rbbt-marq 3.0.0 → 3.0.1

data/install_scripts/rake_includes.rb

@@ -189,7 +189,7 @@ def goterms(org, list, slim, threshold)
   results.
     select{|info| info["S"].to_i  > 2 }.
     select{|info| info["Hyp_c"].to_f < threshold }.
-    collect{|info| info["Items"]}.collect{|id| GO::id2name(id)}
+    collect{|info| info["Items"].first }.collect{|id| GO::id2name(id)}
 end
 
 task 'annotate_GO' do

data/lib/MARQ.rb

@@ -37,35 +37,6 @@ class String
   end
 end
 
-class Array
-  def count_smaller(value)
-    size = self.length
-
-    low = 0
-    last = size - 1
-    hi = size - 1
-    pos = size / 2
-    while true
-      case
-      when value == self[pos]
-        return pos 
-      when pos == last && self[pos] < value
-        return size
-      when pos == 0 && value <= self[pos] 
-        return 0 
-      when  self[pos] < value && value < self[pos + 1]
-        return pos + 1 
-      when  value < self[pos]
-        hi = pos 
-        pos = (pos - low) / 2 + low
-      when self[pos] < value
-        low = pos
-        pos = (hi - pos) / 2 + pos + 1
-      end
-    end
-  end
-end
-
 
 require 'DBcache'
 

data/lib/MARQ/rankproduct.rb

@@ -1,4 +1,4 @@
-require 'MARQ'
+require 'MARQ/util'
 require 'MARQ/main'
 module RankProduct
   def self.ranks(dataset, experiment , from_FC = false, invert = false)

data/lib/MARQ/score.rb

@@ -1,4 +1,5 @@
 require 'png'
+require 'MARQ/util'
 require 'inline'
 
 module Score

data/lib/MARQ/util.rb

@@ -0,0 +1,30 @@
+class Array
+  def count_smaller(value)
+    size = self.length
+
+    low = 0
+    last = size - 1
+    hi = size - 1
+    pos = size / 2
+    while true
+      case
+      when value == self[pos]
+        return pos 
+      when pos == last && self[pos] < value
+        return size
+      when pos == 0 && value <= self[pos] 
+        return 0 
+      when  self[pos] < value && value < self[pos + 1]
+        return pos + 1 
+      when  value < self[pos]
+        hi = pos 
+        pos = (pos - low) / 2 + low
+      when self[pos] < value
+        low = pos
+        pos = (hi - pos) / 2 + pos + 1
+      end
+    end
+  end
+end
+
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-marq
 version: !ruby/object:Gem::Version 
-  version: 3.0.0
+  version: 3.0.1
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-03-09 00:00:00 +01:00
+date: 2010-04-11 00:00:00 +02:00
 default_executable: marq_config
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -324,6 +324,7 @@ files:
 - lib/MARQ/main.rb
 - lib/MARQ/rankproduct.rb
 - lib/MARQ/score.rb
+- lib/MARQ/util.rb
 - tasks/install.rake
 - LICENSE
 - README.rdoc