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JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of
[jalview.git]
/
src
/
jalview
/
analysis
/
NJTree.java
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
542f15e
..
7140867
100644
(file)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-21,7
+21,7
@@
package jalview.analysis;
import jalview.analysis.scoremodels.ScoreModels;
package jalview.analysis;
import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.CigarArray;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.CigarArray;
@@
-224,7
+224,7
@@
public class NJTree
* DOCUMENT ME!
*/
public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
* DOCUMENT ME!
*/
public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
- String pwtype, ScoreModelI sm, int start, int end)
+ String pwtype, DistanceModelI sm, int start, int end)
{
this.sequence = sequence;
this.node = new Vector<SequenceNode>();
{
this.sequence = sequence;
this.node = new Vector<SequenceNode>();
@@
-736,7
+736,7
@@
public class NJTree
*
* @return similarity matrix used to compute tree
*/
*
* @return similarity matrix used to compute tree
*/
- public float[][] findDistances(ScoreModelI _pwmatrix)
+ public float[][] findDistances(DistanceModelI _pwmatrix)
{
float[][] dist = new float[noseqs][noseqs];
{
float[][] dist = new float[noseqs][noseqs];