\ProvidesPackage{LocalDefs}
%\usepackage{german}
\usepackage[pdftex]{graphics}
\usepackage{alltt}
\usepackage{xspace}
\usepackage{command,disstrees}
\usepackage{epsfig}
\usepackage{supertabular}

\newcommand{\Gth}[0]{\textit{Genome\-Threader}\xspace}
\newcommand{\Hmmer}[0]{\textit{HMMER}\xspace}
\newcommand{\Callgth}[0]{\texttt{gth}\xspace}
\newcommand{\Callgthconsensus}[0]{\texttt{gthconsensus}\xspace}
\newcommand{\Callgthsplit}[0]{\texttt{gthsplit}\xspace}
\newcommand{\Callgthgetseq}[0]{\texttt{gthgetseq}\xspace}
\newcommand{\Callgthfilestat}[0]{\texttt{gthfilestat}\xspace}
\newcommand{\Callgthbssmfileinfo}[0]{\texttt{gthbssmfileinfo}\xspace}
\newcommand{\Callgthbssmtrain}[0]{\texttt{gthbssmtrain}\xspace}
\newcommand{\Callgthbssmbuild}[0]{\texttt{gthbssmbuild}\xspace}
\newcommand{\Callgthclean}[0]{\texttt{gthclean.sh}\xspace}
\newcommand{\Callgthsplittwodim}[0]{\texttt{gthsplit2dim.sh}\xspace}
\newcommand{\mkbssmfiles}[0]{\textit{Mkbssmfiles}\xspace}
\newcommand{\gs}[0]{\textit{GeneSeqer}\xspace}
\newcommand{\GStwo}[0]{\textit{GeneSeqer2}\xspace}
\newcommand{\vmatch}[0]{\textit{Vmatch}\xspace}
\newcommand{\callvmatch}[0]{\texttt{vmatch}\xspace}
\newcommand{\mkvtree}[0]{\textit{Mkvtree}\xspace}
\newcommand{\callmkvtree}[0]{\texttt{mkvtree}\xspace}
\newcommand{\splicepredictor}[0]{\textit{SplicePredictor}\xspace}
\newcommand{\exdomino}[0]{\textit{Exdomino}\xspace}
\newcommand{\gap}[0]{\texttt{\symbol{45}}}
\newcommand{\abinitio}[0]{\textit{ab initio}\xspace}
\newcommand{\Abinitio}[0]{\textit{Ab initio}\xspace}
\newcommand{\genscan}[0]{\textit{GENSCAN}\xspace}
\newcommand{\blast}[0]{\textit{BLAST}\xspace}
\newcommand{\blastp}[0]{\textit{BLASTP}\xspace}
\newcommand{\blastx}[0]{\textit{BLASTX}\xspace}
\newcommand{\clustalw}[0]{\textit{CLUSTAL W}\xspace}
\newcommand{\fasta}[0]{\textit{FASTA}\xspace}
\newcommand{\simfour}[0]{\textit{sim4}\xspace}
\newcommand{\genewise}[0]{\textit{GENEWISE}\xspace}
\newcommand{\genegenerator}[0]{\textit{GeneGenerator}\xspace}
\newcommand{\procrustes}[0]{\textit{PROCRUSTES}\xspace}
\newcommand{\5}[0]{5$^\prime$}
\newcommand{\3}[0]{3$^\prime$}
\newcommand{\Adenine}[0]{\texttt{A}}
\newcommand{\Cytosine}[0]{\texttt{C}}
\newcommand{\Guanine}[0]{\texttt{G}}
\newcommand{\Thymine}[0]{\texttt{T}}
\newcommand{\Undetchar}[0]{\texttt{N}}
%\newcommand{\comment}[1]{[\textit{#1}]}
%\newcommand{\comment}[1]{}
%\newcommand{\note}[1]{[\textit{#1}]}
\newcommand{\note}[1]{}
\newcommand{\tobedone}[0]{\emph{To be done.}\xspace}
\newcommand{\manual}[0]{\href{gthmanual.pdf}{manual}}
\newcommand{\documentation}[0]{\href{gthdoc.pdf}{documentation}\xspace}

\newcommand{\fgenes}[0]{\textit{FGENES}\xspace}
\newcommand{\genemark}[0]{\textit{GeneMark.hmm}\xspace}
\newcommand{\genie}[0]{\textit{Genie}\xspace}
\newcommand{\hmmgene}[0]{\textit{HMMgene}\xspace}
\newcommand{\morgan}[0]{\textit{Morgan}\xspace}
\newcommand{\mzef}[0]{\textit{MZEF}\xspace}
\newcommand{\cem}[0]{\textit{CEM}\xspace}
\newcommand{\rosetta}[0]{\textit{ROSETTA}\xspace}
\newcommand{\sgpone}[0]{\textit{SGP-1}\xspace}
\newcommand{\slam}[0]{\textit{SLAM}\xspace}
\newcommand{\twinscan}[0]{\textit{TWINSCAN}\xspace}
\newcommand{\agenda}[0]{\textit{AGenDa}\xspace}

\newcommand{\splint}[0]{\textit{Splint}\xspace}

\newcommand{\polyA}[0]{poly(A)\xspace}
\newcommand{\polyT}[0]{poly(T)\xspace}
\newcommand{\Fastastart}[0]{\texttt{\SY{62}}\xspace}
\newcommand{\Seqformkeyword}[1]{\texttt{\small #1}\index{#1@\texttt{#1}}}
\newcommand{\multieditoparray}[0]{mEOParray\xspace}


\newcommand{\sensitivity}[0]{S_n}
\newcommand{\specificity}[0]{S_p}

\newcommand{\intervalset}[0]{I}
\newcommand{\nucleotidestring}[0]{nuc}
\newcommand{\exonstring}[0]{ex}
\newcommand{\exonpredicate}[0]{exon}
\newcommand{\genestring}[0]{gen}
\newcommand{\true}[0]{\textit{True}\xspace}
\newcommand{\false}[0]{\textit{False}\xspace}
\newcommand{\nucleotidesensitivity}[0]{M_{sens}^{\nucleotidestring}}
\newcommand{\nucleotidespecificity}[0]{M_{spec}^{\nucleotidestring}}
\newcommand{\nonnucleotidesensitivity}[0]{\neg\nucleotidesensitivity}
\newcommand{\nonnucleotidespecificity}[0]{\neg\nucleotidespecificity}
\newcommand{\exonsensitivity}[0]{M_{sens}^{\exonstring}}
\newcommand{\exonspecificity}[0]{M_{spec}^{\exonstring}}
\newcommand{\genesensitivity}[0]{M_{sens}^{\genestring}}
\newcommand{\genespecificity}[0]{M_{spec}^{\genestring}}
\newcommand{\plainsensitivity}[0]{M_{sens}}
\newcommand{\plainspecificity}[0]{M_{spec}}
\newcommand{\truepositive}[0]{\mathit{TP}}
\newcommand{\truenegative}[0]{\mathit{TN}}
\newcommand{\falsepositive}[0]{\mathit{FP}}
\newcommand{\falsenegative}[0]{\mathit{FN}}
\newcommand{\cc}[0]{\mathit{CC}}
\newcommand{\acp}[0]{\mathit{ACP}}
\newcommand{\ac}[0]{\mathit{AC}}
\newcommand{\trueexon}[0]{\mathit{TE}}
\newcommand{\actualexon}[0]{\mathit{AE}}
\newcommand{\missingexon}[0]{\mathit{ME}}
\newcommand{\predictedexon}[0]{\mathit{PE}}
\newcommand{\wrongexon}[0]{\mathit{WE}}
\newcommand{\truegene}[0]{\mathit{TG}}
\newcommand{\actualgene}[0]{\mathit{AG}}
\newcommand{\predictedgene}[0]{\mathit{PG}}
\newcommand{\missinggene}[0]{\mathit{MG}}
\newcommand{\wronggene}[0]{\mathit{WG}}
\newcommand{\gt}[0]{\mathit{GT}}
\newcommand{\ag}[0]{\mathit{AG}}
\newcommand{\gtag}[0]{\mathit{GT-AG}}

\newcommand{\computebordersandscoresfunc}[0]{\texttt{computebordersandscores()}\xspace}
\newcommand{\determinecutoffsfunc}[0]{\texttt{determinecutoffs()}\xspace}

% identifier for basic definitions
\newcommand{\genseqident}[0]{g}
\newcommand{\genchar}[0]{g}
\newcommand{\cdnaseqident}[0]{c}
\newcommand{\cdnachar}[0]{c}
\newcommand{\gensubseqleftident}[0]{i}
\newcommand{\gensubseqrightident}[0]{j}
\newcommand{\numofexons}[0]{k}
\newcommand{\numofgenes}[0]{l}
\newcommand{\leftintervalborder}[0]{a}
\newcommand{\rightintervalborder}[0]{b}
\newcommand{\statusfunctionident}[0]{\varrho}
\newcommand{\exonmappingfunction}[0]{\varphi}
\newcommand{\genseqlength}[0]{n}
\newcommand{\cdnaseqlength}[0]{m}
\newcommand{\coding}[0]{c}
\newcommand{\noncoding}[0]{\mathit{nc}}
\newcommand{\counter}[0]{t}
\newcommand{\predictionchar}[0]{p}
\newcommand{\realitychar}[0]{r}
\newcommand{\predictionstatusfunc}[0]{\statusfunctionident_\predictionchar}
\newcommand{\realitystatusfunc}[0]{\statusfunctionident_\realitychar}
\newcommand{\predictionexon}[0]{\genseqident_\predictionchar^{\exonstring}(\gensubseqleftident,\gensubseqrightident)}
\newcommand{\realityexon}[0]{\genseqident_\realitychar^{\exonstring}(\gensubseqleftident,\gensubseqrightident)}
\newcommand{\adenine}[0]{A}
\newcommand{\cytosine}[0]{C}
\newcommand{\guanine}[0]{G}
\newcommand{\thymine}[0]{T}
\newcommand{\undetchar}[0]{N}
\newcommand{\identity}[0]{\sigma}
\newcommand{\mismatch}[0]{\mu}
\newcommand{\undetcharweight}[0]{\nu}
\newcommand{\deletion}[0]{\delta}
\newcommand{\aligndeffirstseq}[0]{x}
\newcommand{\aligndefsecondseq}[0]{y}


% identifier for DP algorithm
\newcommand{\probchar}[0]{P}
\newcommand{\probinitialexonstate}[0]{\transition_{\exon_1}}
\newcommand{\probdelgen}[0]{\probchar_{\Delta\genseqident}}
\newcommand{\probdonor}[1]{\probchar_{D(#1)}}
\newcommand{\probacceptor}[1]{\probchar_{A(#1)}}
\newcommand{\transition}[0]{\tau}
\newcommand{\exon}[0]{e}
\newcommand{\intron}[0]{i}
\newcommand{\firstcharofA}[0]{X}
\newcommand{\secondcharofA}[0]{Y}
\newcommand{\genseqpos}[0]{u}
\newcommand{\refseqpos}[0]{v}
\newcommand{\stateseqident}[0]{q}
\newcommand{\state}[0]{q}
\newcommand{\statecounter}[0]{w}
\newcommand{\stateseqlength}[0]{o}
\newcommand{\splicedoutput}[0]{s}
\newcommand{\exonmatrix}[0]{E}
\newcommand{\intronmatrix}[0]{I}
\newcommand{\Astates}[0]{\Alpha_{\mathit{states}}}
\newcommand{\wsizezerotransitionweights}[0]{\vartheta}
\newcommand{\wsizedecreasedoutputweights}[0]{\omega}
\newcommand{\cutoffsminexonlen}[0]{\kappa}
\newcommand{\scoreminexonlen}[0]{\lambda}
\newcommand{\minavgsplicesiteprob}[0]{\zeta}
\newcommand{\duplicatecheckarg}[0]{\zeta}
\newcommand{\duplicatecheckmode}[0]{mode\xspace}


% identifier for manual
\newcommand{\Programname}[1]{\texttt{#1}}
\newcommand{\Environmentvariable}[1]{\texttt{\small #1}\index{#1@\texttt{#1}}}
\newcommand{\genseqindex}[0]{genseqfiles\xspace}
\newcommand{\cdnaindex}[0]{cdnafiles\xspace}
\newcommand{\proteinindex}[0]{proteinfiles\xspace}
\newcommand{\leadingmode}[0]{leadingmode\xspace}
\newcommand{\terminalmode}[0]{terminalmode\xspace}
\newcommand{\relaxedmode}[0]{\texttt{RELAXED}\xspace}
\newcommand{\strictmode}[0]{\texttt{STRICT}\xspace}
\newcommand{\minimalmode}[0]{\texttt{MINIMAL}\xspace}

\newcommand{\bssmdir}[0]{BSSMDIR}
\newcommand{\gthdatadir}[0]{GTHDATADIR}
\newcommand{\speciesname}[0]{speciesname\xspace}
\newcommand{\paramfileprefix}[0]{paramfileprefix\xspace}
\newcommand{\scorematrixname}[0]{scorematrixname\xspace}
\newcommand{\showintronmaxlen}[0]{maxintronlen\xspace}
\newcommand{\outputfile}[0]{outputfile}
\newcommand{\smapfile}[0]{smapfile}
\newcommand{\frompos}[0]{i\xspace}
\newcommand{\topos}[0]{j\xspace}
\newcommand{\width}[0]{w\xspace}
\newcommand{\minmatchlen}[0]{\ell\xspace}
\newcommand{\errors}[0]{k\xspace}
\newcommand{\seedlength}[0]{m\xspace}
\newcommand{\exdrop}[0]{x\xspace}
\newcommand{\hdist}[0]{h\xspace}
\newcommand{\dpminexonlength}[0]{\xi\xspace}
\newcommand{\dpminintronlength}[0]{\eta\xspace}
\newcommand{\shortexonpenalty}[0]{\chi\xspace}
\newcommand{\shortintronpenalty}[0]{\psi\xspace}
\newcommand{\firstalshown}[0]{n\xspace}
\newcommand{\minorflength}[0]{o\xspace}
\newcommand{\autointroncutout}[0]{s\xspace}
\newcommand{\icinitialdelta}[0]{d\xspace}
\newcommand{\iciterations}[0]{i\xspace}
\newcommand{\icdeltaincrease}[0]{di\xspace}
\newcommand{\icminremintronlen}[0]{r\xspace}
\newcommand{\Range}[0]{$\Re$\xspace}

\newcommand{\Xdrop}[0]{\mathit{Xdrop}}

%commands for manual
\newcommand{\Showversionfeatures}[1]{\paragraph{\Gth \texttt{#1}:}}

%format types taken from vmotif.tex
\newcommand{\Showformattype}[1]{\textsc{#1}\xspace}
\newcommand{\Fasta}{\Showformattype{Fasta}}
\newcommand{\EMBL}{\Showformattype{Embl}}
\newcommand{\SWISSPROT}{\Showformattype{Swissprot}}
\newcommand{\GENBANK}{\Showformattype{Genbank}}


\newenvironment{Output}%
{%\par%
 %\addvspace{\medskipamount}%
 \begin{sloppy}
 \begin{scriptsize}
 \begin{alltt}}
{\end{alltt}%
 \end{scriptsize}%
 \end{sloppy}
 \addvspace{-\medskipamount}
}

\newenvironment{LargeOutput}%
{\par%
 %\addvspace{\medskipamount}%
 \begin{sloppy}
 \begin{footnotesize}
 \begin{alltt}}
{\end{alltt}%
 \end{footnotesize}%
 \end{sloppy}
 \addvspace{-\medskipamount}
}
