src/jalview/ext/forester/ForesterConversions.java

   1 package jalview.ext.forester;
   2
   3 import jalview.datamodel.SequenceI;
   4 import jalview.math.MatrixI;
   5
   6 import org.forester.evoinference.matrix.distance.DistanceMatrix;
   7 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
   8
   9 public final class ForesterConversions
  10 {
  11   public static org.forester.phylogeny.data.Sequence createForesterSequence(
  12           SequenceI jalviewSequence)
  13   {
  14     org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
  15     if (jalviewSequence.getDescription() != null)
  16     {
  17       foresterSeq.setName(jalviewSequence.getDescription());
  18     }
  19     foresterSeq.setMolecularSequenceAligned(true); // all tree sequences should
  20                                                    // be aligned already
  21     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
  22     if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from
  23                                      // forester itself?)
  24     {
  25       try
  26       {
  27         foresterSeq.setType("protein");
  28       } catch (final PhyloXmlDataFormatException ignore)
  29       {
  30         // do nothing
  31       }
  32
  33     }
  34
  35     return foresterSeq;
  36
  37   }
  38
  39
  40   // public static org.forester.phylogeny.data.Accession
  41   // createForesterAccession(
  42   // SequenceI jalviewSequence)
  43   // {
  44   //
  45   //
  46   // org.forester.phylogeny.data.Accession foresterAcs = new
  47   // org.forester.phylogeny.data.Accession();
  48   //
  49   // return foresterAcs;
  50   // }
  51
  52   public static DistanceMatrix createForesterDistanceMatrix(
  53           final MatrixI jalviewInputMatrix,
  54           final String[] matrixIdentifiers)
  55   {
  56     if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
  57     {
  58       // some kind of warning?
  59     }
  60
  61     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  62             matrixIdentifiers);
  63     return foresterMatrix;
  64
  65   }
  66
  67   public static DistanceMatrix createForesterDistanceMatrix(
  68           final MatrixI jalviewInputMatrix,
  69           final SequenceI[] matrixSequences)
  70   {
  71     if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
  72     {
  73       // some kind of warning?
  74     }
  75     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  76             matrixSequences);
  77     return foresterMatrix;
  78
  79   }
  80 }