1 package jalview.ext.forester;
3 import jalview.datamodel.SequenceI;
4 import jalview.math.MatrixI;
6 import org.forester.evoinference.matrix.distance.DistanceMatrix;
7 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
9 public final class DataConversions
11 public static org.forester.phylogeny.data.Sequence createForesterSequence(
12 final SequenceI jalviewSequence, final boolean sequenceIsAligned)
14 org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
16 if (jalviewSequence.getDescription() != null)
18 foresterSeq.setName(jalviewSequence.getDescription());
21 // all tree sequences should be aligned already
22 foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
24 foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
26 // add checks for DNA or RNA (infer from forester itself?)
27 if (jalviewSequence.isProtein())
31 foresterSeq.setType("protein");
32 } catch (final PhyloXmlDataFormatException ignore)
44 // public static org.forester.phylogeny.data.Accession
45 // createForesterAccession(
46 // SequenceI jalviewSequence)
50 // org.forester.phylogeny.data.Accession foresterAcs = new
51 // org.forester.phylogeny.data.Accession();
53 // return foresterAcs;
56 public static DistanceMatrix createForesterDistanceMatrix(
57 final MatrixI jalviewInputMatrix,
58 final String[] matrixIdentifiers)
61 DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
63 return foresterMatrix;
67 public static DistanceMatrix createForesterDistanceMatrix(
68 final MatrixI jalviewInputMatrix,
69 final SequenceI[] matrixSequences)
71 DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
73 return foresterMatrix;