src/jalview/ext/forester/DataConversions.java

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