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%%
%% 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) 2013 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}[2013/08/01 v0.21 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'.
|
