ulla 0.9.9 → 0.9.9.1
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- data/History.txt +5 -0
- data/Manifest.txt +1 -0
- data/README.rdoc +1 -1
- data/Rakefile +3 -4
- data/lib/array_extensions.rb +16 -0
- data/lib/math_extensions.rb +2 -0
- data/lib/narray_extensions.rb +0 -1
- data/lib/nmatrix_extensions.rb +1 -2
- data/lib/string_extensions.rb +14 -1
- data/lib/ulla.rb +1 -1
- data/lib/ulla/cli.rb +14 -14
- data/lib/ulla/environment.rb +2 -2
- data/lib/ulla/environment_class_hash.rb +1 -1
- data/lib/ulla/heatmap_array.rb +0 -1
- data/ulla.gemspec +3 -6
- metadata +3 -12
data/History.txt
CHANGED
data/Manifest.txt
CHANGED
data/README.rdoc
CHANGED
@@ -24,8 +24,8 @@ http://www-cryst.bioc.cam.ac.uk/ulla
|
|
24
24
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Following RubyGems will be automatically installed if you have rubygems installed on your machine
|
25
25
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|
26
26
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* narray (http://narray.rubyforge.org)
|
27
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-
* facets (http://facets.rubyforge.org)
|
28
27
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* bio (http://bioruby.open-bio.org)
|
28
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+
* Active Support (http://as.rubyonrails.org)
|
29
29
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* RMagick (http://rmagick.rubyforge.org)
|
30
30
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|
31
31
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|
data/Rakefile
CHANGED
@@ -14,10 +14,9 @@ $hoe = Hoe.spec 'ulla' do
|
|
14
14
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self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
|
15
15
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self.rubyforge_name = self.name # TODO this is default value
|
16
16
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self.extra_deps = [
|
17
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-
['narray',
|
18
|
-
['bio',
|
19
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-
['
|
20
|
-
['rmagick', '>= 2.9.1'],
|
17
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+
['narray', '>= 0.5.9.5'],
|
18
|
+
['bio', '>= 1.2.1'],
|
19
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+
['rmagick', '>= 2.9.1'],
|
21
20
|
]
|
22
21
|
end
|
23
22
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@@ -0,0 +1,16 @@
|
|
1
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+
module ArrayExtensions
|
2
|
+
|
3
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+
# from Active Support library
|
4
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+
def sum(identity = 0, &block)
|
5
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+
return identity unless size > 0
|
6
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+
|
7
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+
if block_given?
|
8
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+
map(&block).sum
|
9
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+
else
|
10
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+
inject { |sum, element| sum + element }
|
11
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+
end
|
12
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+
end
|
13
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+
|
14
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+
end
|
15
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+
|
16
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+
Array.send :include, ArrayExtensions
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data/lib/math_extensions.rb
CHANGED
data/lib/narray_extensions.rb
CHANGED
data/lib/nmatrix_extensions.rb
CHANGED
@@ -1,6 +1,5 @@
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1
1
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require 'rubygems'
|
2
2
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require 'narray'
|
3
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-
require 'facets'
|
4
3
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5
4
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begin
|
6
5
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require 'rvg/rvg'
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@@ -19,7 +18,7 @@ module NMatrixExtensions
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19
18
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|
20
19
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("%-3s" % "#") + opts[:col_header].inject("") { |s, a|
|
21
20
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s + ("%#{opts[:col_size]}s" % a)
|
22
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-
} + "\n" + self.to_a.
|
21
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+
} + "\n" + self.to_a.each_with_index.map { |a, i|
|
23
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("%-3s" % opts[:row_header][i]) + a.inject("") { |s, v|
|
24
23
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if v.is_a? Float
|
25
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s + ("%#{opts[:col_size]}.2f" % v)
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data/lib/string_extensions.rb
CHANGED
@@ -1,5 +1,19 @@
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1
1
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module StringExtensions
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2
2
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|
3
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+
unless method_defined?(:blank?)
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+
# from Active Support library
|
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+
def blank?
|
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+
self !~ /\S/
|
7
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+
end
|
8
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+
end
|
9
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+
|
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+
unless method_defined?(:start_with?)
|
11
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+
# from Ruby Facets library
|
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+
def start_with?(prefix)
|
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+
self.index(prefix) == 0
|
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+
end
|
15
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+
end
|
16
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+
|
3
17
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def remove_internal_spaces
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4
18
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gsub(/[\n|\r|\s]+/, '')
|
5
19
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end
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@@ -14,4 +28,3 @@ module StringExtensions
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14
28
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end
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15
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16
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String.send :include, StringExtensions
|
17
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-
|
data/lib/ulla.rb
CHANGED
data/lib/ulla/cli.rb
CHANGED
@@ -4,7 +4,6 @@ require 'logger'
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4
4
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require 'narray'
|
5
5
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require 'bio'
|
6
6
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require 'set'
|
7
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-
require 'facets'
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8
7
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|
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8
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# This is a module for an actual command line interpreter for Ulla
|
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9
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# ---
|
@@ -368,6 +367,7 @@ Options:
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end
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require 'math_extensions'
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+
require 'array_extensions'
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require 'string_extensions'
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require 'narray_extensions'
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require 'nmatrix_extensions'
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@@ -535,7 +535,7 @@ Options:
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535
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ff.rewind
|
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536
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ff.each_entry do |pir|
|
537
537
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if (pir.entry_id == key) && (pir.definition == ec.name)
|
538
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-
labels = pir.data.remove_internal_spaces.split('').
|
538
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+
labels = pir.data.remove_internal_spaces.split('').each_with_index.map do |sym, pos|
|
539
539
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if sym == '-'
|
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540
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'-'
|
541
541
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elsif sym == 'X' || sym == 'x'
|
@@ -562,13 +562,13 @@ Options:
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|
562
562
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if $noweight
|
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563
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ali.each_pair do |id1, seq1|
|
564
564
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if $environment == 1
|
565
|
-
seq1 = seq1.split('').
|
565
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+
seq1 = seq1.split('').each_with_index.map { |aa, pos| aa == $gap ? $ext_gap : env_labels[id1][pos] }.join
|
566
566
|
end
|
567
567
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|
568
568
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ali.each_pair do |id2, seq2|
|
569
569
|
if id1 != id2
|
570
570
|
if $environment == 1
|
571
|
-
seq2 = seq2.split('').
|
571
|
+
seq2 = seq2.split('').each_with_index.map { |aa, pos| aa == $gap ? $ext_gap : env_labels[id2][pos] }.join
|
572
572
|
end
|
573
573
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|
574
574
|
pid = calculate_pid(seq1, seq2, $col_size)
|
@@ -639,7 +639,7 @@ Options:
|
|
639
639
|
ali.each_pair do |key, seq|
|
640
640
|
clusters << [key]
|
641
641
|
if $environment == 1
|
642
|
-
ext_seq = seq.split('').
|
642
|
+
ext_seq = seq.split('').each_with_index.map { |aa, pos| aa == $gap ? $ext_gap : env_labels[key][pos] }.join
|
643
643
|
ext_ali.add_seq(ext_seq, key)
|
644
644
|
end
|
645
645
|
end
|
@@ -988,7 +988,7 @@ HEADER
|
|
988
988
|
end
|
989
989
|
|
990
990
|
# total
|
991
|
-
$outfh.puts '>
|
991
|
+
$outfh.puts '>total'
|
992
992
|
$outfh.puts $tot_cnt_mat.pretty_string(:col_header => $amino_acids,
|
993
993
|
:row_header => $amino_acids,
|
994
994
|
:col_size => mat_col_size > 7 ? mat_col_size : 7)
|
@@ -1132,7 +1132,7 @@ HEADER
|
|
1132
1132
|
end
|
1133
1133
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|
1134
1134
|
if $output == 1
|
1135
|
-
$outfh.puts '>
|
1135
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+
$outfh.puts '>total'
|
1136
1136
|
$outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids,
|
1137
1137
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:row_header => $amino_acids)
|
1138
1138
|
$outfh.close
|
@@ -1197,10 +1197,10 @@ HEADER
|
|
1197
1197
|
#
|
1198
1198
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# p2 and above
|
1199
1199
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#
|
1200
|
-
env_labels = $env_features.
|
1200
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+
env_labels = $env_features.each_with_index.map { |ef, ei| ef.labels.map { |l| "#{ei}#{l}" } }
|
1201
1201
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|
1202
1202
|
if $environment == 1
|
1203
|
-
env_labels += $env_features[1..-1].
|
1203
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+
env_labels += $env_features[1..-1].each_with_index.map { |ef, ei| ef.labels.map { |l| "#{ei + $env_features.size}#{l}" } }
|
1204
1204
|
end
|
1205
1205
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1206
1206
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if $smooth == :partial
|
@@ -1337,7 +1337,7 @@ HEADER
|
|
1337
1337
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entropies = priors.map { |prior| -1.0 * prior.to_a.inject(0.0) { |s, p| p == 0 ? s : s + p * Math::log(p) } }
|
1338
1338
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mod_entropies = entropies.map { |entropy| (entropy_max - entropy) / entropy_max }
|
1339
1339
|
weights = mod_entropies.map { |mod_entropy| mod_entropy / mod_entropies.sum }
|
1340
|
-
weighted_priors = priors.
|
1340
|
+
weighted_priors = priors.each_with_index.map { |prior, i| prior * weights[i] }.sum
|
1341
1341
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|
1342
1342
|
# actual smoothing step
|
1343
1343
|
smooth_prob_arr = NArray.float($amino_acids.size)
|
@@ -1432,9 +1432,9 @@ HEADER
|
|
1432
1432
|
# entropy based weighting priors step
|
1433
1433
|
entropy_max = NMath::log($amino_acids.size)
|
1434
1434
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entropies = priors.map { |prior| -1.0 * prior.to_a.inject(0.0) { |s, p| p == 0 ? s : s + p * Math::log(p) } }
|
1435
|
-
mod_entropies = entropies.
|
1435
|
+
mod_entropies = entropies.each_with_index.map { |entropy, i| (entropy_max - entropies[i]) / entropy_max }
|
1436
1436
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weights = mod_entropies.map { |mod_entropy| mod_entropy / mod_entropies.sum }
|
1437
|
-
weighted_priors = priors.
|
1437
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+
weighted_priors = priors.each_with_index.map { |prior, i| prior * weights[i] }.sum
|
1438
1438
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|
1439
1439
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# smoothing step
|
1440
1440
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smooth_prob_arr = NArray.float($amino_acids.size)
|
@@ -1548,7 +1548,7 @@ HEADER
|
|
1548
1548
|
end
|
1549
1549
|
|
1550
1550
|
if $output == 1
|
1551
|
-
$outfh.puts '>
|
1551
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+
$outfh.puts '>total'
|
1552
1552
|
$outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids,
|
1553
1553
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:row_header => $amino_acids)
|
1554
1554
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$outfh.close
|
@@ -1810,7 +1810,7 @@ HEADER
|
|
1810
1810
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$tot_logo_mat = $tot_logo_mat.round
|
1811
1811
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end
|
1812
1812
|
|
1813
|
-
$outfh.puts ">
|
1813
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+
$outfh.puts ">total #{grp_logo_mats.size}"
|
1814
1814
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$outfh.puts $tot_logo_mat.pretty_string(:col_header => $amino_acids,
|
1815
1815
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:row_header => row_header)
|
1816
1816
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|
data/lib/ulla/environment.rb
CHANGED
@@ -25,9 +25,9 @@ module Ulla
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|
25
25
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|
26
26
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def label_set
|
27
27
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if $direction == 0
|
28
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-
label.split("").
|
28
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+
label.split("").each_with_index.map { |l, i| "#{i}#{l}" }.to_set
|
29
29
|
else
|
30
|
-
label.gsub('-', '').split("").
|
30
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+
label.gsub('-', '').split("").each_with_index.map { |l, i| "#{i}#{l}" }.to_set
|
31
31
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end
|
32
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end
|
33
33
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|
@@ -7,7 +7,7 @@ module Ulla
|
|
7
7
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|
8
8
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def groups_sorted_by_residue_labels
|
9
9
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group_by_non_residue_labels.to_a.sort_by { |env_group|
|
10
|
-
env_group[0].gsub('-', '').split('').
|
10
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+
env_group[0].gsub('-', '').split('').each_with_index.map { |l, i|
|
11
11
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if i < ($env_features.size - 1)
|
12
12
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$env_features[i + 1].labels.index(l)
|
13
13
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else
|
data/lib/ulla/heatmap_array.rb
CHANGED
data/ulla.gemspec
CHANGED
@@ -2,17 +2,17 @@
|
|
2
2
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|
3
3
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Gem::Specification.new do |s|
|
4
4
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s.name = %q{ulla}
|
5
|
-
s.version = "0.9.9"
|
5
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+
s.version = "0.9.9.1"
|
6
6
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|
7
7
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
8
8
|
s.authors = ["Semin Lee"]
|
9
|
-
s.date = %q{2009-08-
|
9
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+
s.date = %q{2009-08-26}
|
10
10
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s.default_executable = %q{ulla}
|
11
11
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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.}
|
12
12
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s.email = ["seminlee@gmail.com"]
|
13
13
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s.executables = ["ulla"]
|
14
14
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s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
|
15
|
-
s.files = ["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"]
|
15
|
+
s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/array_extensions.rb", "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"]
|
16
16
|
s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
|
17
17
|
s.post_install_message = %q{PostInstall.txt}
|
18
18
|
s.rdoc_options = ["--main", "README.rdoc"]
|
@@ -29,20 +29,17 @@ Gem::Specification.new do |s|
|
|
29
29
|
if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
|
30
30
|
s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
|
31
31
|
s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
|
32
|
-
s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
|
33
32
|
s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
|
34
33
|
s.add_development_dependency(%q<hoe>, [">= 2.3.3"])
|
35
34
|
else
|
36
35
|
s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
37
36
|
s.add_dependency(%q<bio>, [">= 1.2.1"])
|
38
|
-
s.add_dependency(%q<facets>, [">= 2.4.5"])
|
39
37
|
s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
40
38
|
s.add_dependency(%q<hoe>, [">= 2.3.3"])
|
41
39
|
end
|
42
40
|
else
|
43
41
|
s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
44
42
|
s.add_dependency(%q<bio>, [">= 1.2.1"])
|
45
|
-
s.add_dependency(%q<facets>, [">= 2.4.5"])
|
46
43
|
s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
47
44
|
s.add_dependency(%q<hoe>, [">= 2.3.3"])
|
48
45
|
end
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: ulla
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.9.9
|
4
|
+
version: 0.9.9.1
|
5
5
|
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: 2009-08-
|
12
|
+
date: 2009-08-26 00:00:00 +01:00
|
13
13
|
default_executable:
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
@@ -32,16 +32,6 @@ dependencies:
|
|
32
32
|
- !ruby/object:Gem::Version
|
33
33
|
version: 1.2.1
|
34
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
35
|
- !ruby/object:Gem::Dependency
|
46
36
|
name: rmagick
|
47
37
|
type: :runtime
|
@@ -83,6 +73,7 @@ files:
|
|
83
73
|
- bin/ulla
|
84
74
|
- config/website.yml
|
85
75
|
- config/website.yml.sample
|
76
|
+
- lib/array_extensions.rb
|
86
77
|
- lib/math_extensions.rb
|
87
78
|
- lib/narray_extensions.rb
|
88
79
|
- lib/nmatrix_extensions.rb
|