommand{\modelingRule}[2] {\sbmlrule{#1}{\mSymbol}{#2}}
% Code examples.
\newcommand{\code}[1]{\literalFont{#1}}
\newcommand{\codeNC}[1]{\literalFontNC{#1}}
\lstset{escapechar=|,%
language=XML,%
columns=fullflexible,%
keepspaces=true,%
backgroundcolor=\color{veryverylightgray},%
rulecolor=\color{sbmlgray},%
frame=single,%
numberstyle=\tiny\sffamily,%
basicstyle=\small\ttfamily\color{black},%
keywordstyle=\ttfamily,%
xleftmargin=3.5pt,%
xrightmargin=3.5pt,%
aboveskip=1\baselineskip,%
belowskip=0.4\baselineskip,%
commentstyle=\footnotesize\itshape\color{mediumgray},%
tabsize=2,%
showstringspaces=false,%
captionpos=b}
\lstdefinestyle{XML}{%
language=XML}
\lstdefinestyle{bash}{%
language=bash}%
\newcommand{\examplespacing}{\renewcommand{\baselinestretch}{0.88}}
\lstnewenvironment{example}[1][]
{\lstset{#1}\examplespacing \csname lst@SetFirstLabel\endcsname}
{\regularspacing \csname lst@SaveFirstLabel\endcsname}
\newcommand{\exampleFile}[2][style=XML]{%
\lstset{#1}\examplespacing\lstinputlisting{#2}\regularspacing}
% Margin note commands.
% The \reversemarginpar is to put notes in the left margin.
\reversemarginpar % Want these be put on the left, not the right.
\newcommand{\notice}{\marginpar{\hspace*{34pt}\raisebox{-0.5ex}{\color{black}\Large\ding{43}}}}