src/jalview/ext/forester/DataConversions.java

   1 package jalview.ext.forester;
   2
   3 import jalview.datamodel.Sequence;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.math.MatrixI;
   6
   7 import org.forester.evoinference.matrix.distance.DistanceMatrix;
   8 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
   9 import org.forester.phylogeny.PhylogenyNode;
  10
  11 public final class DataConversions
  12 {
  13   public static org.forester.phylogeny.data.Sequence createForesterSequence(
  14           final SequenceI jalviewSequence, final boolean sequenceIsAligned)
  15   {
  16     org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
  17
  18     if (jalviewSequence.getDescription() != null)
  19     {
  20       foresterSeq.setName(jalviewSequence.getDescription());
  21     }
  22
  23     // all tree sequences should be aligned already
  24     foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
  25
  26     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
  27
  28     // add checks for DNA or RNA (infer from forester itself?)
  29     if (jalviewSequence.isProtein())
  30     {
  31       try
  32       {
  33         foresterSeq.setType("protein");
  34       } catch (final PhyloXmlDataFormatException ignore)
  35       {
  36         // do nothing
  37       }
  38
  39     }
  40
  41     return foresterSeq;
  42
  43   }
  44
  45   public static SequenceI createJalviewSequence(
  46           PhylogenyNode foresterNode)
  47   {
  48     String seq = foresterNode.getNodeData().getSequence()
  49             .getMolecularSequence();
  50     String seqName = foresterNode.getName();
  51
  52     SequenceI jalviewSeq = new Sequence(seqName, seq, 1,
  53             seq.length() + 1);
  54     return jalviewSeq.deriveSequence();
  55
  56
  57   }
  58
  59
  60   // public static org.forester.phylogeny.data.Accession
  61   // createForesterAccession(
  62   // SequenceI jalviewSequence)
  63   // {
  64   //
  65   //
  66   // org.forester.phylogeny.data.Accession foresterAcs = new
  67   // org.forester.phylogeny.data.Accession();
  68   //
  69   // return foresterAcs;
  70   // }
  71
  72   public static DistanceMatrix createForesterDistanceMatrix(
  73           final MatrixI jalviewInputMatrix,
  74           final String[] matrixIdentifiers)
  75   {
  76
  77     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  78             matrixIdentifiers);
  79     return foresterMatrix;
  80
  81   }
  82
  83   public static DistanceMatrix createForesterDistanceMatrix(
  84           final MatrixI jalviewInputMatrix,
  85           final SequenceI[] matrixSequences)
  86   {
  87     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  88             matrixSequences);
  89     return foresterMatrix;
  90
  91   }
  92
  93
  94 }