src/jalview/ext/forester/ForesterDataConversions.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 ForesterDataConversions
  10 {
  11   public static org.forester.phylogeny.data.Sequence createForesterSequence(
  12           final SequenceI jalviewSequence, final boolean sequenceIsAligned)
  13   {
  14     org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
  15
  16     if (jalviewSequence.getDescription() != null)
  17     {
  18       foresterSeq.setName(jalviewSequence.getDescription());
  19     }
  20     foresterSeq.setMolecularSequenceAligned(sequenceIsAligned); // all tree
  21                                                               // sequences
  22                                                               // should
  23                                                    // be aligned already
  24     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
  25     if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from
  26                                      // forester itself?)
  27     {
  28       try
  29       {
  30         foresterSeq.setType("protein");
  31       } catch (final PhyloXmlDataFormatException ignore)
  32       {
  33         // do nothing
  34       }
  35
  36     }
  37
  38     return foresterSeq;
  39
  40   }
  41
  42
  43   // public static org.forester.phylogeny.data.Accession
  44   // createForesterAccession(
  45   // SequenceI jalviewSequence)
  46   // {
  47   //
  48   //
  49   // org.forester.phylogeny.data.Accession foresterAcs = new
  50   // org.forester.phylogeny.data.Accession();
  51   //
  52   // return foresterAcs;
  53   // }
  54
  55   public static DistanceMatrix createForesterDistanceMatrix(
  56           final MatrixI jalviewInputMatrix,
  57           final String[] matrixIdentifiers)
  58   {
  59     if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
  60     {
  61       // some kind of warning?
  62     }
  63
  64     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  65             matrixIdentifiers);
  66     return foresterMatrix;
  67
  68   }
  69
  70   public static DistanceMatrix createForesterDistanceMatrix(
  71           final MatrixI jalviewInputMatrix,
  72           final SequenceI[] matrixSequences)
  73   {
  74     if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
  75     {
  76       // some kind of warning?
  77     }
  78     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  79             matrixSequences);
  80     return foresterMatrix;
  81
  82   }
  83 }