minimap2 0.0.4 → 0.2.23.1

data/ext/minimap2/tex/bioinfo.cls

@@ -0,0 +1,930 @@
+\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\authoraffliate{\fontfamily{phv}\selectfont}
+\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%
+          \hfill\small\helveticabold\thepage}%
+        }}%
+  \def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}\vss
+        \hbox to \textwidth{\helvetica\thepage\hfill
+          \fontsize{7}{9}\fontshape{n}\selectfont}%
+        }}%
+  \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
+  \global\let\author\relax
+  \global\let\date\relax
+  \global\let\pubyear\relax
+  \global\let\@copyrightline\@empty
+  \global\let\and\relax
+  \@afterindentfalse\@afterheading
+}
+
+\newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
+\setlength{\aboveskipchk}{\z@}%
+
+\def\@maketitle{%
+  \let\footnote\thanks
+  \clearemptydoublepage
+    \checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-3pc}\else\setlength{\aboveskipchk}{-5pc}\fi%for checking oddpage or evenpage top skip%%
+  \vspace*{\aboveskipchk}%
+  \vspace{\dropfromtop}%
+  \hbox to \textwidth{%
+  {\helvetica\itshape\bfseries\fontsize{19}{12}\selectfont {\color{gray}TECHNICAL REPORT}
+    \hfil
+    \if@appnotes APPLICATIONS NOTE\hfil\fi
+    }%
+\enskip  \parbox[b]{11.3pc}{%
+    \helvetica
+    \flushright\fontsize{8}{10}\fontshape{it}\selectfont
+        \hfill
+  }}
+  \rule{\textwidth}{1\p@}\par%
+  \helvetica
+  \hbox to \textwidth{%
+  \parbox[t]{41pc}{%
+    \vspace*{1sp}
+    {\helveticabold\fontsize{16}{21}\selectfont\raggedright \@title \par}%
+    \vspace{4.5\p@}
+    {\authoraffliate\fontsize{11}{13}\selectfont\raggedright \@author \par}%
+        \vspace{4\p@}
+    {\authoraffliate\fontsize{9}{11}\selectfont\raggedright \@address \par}%
+    \vspace{4\p@}
+    %{\helvetica\fontsize{8}{10}\selectfont\raggedright \@history \par}
+    %\vspace{24\p@}
+    %{\helvetica\fontsize{10}{12}\selectfont\raggedright \@editor \par}
+    %\vspace{20\p@}
+    }%
+  }
+  \vspace{4.5\p@}%
+  \rule{\textwidth}{1\p@}%
+  \vspace{12\p@ plus 6\p@ minus 6\p@}%
+  \vspace{\extraspace}
+  }
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%% Abstract %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\newcommand{\absection}[1]{%
+  \par\noindent{\bfseries #1}\space\ignorespaces}
+
+\newenvironment{abstract}{%
+  \begingroup
+  \let\section\absection
+  \fontfamily{\sfdefault}\fontsize{8}{11}\sffamily\selectfont
+  {\fontseries{b}\selectfont ABSTRACT}\par}
+{\endgroup\bigskip\@afterheading\@afterindentfalse\vskip 12pt plus 3pt minus 1pt}
+
+% Section macros
+
+% Lowest level heading that takes a number by default
+\setcounter{secnumdepth}{3}
+
+\renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
+
+\def\section{%
+  \@startsection{section}{1}{\z@}
+  {-22\p@ plus -3\p@}{3\p@}
+  {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
+
+\def\subsection{%
+  \@startsection{subsection}{2}{\z@}
+  {-11\p@ plus -2\p@}{3\p@}
+  {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
+
+\def\subsubsection{%
+  \@startsection{subsubsection}{3}{\z@}
+  %{-11\p@ plus -1\p@}{-1em}
+  {-11\p@ plus -1\p@}{0.001em}
+  {\reset@font\normalfont\normalsize\itshape}}
+
+\def\textcolon{\text{\rm :}}
+
+ \def\paragraph{%
+   \@startsection{paragraph}{4}{\z@}
+   {-6\p@}
+   {-.4em}
+   {\reset@font\itshape}}
+
+% ********************
+% Figures and tables *
+% ********************
+
+% Table and array parameters
+\setlength\arraycolsep{.5em}
+\setlength\tabcolsep{.5em}
+\setlength\arrayrulewidth{.5pt}
+\setlength\doublerulesep{2.5pt}
+\setlength\extrarowheight{\z@}
+\renewcommand\arraystretch{1}
+
+\newlength{\abovecaptionskip}
+\newlength{\belowcaptionskip}
+\setlength{\abovecaptionskip}{13pt}
+\setlength{\belowcaptionskip}{10.5pt}
+
+\long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
+  \begingroup
+  \footnotesize
+  \textbf{#1.}\enskip{#2}\par
+  \endgroup}
+
+\long\def\@tablecaption#1#2{%
+  \begingroup
+  \footnotesize
+  \textbf{#1.}\enskip{#2\strut\par}
+  \endgroup\vspace{\belowcaptionskip}}
+
+% Table rules
+\def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
+   \@tempa\@xhline}
+\def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
+    \hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
+\def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
+   \@tempa\@xhline}
+\def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
+
+\def\thefigure{\@arabic\c@figure}
+\def\fps@figure{tbp}
+\def\ftype@figure{1}
+\def\ext@figure{lof}
+\def\fnum@figure{\figurename~\thefigure}
+\def\figure{\@float{figure}}
+\let\endfigure\end@float
+\@namedef{figure*}{\@dblfloat{figure}}
+\@namedef{endfigure*}{\end@dblfloat}
+\def\thetable{\@arabic\c@table}
+\def\fps@table{tbp}
+\def\ftype@table{2}
+\def\ext@table{lot}
+\def\fnum@table{Table~\thetable}
+\def\table{\let\@makecaption\@tablecaption\let\source\tablesource\@float{table}}
+\def\endtable{\end@float}
+\@namedef{table*}{\let\@makecaption\@tablecaption\@dblfloat{table}}
+\@namedef{endtable*}{\end@dblfloat}
+
+\newif\if@rotate \@rotatefalse
+\newif\if@rotatecenter \@rotatecenterfalse
+\def\rotatecenter{\global\@rotatecentertrue}
+\def\rotateendcenter{\global\@rotatecenterfalse}
+\def\rotate{\global\@rotatetrue}
+\def\endrotate{\global\@rotatefalse}
+\newdimen\rotdimen
+\def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
+    #1 neg exch neg exch translate}}
+\def\rotfinish{\special{ps: currentpoint grestore moveto}}
+\def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
+    \hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
+    \rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
+\def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
+    \hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
+    \rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
+
+\newdimen\tempdime
+\newbox\temptbox
+
+% From ifmtarg.sty
+% Copyright Peter Wilson and Donald Arseneau, 2000
+\begingroup
+\catcode`\Q=3
+\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
+\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
+\long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
+\endgroup
+
+\def\tablesize{\@setfontsize\tablesize{8\p@}{10\p@}}
+
+\newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
+\tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
+{\relax}
+
+\newcommand{\@processtable}[4]{%
+\if@rotate
+\setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
+\begin{minipage}{#4}%
+\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
+\vskip7\p@\noindent
+\parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
+\end{minipage}}\vss}%
+\rotr{4}
+\else
+\hbox to \hsize{\hss\begin{minipage}[t]{#4}%
+\vskip2.9pt
+\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
+\vskip6\p@\noindent
+\parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
+\end{minipage}\hss}\fi}%
+
+\newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
+
+% ******************************
+% List numbering and lettering *
+% ******************************
+\def\labelenumi{{\rm\arabic{enumi}.}}
+\def\theenumi{\arabic{enumi}}
+\def\labelenumii{{\rm\alph{enumii}.}}
+\def\theenumii{\alph{enumii}}
+\def\p@enumii{\theenumi}
+\def\labelenumiii{{\rm(\arabic{enumiii})}}
+\def\theenumiii{\roman{enumiii}}
+\def\p@enumiii{\theenumi(\theenumii)}
+\def\labelenumiv{{\rm(\arabic{enumiv})}}
+\def\theenumiv{\Alph{enumiv}}
+\def\p@enumiv{\p@enumiii\theenumiii}
+\def\labelitemi{{\small$\bullet$}}
+\def\labelitemii{{\small$\bullet$}}
+\def\labelitemiii{{\small$\bullet$}}
+\def\labelitemiv{{\small$\bullet$}}
+
+\def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
+\let\@listi\@listI
+\@listi
+\def\@listii{\topsep\z@\leftmargin\leftmarginii}
+\def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
+\def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
+\def\@listv{\leftmargin\leftmarginv \topsep\z@}
+\def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
+
+\setlength{\leftmargini}{3mm}
+\setlength{\leftmarginii}{\z@}
+\setlength{\leftmarginiii}{\z@}
+\setlength{\leftmarginiv}{\z@}
+
+% Changes to the list parameters for enumerate
+\def\enumargs{%
+   \partopsep     \z@
+   \itemsep       3\p@
+   \parsep        \z@
+   \labelsep      0.5em
+   \listparindent \parindent
+   \itemindent    \z@
+   \topsep 11\p@
+}
+
+\def\enumerate{%
+    \@ifnextchar[{\@numerate}{\@numerate[0]}}
+
+\def\@numerate[#1]{%
+     \ifnum \@enumdepth >3 \@toodeep\else
+     \advance\@enumdepth \@ne
+     \edef\@enumctr{enum\romannumeral\the\@enumdepth}
+     \list{\csname label\@enumctr\endcsname}{%
+       \enumargs
+       \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
+       \usecounter{\@enumctr}
+       \settowidth\labelwidth{#1}
+       \addtolength{\leftmargin}{\labelwidth}
+       \addtolength{\leftmargin}{\labelsep}
+       \def\makelabel##1{\hss \llap{##1}}}%
+     \fi
+   }
+\let\endenumerate\endlist
+
+% Changes to the list parameters for itemize
+\def\itemargs{%
+   \partopsep     \z@
+   \itemsep       3\p@
+   \parsep        \z@
+   \labelsep      0.5em
+   \rightmargin   \z@
+   \listparindent \parindent
+   \itemindent    \z@
+   \topsep11\p@
+}
+
+\def\itemize{%
+    \@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
+
+\def\@itemize[#1]{%
+     \ifnum \@itemdepth >3 \@toodeep\else
+     \advance\@itemdepth \@ne
+     \edef\@itemctr{item\romannumeral\the\@itemdepth}
+     \list{\csname label\@itemctr\endcsname}{%
+       \itemargs
+       \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
+       \settowidth\labelwidth{#1}
+       \addtolength{\leftmargin}{\labelwidth}
+       \addtolength{\leftmargin}{\labelsep}
+       \def\makelabel##1{\hss \llap{##1}}}%
+     \fi
+   }
+\let\enditemize\endlist
+
+\newenvironment{unlist}{%
+  \begin{list}{}%
+    {\setlength{\labelwidth}{\z@}%
+     \setlength{\labelsep}{\z@}%
+     \setlength{\topsep}{\medskipamount}%
+     \setlength{\itemsep}{3\p@}%
+     \setlength{\leftmargin}{2em}%
+     \setlength{\itemindent}{-2em}}}
+{\end{list}}
+
+
+% ***********************
+% Quotes and Quotations *
+% ***********************
+\def\quotation{\par\begin{list}{}{
+      \setlength{\topsep}{\medskipamount}
+      \setlength{\leftmargin}{2em}%
+      \setlength{\rightmargin}{\z@}%
+      \setlength\labelwidth{0pt}%
+      \setlength\labelsep{0pt}%
+      \listparindent\parindent}%
+  \item[]}
+\def\endquotation{\end{list}}
+\let\quote\quotation
+\let\endquote\endquotation
+
+\skip\@mpfootins = \skip\footins
+\fboxsep=6\p@
+\fboxrule=1\p@
+
+% *******************
+% Table of contents *
+% *******************
+\newcommand\@pnumwidth{4em}
+\newcommand\@tocrmarg{2.55em plus 1fil}
+\newcommand\@dotsep{1000}
+\setcounter{tocdepth}{4}
+
+\def\numberline#1{\hbox to \@tempdima{{#1}}}
+
+\def\@authortocline#1#2#3#4#5{%
+  \vskip 1.5\p@
+  \ifnum #1>\c@tocdepth \else
+    {\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
+     \parindent #2\relax\@afterindenttrue
+     \interlinepenalty\@M
+     \leavevmode
+     \@tempdima #3\relax
+     \advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
+     {\itshape #4}\nobreak
+     \leaders\hbox{$\m@th
+        \mkern \@dotsep mu\hbox{.}\mkern \@dotsep
+        mu$}\hfill
+     \nobreak
+     \hb@xt@\@pnumwidth{\hfil}%
+     \par}%
+  \fi}
+
+\newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
+\newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
+\newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
+\newcommand*\l@subsubsection[2]{}
+
+
+
+% ***********
+% Footnotes *
+% ***********
+
+\def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
+\def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
+\newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
+
+% ***********
+% References *
+% ***********
+
+\providecommand{\newblock}{}
+\newenvironment{thebibliography}{%
+  \section{\bibname}%
+  \begingroup
+  \small
+  \begin{list}{}{%
+      \setlength{\topsep}{\z@}%
+      \setlength{\labelsep}{\z@}%
+      \settowidth{\labelwidth}{\z@}%
+      \setlength{\leftmargin}{4mm}%
+      \setlength{\itemindent}{-4mm}}\small}
+{\end{list}\endgroup}
+
+\RequirePackage{natbib}
+
+% **********
+% Appendix *
+% **********
+\newif\ifappend % Are we in the Appendix?
+\def\appendix{\par
+        \setcounter{section}{0}
+        \setcounter{subsection}{0}
+        \appendtrue
+}
+
+%Math parameters
+
+\setlength{\jot}{5\p@}
+\mathchardef\@m=1500   % adapted value
+
+\def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
+  \sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
+
+% Theorems
+\def\th@plain{%
+%%  \let\thm@indent\noindent % no indent
+\thm@headfont{\quad\scshape}% heading font is bold
+\thm@notefont{\upshape\mdseries}% same as heading font
+\thm@headpunct{.}% no period after heading
+\thm@headsep 5\p@ plus\p@ minus\p@\relax
+%%  \let\thm@swap\@gobble
+%%  \thm@preskip\topsep
+%%  \thm@postskip\theorempreskipamount
+\itshape % body font
+}
+
+\vbadness=9999
+\tolerance=9999
+\doublehyphendemerits=10000
+\doublehyphendemerits 640000   % corresponds to badness 800
+\finalhyphendemerits  1000000  % corresponds to badness 1000
+
+\flushbottom
+\frenchspacing
+\ps@headings
+\twocolumn
+
+% Screen PDF compatability
+\newcommand{\medline}[1]{%
+  \unskip\unskip\ignorespaces}
+
+
+%%%%for smaller size text
+\newenvironment{methods}{%
+  \begingroup
+\def\section{%
+  \@startsection{section}{1}{\z@}
+  {-24\p@ plus -3\p@}{4\p@}
+  {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
+ \def\subsection{%
+  \@startsection{subsection}{2}{\z@}
+  {-5\p@ plus -2\p@}{4\p@}
+  {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
+ \def\subsubsection{%
+  \@startsection{subsubsection}{3}{\z@}
+%  {-6\p@ plus -1\p@}{-1em}
+  {-6\p@ plus -1\p@}{0.001em}
+  {\reset@font\normalfont\normalsize\itshape}}
+\footnotesize
+  \par}
+{\par\endgroup\bigskip\@afterheading\@afterindentfalse}
+
+
+
+\graphicspath{{g:/artwork/oup/bioinfo/}}
+
+\language=2
+
+\hyphenation{Figure Table Figures Tables}
+
+\newcommand{\href}[2]{#2}
+
+\renewenvironment{proof}[1][\proofname]{\par
+  \normalfont \topsep6\p@\@plus6\p@\relax
+  \labelsep 0.5em
+  \trivlist
+  \item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
+}{\endtrivlist\@endpefalse}
+
+%%Different Bonds
+
+\def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
+\def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
+\def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
+
+% Author queries
+%\fboxsep=4\p@
+%\fboxrule=0.5\p@
+\newcommand{\query}[2][0pt]{}%
+%  \marginpar{\vspace*{#1}%
+%    {\parbox{\marginparwidth}{%
+%     \raggedright\fontsize{6}{8}\selectfont
+%         #2}}}}
+
+\renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
+
+\endinput