newick-ruby 1.0.3 → 1.0.4

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: c2b1dc3f44e03d60b322225a4699911537e41bbf
+  data.tar.gz: feed13a868431c2d2de44d6acfe05dcc88b13aef
+SHA512:
+  metadata.gz: 3b4b8002b80733ba1ff269b5ddf741d9113d3ee2979c1da2bbe1131424761162f50d3688c90e0299c4e261a188442b1ffe206795e41a3b1a33e413fa72944eec
+  data.tar.gz: 7646b03f2f05cea1fba1bb6dac954164740ee06bc3c9678086aee60567dcbbd2126dba1bfe749b48723dbd35e67b60a8cc9fb3334566598c91d373052514fc13

data/README

@@ -11,12 +11,13 @@ jgi_19094_1366.m000227-Phatr2.tree is an example Newick tree for playing with th
 Let me know what you think:
 
 Jonathan Badger
-J. Craig Venter Institute
+National Cancer Institute (NCI)
 jhbadger@gmail.com
 
 UPDATES:
 1.0.2 -- faster distance matrix calculation
 1.0.3 -- fixed colors in highlights when drawing trees
+1.0.4 -- allow choice of exact or inexact node matching
 
 License
 (The MIT License)

data/bin/newickDraw

@@ -12,6 +12,19 @@ opt.label = false
 opt.highlights = nil
 opt.file = nil
 opt.raw = false
+opt.good = 75
+
+# add string->integer method for array access, as fpdf 1.53 fails without it on ruby 1.9 and higher
+
+class Array
+  def [](key)
+    if key.kind_of?(String)
+      self.at(key.to_i)
+    else
+      self.at(key)
+    end
+  end
+end
 
 ARGV.options {|o|
   o.banner << " tree-file [..tree-file]"
@@ -23,6 +36,7 @@ ARGV.options {|o|
 	  "file with ids to highlight") {|f| opt.file = f} 
   o.on("-l ", "--label ", String, "add label to tree pdf") {|l| opt.label = l}   
   o.on("-r", "--raw", "draw tree with raw names (false)") {opt.raw = true}
+  o.on("-g ", "--goodboot ", Float, "minimum level of a good bootstrap (default #{opt.good})") {|l| opt.good = l}
   begin
     o.parse!
   rescue
@@ -61,5 +75,5 @@ end
 ARGV.each {|arg|
   tree = NewickTree.fromFile(arg)
   tree.draw(arg + ".pdf", "width", linker = :giLink, opt.label, highlights,
-            brackets, opt.raw)
+            brackets, opt.raw, opt.good)
 }

data/lib/Newick.rb

@@ -163,13 +163,13 @@ class NewickNode
   end
 
   # returns node with given name, or nil if not found
-  def findNode(name)
+  def findNode(name, exact=false)
     found = nil
-    if (@name =~/#{name}/)
+    if (exact && @name==name) || (!exact && @name =~/#{name}/)
       found = self
     else
       @children.each do |child|
-        found = child.findNode(name)
+        found = child.findNode(name, exact)
         break if found
       end
     end
@@ -524,9 +524,9 @@ class NewickTree
     return diff1, diff2
   end
 
-  # return node with the given name
-  def findNode(name)
-    return @root.findNode(name)
+  # return node with the given name, exactly if second argument true
+  def findNode(name, exact=false)
+    return @root.findNode(name, exact)
   end
 
   # unroot the tree
@@ -715,7 +715,7 @@ class NewickTree
 
       # returns PDF representation of branching structure of tree
       def draw(pdfFile, boot="width", linker = :giLink, labelName = false,
-        highlights = Hash.new, brackets = nil, rawNames = 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)
@@ -771,7 +771,7 @@ class NewickTree
         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
+            if (child.name.to_f >= goodBoot && boot == "width") # good bootstrap
               pdf.SetLineWidth(lineWidth * 5)
             else
               pdf.SetLineWidth(lineWidth)
@@ -785,7 +785,7 @@ class NewickTree
             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
+            if (child.parent.name.to_f > goodBoot && boot == "width") # good bootstrap
               pdf.SetLineWidth(lineWidth * 5)
             else
               pdf.SetLineWidth(lineWidth)

data/test/tc_Newick.rb

@@ -27,4 +27,10 @@ class TestNewickTree < Test::Unit::TestCase
     tree = NewickTree.new("(A:0.65,(B:0.1,C:0.2)90:0.5);")
     assert_equal(tree.taxa, ["A","B","C"])
   end
-end
+  def test_findNode
+    tree = NewickTree.new("(A12,(A13,A2));")
+    assert_equal(tree.findNode("A1", false).name, "A12")
+    assert_equal(tree.findNode("A1", true), nil)
+    assert_equal(tree.findNode("A13", true).name, "A13")
+  end
+end

metadata

@@ -1,42 +1,33 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: newick-ruby
-version: !ruby/object:Gem::Version 
-  hash: 17
-  prerelease: false
-  segments: 
-  - 1
-  - 0
-  - 3
-  version: 1.0.3
+version: !ruby/object:Gem::Version
+  version: 1.0.4
 platform: ruby
-authors: 
+authors:
 - Jonathan Badger
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2010-12-07 00:00:00 -08:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2015-06-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: fpdf
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 1
-        - 5
-        - 3
+      - !ruby/object:Gem::Version
         version: 1.5.3
   type: :runtime
-  version_requirements: *id001
-description: newick-ruby provides routines for parsing newick-format phylogenetic trees.
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+description: newick-ruby provides routines for parsing newick-format phylogenetic
+  trees.
 email: jhbadger@gmail.com
-executables: 
+executables:
 - newickAlphabetize
 - newickCompare
 - newickDist
@@ -45,12 +36,9 @@ executables:
 - newickReroot
 - newickTaxa
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
-- example/jgi_19094_1366.m000227-Phatr2.tree
-- lib/Newick.rb
+files:
+- README
 - bin/newickAlphabetize
 - bin/newickCompare
 - bin/newickDist
@@ -58,41 +46,31 @@ files:
 - bin/newickReorder
 - bin/newickReroot
 - bin/newickTaxa
-- README
+- example/jgi_19094_1366.m000227-Phatr2.tree
+- lib/Newick.rb
 - test/tc_Newick.rb
-has_rdoc: true
 homepage: http://github.com/jhbadger/Newick-ruby
 licenses: []
-
+metadata: {}
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
   - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
   - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 2.4.5
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: newick-ruby provides routines for parsing newick-format phylogenetic trees.
-test_files: 
+test_files:
 - test/tc_Newick.rb