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Restore file before eclipse changes
[jalview.git]
/
src
/
jalview
/
analysis
/
NJTree.java
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
97b8519
..
6c239be
100755
(executable)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-251,14
+251,14
@@
public class NJTree
{
\r
while (noClus > 2)
\r
{
\r
{
\r
while (noClus > 2)
\r
{
\r
- /* if (type.equals("NJ"))
\r
+ if (type.equals("NJ"))
\r
{
\r
float mind = findMinNJDistance();
\r
}
\r
else
\r
{
\r
float mind = findMinDistance();
\r
{
\r
float mind = findMinNJDistance();
\r
}
\r
else
\r
{
\r
float mind = findMinDistance();
\r
- }*/
\r
+ }
\r
\r
Cluster c = joinClusters(mini, minj);
\r
\r
\r
Cluster c = joinClusters(mini, minj);
\r
\r
@@
-273,7
+273,7
@@
public class NJTree
boolean onefound = false;
\r
\r
int one = -1;
\r
boolean onefound = false;
\r
\r
int one = -1;
\r
- //int two = -1;
\r
+ int two = -1;
\r
\r
for (int i = 0; i < noseqs; i++)
\r
{
\r
\r
for (int i = 0; i < noseqs; i++)
\r
{
\r
@@
-281,7
+281,7
@@
public class NJTree
{
\r
if (onefound == false)
\r
{
\r
{
\r
if (onefound == false)
\r
{
\r
- //two = i;
\r
+ two = i;
\r
onefound = true;
\r
}
\r
else
\r
onefound = true;
\r
}
\r
else
\r
@@
-291,7
+291,7
@@
public class NJTree
}
\r
}
\r
\r
}
\r
}
\r
\r
- // Cluster c = joinClusters(one, two);
\r
+ Cluster c = 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
+375,11
@@
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
+ float ih = 0;
\r
+ float jh = 0;
\r
\r
\r
- //SequenceNode sni = tmpi;
\r
- //SequenceNode snj = tmpj;
\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
+469,8
@@
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
+ 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
@@
-1121,6
+1121,15
@@
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
@@
-1164,3
+1173,4
@@
class Cluster
this.value = value;
\r
}
\r
}
\r
this.value = value;
\r
}
\r
}
\r
+
\r