package jalview.ext.forester;
import jalview.datamodel.SequenceI;
-import jalview.ext.archaeopteryx.TreeNode;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
import jalview.math.MatrixI;
-import java.util.ArrayList;
-import java.util.List;
-
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 List<ExternalTreeNodeI> getConvertedTreeNodes(
- List<PhylogenyNode> aptxNodes)
- {
- List<ExternalTreeNodeI> jalviewNodes = new ArrayList<>();
- for (PhylogenyNode aptxNode : aptxNodes)
- {
- jalviewNodes.add(new TreeNode(aptxNode));
- }
- return jalviewNodes;
- }
+
}