lib/bio/appl/paml/codeml.rb in bio-1.4.3.0001 vs lib/bio/appl/paml/codeml.rb in bio-1.5.0

@@ -35,12 +35,12 @@
   # Example 1:
   #
   #   require 'bio'
   #   # Reads multi-fasta formatted file and gets a Bio::Alignment object.
   #   alignment = Bio::FlatFile.open(Bio::Alignment::MultiFastaFormat,
-  #                                  'example.fst').alignment
+  #                                  'example.fst').next_entry.alignment
   #   # Reads newick tree from a file
-  #   tree = Bio::FlatFile.open(Bio::Newick, 'example.tree').tree
+  #   tree = Bio::FlatFile.open(Bio::Newick, 'example.tree').next_entry.tree
   #   # Creates a Codeml object
   #   codeml = Bio::PAML::Codeml.new
   #   # Sets parameters
   #   codeml.parameters[:runmode] = 0
   #   codeml.parameters[:RateAncestor] = 1