rbbt-dm 1.1.42 → 1.1.43

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: fb33662dd918f39ceb8090b64983a746960c5216
-  data.tar.gz: 5865c507c3ea0468f80a9b80a602b5b7ccc11d73
+  metadata.gz: 270570bf58c397ec1f6da3195f882a5cf73eb1a1
+  data.tar.gz: 4f7232e2c2cddff960f2f9dce6e4279298b53408
 SHA512:
-  metadata.gz: f11deb2301550a9382aca6c9c41fe9ece9e93f2c63c29db84d777b48caec99b3dfeb05e6cc98b4e52f07fa7ea01f312abef81733c9deeafc16694ce6f9449caa
-  data.tar.gz: '0715538b774c7b547c60773c61711539ace35774b7e21813e62fb42aab800946a5ec7002f99e4bf3e1a2030ca837251fc788daf94bee837f6a0a093129567794'
+  metadata.gz: faa0514ae85d537007147f8a1c06367202cffa83c5081b68f9e2e23943b02cc5601160fbcfd32f0c041fd511b2f3116e82b14b5313ba57488297f76a74f77433
+  data.tar.gz: bc1d750d449763f45482318e1f4fe5d54f80c64eb90c3fb08c71d94d282496aa87e54004f309e2c2dac4cc3bc01995880481be490c4bf6510d1e35417276eb85

data/lib/rbbt/network/paths.rb

@@ -1,19 +1,21 @@
-require 'priority_queue'
+require 'fc'
 
 module Paths
 
   def self.dijkstra(adjacency, start_node, end_node = nil, max_steps = nil)
     return nil unless adjacency.include? start_node
 
-    active = PriorityQueue.new         
+    active = FastContainers::PriorityQueue.new(:max)
     distances = Hash.new { 1.0 / 0.0 } 
     parents = Hash.new                 
 
-    active[start_node] << 0
+    active.push(start_node, 0)
     best = 1.0 / 0.0
     until active.empty?
-      u = active.priorities.first
-      distance = active.shift
+      u = active.top
+      distance = active.top_key
+      active.pop
+
       distances[u] = distance
       d = distance + 1
       path = extract_path(parents, start_node, u)
@@ -21,13 +23,12 @@ module Paths
       adjacency[u].each do |v|
         next unless d < distances[v] and d < best # we can't relax this one
         best = d if (String === end_node ? end_node == v : end_node.include?(v))
-        active[v] << d if adjacency.include? v
+        active.push(v,d) if adjacency.include? v
         distances[v] = d
         parents[v] = u
       end    
     end
 
-
     if end_node
       end_node = end_node.select{|n| parents.keys.include? n}.first unless String === end_node
       return nil if not parents.include? end_node
@@ -48,25 +49,28 @@ module Paths
   def self.weighted_dijkstra(adjacency, start_node, end_node = nil, threshold = nil, max_steps = nil)
     return nil unless adjacency.include? start_node
 
-    active = PriorityQueue.new         
+    active = FastContainers::PriorityQueue.new(:max)
     distances = Hash.new { 1.0 / 0.0 } 
     parents = Hash.new                 
 
-    active[start_node] << 0
+    #active[start_node] << 0
+    active.push(start_node, 0)
     best = 1.0 / 0.0
     found = false
     until active.empty?
-      u = active.priorities.first
-      distance = active.shift
+      u = active.top
+      distance = active.top_key
+      active.pop
       distances[u] = distance
       path = extract_path(parents, start_node, u)
       next if path.length > max_steps if max_steps 
       next if not adjacency.include?(u) or (adjacency[u].nil? or adjacency[u].empty? )
       Misc.zip_fields(adjacency[u]).each do |v,node_dist|
+        node_dist = node_dist.to_f
         next if node_dist.nil? or (threshold and node_dist > threshold)
         d = distance + node_dist
         next unless d < distances[v] and d < best # we can't relax this one
-        active[v] << d
+        active.push(v, d)
         distances[v] = d
         parents[v] = u
         if (String === end_node ? end_node == v : end_node.include?(v))

data/test/rbbt/network/test_paths.rb

@@ -7,45 +7,42 @@ require 'set'
 
 class TestNetwork < Test::Unit::TestCase
   def _test_dijsktra
-    string = STRING.protein_protein.tsv :persist => false, :fields => ["Interactor Ensembl Protein ID"], :type => :flat 
-    string.unnamed = true
-
-    start_node = "ENSP00000256078"
-    end_node = "ENSP00000306245"
-
-    path = Paths.dijkstra(string, start_node, [end_node])
-
-    assert path != nil
-    assert path.include? start_node
-    assert path.include? end_node
+    network_txt=<<-EOF
+#: :sep=/\s/#:type=:flat
+#Start End
+N1 N2
+N2 N3 N4
+N4 N5
+    EOF
+    network = TSV.open(StringIO.new(network_txt))
+
+    start_node = "N1"
+    end_node = "N5"
+
+    path = Paths.dijkstra(network, start_node, [end_node])
+    assert_equal %w(N1 N2 N4), path.reverse
   end
 
   def test_weighted_dijsktra
-    string = STRING.protein_protein.tsv 
-    string.unnamed = true
+    network_txt=<<-EOF
+#: :sep=/\s/#:type=:double
+#Start End Score
+N1 N2|N5 1|10
+N2 N3|N4 1|1
+N4 N5 1
+    EOF
+    network = TSV.open(StringIO.new(network_txt))
 
-    string.process "Score" do |scores|
-      scores.collect{|score| 1000 - score.to_i}
-    end
-
-    start_node = "ENSP00000256078"
-    end_node = "ENSP00000306245"
-
-    path = Paths.weighted_dijkstra(string, start_node, end_node)
+    start_node = "N1"
+    end_node = "N5"
 
-    assert path != nil
-    assert path.include? start_node
-    assert path.include? end_node
-    
-    path = Paths.weighted_dijkstra(string, start_node, Set.new([end_node]))
+    path = Paths.weighted_dijkstra(network, start_node, [end_node])
+    assert_equal %w(N1 N2 N4 N5), path.reverse
 
-    assert path != nil
-    assert path.include? start_node
-    assert path.include? end_node
- 
   end
 
-  def _test_random_weighted_dijsktra
+
+  def __test_random_weighted_dijsktra
     string = STRING.protein_protein.tsv 
 
     string.process "Score" do |scores|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.42
+  version: 1.1.43
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-03 00:00:00.000000000 Z
+date: 2018-11-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -39,7 +39,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: priority_queue
+  name: priority_queue_cxx
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -138,18 +138,18 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.13
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: Data-mining and statistics
 test_files:
+- test/test_helper.rb
+- test/rbbt/test_stan.rb
+- test/rbbt/vector/model/test_svm.rb
+- test/rbbt/vector/test_model.rb
 - test/rbbt/network/test_paths.rb
 - test/rbbt/matrix/test_barcode.rb
-- test/rbbt/statistics/test_random_walk.rb
 - test/rbbt/statistics/test_fisher.rb
-- test/rbbt/statistics/test_fdr.rb
 - test/rbbt/statistics/test_hypergeometric.rb
-- test/rbbt/vector/test_model.rb
-- test/rbbt/vector/model/test_svm.rb
-- test/rbbt/test_stan.rb
-- test/test_helper.rb
+- test/rbbt/statistics/test_fdr.rb
+- test/rbbt/statistics/test_random_walk.rb