src/jalview/ext/archaeopteryx/DataConversions.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.datamodel.SequenceI;
   4 import jalview.ext.forester.ForesterMatrix;
   5 import jalview.math.MatrixI;
   6
   7 import org.forester.evoinference.matrix.distance.DistanceMatrix;
   8 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
   9
  10 public final class DataConversions
  11 {
  12   public static org.forester.phylogeny.data.Sequence createForesterSequence(
  13           final SequenceI jalviewSequence, final boolean sequenceIsAligned)
  14   {
  15     org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
  16
  17     if (jalviewSequence.getDescription() != null)
  18     {
  19       foresterSeq.setName(jalviewSequence.getDescription());
  20     }
  21
  22     // all tree sequences should be aligned already
  23     foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
  24
  25     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
  26
  27     // add checks for DNA or RNA (infer from forester itself?)
  28     if (jalviewSequence.isProtein())
  29     {
  30       try
  31       {
  32         foresterSeq.setType("protein");
  33       } catch (final PhyloXmlDataFormatException ignore)
  34       {
  35         // do nothing
  36       }
  37
  38     }
  39
  40     return foresterSeq;
  41
  42   }
  43
  44
  45   // public static org.forester.phylogeny.data.Accession
  46   // createForesterAccession(
  47   // SequenceI jalviewSequence)
  48   // {
  49   //
  50   //
  51   // org.forester.phylogeny.data.Accession foresterAcs = new
  52   // org.forester.phylogeny.data.Accession();
  53   //
  54   // return foresterAcs;
  55   // }
  56
  57   public static DistanceMatrix createForesterDistanceMatrix(
  58           final MatrixI jalviewInputMatrix,
  59           final String[] matrixIdentifiers)
  60   {
  61
  62     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  63             matrixIdentifiers);
  64     return foresterMatrix;
  65
  66   }
  67
  68   public static DistanceMatrix createForesterDistanceMatrix(
  69           final MatrixI jalviewInputMatrix,
  70           final SequenceI[] matrixSequences)
  71   {
  72     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  73             matrixSequences);
  74     return foresterMatrix;
  75
  76   }
  77
  78
  79 }