%% %% This is file `pgfmolbio.chromatogram.tex', %% generated with the docstrip utility. %% %% The original source files were: %% %% pgfmolbio.dtx (with options: `pmb-chr') %% %% Copyright (C) 2011 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}[2011/09/20 v0.1 SCF Chromatograms] \RequireLuaModule{pgfmolbio.chromatogram} \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{% \pgfkeysdef{/pgfmolbio/chromatogram/#1}{% \expandafter\def\csname pmb@chr@#1\endcsname{##1}% }% } \def\@pmb@chr@stylekeydef#1{% \pgfkeysdef{/pgfmolbio/chromatogram/#1}{% \pgfkeys{/pgfmolbio/chromatogram/#1@style/.style={##1}}% }% } \def\@pmb@chr@getkey#1{\csname pmb@chr@#1\endcsname} \@pmb@chr@keydef{sample range} \@pmb@chr@keydef{x unit} \@pmb@chr@keydef{y unit} \@pmb@chr@keydef{samples per line} \@pmb@chr@keydef{baseline skip} \@pmb@chr@stylekeydef{canvas style} \@pmb@chr@keydef{canvas height} \@pmb@chr@stylekeydef{trace A style} \@pmb@chr@stylekeydef{trace C style} \@pmb@chr@stylekeydef{trace G style} \@pmb@chr@stylekeydef{trace T style} \pgfkeysdef{/pgfmolbio/chromatogram/trace style}{% \pgfmolbioset[chromatogram]{ trace A style={#1}, trace C style={#1}, trace G style={#1}, trace T style={#1} }% } \@pmb@chr@keydef{traces drawn} \@pmb@chr@stylekeydef{tick A style} \@pmb@chr@stylekeydef{tick C style} \@pmb@chr@stylekeydef{tick G style} \@pmb@chr@stylekeydef{tick T style} \pgfkeysdef{/pgfmolbio/chromatogram/tick style}{% \pgfmolbioset[chromatogram]{ tick A style={#1}, tick C style={#1}, tick G style={#1}, tick T style={#1} }% } \@pmb@chr@keydef{tick length} \@pmb@chr@keydef{ticks drawn} \@pmb@chr@keydef{base label A text} \@pmb@chr@keydef{base label C text} \@pmb@chr@keydef{base label G text} \@pmb@chr@keydef{base label T text} \@pmb@chr@stylekeydef{base label A style} \@pmb@chr@stylekeydef{base label C style} \@pmb@chr@stylekeydef{base label G style} \@pmb@chr@stylekeydef{base label T style} \pgfkeysdef{/pgfmolbio/chromatogram/base label style}{% \pgfmolbioset[chromatogram]{ base label A style={#1}, base label C style={#1}, base label G style={#1}, base label T style={#1} }% } \@pmb@chr@keydef{base labels drawn} \newif\ifpmb@chr@showbasenumbers \pgfkeys{/pgfmolbio/chromatogram/show base numbers/% .is if=pmb@chr@showbasenumbers} \@pmb@chr@stylekeydef{base number style} \@pmb@chr@keydef{base number range} \@pmb@chr@keydef{probability distance} \@pmb@chr@keydef{probabilities drawn} \@pmb@chr@keydef{probability style function} \pgfkeysdef{/pgfmolbio/chromatogram/bases drawn}{% \pgfmolbioset[chromatogram]{ traces drawn=#1, ticks drawn=#1, base labels drawn=#1, probabilities drawn=#1 }% } \pgfmolbioset[chromatogram]{% sample range=1 to 500 step 1, x unit=0.2mm, y unit=0.01mm, samples per line=500, baseline skip=3cm, canvas style={draw=none, fill=none}, canvas height=2cm, trace A style={pmbTraceGreen}, trace C style={pmbTraceBlue}, trace G style={pmbTraceBlack}, trace T style={pmbTraceRed}, tick A style={thin, pmbTraceGreen}, tick C style={thin, pmbTraceBlue}, tick G style={thin, pmbTraceBlack}, tick T style={thin, pmbTraceRed}, tick length=1mm, base label A text=\strut A, base label C text=\strut C, base label G text=\strut G, base label T text=\strut T, base label A style=% {below=4pt, font=\ttfamily\footnotesize, pmbTraceGreen}, base label C style=% {below=4pt, font=\ttfamily\footnotesize, pmbTraceBlue}, base label G style=% {below=4pt, font=\ttfamily\footnotesize, pmbTraceBlack}, base label T style=% {below=4pt, font=\ttfamily\footnotesize, pmbTraceRed}, show base numbers, base number style={pmbTraceBlack, below=-3pt, font=\sffamily\tiny}, base number range=auto to auto step 10, probability distance=0.8cm, probability style function=nil, bases drawn=ACGT } \newif\ifpmb@chr@tikzpicture \newcommand\pmbchromatogram[2][]{% \@ifundefined{useasboundingbox}% {\pmb@chr@tikzpicturefalse\begin{tikzpicture}}% {\pmb@chr@tikzpicturetrue\begingroup}% \pgfmolbioset[chromatogram]{#1}% \directlua{ pgfmolbio.chromatogram.readScfFile("#2") pgfmolbio.chromatogram.setParameters{ sampleRange = "\@pmb@chr@getkey{sample range}", xUnit = dimen("\@pmb@chr@getkey{x unit}")[1], yUnit = dimen("\@pmb@chr@getkey{y unit}")[1], samplesPerLine = \@pmb@chr@getkey{samples per line}, baselineSkip = dimen("\@pmb@chr@getkey{baseline skip}")[1], canvasHeight = dimen("\@pmb@chr@getkey{canvas height}")[1], tracesDrawn = "\@pmb@chr@getkey{traces drawn}", tickLength = dimen("\@pmb@chr@getkey{tick length}")[1], ticksDrawn = "\@pmb@chr@getkey{ticks drawn}", baseLabelsDrawn = "\@pmb@chr@getkey{base labels drawn}", showBaseNumbers = \ifpmb@chr@showbasenumbers true\else false\fi, baseNumberRange = "\@pmb@chr@getkey{base number range}", probDistance = dimen("\@pmb@chr@getkey{probability distance}")[1], probabilitiesDrawn = "\@pmb@chr@getkey{probabilities drawn}", probStyle = \@pmb@chr@getkey{probability style function} } pgfmolbio.chromatogram.printTikzChromatogram() }% \ifpmb@chr@tikzpicture\endgroup\else\end{tikzpicture}\fi% } \endinput %% %% End of file `pgfmolbio.chromatogram.tex'.