git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve...
[jalview.git]
/
src
/
jalview
/
analysis
/
NJTree.java
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
82e0284
..
522c2b1
100644
(file)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-26,10
+26,8
@@
import jalview.datamodel.SequenceNode;
import jalview.viewmodel.AlignmentViewport;
/**
import jalview.viewmodel.AlignmentViewport;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * This class implements distance calculations used in constructing a Neighbour
+ * Joining tree
*/
public class NJTree extends TreeBuilder
{
*/
public class NJTree extends TreeBuilder
{
@@
-47,16
+45,12
@@
public class NJTree extends TreeBuilder
{
super(av, sm, scoreParameters);
}
{
super(av, sm, scoreParameters);
}
- // private long _lycount = 0, _lylimit = 0;
/**
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
*/
@Override
- protected
- double findMinDistance()
+ protected double findMinDistance()
{
double min = Double.MAX_VALUE;
{
double min = Double.MAX_VALUE;
@@
-84,36
+78,26
@@
public class NJTree extends TreeBuilder
}
/**
}
/**
- * DOCUMENT ME!
- *
- * @param tmpi
- * DOCUMENT ME!
- * @param tmpj
- * DOCUMENT ME!
- * @param dist
- * DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
*/
@Override
- protected
- void findNewDistances(SequenceNode tmpi, SequenceNode tmpj, double dist)
+ protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+ double dist)
{
{
+ nodei.dist = ((dist + ri) - rj) / 2;
+ nodej.dist = (dist - nodei.dist);
- tmpi.dist = ((dist + ri) - rj) / 2;
- tmpj.dist = (dist - tmpi.dist);
-
- if (tmpi.dist < 0)
+ if (nodei.dist < 0)
{
{
- tmpi.dist = 0;
+ nodei.dist = 0;
}
}
- if (tmpj.dist < 0)
+ if (nodej.dist < 0)
{
{
- tmpj.dist = 0;
+ nodej.dist = 0;
}
}
}
}
-
-
/**
* Calculates and saves the distance between the combination of cluster(i) and
* cluster(j) and all other clusters. The new distance to cluster k is
/**
* Calculates and saves the distance between the combination of cluster(i) and
* cluster(j) and all other clusters. The new distance to cluster k is
@@
-124,25
+108,25
@@
public class NJTree extends TreeBuilder
* @param j
*/
@Override
* @param j
*/
@Override
- protected
- void findClusterDistance(int i, int j)
+ protected void findClusterDistance(int i, int j)
{
// New distances from cluster i to others
double[] newdist = new double[noseqs];
{
// New distances from cluster i to others
double[] newdist = new double[noseqs];
-
+
double ijDistance = distances.getValue(i, j);
for (int l = 0; l < noseqs; l++)
{
if ((l != i) && (l != j))
{
double ijDistance = distances.getValue(i, j);
for (int l = 0; l < noseqs; l++)
{
if ((l != i) && (l != j))
{
- newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l) - ijDistance) / 2;
+ newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l)
+ - ijDistance) / 2;
}
else
{
newdist[l] = 0;
}
}
}
else
{
newdist[l] = 0;
}
}
-
+
for (int ii = 0; ii < noseqs; ii++)
{
distances.setValue(i, ii, newdist[ii]);
for (int ii = 0; ii < noseqs; ii++)
{
distances.setValue(i, ii, newdist[ii]);