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bioinfo.cls
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bioinfo.cls
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\newcommand\classname{bioinfo}
\newcommand\lastmodifieddate{2003/02/08}
\newcommand\versionnumber{0.1}
% Are we printing crop marks?
\newif\if@cropmarkson \@cropmarksontrue
\NeedsTeXFormat{LaTeX2e}[2001/06/01]
\ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
\setlength{\paperheight}{11truein}
\setlength{\paperwidth}{8.5truein}
\newif\if@final
\DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}}
\DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}}
\DeclareOption{centre}{\PassOptionsToPackage{center}{crop}}
\DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue}
\DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse}
\DeclareOption{info}{\PassOptionsToPackage{info}{crop}}
\DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}}
\DeclareOption{final}{\global\@finaltrue}
\ExecuteOptions{a4paper,nocrop,centre,info}
\ProcessOptions
% Load all necessary packages
\RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times}
%\RequirePackage[LY1]{fontenc}
%\RequirePackage[LY1,mtbold]{mathtime}
\def\helvetica{\fontfamily{phv}\selectfont}
\def\helveticaitalic{\fontfamily{phv}\itshape\selectfont}
\def\helveticabold{\fontfamily{phv}\bfseries\selectfont}
\def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont}
% Not sure if needed.
\newcommand\@ptsize{0}
% Set twoside printing
\@twosidetrue
% Marginal notes are on the outside edge
\@mparswitchfalse
\reversemarginpar
\renewcommand\normalsize{%
\@setfontsize\normalsize{9}{11}%
\abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
\abovedisplayshortskip \z@ \@plus3\p@
\belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
\belowdisplayskip \abovedisplayskip
\let\@listi\@listI}
\normalsize
\let\@bls\baselineskip
\newcommand\small{%
\@setfontsize\small{9}{11}%
\abovedisplayskip 11\p@ minus 3\p@
\belowdisplayskip \abovedisplayskip
\abovedisplayshortskip \z@ plus 2\p@
\belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@
\def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@
\itemsep \parsep
\topsep 4\p@ plus 2\p@ minus 2\p@}}
\newcommand\footnotesize{%
\@setfontsize\footnotesize{8}{10}%
\abovedisplayskip 6\p@ minus 3\p@
\belowdisplayskip\abovedisplayskip
\abovedisplayshortskip \z@ plus 3\p@
\belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@
\def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@
\parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}}
\def\scriptsize{\@setfontsize\scriptsize{7pt}{9pt}}
\def\tiny{\@setfontsize\tiny{5pt}{7pt}}
\def\large{\@setfontsize\large{11.5pt}{12pt}}
\def\Large{\@setfontsize\Large{14pt}{16}}
\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
\def\huge{\@setfontsize\huge{22pt}{22pt}}
\def\Huge{\@setfontsize\Huge{30pt}{30pt}}
\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
% Line spacing
\setlength\lineskip{1\p@}
\setlength\normallineskip{1\p@}
\renewcommand\baselinestretch{}
% Paragraph dimensions and inter-para spacing
\setlength\parskip{0\p@}
\setlength\parindent{3mm}
% Set inter-para skips
\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
\setlength\medskipamount{6\p@ \@plus 2\p@}
\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
% Page break penalties
\@lowpenalty 51
\@medpenalty 151
\@highpenalty 301
% Disallow widows and orphans
\clubpenalty 10000
\widowpenalty 10000
% Disable page breaks before equations, allow pagebreaks after
% equations and discourage widow lines before equations.
\displaywidowpenalty 100
\predisplaypenalty 10000
\postdisplaypenalty 2500
% Allow breaking the page in the middle of a paragraph
\interlinepenalty 0
% Disallow breaking the page after a hyphenated line
\brokenpenalty 10000
% Hyphenation; don't split words into less than three characters
\lefthyphenmin=3
\righthyphenmin=3
%
% Set page layout dimensions
%
\setlength\headheight{16\p@} % height of running head
\setlength\topmargin{2.9pc} % head margin
\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin
\setlength\topskip{10\p@} % height of first line of text
\setlength\headsep{19\p@} % space below running head --
\setlength\footskip{34\p@} % space above footer line
\setlength\maxdepth{.5\topskip} % pages can be short or deep by half a line?
\setlength\textwidth{42pc} % text measure excluding margins
\setlength\textheight{58\baselineskip} % 54 lines on a full page,
\addtolength\textheight{\topskip} % including the first
% line on the page
% Set the margins
\setlength\marginparsep{3\p@}
\setlength\marginparpush{3\p@}
\setlength\marginparwidth{35\p@}
\setlength\oddsidemargin{4.5pc}
\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
\setlength\@tempdima{\paperwidth}
\addtolength\@tempdima{-\textwidth}
\addtolength\@tempdima{-4.5pc}
\setlength\evensidemargin{\@tempdima}
\addtolength\evensidemargin{-1in}
\setlength\columnsep{1.5pc} % space between columns for double-column text
\setlength\columnseprule{0\p@} % width of rule between two columns
% Footnotes
\setlength\footnotesep{9\p@} % space between footnotes
% space between text and footnote
\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
% Float placement parameters
% The total number of floats that can be allowed on a page.
\setcounter{totalnumber}{10}
% The maximum number of floats at the top and bottom of a page.
\setcounter{topnumber}{5}
\setcounter{bottomnumber}{5}
% The maximum part of the top or bottom of a text page that can be
% occupied by floats. This is set so that at least four lines of text
% fit on the page.
\renewcommand\topfraction{.9}
\renewcommand\bottomfraction{.9}
% The minimum amount of a text page that must be occupied by text.
% This should accomodate four lines of text.
\renewcommand\textfraction{.06}
% The minimum amount of a float page that must be occupied by floats.
\renewcommand\floatpagefraction{.94}
% The same parameters repeated for double column output
\renewcommand\dbltopfraction{.9}
\renewcommand\dblfloatpagefraction{.9}
% Space between floats
\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
% Space between floats and text
\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space above and below an inline figure
\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
% For double column floats
\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
% Space left at top, bottom and inbetween floats on a float page.
\setlength\@fptop{0\p@} % no space above float page figures
\setlength\@fpsep{12\p@ \@plus 1fil}
\setlength\@fpbot{0\p@}
% The same for double column
\setlength\@dblfptop{0\p@}
\setlength\@dblfpsep{12\p@ \@plus 1fil}
\setlength\@dblfpbot{0\p@}
% Override settings in mathtime back to TeX defaults
\DeclareMathSizes{5} {5} {5} {5}
\DeclareMathSizes{6} {6} {5} {5}
\DeclareMathSizes{7} {7} {5} {5}
\DeclareMathSizes{8} {8} {6} {5}
\DeclareMathSizes{9} {9} {6.5} {5}
\DeclareMathSizes{10} {10} {7.5} {5}
\DeclareMathSizes{12} {12} {9} {7}
% Page styles
\def\ps@headings
{%
\def\@oddfoot{\vbox to 12.5\p@{\hbox{\rule{\textwidth}{0.5\p@}}\vss
\hbox to \textwidth{\hfill\helveticabold\small\thepage}%
}}%
\def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
\hbox to \textwidth{\helveticabold\small\thepage\hfill}%
}}%
\def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{8}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont
\strut\leftmark}\hfill}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\@oddhead{\vbox{\hbox to \textwidth{\hfill\fontsize{8}{10}\selectfont
\helveticabold{\fontshape{it}\selectfont\strut\rightmark}}%
\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
\def\titlemark##1{\markboth{##1}{##1}}%
\def\authormark##1{\gdef\leftmark{##1}}%
}
\def\ps@opening
{%
\def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
\hbox to \textwidth{\helvetica
\fontsize{7}{9}\fontshape{n}\selectfont \space %
\hfill\small\helveticabold\thepage}%
}}%
\def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}{1\p@}\vss
\hbox to \textwidth{\helvetica\thepage\hfill
\fontsize{7}{9}\fontshape{n}\selectfont \space }%
}}%
\let\@evenhead\relax
\let\@oddhead\relax}
% Page range
\newif\iflastpagegiven \lastpagegivenfalse
\newcommand\firstpage[1]{%
\gdef\@firstpage{#1}%
\ifnum\@firstpage>\c@page
\setcounter{page}{#1}%
\ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
\else \ifnum\@firstpage<\c@page
\ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
\xdef\@firstpage{\the\c@page}%
}
\def\@firstpage{1}
\def\pagenumbering#1{%
\global\c@page \@ne
\gdef\thepage{\csname @#1\endcsname \c@page}%
\gdef\thefirstpage{%
\csname @#1\endcsname \@firstpage}%
\gdef\thelastpage{%
\csname @#1\endcsname \@lastpage}%
}
\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
\global\lastpagegiventrue}
\def\@lastpage{0}
\def\setlastpage{\iflastpagegiven\else
\edef\@tempa{@lastpage@}%
\expandafter
\ifx \csname \@tempa \endcsname \relax
\gdef\@lastpage{0}%
\else
\xdef\@lastpage{\@nameuse{@lastpage@}}%
\fi
\fi }
\def\writelastpage{%
\iflastpagegiven \else
\immediate\write\@auxout%
{\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
\fi
}
\def\thepagerange{%
\ifnum\@lastpage =0 {\ \bf ???} \else
\ifnum\@lastpage = \@firstpage \ \thefirstpage\else
\thefirstpage--\thelastpage \fi\fi}
\AtBeginDocument{\setlastpage
\pagenumbering{arabic}%
}
\AtEndDocument{%
\writelastpage
\if@final
\clearemptydoublepage
\else
\clearpage
\fi}
%
% Sectional units
%
% Counters
\newcounter{section}
\newcounter{subsection}[section]
\newcounter{subsubsection}[subsection]
\newcounter{paragraph}[subsubsection]
\newcounter{subparagraph}[paragraph]
\newcounter{figure}
\newcounter{table}
% Form of the numbers
\newcommand\thepage{\arabic{page}}
\renewcommand\thesection{\arabic{section}}
\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
\renewcommand\theequation{\arabic{equation}}
% Form of the words
\newcommand\contentsname{Contents}
\newcommand\listfigurename{List of Figures}
\newcommand\listtablename{List of Tables}
\newcommand\partname{Part}
\newcommand\appendixname{Appendix}
\newcommand\abstractname{Abstract}
\newcommand\refname{References}
\newcommand\bibname{References}
\newcommand\indexname{Index}
\newcommand\figurename{Fig.}
\newcommand\tablename{Table}
% Clearemptydoublepage should really clear the running heads too
\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
% Frontmatter, mainmatter and backmatter
\newif\if@mainmatter \@mainmattertrue
\newcommand\frontmatter{%
\clearpage
\@mainmatterfalse
\pagenumbering{roman}}
\newcommand\mainmatter{%
\clearpage
\@mainmattertrue
\pagenumbering{arabic}}
\newcommand\backmatter{%
\clearpage
\@mainmatterfalse}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% TITLE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newlength{\dropfromtop}
\setlength{\dropfromtop}{\z@}
% Application Notes
\newif\if@appnotes
\newcommand{\application}{%
% \setlength{\dropfromtop}{-2.25pc}%
\global\@appnotestrue}
\long\def\title{\@ifnextchar[{\short@title}{\@@title}}
\def\short@title[#1]{\titlemark{#1}\@@@title}
\def\@@title#1{\authormark{#1}\@@@title{#1}}
\long\def\@@@title#1{\gdef\@title{#1}}
\long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
\def\short@uthor[#1]{\authormark{#1}\@@author}
\def\@uthor#1{\authormark{#1}\@@author{#1}}
\long\def\@@author#1{\gdef\@author{#1}}
\def\vol#1{\global\def\@vol{#1}}
\def\issue#1{\global\def\@issue{#1}}
\def\address#1{\global\def\@issue{#1}}
\def\history#1{\global\def\@history{#1}}
\def\editor#1{\global\def\@editor{#1}}
\def\pubyear#1{\global\def\@pubyear{#1}}
\def\copyrightyear#1{\global\def\@copyrightyear{#1}}
\def\address#1{\global\def\@address{#1}}
\def\DOI#1{\global\def\@DOI{#1}}
\definecolor{gray}{cmyk}{0, 0, 0, 0.15}
\newlength{\extraspace}
\setlength{\extraspace}{\z@}
\newcommand\maketitle{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 3mm\noindent
% \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
\@textsuperscript{\normalfont\@thefnmark}##1}%
\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{opening}\@thanks
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@address\@empty
\global\let\@history\@empty
\global\let\@editor\@empty
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@pubyear\@empty
\global\let\address\relax
\global\let\history\relax
\global\let\editor\relax
\global\let\title\relax
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{\helvetica\itshape\bfseries\fontsize{19}{12}\selectfont {\color{gray}Original Research Articles}
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\if@appnotes APPLICATIONS NOTE\hfil\fi
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%% Abstract %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% ********************
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% ********************
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% From ifmtarg.sty
% Copyright Peter Wilson and Donald Arseneau, 2000
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% ******************************
% List numbering and lettering *
% ******************************
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\def\makelabel##1{\hss \llap{##1}}}%
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% Changes to the list parameters for itemize
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\partopsep \z@
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\parsep \z@
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\def\itemize{%
\@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
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\def\makelabel##1{\hss \llap{##1}}}%
\fi
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\let\enditemize\endlist
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% ***********************
% Quotes and Quotations *
% ***********************
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\setlength\labelwidth{0pt}%
\setlength\labelsep{0pt}%
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\fboxrule=1\p@
% *******************
% Table of contents *
% *******************
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\newcommand\@dotsep{1000}
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% ***********
% Footnotes *
% ***********
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% ***********
% References *
% ***********
\providecommand{\newblock}{}
\newenvironment{thebibliography}{%
\section{\bibname}%
\begingroup
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{\end{list}\endgroup}
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% **********
% Appendix *
% **********
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% Screen PDF compatability
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%%%%for smaller size text
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\def\section{%
\@startsection{section}{1}{\z@}
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{\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
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\@startsection{subsection}{2}{\z@}
{-5\p@ plus -2\p@}{4\p@}
{\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
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{-6\p@ plus -1\p@}{-1em}
{\reset@font\normalfont\normalsize\itshape}}
\footnotesize
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\hyphenation{Figure Table Figures Tables}
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