From 501d1837aeddc838bf1ea0898f94d6b9435aa205 Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Thu, 18 Oct 2012 22:52:50 +0000 Subject: pgfmolbio 0.2 (7oct12) git-svn-id: svn://tug.org/texlive/trunk@28023 c570f23f-e606-0410-a88d-b1316a301751 --- Master/texmf-dist/doc/lualatex/pgfmolbio/README | 9 ++- .../doc/lualatex/pgfmolbio/SampleGff.gff | 14 ++++ .../doc/lualatex/pgfmolbio/SampleUniprot.txt | 19 +++++ .../doc/lualatex/pgfmolbio/pgfmolbio.lua | 80 +++++++++++++++++++++ .../doc/lualatex/pgfmolbio/pgfmolbio.pdf | Bin 386065 -> 853848 bytes 5 files changed, 117 insertions(+), 5 deletions(-) create mode 100644 Master/texmf-dist/doc/lualatex/pgfmolbio/SampleGff.gff create mode 100644 Master/texmf-dist/doc/lualatex/pgfmolbio/SampleUniprot.txt create mode 100644 Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.lua (limited to 'Master/texmf-dist/doc/lualatex/pgfmolbio') 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 Binary files a/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf and b/Master/texmf-dist/doc/lualatex/pgfmolbio/pgfmolbio.pdf differ -- cgit v1.2.3