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Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeModel.java
diff --git
a/src/jalview/analysis/TreeModel.java
b/src/jalview/analysis/TreeModel.java
index
1725adc
..
0e57a58
100644
(file)
--- a/
src/jalview/analysis/TreeModel.java
+++ b/
src/jalview/analysis/TreeModel.java
@@
-20,7
+20,6
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
@@
-81,7
+80,7
@@
public class TreeModel
public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
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;
treefile.HasBootstrap(), treefile.HasRootDistance());
seqData = odata;
@@
-95,7
+94,7
@@
public class TreeModel
*/
public TreeModel(TreeBuilder tree)
{
*/
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();
}
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
@@
-109,7
+108,7
@@
public class TreeModel
* @param hasBoot
* @param hasRootDist
*/
* @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;
boolean hasBoot, boolean hasRootDist)
{
this.sequences = seqs;
@@
-142,7
+141,7
@@
public class TreeModel
while (i < leaves.size())
{
// TODO - decide if we get rid of the polymorphism here ?
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;
realnam = j.getName();
nam = null;
@@
-312,8
+311,7
@@
public class TreeModel
*
* @return Vector of leaf nodes on binary tree
*/
*
* @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)
{
{
if (nd == null)
{
@@
-333,8
+331,8
@@
public class TreeModel
* TODO: Identify internal nodes... if (node.isSequenceLabel()) {
* leaves.addElement(node); }
*/
* 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;
}
return leaves;
@@
-410,8
+408,8
@@
public class TreeModel
}
else
{
}
else
{
- _groupNodes(groups, (SequenceNode) nd.left(), threshold);
- _groupNodes(groups, (SequenceNode) nd.right(), threshold);
+ _groupNodes(groups, nd.left(), threshold);
+ _groupNodes(groups, nd.right(), threshold);
}
}
}
}