import jalview.datamodel.SequenceI;
import jalview.math.MatrixI;
-import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
-import org.forester.msa.Msa;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
protected MatrixI distances;
- protected Msa msa;
-
- protected SymmetricalDistanceMatrixParser distanceParser = SymmetricalDistanceMatrixParser
- .createInstance();
+ {
+ this.aptxTree = new Phylogeny();
+ }
public ArchaeopteryxTreeBuilder()
{
this.rootNode = new PhylogenyNode();
- this.aptxTree = new Phylogeny();
}
{
this.rootNode = treeRoot;
- this.aptxTree = new Phylogeny();
}
public Phylogeny buildAptxTree(TreeBuilder tree)
{
this.sequences = tree.getSequences();
- aptxTree.setName("word");
+ this.distances = tree.getDistances();
+
+ aptxTree.setName(
+ "PLEASE FIX ME reheaheth35yheqhb3q5hyq3bt3q5u4jwqjwuh6");
+
+ // final NeighborJoiningF nj = NeighborJoiningF.createInstance(false, 5);
+
+ //
+ // final Phylogeny phy = nj.execute(JalviewMatrixToForesterMatrix
+ // .convertJalviewToForester(distances));
+
return buildAptxTree(sequences);
}
for (SequenceI sequence : sequences)
{
- PhylogenyNode treeNode = new PhylogenyNode();
- treeNode.setName(sequence.getName());
+ PhylogenyNode treeNode = new PhylogenyNode(sequence.getName());
rootNode.addAsChild(treeNode);
}
}
+
/**
* Formats a localised title for the tree panel, like
* <p>