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JAL-4090 JAL-1551 spotlessApply
[jalview.git]
/
src
/
jalview
/
analysis
/
AverageDistanceEngine.java
diff --git
a/src/jalview/analysis/AverageDistanceEngine.java
b/src/jalview/analysis/AverageDistanceEngine.java
index
d81dd44
..
286d589
100644
(file)
--- a/
src/jalview/analysis/AverageDistanceEngine.java
+++ b/
src/jalview/analysis/AverageDistanceEngine.java
@@
-55,8
+55,10
@@
public class AverageDistanceEngine extends TreeEngine
/**
* compute cosine distance matrix for a given contact matrix and create a
* UPGMA tree
/**
* compute cosine distance matrix for a given contact matrix and create a
* UPGMA tree
+ *
* @param cm
* @param cm
- * @param cosineOrDifference false - dot product : true - L1
+ * @param cosineOrDifference
+ * false - dot product : true - L1
*/
public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa,
ContactMatrixI cm, boolean cosineOrDifference)
*/
public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa,
ContactMatrixI cm, boolean cosineOrDifference)
@@
-64,12
+66,11
@@
public class AverageDistanceEngine extends TreeEngine
this.av = av;
this.aa = aa;
this.cm = cm;
this.av = av;
this.aa = aa;
this.cm = cm;
- mode = (cosineOrDifference) ? 1 :0;
+ mode = (cosineOrDifference) ? 1 : 0;
calculate(cm);
}
calculate(cm);
}
-
public void calculate(ContactMatrixI cm)
{
this.cm = cm;
public void calculate(ContactMatrixI cm)
{
this.cm = cm;
@@
-103,7
+104,7
@@
public class AverageDistanceEngine extends TreeEngine
// compute distance matrix element
ContactListI ith = cm.getContactList(i);
distances.setValue(i, i, 0);
// compute distance matrix element
ContactListI ith = cm.getContactList(i);
distances.setValue(i, i, 0);
- if (ith==null)
+ if (ith == null)
{
continue;
}
{
continue;
}