package jalview.ext.archaeopteryx; import jalview.analysis.TreeBuilder; import jalview.datamodel.SequenceI; import jalview.ext.forester.ForesterMatrix; import jalview.util.MessageManager; import org.forester.evoinference.distance.NeighborJoiningF; import org.forester.evoinference.matrix.distance.DistanceMatrix; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyNode; public class ArchaeopteryxTreeConverter { protected final SequenceI[] sequences; private Phylogeny aptxTree; private PhylogenyNode rootNode; protected final DistanceMatrix distances; protected final TreeBuilder jalviewTree; public String treeTitle; public ArchaeopteryxTreeConverter(final TreeBuilder calculatedTree) { jalviewTree = calculatedTree; sequences = jalviewTree.getSequences(); distances = ForesterMatrix.convertJalviewToForester( jalviewTree.testDistances, sequences); aptxTree = new Phylogeny(); rootNode = new PhylogenyNode(); } public Phylogeny buildAptxTree(final PhylogenyNode treeRoot) { rootNode = treeRoot; buildAptxTree(); return aptxTree; } public Phylogeny buildAptxTree() { NeighborJoiningF foresterClustering = NeighborJoiningF .createInstance(); aptxTree = foresterClustering.execute(distances); treeTitle = generateTreeName(); aptxTree.setName(treeTitle); return aptxTree; } private Phylogeny clusterNodes() { return aptxTree; } /** * Formats a localised title for the tree panel, like *
* Neighbour Joining Using BLOSUM62 *
* For a tree loaded from file, just uses the file name
*
* @return
*/
public String generateTreeName()
{
if (treeTitle != null) // will currently never happen, loaded tree file will
// take a different path
{
return treeTitle;
}
else
{
/*
* i18n description of Neighbour Joining or Average Distance method
*/
String treecalcnm = MessageManager
.getString("label.tree_calc_" + jalviewTree.getClass()
.getSimpleName().substring(0, 2).toLowerCase());
/*
* short score model name (long description can be too long)
*/
String smn = jalviewTree.getScoreModel().getName();
/*
* put them together as