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JAL-2490 performant findFeaturesAtRes
[jalview.git]
/
src
/
jalview
/
analysis
/
AverageDistanceTree.java
diff --git
a/src/jalview/analysis/AverageDistanceTree.java
b/src/jalview/analysis/AverageDistanceTree.java
index
7e3cfe1
..
907109e
100644
(file)
--- a/
src/jalview/analysis/AverageDistanceTree.java
+++ b/
src/jalview/analysis/AverageDistanceTree.java
@@
-5,6
+5,10
@@
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceNode;
import jalview.viewmodel.AlignmentViewport;
import jalview.datamodel.SequenceNode;
import jalview.viewmodel.AlignmentViewport;
+/**
+ * This class implements distance calculations used in constructing a Average
+ * Distance tree (also known as UPGMA)
+ */
public class AverageDistanceTree extends TreeBuilder
{
/**
public class AverageDistanceTree extends TreeBuilder
{
/**
@@
-55,17
+59,11
@@
public class AverageDistanceTree extends TreeBuilder
{
distances.setValue(i, ii, newdist[ii]);
distances.setValue(ii, i, newdist[ii]);
{
distances.setValue(i, ii, newdist[ii]);
distances.setValue(ii, i, newdist[ii]);
- System.out.println(String.format(
- "findClusterDistance(%d, %d) newdist to %d is %f", i, j, ii,
- newdist[ii]));
}
}
/**
}
}
/**
- * Returns the minimum distance between two clusters, and also sets the
- * indices of the clusters in fields mini and minj
- *
- * @return DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
protected double findMinDistance()
*/
@Override
protected double findMinDistance()
@@
-88,30
+86,21
@@
public class AverageDistanceTree extends TreeBuilder
}
}
}
}
}
}
- System.out.println("findMinDistance found " + min + " at " + mini + ","
- + minj);
return min;
}
/**
return min;
}
/**
- * DOCUMENT ME!
- *
- * @param tmpi
- * DOCUMENT ME!
- * @param tmpj
- * DOCUMENT ME!
- * @param dist
- * DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
*/
@Override
- protected void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+ protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
double dist)
{
double ih = 0;
double jh = 0;
double dist)
{
double ih = 0;
double jh = 0;
- SequenceNode sni = tmpi;
- SequenceNode snj = tmpj;
+ SequenceNode sni = nodei;
+ SequenceNode snj = nodej;
while (sni != null)
{
while (sni != null)
{
@@
-125,10
+114,8
@@
public class AverageDistanceTree extends TreeBuilder
snj = (SequenceNode) snj.left();
}
snj = (SequenceNode) snj.left();
}
- tmpi.dist = ((dist / 2) - ih);
- tmpj.dist = ((dist / 2) - jh);
- System.out.println("findNewDistances set tmpi to " + tmpi.dist
- + ", tmpj to " + tmpj.dist);
+ nodei.dist = ((dist / 2) - ih);
+ nodej.dist = ((dist / 2) - jh);
}
}
}
}