\documentclass[11pt,titlepage]{article}
\usepackage{skaff,LocalDefs}

\date{\today\\[1mm]
\begin{minipage}[t]{0.75\linewidth}
This is the documentation of library functions compiled into 
the archives \texttt{libkurtz-basic.a}, \texttt{libkurtz.a},
\texttt{libmkvtree.a} and \texttt{libvmatch.a}. 
The include file used for compiling these
library can be found in directory \texttt{include}.  
The library files for \texttt{libkurtz.a} are in the directory \texttt{lib}. 
The library files for \texttt{libvmkvtree.a} are in the directory 
\texttt{virtual/Mkvtree}. 
The library files for \texttt{libvmatch.a} are in the directory 
\texttt{virtual/Vmatch}. 
For each library file, say \texttt{libfile.c} there exists a corresponding
file \texttt{include/libfile.pr} containing the header of the functions
exported from \texttt{libfile.c}.
The PDF-version of this document comes with hyperlinks,
linking type names, function names, and macro names to their definition. 
The acrobat reader \texttt{acroread} conveniently allows navigating along
these links. If you encounter broken or missing links, please contact the
author at \texttt{kurtz@zbh.uni-hamburg.de}. Other comments
are also welcome.
\end{minipage}
}

\makeindex
\begin{document}

\maketitle
\newpage
\pagestyle{headings}
\pagenumbering{Roman}
\tableofcontents
\newpage
\pagenumbering{arabic}
\setcounter{page}{1}

\section{Basic Definition}%%%
\Showheaderfile{types}{March 2001}
\Showheaderfile{absdef}{April 2001}
\Showheaderfile{chardef}{January 2001}
\Showheaderfile{maxfiles}{January 2001}
\Showheaderfile{megabytes}{February 2000}
\Showheaderfile{divmodmul}{February 2003}
\Showheaderfile{minmax}{June 1994}
\Showheaderfile{scoredef}{January 2000}
\Showheaderfile{fopen}{June 1999}
\Showheaderfile{mumcand}{March 2003}
\Showheaderfile{safecast}{May 2003}
\Showheaderfile{safeadd}{March 2003}
\Showheaderfile{safemult}{March 2003}
\Showheaderfile{evaluedef}{March 2003}
\Showheaderfile{visible}{March 1994}

\section{Debugging Messages}%%%
\Showheaderfile{debugdef}{March 1999}
\Showcodefile{debug}{March 1997}

\section{Error Messages}%%%
\Showheaderfile{errordef}{December 1999}
\Showcodefile{seterror}{January 1999}

\section{Option Processing}%%%
\Showheaderfile{optdesc}{March 1998}
\Showcodefile{procopt}{October 1999}

\section{Numbers}%%%
\Showheaderfile{logbase}{February 2000}

\section{Space Management}%%%
\Showheaderfile{spacedef}{January 2000}
\Showcodefile{space}{February 2001}
\Showcodefile{mapfile}{May 2000}
\Showheaderfile{arraydef}{May 2000}

\section{File Management}%%%
\Showheaderfile{fhandledef}{November 2003}
\Showcodefile{filehandle}{November 2003}
\Showcodefile{outindextab}{March 2000}
\Showcodefile{readgzip}{May 2003}
%\Showcodefile{recvirt}{June 2000}

\section{Alphabets}%%%
\Showheaderfile{alphadef}{March 2001}
\Showcodefile{alphabet}{March 2000}
\Showcodefile{codon}{March 2001}
\Showheaderfile{compl}{May 2002}

\section{Multiple Sequences}%%%
\Showcodefile{getfasta}{March 2000}
\Showheaderfile{multidef}{March 2000}
\Showcodefile{multiseq}{July 2000}
\Showcodefile{multiseq-adv}{July 2000}

\section{Dynamic Programming}%%%
\Showcodefile{uedist}{Nov 1999}
\Showcodefile{dpacp}{Nov 2003}
\Showcodefile{extendHD}{March 2000}
\Showcodefile{extendED}{March 2000}
\Showheaderfile{frontdef}{June 1999}
\Showcodefile{front}{June 1999}
\Showcodefile{frontSEP}{June 1999}
\Showcodefile{galign}{June 1999}
\Showcodefile{xdropal1}{March 2001}
\Showcodefile{xdropal2}{March 2001}

\section{Virtual Suffix Trees}%%%
\Showheaderfile{virtualdef}{June 2000}
\Showcodefile{readvirt}{June 2000}
\Showcodefile{vnodes}{June 2000}
\Showcodefile{readmulti}{December 2000}
\Showcodefile{accvirt}{December 2001}
\Showcodefile{mkskip}{October 2000}
\Showcodefile{binsplitvn}{December 2001}

\section{Matches}%%%
\Showheaderfile{match}{September 2000}
\Showheaderfile{select}{January 2002}
\Showcodefile{extcmp}{September 2000}
\Showcodefile{bestmatch}{September 2000}
\Showcodefile{mcontain}{October 2000}
\Showcodefile{maxpref}{July 2000}
\Showcodefile{mkcld}{July 2000}

\section{Alignments}%%%
\Showheaderfile{alignment}{March 2001}
\Showcodefile{showalign}{November 2000}

\section{Bit Vector Manipulation}%%%
\Showheaderfile{dpbitvec}{October 1999}
\Showcodefile{dpvecdbg}{October 1999}
\Showheaderfile{intbits}{January 1998}
\Showcodefile{showibit}{January 1998}

\section{Xdrop Algorithms}%%%
\Showheaderfile{xdropdef}{March 2001}
\Showcodefile{xdrop}{March 2001}

\section{Clustering}%%%
\Showheaderfile{clusterdef}{February 2001}
\Showcodefile{cluster}{February 2001}

\section{Queues}%%%
\Showcodefile{queue}{February 1999}

\section{Sorting and Searching}%%%
\Showcodefile{binsearch}{April 1997}
\Showcodefile{bmhfun}{July 2000}
\Showcodefile{matsort}{May 2001}
\Showcodefile{remdups}{May 2001}
\Showheaderfile{redblackdef}{May 2003}
\Showcodefile{redblack}{May 2003}
\Showcodefile{dictmaxsize}{May 2003}

\section{Miscallaneous}%%%
\Showcodefile{bwtcode}{May 2000}
\Showheaderfile{iubdef}{February 1999}
\Showheaderfile{dlopen}{March 2003}
\Showheaderfile{experim}{March 2000}
\Showheaderfile{args}{July 1994}
\Showcodefile{distri}{May 2000}
\Showcodefile{clock}{May 2000}
\Showcodefile{emptyln}{March 1997}
\Showcodefile{evalues}{November 1999}
\Showcodefile{applall}{July 2000}
\Showcodefile{getbasename}{June 2000}
\Showcodefile{getdirname}{June 2000}
\Showcodefile{splitargs}{December 2000}
\Showcodefile{checkonoff}{December 2000}
\Showcodefile{cleanMUMcand}{July 2002}
\Showcodefile{reverse}{May 2001}
%\Showcodefile{searchpath}{May 2001}

\section{The Vmatch Library}

\Showheaderfile{outinfo}{November 2000}
\Showheaderfile{mparms}{January 2001}
\Showheaderfile{matchtask}{January 2001}
\Showheaderfile{matchstate}{January 2001}
\Showcodefile{detmatch}{December 2000}
\Showcodefile{echomatch}{October 2000}

\newpage
\FILEINFO{\Indexheader}{Stefan Kurtz}{March 2001}

\input{vstree.ind}

\end{document}
