%%
%% 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) 2024 by Wolfgang Esser-Skala
%% 
%% This work may be distributed and/or modified under the
%% conditions of the LaTeX Project Public License, either version 1.3c
%% of this license or (at your option) any later version.
%% The latest version of this license is in
%%   https://www.latex-project.org/lppl.txt
%% and version 1.3c or later is part of all distributions of LaTeX
%% version 2008/05/04 or later.
%% 
\ProvidesFile{pgfmolbio.chromatogram.tex}[2024/06/17 v0.21a 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'.