% % % BIOINF document class % % last revision 2010-02-15 by Ulrich Bodenhofer % % \NeedsTeXFormat{LaTeX2e}[1995/12/01] \ProvidesClass{bioinf}[2010/02/15] \def\bioinf@basisclass{article} \newif\ifbasisclassdefined \basisclassdefinedfalse % % declare options for three basis classes % \DeclareOption{article}{\ifbasisclassdefined \ClassError{bioinf}{You may only supply one basis class.}{Remove the `article' option} \fi \def\bioinf@basisclass{article}\basisclassdefinedtrue} \DeclareOption{report}{\ifbasisclassdefined \ClassError{bioinf}{You may only supply one basis class.}{Remove the `report' option} \fi \def\bioinf@basisclass{report}\basisclassdefinedtrue} \DeclareOption{book}{\ifbasisclassdefined \ClassError{bioinf}{You may only supply one basis class.}{Remove the `book' option} \fi \def\bioinf@basisclass{book}\basisclassdefinedtrue} % % forward all other options to document class article % \DeclareOption*{{\ClassError{bioinf}{Option `\CurrentOption' not supported for BIOINF document class.}{Remove the `\CurrentOption' option}}} % % process options % \ProcessOptions\relax % % load document class article (always with options a4paper and titlepage) % \LoadClass[a4paper,11pt,twoside]{\bioinf@basisclass} \typeout{=============================================================}% \typeout{BIOINF document class loaded with basis class '\bioinf@basisclass'}% \typeout{=============================================================}% % % font customizations % \renewcommand{\encodingdefault}{T1} \renewcommand{\rmdefault}{ptm} \renewcommand{\sfdefault}{phv} \renewcommand{\ttdefault}{cmtt} \fontencoding{T1}\selectfont % % customization of item marks % \renewcommand{\labelitemi}{\rule[0.2ex]{0.8ex}{0.8ex}} \renewcommand{\labelitemii}{$\m@th\bullet$} % % include of additional packages % \RequirePackage{color} \RequirePackage{graphicx} \RequirePackage{ifthen} % % setup of page format % \setlength{\evensidemargin}{-1in} \setlength{\oddsidemargin}{-1in} \setlength{\topmargin}{-1in} \addtolength\evensidemargin{30mm} \addtolength\oddsidemargin{30mm} \addtolength\topmargin{28mm} \setlength{\textwidth}{150mm} \setlength{\headheight}{12pt} \setlength{\headsep}{8mm} \setlength{\textheight}{222mm} \ifx\pdfoutput\undefined \relax \else \setlength{\pdfpagewidth}{21cm} \setlength{\pdfpageheight}{29.7cm} \fi % % setup of customized headings style and listings % \input{bioinf-\bioinf@basisclass.txi} % % set page style % \pagestyle{headings} % % adjust parskip % \setlength{\parskip}{5pt plus 2pt minus 1pt} % % define colors and color commands % \definecolor{biowh}{rgb}{1.00,1.00,1.00} \definecolor{biobl}{rgb}{0.00,0.00,0.00} \definecolor{bioaz}{rgb}{0.204,0.325,0.631} \definecolor{biove}{rgb}{0.24,0.63,0.37} \definecolor{bioli}{rgb}{0.667,0.9333,0.667} \newcommand{\blue}{\color{bioaz}} \newcommand{\green}{\color{biove}} % % define BIOINF title page commands % \newcommand{\customtitlepage}[2]{% \thispagestyle{empty} #2 \vfill \noindent\makebox[0pt][l]{% \setlength{\unitlength}{1cm} \begin{picture}(0,0)(2,2.4) %\put(0,25.5){\makebox(0,0)[lb]{\color{bioli}\rule{19cm}{2.2cm}}} \put(19,25.5){\makebox(0,0)[rb]{\includegraphics[width=19cm]{bioinf-bar}}} \put(0.3,26.0){\makebox(0,0)[l]{\color{bioaz}\fontfamily{phv}\bfseries\large% Institute of Bioinformatics, Johannes Kepler University Linz}} \put(0.3,26.9){\makebox(0,0)[l]{\color{bioaz}\fontfamily{phv}\bfseries\Huge #1}} \put(0,1.6){\makebox(0,0)[lb]{\color{bioli}\rule{19cm}{1mm}}} \put(0,0){\makebox(0,0)[lb]{\fontfamily{phv}\normalsize\begin{tabular}[b]{l} Institute of Bioinformatics\\ Johannes Kepler University Linz\\ A-4040 Linz, Austria \end{tabular}}} \put(9.5,0.4){\makebox(0,0)[cb]{\includegraphics[height=0.8cm]{JKU_EN_noName}}} \put(19,0){\makebox(0,0)[rb]{\fontfamily{phv}\normalsize\begin{tabular}[b]{r} Tel. +43 732 2468 4520\\ Fax +43 732 2468 4539\\ http://www.bioinf.jku.at \end{tabular}}} %\put(0,24.5){\makebox(0,0)[lt]{\noindent\begin{minipage}{19cm} %#2 %\end{minipage}}} \end{picture}}\newpage} \def\bioinf@number{} \def\bioinf@keywords{} \def\bioinf@abstract{} \def\bioinf@citation{} \def\bioinf@affiliation{} \newcommand{\affiliation}[1]{\def\bioinf@affiliation{#1}} \newcommand{\pubnumber}[1]{\def\bioinf@number{#1}} \newcommand{\setkeywords}[1]{\def\bioinf@keywords{#1}} \newcommand{\setabstract}[1]{\def\bioinf@abstract{#1}} \newcommand{\setcitation}[1]{\def\bioinf@citation{#1}} \newcommand{\affilmark}[1]{\textsuperscript{\scriptsize #1}} \newcommand{\doi}[1]{% \ifx\href\undefined doi:#1 \else \href{http://dx.doi.org/#1}{doi:#1} \fi} \newcommand{\email}[1]{\ifx\href\undefined {\em #1} \else \href{mailto:#1}{{\em #1}} \fi} \newcommand{\reporttitlepage}[1]{\customtitlepage{#1}{% \mbox{ } \vfill \begin{center} \sffamily\bfseries\LARGE\@title \end{center} \begin{center} {\sffamily\bfseries\large\@author}\\[2mm] \ifx\@empty\bioinf@affiliation \relax \else {\sffamily\normalsize\bioinf@affiliation} \end{center} \fi \vspace{1.5cm} \ifthenelse{\equal{}{\bioinf@abstract}}{% \relax }{% \centerline{\rule{15cm}{1pt}}\vspace{2mm} \centerline{\begin{minipage}[b]{15cm} \noindent{\bf Abstract --- } \bioinf@abstract \end{minipage}} \ifx\@empty\bioinf@keywords \vspace{-1.5mm}\centerline{\rule{15cm}{1pt}} \fi } \ifthenelse{\equal{}{\bioinf@keywords}}{% \relax }{% \ifx\@empty\bioinf@abstract \centerline{\rule{15cm}{1pt}}\vspace{2mm} \else \vspace{5mm} \fi \centerline{\begin{minipage}[b]{15cm} \noindent{\bf Key words --- } \bioinf@keywords \end{minipage}} \vspace{-1.5mm}\centerline{\rule{15cm}{1pt}} } \ifthenelse{\equal{}{\bioinf@citation}}{% \relax }{% \vspace{2cm} \centerline{\begin{minipage}[b]{15cm} \noindent{\bf Citation: } \bioinf@citation \end{minipage}} } \vfill}} \newcommand{\researchreporttitlepage}{\reporttitlepage{Research Report \bioinf@number}} \newcommand{\techreporttitlepage}{\reporttitlepage{Technical Report \bioinf@number}} \newcommand{\preprinttitlepage}{\reporttitlepage{Publication Preprint}{}} \newcommand{\reprinttitlepage}{\reporttitlepage{Publication Reprint}{}} \newcommand{\manualtitlepage}[1][]{\customtitlepage{Software Manual}{% \mbox{ } \vfill \begin{center} \sffamily\bfseries\LARGE\@title \end{center} \ifthenelse{\equal{\@author}{}}{}{\begin{center} {\sffamily\bfseries\large\@author}\\[2mm] \ifx\@empty\bioinf@affiliation \relax \else {\sffamily\normalsize\bioinf@affiliation} \end{center} \fi} \vspace{1cm} \begin{center} {\Large\sffamily\bfseries #1} \end{center} \vfill \mbox{ }}} \newcommand{\lecturenotestitlepage}[1][]{\customtitlepage{Lecture Notes}{% \ifthenelse{\equal{#1}{}}{% \vspace*{2cm} \begin{center} \sffamily\bfseries\huge \@title \end{center} \vspace{2cm} \begin{center} \sffamily\bfseries\Large \@author \end{center} \vfill \mbox{ }}{% {\LARGE\sffamily\bfseries\mbox{ } \vfill \begin{center} #1 \end{center} \vfill \vfill \mbox{ }}}}} \newcommand{\copyrightpage}[1][]{% \clearpage \mbox{ } \vfill \vfill \noindent{\large \textcircled{c} \ifthenelse{\equal{#1}{}}{% \@author}{% #1}}\\[7mm] \noindent \BIOINFCopyrightNotice\thispagestyle{empty} \vfill \mbox{ } \clearpage} \newcommand{\BIOINFCopyrightNotice}{This material, no matter whether in printed or electronic form, may be used for personal and educational use only. Any reproduction of this manuscript, no matter whether as a whole or in parts, no matter whether in printed or in electronic form, requires explicit prior acceptance of the author.} \endinput % % end of scch-tr.cls %