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authorKarl Berry <karl@freefriends.org>2012-10-18 22:52:50 +0000
committerKarl Berry <karl@freefriends.org>2012-10-18 22:52:50 +0000
commit501d1837aeddc838bf1ea0898f94d6b9435aa205 (patch)
tree4eaea5c3364c6e11708179ed88ed224158f88e86 /Master/texmf-dist/doc/lualatex
parent3ab72bbc8f60fc642a7dd422ed357c1b5dc0ec23 (diff)
pgfmolbio 0.2 (7oct12)
git-svn-id: svn://tug.org/texlive/trunk@28023 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist/doc/lualatex')
-rw-r--r--Master/texmf-dist/doc/lualatex/pgfmolbio/README9
-rw-r--r--Master/texmf-dist/doc/lualatex/pgfmolbio/SampleGff.gff14
-rw-r--r--Master/texmf-dist/doc/lualatex/pgfmolbio/SampleUniprot.txt19
-rw-r--r--Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua80
-rw-r--r--Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdfbin386065 -> 853848 bytes
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
Binary files differ