src/jalview/ext/forester/DataConversions.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 DataConversions
  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
  24                                                                 // already
  25     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
  26     if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from
  27                                      // forester itself?)
  28     {
  29       try
  30       {
  31         foresterSeq.setType("protein");
  32       } catch (final PhyloXmlDataFormatException ignore)
  33       {
  34         // do nothing
  35       }
  36
  37     }
  38
  39     return foresterSeq;
  40
  41   }
  42
  43
  44   // public static org.forester.phylogeny.data.Accession
  45   // createForesterAccession(
  46   // SequenceI jalviewSequence)
  47   // {
  48   //
  49   //
  50   // org.forester.phylogeny.data.Accession foresterAcs = new
  51   // org.forester.phylogeny.data.Accession();
  52   //
  53   // return foresterAcs;
  54   // }
  55
  56   public static DistanceMatrix createForesterDistanceMatrix(
  57           final MatrixI jalviewInputMatrix,
  58           final String[] matrixIdentifiers)
  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     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  72             matrixSequences);
  73     return foresterMatrix;
  74
  75   }
  76 }