semin-ulla 0.9.3 → 0.9.4
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- data/.autotest +5 -0
- data/History.txt +8 -0
- data/Manifest.txt +2 -53
- data/README.rdoc +5 -6
- data/lib/ulla/cli.rb +5 -7
- data/lib/ulla.rb +1 -1
- data/ulla.gemspec +53 -0
- data/website/index.html +11 -1
- data/website/index.txt +0 -1
- metadata +5 -56
- data/.gitignore +0 -8
data/.autotest
ADDED
data/History.txt
CHANGED
@@ -1,3 +1,11 @@
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== 0.9.4 18/03/2009
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* Fixed a bug for environment label and residue name when --cys 2 is set
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== 0.9.3 23/2/2009
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* Egor has been renamed to Ulla!
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== 0.9.0 13/2/2009
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* Added --heatmap option for heat map generation from substitution tables
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data/Manifest.txt
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.git/refs/remotes/origin/HEAD
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.gitignore
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.autotest
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History.txt
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Manifest.txt
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PostInstall.txt
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@@ -83,6 +31,7 @@ test/test_ulla.rb
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test/ulla/test_cli.rb
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test/ulla/test_environment_class_hash.rb
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test/ulla/test_environment_feature.rb
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ulla.gemspec
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website/index.html
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website/index.txt
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website/javascripts/rounded_corners_lite.inc.js
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data/README.rdoc
CHANGED
@@ -94,7 +94,7 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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== Usage
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1. Prepare an environmental class definition file. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES).
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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
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~user $ cat classdef.dat
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#
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@@ -104,7 +104,7 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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secondary structure and phi angle;HEPC;HEPC;T;F
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solvent accessibility;TF;Aa;F;F
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-
2. Prepare structural alignments and their annotations of above environmental classes in PIR format.
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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
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~user $ cat sample1.tem
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>P1;1mnma
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@@ -153,13 +153,13 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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~user $ ulla -l TEMLIST --output 2 -o substlogo.mat
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-
7. To produce substitution
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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.)
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~user $ ulla -l TEMLIST --pidmin 60 --pidmax 80 --output 1
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8. To change the clustering level (default 60), type
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8. To change the clustering level (default 60) to PID 80, type
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~user $ ulla -l TEMLIST --weight 80 --output
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~user $ ulla -l TEMLIST --weight 80 --output 1
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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.
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@@ -235,7 +235,6 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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== TODO
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* Substitution table generation considering both the source and the target environmental classes
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-
* Remove dependency on NMatrix package
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== Repository
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data/lib/ulla/cli.rb
CHANGED
@@ -502,9 +502,7 @@ Options:
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'X'
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else
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if ei == 0 # Amino Acid Environment Feature
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-
(disulphide.has_key?(key) &&
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-
(disulphide[key][pos] == 'F') &&
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-
(sym == 'C')) ? 'J' : sym
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+
(disulphide.has_key?(key) && (disulphide[key][pos] == 'F') && (sym == 'C') && ($cys != 2)) ? 'J' : sym
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else
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ec.labels[ec.symbols.index(sym)]
|
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end
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@@ -569,8 +567,8 @@ Options:
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567
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next
|
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end
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-
aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C')) ? 'J' : aa1
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-
aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C')) ? 'J' : aa2
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+
aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C') && ($cys != 2)) ? 'J' : aa1
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+
aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C') && ($cys != 2)) ? 'J' : aa2
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if $cst_features.empty?
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$env_classes[env_labels[id1][pos]].increase_residue_count(aa2)
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@@ -684,8 +682,8 @@ Options:
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next
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end
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-
aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C')) ? 'J' : aa1
|
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-
aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C')) ? 'J' : aa2
|
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+
aa1 = (disulphide.has_key?(id1) && (disulphide[id1][pos] == 'F') && (aa1 == 'C') && ($cys != 2)) ? 'J' : aa1
|
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aa2 = (disulphide.has_key?(id2) && (disulphide[id2][pos] == 'F') && (aa2 == 'C') && ($cys != 2)) ? 'J' : aa2
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cnt1 = 1.0 / cluster1.size
|
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cnt2 = 1.0 / cluster2.size
|
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jnt_cnt = cnt1 * cnt2
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data/lib/ulla.rb
CHANGED
data/ulla.gemspec
ADDED
@@ -0,0 +1,53 @@
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = %q{ulla}
|
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s.version = "0.9.4"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Semin Lee"]
|
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s.date = %q{2009-03-18}
|
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s.default_executable = %q{ulla}
|
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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.}
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s.email = ["seminlee@gmail.com"]
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s.executables = ["ulla"]
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s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
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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"]
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s.has_rdoc = true
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s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
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s.post_install_message = %q{PostInstall.txt}
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s.rdoc_options = ["--main", "README.rdoc"]
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s.require_paths = ["lib"]
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s.rubyforge_project = %q{ulla}
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+
s.rubygems_version = %q{1.3.1}
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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.}
|
24
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+
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"]
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+
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if s.respond_to? :specification_version then
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
|
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s.specification_version = 2
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+
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
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+
s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
|
32
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+
s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
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+
s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
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+
s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
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35
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+
s.add_development_dependency(%q<newgem>, [">= 1.3.0"])
|
36
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+
s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
|
37
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+
else
|
38
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+
s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
39
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+
s.add_dependency(%q<bio>, [">= 1.2.1"])
|
40
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+
s.add_dependency(%q<facets>, [">= 2.4.5"])
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+
s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
42
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+
s.add_dependency(%q<newgem>, [">= 1.3.0"])
|
43
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+
s.add_dependency(%q<hoe>, [">= 1.8.0"])
|
44
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+
end
|
45
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+
else
|
46
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+
s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
47
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+
s.add_dependency(%q<bio>, [">= 1.2.1"])
|
48
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+
s.add_dependency(%q<facets>, [">= 2.4.5"])
|
49
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+
s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
50
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+
s.add_dependency(%q<newgem>, [">= 1.3.0"])
|
51
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+
s.add_dependency(%q<hoe>, [">= 1.8.0"])
|
52
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+
end
|
53
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end
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data/website/index.html
CHANGED
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</head>
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<body>
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<p>
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-
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://
|
12
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+
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.
|
13
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</p>
|
14
14
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- Semin
|
15
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+
<script type="text/javascript">
|
16
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+
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
|
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+
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
|
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</script>
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<script type="text/javascript">
|
20
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+
try {
|
21
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+
var pageTracker = _gat._getTracker("UA-7633498-1");
|
22
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+
pageTracker._trackPageview();
|
23
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+
} catch(err) {}
|
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+
</script>
|
15
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</body>
|
16
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</html>
|
data/website/index.txt
CHANGED
@@ -30,7 +30,6 @@ Following RubyGems will be automatically installed if you have rubygems installe
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30
30
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* narray (http://narray.rubyforge.org/)
|
31
31
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* facets (http://facets.rubyforge.org/)
|
32
32
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* bio (http://bioruby.open-bio.org/)
|
33
|
-
* simple_memoize (http://github.com/JackDanger/simple_memoize/tree/master)
|
34
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|
35
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|
36
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h2. Basic Usage
|
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: semin-ulla
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.9.
|
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+
version: 0.9.4
|
5
5
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platform: ruby
|
6
6
|
authors:
|
7
7
|
- Semin Lee
|
@@ -9,7 +9,7 @@ autorequire:
|
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
11
|
|
12
|
-
date: 2009-
|
12
|
+
date: 2009-03-18 00:00:00 -07:00
|
13
13
|
default_executable: ulla
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
@@ -60,7 +60,7 @@ dependencies:
|
|
60
60
|
requirements:
|
61
61
|
- - ">="
|
62
62
|
- !ruby/object:Gem::Version
|
63
|
-
version: 1.
|
63
|
+
version: 1.3.0
|
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- .autotest
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- PostInstall.txt
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@@ -171,6 +119,7 @@ files:
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+
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