{\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
+ }*/\r
\r
Cluster c = joinClusters(mini, minj);\r
\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
if (onefound == false)\r
{\r
- two = i;\r
+ //two = i;\r
onefound = true;\r
}\r
else\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
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
- 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
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
}\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