public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
- this(seqs, treefile.getTree(), treefile.HasDistances(),
+ this(seqs, treefile.getTree(), treefile.HasDistances(),
treefile.HasBootstrap(), treefile.HasRootDistance());
seqData = odata;
*/
public TreeModel(TreeBuilder tree)
{
- this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
+ this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
while (i < leaves.size())
{
// TODO - decide if we get rid of the polymorphism here ?
- j = (SequenceNode)leaves.elementAt(i++);
+ j = (SequenceNode) leaves.elementAt(i++);
realnam = j.getName();
nam = null;
*
* @return Vector of leaf nodes on binary tree
*/
- Vector<BinaryNode> findLeaves(BinaryNode nd,
- Vector<BinaryNode> leaves)
+ Vector<BinaryNode> findLeaves(BinaryNode nd, Vector<BinaryNode> leaves)
{
if (nd == null)
{
}
else
{
- _groupNodes(groups, (SequenceNode) nd.left(), threshold);
- _groupNodes(groups, (SequenceNode) nd.right(), threshold);
+ _groupNodes(groups, nd.left(), threshold);
+ _groupNodes(groups, nd.right(), threshold);
}
}