added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 8019def31cad9acc54c1308171bf796e949890a1..56ce8bb19e19d10b7181512b31d422d3d6b2a32f 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -288,7 +288,7 @@ int ClusterCommand::execute(){
                
                read->read(nameMap);
                list = read->getListVector();
-               matrix = read->getMatrix();
+               matrix = read->getDMatrix();
                rabund = new RAbundVector(list->getRAbundVector());
                delete read;
                
@@ -333,7 +333,7 @@ int ClusterCommand::execute(){
                loops = 0;
                double saveCutoff = cutoff;
                
-               while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
+               while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){  
                
                        if (m->control_pressed) { //clean up
                                delete list; delete matrix; delete rabund; delete cluster;
@@ -353,8 +353,8 @@ int ClusterCommand::execute(){
                        loops++;
 
                        cluster->update(cutoff);
-       
-                       float dist = matrix->getSmallDist();
+            
+            float dist = matrix->getSmallDist();
                        float rndDist;
                        if (hard) {
                                rndDist = m->ceilDist(dist, precision);