Class: NewickTree

Inherits:
Object
  • Object
show all
Defined in:
lib/Newick.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(treeString) ⇒ NewickTree

Returns a new instance of NewickTree.



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# File 'lib/Newick.rb', line 351

def initialize(treeString)
  tokenizer = NewickTokenizer.new(treeString)
  @root = buildTree(nil, tokenizer)
end

Instance Attribute Details

#root ⇒ Object (readonly)

Returns the value of attribute root.



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# File 'lib/Newick.rb', line 350

def root
  @root
end

Class Method Details

.fromFile(fileName) ⇒ Object

create new NewickTree from tree stored in file



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# File 'lib/Newick.rb', line 357

def NewickTree.fromFile(fileName)
  treeString = ""
  inFile = File.new(fileName)
  inFile.each do |line|
    treeString += line.chomp
  end
  inFile.close
  treeString.gsub!(/\[[^\]]*\]/,"") # remove comments before parsing
  return NewickTree.new(treeString)
end

Instance Method Details

#addBootStrap(bootClades) ⇒ Object

add bootstrap values (given in clade arrays) to a tree



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# File 'lib/Newick.rb', line 642

def addBootStrap(bootClades)
  @root.descendants.each do |clade|
    next if clade.leaf?
    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

#addECnums(alignFile) ⇒ Object

add EC numbers from alignment



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# File 'lib/Newick.rb', line 589

def addECnums(alignFile)
  ec = Hash.new
  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
    end
  end
  unAlias(ec)
end

#alias(aliasFile = nil, longAlias = false) ⇒ Object

renames nodes and creates an alias file, returning aliased tree and hash



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# File 'lib/Newick.rb', line 432

def alias(aliasFile = nil, longAlias = false)
  ali = Hash.new
  aliF = File.new(aliasFile, "w") if (!aliasFile.nil?)
  if (longAlias)
    taxon = "SEQ" + "0"* taxa.sort {|x,y| x.length <=> y.length}.last.length
  else
    taxon =  "SEQ0000001"
  end
  @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!
    end
  end
  aliF.close if (!aliasFile.nil?)
  return self, ali
end

#buildTree(parent, tokenizer) ⇒ Object

internal function used for building tree structure from string



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# File 'lib/Newick.rb', line 369

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
    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 
    else
      raise NewickParseError, 
      "Expected '(' or label but found: #{token.value}"
    end
  end
end

#calcPos(yUnit) ⇒ Object

calculates leaf node positions (backwards from leaves, given spacing)



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# File 'lib/Newick.rb', line 683

def calcPos(yUnit)
    yPos = 0.25
    @root.reorder
    leaves = @root.leaves.sort {|x, y| x.nodesToNode(y) <=> y.nodesToNode(x)}
    leaves.each do |leaf|
leaf.y = yPos
yPos += yUnit
    end
    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
end

#clades(bootstrap = false) ⇒ Object

returns array of arrays representing the tree clades



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# File 'lib/Newick.rb', line 633

def clades(bootstrap = false)
  clades = []
  @root.descendants.each do |clade|
    clades.push(clade.taxa(bootstrap)) if (!clade.children.empty?)
  end
  return clades
end

#compare(tree) ⇒ Object

returns lists of clades different between two trees



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# File 'lib/Newick.rb', line 502

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 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
  return diff1, diff2
end

#distanceMatrix(verbose = nil) ⇒ Object

returns a 2D hash of pairwise distances on tree



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# File 'lib/Newick.rb', line 476

def distanceMatrix(verbose = nil)
  dMatrix = Hash.new
  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

#draw(pdfFile, boot = "width", linker = :giLink, labelName = false, highlights = Hash.new, brackets = nil, rawNames = false, goodBoot = 75) ⇒ Object

returns PDF representation of branching structure of tree



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# File 'lib/Newick.rb', line 717

def draw(pdfFile, boot="width", linker = :giLink, labelName = false,
  highlights = Hash.new, brackets = nil, rawNames = false, goodBoot = 75)
  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 = 6
    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
    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 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_f >= goodBoot && 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_f > goodBoot && 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
    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

#findNode(name, exact = false) ⇒ Object

return node with the given name, exactly if second argument true



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# File 'lib/Newick.rb', line 528

def findNode(name, exact=false)
  return @root.findNode(name, exact)
end

#fixPhylip ⇒ Object

Fixes PHYLIP’s mistake of using branch lengths and not node values



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# File 'lib/Newick.rb', line 671

def fixPhylip
  @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

#giLink(entry) ⇒ Object

function to generate gi link to ncbi for draw, below



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# File 'lib/Newick.rb', line 706

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

#midpointRoot ⇒ Object

root the tree on midpoint distance



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# File 'lib/Newick.rb', line 604

def midpointRoot
  unroot
  org1, org2, dist = mostDistantLeaves
  midDist = dist / 2.0
  return self if (midDist == 0)
  if (org1.distToAncestor(@root) > org2.distToAncestor(@root))
    node = org1
  else
    node = org2
  end
  distTraveled = 0
  while(!node.nil?)
    distTraveled += node.edgeLen
    break if (distTraveled >= midDist)
    node = node.parent
  end
  oldDist = node.edgeLen
  left, right = node, node.parent
  right.removeChild(node)
  right.reverseChildParent
  left.edgeLen = distTraveled - midDist
  right.edgeLen = oldDist - left.edgeLen
  @root = NewickNode.new("", 0)
  @root.addChild(left)
  @root.addChild(right)
  return self
end

#mostDistantLeaves ⇒ Object

returns the two most distant leaves and their distance apart



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# File 'lib/Newick.rb', line 565

def mostDistantLeaves
  greatestDist = 0
  dist = Hash.new
  org1, org2 = nil, nil
  @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)
      dist[node2][node1] = dist[node1][node2]
      if (dist[node1][node2] > greatestDist)
        org1 = node1
        org2 = node2
        greatestDist = dist[node1][node2]
      end
    end
  end
  return org1, org2, greatestDist
end

#reAlias(aliasNames) ⇒ Object

renames nodes according to inverse alias hash



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# File 'lib/Newick.rb', line 461

def reAlias(aliasNames)
  @root.descendants.each do |node|
    aliasNames.keys.each do |key|
      node.name = key if (aliasNames[key] == node.name)
    end
  end
  return self
end

#relatives(taxon) ⇒ Object

return array of arrays of taxa representing relatives at each level



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# File 'lib/Newick.rb', line 655

def relatives(taxon)
  node = findNode(taxon)
  if (node.nil?)
    return nil
  else
    relatives = []
    while(!node.parent.nil?)
      relatives.push(node.parent.taxa - node.taxa)
      node = node.parent
    end
    return relatives
  end
end

#reorder ⇒ Object

reorders leaves alphabetically and size



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# File 'lib/Newick.rb', line 426

def reorder
  @root.reorder
  return self
end

#reroot(node) ⇒ Object

root the tree on a given node



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# File 'lib/Newick.rb', line 548

def reroot(node)
  unroot
  left = node
  right = left.parent
  right.removeChild(node)
  right.reverseChildParent
  if (left.edgeLen != 0)
    right.edgeLen = left.edgeLen / 2.0
    left.edgeLen = right.edgeLen
  end
  @root = NewickNode.new("", 0)
  @root.addChild(left)
  @root.addChild(right)
  return self
end

#taxa ⇒ Object

return array of all taxa in tree



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# File 'lib/Newick.rb', line 471

def taxa
  return @root.taxa
end

#to_s(showLen = true, bootStrap = "node") ⇒ Object

return string representation of tree



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# File 'lib/Newick.rb', line 414

def to_s(showLen = true, bootStrap = "node")
  return @root.to_s(showLen, bootStrap) + ";"
end

#unAlias(aliasNames) ⇒ Object

renames nodes according to alias hash



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# File 'lib/Newick.rb', line 453

def unAlias(aliasNames)
  @root.descendants.each do |node|
    node.name = aliasNames[node.name] if (!aliasNames[node.name].nil?)
  end
  return self
end

#unroot ⇒ Object

unroot the tree



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# File 'lib/Newick.rb', line 533

def unroot
  if (@root.children.size != 2)
    return self # already unrooted
  end
  left, right = @root.children
  left, right = right, left if (right.leaf?) # don't uproot leaf side   
  left.edgeLen += right.edgeLen
  right.children.each do |child|
    @root.addChild(child)
  end
  @root.removeChild(right)
  return self
end

#write(fileName, showLen = true, bootStrap = "node") ⇒ Object

write string representation of tree to file



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# File 'lib/Newick.rb', line 419

def write(fileName, showLen = true, bootStrap = "node")
  file = File.new(fileName, "w")
  file.print @root.to_s(showLen, bootStrap) + ";\n"
  file.close
end