pgfmolbio 0.2 (7oct12)

git-svn-id: svn://tug.org/texlive/trunk@28023 c570f23f-e606-0410-a88d-b1316a301751

5 files changed, 117 insertions, 5 deletions

diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/README b/Master/texmf-dist/doc/lualatex/pgfmolbio/README
index c2f28947af5..824c1ff68b8 100644
--- a/Master/texmf-dist/doc/lualatex/pgfmolbio/README
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/README
@@ -1,13 +1,12 @@
-The pgfmolbio package
+The pgfmolbio package v0.2
 ------------------------------------------------------------------------------
 This package is released under the LaTeX Project Public License v1.3c or later
 (see http://www.latex-project.org/lppl.txt).
 
 
 The experimental package pgfmolbio draws graphs typically found in
-molecular biology texts. Currently, the package contains one module,
-which creates DNA sequencing chromatograms from files in standard
-chromatogram format (scf).
+molecular biology texts. Currently, the package contains modules
+for drawing DNA sequencing chromatograms and protein domain diagrams.
 
 The package requires pgf/TikZ (http://tug.ctan.org/pkg/pgf)
 and LuaTeX (http://www.luatex.org).
@@ -16,4 +15,4 @@ Installation: Run pgfmolbio.ins through LaTeX and follow the instructions.
 
 --
 Wolfgang Skala
-September 20th, 2011
+October 1st, 2012
diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/SampleGff.gff b/Master/texmf-dist/doc/lualatex/pgfmolbio/SampleGff.gff
new file mode 100644
index 00000000000..0c6754989fe
--- /dev/null
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/SampleGff.gff
@@ -0,0 +1,14 @@
+##gff-version 3
+##sequence-region TestProtein 1 200
+TestProtein	TheDatabase	disulfide	5	45	.	.	.	Disulfide 1
+TestProtein	TheDatabase	disulfide	30	122	.	.	.	Disulfide 2
+TestProtein	TheDatabase	disulfide	51	99	.	.	.	Disulfide 3
+TestProtein	TheDatabase	domain	10	40	.	.	.	Domain 1
+TestProtein	TheDatabase	domain	60	120	.	.	.	Domain 2
+TestProtein	TheDatabase	domain	135	178	.	.	.	Domain 3
+TestProtein	TheDatabase	beta strand	15	23	.	.	.	Strand 1
+TestProtein	TheDatabase	beta strand	25	32	.	.	.	Strand 2
+TestProtein	TheDatabase	alpha helix	60	75	.	.	.	Helix 1
+TestProtein	TheDatabase	alpha helix	80	108	.	.	.	Helix 1
+TestProtein	TheDatabase	carbohydrate	151	151	.	.	.	Sugar 1
+TestProtein	TheDatabase	carbohydrate	183	183	.	.	.	Sugar 2
\ No newline at end of file
diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/SampleUniprot.txt b/Master/texmf-dist/doc/lualatex/pgfmolbio/SampleUniprot.txt
new file mode 100644
index 00000000000..ca0f6b98eca
--- /dev/null
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/SampleUniprot.txt
@@ -0,0 +1,19 @@
+ID   TestProtein  Reviewed;        200 AA.
+FT   DISULFID      5     45       Disulfide 1
+FT   DISULFID     30    122       Disulfide 2
+FT   DISULFID     51     99       Disulfide 3
+FT   DOMAIN       10     40       Domain 1
+FT   DOMAIN       60    120       Domain 2
+FT   DOMAIN      135    178       Domain 3
+FT   STRAND       15     23       Strand 1
+FT   STRAND       25     32       Strand 2
+FT   HELIX        60     75       Helix 1
+FT   HELIX        80    108       Helix 2
+FT   CARBOHYD    151    151       Sugar 1
+FT   CARBOHYD    183    183       Sugar 2
+SQ   SEQUENCE   200 AA;   22041 MW;  00A52FE2EC5431D9 CRC64;
+     MGSKRSVPSR HRSLTTYEVM FAVLFVILVA LCAGLIAVSW LSIQGSVKDA AFGKSHEARG
+     TLKIISGATY NPHLQDKLSV DFKVLAFDIQ QMIDDIFQSS NLKNEYKNSR VLQFENGSII
+     VIFDLLFDQW VSDKNVKEEL IQGIEANKSS QLVTFHIDLN SIDITASLEN FSTISPATTS
+     EKLTTSIPLA TPGNVSIECP
+//
\ No newline at end of file
diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua
new file mode 100644
index 00000000000..2fe66b4090f
--- /dev/null
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua
@@ -0,0 +1,80 @@
+--
+-- This is file `pgfmolbio.lua',
+-- generated with the docstrip utility.
+--
+-- The original source files were:
+--
+-- pgfmolbio.dtx  (with options: `pgfmolbio-lua')
+--
+-- Copyright (C) 2012 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.
+--
+module("pgfmolbio", package.seeall)
+
+
+if luatexbase then
+  luatexbase.provides_module({
+    name          = "pgfmolbio",
+    version       = 0.2,
+    date          = "2012/10/01",
+    description   = "Molecular biology graphs wit LuaLaTeX",
+    author        = "Wolfgang Skala",
+    copyright     = "Wolfgang Skala",
+    license       = "LPPL",
+  })
+end
+
+local coordUnit, coordFmtStr
+
+function setCoordinateFormat(unit, fmtString)
+  coordUnit = unit
+  coordFmtStr = fmtString
+end
+
+function stringToDim(x)
+  if type(x) == "string" then
+    return dimen(x)[1]
+  end
+end
+
+function dimToString(x)
+  return number.todimen(x, coordUnit, coordFmtStr)
+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))
+  end
+  return unpack(result)
+end
+
+function packageWarning(message)
+  tex.sprint("\\PackageWarning{pgfmolbio}{" .. message .. "}")
+end
+
+function packageError(message)
+  tex.error("Package pgfmolbio Error: " .. message)
+  errorCatched = true
+end
+
+errorCatched = false
+
+if not string.trim then
+  string.trim = function(self)
+    return self:match("^%s*(.-)%s*$")
+  end
+end
+
+outputFileId = 0
+--
+-- End of file `pgfmolbio.lua'.
diff --git a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf
index 749c9ec9341..f64765d15a0 100644
--- a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf
+++ b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf