ulla 0.9.9.1 → 0.9.9.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (20) hide show
  1. checksums.yaml +7 -0
  2. data/History.txt +1 -1
  3. data/Manifest.txt +4 -0
  4. data/PostInstall.txt +1 -1
  5. data/README.rdoc +6 -7
  6. data/Rakefile +2 -2
  7. data/lib/narray_extensions.rb +0 -3
  8. data/lib/nmatrix_extensions.rb +0 -11
  9. data/lib/ulla.rb +45 -1
  10. data/lib/ulla/cli.rb +192 -89
  11. data/lib/ulla/esst.rb +32 -0
  12. data/lib/ulla/essts.rb +84 -0
  13. data/lib/ulla/heatmap_array.rb +0 -12
  14. data/lib/ulla/joy_tem.rb +63 -0
  15. data/lib/ulla/sequence.rb +7 -0
  16. data/script/txt2html +5 -5
  17. data/ulla.gemspec +3 -3
  18. data/website/index.html +286 -19
  19. data/website/stylesheets/screen.css +80 -81
  20. metadata +109 -71
data/website/stylesheets/screen.css CHANGED
@@ -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: []