ulla 0.9.9.1 → 0.9.9.2
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- checksums.yaml +7 -0
- data/History.txt +1 -1
- data/Manifest.txt +4 -0
- data/PostInstall.txt +1 -1
- data/README.rdoc +6 -7
- data/Rakefile +2 -2
- data/lib/narray_extensions.rb +0 -3
- data/lib/nmatrix_extensions.rb +0 -11
- data/lib/ulla.rb +45 -1
- data/lib/ulla/cli.rb +192 -89
- data/lib/ulla/esst.rb +32 -0
- data/lib/ulla/essts.rb +84 -0
- data/lib/ulla/heatmap_array.rb +0 -12
- data/lib/ulla/joy_tem.rb +63 -0
- data/lib/ulla/sequence.rb +7 -0
- data/script/txt2html +5 -5
- data/ulla.gemspec +3 -3
- data/website/index.html +286 -19
- data/website/stylesheets/screen.css +80 -81
- metadata +109 -71
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#main {
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table {
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#version {
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#version a {
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.clickable {
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cursor: hand;
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}
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#twitter_search {
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#twitter_search center b {
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metadata
CHANGED
@@ -1,70 +1,114 @@
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-
--- !ruby/object:Gem::Specification
|
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--- !ruby/object:Gem::Specification
|
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name: ulla
|
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version: !ruby/object:Gem::Version
|
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version: 0.9.9.
|
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version: !ruby/object:Gem::Version
|
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version: 0.9.9.2
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platform: ruby
|
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authors:
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authors:
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- Semin Lee
|
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8
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autorequire:
|
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9
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bindir: bin
|
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cert_chain: []
|
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-
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-
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dependencies:
|
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-
- !ruby/object:Gem::Dependency
|
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date: 2016-02-04 00:00:00.000000000 Z
|
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dependencies:
|
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- !ruby/object:Gem::Dependency
|
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name: narray
|
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requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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- - ">="
|
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- !ruby/object:Gem::Version
|
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version: 0.5.9.5
|
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type: :runtime
|
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-
|
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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- - ">="
|
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-
- !ruby/object:Gem::Version
|
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+
- !ruby/object:Gem::Version
|
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version: 0.5.9.5
|
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-
|
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-
- !ruby/object:Gem::Dependency
|
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+
- !ruby/object:Gem::Dependency
|
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name: bio
|
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requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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+
- - ">="
|
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+
- !ruby/object:Gem::Version
|
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+
version: 1.2.1
|
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type: :runtime
|
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-
|
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-
version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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prerelease: false
|
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+
version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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- - ">="
|
32
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-
- !ruby/object:Gem::Version
|
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+
- !ruby/object:Gem::Version
|
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version: 1.2.1
|
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-
|
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-
- !ruby/object:Gem::Dependency
|
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+
- !ruby/object:Gem::Dependency
|
36
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name: rmagick
|
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+
requirement: !ruby/object:Gem::Requirement
|
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+
requirements:
|
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+
- - ">="
|
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+
- !ruby/object:Gem::Version
|
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+
version: 2.9.1
|
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type: :runtime
|
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-
|
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
|
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+
requirements:
|
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- - ">="
|
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-
- !ruby/object:Gem::Version
|
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+
- !ruby/object:Gem::Version
|
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version: 2.9.1
|
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-
|
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-
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-
|
55
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+
- !ruby/object:Gem::Dependency
|
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name: rdoc
|
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requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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+
- - "~>"
|
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+
- !ruby/object:Gem::Version
|
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+
version: '4.0'
|
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+
type: :development
|
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+
prerelease: false
|
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+
version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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+
- - "~>"
|
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+
- !ruby/object:Gem::Version
|
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version: '4.0'
|
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+
- !ruby/object:Gem::Dependency
|
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name: newgem
|
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+
requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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+
- - ">="
|
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+
- !ruby/object:Gem::Version
|
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+
version: 1.5.3
|
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type: :development
|
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-
|
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-
version_requirements: !ruby/object:Gem::Requirement
|
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-
requirements:
|
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
51
80
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- - ">="
|
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-
- !ruby/object:Gem::Version
|
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-
version:
|
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-
|
55
|
-
|
56
|
-
|
81
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+
- !ruby/object:Gem::Version
|
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+
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
|
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|
+
requirements:
|
94
|
+
- - "~>"
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: '3.14'
|
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+
description: "'ulla' is a program for calculating environment-specific substitution
|
98
|
+
tables from user providing environmental class definitions and sequence alignments
|
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|
+
with the annotations of the environment classes."
|
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|
+
email:
|
57
101
|
- seminlee@gmail.com
|
58
|
-
executables:
|
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+
executables:
|
59
103
|
- ulla
|
60
104
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extensions: []
|
61
|
-
|
62
|
-
extra_rdoc_files:
|
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+
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
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+
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
|
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|
+
- lib/ulla/joy_tem.rb
|
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|
+
- 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
|
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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
|
- - ">="
|
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|
-
- !ruby/object:Gem::Version
|
121
|
-
version:
|
122
|
-
|
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|
-
|
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:
|
128
|
-
version:
|
173
|
+
- !ruby/object:Gem::Version
|
174
|
+
version: '0'
|
129
175
|
requirements: []
|
130
|
-
|
131
|
-
|
132
|
-
rubygems_version: 1.3.5
|
176
|
+
rubyforge_project:
|
177
|
+
rubygems_version: 2.4.5.1
|
133
178
|
signing_key:
|
134
|
-
specification_version:
|
135
|
-
summary: "'ulla' is a program for calculating environment-specific substitution tables
|
136
|
-
|
137
|
-
|
138
|
-
|
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: []
|