Phylip output

TODO

@@ -0,0 +1,2 @@
+- Island masking assumes one unique element, maybe consider a
+  neighbour. The example in test/data is rather a good one.

lib/bio-alignment.rb

@@ -12,3 +12,4 @@
 require 'bio-alignment/alignment'
 require 'bio-alignment/format/text'
 require 'bio-alignment/format/fasta'
+require 'bio-alignment/format/phylip'

lib/bio-alignment/edit/edit_rows.rb

@@ -24,7 +24,7 @@ def mark_row_elements &block
         aln = markrows_clone
         aln.rows.each_with_index do | row,rownum |
           new_seq = block.call(Coerce::to_elements(row),rownum)
-          p [rownum,new_seq,row]
+          # p [rownum,new_seq,row]
           aln.rows[rownum] = new_seq
         end
         aln

lib/bio-alignment/format/phylip.rb

@@ -0,0 +1,25 @@
+module Bio
+  module BioAlignment
+    module PhylipOutput
+      # Calculate header info from alignment and return as string
+      def PhylipOutput::header alignment
+        "#{alignment.size} #{alignment[0].length}\n"
+      end
+
+      # Output sequence PAML style and return as a multi-line string
+      def PhylipOutput::to_paml seq, size=60
+        buf = seq.id+"\n"
+        coding = if seq.kind_of?(CodonSequence) 
+                 seq.to_nt
+               else
+                 seq.to_s
+               end
+        coding.scan(/.{1,#{size}}/).each do | section |
+          buf += section + "\n"
+        end
+        buf
+      end
+    end
+  end
+end
+