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JAL-4134 - refactor tree calculation code to work with binaryNode base type.
[jalview.git]
/
src
/
jalview
/
analysis
/
AverageDistanceTree.java
diff --git
a/src/jalview/analysis/AverageDistanceTree.java
b/src/jalview/analysis/AverageDistanceTree.java
index
c726627
..
760962e
100644
(file)
--- a/
src/jalview/analysis/AverageDistanceTree.java
+++ b/
src/jalview/analysis/AverageDistanceTree.java
@@
-22,7
+22,7
@@
package jalview.analysis;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.datamodel.SequenceNode;
+import jalview.datamodel.BinaryNode;
import jalview.viewmodel.AlignmentViewport;
/**
import jalview.viewmodel.AlignmentViewport;
/**
@@
-113,25
+113,25
@@
public class AverageDistanceTree extends TreeBuilder
* {@inheritDoc}
*/
@Override
* {@inheritDoc}
*/
@Override
- protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+ protected void findNewDistances(BinaryNode nodei, BinaryNode nodej,
double dist)
{
double ih = 0;
double jh = 0;
double dist)
{
double ih = 0;
double jh = 0;
- SequenceNode sni = nodei;
- SequenceNode snj = nodej;
+ BinaryNode sni = nodei;
+ BinaryNode snj = nodej;
while (sni != null)
{
ih = ih + sni.dist;
while (sni != null)
{
ih = ih + sni.dist;
- sni = (SequenceNode) sni.left();
+ sni = (BinaryNode) sni.left();
}
while (snj != null)
{
jh = jh + snj.dist;
}
while (snj != null)
{
jh = jh + snj.dist;
- snj = (SequenceNode) snj.left();
+ snj = (BinaryNode) snj.left();
}
nodei.dist = ((dist / 2) - ih);
}
nodei.dist = ((dist / 2) - ih);