Merge commit 'blessed/master'

lib/bio/appl/paml/codeml/report.rb

@@ -34,12 +34,13 @@ class Codeml
     # report.tree_lengh # => Estimated phylogetic tree length
     class Report
 
-      attr_reader :tree_log_likelihood, :tree_length, :alpha
+      attr_reader :tree_log_likelihood, :tree_length, :alpha, :tree
 
       def initialize(codeml_report)
         @tree_log_likelihood = pull_tree_log_likelihood(codeml_report)
         @tree_length = pull_tree_length(codeml_report)
         @alpha = pull_alpha(codeml_report)
+        @tree = pull_tree(codeml_report)
       end
 
       private
@@ -57,6 +58,10 @@ def pull_alpha(text)
         text[/alpha .+ =\s+(-?\d+(\.\d+)?)/,1].to_f
       end
 
+      def pull_tree(text)
+        text[/([^\n]+)\n\nDetailed/m,1]
+      end
+
     end # End Report
   end # End Codeml
 end # End Bio::PAML

test/unit/bio/appl/paml/codeml/test_report.rb

@@ -34,4 +34,9 @@ def test_alpha
     assert_equal(0.58871, @example_report.alpha)
   end
 
+  def test_tree
+    tree = "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"
+    assert_equal(tree, @example_report.tree)
+  end
+
 end