Class PHYLIPExporter

  • All Implemented Interfaces:
    AlignmentExporter, TreeExporter

    public class PHYLIPExporter
    extends java.lang.Object
    implements AlignmentExporter, TreeExporter
    Export alignment to Phylip format. Must be one of the most braindead format around. Try to output something that hopefuly any "Phylip supported" variant can read - up to 9 name chars, followed by a blank, followed by sequence on one line.
    Version:
    $Id: PHYLIPExporter.java 841 2007-11-11 21:36:42Z twobeers $
    Author:
    Joseph Heled
    • Constructor Summary

      Constructors 
      Constructor Description
      PHYLIPExporter​(java.io.Writer writer)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void exportAlignment​(Alignment alignment)
      export one alignment.
      void exportTree​(Tree tree)
      Export a single tree
      void exportTrees​(java.util.Collection<? extends Tree> trees)
      Export a collection of trees
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • PHYLIPExporter

        public PHYLIPExporter​(java.io.Writer writer)
        Parameters:
        writer - where export text goes
    • Method Detail

      • exportAlignment

        public void exportAlignment​(Alignment alignment)
                             throws java.io.IOException
        Description copied from interface: AlignmentExporter
        export one alignment.
        Specified by:
        exportAlignment in interface AlignmentExporter
        Parameters:
        alignment - to export
        Throws:
        java.io.IOException
      • exportTree

        public void exportTree​(Tree tree)
                        throws java.io.IOException
        Description copied from interface: TreeExporter
        Export a single tree
        Specified by:
        exportTree in interface TreeExporter
        Throws:
        java.io.IOException
      • exportTrees

        public void exportTrees​(java.util.Collection<? extends Tree> trees)
                         throws java.io.IOException
        Description copied from interface: TreeExporter
        Export a collection of trees
        Specified by:
        exportTrees in interface TreeExporter
        Throws:
        java.io.IOException