src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.TreeBuilder;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.math.MatrixI;
   6
   7 import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
   8 import org.forester.msa.Msa;
   9 import org.forester.phylogeny.Phylogeny;
  10 import org.forester.phylogeny.PhylogenyNode;
  11
  12 public class ArchaeopteryxTreeBuilder // cannot inherit
  13                                                         // TreeBuilder as that
  14                                                         // demands the use of
  15                                                         // SequenceNode (instead
  16                                                         // of PhylogenyNode)
  17 {
  18   protected SequenceI[] sequences;
  19
  20   private Phylogeny aptxTree;
  21
  22   private PhylogenyNode rootNode;
  23
  24   protected MatrixI distances;
  25
  26   protected Msa msa;
  27
  28   protected SymmetricalDistanceMatrixParser distanceParser = SymmetricalDistanceMatrixParser
  29           .createInstance();
  30
  31
  32   public ArchaeopteryxTreeBuilder()
  33   {
  34
  35     this.rootNode = new PhylogenyNode();
  36     this.aptxTree = new Phylogeny();
  37
  38   }
  39
  40   public ArchaeopteryxTreeBuilder(PhylogenyNode treeRoot)
  41   {
  42
  43     this.rootNode = treeRoot;
  44     this.aptxTree = new Phylogeny();
  45
  46   }
  47
  48   public Phylogeny buildAptxTree(TreeBuilder tree)
  49   {
  50   this.sequences= tree.getSequences();
  51     return buildAptxTree(sequences);
  52
  53   }
  54
  55   public Phylogeny buildAptxTree(SequenceI[] sequences)
  56   {
  57
  58     for (SequenceI sequence : sequences)
  59     {
  60       PhylogenyNode treeNode = new PhylogenyNode();
  61       treeNode.setName(sequence.getName());
  62       rootNode.addAsChild(treeNode);
  63
  64     }
  65     aptxTree.setRoot(rootNode);
  66     return aptxTree;
  67
  68   }
  69 }