%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % DO NOT MAKE ANY CHANGES TO THIS DOCUMENT! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % %%% Scribing Document Class %%% %%% This document class is much like the article class. %%% These are the preamble commands provided by this document class: %%% %%% \lecturenumber{number} % sequence number %%% \lecturetitle{title} % title describing lecture topic %%% \lecturedate{date} % date on which lecture was delivered %%% \lecturescribe{name} % name of individual scribing lecture %%% %%% The class also provides a number of new theorems, commands, and %%% environments, including: %%% %%% \urlclick{url} %%% \figureadd{basename}{label}{caption} %%% \figureaddnostretch{basename}{label}{caption} %%% \ProvidesClass{scribing} \LoadClass{article} %------------------------------------------------------------------- \newif\ifpdf \ifx\pdfoutput\undefined \pdffalse % we are not running PDFLaTeX \else \pdfoutput=1 % we are running PDFLaTeX \pdftrue \fi %------------------------------------------------------------------- \ifpdf \usepackage[pdftex, colorlinks=true, urlcolor=rltblue, % \href{...}{...} filecolor=rltgreen, % \href*{...} linkcolor=rltred, % \ref{...} and \pageref{...} citecolor=rltbrightgreen, % \cite{...} anchorcolor=rltbrightblue, % ??? menucolor=rltdarkblue, % ??? pdftitle={CPS260/BGT204 Lecture Notes}, pdfauthor={Pankaj K. Agarwal, Duke University}, pdfsubject={Algorithms in Computational Biology}, pdfkeywords={algorithms computational biology bioinformatics course lecture notes education}, pagebackref, pdfpagemode=None, bookmarksopen=true]{hyperref} \pdfcompresslevel=9 \usepackage[pdftex]{graphicx} \usepackage{thumbpdf} \else \usepackage[ colorlinks=true, urlcolor=rltblue, % \href{...}{...} filecolor=rltgreen, % \href*{...} linkcolor=rltred, % \ref{...} and \pageref{...} citecolor=rltbrightgreen, % \cite{...} anchorcolor=rltbrightblue, % ??? menucolor=rltdarkblue]{hyperref} % ??? \usepackage[dvips]{graphicx} \fi %------------------------------------------------------------------- \usepackage{color} \definecolor{rltbrightred}{rgb}{1,0,0} \definecolor{rltred}{rgb}{0.75,0,0} \definecolor{rltdarkred}{rgb}{0.5,0,0} % \definecolor{rltbrightgreen}{rgb}{0,0.75,0} \definecolor{rltgreen}{rgb}{0,0.5,0} \definecolor{rltdarkgreen}{rgb}{0,0,0.25} % \definecolor{rltbrightblue}{rgb}{0,0,1} \definecolor{rltblue}{rgb}{0,0,0.75} \definecolor{rltdarkblue}{rgb}{0,0,0.5} %------------------------------------------------------------------- \textwidth=6in \oddsidemargin=0.25in \evensidemargin=0.25in \topmargin=-0.1in \footskip=0.8in \parindent=0.0cm \parskip=0.3cm \textheight=8.00in \setcounter{tocdepth}{3} \setcounter{secnumdepth}{2} \sloppy \newcommand{\lecturenumber}[1]{% \newcommand{\lecnumber}{#1} } \newcommand{\lecturetitle}[1]{% \newcommand{\lectitle}{#1} } \newcommand{\lecturedate}[1]{% \newcommand{\lecdate}{#1} } \newcommand{\lecturescribe}[1]{% \newcommand{\lecscribe}{#1} } \newcommand{\urlclick}[1]{\href{#1}{\emph{#1}}} \newcommand{\figureadd}[3]{% \begin{figure}[ht] \begin{center} \includegraphics[width=\textwidth]{#1} \caption{#3} \label{#2} \end{center} \end{figure} } \newcommand{\figureaddnostretch}[3]{% \begin{figure}[ht] \begin{center} \includegraphics{#1} \caption{#3} \label{#2} \end{center} \end{figure} } \newtheorem{theorem}{Theorem} \newtheorem{corollary}{Corollary} \newtheorem{lemma}{Lemma} \newtheorem{claim}{Claim} \newtheorem{fact}{Fact} \newtheorem{definition}{Definition} \newtheorem{assumption}{Assumption} \newtheorem{observation}{Observation} \newtheorem{example}{Example} \newcommand{\qed}{\rule{7pt}{7pt}} \newenvironment{proof}{\noindent{\bf Proof:}}{\qed\bigskip} \newenvironment{proof_sketch}{\noindent{\bf Sketch of Proof}\hspace*{1em}}{\qed\bigskip} \renewcommand{\thepage}{\lecnumber-\arabic{page}} \renewcommand{\thesection}{\lecnumber.\arabic{section}} \renewcommand{\theequation}{\lecnumber.\arabic{equation}} \renewcommand{\thefigure}{\lecnumber.\arabic{figure}} \renewcommand{\thetable}{\lecnumber.\arabic{table}} \pagestyle{myheadings} \thispagestyle{plain} \setcounter{page}{1} \AtBeginDocument{% \begin{center} \framebox{% \vbox{% \textbf{CPS260/BGT204.1 Algorithms in Computational Biology \hfill \lecdate}\\ \vspace{1.2em} \textbf{\Large Lecture \lecnumber: \lectitle}\\ \vspace{1em} \textsl{Lecturer: Pankaj K. Agarwal \hfill Scribe: \lecscribe}\\ \vspace{1em} } } \end{center} \vspace*{4mm} \markboth{Lecture \lecnumber: \lecdate}{Lecture \lecnumber: \lecdate} \noindent } \def\etal{\emph{et al.}}