BioInfo/BS-Seq/bwa-meth/paper/bioinfo.cls

   1 \newcommand\classname{bioinfo}
   2 \newcommand\lastmodifieddate{2003/02/08}
   3 \newcommand\versionnumber{0.1}
   4
   5 % Are we printing crop marks?
   6 \newif\if@cropmarkson \@cropmarksontrue
   7
   8 \NeedsTeXFormat{LaTeX2e}[2001/06/01]
   9 \ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
  10
  11 \setlength{\paperheight}{11truein}
  12 \setlength{\paperwidth}{8.5truein}
  13
  14 \newif\if@final
  15
  16 \DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}}
  17 \DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}}
  18 \DeclareOption{centre}{\PassOptionsToPackage{center}{crop}}
  19 \DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue}
  20 \DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse}
  21 \DeclareOption{info}{\PassOptionsToPackage{info}{crop}}
  22 \DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}}
  23 \DeclareOption{final}{\global\@finaltrue}
  24
  25 \ExecuteOptions{a4paper,nocrop,centre,info}
  26
  27 \ProcessOptions
  28
  29 % Load all necessary packages
  30 \RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times}
  31 %\RequirePackage[LY1]{fontenc}
  32 %\RequirePackage[LY1,mtbold]{mathtime}
  33 \def\helvetica{\fontfamily{phv}\selectfont}
  34 \def\helveticaitalic{\fontfamily{phv}\itshape\selectfont}
  35 \def\helveticabold{\fontfamily{phv}\bfseries\selectfont}
  36 \def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont}
  37
  38 % Not sure if needed.
  39 \newcommand\@ptsize{0}
  40
  41 % Set twoside printing
  42 \@twosidetrue
  43
  44 % Marginal notes are on the outside edge
  45 \@mparswitchfalse
  46
  47 \reversemarginpar
  48
  49 \renewcommand\normalsize{%
  50    \@setfontsize\normalsize{9}{11}%
  51    \abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
  52    \abovedisplayshortskip \z@ \@plus3\p@
  53    \belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
  54    \belowdisplayskip \abovedisplayskip
  55    \let\@listi\@listI}
  56 \normalsize
  57 \let\@bls\baselineskip
  58
  59 \newcommand\small{%
  60     \@setfontsize\small{9}{11}%
  61     \abovedisplayskip 11\p@ minus 3\p@
  62     \belowdisplayskip \abovedisplayskip
  63     \abovedisplayshortskip \z@ plus 2\p@
  64     \belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@
  65     \def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@
  66        \itemsep \parsep
  67        \topsep 4\p@ plus 2\p@ minus 2\p@}}
  68
  69 \newcommand\footnotesize{%
  70     \@setfontsize\footnotesize{8}{10}%
  71     \abovedisplayskip 6\p@ minus 3\p@
  72     \belowdisplayskip\abovedisplayskip
  73     \abovedisplayshortskip \z@ plus 3\p@
  74     \belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@
  75     \def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@
  76        \parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}}
  77
  78 \def\scriptsize{\@setfontsize\scriptsize{7pt}{9pt}}
  79 \def\tiny{\@setfontsize\tiny{5pt}{7pt}}
  80 \def\large{\@setfontsize\large{11.5pt}{12pt}}
  81 \def\Large{\@setfontsize\Large{14pt}{16}}
  82 \def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
  83 \def\huge{\@setfontsize\huge{22pt}{22pt}}
  84 \def\Huge{\@setfontsize\Huge{30pt}{30pt}}
  85
  86 \DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
  87 \DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
  88 \DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
  89 \DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
  90 \DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
  91 \DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
  92 \DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
  93
  94 % Line spacing
  95 \setlength\lineskip{1\p@}
  96 \setlength\normallineskip{1\p@}
  97 \renewcommand\baselinestretch{}
  98
  99 % Paragraph dimensions and inter-para spacing
 100 \setlength\parskip{0\p@}
 101 \setlength\parindent{3mm}
 102
 103 % Set inter-para skips
 104 \setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
 105 \setlength\medskipamount{6\p@ \@plus 2\p@}
 106 \setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
 107
 108 % Page break penalties
 109 \@lowpenalty   51
 110 \@medpenalty  151
 111 \@highpenalty 301
 112
 113 % Disallow widows and orphans
 114 \clubpenalty 10000
 115 \widowpenalty 10000
 116
 117 % Disable page breaks before equations, allow pagebreaks after
 118 % equations and discourage widow lines before equations.
 119 \displaywidowpenalty 100
 120 \predisplaypenalty   10000
 121 \postdisplaypenalty  2500
 122
 123 % Allow breaking the page in the middle of a paragraph
 124 \interlinepenalty 0
 125
 126 % Disallow breaking the page after a hyphenated line
 127 \brokenpenalty 10000
 128
 129 % Hyphenation; don't split words into less than three characters
 130 \lefthyphenmin=3
 131 \righthyphenmin=3
 132
 133 %
 134 % Set page layout dimensions
 135 %
 136 \setlength\headheight{16\p@}        % height of running head
 137 \setlength\topmargin{2.9pc}         % head margin
 138 \addtolength\topmargin{-1in}        % subtract out the 1 inch driver margin
 139
 140 \setlength\topskip{10\p@}           % height of first line of text
 141 \setlength\headsep{19\p@}        %   space below running head --
 142
 143 \setlength\footskip{34\p@}          % space above footer line
 144 \setlength\maxdepth{.5\topskip}     % pages can be short or deep by half a line?
 145
 146 \setlength\textwidth{42pc}          % text measure excluding margins
 147
 148 \setlength\textheight{58\baselineskip} % 54 lines on a full page,
 149 \addtolength\textheight{\topskip}      %   including the first
 150                                        %   line on the page
 151
 152 % Set the margins
 153 \setlength\marginparsep{3\p@}
 154 \setlength\marginparpush{3\p@}
 155 \setlength\marginparwidth{35\p@}
 156
 157 \setlength\oddsidemargin{4.5pc}
 158 \addtolength\oddsidemargin{-1in}     % subtract out the 1 inch driver margin
 159 \setlength\@tempdima{\paperwidth}
 160 \addtolength\@tempdima{-\textwidth}
 161 \addtolength\@tempdima{-4.5pc}
 162 \setlength\evensidemargin{\@tempdima}
 163 \addtolength\evensidemargin{-1in}
 164
 165 \setlength\columnsep{1.5pc}          % space between columns for double-column text
 166 \setlength\columnseprule{0\p@}       % width of rule between two columns
 167
 168 % Footnotes
 169 \setlength\footnotesep{9\p@}      % space between footnotes
 170 % space between text and footnote
 171 \setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
 172
 173 % Float placement parameters
 174
 175 % The total number of floats that can be allowed on a page.
 176 \setcounter{totalnumber}{10}
 177 % The maximum number of floats at the top and bottom of a page.
 178 \setcounter{topnumber}{5}
 179 \setcounter{bottomnumber}{5}
 180 % The maximum part of the top or bottom of a text page that can be
 181 % occupied by floats. This is set so that at least four lines of text
 182 % fit on the page.
 183 \renewcommand\topfraction{.9}
 184 \renewcommand\bottomfraction{.9}
 185 % The minimum amount of a text page that must be occupied by text.
 186 % This should accomodate four lines of text.
 187 \renewcommand\textfraction{.06}
 188 % The minimum amount of a float page that must be occupied by floats.
 189 \renewcommand\floatpagefraction{.94}
 190
 191 % The same parameters repeated for double column output
 192 \renewcommand\dbltopfraction{.9}
 193 \renewcommand\dblfloatpagefraction{.9}
 194
 195 % Space between floats
 196 \setlength\floatsep    {12\p@ \@plus 2\p@ \@minus 2\p@}
 197 % Space between floats and text
 198 \setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
 199 % Space above and below an inline figure
 200 \setlength\intextsep   {18\p@ \@plus 2\p@ \@minus 2\p@}
 201
 202 % For double column floats
 203 \setlength\dblfloatsep    {12\p@ \@plus 2\p@ \@minus 2\p@}
 204 \setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
 205
 206 % Space left at top, bottom and inbetween floats on a float page.
 207 \setlength\@fptop{0\p@}         % no space above float page figures
 208 \setlength\@fpsep{12\p@ \@plus 1fil}
 209 \setlength\@fpbot{0\p@}
 210
 211 % The same for double column
 212 \setlength\@dblfptop{0\p@}
 213 \setlength\@dblfpsep{12\p@ \@plus 1fil}
 214 \setlength\@dblfpbot{0\p@}
 215
 216 % Override settings in mathtime back to TeX defaults
 217 \DeclareMathSizes{5}     {5}   {5}  {5}
 218 \DeclareMathSizes{6}     {6}   {5}  {5}
 219 \DeclareMathSizes{7}     {7}   {5}  {5}
 220 \DeclareMathSizes{8}     {8}   {6}  {5}
 221 \DeclareMathSizes{9}     {9}   {6.5}  {5}
 222 \DeclareMathSizes{10}   {10}   {7.5}  {5}
 223 \DeclareMathSizes{12}   {12}   {9}  {7}
 224
 225 % Page styles
 226 \def\ps@headings
 227   {%
 228   \def\@oddfoot{\vbox to 12.5\p@{\hbox{\rule{\textwidth}{0.5\p@}}\vss
 229         \hbox to \textwidth{\hfill\helveticabold\small\thepage}%
 230         }}%
 231   \def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
 232         \hbox to \textwidth{\helveticabold\small\thepage\hfill}%
 233         }}%
 234   \def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{8}{10}\selectfont
 235         \helveticabold{\fontshape{it}\selectfont
 236         \strut\leftmark}\hfill}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
 237   \def\@oddhead{\vbox{\hbox to \textwidth{\hfill\fontsize{8}{10}\selectfont
 238         \helveticabold{\fontshape{it}\selectfont\strut\rightmark}}%
 239         \vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
 240   \def\titlemark##1{\markboth{##1}{##1}}%
 241   \def\authormark##1{\gdef\leftmark{##1}}%
 242   }
 243
 244 \def\ps@opening
 245   {%
 246   \def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
 247         \hbox to \textwidth{\helvetica
 248         \fontsize{7}{9}\fontshape{n}\selectfont \copyright\space Oxford University Press \@copyrightyear.%
 249           \hfill\small\helveticabold\thepage}%
 250         }}%
 251   \def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}{1\p@}\vss
 252         \hbox to \textwidth{\helvetica\thepage\hfill
 253           \fontsize{7}{9}\fontshape{n}\selectfont \copyright\space Oxford University Press \@copyrightyear.}%
 254         }}%
 255   \let\@evenhead\relax
 256   \let\@oddhead\relax}
 257
 258 % Page range
 259 \newif\iflastpagegiven   \lastpagegivenfalse
 260 \newcommand\firstpage[1]{%
 261   \gdef\@firstpage{#1}%
 262   \ifnum\@firstpage>\c@page
 263     \setcounter{page}{#1}%
 264     \ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
 265   \else \ifnum\@firstpage<\c@page
 266     \ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
 267     \xdef\@firstpage{\the\c@page}%
 268     }
 269 \def\@firstpage{1}
 270 \def\pagenumbering#1{%
 271     \global\c@page \@ne
 272     \gdef\thepage{\csname @#1\endcsname \c@page}%
 273     \gdef\thefirstpage{%
 274             \csname @#1\endcsname \@firstpage}%
 275     \gdef\thelastpage{%
 276             \csname @#1\endcsname \@lastpage}%
 277     }
 278
 279 \newcommand\lastpage[1]{\xdef\@lastpage{#1}%
 280   \global\lastpagegiventrue}
 281 \def\@lastpage{0}
 282 \def\setlastpage{\iflastpagegiven\else
 283     \edef\@tempa{@lastpage@}%
 284     \expandafter
 285     \ifx \csname \@tempa \endcsname \relax
 286         \gdef\@lastpage{0}%
 287     \else
 288         \xdef\@lastpage{\@nameuse{@lastpage@}}%
 289         \fi
 290     \fi }
 291 \def\writelastpage{%
 292     \iflastpagegiven \else
 293     \immediate\write\@auxout%
 294     {\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
 295     \fi
 296     }
 297 \def\thepagerange{%
 298   \ifnum\@lastpage =0 {\ \bf ???} \else
 299   \ifnum\@lastpage = \@firstpage \ \thefirstpage\else
 300   \thefirstpage--\thelastpage \fi\fi}
 301
 302 \AtBeginDocument{\setlastpage
 303      \pagenumbering{arabic}%
 304    }
 305 \AtEndDocument{%
 306     \writelastpage
 307     \if@final
 308     \clearemptydoublepage
 309     \else
 310     \clearpage
 311     \fi}
 312
 313 %
 314 % Sectional units
 315 %
 316
 317 % Counters
 318 \newcounter{section}
 319 \newcounter{subsection}[section]
 320 \newcounter{subsubsection}[subsection]
 321 \newcounter{paragraph}[subsubsection]
 322 \newcounter{subparagraph}[paragraph]
 323 \newcounter{figure}
 324 \newcounter{table}
 325
 326 % Form of the numbers
 327 \newcommand\thepage{\arabic{page}}
 328 \renewcommand\thesection{\arabic{section}}
 329 \renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
 330 \renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
 331 \renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
 332 \renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
 333 \renewcommand\theequation{\arabic{equation}}
 334
 335 % Form of the words
 336 \newcommand\contentsname{Contents}
 337 \newcommand\listfigurename{List of Figures}
 338 \newcommand\listtablename{List of Tables}
 339 \newcommand\partname{Part}
 340 \newcommand\appendixname{Appendix}
 341 \newcommand\abstractname{Abstract}
 342 \newcommand\refname{References}
 343 \newcommand\bibname{References}
 344 \newcommand\indexname{Index}
 345 \newcommand\figurename{Fig.}
 346 \newcommand\tablename{Table}
 347
 348 % Clearemptydoublepage should really clear the running heads too
 349 \newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
 350
 351 % Frontmatter, mainmatter and backmatter
 352
 353 \newif\if@mainmatter \@mainmattertrue
 354
 355 \newcommand\frontmatter{%
 356   \clearpage
 357   \@mainmatterfalse
 358   \pagenumbering{roman}}
 359
 360 \newcommand\mainmatter{%
 361   \clearpage
 362   \@mainmattertrue
 363   \pagenumbering{arabic}}
 364
 365 \newcommand\backmatter{%
 366   \clearpage
 367   \@mainmatterfalse}
 368
 369 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% TITLE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 370 \newlength{\dropfromtop}
 371 \setlength{\dropfromtop}{\z@}
 372
 373 % Application Notes
 374 \newif\if@appnotes
 375 \newcommand{\application}{%
 376 %  \setlength{\dropfromtop}{-2.25pc}%
 377   \global\@appnotestrue}
 378
 379 \long\def\title{\@ifnextchar[{\short@title}{\@@title}}
 380 \def\short@title[#1]{\titlemark{#1}\@@@title}
 381 \def\@@title#1{\authormark{#1}\@@@title{#1}}
 382 \long\def\@@@title#1{\gdef\@title{#1}}
 383
 384 \long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
 385 \def\short@uthor[#1]{\authormark{#1}\@@author}
 386 \def\@uthor#1{\authormark{#1}\@@author{#1}}
 387 \long\def\@@author#1{\gdef\@author{#1}}
 388
 389 \def\vol#1{\global\def\@vol{#1}}
 390 \def\issue#1{\global\def\@issue{#1}}
 391 \def\address#1{\global\def\@issue{#1}}
 392 \def\history#1{\global\def\@history{#1}}
 393 \def\editor#1{\global\def\@editor{#1}}
 394 \def\pubyear#1{\global\def\@pubyear{#1}}
 395 \def\copyrightyear#1{\global\def\@copyrightyear{#1}}
 396 \def\address#1{\global\def\@address{#1}}
 397 \def\DOI#1{\global\def\@DOI{#1}}
 398
 399 \definecolor{gray}{cmyk}{0, 0, 0, 0.15}
 400 \newlength{\extraspace}
 401 \setlength{\extraspace}{\z@}
 402
 403 \newcommand\maketitle{\par
 404   \begingroup
 405     \renewcommand\thefootnote{\@fnsymbol\c@footnote}%
 406     \def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
 407     \long\def\@makefntext##1{\parindent 3mm\noindent
 408 %      \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
 409       \@textsuperscript{\normalfont\@thefnmark}##1}%
 410     \if@twocolumn
 411       \ifnum \col@number=\@ne
 412         \@maketitle
 413       \else
 414         \twocolumn[\@maketitle]%
 415       \fi
 416     \else
 417       \newpage
 418       \global\@topnum\z@   % Prevents figures from going at top of page.
 419       \@maketitle
 420     \fi
 421     \thispagestyle{opening}\@thanks
 422   \endgroup
 423   \setcounter{footnote}{0}%
 424   \global\let\thanks\relax
 425   \global\let\maketitle\relax
 426   \global\let\@maketitle\relax
 427   \global\let\@address\@empty
 428   \global\let\@history\@empty
 429   \global\let\@editor\@empty
 430   \global\let\@thanks\@empty
 431   \global\let\@author\@empty
 432   \global\let\@date\@empty
 433   \global\let\@title\@empty
 434   \global\let\@pubyear\@empty
 435   \global\let\address\relax
 436   \global\let\history\relax
 437   \global\let\editor\relax
 438   \global\let\title\relax
 439   \global\let\author\relax
 440   \global\let\date\relax
 441   \global\let\pubyear\relax
 442   \global\let\@copyrightline\@empty
 443   \global\let\and\relax
 444   \@afterindentfalse\@afterheading
 445 }
 446
 447 \newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
 448 \setlength{\aboveskipchk}{\z@}%
 449
 450 \def\@maketitle{%
 451   \let\footnote\thanks
 452   \clearemptydoublepage
 453     \checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-3pc}\else\setlength{\aboveskipchk}{-5pc}\fi%for checking oddpage or evenpage top skip%%
 454   \vspace*{\aboveskipchk}%
 455   \vspace{\dropfromtop}%
 456   \hbox to \textwidth{%
 457   {\helvetica\itshape\bfseries\fontsize{19}{12}\selectfont {\color{gray}BIOINFORMATICS}
 458     \hfil
 459     \if@appnotes APPLICATIONS NOTE\hfil\fi
 460     }%
 461 \enskip  \parbox[b]{11.3pc}{%
 462     \helvetica
 463     \flushright\fontsize{8}{10}\fontshape{it}\selectfont
 464         Vol. 00\ no. 00 \@pubyear\\
 465         \hfill Pages \thepagerange
 466   }}
 467   \rule{\textwidth}{1\p@}\par%
 468   \helvetica
 469   \hbox to \textwidth{%
 470   \parbox[t]{36.5pc}{%
 471     \vspace*{1sp}
 472     {\helveticabold\fontsize{16}{21}\selectfont\raggedright \@title \par}%
 473     \vspace{4.5\p@}
 474     {\helvetica\fontsize{13}{15}\selectfont\raggedright \@author \par}%
 475         \vspace{4\p@}
 476     {\helvetica\fontsize{10}{12}\selectfont\raggedright \@address \par}%
 477     \vspace{4\p@}
 478     {\helvetica\fontsize{8}{10}\selectfont\raggedright \@history \par}
 479     \vspace{24\p@}
 480     {\helvetica\fontsize{10}{12}\selectfont\raggedright \@editor \par}
 481     %\vspace{20\p@}
 482     }%
 483   }
 484   \vspace{14.5\p@}%
 485   \rule{\textwidth}{1\p@}%
 486   \vspace{12\p@ plus 6\p@ minus 6\p@}%
 487   \vspace{\extraspace}
 488   }
 489 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 490
 491 %%%%%%%%%%%%%%%%%%%%%%%%%%%% Abstract %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 492 \newcommand{\absection}[1]{%
 493   \par\noindent{\bfseries #1}\space\ignorespaces}
 494
 495 \newenvironment{abstract}{%
 496   \begingroup
 497   \let\section\absection
 498   \fontfamily{\sfdefault}\fontsize{8}{11}\sffamily\selectfont
 499   {\fontseries{b}\selectfont ABSTRACT}\par}
 500 {\endgroup\bigskip\@afterheading\@afterindentfalse\vskip 12pt plus 3pt minus 1pt}
 501
 502 % Section macros
 503
 504 % Lowest level heading that takes a number by default
 505 \setcounter{secnumdepth}{3}
 506
 507 \renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
 508
 509 \def\section{%
 510   \@startsection{section}{1}{\z@}
 511   {-22\p@ plus -3\p@}{3\p@}
 512   {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
 513
 514 \def\subsection{%
 515   \@startsection{subsection}{2}{\z@}
 516   {-11\p@ plus -2\p@}{3\p@}
 517   {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
 518
 519 \def\subsubsection{%
 520   \@startsection{subsubsection}{3}{\z@}
 521   {-11\p@ plus -1\p@}{-1em}
 522   {\reset@font\normalfont\normalsize\itshape}}
 523
 524 \def\textcolon{\text{\rm :}}
 525
 526  \def\paragraph{%
 527    \@startsection{paragraph}{4}{\z@}
 528    {-6\p@}
 529    {-.4em}
 530    {\reset@font\itshape}}
 531
 532 % ********************
 533 % Figures and tables *
 534 % ********************
 535
 536 % Table and array parameters
 537 \setlength\arraycolsep{.5em}
 538 \setlength\tabcolsep{.5em}
 539 \setlength\arrayrulewidth{.5pt}
 540 \setlength\doublerulesep{2.5pt}
 541 \setlength\extrarowheight{\z@}
 542 \renewcommand\arraystretch{1}
 543
 544 \newlength{\abovecaptionskip}
 545 \newlength{\belowcaptionskip}
 546 \setlength{\abovecaptionskip}{13pt}
 547 \setlength{\belowcaptionskip}{10.5pt}
 548
 549 \long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
 550   \begingroup
 551   \footnotesize
 552   \textbf{#1.}\enskip{#2}\par
 553   \endgroup}
 554
 555 \long\def\@tablecaption#1#2{%
 556   \begingroup
 557   \footnotesize
 558   \textbf{#1.}\enskip{#2\strut\par}
 559   \endgroup\vspace{\belowcaptionskip}}
 560
 561 % Table rules
 562 \def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
 563    \@tempa\@xhline}
 564 \def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
 565     \hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
 566 \def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
 567    \@tempa\@xhline}
 568 \def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
 569
 570 \def\thefigure{\@arabic\c@figure}
 571 \def\fps@figure{tbp}
 572 \def\ftype@figure{1}
 573 \def\ext@figure{lof}
 574 \def\fnum@figure{\figurename~\thefigure}
 575 \def\figure{\@float{figure}}
 576 \let\endfigure\end@float
 577 \@namedef{figure*}{\@dblfloat{figure}}
 578 \@namedef{endfigure*}{\end@dblfloat}
 579 \def\thetable{\@arabic\c@table}
 580 \def\fps@table{tbp}
 581 \def\ftype@table{2}
 582 \def\ext@table{lot}
 583 \def\fnum@table{Table~\thetable}
 584 \def\table{\let\@makecaption\@tablecaption\let\source\tablesource\@float{table}}
 585 \def\endtable{\end@float}
 586 \@namedef{table*}{\let\@makecaption\@tablecaption\@dblfloat{table}}
 587 \@namedef{endtable*}{\end@dblfloat}
 588
 589 \newif\if@rotate \@rotatefalse
 590 \newif\if@rotatecenter \@rotatecenterfalse
 591 \def\rotatecenter{\global\@rotatecentertrue}
 592 \def\rotateendcenter{\global\@rotatecenterfalse}
 593 \def\rotate{\global\@rotatetrue}
 594 \def\endrotate{\global\@rotatefalse}
 595 \newdimen\rotdimen
 596 \def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
 597     #1 neg exch neg exch translate}}
 598 \def\rotfinish{\special{ps: currentpoint grestore moveto}}
 599 \def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
 600     \hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
 601     \rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
 602 \def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
 603     \hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
 604     \rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
 605
 606 \newdimen\tempdime
 607 \newbox\temptbox
 608
 609 % From ifmtarg.sty
 610 % Copyright Peter Wilson and Donald Arseneau, 2000
 611 \begingroup
 612 \catcode`\Q=3
 613 \long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
 614 \long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
 615 \long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
 616 \endgroup
 617
 618 \def\tablesize{\@setfontsize\tablesize{8\p@}{10\p@}}
 619
 620 \newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
 621 \tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
 622 {\relax}
 623
 624 \newcommand{\@processtable}[4]{%
 625 \if@rotate
 626 \setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
 627 \begin{minipage}{#4}%
 628 \@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
 629 \vskip7\p@\noindent
 630 \parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
 631 \end{minipage}}\vss}%
 632 \rotr{4}
 633 \else
 634 \hbox to \hsize{\hss\begin{minipage}[t]{#4}%
 635 \vskip2.9pt
 636 \@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
 637 \vskip6\p@\noindent
 638 \parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
 639 \end{minipage}\hss}\fi}%
 640
 641 \newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
 642
 643 % ******************************
 644 % List numbering and lettering *
 645 % ******************************
 646 \def\labelenumi{{\rm\arabic{enumi}.}}
 647 \def\theenumi{\arabic{enumi}}
 648 \def\labelenumii{{\rm\alph{enumii}.}}
 649 \def\theenumii{\alph{enumii}}
 650 \def\p@enumii{\theenumi}
 651 \def\labelenumiii{{\rm(\arabic{enumiii})}}
 652 \def\theenumiii{\roman{enumiii}}
 653 \def\p@enumiii{\theenumi(\theenumii)}
 654 \def\labelenumiv{{\rm(\arabic{enumiv})}}
 655 \def\theenumiv{\Alph{enumiv}}
 656 \def\p@enumiv{\p@enumiii\theenumiii}
 657 \def\labelitemi{{\small$\bullet$}}
 658 \def\labelitemii{{\small$\bullet$}}
 659 \def\labelitemiii{{\small$\bullet$}}
 660 \def\labelitemiv{{\small$\bullet$}}
 661
 662 \def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
 663 \let\@listi\@listI
 664 \@listi
 665 \def\@listii{\topsep\z@\leftmargin\leftmarginii}
 666 \def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
 667 \def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
 668 \def\@listv{\leftmargin\leftmarginv \topsep\z@}
 669 \def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
 670
 671 \setlength{\leftmargini}{3mm}
 672 \setlength{\leftmarginii}{\z@}
 673 \setlength{\leftmarginiii}{\z@}
 674 \setlength{\leftmarginiv}{\z@}
 675
 676 % Changes to the list parameters for enumerate
 677 \def\enumargs{%
 678    \partopsep     \z@
 679    \itemsep       3\p@
 680    \parsep        \z@
 681    \labelsep      0.5em
 682    \listparindent \parindent
 683    \itemindent    \z@
 684    \topsep 11\p@
 685 }
 686
 687 \def\enumerate{%
 688     \@ifnextchar[{\@numerate}{\@numerate[0]}}
 689
 690 \def\@numerate[#1]{%
 691      \ifnum \@enumdepth >3 \@toodeep\else
 692      \advance\@enumdepth \@ne
 693      \edef\@enumctr{enum\romannumeral\the\@enumdepth}
 694      \list{\csname label\@enumctr\endcsname}{%
 695        \enumargs
 696        \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
 697        \usecounter{\@enumctr}
 698        \settowidth\labelwidth{#1}
 699        \addtolength{\leftmargin}{\labelwidth}
 700        \addtolength{\leftmargin}{\labelsep}
 701        \def\makelabel##1{\hss \llap{##1}}}%
 702      \fi
 703    }
 704 \let\endenumerate\endlist
 705
 706 % Changes to the list parameters for itemize
 707 \def\itemargs{%
 708    \partopsep     \z@
 709    \itemsep       3\p@
 710    \parsep        \z@
 711    \labelsep      0.5em
 712    \rightmargin   \z@
 713    \listparindent \parindent
 714    \itemindent    \z@
 715    \topsep11\p@
 716 }
 717
 718 \def\itemize{%
 719     \@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
 720
 721 \def\@itemize[#1]{%
 722      \ifnum \@itemdepth >3 \@toodeep\else
 723      \advance\@itemdepth \@ne
 724      \edef\@itemctr{item\romannumeral\the\@itemdepth}
 725      \list{\csname label\@itemctr\endcsname}{%
 726        \itemargs
 727        \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
 728        \settowidth\labelwidth{#1}
 729        \addtolength{\leftmargin}{\labelwidth}
 730        \addtolength{\leftmargin}{\labelsep}
 731        \def\makelabel##1{\hss \llap{##1}}}%
 732      \fi
 733    }
 734 \let\enditemize\endlist
 735
 736 \newenvironment{unlist}{%
 737   \begin{list}{}%
 738     {\setlength{\labelwidth}{\z@}%
 739      \setlength{\labelsep}{\z@}%
 740      \setlength{\topsep}{\medskipamount}%
 741      \setlength{\itemsep}{3\p@}%
 742      \setlength{\leftmargin}{2em}%
 743      \setlength{\itemindent}{-2em}}}
 744 {\end{list}}
 745
 746
 747 % ***********************
 748 % Quotes and Quotations *
 749 % ***********************
 750 \def\quotation{\par\begin{list}{}{
 751       \setlength{\topsep}{\medskipamount}
 752       \setlength{\leftmargin}{2em}%
 753       \setlength{\rightmargin}{\z@}%
 754       \setlength\labelwidth{0pt}%
 755       \setlength\labelsep{0pt}%
 756       \listparindent\parindent}%
 757   \item[]}
 758 \def\endquotation{\end{list}}
 759 \let\quote\quotation
 760 \let\endquote\endquotation
 761
 762 \skip\@mpfootins = \skip\footins
 763 \fboxsep=6\p@
 764 \fboxrule=1\p@
 765
 766 % *******************
 767 % Table of contents *
 768 % *******************
 769 \newcommand\@pnumwidth{4em}
 770 \newcommand\@tocrmarg{2.55em plus 1fil}
 771 \newcommand\@dotsep{1000}
 772 \setcounter{tocdepth}{4}
 773
 774 \def\numberline#1{\hbox to \@tempdima{{#1}}}
 775
 776 \def\@authortocline#1#2#3#4#5{%
 777   \vskip 1.5\p@
 778   \ifnum #1>\c@tocdepth \else
 779     {\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
 780      \parindent #2\relax\@afterindenttrue
 781      \interlinepenalty\@M
 782      \leavevmode
 783      \@tempdima #3\relax
 784      \advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
 785      {\itshape #4}\nobreak
 786      \leaders\hbox{$\m@th
 787         \mkern \@dotsep mu\hbox{.}\mkern \@dotsep
 788         mu$}\hfill
 789      \nobreak
 790      \hb@xt@\@pnumwidth{\hfil}%
 791      \par}%
 792   \fi}
 793
 794 \newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
 795 \newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
 796 \newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
 797 \newcommand*\l@subsubsection[2]{}
 798
 799
 800
 801 % ***********
 802 % Footnotes *
 803 % ***********
 804
 805 \def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
 806 \def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
 807 \newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
 808
 809 % ***********
 810 % References *
 811 % ***********
 812
 813 \providecommand{\newblock}{}
 814 \newenvironment{thebibliography}{%
 815   \section{\bibname}%
 816   \begingroup
 817   \small
 818   \begin{list}{}{%
 819       \setlength{\topsep}{\z@}%
 820       \setlength{\labelsep}{\z@}%
 821       \settowidth{\labelwidth}{\z@}%
 822       \setlength{\leftmargin}{4mm}%
 823       \setlength{\itemindent}{-4mm}}\small}
 824 {\end{list}\endgroup}
 825
 826 \RequirePackage{natbib}
 827
 828 % **********
 829 % Appendix *
 830 % **********
 831 \newif\ifappend % Are we in the Appendix?
 832 \def\appendix{\par
 833         \setcounter{section}{0}
 834         \setcounter{subsection}{0}
 835         \appendtrue
 836 }
 837
 838 %Math parameters
 839
 840 \setlength{\jot}{5\p@}
 841 \mathchardef\@m=1500   % adapted value
 842
 843 \def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
 844   \sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
 845
 846 % Theorems
 847 \def\th@plain{%
 848 %%  \let\thm@indent\noindent % no indent
 849 \thm@headfont{\quad\scshape}% heading font is bold
 850 \thm@notefont{\upshape\mdseries}% same as heading font
 851 \thm@headpunct{.}% no period after heading
 852 \thm@headsep 5\p@ plus\p@ minus\p@\relax
 853 %%  \let\thm@swap\@gobble
 854 %%  \thm@preskip\topsep
 855 %%  \thm@postskip\theorempreskipamount
 856 \itshape % body font
 857 }
 858
 859 \vbadness=9999
 860 \tolerance=9999
 861 \doublehyphendemerits=10000
 862 \doublehyphendemerits 640000   % corresponds to badness 800
 863 \finalhyphendemerits  1000000  % corresponds to badness 1000
 864
 865 \flushbottom
 866 \frenchspacing
 867 \ps@headings
 868 \twocolumn
 869
 870 % Screen PDF compatability
 871 \newcommand{\medline}[1]{%
 872   \unskip\unskip\ignorespaces}
 873
 874
 875 %%%%for smaller size text
 876 \newenvironment{methods}{%
 877   \begingroup
 878 \def\section{%
 879   \@startsection{section}{1}{\z@}
 880   {-24\p@ plus -3\p@}{4\p@}
 881   {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
 882  \def\subsection{%
 883   \@startsection{subsection}{2}{\z@}
 884   {-5\p@ plus -2\p@}{4\p@}
 885   {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
 886  \def\subsubsection{%
 887   \@startsection{subsubsection}{3}{\z@}
 888   {-6\p@ plus -1\p@}{-1em}
 889   {\reset@font\normalfont\normalsize\itshape}}
 890 \footnotesize
 891   \par}
 892 {\par\endgroup\bigskip\@afterheading\@afterindentfalse}
 893
 894
 895
 896 \graphicspath{{g:/artwork/oup/bioinfo/}}
 897
 898 \language=2
 899
 900 \hyphenation{Figure Table Figures Tables}
 901
 902 \newcommand{\href}[2]{#2}
 903
 904 \renewenvironment{proof}[1][\proofname]{\par
 905   \normalfont \topsep6\p@\@plus6\p@\relax
 906   \labelsep 0.5em
 907   \trivlist
 908   \item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
 909 }{\endtrivlist\@endpefalse}
 910
 911 %%Different Bonds
 912
 913 \def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
 914 \def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
 915 \def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
 916
 917 % Author queries
 918 %\fboxsep=4\p@
 919 %\fboxrule=0.5\p@
 920 \newcommand{\query}[2][0pt]{}%
 921 %  \marginpar{\vspace*{#1}%
 922 %    {\parbox{\marginparwidth}{%
 923 %     \raggedright\fontsize{6}{8}\selectfont
 924 %         #2}}}}
 925
 926 \renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
 927
 928 \endinput