1 package jalview.ext.forester;
3 import jalview.datamodel.Sequence;
4 import jalview.datamodel.SequenceI;
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)
44 public static SequenceI createJalviewSequence(
45 org.forester.phylogeny.data.Sequence foresterSeq)
47 String seq = foresterSeq.getMolecularSequence();
48 SequenceI jalviewSeq = new Sequence(foresterSeq.getName(), seq, 1,
55 // public static org.forester.phylogeny.data.Accession
56 // createForesterAccession(
57 // SequenceI jalviewSequence)
61 // org.forester.phylogeny.data.Accession foresterAcs = new
62 // org.forester.phylogeny.data.Accession();
64 // return foresterAcs;
67 public static DistanceMatrix createForesterDistanceMatrix(
68 final MatrixI jalviewInputMatrix,
69 final String[] matrixIdentifiers)
72 DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
74 return foresterMatrix;
78 public static DistanceMatrix createForesterDistanceMatrix(
79 final MatrixI jalviewInputMatrix,
80 final SequenceI[] matrixSequences)
82 DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
84 return foresterMatrix;