package jalview.ext.forester;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.math.MatrixI;
import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.phylogeny.PhylogenyNode;
public final class DataConversions
{
{
foresterSeq.setName(jalviewSequence.getDescription());
}
- foresterSeq.setMolecularSequenceAligned(sequenceIsAligned); // all tree
- // sequences
- // should
- // be aligned
- // already
+
+ // all tree sequences should be aligned already
+ foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
+
foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
- if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from
- // forester itself?)
+
+ // add checks for DNA or RNA (infer from forester itself?)
+ if (jalviewSequence.isProtein())
{
try
{
}
+ public static SequenceI createJalviewSequence(
+ PhylogenyNode foresterNode)
+ {
+ String seq = foresterNode.getNodeData().getSequence()
+ .getMolecularSequence();
+ String seqName = foresterNode.getName();
+
+ SequenceI jalviewSeq = new Sequence(seqName, seq, 1,
+ seq.length() + 1);
+ return jalviewSeq.deriveSequence();
+
+
+ }
+
// public static org.forester.phylogeny.data.Accession
// createForesterAccession(
return foresterMatrix;
}
+
+
}