bio-nwk 0.1.3 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8d9592e998026208adab8760c3c98f61c7dca740ede2e2634146252abeea18cc
-  data.tar.gz: be558a160cdc49fed06d255f84f72bde9a062c2ca7a8422db865292c86a2a9aa
+  metadata.gz: b5f845416e561baa214dee9ad326763f784b5ca2f891bdb01c4deb9572f9ca23
+  data.tar.gz: e7720ae89b70955493c510b4291ae8f2125e00a6d83e88d4274fa8b3490b137a
 SHA512:
-  metadata.gz: 92351aaa11e1743679f87aebaa0919dee8c903378b819e1ea857fea1f4066c1276485ab0328dc50e63fcdee0dd3ba3bb7fd3160aab4a6b184318ddc0f4d1a219
-  data.tar.gz: a48f163a2a2498c50971f45f922fe6062bdc698dd06a2a762daed8311a8528c3133800d5a3f3b290da1e22f0454cb59ac66f895a52526cd815230b610b7be96a
+  metadata.gz: a252ea335e65cbf252f3482a5fb93d5c33499df3cc401932de7db4c491628c1e3c72e9628613cf66bc632a9723bf2c541cd76c583c8aca3e8d1a456d17d71676
+  data.tar.gz: 960aa5a028aa7d475654d80683983f0b2f1900aaa665f09a37fa776d67bec11992ed0b9328c9d1aeb2a9fbf1bf884ee39629236f2ab70e41b6445289e3b95cdc

data/lib/bio/nwk/version.rb

@@ -1,5 +1,5 @@
 module Bio
   module Nwk
-    VERSION = "0.1.3"
+    VERSION = "0.1.4"
   end
 end

data/lib/bio/nwk.rb

@@ -7,6 +7,7 @@ class Bio::Tree
   DELIMITER = ';'
   attr_accessor :tip2index, :index2tip
 
+
   def tips(node)
     rv = Array.new
     if node.isTip?(self)
@@ -17,16 +18,19 @@ class Bio::Tree
     return(rv)
   end
 
+
   def all_nodes_of_subtree(node)
     [leaves(node), tips(node)].flatten
   end
 
+
   def cleanName!
     allTips.each do |tip|
       tip.name.gsub!(' ', '_')
     end
   end
 
+
   def twoTaxaNode(node)
     if node.isTip?(self)
       return(node)
@@ -34,6 +38,7 @@ class Bio::Tree
       return children(node).map{|child|tips(child).sort_by{|i|i.name}.shift}.sort_by{|i|i.name}
     end
   end
+
   
   def twoTaxaNodeName(node)
     if node.isTip?(self)
@@ -43,6 +48,7 @@ class Bio::Tree
     end
   end
 
+
   def twoTaxaNodeNameStr(node, sep='|')
     a = twoTaxaNodeName(node)
     if a.is_a?(Array)
@@ -52,6 +58,7 @@ class Bio::Tree
     end
   end
 
+
   def sisters(node)
     if node == root
       return([])
@@ -60,10 +67,12 @@ class Bio::Tree
     end
   end
 
+
   def sister(node)
     return(sisters(node)[0])
   end
 
+
   def internal_nodes
     a = Array.new
     nodes.each do |node|
@@ -74,6 +83,7 @@ class Bio::Tree
     return(a)
   end
 
+
   def allSubtreeRepresentatives
     arr = Array.new
     nodes.each do |node|
@@ -82,6 +92,7 @@ class Bio::Tree
     return(arr)
   end
 
+
   def allTips
     a = Array.new
     nodes.each do |node|
@@ -90,6 +101,7 @@ class Bio::Tree
     return(a)
   end
 
+
   def outputNexus(isTranslate=false, isTip2Index=false)
     puts "#NEXUS"
     puts
@@ -101,6 +113,7 @@ class Bio::Tree
     newickIndexToTip if isTip2Index
   end
 
+
   def cleanNewick
     output = output_newick
     output.gsub!(/[\n\s]/, '')
@@ -108,6 +121,7 @@ class Bio::Tree
     return(output)
   end
 
+
   def tipToIndex
     @tip2index = Hash.new
     @index2tip = Hash.new
@@ -117,6 +131,7 @@ class Bio::Tree
     end
   end
 
+
   def newickTipToIndex()
     tipToIndex
     allTips.each do |tip|
@@ -125,6 +140,7 @@ class Bio::Tree
     end
   end
 
+
   def newickIndexToTip()
     tipToIndex if @index2tip.empty?
     allTips.each do |tip|
@@ -133,6 +149,7 @@ class Bio::Tree
     end
   end
 
+
   def getAlldistances()
     distances = Array.new
     each_edge do |node0, node1, edge|
@@ -142,6 +159,7 @@ class Bio::Tree
     return(distances)
   end
 
+
   def normalizeBranchLength!()
     min, max = getAlldistances().minmax
     each_edge do |node0, node1, edge|
@@ -149,6 +167,7 @@ class Bio::Tree
     end
   end
 
+
   def normalizeBranchLengthGainAndLoss!()
     min, max = getAlldistances().select{|i|i>=0}.minmax
     each_edge do |node0, node1, edge|
@@ -161,6 +180,27 @@ class Bio::Tree
     end
   end
 
+
+  def getNameTipRela()
+    tip2name, name2tip = [Hash.new, Hash.new]
+    allTips.each do |tip|
+      tip2name[tip] = tip.name
+      name2tip[tip.name] = tip
+    end
+    return([name2tip, tip2name])
+  end
+
+
+  def getNameNodeRela()
+    node2name, name2node = [Hash.new, Hash.new]
+    nodes.each do |node|
+      node2name[node] = node.name
+      name2node[node.name] = node
+    end
+    return([name2node, node2name])
+  end
+
+
   private
   def translate
     #  TRANSLATE
@@ -212,3 +252,4 @@ def getTreeObjFromMcmctree(tree_file)
   return([first_line, treeio])
 end
 
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-nwk
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
 platform: ruby
 authors:
 - Sishuo Wang
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2022-03-14 00:00:00.000000000 Z
+date: 2022-04-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler