1 package jalview.ext.archaeopteryx;
3 import jalview.datamodel.SequenceI;
4 import jalview.ext.forester.ForesterMatrix;
5 import jalview.math.MatrixI;
7 import org.forester.evoinference.matrix.distance.DistanceMatrix;
8 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
10 public final class DataConversions
12 public static org.forester.phylogeny.data.Sequence createForesterSequence(
13 final SequenceI jalviewSequence, final boolean sequenceIsAligned)
15 org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
17 if (jalviewSequence.getDescription() != null)
19 foresterSeq.setName(jalviewSequence.getDescription());
22 // all tree sequences should be aligned already
23 foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
25 foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
27 // add checks for DNA or RNA (infer from forester itself?)
28 if (jalviewSequence.isProtein())
32 foresterSeq.setType("protein");
33 } catch (final PhyloXmlDataFormatException ignore)
45 // public static org.forester.phylogeny.data.Accession
46 // createForesterAccession(
47 // SequenceI jalviewSequence)
51 // org.forester.phylogeny.data.Accession foresterAcs = new
52 // org.forester.phylogeny.data.Accession();
54 // return foresterAcs;
57 public static DistanceMatrix createForesterDistanceMatrix(
58 final MatrixI jalviewInputMatrix,
59 final String[] matrixIdentifiers)
62 DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
64 return foresterMatrix;
68 public static DistanceMatrix createForesterDistanceMatrix(
69 final MatrixI jalviewInputMatrix,
70 final SequenceI[] matrixSequences)
72 DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
74 return foresterMatrix;