newick-ruby 1.0.1 → 1.0.2

data/README

@@ -14,6 +14,8 @@ Jonathan Badger
 J. Craig Venter Institute
 jhbadger@gmail.com
 
+UPDATES:
+1.0.2 -- faster distance matrix calculation
 
 License
 (The MIT License)

data/bin/newickDist

@@ -1,16 +1,33 @@
 #!/usr/bin/env ruby
 
 require 'Newick'
+require 'optparse'
+require 'ostruct'
+
+opt = OpenStruct.new
+opt.verbose = false
+
+ARGV.options {|opts|
+  opts.banner << " tree-file"
+  opts.on("-v", "--verbose", "show progress") {|t| opt.verbose = t} 
+  begin
+    opts.parse!
+  rescue
+    STDERR.puts $!.message
+    STDERR.puts opts
+    exit(1)
+  end
+  if (ARGV.size < 1)
+    STDERR.puts opts
+    exit(1)
+  end
+}
 
-if (ARGV.size != 1)
-  STDERR.printf("usage: %s tree-file\n", $0)
-  exit(1)
-end
 
 file = ARGV.pop
 
 tree = NewickTree.fromFile(file)
-dMatrix = tree.distanceMatrix
+dMatrix = tree.distanceMatrix(opt.verbose)
 
 printf("    %d\n", dMatrix.keys.size)
 dMatrix.keys.each {|key1|

data/lib/Newick.rb

@@ -8,7 +8,7 @@ class NewickToken
   attr_reader :type
   # string value of token
   attr_reader :value
-  
+
   def initialize(type, value)
     @type = type
     @value = value
@@ -19,7 +19,7 @@ end
 
 # Splits a Newick tree string into tokens that NewickTree uses
 class NewickTokenizer
-  
+
   def initialize(str)
     @str = str
     @pos = 0
@@ -45,17 +45,17 @@ class NewickTokenizer
       return NewickToken.new("SYMBOL", c)
     elsif (c == ":")
       if (@str.index((/([0-9|\.|\-|e|E]+)/), @pos) == @pos)
-	@pos += $1.length
-	return NewickToken.new("WEIGHT", $1)
+        @pos += $1.length
+        return NewickToken.new("WEIGHT", $1)
       else
-	raise NewickParseError, "Illegal weight at pos #{@pos} of #{@str}"
+        raise NewickParseError, "Illegal weight at pos #{@pos} of #{@str}"
       end
     elsif (c == "'")
       if (@str.index(/(\'[^\']*\')/, @pos - 1) == @pos - 1)
-	@pos += $1.length - 1
-	return NewickToken.new("LABEL", $1)
+        @pos += $1.length - 1
+        return NewickToken.new("LABEL", $1)
       else
-	raise NewickParseError, "Illegal label at pos #{@pos} of #{@str}"
+        raise NewickParseError, "Illegal label at pos #{@pos} of #{@str}"
       end
     elsif (@str.index(/([^,():]+)/, @pos - 1) == @pos - 1)
       @pos += $1.length - 1
@@ -112,10 +112,10 @@ class NewickNode
     s = ""
     if (!leaf?)
       s += "("
-      @children.each {|child|
-	s += child.to_s(showLen, bootStrap)
-	s += "," if (child != @children.last)
-      }
+      @children.each do |child|
+        s += child.to_s(showLen, bootStrap)
+        s += "," if (child != @children.last)
+      end
       s += ")"
     end
     if (leaf? || bootStrap == "node")
@@ -133,32 +133,32 @@ class NewickNode
     taxa = []
     if (!leaf?)
       taxa.push(@name) if (bootstrap)
-      @children.each {|child|
-	child.taxa.each {|taxon|
-	  taxa.push(taxon)
-	}
-      }
+      @children.each do |child|
+        child.taxa.each do |taxon|
+          taxa.push(taxon)
+        end
+      end
     else
       taxa.push(name)
     end
     return taxa.sort
   end
-  
+
   # returns array of leaves (taxa) are contained in the node
   def leaves
     nodes = []
-    descendants.each {|node|
+    descendants.each do |node|
       nodes.push(node) if (node.leaf?)
-    }
+    end
     return nodes
   end
 
   # returns array of non leaves (taxa) that are contained in the node
   def intNodes
     nodes = []
-    descendants.each {|child|
+    descendants.each do  |child|
       nodes.push(child) if (!child.leaf?)
-    }
+    end
     return nodes
   end
 
@@ -168,10 +168,10 @@ class NewickNode
     if (@name =~/#{name}/)
       found = self
     else
-      @children.each {|child|
-	found = child.findNode(name)
-	break if found
-      }
+      @children.each do |child|
+        found = child.findNode(name)
+        break if found
+      end
     end
     return found
   end
@@ -188,7 +188,7 @@ class NewickNode
     oldParent.edgeLen = @edgeLen
     @edgeLen = 0
   end
-  
+
   # True if given node is child (or grandchild, etc.) of self. False otherwise
   def include?(node)
     while(node.parent != nil)
@@ -210,12 +210,12 @@ class NewickNode
   # returns array of all descendant nodes
   def descendants
     descendants = []
-    @children.each {|child|
+    @children.each do |child|
       descendants.push(child)
-      child.descendants.each {|grandchild|
-	descendants.push(grandchild)
-      }
-    }
+      child.descendants.each do |grandchild|
+        descendants.push(grandchild)
+      end
+    end
     return descendants
   end
 
@@ -225,24 +225,24 @@ class NewickNode
     if (parent.nil?)
       return siblings
     else
-      @parent.children.each {|child|
+      @parent.children.each do |child|
         siblings.push(child) if (child!=self)
-      }
+      end
       return siblings
     end
   end
 
- # reorders descendant nodes alphabetically and by size
+  # reorders descendant nodes alphabetically and by size
   def reorder
     return if (@children.empty?)
     @children.sort! {|x, y| x.name <=> y.name}
-    @children.each {|child|
+    @children.each do |child|
       child.reorder
-    }
+    end
     return self
   end
 
-  
+
 
   # returns the last common ancestor node of self and given node
   def lca(node)
@@ -265,7 +265,7 @@ class NewickNode
     end
     return dist
   end
-  
+
 
   # returns number of nodes to the ancestor node
   def nodesToAncestor(ancestor)
@@ -280,7 +280,7 @@ class NewickNode
     end
   end
 
-  
+
   # returns number of nodes to other node
   def nodesToNode(node)
     lca = lca(node)
@@ -296,9 +296,9 @@ class NewickNode
   # calculates node Y positions
   def calcYPos
     ySum = 0
-    @children.each {|child|
+    @children.each do |child|
       ySum += child.y
-    }
+    end
     @y = ySum / @children.size
   end
 
@@ -311,36 +311,36 @@ class NewickNode
       @x = parent.x + @edgeLen
     end
     if (!leaf?)
-      @children.each {|child|
+      @children.each do |child|
         child.calcXPos
-      }
+      end
     end
   end
 
   # returns the maximum X value in node
   def xMax
     xMax = 0
-    children.each {|child|
+    children.each do |child|
       xMax = child.edgeLen if (child.x > xMax)
-    }
+    end
     return xMax
   end
 
   # returns the maximum Y value in node
   def yMax
     yMax = 0
-    children.each {|child|
+    children.each do |child|
       yMax = child.y if (child.y > yMax)
-    }
+    end
     return yMax
   end
 
   # returns the minimum Y value in node
   def yMin
     yMin = 1e6
-    children.each {|child|
+    children.each do |child|
       yMin = child.y if (child.y < yMin)
-    }
+    end
     return yMin
   end
 
@@ -357,9 +357,9 @@ class NewickTree
   def NewickTree.fromFile(fileName)
     treeString = ""
     inFile = File.new(fileName)
-    inFile.each {|line|
+    inFile.each do |line|
       treeString += line.chomp
-    }
+    end
     inFile.close
     treeString.gsub!(/\[[^\]]*\]/,"") # remove comments before parsing
     return NewickTree.new(treeString)
@@ -369,43 +369,43 @@ class NewickTree
   def buildTree(parent, tokenizer)
     while (!(token = tokenizer.nextToken).nil?)
       if (token.type == "LABEL")
-	name = token.value
-	edgeLen = 0
-	if (tokenizer.peekToken.type == "WEIGHT")
-	  edgeLen = tokenizer.nextToken.value.to_f
-	end
-	node = NewickNode.new(name, edgeLen)
-	return node
+        name = token.value
+        edgeLen = 0
+        if (tokenizer.peekToken.type == "WEIGHT")
+          edgeLen = tokenizer.nextToken.value.to_f
+        end
+        node = NewickNode.new(name, edgeLen)
+        return node
       elsif (token.value == "(")
-	node = NewickNode.new("", 0)
-	forever = true
-	while (forever)
-	  child = buildTree(node, tokenizer)
-	  node.addChild(child)
-	  break if tokenizer.peekToken.value != ","
-	  tokenizer.nextToken
-	end
-	if (tokenizer.nextToken.value != ")")
-	  raise NewickParseError, "Expected ')' but found: #{token.value}"
-	else
-	  peek = tokenizer.peekToken
-	  if (peek.value == ")" || peek.value == "," || peek.value == ";")
-	    return node
-	  elsif (peek.type == "WEIGHT")
-	    node.edgeLen = tokenizer.nextToken.value.to_f
-	    return node
-	  elsif (peek.type == "LABEL")
-	    token = tokenizer.nextToken
-	    node.name = token.value
-	    if (tokenizer.peekToken.type == "WEIGHT")
-	      node.edgeLen = tokenizer.nextToken.value.to_f
-	    end
-	    return node
-	  end
-	end 
+        node = NewickNode.new("", 0)
+        forever = true
+        while (forever)
+          child = buildTree(node, tokenizer)
+          node.addChild(child)
+          break if tokenizer.peekToken.value != ","
+          tokenizer.nextToken
+        end
+        if (tokenizer.nextToken.value != ")")
+          raise NewickParseError, "Expected ')' but found: #{token.value}"
+        else
+          peek = tokenizer.peekToken
+          if (peek.value == ")" || peek.value == "," || peek.value == ";")
+            return node
+          elsif (peek.type == "WEIGHT")
+            node.edgeLen = tokenizer.nextToken.value.to_f
+            return node
+          elsif (peek.type == "LABEL")
+            token = tokenizer.nextToken
+            node.name = token.value
+            if (tokenizer.peekToken.type == "WEIGHT")
+              node.edgeLen = tokenizer.nextToken.value.to_f
+            end
+            return node
+          end
+        end 
       else
-	raise NewickParseError, 
-	  "Expected '(' or label but found: #{token.value}"
+        raise NewickParseError, 
+        "Expected '(' or label but found: #{token.value}"
       end
     end
   end
@@ -437,33 +437,33 @@ class NewickTree
     else
       taxon =  "SEQ0000001"
     end
-    @root.descendants.each {|node|
+    @root.descendants.each do |node|
       if (node.name != "" && node.name.to_i == 0)
-	ali[taxon] = node.name
-	aliF.printf("%s\t%s\n", taxon, node.name) if (!aliasFile.nil?)
-	node.name = taxon.dup
-	taxon.succ!
+        ali[taxon] = node.name
+        aliF.printf("%s\t%s\n", taxon, node.name) if (!aliasFile.nil?)
+        node.name = taxon.dup
+        taxon.succ!
       end
-    }
+    end
     aliF.close if (!aliasFile.nil?)
     return self, ali
   end
 
   # renames nodes according to alias hash
   def unAlias(aliasNames)
-    @root.descendants.each {|node|
+    @root.descendants.each do |node|
       node.name = aliasNames[node.name] if (!aliasNames[node.name].nil?)
-    }
+    end
     return self
   end
 
   # renames nodes according to inverse alias hash 
   def reAlias(aliasNames)
-    @root.descendants.each {|node|
-      aliasNames.keys.each {|key|
+    @root.descendants.each do |node|
+      aliasNames.keys.each do |key|
         node.name = key if (aliasNames[key] == node.name)
-      }
-    }
+      end
+    end
     return self
   end
 
@@ -473,22 +473,28 @@ class NewickTree
   end
 
   # returns a 2D hash of pairwise distances on tree
-  def distanceMatrix
+  def distanceMatrix(verbose = nil)
     dMatrix = Hash.new
-    @root.taxa.each {|taxon1|
-      dMatrix[taxon1] = Hash.new
-      taxon1Node = @root.findNode(taxon1)
-      @root.taxa.each {|taxon2|
-	if (taxon1 == taxon2)
-	  dMatrix[taxon1][taxon2] = 0.0
-	else
-	  taxon2Node = @root.findNode(taxon2)
-	  lca = taxon1Node.lca(taxon2Node)
-	  dMatrix[taxon1][taxon2] = taxon1Node.distToAncestor(lca) + 
-	    taxon2Node.distToAncestor(lca)
-	end
-      }
-    }
+    leaves = root.leaves
+    num = (leaves.size)**2
+    numpercent = num/100
+    count = 0
+    
+    leaves.each do |leaf1|
+      dMatrix[leaf1.name] = Hash.new
+      leaves.each do |leaf2|
+        count += 1
+        if (verbose && count % numpercent == 0)
+          STDERR.printf("Processing %s %s (%d of %d)\n", leaf1.name, leaf2.name, count, num)
+        end 
+        if (leaf1 == leaf2)
+          dMatrix[leaf1.name][leaf2.name] = 0.0
+        else
+          lca = leaf1.lca(leaf2)
+          dMatrix[leaf1.name][leaf2.name] = leaf1.distToAncestor(lca) + leaf2.distToAncestor(lca)
+        end
+      end
+    end
     return dMatrix
   end
 
@@ -496,22 +502,22 @@ class NewickTree
   def compare(tree)
     tree1 = self.dup.unroot
     tree2 = tree.dup.unroot
-    
+
     diff1 = []
     diff2 = []
     if (tree1.taxa == tree2.taxa)
       clades1 = tree1.clades
       clades2 = tree2.clades
-      clades1.each {|clade|
-	if (!clades2.include?(clade))
-	  diff1.push(clade)
-	end
-      }
-      clades2.each {|clade|
-	if (!clades1.include?(clade))
-	  diff2.push(clade)
-	end
-      }
+      clades1.each do |clade|
+        if (!clades2.include?(clade))
+          diff1.push(clade)
+        end
+      end
+      clades2.each do |clade|
+        if (!clades1.include?(clade))
+          diff2.push(clade)
+        end
+      end
     else
       raise NewickParseError, "The trees have different taxa!"
     end
@@ -531,9 +537,9 @@ class NewickTree
     left, right = @root.children
     left, right = right, left if (right.leaf?) # don't uproot leaf side   
     left.edgeLen += right.edgeLen
-    right.children.each {|child|
+    right.children.each do |child|
       @root.addChild(child)
-    }
+    end
     @root.removeChild(right)
     return self
   end
@@ -560,37 +566,37 @@ class NewickTree
     greatestDist = 0
     dist = Hash.new
     org1, org2 = nil, nil
-    @root.leaves.each {|node1|
-      @root.leaves.each {|node2|
+    @root.leaves.each do |node1|
+      @root.leaves.each do |node2|
         dist[node1] = Hash.new if dist[node1].nil?
         dist[node2] = Hash.new if dist[node2].nil?
         next if (!dist[node1][node2].nil?)
         lca = node1.lca(node2)
         dist[node1][node2] = node1.distToAncestor(lca) + 
-                                node2.distToAncestor(lca)
+        node2.distToAncestor(lca)
         dist[node2][node1] = dist[node1][node2]
         if (dist[node1][node2] > greatestDist)
           org1 = node1
           org2 = node2
           greatestDist = dist[node1][node2]
-	end
-      }
-    }
+        end
+      end
+    end
     return org1, org2, greatestDist
   end
 
   # add EC numbers from alignment
   def addECnums(alignFile)
     ec = Hash.new
-    File.new(alignFile).each {|line|
+    File.new(alignFile).each do |line|
       if (line =~ /^>/)
-	definition = line.chomp[1..line.length]
-	name = definition.split(" ").first
-	if (definition =~ /\[EC:([0-9|\.]*)/)
-	  ec[name] = name + "_" + $1
-	end
+        definition = line.chomp[1..line.length]
+        name = definition.split(" ").first
+        if (definition =~ /\[EC:([0-9|\.]*)/)
+          ec[name] = name + "_" + $1
+        end
       end
-    }
+    end
     unAlias(ec)
   end
 
@@ -626,23 +632,23 @@ class NewickTree
   # returns array of arrays representing the tree clades
   def clades(bootstrap = false)
     clades = []
-    @root.descendants.each {|clade|
+    @root.descendants.each do |clade|
       clades.push(clade.taxa(bootstrap)) if (!clade.children.empty?)
-    }
+    end
     return clades
   end
 
   # add bootstrap values (given in clade arrays) to a tree
   def addBootStrap(bootClades)
-    @root.descendants.each {|clade|
+    @root.descendants.each do |clade|
       next if clade.leaf?
-      bootClades.each {|bClade|
-	boot, rest = bClade.first, bClade[1..bClade.size - 1]
-	if (rest == clade.taxa ) # same clade found
-	  clade.name = boot
-	end
-      }
-    }
+      bootClades.each do |bClade|
+        boot, rest = bClade.first, bClade[1..bClade.size - 1]
+        if (rest == clade.taxa ) # same clade found
+          clade.name = boot
+        end
+      end
+    end
   end
 
   # return array of arrays of taxa representing relatives at each level
@@ -653,23 +659,23 @@ class NewickTree
     else
       relatives = []
       while(!node.parent.nil?)
-	relatives.push(node.parent.taxa - node.taxa)
-	node = node.parent
+        relatives.push(node.parent.taxa - node.taxa)
+        node = node.parent
       end
       return relatives
     end
   end
 
-  
+
   # Fixes PHYLIP's mistake of using branch lengths and not node values
   def fixPhylip
-    @root.descendants.each {|child|
+    @root.descendants.each do |child|
       br = child.edgeLen.to_i
       child.edgeLen = 0
       if (br > 0 && !child.leaf?)
         child.name = br.to_s
       end
-    }
+    end
   end
 
 
@@ -678,189 +684,189 @@ class NewickTree
     yPos = 0.25
     @root.reorder
     leaves = @root.leaves.sort {|x, y| x.nodesToNode(y) <=> y.nodesToNode(x)}
-    leaves.each {|leaf|
+    leaves.each do |leaf|
       leaf.y = yPos
       yPos += yUnit
-    }
-    nodes =  @root.intNodes.sort{|x, y| y.nodesToAncestor(@root) <=> 
-                                       x.nodesToAncestor(@root)}
-    nodes.each {|node|
-      node.calcYPos
-    }
-    @root.calcYPos
-    @root.calcXPos
-    nodes =  @root.intNodes.sort{|x, y| x.nodesToAncestor(@root) <=> 
-                                       y.nodesToAncestor(@root)}
-    nodes.each {|node|
-      @root.calcXPos # (forwards from root)
-    }
-  end
-
-  # function to generate gi link to ncbi for draw, below
-  def giLink(entry)
-    ncbiLink = "http://www.ncbi.nlm.nih.gov/entrez/"
-    protLink = "viewer.fcgi?db=protein&val="
-    if (entry =~ /^gi[\_]*([0-9]*)/ || entry =~ /(^[A-Z|0-9]*)\|/)
-      return ncbiLink + protLink + $1
-    else
-      return nil
     end
-  end
-  
-  # returns PDF representation of branching structure of tree
-  def draw(pdfFile, boot="width", linker = :giLink, labelName = false,
-	   highlights = Hash.new, brackets = nil, rawNames = false)
-	  colors = {"goldenrod4"=>[139, 105, 20], "lightcyan"=>[224, 255, 255], "rosybrown1"=>[255, 193, 193], "sienna1"=>[255, 130, 71], "lavender"=>[230, 230, 250], "rosybrown2"=>[238, 180, 180], "wheat1"=>[255, 231, 186], "linen"=>[250, 240, 230], "beige"=>[245, 245, 220], "sienna2"=>[238, 121, 66], "paleturquoise1"=>[187, 255, 255], "pink1"=>[255, 181, 197], "wheat2"=>[238, 216, 174], "violetred"=>[208, 32, 144], "palegreen"=>[152, 251, 152], "gray50"=>[127, 127, 127], "rosybrown3"=>[205, 155, 155], "sienna3"=>[205, 104, 57], "paleturquoise2"=>[174, 238, 238], "green1"=>[0, 255, 0], "pink2"=>[238, 169, 184], "wheat3"=>[205, 186, 150], "lightskyblue1"=>[176, 226, 255], "gray51"=>[130, 130, 130], "rosybrown4"=>[139, 105, 105], "sienna4"=>[139, 71, 38], "paleturquoise3"=>[150, 205, 205], "green2"=>[0, 238, 0], "pink3"=>[205, 145, 158], "wheat4"=>[139, 126, 102], "lightskyblue2"=>[164, 211, 238], "yellow1"=>[255, 255, 0], "sgilightgray"=>[170, 170, 170], "paleturquoise4"=>[102, 139, 139], "green3"=>[0, 205, 0], "pink4"=>[139, 99, 108], "lightskyblue3"=>[141, 182, 205], "yellow2"=>[238, 238, 0], "gray52"=>[133, 133, 133], "mediumorchid"=>[186, 85, 211], "green4"=>[0, 139, 0], "lightskyblue4"=>[96, 123, 139], "ivory1"=>[255, 255, 240], "yellow3"=>[205, 205, 0], "plum1"=>[255, 187, 255], "lightblue1"=>[191, 239, 255], "seashell1"=>[255, 245, 238], "gray53"=>[135, 135, 135], "ivory2"=>[238, 238, 224], "violetred1"=>[255, 62, 150], "plum2"=>[238, 174, 238], "lightblue2"=>[178, 223, 238], "seashell2"=>[238, 229, 222], "gray54"=>[138, 138, 138], "white"=>[255, 255, 255], "mediumslateblue"=>[123, 104, 238], "ivory3"=>[205, 205, 193], "yellow4"=>[139, 139, 0], "lightcyan1"=>[224, 255, 255], "plum3"=>[205, 150, 205], "lightslateblue"=>[132, 112, 255], "lightblue3"=>[154, 192, 205], "seashell3"=>[205, 197, 191], "gray55"=>[140, 140, 140], "ivory4"=>[139, 139, 131], "lightcyan2"=>[209, 238, 238], "violetred2"=>[238, 58, 140], "peru"=>[205, 133, 63], "lightblue4"=>[104, 131, 139], "seashell4"=>[139, 134, 130], "gray56"=>[143, 143, 143], "flesh"=>[255, 125, 64], "lightcyan3"=>[180, 205, 205], "violetred3"=>[205, 50, 120], "plum4"=>[139, 102, 139], "lightblue"=>[173, 216, 230], "gray57"=>[145, 145, 145], "coral"=>[255, 127, 80], "cadmiumorange"=>[255, 97, 3], "khaki1"=>[255, 246, 143], "lightcyan4"=>[122, 139, 139], "violetred4"=>[139, 34, 82], "lightslategray"=>[119, 136, 153], "gray58"=>[148, 148, 148], "sgigray32"=>[81, 81, 81], "khaki2"=>[238, 230, 133], "dodgerblue1"=>[30, 144, 255], "lavenderblush1"=>[255, 240, 245], "gray59"=>[150, 150, 150], "khaki3"=>[205, 198, 115], "dodgerblue2"=>[28, 134, 238], "lavenderblush2"=>[238, 224, 229], "banana"=>[227, 207, 87], "khaki4"=>[139, 134, 78], "dodgerblue3"=>[24, 116, 205], "lavenderblush3"=>[205, 193, 197], "cyan2"=>[0, 238, 238], "cadetblue"=>[95, 158, 160], "cadmiumyellow"=>[255, 153, 18], "mediumpurple"=>[147, 112, 219], "dodgerblue4"=>[16, 78, 139], "lavenderblush4"=>[139, 131, 134], "cyan3"=>[0, 205, 205], "silver"=>[192, 192, 192], "sgigray36"=>[91, 91, 91], "cyan4"=>[0, 139, 139], "deeppink1"=>[255, 20, 147], "burntumber"=>[138, 51, 36], "deeppink2"=>[238, 18, 137], "aliceblue"=>[240, 248, 255], "rosybrown"=>[188, 143, 143], "aquamarine"=>[127, 255, 212], "plum"=>[221, 160, 221], "deeppink3"=>[205, 16, 118], "darkgoldenrod"=>[184, 134, 11], "darkslategray1"=>[151, 255, 255], "chartreuse1"=>[127, 255, 0], "deeppink4"=>[139, 10, 80], "antiquewhite"=>[250, 235, 215], "darkslategray2"=>[141, 238, 238], "chartreuse2"=>[118, 238, 0], "darkslategray3"=>[121, 205, 205], "raspberry"=>[135, 38, 87], "chartreuse3"=>[102, 205, 0], "darkslategray4"=>[82, 139, 139], "chartreuse4"=>[69, 139, 0], "lightsalmon"=>[255, 160, 122], "warmgrey"=>[128, 128, 105], "cobalt"=>[61, 89, 171], "pink"=>[255, 192, 203], "orangered"=>[255, 69, 0], "indianred"=>[205, 92, 92], "palegreen1"=>[154, 255, 154], "red1"=>[255, 0, 0], "darkorange1"=>[255, 127, 0], "palegreen2"=>[144, 238, 144], "darkorchid"=>[153, 50, 204], "red2"=>[238, 0, 0], "darkorange2"=>[238, 118, 0], "palegreen3"=>[124, 205, 124], "goldenrod"=>[218, 165, 32], "red3"=>[205, 0, 0], "tomato1"=>[255, 99, 71], "yellowgreen"=>[154, 205, 50], "darkorange3"=>[205, 102, 0], "palegreen4"=>[84, 139, 84], "gray30"=>[77, 77, 77], "red4"=>[139, 0, 0], "tomato2"=>[238, 92, 66], "darkorange4"=>[139, 69, 0], "antiquewhite1"=>[255, 239, 219], "gray31"=>[79, 79, 79], "brown"=>[165, 42, 42], "tomato3"=>[205, 79, 57], "thistle1"=>[255, 225, 255], "antiquewhite2"=>[238, 223, 204], "darkolivegreen1"=>[202, 255, 112], "gray32"=>[82, 82, 82], "gray80"=>[204, 204, 204], "tomato4"=>[139, 54, 38], "sepia"=>[94, 38, 18], "thistle2"=>[238, 210, 238], "deepskyblue"=>[0, 191, 255], "antiquewhite3"=>[205, 192, 176], "darkolivegreen2"=>[188, 238, 104], "cornflowerblue"=>[100, 149, 237], "gray33"=>[84, 84, 84], "gray81"=>[207, 207, 207], "thistle3"=>[205, 181, 205], "peachpuff"=>[255, 218, 185], "steelblue1"=>[99, 184, 255], "antiquewhite4"=>[139, 131, 120], "darkolivegreen3"=>[162, 205, 90], "gray34"=>[87, 87, 87], "gray82"=>[209, 209, 209], "maroon"=>[128, 0, 0], "thistle4"=>[139, 123, 139], "springgreen1"=>[0, 238, 118], "steelblue2"=>[92, 172, 238], "darkolivegreen4"=>[110, 139, 61], "gray35"=>[89, 89, 89], "gray83"=>[212, 212, 212], "springgreen2"=>[0, 205, 102], "steelblue3"=>[79, 148, 205], "steelblue"=>[70, 130, 180], "gray36"=>[92, 92, 92], "gray84"=>[214, 214, 214], "springgreen3"=>[0, 139, 69], "steelblue4"=>[54, 100, 139], "gray37"=>[94, 94, 94], "blue2"=>[0, 0, 238], "darkturquoise"=>[0, 206, 209], "gray38"=>[97, 97, 97], "gray85"=>[217, 217, 217], "sgigray12"=>[30, 30, 30], "blanchedalmond"=>[255, 235, 205], "violet"=>[238, 130, 238], "blue3"=>[0, 0, 205], "gray39"=>[99, 99, 99], "gray86"=>[219, 219, 219], "burlywood1"=>[255, 211, 155], "navy"=>[0, 0, 128], "darkviolet"=>[148, 0, 211], "blue4"=>[0, 0, 139], "gray87"=>[222, 222, 222], "burlywood2"=>[238, 197, 145], "floralwhite"=>[255, 250, 240], "turquoise"=>[64, 224, 208], "darkorange"=>[255, 140, 0], "gray88"=>[224, 224, 224], "burlywood3"=>[205, 170, 125], "gray89"=>[227, 227, 227], "dimgray"=>[105, 105, 105], "sgigray16"=>[40, 40, 40], "snow"=>[255, 250, 250], "burlywood4"=>[139, 115, 85], "mediumvioletred"=>[199, 21, 133], "seagreen"=>[46, 139, 87], "purple1"=>[155, 48, 255], "lightsteelblue1"=>[202, 225, 255], "purple2"=>[145, 44, 238], "orangered1"=>[255, 69, 0], "lightsteelblue2"=>[188, 210, 238], "purple3"=>[125, 38, 205], "cyan/aqua"=>[0, 255, 255], "orangered2"=>[238, 64, 0], "lightsteelblue3"=>[162, 181, 205], "purple4"=>[85, 26, 139], "orangered3"=>[205, 55, 0], "fuchsia"=>[255, 0, 255], "lightsteelblue4"=>[110, 123, 139], "mistyrose1"=>[255, 228, 225], "orangered4"=>[139, 37, 0], "darkorchid1"=>[191, 62, 255], "lemonchiffon1"=>[255, 250, 205], "mistyrose2"=>[238, 213, 210], "darkorchid2"=>[178, 58, 238], "lemonchiffon2"=>[238, 233, 191], "mistyrose3"=>[205, 183, 181], "royalblue"=>[65, 105, 225], "darkorchid3"=>[154, 50, 205], "lemonchiffon3"=>[205, 201, 165], "sgiolivedrab"=>[142, 142, 56], "mistyrose4"=>[139, 125, 123], "darkorchid4"=>[104, 34, 139], "peachpuff1"=>[255, 218, 185], "mediumseagreen"=>[60, 179, 113], "lemonchiffon4"=>[139, 137, 112], "lightgreen"=>[144, 238, 144], "peachpuff2"=>[238, 203, 173], "peachpuff3"=>[205, 175, 149], "peachpuff4"=>[139, 119, 101], "lightsteelblue"=>[176, 196, 222], "skyblue"=>[135, 206, 235], "gray10"=>[26, 26, 26], "magenta"=>[255, 0, 255], "turquoise1"=>[0, 245, 255], "gray11"=>[28, 28, 28], "turquoise2"=>[0, 229, 238], "chartreuse"=>[127, 255, 0], "navajowhite"=>[255, 222, 173], "ghostwhite"=>[248, 248, 255], "gray12"=>[31, 31, 31], "gray60"=>[153, 153, 153], "melon"=>[227, 168, 105], "turquoise3"=>[0, 197, 205], "gray13"=>[33, 33, 33], "gray61"=>[156, 156, 156], "coral1"=>[255, 114, 86], "turquoise4"=>[0, 134, 139], "gray14"=>[36, 36, 36], "gray62"=>[158, 158, 158], "sgiteal"=>[56, 142, 142], "coral2"=>[238, 106, 80], "honeydew"=>[240, 255, 240], "gray1"=>[3, 3, 3], "gray15"=>[38, 38, 38], "firebrick"=>[178, 34, 34], "coral3"=>[205, 91, 69], "lightpink"=>[255, 182, 193], "gray2"=>[5, 5, 5], "gray16"=>[41, 41, 41], "gray63"=>[161, 161, 161], "coral4"=>[139, 62, 47], "mediumblue"=>[0, 0, 205], "gray3"=>[8, 8, 8], "gray17"=>[43, 43, 43], "gray64"=>[163, 163, 163], "blueviolet"=>[138, 43, 226], "darkgreen"=>[0, 100, 0], "gray4"=>[10, 10, 10], "gray18"=>[46, 46, 46], "gray65"=>[166, 166, 166], "deepskyblue1"=>[0, 191, 255], "gray5"=>[13, 13, 13], "gray19"=>[48, 48, 48], "gray66"=>[168, 168, 168], "mediumspringgreen"=>[0, 250, 154], "darkkhaki"=>[189, 183, 107], "lightgoldenrodyellow"=>[250, 250, 210], "orange"=>[255, 128, 0], "deepskyblue2"=>[0, 178, 238], "gray6"=>[15, 15, 15], "gray67"=>[171, 171, 171], "mediumturquoise"=>[72, 209, 204], "deepskyblue3"=>[0, 154, 205], "turquoiseblue"=>[0, 199, 140], "gray7"=>[18, 18, 18], "gray68"=>[173, 173, 173], "orchid"=>[218, 112, 214], "burlywood"=>[222, 184, 135], "thistle"=>[216, 191, 216], "mediumpurple1"=>[171, 130, 255], "deepskyblue4"=>[0, 104, 139], "gray8"=>[20, 20, 20], "gray69"=>[176, 176, 176], "palevioletred"=>[219, 112, 147], "sandybrown"=>[244, 164, 96], "mediumpurple2"=>[159, 121, 238], "yellow"=>[255, 255, 0], "darkgoldenrod1"=>[255, 185, 15], "gray9"=>[23, 23, 23], "darkseagreen"=>[143, 188, 143], "mediumpurple3"=>[137, 104, 205], "darkgoldenrod2"=>[238, 173, 14], "sgigray92"=>[234, 234, 234], "mediumpurple4"=>[93, 71, 139], "darkgoldenrod3"=>[205, 149, 12], "mediumaquamarine"=>[102, 205, 170], "firebrick1"=>[255, 48, 48], "tomato"=>[255, 99, 71], "darkgoldenrod4"=>[139, 101, 8], "gray"=>[128, 128, 128], "firebrick2"=>[238, 44, 44], "palegoldenrod"=>[238, 232, 170], "moccasin"=>[255, 228, 181], "firebrick3"=>[205, 38, 38], "snow1"=>[255, 250, 250], "sgigray96"=>[244, 244, 244], "firebrick4"=>[139, 26, 26], "snow2"=>[238, 233, 233], "papayawhip"=>[255, 239, 213], "snow3"=>[205, 201, 201], "eggshell"=>[252, 230, 201], "snow4"=>[139, 137, 137], "tan"=>[210, 180, 140], "peacock"=>[51, 161, 201], "gold1"=>[255, 215, 0], "slateblue1"=>[131, 111, 255], "springgreen"=>[0, 255, 127], "ivoryblack"=>[41, 36, 33], "gold2"=>[238, 201, 0], "honeydew1"=>[240, 255, 240], "greenyellow"=>[173, 255, 47], "slateblue2"=>[122, 103, 238], "gainsboro"=>[220, 220, 220], "azure"=>[240, 255, 255], "gold3"=>[205, 173, 0], "oldlace"=>[253, 245, 230], "honeydew2"=>[224, 238, 224], "gold4"=>[139, 117, 0], "honeydew3"=>[193, 205, 193], "slateblue3"=>[105, 89, 205], "green"=>[0, 128, 0], "skyblue1"=>[135, 206, 255], "honeydew4"=>[131, 139, 131], "cadetblue1"=>[152, 245, 255], "slateblue4"=>[71, 60, 139], "sienna"=>[160, 82, 45], "darksalmon"=>[233, 150, 122], "skyblue2"=>[126, 192, 238], "cadetblue2"=>[142, 229, 238], "sapgreen"=>[48, 128, 20], "gray40"=>[102, 102, 102], "skyblue3"=>[108, 166, 205], "midnightblue"=>[25, 25, 112], "blue"=>[0, 0, 255], "cadetblue3"=>[122, 197, 205], "sgichartreuse"=>[113, 198, 113], "skyblue4"=>[74, 112, 139], "cadetblue4"=>[83, 134, 139], "lime"=>[0, 255, 0], "gray90"=>[229, 229, 229], "gray42"=>[105, 105, 105], "mistyrose"=>[255, 228, 225], "burntsienna"=>[138, 54, 15], "ivory"=>[255, 255, 240], "gray43"=>[110, 110, 110], "gray91"=>[232, 232, 232], "darkcyan"=>[0, 139, 139], "gray44"=>[112, 112, 112], "gray92"=>[235, 235, 235], "lawngreen"=>[124, 252, 0], "gray45"=>[115, 115, 115], "gray93"=>[237, 237, 237], "palevioletred1"=>[255, 130, 171], "saddlebrown"=>[139, 69, 19], "lavenderblush"=>[255, 240, 245], "gray46"=>[117, 117, 117], "gray94"=>[240, 240, 240], "palevioletred2"=>[238, 121, 159], "khaki"=>[240, 230, 140], "paleturquoise"=>[174, 238, 238], "gray47"=>[120, 120, 120], "gray95"=>[242, 242, 242], "carrot"=>[237, 145, 33], "palevioletred3"=>[205, 104, 137], "lightsalmon1"=>[255, 160, 122], "olivedrab"=>[107, 142, 35], "gray48"=>[122, 122, 122], "palevioletred4"=>[139, 71, 93], "wheat"=>[245, 222, 179], "lightsalmon2"=>[238, 149, 114], "powderblue"=>[176, 224, 230], "gray49"=>[125, 125, 125], "gray96"=>[245, 245, 245], "red"=>[255, 0, 0], "brown1"=>[255, 64, 64], "lightsalmon3"=>[205, 129, 98], "manganeseblue"=>[3, 168, 158], "gray97"=>[247, 247, 247], "brown2"=>[238, 59, 59], "lightsalmon4"=>[139, 87, 66], "olive"=>[128, 128, 0], "gray98"=>[250, 250, 250], "lightgrey"=>[211, 211, 211], "sgigray72"=>[183, 183, 183], "brown3"=>[205, 51, 51], "gold"=>[255, 215, 0], "mintcream"=>[245, 255, 250], "gray99"=>[252, 252, 252], "brown4"=>[139, 35, 35], "sgidarkgray"=>[85, 85, 85], "magenta2"=>[238, 0, 238], "sgigray76"=>[193, 193, 193], "magenta3"=>[205, 0, 205], "dodgerblue"=>[30, 144, 255], "magenta4"=>[139, 0, 139], "cobaltgreen"=>[61, 145, 64], "sgisalmon"=>[198, 113, 113], "emeraldgreen"=>[0, 201, 87], "sgibrightgray"=>[197, 193, 170], "darkred"=>[139, 0, 0], "rawsienna"=>[199, 97, 20], "seagreen1"=>[84, 255, 159], "lightyellow"=>[255, 255, 224], "olivedrab1"=>[192, 255, 62], "orchid1"=>[255, 131, 250], "seashell"=>[255, 245, 238], "seagreen2"=>[78, 238, 148], "bisque1"=>[255, 228, 196], "olivedrab2"=>[179, 238, 58], "orchid2"=>[238, 122, 233], "azure1"=>[240, 255, 255], "seagreen3"=>[67, 205, 128], "bisque2"=>[238, 213, 183], "whitesmoke"=>[245, 245, 245], "olivedrab3"=>[154, 205, 50], "orchid3"=>[205, 105, 201], "azure2"=>[224, 238, 238], "lightpink1"=>[255, 174, 185], "lightgoldenrod1"=>[255, 236, 139], "bisque3"=>[205, 183, 158], "olivedrab4"=>[105, 139, 34], "orchid4"=>[139, 71, 137], "purple"=>[128, 0, 128], "lemonchiffon"=>[255, 250, 205], "azure3"=>[193, 205, 205], "lightpink2"=>[238, 162, 173], "seagreen4"=>[46, 139, 87], "forestgreen"=>[34, 139, 34], "lightgoldenrod2"=>[238, 220, 130], "bisque4"=>[139, 125, 107], "sgislateblue"=>[113, 113, 198], "azure4"=>[131, 139, 139], "lightpink3"=>[205, 140, 149], "lightgoldenrod3"=>[205, 190, 112], "gray20"=>[51, 51, 51], "sgibeet"=>[142, 56, 142], "limegreen"=>[50, 205, 50], "orange1"=>[255, 165, 0], "lightpink4"=>[139, 95, 101], "lightgoldenrod4"=>[139, 129, 76], "gray21"=>[54, 54, 54], "orange2"=>[238, 154, 0], "gray22"=>[56, 56, 56], "gray70"=>[179, 179, 179], "orange3"=>[205, 133, 0], "gray23"=>[59, 59, 59], "gray71"=>[181, 181, 181], "orange4"=>[139, 90, 0], "lightseagreen"=>[32, 178, 170], "bisque"=>[255, 228, 196], "gray24"=>[61, 61, 61], "gray72"=>[184, 184, 184], "darkslateblue"=>[72, 61, 139], "gray25"=>[64, 64, 64], "gray73"=>[186, 186, 186], "lightcoral"=>[240, 128, 128], "tan1"=>[255, 165, 79], "gray26"=>[66, 66, 66], "black"=>[0, 0, 0], "tan2"=>[238, 154, 73], "gray27"=>[69, 69, 69], "gray74"=>[189, 189, 189], "teal"=>[0, 128, 128], "tan3"=>[205, 133, 63], "aquamarine1"=>[127, 255, 212], "gray28"=>[71, 71, 71], "gray75"=>[191, 191, 191], "tan4"=>[139, 90, 43], "darkmagenta"=>[139, 0, 139], "aquamarine2"=>[118, 238, 198], "gray29"=>[74, 74, 74], "gray76"=>[194, 194, 194], "indianred1"=>[255, 106, 106], "chocolate"=>[210, 105, 30], "aquamarine3"=>[102, 205, 170], "gray77"=>[196, 196, 196], "indianred2"=>[238, 99, 99], "slategray1"=>[198, 226, 255], "chocolate1"=>[255, 127, 36], "aquamarine4"=>[69, 139, 116], "gray78"=>[199, 199, 199], "sgigray52"=>[132, 132, 132], "indianred3"=>[205, 85, 85], "salmon"=>[250, 128, 114], "darkblue"=>[0, 0, 139], "lightyellow1"=>[255, 255, 224], "slategray2"=>[185, 211, 238], "chocolate2"=>[238, 118, 33], "gray79"=>[201, 201, 201], "indianred4"=>[139, 58, 58], "hotpink"=>[255, 105, 180], "brick"=>[156, 102, 31], "lightyellow2"=>[238, 238, 209], "slategray3"=>[159, 182, 205], "chocolate3"=>[205, 102, 29], "darkgray"=>[169, 169, 169], "lightyellow3"=>[205, 205, 180], "darkolivegreen"=>[85, 107, 47], "slategray4"=>[108, 123, 139], "chocolate4"=>[139, 69, 19], "salmon1"=>[255, 140, 105], "deeppink"=>[255, 20, 147], "indigo"=>[75, 0, 130], "darkslategray"=>[47, 79, 79], "navajowhite1"=>[255, 222, 173], "lightyellow4"=>[139, 139, 122], "royalblue1"=>[72, 118, 255], "slateblue"=>[106, 90, 205], "maroon1"=>[255, 52, 179], "sgigray56"=>[142, 142, 142], "salmon2"=>[238, 130, 98], "navajowhite2"=>[238, 207, 161], "coldgrey"=>[128, 138, 135], "royalblue2"=>[67, 110, 238], "cornsilk1"=>[255, 248, 220], "maroon2"=>[238, 48, 167], "salmon3"=>[205, 112, 84], "navajowhite3"=>[205, 179, 139], "royalblue3"=>[58, 95, 205], "cornsilk2"=>[238, 232, 205], "maroon3"=>[205, 41, 144], "slategray"=>[112, 128, 144], "salmon4"=>[139, 76, 57], "navajowhite4"=>[139, 121, 94], "royalblue4"=>[39, 64, 139], "darkseagreen1"=>[193, 255, 193], "cornsilk3"=>[205, 200, 177], "maroon4"=>[139, 28, 98], "hotpink1"=>[255, 110, 180], "mediumorchid1"=>[224, 102, 255], "darkseagreen2"=>[180, 238, 180], "cornsilk4"=>[139, 136, 120], "mint"=>[189, 252, 201], "hotpink2"=>[238, 106, 167], "sgilightblue"=>[125, 158, 192], "goldenrod1"=>[255, 193, 37], "mediumorchid2"=>[209, 95, 238], "darkseagreen3"=>[155, 205, 155], "hotpink3"=>[205, 96, 144], "goldenrod2"=>[238, 180, 34], "mediumorchid3"=>[180, 82, 205], "darkseagreen4"=>[105, 139, 105], "hotpink4"=>[139, 58, 98], "crimson"=>[220, 20, 60], "lightskyblue"=>[135, 206, 250], "goldenrod3"=>[205, 155, 29], "mediumorchid4"=>[122, 55, 139], "cornsilk"=>[255, 248, 220]}
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-    pdf.SetTitle(pdfFile)
-    pdf.SetCreator("newickDraw")
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-      yUnit = 0.030
-      lineWidth = 0.0015
-    else
-      fontSize = 0.5
-      yUnit = 0.020
-      lineWidth = 0.0010
-    end
-    bootScale = 0.5 * fontSize
-    pdf.SetFont('Times','B', fontSize)
-    calcPos(yUnit) # calculate node pos before drawing
-    max = 0
-    @root.leaves.each {|leaf|
-      d = leaf.distToAncestor(@root)
-      max = d if (max < d)
-    }
-    xScale = 10.0/max
-    xOffSet = 0.25
-    pdf.SetLineWidth(lineWidth)
-    pdf.SetTextColor(0, 0, 0)
-    pdf.Line(0, @root.y, xOffSet, @root.y)
-    pdf.Line(xOffSet, @root.yMin, xOffSet, @root.yMax)
-    @root.descendants.each {|child|
-      if (!child.leaf?)
-        if (child.name.to_i > 75 && boot == "width") # good bootstrap
-          pdf.SetLineWidth(lineWidth * 5)
-        else
-          pdf.SetLineWidth(lineWidth)
+    nodes =  @root.intNodes.sort{|x, y| y.nodesToAncestor(@root) <=> 
+      x.nodesToAncestor(@root)}
+      nodes.each do |node|
+        node.calcYPos
+      end
+      @root.calcYPos
+      @root.calcXPos
+      nodes =  @root.intNodes.sort{|x, y| x.nodesToAncestor(@root) <=> 
+        y.nodesToAncestor(@root)}
+        nodes.each do |node|
+          @root.calcXPos # (forwards from root)
         end
-	      bootX = xOffSet + child.x*xScale 
-	      bootY = ((child.yMin + child.yMax) / 2.0) 
-	      pdf.SetXY(bootX, bootY) 
-	      pdf.SetFont('Times','B', bootScale)
-	      pdf.Write(0, child.name.to_s)
-	      pdf.SetFont('Times','B', fontSize)
-        pdf.Line(xOffSet + child.x*xScale, child.yMin, 
-          xOffSet + child.x*xScale, child.yMax)
-      else
-        if (child.parent.name.to_i > 75 && boot == "width") # good bootstrap
-          pdf.SetLineWidth(lineWidth * 5)
+      end
+
+      # function to generate gi link to ncbi for draw, below
+      def giLink(entry)
+        ncbiLink = "http://www.ncbi.nlm.nih.gov/entrez/"
+        protLink = "viewer.fcgi?db=protein&val="
+        if (entry =~ /^gi[\_]*([0-9]*)/ || entry =~ /(^[A-Z|0-9]*)\|/)
+          return ncbiLink + protLink + $1
         else
-          pdf.SetLineWidth(lineWidth)
+          return nil
         end
-        pdf.SetXY(xOffSet + child.x*xScale, child.y)
-	      efields = child.name.split("__")
-        entry, species = efields.first, efields.last
-	      if (entry =~/\{([^\}]*)\}/)
-	        species = $1
-	      end
-        species = entry if species.nil? && !rawNames
-        species = child.name if rawNames
-	      hl = false
-	      highlights.keys.each{|highlight|
-	        hl = highlights[highlight] if (entry.index(highlight))
-	      } 
-        if (pdfFile.index(entry)) # name of query taxon
-          pdf.SetTextColor(colors["red"][0], colors["red"][1], colors["red"][2]) 
-          pdf.Write(0, entry) 
-          pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) 
-        elsif (linker && link = send(linker, entry)) 
-	        pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl 
-	        pdf.Write(0, species, link)
-	        pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl 
-        elsif (!species.nil?)
-          pdf.SetTextColor(colors[hl][0], colors[hl][1], colors[hl][2]) if hl 
-          pdf.Write(0, species) 
-          pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl 
+      end
+
+      # returns PDF representation of branching structure of tree
+      def draw(pdfFile, boot="width", linker = :giLink, labelName = false,
+        highlights = Hash.new, brackets = nil, rawNames = false)
+        colors = {"goldenrod4"=>[139, 105, 20], "lightcyan"=>[224, 255, 255], "rosybrown1"=>[255, 193, 193], "sienna1"=>[255, 130, 71], "lavender"=>[230, 230, 250], "rosybrown2"=>[238, 180, 180], "wheat1"=>[255, 231, 186], "linen"=>[250, 240, 230], "beige"=>[245, 245, 220], "sienna2"=>[238, 121, 66], "paleturquoise1"=>[187, 255, 255], "pink1"=>[255, 181, 197], "wheat2"=>[238, 216, 174], "violetred"=>[208, 32, 144], "palegreen"=>[152, 251, 152], "gray50"=>[127, 127, 127], "rosybrown3"=>[205, 155, 155], "sienna3"=>[205, 104, 57], "paleturquoise2"=>[174, 238, 238], "green1"=>[0, 255, 0], "pink2"=>[238, 169, 184], "wheat3"=>[205, 186, 150], "lightskyblue1"=>[176, 226, 255], "gray51"=>[130, 130, 130], "rosybrown4"=>[139, 105, 105], "sienna4"=>[139, 71, 38], "paleturquoise3"=>[150, 205, 205], "green2"=>[0, 238, 0], "pink3"=>[205, 145, 158], "wheat4"=>[139, 126, 102], "lightskyblue2"=>[164, 211, 238], "yellow1"=>[255, 255, 0], "sgilightgray"=>[170, 170, 170], "paleturquoise4"=>[102, 139, 139], "green3"=>[0, 205, 0], "pink4"=>[139, 99, 108], "lightskyblue3"=>[141, 182, 205], "yellow2"=>[238, 238, 0], "gray52"=>[133, 133, 133], "mediumorchid"=>[186, 85, 211], "green4"=>[0, 139, 0], "lightskyblue4"=>[96, 123, 139], "ivory1"=>[255, 255, 240], "yellow3"=>[205, 205, 0], "plum1"=>[255, 187, 255], "lightblue1"=>[191, 239, 255], "seashell1"=>[255, 245, 238], "gray53"=>[135, 135, 135], "ivory2"=>[238, 238, 224], "violetred1"=>[255, 62, 150], "plum2"=>[238, 174, 238], "lightblue2"=>[178, 223, 238], "seashell2"=>[238, 229, 222], "gray54"=>[138, 138, 138], "white"=>[255, 255, 255], "mediumslateblue"=>[123, 104, 238], "ivory3"=>[205, 205, 193], "yellow4"=>[139, 139, 0], "lightcyan1"=>[224, 255, 255], "plum3"=>[205, 150, 205], "lightslateblue"=>[132, 112, 255], "lightblue3"=>[154, 192, 205], "seashell3"=>[205, 197, 191], "gray55"=>[140, 140, 140], "ivory4"=>[139, 139, 131], "lightcyan2"=>[209, 238, 238], "violetred2"=>[238, 58, 140], "peru"=>[205, 133, 63], "lightblue4"=>[104, 131, 139], "seashell4"=>[139, 134, 130], "gray56"=>[143, 143, 143], "flesh"=>[255, 125, 64], "lightcyan3"=>[180, 205, 205], "violetred3"=>[205, 50, 120], "plum4"=>[139, 102, 139], "lightblue"=>[173, 216, 230], "gray57"=>[145, 145, 145], "coral"=>[255, 127, 80], "cadmiumorange"=>[255, 97, 3], "khaki1"=>[255, 246, 143], "lightcyan4"=>[122, 139, 139], "violetred4"=>[139, 34, 82], "lightslategray"=>[119, 136, 153], "gray58"=>[148, 148, 148], "sgigray32"=>[81, 81, 81], "khaki2"=>[238, 230, 133], "dodgerblue1"=>[30, 144, 255], "lavenderblush1"=>[255, 240, 245], "gray59"=>[150, 150, 150], "khaki3"=>[205, 198, 115], "dodgerblue2"=>[28, 134, 238], "lavenderblush2"=>[238, 224, 229], "banana"=>[227, 207, 87], "khaki4"=>[139, 134, 78], "dodgerblue3"=>[24, 116, 205], "lavenderblush3"=>[205, 193, 197], "cyan2"=>[0, 238, 238], "cadetblue"=>[95, 158, 160], "cadmiumyellow"=>[255, 153, 18], "mediumpurple"=>[147, 112, 219], "dodgerblue4"=>[16, 78, 139], "lavenderblush4"=>[139, 131, 134], "cyan3"=>[0, 205, 205], "silver"=>[192, 192, 192], "sgigray36"=>[91, 91, 91], "cyan4"=>[0, 139, 139], "deeppink1"=>[255, 20, 147], "burntumber"=>[138, 51, 36], "deeppink2"=>[238, 18, 137], "aliceblue"=>[240, 248, 255], "rosybrown"=>[188, 143, 143], "aquamarine"=>[127, 255, 212], "plum"=>[221, 160, 221], "deeppink3"=>[205, 16, 118], "darkgoldenrod"=>[184, 134, 11], "darkslategray1"=>[151, 255, 255], "chartreuse1"=>[127, 255, 0], "deeppink4"=>[139, 10, 80], "antiquewhite"=>[250, 235, 215], "darkslategray2"=>[141, 238, 238], "chartreuse2"=>[118, 238, 0], "darkslategray3"=>[121, 205, 205], "raspberry"=>[135, 38, 87], "chartreuse3"=>[102, 205, 0], "darkslategray4"=>[82, 139, 139], "chartreuse4"=>[69, 139, 0], "lightsalmon"=>[255, 160, 122], "warmgrey"=>[128, 128, 105], "cobalt"=>[61, 89, 171], "pink"=>[255, 192, 203], "orangered"=>[255, 69, 0], "indianred"=>[205, 92, 92], "palegreen1"=>[154, 255, 154], "red1"=>[255, 0, 0], "darkorange1"=>[255, 127, 0], "palegreen2"=>[144, 238, 144], "darkorchid"=>[153, 50, 204], "red2"=>[238, 0, 0], "darkorange2"=>[238, 118, 0], "palegreen3"=>[124, 205, 124], "goldenrod"=>[218, 165, 32], "red3"=>[205, 0, 0], "tomato1"=>[255, 99, 71], "yellowgreen"=>[154, 205, 50], "darkorange3"=>[205, 102, 0], "palegreen4"=>[84, 139, 84], "gray30"=>[77, 77, 77], "red4"=>[139, 0, 0], "tomato2"=>[238, 92, 66], "darkorange4"=>[139, 69, 0], "antiquewhite1"=>[255, 239, 219], "gray31"=>[79, 79, 79], "brown"=>[165, 42, 42], "tomato3"=>[205, 79, 57], "thistle1"=>[255, 225, 255], "antiquewhite2"=>[238, 223, 204], "darkolivegreen1"=>[202, 255, 112], "gray32"=>[82, 82, 82], "gray80"=>[204, 204, 204], "tomato4"=>[139, 54, 38], "sepia"=>[94, 38, 18], "thistle2"=>[238, 210, 238], "deepskyblue"=>[0, 191, 255], "antiquewhite3"=>[205, 192, 176], "darkolivegreen2"=>[188, 238, 104], "cornflowerblue"=>[100, 149, 237], "gray33"=>[84, 84, 84], "gray81"=>[207, 207, 207], "thistle3"=>[205, 181, 205], "peachpuff"=>[255, 218, 185], "steelblue1"=>[99, 184, 255], "antiquewhite4"=>[139, 131, 120], "darkolivegreen3"=>[162, 205, 90], "gray34"=>[87, 87, 87], "gray82"=>[209, 209, 209], "maroon"=>[128, 0, 0], "thistle4"=>[139, 123, 139], "springgreen1"=>[0, 238, 118], "steelblue2"=>[92, 172, 238], "darkolivegreen4"=>[110, 139, 61], "gray35"=>[89, 89, 89], "gray83"=>[212, 212, 212], "springgreen2"=>[0, 205, 102], "steelblue3"=>[79, 148, 205], "steelblue"=>[70, 130, 180], "gray36"=>[92, 92, 92], "gray84"=>[214, 214, 214], "springgreen3"=>[0, 139, 69], "steelblue4"=>[54, 100, 139], "gray37"=>[94, 94, 94], "blue2"=>[0, 0, 238], "darkturquoise"=>[0, 206, 209], "gray38"=>[97, 97, 97], "gray85"=>[217, 217, 217], "sgigray12"=>[30, 30, 30], "blanchedalmond"=>[255, 235, 205], "violet"=>[238, 130, 238], "blue3"=>[0, 0, 205], "gray39"=>[99, 99, 99], "gray86"=>[219, 219, 219], "burlywood1"=>[255, 211, 155], "navy"=>[0, 0, 128], "darkviolet"=>[148, 0, 211], "blue4"=>[0, 0, 139], "gray87"=>[222, 222, 222], "burlywood2"=>[238, 197, 145], "floralwhite"=>[255, 250, 240], "turquoise"=>[64, 224, 208], "darkorange"=>[255, 140, 0], "gray88"=>[224, 224, 224], "burlywood3"=>[205, 170, 125], "gray89"=>[227, 227, 227], "dimgray"=>[105, 105, 105], "sgigray16"=>[40, 40, 40], "snow"=>[255, 250, 250], "burlywood4"=>[139, 115, 85], "mediumvioletred"=>[199, 21, 133], "seagreen"=>[46, 139, 87], "purple1"=>[155, 48, 255], "lightsteelblue1"=>[202, 225, 255], "purple2"=>[145, 44, 238], "orangered1"=>[255, 69, 0], "lightsteelblue2"=>[188, 210, 238], "purple3"=>[125, 38, 205], "cyan/aqua"=>[0, 255, 255], "orangered2"=>[238, 64, 0], "lightsteelblue3"=>[162, 181, 205], "purple4"=>[85, 26, 139], "orangered3"=>[205, 55, 0], "fuchsia"=>[255, 0, 255], "lightsteelblue4"=>[110, 123, 139], "mistyrose1"=>[255, 228, 225], "orangered4"=>[139, 37, 0], "darkorchid1"=>[191, 62, 255], "lemonchiffon1"=>[255, 250, 205], "mistyrose2"=>[238, 213, 210], "darkorchid2"=>[178, 58, 238], "lemonchiffon2"=>[238, 233, 191], "mistyrose3"=>[205, 183, 181], "royalblue"=>[65, 105, 225], "darkorchid3"=>[154, 50, 205], "lemonchiffon3"=>[205, 201, 165], "sgiolivedrab"=>[142, 142, 56], "mistyrose4"=>[139, 125, 123], "darkorchid4"=>[104, 34, 139], "peachpuff1"=>[255, 218, 185], "mediumseagreen"=>[60, 179, 113], "lemonchiffon4"=>[139, 137, 112], "lightgreen"=>[144, 238, 144], "peachpuff2"=>[238, 203, 173], "peachpuff3"=>[205, 175, 149], "peachpuff4"=>[139, 119, 101], "lightsteelblue"=>[176, 196, 222], "skyblue"=>[135, 206, 235], "gray10"=>[26, 26, 26], "magenta"=>[255, 0, 255], "turquoise1"=>[0, 245, 255], "gray11"=>[28, 28, 28], "turquoise2"=>[0, 229, 238], "chartreuse"=>[127, 255, 0], "navajowhite"=>[255, 222, 173], "ghostwhite"=>[248, 248, 255], "gray12"=>[31, 31, 31], "gray60"=>[153, 153, 153], "melon"=>[227, 168, 105], "turquoise3"=>[0, 197, 205], "gray13"=>[33, 33, 33], "gray61"=>[156, 156, 156], "coral1"=>[255, 114, 86], "turquoise4"=>[0, 134, 139], "gray14"=>[36, 36, 36], "gray62"=>[158, 158, 158], "sgiteal"=>[56, 142, 142], "coral2"=>[238, 106, 80], "honeydew"=>[240, 255, 240], "gray1"=>[3, 3, 3], "gray15"=>[38, 38, 38], "firebrick"=>[178, 34, 34], "coral3"=>[205, 91, 69], "lightpink"=>[255, 182, 193], "gray2"=>[5, 5, 5], "gray16"=>[41, 41, 41], "gray63"=>[161, 161, 161], "coral4"=>[139, 62, 47], "mediumblue"=>[0, 0, 205], "gray3"=>[8, 8, 8], "gray17"=>[43, 43, 43], "gray64"=>[163, 163, 163], "blueviolet"=>[138, 43, 226], "darkgreen"=>[0, 100, 0], "gray4"=>[10, 10, 10], "gray18"=>[46, 46, 46], "gray65"=>[166, 166, 166], "deepskyblue1"=>[0, 191, 255], "gray5"=>[13, 13, 13], "gray19"=>[48, 48, 48], "gray66"=>[168, 168, 168], "mediumspringgreen"=>[0, 250, 154], "darkkhaki"=>[189, 183, 107], "lightgoldenrodyellow"=>[250, 250, 210], "orange"=>[255, 128, 0], "deepskyblue2"=>[0, 178, 238], "gray6"=>[15, 15, 15], "gray67"=>[171, 171, 171], "mediumturquoise"=>[72, 209, 204], "deepskyblue3"=>[0, 154, 205], "turquoiseblue"=>[0, 199, 140], "gray7"=>[18, 18, 18], "gray68"=>[173, 173, 173], "orchid"=>[218, 112, 214], "burlywood"=>[222, 184, 135], "thistle"=>[216, 191, 216], "mediumpurple1"=>[171, 130, 255], "deepskyblue4"=>[0, 104, 139], "gray8"=>[20, 20, 20], "gray69"=>[176, 176, 176], "palevioletred"=>[219, 112, 147], "sandybrown"=>[244, 164, 96], "mediumpurple2"=>[159, 121, 238], "yellow"=>[255, 255, 0], "darkgoldenrod1"=>[255, 185, 15], "gray9"=>[23, 23, 23], "darkseagreen"=>[143, 188, 143], "mediumpurple3"=>[137, 104, 205], "darkgoldenrod2"=>[238, 173, 14], "sgigray92"=>[234, 234, 234], "mediumpurple4"=>[93, 71, 139], "darkgoldenrod3"=>[205, 149, 12], "mediumaquamarine"=>[102, 205, 170], "firebrick1"=>[255, 48, 48], "tomato"=>[255, 99, 71], "darkgoldenrod4"=>[139, 101, 8], "gray"=>[128, 128, 128], "firebrick2"=>[238, 44, 44], "palegoldenrod"=>[238, 232, 170], "moccasin"=>[255, 228, 181], "firebrick3"=>[205, 38, 38], "snow1"=>[255, 250, 250], "sgigray96"=>[244, 244, 244], "firebrick4"=>[139, 26, 26], "snow2"=>[238, 233, 233], "papayawhip"=>[255, 239, 213], "snow3"=>[205, 201, 201], "eggshell"=>[252, 230, 201], "snow4"=>[139, 137, 137], "tan"=>[210, 180, 140], "peacock"=>[51, 161, 201], "gold1"=>[255, 215, 0], "slateblue1"=>[131, 111, 255], "springgreen"=>[0, 255, 127], "ivoryblack"=>[41, 36, 33], "gold2"=>[238, 201, 0], "honeydew1"=>[240, 255, 240], "greenyellow"=>[173, 255, 47], "slateblue2"=>[122, 103, 238], "gainsboro"=>[220, 220, 220], "azure"=>[240, 255, 255], "gold3"=>[205, 173, 0], "oldlace"=>[253, 245, 230], "honeydew2"=>[224, 238, 224], "gold4"=>[139, 117, 0], "honeydew3"=>[193, 205, 193], "slateblue3"=>[105, 89, 205], "green"=>[0, 128, 0], "skyblue1"=>[135, 206, 255], "honeydew4"=>[131, 139, 131], "cadetblue1"=>[152, 245, 255], "slateblue4"=>[71, 60, 139], "sienna"=>[160, 82, 45], "darksalmon"=>[233, 150, 122], "skyblue2"=>[126, 192, 238], "cadetblue2"=>[142, 229, 238], "sapgreen"=>[48, 128, 20], "gray40"=>[102, 102, 102], "skyblue3"=>[108, 166, 205], "midnightblue"=>[25, 25, 112], "blue"=>[0, 0, 255], "cadetblue3"=>[122, 197, 205], "sgichartreuse"=>[113, 198, 113], "skyblue4"=>[74, 112, 139], "cadetblue4"=>[83, 134, 139], "lime"=>[0, 255, 0], "gray90"=>[229, 229, 229], "gray42"=>[105, 105, 105], "mistyrose"=>[255, 228, 225], "burntsienna"=>[138, 54, 15], "ivory"=>[255, 255, 240], "gray43"=>[110, 110, 110], "gray91"=>[232, 232, 232], "darkcyan"=>[0, 139, 139], "gray44"=>[112, 112, 112], "gray92"=>[235, 235, 235], "lawngreen"=>[124, 252, 0], "gray45"=>[115, 115, 115], "gray93"=>[237, 237, 237], "palevioletred1"=>[255, 130, 171], "saddlebrown"=>[139, 69, 19], "lavenderblush"=>[255, 240, 245], "gray46"=>[117, 117, 117], "gray94"=>[240, 240, 240], "palevioletred2"=>[238, 121, 159], "khaki"=>[240, 230, 140], "paleturquoise"=>[174, 238, 238], "gray47"=>[120, 120, 120], "gray95"=>[242, 242, 242], "carrot"=>[237, 145, 33], "palevioletred3"=>[205, 104, 137], "lightsalmon1"=>[255, 160, 122], "olivedrab"=>[107, 142, 35], "gray48"=>[122, 122, 122], "palevioletred4"=>[139, 71, 93], "wheat"=>[245, 222, 179], "lightsalmon2"=>[238, 149, 114], "powderblue"=>[176, 224, 230], "gray49"=>[125, 125, 125], "gray96"=>[245, 245, 245], "red"=>[255, 0, 0], "brown1"=>[255, 64, 64], "lightsalmon3"=>[205, 129, 98], "manganeseblue"=>[3, 168, 158], "gray97"=>[247, 247, 247], "brown2"=>[238, 59, 59], "lightsalmon4"=>[139, 87, 66], "olive"=>[128, 128, 0], "gray98"=>[250, 250, 250], "lightgrey"=>[211, 211, 211], "sgigray72"=>[183, 183, 183], "brown3"=>[205, 51, 51], "gold"=>[255, 215, 0], "mintcream"=>[245, 255, 250], "gray99"=>[252, 252, 252], "brown4"=>[139, 35, 35], "sgidarkgray"=>[85, 85, 85], "magenta2"=>[238, 0, 238], "sgigray76"=>[193, 193, 193], "magenta3"=>[205, 0, 205], "dodgerblue"=>[30, 144, 255], "magenta4"=>[139, 0, 139], "cobaltgreen"=>[61, 145, 64], "sgisalmon"=>[198, 113, 113], "emeraldgreen"=>[0, 201, 87], "sgibrightgray"=>[197, 193, 170], "darkred"=>[139, 0, 0], "rawsienna"=>[199, 97, 20], "seagreen1"=>[84, 255, 159], "lightyellow"=>[255, 255, 224], "olivedrab1"=>[192, 255, 62], "orchid1"=>[255, 131, 250], "seashell"=>[255, 245, 238], "seagreen2"=>[78, 238, 148], "bisque1"=>[255, 228, 196], "olivedrab2"=>[179, 238, 58], "orchid2"=>[238, 122, 233], "azure1"=>[240, 255, 255], "seagreen3"=>[67, 205, 128], "bisque2"=>[238, 213, 183], "whitesmoke"=>[245, 245, 245], "olivedrab3"=>[154, 205, 50], "orchid3"=>[205, 105, 201], "azure2"=>[224, 238, 238], "lightpink1"=>[255, 174, 185], "lightgoldenrod1"=>[255, 236, 139], "bisque3"=>[205, 183, 158], "olivedrab4"=>[105, 139, 34], "orchid4"=>[139, 71, 137], "purple"=>[128, 0, 128], "lemonchiffon"=>[255, 250, 205], "azure3"=>[193, 205, 205], "lightpink2"=>[238, 162, 173], "seagreen4"=>[46, 139, 87], "forestgreen"=>[34, 139, 34], "lightgoldenrod2"=>[238, 220, 130], "bisque4"=>[139, 125, 107], "sgislateblue"=>[113, 113, 198], "azure4"=>[131, 139, 139], "lightpink3"=>[205, 140, 149], "lightgoldenrod3"=>[205, 190, 112], "gray20"=>[51, 51, 51], "sgibeet"=>[142, 56, 142], "limegreen"=>[50, 205, 50], "orange1"=>[255, 165, 0], "lightpink4"=>[139, 95, 101], "lightgoldenrod4"=>[139, 129, 76], "gray21"=>[54, 54, 54], "orange2"=>[238, 154, 0], "gray22"=>[56, 56, 56], "gray70"=>[179, 179, 179], "orange3"=>[205, 133, 0], "gray23"=>[59, 59, 59], "gray71"=>[181, 181, 181], "orange4"=>[139, 90, 0], "lightseagreen"=>[32, 178, 170], "bisque"=>[255, 228, 196], "gray24"=>[61, 61, 61], "gray72"=>[184, 184, 184], "darkslateblue"=>[72, 61, 139], "gray25"=>[64, 64, 64], "gray73"=>[186, 186, 186], "lightcoral"=>[240, 128, 128], "tan1"=>[255, 165, 79], "gray26"=>[66, 66, 66], "black"=>[0, 0, 0], "tan2"=>[238, 154, 73], "gray27"=>[69, 69, 69], "gray74"=>[189, 189, 189], "teal"=>[0, 128, 128], "tan3"=>[205, 133, 63], "aquamarine1"=>[127, 255, 212], "gray28"=>[71, 71, 71], "gray75"=>[191, 191, 191], "tan4"=>[139, 90, 43], "darkmagenta"=>[139, 0, 139], "aquamarine2"=>[118, 238, 198], "gray29"=>[74, 74, 74], "gray76"=>[194, 194, 194], "indianred1"=>[255, 106, 106], "chocolate"=>[210, 105, 30], "aquamarine3"=>[102, 205, 170], "gray77"=>[196, 196, 196], "indianred2"=>[238, 99, 99], "slategray1"=>[198, 226, 255], "chocolate1"=>[255, 127, 36], "aquamarine4"=>[69, 139, 116], "gray78"=>[199, 199, 199], "sgigray52"=>[132, 132, 132], "indianred3"=>[205, 85, 85], "salmon"=>[250, 128, 114], "darkblue"=>[0, 0, 139], "lightyellow1"=>[255, 255, 224], "slategray2"=>[185, 211, 238], "chocolate2"=>[238, 118, 33], "gray79"=>[201, 201, 201], "indianred4"=>[139, 58, 58], "hotpink"=>[255, 105, 180], "brick"=>[156, 102, 31], "lightyellow2"=>[238, 238, 209], "slategray3"=>[159, 182, 205], "chocolate3"=>[205, 102, 29], "darkgray"=>[169, 169, 169], "lightyellow3"=>[205, 205, 180], "darkolivegreen"=>[85, 107, 47], "slategray4"=>[108, 123, 139], "chocolate4"=>[139, 69, 19], "salmon1"=>[255, 140, 105], "deeppink"=>[255, 20, 147], "indigo"=>[75, 0, 130], "darkslategray"=>[47, 79, 79], "navajowhite1"=>[255, 222, 173], "lightyellow4"=>[139, 139, 122], "royalblue1"=>[72, 118, 255], "slateblue"=>[106, 90, 205], "maroon1"=>[255, 52, 179], "sgigray56"=>[142, 142, 142], "salmon2"=>[238, 130, 98], "navajowhite2"=>[238, 207, 161], "coldgrey"=>[128, 138, 135], "royalblue2"=>[67, 110, 238], "cornsilk1"=>[255, 248, 220], "maroon2"=>[238, 48, 167], "salmon3"=>[205, 112, 84], "navajowhite3"=>[205, 179, 139], "royalblue3"=>[58, 95, 205], "cornsilk2"=>[238, 232, 205], "maroon3"=>[205, 41, 144], "slategray"=>[112, 128, 144], "salmon4"=>[139, 76, 57], "navajowhite4"=>[139, 121, 94], "royalblue4"=>[39, 64, 139], "darkseagreen1"=>[193, 255, 193], "cornsilk3"=>[205, 200, 177], "maroon4"=>[139, 28, 98], "hotpink1"=>[255, 110, 180], "mediumorchid1"=>[224, 102, 255], "darkseagreen2"=>[180, 238, 180], "cornsilk4"=>[139, 136, 120], "mint"=>[189, 252, 201], "hotpink2"=>[238, 106, 167], "sgilightblue"=>[125, 158, 192], "goldenrod1"=>[255, 193, 37], "mediumorchid2"=>[209, 95, 238], "darkseagreen3"=>[155, 205, 155], "hotpink3"=>[205, 96, 144], "goldenrod2"=>[238, 180, 34], "mediumorchid3"=>[180, 82, 205], "darkseagreen4"=>[105, 139, 105], "hotpink4"=>[139, 58, 98], "crimson"=>[220, 20, 60], "lightskyblue"=>[135, 206, 250], "goldenrod3"=>[205, 155, 29], "mediumorchid4"=>[122, 55, 139], "cornsilk"=>[255, 248, 220]}
+        pdf=FPDF.new('P', "cm")
+        pdf.SetTitle(pdfFile)
+        pdf.SetCreator("newickDraw")
+        pdf.SetAuthor(ENV["USER"]) if (!ENV["USER"].nil?)
+        pdf.AddPage
+        yUnit = nil
+        lineWidth = nil
+        fontSize = nil
+        bootScale = 0.6
+        if (taxa.size < 30)
+          fontSize = 10
+          yUnit = 0.5
+          lineWidth = 0.02
+        elsif (taxa.size < 60)
+          fontSize = 8
+          yUnit = 0.25
+          lineWidth = 0.01
+        elsif (taxa.size < 150)
+          fontSize = 8
+          yUnit = 0.197
+          lineWidth = 0.01
+        elsif (taxa.size < 300)
+          fontSize = 2
+          yUnit = 0.09
+          lineWidth = 0.005
+        elsif (taxa.size < 400)
+          fontSize = 2
+          yUnit = 0.055
+          lineWidth = 0.002
+        elsif (taxa.size < 800)
+          fontSize = 1
+          yUnit = 0.030
+          lineWidth = 0.0015
         else
-          pdf.SetTextColor(colors[hl][0], colors[hl][1], colors[hl][2]) if hl 
-          pdf.Write(0, entry) 
-          pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl  
+          fontSize = 0.5
+          yUnit = 0.020
+          lineWidth = 0.0010
         end
-      end
-      pdf.Line(xOffSet + child.parent.x*xScale, child.y, 
-        xOffSet + child.x*xScale, child.y)
-      }
-      if (labelName)
-        pdf.SetFont('Times','B', 24)
-        pdf.SetXY(0, pdf.GetY + 1)
-        pdf.Write(0, labelName)
-      end
-      if (brackets)
-        brackets.each {|bracket|
-          x, y1, y2, label, r, p = bracket
-          next if label.nil?
-          pdf.SetLineWidth(lineWidth * 5)
-          pdf.SetFont('Times','B', fontSize*1.5)
-          pdf.Line(x, y1, x, y2)
-          pdf.Line(x, y1, x - 0.3, y1)
-          pdf.Line(x, y2, x - 0.3, y2)
-          pdf.SetXY(x, (y1+y2)/2)
-          pdf.Write(0, label)
-          if (r == "r")
-            pdf.SetTextColor(255, 0, 0) 
-            pdf.SetXY(x + 1.8, -0.65+(y1+y2)/2)
-            pdf.SetFont('Times','B', fontSize*10)
-            pdf.Write(0, " .")
-            pdf.SetTextColor(0, 0, 0)
+        bootScale = 0.5 * fontSize
+        pdf.SetFont('Times','B', fontSize)
+        calcPos(yUnit) # calculate node pos before drawing
+        max = 0
+        @root.leaves.each do |leaf|
+          d = leaf.distToAncestor(@root)
+          max = d if (max < d)
+        end
+        xScale = 10.0/max
+        xOffSet = 0.25
+        pdf.SetLineWidth(lineWidth)
+        pdf.SetTextColor(0, 0, 0)
+        pdf.Line(0, @root.y, xOffSet, @root.y)
+        pdf.Line(xOffSet, @root.yMin, xOffSet, @root.yMax)
+        @root.descendants.each do |child|
+          if (!child.leaf?)
+            if (child.name.to_i > 75 && boot == "width") # good bootstrap
+              pdf.SetLineWidth(lineWidth * 5)
+            else
+              pdf.SetLineWidth(lineWidth)
+            end
+            bootX = xOffSet + child.x*xScale 
+            bootY = ((child.yMin + child.yMax) / 2.0) 
+            pdf.SetXY(bootX, bootY) 
+            pdf.SetFont('Times','B', bootScale)
+            pdf.Write(0, child.name.to_s)
+            pdf.SetFont('Times','B', fontSize)
+            pdf.Line(xOffSet + child.x*xScale, child.yMin, 
+            xOffSet + child.x*xScale, child.yMax)
+          else
+            if (child.parent.name.to_i > 75 && boot == "width") # good bootstrap
+              pdf.SetLineWidth(lineWidth * 5)
+            else
+              pdf.SetLineWidth(lineWidth)
+            end
+            pdf.SetXY(xOffSet + child.x*xScale, child.y)
+            efields = child.name.split("__")
+            entry, species = efields.first, efields.last
+            if (entry =~/\{([^\}]*)\}/)
+              species = $1
+            end
+            species = entry if species.nil? && !rawNames
+            species = child.name if rawNames
+            hl = false
+            highlights.keys.each do |highlight|
+              hl = highlights[highlight] if (entry.index(highlight))
+            end
+            if (pdfFile.index(entry)) # name of query taxon
+              pdf.SetTextColor(colors["red"][0], colors["red"][1], colors["red"][2]) 
+              pdf.Write(0, entry) 
+              pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) 
+            elsif (linker && link = send(linker, entry)) 
+              pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl 
+              pdf.Write(0, species, link)
+              pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl 
+            elsif (!species.nil?)
+              pdf.SetTextColor(colors[hl][0], colors[hl][1], colors[hl][2]) if hl 
+              pdf.Write(0, species) 
+              pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl 
+            else
+              pdf.SetTextColor(colors[hl][0], colors[hl][1], colors[hl][2]) if hl 
+              pdf.Write(0, entry) 
+              pdf.SetTextColor(colors["black"][0], colors["black"][1], colors["black"][2]) if hl  
+            end
           end
-          if (p == "p" || r == "p")
-            pdf.SetTextColor(255, 0, 255) 
-            pdf.SetXY(x + 2.3, -0.65+(y1+y2)/2)
-            pdf.SetFont('Times','B', fontSize*10)
-            pdf.Write(0, " .")
-            pdf.SetTextColor(0, 0, 0)
+          pdf.Line(xOffSet + child.parent.x*xScale, child.y, 
+          xOffSet + child.x*xScale, child.y)
+        end
+        if (labelName)
+          pdf.SetFont('Times','B', 24)
+          pdf.SetXY(0, pdf.GetY + 1)
+          pdf.Write(0, labelName)
+        end
+        if (brackets)
+          brackets.each do |bracket|
+            x, y1, y2, label, r, p = bracket
+            next if label.nil?
+            pdf.SetLineWidth(lineWidth * 5)
+            pdf.SetFont('Times','B', fontSize*1.5)
+            pdf.Line(x, y1, x, y2)
+            pdf.Line(x, y1, x - 0.3, y1)
+            pdf.Line(x, y2, x - 0.3, y2)
+            pdf.SetXY(x, (y1+y2)/2)
+            pdf.Write(0, label)
+            if (r == "r")
+              pdf.SetTextColor(255, 0, 0) 
+              pdf.SetXY(x + 1.8, -0.65+(y1+y2)/2)
+              pdf.SetFont('Times','B', fontSize*10)
+              pdf.Write(0, " .")
+              pdf.SetTextColor(0, 0, 0)
+            end
+            if (p == "p" || r == "p")
+              pdf.SetTextColor(255, 0, 255) 
+              pdf.SetXY(x + 2.3, -0.65+(y1+y2)/2)
+              pdf.SetFont('Times','B', fontSize*10)
+              pdf.Write(0, " .")
+              pdf.SetTextColor(0, 0, 0)
+            end
           end
-        }
+        end
+        pdf.SetLineWidth(lineWidth * 5)
+        pdf.Line(1, pdf.GetY + 1, 1 + 0.1*xScale, pdf.GetY + 1) 
+        pdf.SetFont('Times','B', fontSize)
+        pdf.SetXY(1 + 0.1*xScale, pdf.GetY + 1)
+        pdf.Write(0, "0.1")
+        if (pdfFile =~/^--/)
+          return pdf.Output
+        else
+          pdf.Output(pdfFile)
+        end
       end
-      pdf.SetLineWidth(lineWidth * 5)
-      pdf.Line(1, pdf.GetY + 1, 1 + 0.1*xScale, pdf.GetY + 1) 
-      pdf.SetFont('Times','B', fontSize)
-      pdf.SetXY(1 + 0.1*xScale, pdf.GetY + 1)
-      pdf.Write(0, "0.1")
-      if (pdfFile =~/^--/)
-        return pdf.Output
-      else
-        pdf.Output(pdfFile)
     end
-  end
-end
 
 
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: newick-ruby
 version: !ruby/object:Gem::Version 
-  hash: 21
+  hash: 19
   prerelease: false
   segments: 
   - 1
   - 0
-  - 1
-  version: 1.0.1
+  - 2
+  version: 1.0.2
 platform: ruby
 authors: 
 - Jonathan Badger
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-08-02 00:00:00 -07:00
+date: 2010-11-08 00:00:00 -08:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency