ulla 0.9.9.1 → 0.9.9.2

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@@ -1,89 +1,89 @@
1
1
  body {
2
- background-color: #8DBD82;
3
- font-family: "Georgia", sans-serif;
4
- font-size: 16px;
5
- line-height: 1.6em;
6
- padding: 1.6em 0 0 0;
7
- color: #333;
2
+ background-color: #8DBD82;
3
+ font-family: "Georgia", "Optima", "Lucida Grande", sans-serif;
4
+ font-size: 16px;
5
+ line-height: 1.6em;
6
+ padding: 1.6em 0 0 0;
7
+ color: #333;
8
8
  }
9
9
  h1, h2, h3, h4, h5, h6 {
10
- color: #444;
10
+ color: #444;
11
11
  }
12
12
  h1 {
13
- font-family: sans-serif;
14
- font-weight: normal;
15
- font-size: 4em;
16
- line-height: 0.8em;
17
- letter-spacing: -0.1ex;
18
- margin: 5px;
13
+ font-weight: bold;
14
+ font-size: 4em;
15
+ line-height: 0.8em;
16
+ letter-spacing: -0.1ex;
17
+ margin: 5px;
19
18
  }
20
19
  li {
21
- padding: 0;
22
- margin: 0;
23
- list-style-type: square;
20
+ padding: 0;
21
+ margin: 0;
22
+ list-style-type: square;
24
23
  }
25
24
  a {
26
- color: #5E5AFF;
27
- background-color: #A1DDB1;
28
- font-weight: normal;
29
- text-decoration: underline;
25
+ color: #0000FF;
26
+ font-weight: normal;
27
+ text-decoration: underline;
30
28
  }
31
29
  blockquote {
32
- font-size: 90%;
33
- font-style: italic;
34
- border-left: 1px solid #111;
35
- padding-left: 1em;
30
+ font-size: 90%;
31
+ font-style: italic;
32
+ border-left: 1px solid #111;
33
+ padding-left: 1em;
36
34
  }
37
35
  .caps {
38
- font-size: 80%;
36
+ font-size: 80%;
39
37
  }
40
38
 
41
39
  #main {
42
- width: 55em;
43
- padding: 0;
44
- margin: 0 auto;
40
+ width: 55em;
41
+ padding: 0;
42
+ margin: 0 auto;
45
43
  }
46
44
  .coda {
47
- text-align: right;
48
- color: #77f;
49
- font-size: smaller;
45
+ text-align: right;
46
+ color: #77f;
47
+ font-size: smaller;
50
48
  }
51
49
 
52
50
  table {
53
- font-size: 90%;
54
- line-height: 1.4em;
55
- color: #ff8;
56
- background-color: #111;
57
- padding: 2px 10px 2px 10px;
58
- border-style: dashed;
51
+ font-size: 90%;
52
+ line-height: 1.4em;
53
+ color: #ff8;
54
+ background-color: #111;
55
+ padding: 2px 10px 2px 10px;
56
+ border-style: dashed;
59
57
  }
60
58
 
61
59
  th {
62
- color: #fff;
60
+ color: #fff;
63
61
  }
64
62
 
65
63
  td {
66
- padding: 2px 10px 2px 10px;
64
+ padding: 2px 10px 2px 10px;
67
65
  }
68
66
 
69
67
  .success {
70
- color: #0CC52B;
68
+ color: #0CC52B;
71
69
  }
72
70
 
73
71
  .failed {
74
- color: #E90A1B;
72
+ color: #E90A1B;
75
73
  }
76
74
 
77
75
  .unknown {
78
- color: #995000;
76
+ color: #995000;
79
77
  }
80
78
  pre, code {
81
- font-family: monospace;
82
- font-size: 90%;
83
- line-height: 1.4em;
84
- color: #ff8;
85
- background-color: #111;
86
- padding: 2px 10px 2px 10px;
79
+ font-family: courier, monospace;
80
+ font-size: 85%;
81
+ line-height: 1.4em;
82
+ color: #ff8;
83
+ background-color: #111;
84
+ /*width: 40em;*/
85
+ overflow: auto;
86
+ padding: 2px 10px 2px 10px;
87
87
  }
88
88
  .comment { color: #aaa; font-style: italic; }
89
89
  .keyword { color: #eff; font-weight: bold; }
@@ -97,62 +97,61 @@ pre, code {
97
97
  .expr { color: #227; }
98
98
 
99
99
  .sidebar {
100
- float: right;
100
+ float: right;
101
101
  }
102
102
 
103
103
  #version {
104
- width: 217px;
105
- text-align: right;
106
- font-family: sans-serif;
107
- font-weight: normal;
108
- color: #141331;
109
- padding: 15px 20px 10px 20px;
110
- margin: 0 auto;
111
- margin-top: 15px;
112
- background-color: #9A5535;
113
- border: 3px solid #7E393E;
104
+ width: 217px;
105
+ text-align: right;
106
+ font-weight: normal;
107
+ color: #141331;
108
+ padding: 15px 20px 10px 20px;
109
+ margin: 0 auto;
110
+ margin-top: 15px;
111
+ background-color: #9A5535;
112
+ border: 3px solid #7E393E;
114
113
  }
115
114
 
116
115
  #version .numbers {
117
- display: block;
118
- font-size: 4em;
119
- line-height: 0.8em;
120
- letter-spacing: -0.1ex;
121
- margin-bottom: 15px;
116
+ display: block;
117
+ font-size: 4em;
118
+ line-height: 0.8em;
119
+ letter-spacing: -0.1ex;
120
+ margin-bottom: 15px;
122
121
  }
123
122
 
124
123
  #version p {
125
- text-decoration: none;
126
- color: #F1F4FF;
127
- background-color: #9A5535;
128
- margin: 0;
129
- padding: 0;
124
+ text-decoration: none;
125
+ color: #F1F4FF;
126
+ background-color: #9A5535;
127
+ margin: 0;
128
+ padding: 0;
130
129
  }
131
130
 
132
131
  #version a {
133
- text-decoration: none;
134
- color: #F1F4FF;
135
- background-color: #9A5535;
132
+ text-decoration: none;
133
+ color: #F1F4FF;
134
+ background-color: #9A5535;
136
135
  }
137
136
 
138
137
  .clickable {
139
- cursor: pointer;
140
- cursor: hand;
138
+ cursor: pointer;
139
+ cursor: hand;
141
140
  }
142
141
 
143
142
  #twitter_search {
144
- margin: 40px 0 10px 15px;
145
- color: #F1F4FF;
146
- background-color: #9A5535;
147
- border: 3px solid #7E393E;
143
+ margin: 40px 0 10px 15px;
144
+ color: #F1F4FF;
145
+ background-color: #9A5535;
146
+ border: 3px solid #7E393E;
148
147
  }
149
148
 
150
149
  #twitter_search h3 {
151
- color: #F1F4FF;
152
- margin-bottom: 0px;
150
+ color: #F1F4FF;
151
+ margin-bottom: 0px;
153
152
  }
154
153
 
155
154
  #twitter_search center b {
156
- display: none;
155
+ display: none;
157
156
  }
158
157
 
metadata CHANGED
@@ -1,70 +1,114 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: ulla
3
- version: !ruby/object:Gem::Version
4
- version: 0.9.9.1
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.9.9.2
5
5
  platform: ruby
6
- authors:
6
+ authors:
7
7
  - Semin Lee
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
-
12
- date: 2009-08-26 00:00:00 +01:00
13
- default_executable:
14
- dependencies:
15
- - !ruby/object:Gem::Dependency
11
+ date: 2016-02-04 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
16
14
  name: narray
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - ">="
18
+ - !ruby/object:Gem::Version
19
+ version: 0.5.9.5
17
20
  type: :runtime
18
- version_requirement:
19
- version_requirements: !ruby/object:Gem::Requirement
20
- requirements:
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
21
24
  - - ">="
22
- - !ruby/object:Gem::Version
25
+ - !ruby/object:Gem::Version
23
26
  version: 0.5.9.5
24
- version:
25
- - !ruby/object:Gem::Dependency
27
+ - !ruby/object:Gem::Dependency
26
28
  name: bio
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ">="
32
+ - !ruby/object:Gem::Version
33
+ version: 1.2.1
27
34
  type: :runtime
28
- version_requirement:
29
- version_requirements: !ruby/object:Gem::Requirement
30
- requirements:
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
31
38
  - - ">="
32
- - !ruby/object:Gem::Version
39
+ - !ruby/object:Gem::Version
33
40
  version: 1.2.1
34
- version:
35
- - !ruby/object:Gem::Dependency
41
+ - !ruby/object:Gem::Dependency
36
42
  name: rmagick
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - ">="
46
+ - !ruby/object:Gem::Version
47
+ version: 2.9.1
37
48
  type: :runtime
38
- version_requirement:
39
- version_requirements: !ruby/object:Gem::Requirement
40
- requirements:
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
41
52
  - - ">="
42
- - !ruby/object:Gem::Version
53
+ - !ruby/object:Gem::Version
43
54
  version: 2.9.1
44
- version:
45
- - !ruby/object:Gem::Dependency
46
- name: hoe
55
+ - !ruby/object:Gem::Dependency
56
+ name: rdoc
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - "~>"
60
+ - !ruby/object:Gem::Version
61
+ version: '4.0'
62
+ type: :development
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - "~>"
67
+ - !ruby/object:Gem::Version
68
+ version: '4.0'
69
+ - !ruby/object:Gem::Dependency
70
+ name: newgem
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - ">="
74
+ - !ruby/object:Gem::Version
75
+ version: 1.5.3
47
76
  type: :development
48
- version_requirement:
49
- version_requirements: !ruby/object:Gem::Requirement
50
- requirements:
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
51
80
  - - ">="
52
- - !ruby/object:Gem::Version
53
- version: 2.3.3
54
- version:
55
- 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."
56
- email:
81
+ - !ruby/object:Gem::Version
82
+ version: 1.5.3
83
+ - !ruby/object:Gem::Dependency
84
+ name: hoe
85
+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - "~>"
88
+ - !ruby/object:Gem::Version
89
+ version: '3.14'
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
94
+ - - "~>"
95
+ - !ruby/object:Gem::Version
96
+ version: '3.14'
97
+ description: "'ulla' is a program for calculating environment-specific substitution
98
+ tables from user providing environmental class definitions and sequence alignments
99
+ with the annotations of the environment classes."
100
+ email:
57
101
  - seminlee@gmail.com
58
- executables:
102
+ executables:
59
103
  - ulla
60
104
  extensions: []
61
-
62
- extra_rdoc_files:
105
+ extra_rdoc_files:
63
106
  - History.txt
64
107
  - Manifest.txt
65
108
  - PostInstall.txt
109
+ - README.rdoc
66
110
  - website/index.txt
67
- files:
111
+ files:
68
112
  - History.txt
69
113
  - Manifest.txt
70
114
  - PostInstall.txt
@@ -84,7 +128,11 @@ files:
84
128
  - lib/ulla/environment_class_hash.rb
85
129
  - lib/ulla/environment_feature.rb
86
130
  - lib/ulla/environment_feature_array.rb
131
+ - lib/ulla/esst.rb
132
+ - lib/ulla/essts.rb
87
133
  - lib/ulla/heatmap_array.rb
134
+ - lib/ulla/joy_tem.rb
135
+ - lib/ulla/sequence.rb
88
136
  - script/console
89
137
  - script/destroy
90
138
  - script/generate
@@ -104,42 +152,32 @@ files:
104
152
  - website/javascripts/rounded_corners_lite.inc.js
105
153
  - website/stylesheets/screen.css
106
154
  - website/template.html.erb
107
- has_rdoc: true
108
155
  homepage: http://www-cryst.bioc.cam.ac.uk/ulla
109
- licenses: []
110
-
156
+ licenses:
157
+ - MIT
158
+ metadata: {}
111
159
  post_install_message: PostInstall.txt
112
- rdoc_options:
113
- - --main
160
+ rdoc_options:
161
+ - "--main"
114
162
  - README.rdoc
115
- require_paths:
163
+ require_paths:
116
164
  - lib
117
- required_ruby_version: !ruby/object:Gem::Requirement
118
- requirements:
165
+ required_ruby_version: !ruby/object:Gem::Requirement
166
+ requirements:
119
167
  - - ">="
120
- - !ruby/object:Gem::Version
121
- version: "0"
122
- version:
123
- required_rubygems_version: !ruby/object:Gem::Requirement
124
- requirements:
168
+ - !ruby/object:Gem::Version
169
+ version: '0'
170
+ required_rubygems_version: !ruby/object:Gem::Requirement
171
+ requirements:
125
172
  - - ">="
126
- - !ruby/object:Gem::Version
127
- version: "0"
128
- version:
173
+ - !ruby/object:Gem::Version
174
+ version: '0'
129
175
  requirements: []
130
-
131
- rubyforge_project: ulla
132
- rubygems_version: 1.3.5
176
+ rubyforge_project:
177
+ rubygems_version: 2.4.5.1
133
178
  signing_key:
134
- specification_version: 3
135
- 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."
136
- test_files:
137
- - test/test_math_extensions.rb
138
- - test/test_narray_extensions.rb
139
- - test/test_nmatrix_extensions.rb
140
- - test/test_string_extensions.rb
141
- - test/ulla/test_cli.rb
142
- - test/ulla/test_environment_class_hash.rb
143
- - test/ulla/test_environment_feature.rb
144
- - test/test_helper.rb
145
- - test/test_ulla.rb
179
+ specification_version: 4
180
+ summary: "'ulla' is a program for calculating environment-specific substitution tables
181
+ from user providing environmental class definitions and sequence alignments with
182
+ the annotations of the environment classes."
183
+ test_files: []