summaryrefslogtreecommitdiff
path: root/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex
diff options
context:
space:
mode:
Diffstat (limited to 'Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex')
-rw-r--r--Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex185
1 files changed, 185 insertions, 0 deletions
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'.