iroki 0.0.15 → 0.0.16

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 5a9b674ae4df9732e0925d66c98e586c97ef4759
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+  data.tar.gz: 6a18a69751a71d0947f630ef3eabe276d1cc0d6c
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+  data.tar.gz: d28bee6b62b0973de7da3daefa58da5883363f913451628c40350a5f77ec2e7ac6228b928d1a78bf6edaf431c65cdf54e689e30878bc1f0731404fc55a0df63b

data/README.md

@@ -139,3 +139,8 @@ Add `reorder_nodes` script.
 ### 0.0.15 ###
 
 - `.ruby-version` file was being weird when user didn't have the correct ruby
+
+### 0.0.16 ###
+
+- Allow unusual characters in label names ([GitHub issue](https://github.com/mooreryan/iroki/issues/2))
+- Fix no method `clean` bug ([GitHub issue](https://github.com/mooreryan/iroki/issues/3))

data/assets/images/iroki_text.svg

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0" y="0" width="362.268" height="256" viewBox="0, 0, 362.268, 256">
+  <g id="Layer_1">
+    <g>
+      <text transform="matrix(1, 0, 0, 1, 181.134, 212.5)">
+        <tspan x="-144.702" y="-9.5" font-family="Raleway-Thin" font-size="36" fill="#000000">Phylogenetic Tree</tspan>
+        <tspan x="-91.458" y="32.5" font-family="Raleway-Thin" font-size="36" fill="#000000">Customizer</tspan>
+      </text>
+      <text transform="matrix(1, 0, 0, 1, 181.134, 84.5)">
+        <tspan x="-129.384" y="50.5" font-family="Raleway-Thin" font-size="144" fill="#000000">Iroki</tspan>
+      </text>
+      <path d="M14.634,160 L348.634,160" fill-opacity="0" stroke="#000000" stroke-width="1.5"/>
+    </g>
+  </g>
+</svg>

data/assets/images/iroki_text_omni.svg

@@ -0,0 +1,3 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xl="http://www.w3.org/1999/xlink" version="1.1" viewBox="0 -18 362 274" width="362pt" height="274pt" xmlns:dc="http://purl.org/dc/elements/1.1/"><metadata> Produced by OmniGraffle 6.6 <dc:date>2016-08-08 18:14:28 +0000</dc:date></metadata><defs><font-face font-family="Raleway" font-size="36" panose-1="2 11 2 3 3 1 1 6 0 3" units-per-em="1000" underline-position="-75" underline-thickness="50" slope="0" x-height="528" cap-height="715" ascent="940.00244" descent="-233.99353" font-weight="300" font-stretch="condensed"><font-face-src><font-face-name name="Raleway-Thin"/></font-face-src></font-face><font-face font-family="Raleway" font-size="144" panose-1="2 11 2 3 3 1 1 6 0 3" units-per-em="1000" underline-position="-75" underline-thickness="50" slope="0" x-height="528" cap-height="715" ascent="940.00244" descent="-233.99353" font-weight="300" font-stretch="condensed"><font-face-src><font-face-name name="Raleway-Thin"/></font-face-src></font-face></defs><g stroke="none" stroke-opacity="1" stroke-dasharray="none" fill="none" fill-opacity="1"><title>Canvas 1</title><g><title>Layer 1</title><text transform="translate(31.63405 161.5)" fill="black"><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="0" y="34" textLength="42.624">Ph</tspan><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="42.12" y="34" textLength="132.48">ylogene</tspan><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="174.456" y="34" textLength="46.152">tic </tspan><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="219.6" y="34" textLength="21.6">T</tspan><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="237.24" y="34" textLength="11.628">r</tspan><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="247.932" y="34" textLength="50.868">ee </tspan></text><text transform="translate(84.87805 203.5)" fill="black"><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="0" y="34" textLength="73.404">Cust</tspan><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="72.936" y="34" textLength="78.12">omiz</tspan><tspan font-family="Raleway" font-size="36" font-weight="300" font-stretch="condensed" fill="black" x="150.552" y="34" textLength="32.364">er</tspan></text><text transform="translate(51.63405 -8.5)" fill="black"><tspan font-family="Raleway" font-size="144" font-weight="300" font-stretch="condensed" fill="black" x="0" y="135" textLength="77.904">Ir</tspan><tspan font-family="Raleway" font-size="144" font-weight="300" font-stretch="condensed" fill="black" x="74.16" y="135" textLength="184.608">oki</tspan></text><line x1="14.17608" y1="153" x2="348.17604" y2="153" stroke="black" stroke-linecap="round" stroke-linejoin="miter" stroke-width="1"/></g></g></svg>

data/lib/iroki.rb

@@ -19,6 +19,7 @@
 require "abort_if"
 
 require "iroki/biom"
+require "iroki/tree"
 require "iroki/version"
 
 require "iroki/const/const"

data/lib/iroki/core_ext/file/file.rb

@@ -67,7 +67,7 @@ module Iroki
             assert pattern, "found no pattern"
 
             if exact_matching # TODO should this really be everytime?
-              pattern = pattern.clean
+              pattern = pattern#.clean_name
             else
               # TODO flag bad regexp
               pattern = Regexp.new pattern
@@ -127,6 +127,95 @@ module Iroki
         patterns
       end
 
+      def parse_color_map_iroki( fname,
+                                iroki_to_name,
+                                exact_matching: true,
+                                auto_color: false)
+
+
+        check_file fname, :color_map
+
+        name_to_iroki = iroki_to_name.invert
+
+        patterns = {}
+        Object::File.open(fname, "rt").each_line do |line|
+          unless line.start_with? "#"
+            label_tag = ""
+            branch_tag = ""
+
+            pattern, label_color, branch_color = line.chomp.split "\t"
+
+            # color = "black" if color.nil? || color.empty?
+
+            assert pattern, "found no pattern"
+
+            if exact_matching # TODO should this really be everytime?
+            # pattern = pattern.clean_name
+              if name_to_iroki.has_key? pattern
+                pattern = name_to_iroki[pattern]
+              else
+                assert false, "String '#{pattern}' has no match in #{name_to_iroki.inspect}"
+              end
+            else
+              # TODO flag bad regexp
+              pattern = Regexp.new pattern
+            end
+
+            if color_given?(label_color) && color_given?(branch_color)
+              abort_if(has_label_tag?(label_color) &&
+                       has_label_tag?(branch_color),
+                       "Label tag specified twice for '#{line}'")
+
+              abort_if(has_branch_tag?(label_color) &&
+                       has_branch_tag?(branch_color),
+                       "Branch tag specified twice for '#{line}'")
+            end
+
+            if color_given?(label_color) && !color_given?(branch_color)
+              if (color = has_label_tag? label_color)
+                label_tag = Iroki::Color.get_tag color, auto_color
+              elsif (color = has_branch_tag? label_color)
+                branch_tag = Iroki::Color.get_tag color, auto_color
+              else
+                label_tag = Iroki::Color.get_tag label_color, auto_color
+                branch_tag = Iroki::Color.get_tag label_color, auto_color
+              end
+            else
+              if color_given? label_color
+                if (color = has_label_tag? label_color)
+                  label_tag = Iroki::Color.get_tag color, auto_color
+                elsif (color = has_branch_tag? label_color)
+                  branch_tag = Iroki::Color.get_tag color, auto_color
+                else
+                  label_tag = Iroki::Color.get_tag label_color, auto_color
+                end
+              end
+
+              if color_given? branch_color
+                if (color = has_branch_tag? branch_color)
+                  branch_tag = Iroki::Color.get_tag color, auto_color
+                elsif (color = has_label_tag? branch_color)
+                  label_tag = Iroki::Color.get_tag color, auto_color
+                else
+                  branch_tag = Iroki::Color.get_tag branch_color, auto_color
+                end
+              end
+            end
+
+            # if auto_color
+            #   patterns[pattern] = "[&!color=\"#{auto_colors[color]}\"]"
+            # else
+            #   patterns[pattern] = Iroki::Color.get_tag color, auto_color
+            # end
+
+            patterns[pattern] = { label: label_tag, branch: branch_tag }
+          end
+        end
+
+        patterns
+      end
+
+
       def parse_name_map fname
         check_file fname, :name_map
 
@@ -142,8 +231,8 @@ module Iroki
             abort_if newname.nil? || newname.empty?,
                      "Column 2 missing for line: #{line.inspect}"
 
-            oldname = oldname.clean
-            newname = newname.clean
+            # oldname = oldname.clean_name
+            # newname = newname.clean_name
 
             abort_if name_map.has_key?(oldname),
                      "#{oldname} is repeated in column 1"

data/lib/iroki/core_ext/string/string.rb

@@ -2,29 +2,53 @@ module Iroki
   module CoreExt
     module String
 
+      def has_color?
+        self.match(/(.*)(\[&!color="#[0-9A-Fa-f]{6}"\])/)
+      end
+      alias already_checked? has_color?
+
       def hex?
         self.match(/^#[0-9A-Fa-f]{6}$/)
       end
 
       def clean
-        self.strip.gsub(/[^\p{Alnum}_]+/, "_").gsub(/_+/, "_")
+        # puts %Q{clean: #{self}, #{self.gsub(/'/, '"')}}
+        self.gsub(/'/, '"')
       end
 
-      def has_color?
-        self.match(/(.*)(\[&!color="#[0-9A-Fa-f]{6}"\])/)
+      def single_quote
+        if self.match /\A'.*'\Z/
+          # puts %Q{single_quote if: #{self}, outputing #{self.dup}}
+          self.dup
+        else
+          # puts %Q{single_quote else: #{self}, returning '#{self.clean}'}
+          %Q['#{self.clean}']
+        end
       end
-      alias already_checked? has_color?
 
       def clean_name
         if (match = self.has_color?)
           name = match[1]
           color = match[2]
 
-          name.clean + color
+          # puts %Q{clean_name if: #{self}, returning #{name.single_quote + color}}
+          name.single_quote + color
+          # name + color
         else
-          self.clean
+          # puts %Q{clean_name else: #{self}, returning #{self.single_quote}}
+          self.single_quote
         end
       end
+
+      def clean_strict
+        self.strip.gsub(/[^\p{Alnum}_]+/, "_").gsub(/_+/, "_")
+      end
+
+
+      def has_single_quote?
+        self.match(/'/)
+      end
+
     end
   end
 end

data/lib/iroki/main/main.rb

@@ -20,6 +20,121 @@ require "bio"
 require "set"
 require "trollop"
 
+module Bio
+  class Tree
+    # formats Newick label (unquoted_label or quoted_label)
+    def __to_newick_format_label(str, options)
+      if __get_option(:parser, options) == :naive then
+        return str.to_s
+      end
+
+      str = str.to_s
+      if /([\(\)\,\:\[\]\_\'\x00-\x1f\x7f])/ =~ str then
+        # quoted_label
+        if __get_option(:parser, options) == :iroki
+          return str
+        else
+          return "\'" + str.gsub(/\'/, "\'\'") + "\'"
+        end
+      end
+      # unquoted_label
+      return str.gsub(/ /, '_')
+    end
+    private :__to_newick_format_label
+  end
+
+  class Newick
+    # splits string to tokens
+    def __parse_newick_tokenize(str, options)
+      str = str.chop if str[-1..-1] == ';'
+      # http://evolution.genetics.washington.edu/phylip/newick_doc.html
+      # quoted_label ==> ' string_of_printing_characters '
+      # single quote in quoted_label is '' (two single quotes)
+      #
+
+      if __get_option(:parser, options) == :naive then
+        ary = str.split(/([\(\)\,\:\[\]])/)
+        ary.collect! { |x| x.strip!; x.empty? ? nil : x }
+        ary.compact!
+        ary.collect! do |x|
+          if /\A([\(\)\,\:\[\]])\z/ =~ x then
+            x.intern
+          else
+            x
+          end
+        end
+        return ary
+      end
+
+      tokens = []
+      ss = StringScanner.new(str)
+
+      while !(ss.eos?)
+        if ss.scan(/\s+/) then
+          # do nothing
+
+        elsif ss.scan(/[\(\)\,\:\[\]]/) then
+          # '(' or ')' or ',' or ':' or '[' or ']'
+          t = ss.matched
+          tokens.push t.intern
+
+        elsif ss.scan(/\'/) then
+          # quoted_label
+          t = ''
+          while true
+            if ss.scan(/([^\']*)\'/) then
+              t.concat ss[1]
+              if  ss.scan(/\'/) then
+                # single quote in quoted_label
+                t.concat ss.matched
+              else
+                break
+              end
+            else
+              # incomplete quoted_label?
+              break
+            end
+          end #while true
+          unless ss.match?(/\s*[\(\)\,\:\[\]]/) or ss.match?(/\s*\z/) then
+            # label continues? (illegal, but try to rescue)
+            if ss.scan(/[^\(\)\,\:\[\]]+/) then
+              t.concat ss.matched.lstrip
+            end
+          end
+          tokens.push t
+
+        elsif ss.scan(/[^\(\)\,\:\[\]]+/) then
+          # unquoted_label
+          t = ss.matched.strip
+          t.gsub!(/[\r\n]/, '')
+
+          unless __get_option(:parser, options) == :iroki then
+            # unquoted underscore should be converted to blank
+            t.gsub!(/\_/, ' ')
+          end
+          tokens.push t unless t.empty?
+
+        else
+          # unquoted_label in end of string
+          t = ss.rest.strip
+          t.gsub!(/[\r\n]/, '')
+
+          unless __get_option(:parser, options) == :iroki then
+            # unquoted underscore should be converted to blank
+            t.gsub!(/\_/, ' ')
+          end
+
+          tokens.push t unless t.empty?
+          ss.terminate
+
+        end
+      end #while !(ss.eos?)
+
+      tokens
+    end
+  end
+end
+
 module Iroki
   module Main
     def self.main(color_branches: nil,
@@ -56,6 +171,7 @@ module Iroki
       abort_if single_color && biom_f.nil?,
                "--single-color was passed but no biom file was given"
 
+      # this should be allowed
       abort_if biom_f && color_map_f,
                "--color-map and --biom-file cannot both be specified. Try iroki --help for help."
 
@@ -92,12 +208,50 @@ module Iroki
                name_map_f.nil?,
                "Newick file was given but no other files were given")
 
-      # get the color patterns
-      if color_f
-        patterns = parse_color_map color_f,
-                                   exact_matching: exact,
-                                   auto_color: auto_color_hash
+      # treeio = Bio::FlatFile.open(Bio::Newick, newick)
+
+      # newick = treeio.next_entry
+      str = File.read newick
+      newick = Bio::Newick.new str, parser: :iroki
+      tree = newick.tree
+
+      # puts [:tree_first_parsed, tree.newick(indent: false)]
+
+      iroki_to_name = Iroki::Tree.change_names tree
+
+
+      #################################################################
+      # parse name map
+      ################
+
+      if name_map_f
+        name_map = parse_name_map name_map_f
       else
+        name_map = nil
+      end
+
+      if name_map_f && color_map_f.nil? && biom_f.nil? # just name map
+        # put node names back
+      end
+
+      ################
+      # parse name map
+      #################################################################
+
+      if name_map_f && color_map_f.nil? && biom_f.nil?
+        AbortIf.logger.info "Only renaming was requested."
+      end
+
+      #################################################################
+      # get color patterns
+      ####################
+
+      if color_f
+        patterns = parse_color_map_iroki color_f,
+                                         iroki_to_name,
+                                         exact_matching: exact,
+                                         auto_color: auto_color_hash
+      elsif biom_f
         samples, counts, is_single_group = Biom.open(biom_f, "rt").parse
 
         if is_single_group
@@ -107,45 +261,59 @@ module Iroki
           g2_counts = counts.map(&:last)
           patterns = TwoGroupGradient.new(samples, g1_counts, g2_counts).patterns
         end
+
+        # these patterns have the original name for the key, so change
+        # the key to the iroki name
+        name_to_iroki = iroki_to_name.invert
+        h = {}
+        patterns.each do |name, val|
+          h[name_to_iroki[name]] = val
+        end
+
+        patterns = h
+      else
+        patterns = nil
       end
 
-      treeio = Bio::FlatFile.open(Bio::Newick, newick)
+      ####################
+      # get color patterns
+      #################################################################
 
-      newick = treeio.next_entry
-      tree = newick.tree
+
+      # puts [:tree_after_change_names, tree.newick(indent: false)]
+      nil_val = { label: "", branch: "" }
 
       # do this first cos everything after will use the "new" names
-      if name_map_f
-        name_map = parse_name_map name_map_f
+      # if name_map_f
+      #   name_map = parse_name_map name_map_f
 
-        tree.collect_node! do |node|
-          unless node.name.nil?
-            # every name is cleaned no matter what
-            node.name = clean node.name
+      #   tree.collect_node! do |node|
+      #     unless node.name.nil?
+      #       # every name is cleaned no matter what
+      #       # node.name = node.name.clean_name
 
-            if name_map.has_key?(node.name)
-              node.name = name_map[node.name]
-            end
-          end
+      #       if name_map.has_key?(node.name)
+      #         node.name = name_map[node.name]
+      #       end
+      #     end
 
-          node
-        end
-      end
+      #     node
+      #   end
+      # end
 
       leaves_with_names = tree.leaves.reject { |leaf| leaf.name.nil? }
       if color_taxa_names
         leaves = leaves_with_names.map do |n|
-          name = n.name.clean_name
+          name = n.name#.clean_name
 
-          if (color = add_color_to_leaf_branch(patterns, name, exact))
-            name + color[:label]
+          if (color = add_color_to_leaf_branch(patterns, name, exact, iroki_to_name))
+            name.single_quote + color[:label]
           else
-            name
+            name.single_quote
           end
         end
       else
-        leaves = leaves_with_names.
-                 map { |n| n.name.clean_name }
+        leaves = leaves_with_names.map { |n| n.name.single_quote }
       end
 
       if color_branches
@@ -155,35 +323,49 @@ module Iroki
           n += 1
           $stderr.printf "Node: %d of %d\r", n, total
 
-          color_nodes patterns, tree, node, exact
+          color_nodes patterns, tree, node, exact, iroki_to_name
         end
       end
       $stderr.puts
 
-      if remove_bootstraps_below
-        tree.collect_node! do |node|
-          if node.bootstrap && node.bootstrap < remove_bootstraps_below
-            node.bootstrap_string = ""
-          end
-
-          node
+      # if remove_bootstraps_below
+      #   tree.collect_node! do |node|
+      #     if node.bootstrap && node.bootstrap < remove_bootstraps_below
+      #       node.bootstrap_string = ""
+      #     end
+
+      #     node
+      #   end
+      # end
+
+      tre_str = tree.newick(indent: false)
+      # tree.each_node do |node|
+      #   p [:node, node.name]
+      # end
+      # puts [:tree_str, tre_str]
+      # puts [:iroki_to_name, iroki_to_name]
+      # puts [:after_change, Iroki::Tree.gsub_iroki_newick_string(tre_str, iroki_to_name)]
+
+      # this hash can be used regardless of whether a name map was used
+      silly_iroki_to_name = {}
+      iroki_to_name.each do |iname, oldname|
+        if name_map && name_map.has_key?(oldname)
+          silly_iroki_to_name[iname] = name_map[oldname]
+        else
+          silly_iroki_to_name[iname] = oldname
         end
       end
 
-
-
-      tre_str = tree.newick(indent: false).gsub(/'/, '')
-
       nexus = "#NEXUS
 begin taxa;
 dimensions ntax=#{leaves.count};
 taxlabels
-#{leaves.join("\n")}
+#{leaves.join("\n").gsub(/iroki[0-9]+iroki/, silly_iroki_to_name)}
 ;
 end;
 
 begin trees;
-  tree tree_1 = [&R] #{tre_str}
+  tree tree_1 = [&R] #{Iroki::Tree.gsub_iroki_newick_string tre_str, silly_iroki_to_name}
 end;
 
 #{FIG}"

data/lib/iroki/tree.rb

@@ -0,0 +1,92 @@
+module Iroki
+  class Tree
+    def self.iroki_name idx
+      "iroki#{idx}iroki"
+    end
+
+    # @note The newick standard changes unquoted underscores to spaces
+    #
+    # @note The reason we have to bother with this is because when the
+    #   bioruby parser calls the __to_newick method, it does some
+    #   annoying things to the output and changes the names. Making
+    #   the names like this lets us easily gsub the names to what they
+    #   should be after the name map.
+    #
+    # @param [Bio::Tree] a bio ruby tree object
+    #
+    # @return [Hash] iroki_name (string) => quoted_orig_name (string)
+    def self.change_names tree
+      idx = -1
+      realname = {}
+      tree.each_node do |node|
+        if node.name && !node.name.empty?
+          idx += 1
+
+          realname[iroki_name(idx)] = %Q{#{node.name}}
+
+          node.name = iroki_name(idx)
+        end
+      end
+
+      realname
+    end
+
+    def self.combine_hashes h1, h2, nil_val=nil
+      h_new = {}
+      h1.each do |h1_key, h1_val|
+        if h2.has_key? h1_val
+          h_new[h1_key] = h2[h1_val]
+        else
+          h_new[h1_key] = nil_val
+        end
+      end
+
+      h_new
+    end
+
+    def self.quoted_vals hash
+      # p [:a, hash.values]
+      # p [:b, hash.values.map(&:single_quote)]
+      hash.values.map(&:single_quote)
+    end
+
+    def self.gsub_iroki_newick_string tre_str, iroki_to_name, name_map=nil
+      if name_map
+        vals = self.quoted_vals name_map
+        name_map_quoted = Hash[name_map.keys.zip(vals)]
+
+        iroki_to_new_name = self.combine_hashes iroki_to_name, name_map_quoted
+      else
+        vals = self.quoted_vals iroki_to_name
+
+        iroki_to_new_name = Hash[iroki_to_name.keys.zip(vals)]
+      end
+
+      tre_str.gsub(/iroki[0-9]+iroki/, iroki_to_new_name)
+    end
+
+    def self.iroki_to_color iroki_to_name, color_map, name_map, nil_val=nil
+      if name_map
+        old_names = name_map.keys
+        new_names = name_map.values
+
+        color_map_is_for_old_names = color_map.keys.all? { |key| old_names.include? key }
+        color_map_is_for_new_names = color_map.keys.all? { |key| new_names.include? key }
+
+        if color_map_is_for_old_names
+          iroki_to_color = self.combine_hashes iroki_to_name, color_map, nil_val
+        elsif color_map_is_for_new_names
+          iroki_to_new_name = self.combine_hashes iroki_to_name, name_map
+
+          iroki_to_color = self.combine_hashes iroki_to_new_name, color_map, nil_val
+        else # some old, some new
+          abort_if true, "The color map has both old and new names in the first column."
+        end
+
+        iroki_to_color
+      else # no name map
+        self.combine_hashes iroki_to_name, color_map, nil_val
+      end
+    end
+  end
+end

data/lib/iroki/utils/utils.rb

@@ -22,7 +22,7 @@ module Iroki
       tree.children(node).empty?
     end
 
-    def add_color_to_leaf_branch patterns, node, exact
+    def add_color_to_leaf_branch patterns, node, exact, iroki_to_name=nil
       num_matches = 0
       color = nil
       already_matched = false
@@ -37,7 +37,9 @@ module Iroki
           return nil
         end
       else
-        node_s = node.to_s
+        assert iroki_to_name, "iroki_to_name arg is nil"
+        assert iroki_to_name[node.to_s], "iroki_to_name is missing #{node.to_s}"
+        node_s = iroki_to_name[node.to_s]
 
         patterns.each do |pattern, this_color|
           if node_s =~ pattern
@@ -61,13 +63,15 @@ module Iroki
       end
     end
 
-    def color_nodes patterns, tree, node, exact
+    def color_nodes patterns, tree, node, exact, iroki_to_name
       # # check if it needs color, if so set the color
       # color = add_color_to_leaf_branch patterns, node, exact
 
       # clean the name no matter what
       if node.name
-        node.name = node.name.clean_name
+        # puts "before haha: #{node.name}"
+        node.name = node.name #.clean_name
+        # puts "after  haha: #{node.name}"
       else
         node.name = nil
       end
@@ -82,16 +86,18 @@ module Iroki
 
         # NOTE: this was originally before cleaning the node name a
         # couple lines up, does it matter that it is after?
-        color = add_color_to_leaf_branch patterns, node, exact
+        color = add_color_to_leaf_branch patterns, node, exact, iroki_to_name
 
         # add color to the name
+        # p [:before, node.name]
         node.name = node.name + color[:branch] if color
+        # p [:after, node.name]
       elsif !leaf?(tree, node)
         children = tree.children(node) # get the children
         children_colors = []
         children.each do |child|
           # recurse to color the child if needed
-          color_nodes patterns, tree, child, exact
+          color_nodes patterns, tree, child, exact, iroki_to_name
           children_colors << get_color(child) # add color of the child
         end
 

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.15"
+  VERSION = "0.0.16"
   COPYRIGHT = "2015 - 2016 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.15
+  version: 0.0.16
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-08-05 00:00:00.000000000 Z
+date: 2016-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -187,6 +187,13 @@ files:
 - assets/images/iroki_logo2.idraw
 - assets/images/iroki_logo2.png
 - assets/images/iroki_logo2.svg
+- assets/images/iroki_text.graffle
+- assets/images/iroki_text.idraw
+- assets/images/iroki_text.pdf
+- assets/images/iroki_text.png
+- assets/images/iroki_text.svg
+- assets/images/iroki_text_omni.pdf
+- assets/images/iroki_text_omni.svg
 - bin/console
 - bin/iroki_docker
 - bin/setup
@@ -207,6 +214,7 @@ files:
 - lib/iroki/core_ext/hash/hash.rb
 - lib/iroki/core_ext/string/string.rb
 - lib/iroki/main/main.rb
+- lib/iroki/tree.rb
 - lib/iroki/utils/utils.rb
 - lib/iroki/version.rb
 homepage: https://github.com/mooreryan/iroki