public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
- this(seqs, treefile.getTree(), treefile.HasDistances(),
- treefile.HasBootstrap(), treefile.HasRootDistance());
+ this(seqs, treefile.getTree(), treefile.hasDistances(),
+ treefile.hasBootstrap(), treefile.hasRootDistance());
seqData = odata;
associateLeavesToSequences(seqs);
this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
+
}
/**
SequenceNode j;
SequenceI nam;
String realnam;
- Vector<SequenceI> one2many = new Vector<SequenceI>();
+ Vector<SequenceI> one2many = new Vector<>();
// int countOne2Many = 0;
while (i < leaves.size())
{
*/
public Vector<SequenceNode> findLeaves(SequenceNode nd)
{
- Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+ Vector<SequenceNode> leaves = new Vector<>();
findLeaves(nd, leaves);
return leaves;
}
*/
public List<SequenceNode> groupNodes(float threshold)
{
- List<SequenceNode> groups = new ArrayList<SequenceNode>();
+ List<SequenceNode> groups = new ArrayList<>();
_groupNodes(groups, getTopNode(), threshold);
return groups;
}