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[jalview.git]
/
src
/
jalview
/
analysis
/
NJTree.java
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
71d6737
..
0683265
100755
(executable)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-253,11
+253,11
@@
public class NJTree
{
\r
if (type.equals("NJ"))
\r
{
\r
{
\r
if (type.equals("NJ"))
\r
{
\r
- float mind = findMinNJDistance();
\r
+ findMinNJDistance();
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- float mind = findMinDistance();
\r
+ findMinDistance();
\r
}
\r
\r
Cluster c = joinClusters(mini, minj);
\r
}
\r
\r
Cluster c = joinClusters(mini, minj);
\r
@@
-291,7
+291,7
@@
public class NJTree
}
\r
}
\r
\r
}
\r
}
\r
\r
- Cluster c = joinClusters(one, two);
\r
+ joinClusters(one, two);
\r
top = (SequenceNode) (node.elementAt(one));
\r
\r
reCount(top);
\r
top = (SequenceNode) (node.elementAt(one));
\r
\r
reCount(top);
\r
@@
-375,11
+375,6
@@
public class NJTree
public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
\r
float dist)
\r
{
\r
public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
\r
float dist)
\r
{
\r
- float ih = 0;
\r
- float jh = 0;
\r
-
\r
- SequenceNode sni = tmpi;
\r
- SequenceNode snj = tmpj;
\r
\r
tmpi.dist = ((dist + ri) - rj) / 2;
\r
tmpj.dist = (dist - tmpi.dist);
\r
\r
tmpi.dist = ((dist + ri) - rj) / 2;
\r
tmpj.dist = (dist - tmpi.dist);
\r
@@
-469,8
+464,6
@@
public class NJTree
*/
\r
public void findClusterNJDistance(int i, int j)
\r
{
\r
*/
\r
public void findClusterNJDistance(int i, int j)
\r
{
\r
- int noi = ((Cluster) cluster.elementAt(i)).value.length;
\r
- int noj = ((Cluster) cluster.elementAt(j)).value.length;
\r
\r
// New distances from cluster to others
\r
float[] newdist = new float[noseqs];
\r
\r
// New distances from cluster to others
\r
float[] newdist = new float[noseqs];
\r
@@
-665,7
+658,7
@@
public class NJTree
AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
- as.printAlignment();
\r
+ as.printAlignment(System.out);
\r
distance[i][j] = (float) as.maxscore;
\r
\r
if (max < distance[i][j])
\r
distance[i][j] = (float) as.maxscore;
\r
\r
if (max < distance[i][j])
\r
@@
-1121,15
+1114,6
@@
public class NJTree
}
\r
}
\r
\r
}
\r
}
\r
\r
- /**
\r
- * DOCUMENT ME!
\r
- *
\r
- * @param node DOCUMENT ME!
\r
- */
\r
- public void setMaxDist(SequenceNode node)
\r
- {
\r
- this.maxdist = maxdist;
\r
- }
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r
@@
-1173,3
+1157,4
@@
class Cluster
this.value = value;
\r
}
\r
}
\r
this.value = value;
\r
}
\r
}
\r
+
\r