*/
package jalview.analysis;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
- this(seqs, (SequenceNode) treefile.getTree(), treefile.HasDistances(),
+ this(seqs, treefile.getTree(), treefile.HasDistances(),
treefile.HasBootstrap(), treefile.HasRootDistance());
seqData = odata;
*/
public TreeModel(TreeBuilder tree)
{
- this(tree.getSequences(), (SequenceNode) tree.getTopNode(), tree.hasDistances(),
+ this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
* @param hasBoot
* @param hasRootDist
*/
- public TreeModel(SequenceI[] seqs, SequenceNode root, boolean hasDist,
+ public TreeModel(SequenceI[] seqs, BinaryNode root, boolean hasDist,
boolean hasBoot, boolean hasRootDist)
{
this.sequences = seqs;
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)
{
* TODO: Identify internal nodes... if (node.isSequenceLabel()) {
* leaves.addElement(node); }
*/
- findLeaves((SequenceNode) nd.left(), leaves);
- findLeaves((SequenceNode) nd.right(), leaves);
+ findLeaves(nd.left(), leaves);
+ findLeaves(nd.right(), leaves);
}
return leaves;
}
else
{
- _groupNodes(groups, (SequenceNode) nd.left(), threshold);
- _groupNodes(groups, (SequenceNode) nd.right(), threshold);
+ _groupNodes(groups, nd.left(), threshold);
+ _groupNodes(groups, nd.right(), threshold);
}
}