pgfmolbio (31jul13)

git-svn-id: svn://tug.org/texlive/trunk@31334 c570f23f-e606-0410-a88d-b1316a301751

11 files changed, 36 insertions, 32 deletions

diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/README b/Master/texmf-dist/doc/lualatex/pgfmolbio/README
index 824c1ff68b8..291e363151e 100644
--- a/Master/texmf-dist/doc/lualatex/pgfmolbio/README
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/README
@@ -1,4 +1,4 @@
-The pgfmolbio package v0.2
+The pgfmolbio package v0.21
 ------------------------------------------------------------------------------
 This package is released under the LaTeX Project Public License v1.3c or later
 (see http://www.latex-project.org/lppl.txt).
@@ -15,4 +15,4 @@ Installation: Run pgfmolbio.ins through LaTeX and follow the instructions.
 
 --
 Wolfgang Skala
-October 1st, 2012
+August 1st, 2013
diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua
index 2fe66b4090f..d0c45c74595 100644
--- a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua
@@ -6,7 +6,7 @@
 --
 -- pgfmolbio.dtx  (with options: `pgfmolbio-lua')
 --
--- Copyright (C) 2012 by Wolfgang Skala
+-- 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
@@ -51,9 +51,11 @@ end
 function getRange(rangeInput, ...)
   if type(rangeInput) ~= "string" then return end
   local result = {}
-  for _, v in ipairs(arg) do
-    if type(v) ~= "string" then return end
-    table.insert(result, rangeInput:match(v))
+  local matchStrings = table.pack(...)
+  for i = 1, matchStrings.n do
+    if type(matchStrings[i]) == "string" then
+      table.insert(result, rangeInput:match(matchStrings[i]))
+    end
   end
   return unpack(result)
 end
diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf
index f64765d15a0..4139932d7f9 100644
--- a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf
diff --git a/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.dtx b/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.dtx
index 95c27940ce2..eb4fc315258 100644
--- a/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.dtx
+++ b/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.dtx
@@ -1,6 +1,6 @@
 % \iffalse meta-comment
 %
-% Copyright (C) 2012 by Wolfgang Skala
+% 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
@@ -13,14 +13,14 @@
 % \fi
 %
 % \iffalse
-%<pgfmolbio-tex>\ProvidesPackage{pgfmolbio}[2012/10/01 v0.2 Molecular biology graphs with TikZ]
+%<pgfmolbio-tex>\ProvidesPackage{pgfmolbio}[2013/08/01 v0.21 Molecular biology graphs with TikZ]
 %<pgfmolbio-tex>\NeedsTeXFormat{LaTeX2e}[1999/12/01]
 %<pgfmolbio-lua>module("pgfmolbio", package.seeall)
-%<pmb-chr-tex>\ProvidesFile{pgfmolbio.chromatogram.tex}[2012/10/01 v0.2 SCF chromatograms]
+%<pmb-chr-tex>\ProvidesFile{pgfmolbio.chromatogram.tex}[2013/08/01 v0.21 SCF chromatograms]
 %<pmb-chr-lua>module("pgfmolbio.chromatogram", package.seeall)
-%<pmb-dom-tex>\ProvidesFile{pgfmolbio.domains.tex}[2012/10/01 v0.2 Protein domains]
+%<pmb-dom-tex>\ProvidesFile{pgfmolbio.domains.tex}[2013/08/01 v0.21 Protein domains]
 %<pmb-dom-lua>module("pgfmolbio.domains", package.seeall)
-%<pmb-con-tex>\ProvidesFile{pgfmolbio.convert.tex}[2012/10/01 v0.2 pgfmolbio graph conversion]
+%<pmb-con-tex>\ProvidesFile{pgfmolbio.convert.tex}[2013/08/01 v0.21 pgfmolbio graph conversion]
 %
 %<*driver>
 \documentclass[captions=tableheading,cleardoublepage=empty,titlepage=false]{scrreprt}
@@ -1791,8 +1791,8 @@
 % You can change the format of the coordinates by the following keys:
 % 
 % \DescribeOption{}{coordinate unit}{mm}<unit>
-% \DescribeOption{}{coordinate format string}{\%s\%s}<format string>\relax
-% \pkg{pgfmolbio} internally calculates dimensions in scaled points, but usually converts them before returning them to \TeX. To this end, it selects the \meta{unit} stored in \opt{coordinate unit} (any of the standard \TeX\ units of measurement: \texttt{bp}, \texttt{cc}, \texttt{cm}, \texttt{dd}, \texttt{in}, \texttt{mm}, \texttt{pc}, \texttt{pt} or \texttt{sp}). In addition, the package formats the dimension according to the \meta{format string} given by \opt{coordinate format string}. This string basically follows the syntax of C's \texttt{printf} function, as described in the Lua reference manual.
+% \DescribeOption{}{coordinate format string}{\letterpercent s\letterpercent s}<format string>\relax
+% \pkg{pgfmolbio} internally calculates dimensions in scaled points, but usually converts them before returning them to \TeX. To this end, it selects the \meta{unit} stored in \opt{coordinate unit} (any of the standard \TeX\ units of measurement: \texttt{bp}, \texttt{cc}, \texttt{cm}, \texttt{dd}, \texttt{in}, \texttt{mm}, \texttt{pc}, \texttt{pt} or \texttt{sp}). In addition, the package formats the dimension according to the \meta{format string} given by \opt{coordinate format string}. This string basically follows the syntax of C's \texttt{printf} function, as described in the Lua reference manual. (Note: Use |\letterpercent| instead of \texttt{\%}, since \TeX\ treats anything following a percent character as comment.)
 % 
 % Depending on the values of \opt{coordinate unit} and \opt{coordinate format string}, dimensions will be printed in different ways (Table~\ref{tab:CoordFormat}).
 % 
@@ -2067,7 +2067,7 @@
 % We introduce two package-wide keys.
 %    \begin{macrocode}
 \pgfkeyssetvalue{/pgfmolbio/coordinate unit}{mm}
-\pgfkeyssetvalue{/pgfmolbio/coordinate format string}{\%s\%s}
+\pgfkeyssetvalue{/pgfmolbio/coordinate format string}{\letterpercent s\letterpercent s}
 
 %    \end{macrocode}
 % Furthermore, we define two scratch token registers. Strictly speaking, the two conditionals belong to the \module{convert} module, but all modules need to know them.
@@ -2149,14 +2149,16 @@ function dimToString(x)
 end
 
 %    \end{macrocode}
-% §getRange§ extracts a variable number of strings from §rangeInput§ by applying the regular expressions in its §arg§ table. §rangeInput§ contains the values of any of the \opt{... range} keys.
+% §getRange§ extracts a variable number of strings from §rangeInput§ by applying the regular expressions in the table §matchStrings§, which derives from the varargs. §rangeInput§ contains the values of any of the \opt{... range} keys.
 %    \begin{macrocode}
 function getRange(rangeInput, ...)
   if type(rangeInput) ~= "string" then return end
   local result = {}
-  for _, v in ipairs(arg) do
-    if type(v) ~= "string" then return end
-    table.insert(result, rangeInput:match(v))
+  local matchStrings = table.pack(...)
+  for i = 1, matchStrings.n do
+    if type(matchStrings[i]) == "string" then
+      table.insert(result, rangeInput:match(matchStrings[i]))
+    end
   end
   return unpack(result)
 end
diff --git a/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.ins b/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.ins
index 5729ed29b2a..94e88bfb815 100644
--- a/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.ins
+++ b/Master/texmf-dist/source/lualatex/pgfmolbio/pgfmolbio.ins
@@ -1,6 +1,6 @@
 % pgfmolbio.ins
 %%
-%% Copyright (C) 2012 by Wolfgang Skala
+%% 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
@@ -25,7 +25,7 @@
 
 \preamble
 
-Copyright (C) 2012 by Wolfgang Skala
+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
@@ -43,7 +43,7 @@ version 2005/12/01 or later.
 -- generated with the docstrip utility.^^J%
 \ReferenceLines%
 --^^J%
--- Copyright (C) 2012 by Wolfgang Skala^^J%
+-- Copyright (C) 2013 by Wolfgang Skala^^J%
 --^^J%
 -- This work may be distributed and/or modified under the^^J%
 -- conditions of the LaTeX Project Public License, either version 1.3^^J%
diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua
index 4919aeab702..7c1eae02177 100644
--- a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua
+++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua
@@ -6,7 +6,7 @@
 --
 -- pgfmolbio.dtx  (with options: `pmb-chr-lua')
 --
--- Copyright (C) 2012 by Wolfgang Skala
+-- 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
diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex
index a895f89603a..32cd1c4e867 100644
--- a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex
+++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.tex
@@ -6,7 +6,7 @@
 %%
 %% pgfmolbio.dtx  (with options: `pmb-chr-tex')
 %% 
-%% Copyright (C) 2012 by Wolfgang Skala
+%% 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
@@ -16,7 +16,7 @@
 %% and version 1.3 or later is part of all distributions of LaTeX
 %% version 2005/12/01 or later.
 %% 
-\ProvidesFile{pgfmolbio.chromatogram.tex}[2012/10/01 v0.2 SCF chromatograms]
+\ProvidesFile{pgfmolbio.chromatogram.tex}[2013/08/01 v0.21 SCF chromatograms]
 
 
 \ifluatex
diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.convert.tex b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.convert.tex
index 557dc333d65..49a77fe6986 100644
--- a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.convert.tex
+++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.convert.tex
@@ -6,7 +6,7 @@
 %%
 %% pgfmolbio.dtx  (with options: `pmb-con-tex')
 %% 
-%% Copyright (C) 2012 by Wolfgang Skala
+%% 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
@@ -16,7 +16,7 @@
 %% and version 1.3 or later is part of all distributions of LaTeX
 %% version 2005/12/01 or later.
 %% 
-\ProvidesFile{pgfmolbio.convert.tex}[2012/10/01 v0.2 pgfmolbio graph conversion]
+\ProvidesFile{pgfmolbio.convert.tex}[2013/08/01 v0.21 pgfmolbio graph conversion]
 
 
 \pdfdraftmode1
diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.lua b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.lua
index 905c6d688e0..88d8907aa83 100644
--- a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.lua
+++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.lua
@@ -6,7 +6,7 @@
 --
 -- pgfmolbio.dtx  (with options: `pmb-dom-lua')
 --
--- Copyright (C) 2012 by Wolfgang Skala
+-- 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
diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.tex b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.tex
index 104d92763dc..4fe6bcae04e 100644
--- a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.tex
+++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.domains.tex
@@ -6,7 +6,7 @@
 %%
 %% pgfmolbio.dtx  (with options: `pmb-dom-tex')
 %% 
-%% Copyright (C) 2012 by Wolfgang Skala
+%% 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
@@ -16,7 +16,7 @@
 %% and version 1.3 or later is part of all distributions of LaTeX
 %% version 2005/12/01 or later.
 %% 
-\ProvidesFile{pgfmolbio.domains.tex}[2012/10/01 v0.2 Protein domains]
+\ProvidesFile{pgfmolbio.domains.tex}[2013/08/01 v0.21 Protein domains]
 
 
 \ProvidesFile{pgfmolbio.domains.tex}[2012/10/01 v0.2 Protein Domains]
diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.sty b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.sty
index a841ec2d6ea..cb3479cb2ea 100644
--- a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.sty
+++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.sty
@@ -6,7 +6,7 @@
 %%
 %% pgfmolbio.dtx  (with options: `pgfmolbio-tex')
 %% 
-%% Copyright (C) 2012 by Wolfgang Skala
+%% 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
@@ -16,7 +16,7 @@
 %% and version 1.3 or later is part of all distributions of LaTeX
 %% version 2005/12/01 or later.
 %% 
-\ProvidesPackage{pgfmolbio}[2012/10/01 v0.2 Molecular biology graphs with TikZ]
+\ProvidesPackage{pgfmolbio}[2013/08/01 v0.21 Molecular biology graphs with TikZ]
 \NeedsTeXFormat{LaTeX2e}[1999/12/01]
 
 
@@ -56,7 +56,7 @@
 }
 
 \pgfkeyssetvalue{/pgfmolbio/coordinate unit}{mm}
-\pgfkeyssetvalue{/pgfmolbio/coordinate format string}{\%s\%s}
+\pgfkeyssetvalue{/pgfmolbio/coordinate format string}{\letterpercent s\letterpercent s}
 
 \newtoks\@pmb@toksa
 \newtoks\@pmb@toksb