semin-ulla 0.9.3
Sign up to get free protection for your applications and to get access to all the features.
- data/.gitignore +8 -0
- data/History.txt +38 -0
- data/Manifest.txt +90 -0
- data/PostInstall.txt +5 -0
- data/README.rdoc +259 -0
- data/Rakefile +32 -0
- data/bin/ulla +10 -0
- data/config/website.yml +2 -0
- data/config/website.yml.sample +2 -0
- data/lib/math_extensions.rb +7 -0
- data/lib/narray_extensions.rb +22 -0
- data/lib/nmatrix_extensions.rb +245 -0
- data/lib/string_extensions.rb +17 -0
- data/lib/ulla/cli.rb +1742 -0
- data/lib/ulla/environment.rb +34 -0
- data/lib/ulla/environment_class_hash.rb +20 -0
- data/lib/ulla/environment_feature.rb +26 -0
- data/lib/ulla/environment_feature_array.rb +12 -0
- data/lib/ulla/heatmap_array.rb +111 -0
- data/lib/ulla.rb +6 -0
- data/script/console +10 -0
- data/script/destroy +14 -0
- data/script/generate +14 -0
- data/script/txt2html +71 -0
- data/test/test_helper.rb +2 -0
- data/test/test_math_extensions.rb +11 -0
- data/test/test_narray_extensions.rb +14 -0
- data/test/test_nmatrix_extensions.rb +16 -0
- data/test/test_string_extensions.rb +11 -0
- data/test/test_ulla.rb +11 -0
- data/test/ulla/test_cli.rb +9 -0
- data/test/ulla/test_environment_class_hash.rb +25 -0
- data/test/ulla/test_environment_feature.rb +29 -0
- data/website/index.html +16 -0
- data/website/index.txt +217 -0
- data/website/javascripts/rounded_corners_lite.inc.js +285 -0
- data/website/stylesheets/screen.css +158 -0
- data/website/template.html.erb +57 -0
- metadata +215 -0
|
@@ -0,0 +1,57 @@
|
|
|
1
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
|
2
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
|
3
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
4
|
+
<head>
|
|
5
|
+
<link rel="stylesheet" href="stylesheets/screen.css" type="text/css" media="screen" />
|
|
6
|
+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
7
|
+
<title>
|
|
8
|
+
<%= title %>
|
|
9
|
+
</title>
|
|
10
|
+
<script src="javascripts/rounded_corners_lite.inc.js" type="text/javascript"></script>
|
|
11
|
+
<style>
|
|
12
|
+
|
|
13
|
+
</style>
|
|
14
|
+
<script type="text/javascript">
|
|
15
|
+
window.onload = function() {
|
|
16
|
+
settings = {
|
|
17
|
+
tl: { radius: 10 },
|
|
18
|
+
tr: { radius: 10 },
|
|
19
|
+
bl: { radius: 10 },
|
|
20
|
+
br: { radius: 10 },
|
|
21
|
+
antiAlias: true,
|
|
22
|
+
autoPad: true,
|
|
23
|
+
validTags: ["div"]
|
|
24
|
+
}
|
|
25
|
+
var versionBox = new curvyCorners(settings, document.getElementById("version"));
|
|
26
|
+
versionBox.applyCornersToAll();
|
|
27
|
+
}
|
|
28
|
+
</script>
|
|
29
|
+
</head>
|
|
30
|
+
<body>
|
|
31
|
+
<div id="main">
|
|
32
|
+
|
|
33
|
+
<h1><%= title %></h1>
|
|
34
|
+
<div class="sidebar">
|
|
35
|
+
<div id="version" class="clickable" onclick='document.location = "<%= download %>"; return false'>
|
|
36
|
+
<p>Get Version</p>
|
|
37
|
+
<a href="<%= download %>" class="numbers"><%= version %></a>
|
|
38
|
+
</div>
|
|
39
|
+
</div>
|
|
40
|
+
<%= body %>
|
|
41
|
+
<p class="coda">
|
|
42
|
+
Semin Lee, <%= modified.pretty %><br>
|
|
43
|
+
Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
|
|
44
|
+
</p>
|
|
45
|
+
</div>
|
|
46
|
+
|
|
47
|
+
<!-- insert site tracking codes here, like Google Urchin -->
|
|
48
|
+
<script type="text/javascript">
|
|
49
|
+
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
|
|
50
|
+
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
|
|
51
|
+
</script>
|
|
52
|
+
<script type="text/javascript">
|
|
53
|
+
var pageTracker = _gat._getTracker("UA-6291956-1");
|
|
54
|
+
pageTracker._trackPageview();
|
|
55
|
+
</script>
|
|
56
|
+
</body>
|
|
57
|
+
</html>
|
metadata
ADDED
|
@@ -0,0 +1,215 @@
|
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
|
2
|
+
name: semin-ulla
|
|
3
|
+
version: !ruby/object:Gem::Version
|
|
4
|
+
version: 0.9.3
|
|
5
|
+
platform: ruby
|
|
6
|
+
authors:
|
|
7
|
+
- Semin Lee
|
|
8
|
+
autorequire:
|
|
9
|
+
bindir: bin
|
|
10
|
+
cert_chain: []
|
|
11
|
+
|
|
12
|
+
date: 2009-02-23 00:00:00 -08:00
|
|
13
|
+
default_executable: ulla
|
|
14
|
+
dependencies:
|
|
15
|
+
- !ruby/object:Gem::Dependency
|
|
16
|
+
name: narray
|
|
17
|
+
type: :runtime
|
|
18
|
+
version_requirement:
|
|
19
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
20
|
+
requirements:
|
|
21
|
+
- - ">="
|
|
22
|
+
- !ruby/object:Gem::Version
|
|
23
|
+
version: 0.5.9.5
|
|
24
|
+
version:
|
|
25
|
+
- !ruby/object:Gem::Dependency
|
|
26
|
+
name: bio
|
|
27
|
+
type: :runtime
|
|
28
|
+
version_requirement:
|
|
29
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
30
|
+
requirements:
|
|
31
|
+
- - ">="
|
|
32
|
+
- !ruby/object:Gem::Version
|
|
33
|
+
version: 1.2.1
|
|
34
|
+
version:
|
|
35
|
+
- !ruby/object:Gem::Dependency
|
|
36
|
+
name: facets
|
|
37
|
+
type: :runtime
|
|
38
|
+
version_requirement:
|
|
39
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
40
|
+
requirements:
|
|
41
|
+
- - ">="
|
|
42
|
+
- !ruby/object:Gem::Version
|
|
43
|
+
version: 2.4.5
|
|
44
|
+
version:
|
|
45
|
+
- !ruby/object:Gem::Dependency
|
|
46
|
+
name: rmagick
|
|
47
|
+
type: :runtime
|
|
48
|
+
version_requirement:
|
|
49
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
50
|
+
requirements:
|
|
51
|
+
- - ">="
|
|
52
|
+
- !ruby/object:Gem::Version
|
|
53
|
+
version: 2.9.1
|
|
54
|
+
version:
|
|
55
|
+
- !ruby/object:Gem::Dependency
|
|
56
|
+
name: newgem
|
|
57
|
+
type: :development
|
|
58
|
+
version_requirement:
|
|
59
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
60
|
+
requirements:
|
|
61
|
+
- - ">="
|
|
62
|
+
- !ruby/object:Gem::Version
|
|
63
|
+
version: 1.2.3
|
|
64
|
+
version:
|
|
65
|
+
- !ruby/object:Gem::Dependency
|
|
66
|
+
name: hoe
|
|
67
|
+
type: :development
|
|
68
|
+
version_requirement:
|
|
69
|
+
version_requirements: !ruby/object:Gem::Requirement
|
|
70
|
+
requirements:
|
|
71
|
+
- - ">="
|
|
72
|
+
- !ruby/object:Gem::Version
|
|
73
|
+
version: 1.8.0
|
|
74
|
+
version:
|
|
75
|
+
description: "'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."
|
|
76
|
+
email:
|
|
77
|
+
- seminlee@gmail.com
|
|
78
|
+
executables:
|
|
79
|
+
- ulla
|
|
80
|
+
extensions: []
|
|
81
|
+
|
|
82
|
+
extra_rdoc_files:
|
|
83
|
+
- History.txt
|
|
84
|
+
- Manifest.txt
|
|
85
|
+
- PostInstall.txt
|
|
86
|
+
- README.rdoc
|
|
87
|
+
- website/index.txt
|
|
88
|
+
files:
|
|
89
|
+
- .git/COMMIT_EDITMSG
|
|
90
|
+
- .git/HEAD
|
|
91
|
+
- .git/config
|
|
92
|
+
- .git/description
|
|
93
|
+
- .git/hooks/applypatch-msg.sample
|
|
94
|
+
- .git/hooks/commit-msg.sample
|
|
95
|
+
- .git/hooks/post-commit.sample
|
|
96
|
+
- .git/hooks/post-receive.sample
|
|
97
|
+
- .git/hooks/post-update.sample
|
|
98
|
+
- .git/hooks/pre-applypatch.sample
|
|
99
|
+
- .git/hooks/pre-commit.sample
|
|
100
|
+
- .git/hooks/pre-rebase.sample
|
|
101
|
+
- .git/hooks/prepare-commit-msg.sample
|
|
102
|
+
- .git/hooks/update.sample
|
|
103
|
+
- .git/index
|
|
104
|
+
- .git/info/exclude
|
|
105
|
+
- .git/logs/HEAD
|
|
106
|
+
- .git/logs/refs/heads/master
|
|
107
|
+
- .git/logs/refs/remotes/origin/HEAD
|
|
108
|
+
- .git/objects/06/9494e479f28b5751fb135b8e55e8fef3d3a02e
|
|
109
|
+
- .git/objects/22/0df784191ad94983ca1d943e49fe482c9d1069
|
|
110
|
+
- .git/objects/3b/b6f2b7f563175a13a0ccd723aab761552f448b
|
|
111
|
+
- .git/objects/41/f48aefb4d7a6a87eb423eaae77ae1e8a58dd6c
|
|
112
|
+
- .git/objects/44/d1f1782e3ea1d9fd2f9054784b53e8e810a8ca
|
|
113
|
+
- .git/objects/4f/364c2eac29f5c7fcbf06419c4f58074cd32ace
|
|
114
|
+
- .git/objects/57/1326145a7a4b3e58f3d3008ba343135f213b05
|
|
115
|
+
- .git/objects/6c/4f0844f62b7345f0651b0fb2829a8f157469fb
|
|
116
|
+
- .git/objects/73/8dc79450de050f12d48a32602f2ddbe6807029
|
|
117
|
+
- .git/objects/7b/4acb3aee6616d80e295ee21fe8bb7ee93ebe96
|
|
118
|
+
- .git/objects/9e/0a9235b0d70a8029098070007fb414cb52504e
|
|
119
|
+
- .git/objects/9e/bfcad2906aac4a23a7c9689a47b76723f5d152
|
|
120
|
+
- .git/objects/a6/578c95f2f474303464b572e9dac716432472b2
|
|
121
|
+
- .git/objects/a8/65ef5700ff04601c6fc40fa5ede3cc25534723
|
|
122
|
+
- .git/objects/aa/285cb176668c5e49c54c6e1d3cc27bd47fd4f4
|
|
123
|
+
- .git/objects/b8/e3828a1082137c4aa4595386bdfb73e3c75b9d
|
|
124
|
+
- .git/objects/c2/fb6afc000952b56354fe195682645000d2aea2
|
|
125
|
+
- .git/objects/c4/a0553ca0e3c4628e688ecb5e3304a8a8ac0c28
|
|
126
|
+
- .git/objects/c8/d49f83c4a32cff2d87dd4aa5f83eb7aac3a753
|
|
127
|
+
- .git/objects/ca/c25e8049075ed4bff993705acb4750b2b62ba9
|
|
128
|
+
- .git/objects/d2/ff2e939339eb3fb776e064c258e71dfa1cf396
|
|
129
|
+
- .git/objects/d7/cedf9e2a8ff35b5d7dafdc0f20daed9c65ce44
|
|
130
|
+
- .git/objects/e2/e81af59e3a6c4aa8daac62add62860ae776ba4
|
|
131
|
+
- .git/objects/e5/7c47d183ce5dda1a944c7ee1c19c8a0c4bb278
|
|
132
|
+
- .git/objects/eb/f4a4e1e50bb30731597f776e56b0ccb0c9959f
|
|
133
|
+
- .git/objects/f6/39d6f6cf883fde4b9052012919c1df3288c7da
|
|
134
|
+
- .git/objects/f8/2346f308f49053df108b7c31ac3089e8b4b4ac
|
|
135
|
+
- .git/objects/fb/4b193bb1cbe9041d2f00176f6caa6acfb1fc12
|
|
136
|
+
- .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.idx
|
|
137
|
+
- .git/objects/pack/pack-aebf617a0b8e016433238d2f21f542bc5b21bd15.pack
|
|
138
|
+
- .git/packed-refs
|
|
139
|
+
- .git/refs/heads/master
|
|
140
|
+
- .git/refs/remotes/origin/HEAD
|
|
141
|
+
- .gitignore
|
|
142
|
+
- History.txt
|
|
143
|
+
- Manifest.txt
|
|
144
|
+
- PostInstall.txt
|
|
145
|
+
- README.rdoc
|
|
146
|
+
- Rakefile
|
|
147
|
+
- bin/ulla
|
|
148
|
+
- config/website.yml
|
|
149
|
+
- config/website.yml.sample
|
|
150
|
+
- lib/math_extensions.rb
|
|
151
|
+
- lib/narray_extensions.rb
|
|
152
|
+
- lib/nmatrix_extensions.rb
|
|
153
|
+
- lib/string_extensions.rb
|
|
154
|
+
- lib/ulla.rb
|
|
155
|
+
- lib/ulla/cli.rb
|
|
156
|
+
- lib/ulla/environment.rb
|
|
157
|
+
- lib/ulla/environment_class_hash.rb
|
|
158
|
+
- lib/ulla/environment_feature.rb
|
|
159
|
+
- lib/ulla/environment_feature_array.rb
|
|
160
|
+
- lib/ulla/heatmap_array.rb
|
|
161
|
+
- script/console
|
|
162
|
+
- script/destroy
|
|
163
|
+
- script/generate
|
|
164
|
+
- script/txt2html
|
|
165
|
+
- test/test_helper.rb
|
|
166
|
+
- test/test_math_extensions.rb
|
|
167
|
+
- test/test_narray_extensions.rb
|
|
168
|
+
- test/test_nmatrix_extensions.rb
|
|
169
|
+
- test/test_string_extensions.rb
|
|
170
|
+
- test/test_ulla.rb
|
|
171
|
+
- test/ulla/test_cli.rb
|
|
172
|
+
- test/ulla/test_environment_class_hash.rb
|
|
173
|
+
- test/ulla/test_environment_feature.rb
|
|
174
|
+
- website/index.html
|
|
175
|
+
- website/index.txt
|
|
176
|
+
- website/javascripts/rounded_corners_lite.inc.js
|
|
177
|
+
- website/stylesheets/screen.css
|
|
178
|
+
- website/template.html.erb
|
|
179
|
+
has_rdoc: true
|
|
180
|
+
homepage: http://www-cryst.bioc.cam.ac.uk/ulla
|
|
181
|
+
post_install_message: PostInstall.txt
|
|
182
|
+
rdoc_options:
|
|
183
|
+
- --main
|
|
184
|
+
- README.rdoc
|
|
185
|
+
require_paths:
|
|
186
|
+
- lib
|
|
187
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
|
188
|
+
requirements:
|
|
189
|
+
- - ">="
|
|
190
|
+
- !ruby/object:Gem::Version
|
|
191
|
+
version: "0"
|
|
192
|
+
version:
|
|
193
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
194
|
+
requirements:
|
|
195
|
+
- - ">="
|
|
196
|
+
- !ruby/object:Gem::Version
|
|
197
|
+
version: "0"
|
|
198
|
+
version:
|
|
199
|
+
requirements: []
|
|
200
|
+
|
|
201
|
+
rubyforge_project: ulla
|
|
202
|
+
rubygems_version: 1.2.0
|
|
203
|
+
signing_key:
|
|
204
|
+
specification_version: 2
|
|
205
|
+
summary: "'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."
|
|
206
|
+
test_files:
|
|
207
|
+
- test/test_math_extensions.rb
|
|
208
|
+
- test/test_narray_extensions.rb
|
|
209
|
+
- test/test_nmatrix_extensions.rb
|
|
210
|
+
- test/test_string_extensions.rb
|
|
211
|
+
- test/ulla/test_cli.rb
|
|
212
|
+
- test/ulla/test_environment_class_hash.rb
|
|
213
|
+
- test/ulla/test_environment_feature.rb
|
|
214
|
+
- test/test_helper.rb
|
|
215
|
+
- test/test_ulla.rb
|