%% %% This is file `pgfmolbio.chromatogram.tex', %% generated with the docstrip utility. %% %% The original source files were: %% %% pgfmolbio.dtx (with options: `pmb-chr-tex') %% %% Copyright (C) 2012 by Wolfgang Skala %% %% This work may be distributed and/or modified under the %% conditions of the LaTeX Project Public License, either version 1.3 %% of this license or (at your option) any later version. %% The latest version of this license is in %% http://www.latex-project.org/lppl.txt %% and version 1.3 or later is part of all distributions of LaTeX %% version 2005/12/01 or later. %% \ProvidesFile{pgfmolbio.chromatogram.tex}[2012/10/01 v0.2 SCF chromatograms] \ifluatex \RequireLuaModule{pgfmolbio.chromatogram} \fi \definecolor{pmbTraceGreen}{RGB}{34,114,46} \definecolor{pmbTraceBlue}{RGB}{48,37,199} \definecolor{pmbTraceBlack}{RGB}{0,0,0} \definecolor{pmbTraceRed}{RGB}{191,27,27} \definecolor{pmbTraceYellow}{RGB}{233,230,0} \def\@pmb@chr@keydef#1#2{% \pgfkeyssetvalue{/pgfmolbio/chromatogram/#1}{#2}% } \def\@pmb@chr@stylekeydef#1#2{% \pgfkeys{/pgfmolbio/chromatogram/#1/.style={#2}}% } \def\@pmb@chr@getkey#1{% \pgfkeysvalueof{/pgfmolbio/chromatogram/#1}% } \@pmb@chr@keydef{sample range}{1-500 step 1} \@pmb@chr@keydef{x unit}{0.2mm} \@pmb@chr@keydef{y unit}{0.01mm} \@pmb@chr@keydef{samples per line}{500} \@pmb@chr@keydef{baseline skip}{3cm} \@pmb@chr@stylekeydef{canvas style}{draw=none, fill=none} \@pmb@chr@keydef{canvas height}{2cm} \@pmb@chr@stylekeydef{trace A style}{pmbTraceGreen} \@pmb@chr@stylekeydef{trace C style}{pmbTraceBlue} \@pmb@chr@stylekeydef{trace G style}{pmbTraceBlack} \@pmb@chr@stylekeydef{trace T style}{pmbTraceRed} \pgfmolbioset[chromatogram]{% trace style/.code=\pgfkeysalso{ trace A style/.style={#1}, trace C style/.style={#1}, trace G style/.style={#1}, trace T style/.style={#1} }% } \@pmb@chr@keydef{traces drawn}{} \@pmb@chr@stylekeydef{tick A style}{thin, pmbTraceGreen} \@pmb@chr@stylekeydef{tick C style}{thin, pmbTraceBlue} \@pmb@chr@stylekeydef{tick G style}{thin, pmbTraceBlack} \@pmb@chr@stylekeydef{tick T style}{thin, pmbTraceRed} \pgfmolbioset[chromatogram]{% tick style/.code=\pgfkeysalso{ tick A style/.style={#1}, tick C style/.style={#1}, tick G style/.style={#1}, tick T style/.style={#1} }% } \@pmb@chr@keydef{tick length}{1mm} \@pmb@chr@keydef{ticks drawn}{} \@pmb@chr@keydef{base label A text}{\strut A} \@pmb@chr@keydef{base label C text}{\strut C} \@pmb@chr@keydef{base label G text}{\strut G} \@pmb@chr@keydef{base label T text}{\strut T} \@pmb@chr@stylekeydef{base label A style}% {below=4pt, font=\ttfamily\footnotesize, pmbTraceGreen} \@pmb@chr@stylekeydef{base label C style}% {below=4pt, font=\ttfamily\footnotesize, pmbTraceBlue} \@pmb@chr@stylekeydef{base label G style}% {below=4pt, font=\ttfamily\footnotesize, pmbTraceBlack} \@pmb@chr@stylekeydef{base label T style}% {below=4pt, font=\ttfamily\footnotesize, pmbTraceRed} \pgfmolbioset[chromatogram]{% base label style/.code=\pgfkeysalso{ base label A style/.style={#1}, base label C style/.style={#1}, base label G style/.style={#1}, base label T style/.style={#1} }% } \@pmb@chr@keydef{base labels drawn}{} \newif\ifpmb@chr@showbasenumbers \pgfmolbioset[chromatogram]{% show base numbers/.is if=pmb@chr@showbasenumbers, show base numbers } \@pmb@chr@stylekeydef{base number style}% {pmbTraceBlack, below=-3pt, font=\sffamily\tiny} \@pmb@chr@keydef{base number range}{auto-auto step 10} \@pmb@chr@keydef{probability distance}{0.8cm} \@pmb@chr@keydef{probabilities drawn}{} \@pmb@chr@keydef{probability style function}{nil} \pgfmolbioset[chromatogram]{ bases drawn/.code=\pgfkeysalso{ traces drawn=#1, ticks drawn=#1, base labels drawn=#1, probabilities drawn=#1 }, bases drawn=ACGT } \ifluatex\else\expandafter\endinput\fi \newif\ifpmb@chr@tikzpicture \newcommand\pmbchromatogram[2][]{% \@ifundefined{useasboundingbox}% {\pmb@chr@tikzpicturefalse\begin{tikzpicture}}% {\pmb@chr@tikzpicturetrue\begingroup}% \pgfmolbioset[chromatogram]{#1}% \directlua{ pmbChromatogram = pgfmolbio.chromatogram.Chromatogram:new() pmbChromatogram:readScfFile("#2") pmbChromatogram:setParameters{ sampleRange = "\@pmb@chr@getkey{sample range}", xUnit = "\@pmb@chr@getkey{x unit}", yUnit = "\@pmb@chr@getkey{y unit}", samplesPerLine = "\@pmb@chr@getkey{samples per line}", baselineSkip = "\@pmb@chr@getkey{baseline skip}", canvasHeight = "\@pmb@chr@getkey{canvas height}", tracesDrawn = "\@pmb@chr@getkey{traces drawn}", tickLength = "\@pmb@chr@getkey{tick length}", ticksDrawn = "\@pmb@chr@getkey{ticks drawn}", baseLabelsDrawn = "\@pmb@chr@getkey{base labels drawn}", showBaseNumbers = "\ifpmb@chr@showbasenumbers true\else false\fi", probDistance = "\@pmb@chr@getkey{probability distance}", probabilitiesDrawn = "\@pmb@chr@getkey{probabilities drawn}", probStyle = \@pmb@chr@getkey{probability style function} } pmbChromatogram:setParameters{ baseNumberRange = "\@pmb@chr@getkey{base number range}", } pgfmolbio.setCoordinateFormat( "\pgfkeysvalueof{/pgfmolbio/coordinate unit}", "\pgfkeysvalueof{/pgfmolbio/coordinate format string}" ) \ifpmb@loadmodule@convert local filename = "\pgfkeysvalueof{/pgfmolbio/convert/output file name}" if filename == "(auto)" then filename = "pmbconverted" .. pgfmolbio.outputFileId end filename = filename .. ".\pgfkeysvalueof{/pgfmolbio/convert/output file extension}" outputFile, ioError = io.open(filename, "w") if ioError then tex.error(ioError) end tex.sprint = function (a) outputFile:write(a) end tex.sprint("\string\\begin{tikzpicture}") pmbChromatogram:printTikzChromatogram() tex.sprint("\string\n\string\\end{tikzpicture}") outputFile:close() pgfmolbio.outputFileId = pgfmolbio.outputFileId + 1 \else pmbChromatogram:printTikzChromatogram() \fi }% \ifpmb@chr@tikzpicture\endgroup\else\end{tikzpicture}\fi% } \endinput %% %% End of file `pgfmolbio.chromatogram.tex'.