semin-ulla 0.9.3 → 0.9.4

data/.autotest

@@ -0,0 +1,5 @@
+#require 'autotest/screen'
+
+#Autotest::Screen.statusline = '%H %`%-w%{=b bw}%n %t%{-}%+w (your statusline)'
+#Autotest::Screen.statusline = '%{=b}%{G} Screen(s): %{b}%w %=%{kG}%C%A  %D, %M/%d/%Y (your statusline)'
+

data/History.txt

@@ -1,3 +1,11 @@
+== 0.9.4 18/03/2009
+
+* Fixed a bug for environment label and residue name when --cys 2 is set
+
+== 0.9.3 23/2/2009
+
+* Egor has been renamed to Ulla!
+
 == 0.9.0 13/2/2009
 
 * Added --heatmap option for heat map generation from substitution tables

data/Manifest.txt

@@ -1,56 +1,4 @@
-.git/COMMIT_EDITMSG
-.git/HEAD
-.git/config
-.git/description
-.git/hooks/applypatch-msg.sample
-.git/hooks/commit-msg.sample
-.git/hooks/post-commit.sample
-.git/hooks/post-receive.sample
-.git/hooks/post-update.sample
-.git/hooks/pre-applypatch.sample
-.git/hooks/pre-commit.sample
-.git/hooks/pre-rebase.sample
-.git/hooks/prepare-commit-msg.sample
-.git/hooks/update.sample
-.git/index
-.git/info/exclude
-.git/logs/HEAD
-.git/logs/refs/heads/master
-.git/logs/refs/remotes/origin/HEAD
-.git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e
-.git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069
-.git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b
-.git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c
-.git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca
-.git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace
-.git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05
-.git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb
-.git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029
-.git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96
-.git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e
-.git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152
-.git/objects/a6/578c95f2f474303464b572e9dac716432472b2
-.git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723
-.git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4
-.git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d
-.git/objects/c2/fb6afc000952b56354fe195682645000d2aea2
-.git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28
-.git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753
-.git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9
-.git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396
-.git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44
-.git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4
-.git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278
-.git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f
-.git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da
-.git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac
-.git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12
-.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx
-.git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack
-.git/packed-refs
-.git/refs/heads/master
-.git/refs/remotes/origin/HEAD
-.gitignore
+.autotest
 History.txt
 Manifest.txt
 PostInstall.txt
@@ -83,6 +31,7 @@ test/test_ulla.rb
 test/ulla/test_cli.rb
 test/ulla/test_environment_class_hash.rb
 test/ulla/test_environment_feature.rb
+ulla.gemspec
 website/index.html
 website/index.txt
 website/javascripts/rounded_corners_lite.inc.js

data/README.rdoc

@@ -94,7 +94,7 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
 
 == Usage
 
-1. Prepare an environmental class definition file. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES).
+1. Prepare an environmental class definition file. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES). You can download a sample environmental class definition file from http://www-cryst.bioc.cam.ac.uk/~kenji/subst/classdef.dat 
 
         ~user $ cat classdef.dat
         #
@@ -104,7 +104,7 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
         secondary structure and phi angle;HEPC;HEPC;T;F
         solvent accessibility;TF;Aa;F;F
 
-2. Prepare structural alignments and their annotations of above environmental classes in PIR format.
+2. Prepare structural alignments and their annotations of above environmental classes in PIR format. You can download sample alignments from http://www-cryst.bioc.cam.ac.uk/~kenji/subst/alltem-allmask.tar.gz
 
         ~user $ cat sample1.tem
         >P1;1mnma
@@ -153,13 +153,13 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
 
         ~user $ ulla -l TEMLIST --output 2 -o substlogo.mat
 
-7. To produce substitution data only from the sequence pairs within a given PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
+7. To produce substitution probability matrices only from the sequence pairs within a certain PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
 
         ~user $ ulla -l TEMLIST --pidmin 60 --pidmax 80 --output 1
 
-8. To change the clustering level (default 60), type
+8. To change the clustering level (default 60) to PID 80, type
 
-        ~user $ ulla -l TEMLIST --weight 80 --output 2
+        ~user $ ulla -l TEMLIST --weight 80 --output 1
 
 9. In case positions are masked with the character 'X' in any environmental features, all mutations from/to the position will be excluded from the calculation of substitution counts.
 
@@ -235,7 +235,6 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
 == TODO
 
 * Substitution table generation considering both the source and the target environmental classes
-* Remove dependency on NMatrix package
 
 == Repository
 

data/lib/ulla/cli.rb

@@ -502,9 +502,7 @@ Options:
                       'X'
                     else
                       if ei == 0 # Amino Acid Environment Feature
-                        (disulphide.has_key?(key) &&
-                         (disulphide[key][pos] == 'F') &&
-                         (sym == 'C')) ? 'J' : sym
+                        (disulphide.has_key?(key) && (disulphide[key][pos] == 'F') && (sym == 'C') && ($cys != 2)) ? 'J' : sym
                       else
                         ec.labels[ec.symbols.index(sym)]
                       end
@@ -569,8 +567,8 @@ Options:
                       next
                     end
 
-                    aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C')) ? 'J' : aa1
-                    aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C')) ? 'J' : aa2
+                    aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C') && ($cys != 2)) ? 'J' : aa1
+                    aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C') && ($cys != 2)) ? 'J' : aa2
 
                     if $cst_features.empty?
                       $env_classes[env_labels[id1][pos]].increase_residue_count(aa2)
@@ -684,8 +682,8 @@ Options:
                       next
                     end
 
-                    aa1   = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C')) ? 'J' : aa1
-                    aa2   = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C')) ? 'J' : aa2
+                    aa1   = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C') && ($cys != 2)) ? 'J' : aa1
+                    aa2   = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C') && ($cys != 2)) ? 'J' : aa2
                     cnt1  = 1.0 / cluster1.size
                     cnt2  = 1.0 / cluster2.size
                     jnt_cnt = cnt1 * cnt2

data/lib/ulla.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Ulla
-  VERSION = '0.9.3'
+  VERSION = '0.9.4'
 end

data/ulla.gemspec

@@ -0,0 +1,53 @@
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{ulla}
+  s.version = "0.9.4"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Semin Lee"]
+  s.date = %q{2009-03-18}
+  s.default_executable = %q{ulla}
+  s.description = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
+  s.email = ["seminlee@gmail.com"]
+  s.executables = ["ulla"]
+  s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
+  s.files = [".autotest", "History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
+  s.has_rdoc = true
+  s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
+  s.post_install_message = %q{PostInstall.txt}
+  s.rdoc_options = ["--main", "README.rdoc"]
+  s.require_paths = ["lib"]
+  s.rubyforge_project = %q{ulla}
+  s.rubygems_version = %q{1.3.1}
+  s.summary = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
+  s.test_files = ["test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "test/test_helper.rb", "test/test_ulla.rb"]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 2
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_development_dependency(%q<newgem>, [">= 1.3.0"])
+      s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
+    else
+      s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_dependency(%q<newgem>, [">= 1.3.0"])
+      s.add_dependency(%q<hoe>, [">= 1.8.0"])
+    end
+  else
+    s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+    s.add_dependency(%q<bio>, [">= 1.2.1"])
+    s.add_dependency(%q<facets>, [">= 2.4.5"])
+    s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+    s.add_dependency(%q<newgem>, [">= 1.3.0"])
+    s.add_dependency(%q<hoe>, [">= 1.8.0"])
+  end
+end

data/website/index.html

@@ -9,8 +9,18 @@
 </head>
 <body>
     <p>
-    Egor has been renamed to Ulla, and an official web site for Ulla will be available when our new web contents management system is ready. Until then, this page will be redirected to its Git repository, <a href="http://http://github.com/semin/ulla/">http://github.com/semin/ulla</a> in 5 seconds.
+    Egor has been renamed to Ulla, and an official web site for Ulla will be available when our new web contents management system is ready. Until then, this page will be redirected to its Git repository, <a href="http://github.com/semin/ulla/">http://github.com/semin/ulla</a> in 5 seconds.
     </p>
     - Semin
+    <script type="text/javascript">
+        var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+        document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+    </script>
+    <script type="text/javascript">
+        try {
+            var pageTracker = _gat._getTracker("UA-7633498-1");
+            pageTracker._trackPageview();
+        } catch(err) {}
+    </script>
 </body>
 </html>

data/website/index.txt

@@ -30,7 +30,6 @@ Following RubyGems will be automatically installed if you have rubygems installe
 * narray (http://narray.rubyforge.org/)
 * facets (http://facets.rubyforge.org/)
 * bio (http://bioruby.open-bio.org/)
-* simple_memoize (http://github.com/JackDanger/simple_memoize/tree/master)
 
 
 h2. Basic Usage

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: semin-ulla
 version: !ruby/object:Gem::Version 
-  version: 0.9.3
+  version: 0.9.4
 platform: ruby
 authors: 
 - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-02-23 00:00:00 -08:00
+date: 2009-03-18 00:00:00 -07:00
 default_executable: ulla
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -60,7 +60,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.2.3
+        version: 1.3.0
     version: 
 - !ruby/object:Gem::Dependency 
   name: hoe
@@ -86,59 +86,7 @@ extra_rdoc_files:
 - README.rdoc
 - website/index.txt
 files: 
-- .git/COMMIT_EDITMSG
-- .git/HEAD
-- .git/config
-- .git/description
-- .git/hooks/applypatch-msg.sample
-- .git/hooks/commit-msg.sample
-- .git/hooks/post-commit.sample
-- .git/hooks/post-receive.sample
-- .git/hooks/post-update.sample
-- .git/hooks/pre-applypatch.sample
-- .git/hooks/pre-commit.sample
-- .git/hooks/pre-rebase.sample
-- .git/hooks/prepare-commit-msg.sample
-- .git/hooks/update.sample
-- .git/index
-- .git/info/exclude
-- .git/logs/HEAD
-- .git/logs/refs/heads/master
-- .git/logs/refs/remotes/origin/HEAD
-- .git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e
-- .git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069
-- .git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b
-- .git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c
-- .git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca
-- .git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace
-- .git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05
-- .git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb
-- .git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029
-- .git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96
-- .git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e
-- .git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152
-- .git/objects/a6/578c95f2f474303464b572e9dac716432472b2
-- .git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723
-- .git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4
-- .git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d
-- .git/objects/c2/fb6afc000952b56354fe195682645000d2aea2
-- .git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28
-- .git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753
-- .git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9
-- .git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396
-- .git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44
-- .git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4
-- .git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278
-- .git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f
-- .git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da
-- .git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac
-- .git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12
-- .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx
-- .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack
-- .git/packed-refs
-- .git/refs/heads/master
-- .git/refs/remotes/origin/HEAD
-- .gitignore
+- .autotest
 - History.txt
 - Manifest.txt
 - PostInstall.txt
@@ -171,6 +119,7 @@ files:
 - test/ulla/test_cli.rb
 - test/ulla/test_environment_class_hash.rb
 - test/ulla/test_environment_feature.rb
+- ulla.gemspec
 - website/index.html
 - website/index.txt
 - website/javascripts/rounded_corners_lite.inc.js

data/.gitignore

@@ -1,8 +0,0 @@
-pkg
-doc
-.DS_Store
-tmp
-data
-*.log
-*.swp
-*~