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diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex new file mode 100644 index 00000000000..4aff5ef075c --- /dev/null +++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex @@ -0,0 +1,185 @@ +%% +%% 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'. |