added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 7484a621645c2449bfc9f158a391549f33da71dd..5e6a9b45aea94babdb66d7c928f48b323e88d573 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -154,7 +154,7 @@ int ClusterCommand::execute(){
                double saveCutoff = cutoff;
                
                while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
-               
+       
                        if (m->control_pressed) { //clean up
                                delete globaldata->gSparseMatrix;  globaldata->gSparseMatrix = NULL;
                                delete globaldata->gListVector;  globaldata->gListVector = NULL;
@@ -176,6 +176,7 @@ int ClusterCommand::execute(){
                        loops++;
 
                        cluster->update(cutoff);
+       
                        float dist = matrix->getSmallDist();
                        float rndDist = roundDist(dist, precision);
 
@@ -209,7 +210,7 @@ int ClusterCommand::execute(){
                //delete globaldata's copy of the sparsematrix and listvector to free up memory
                delete globaldata->gSparseMatrix;  globaldata->gSparseMatrix = NULL;
                delete globaldata->gListVector;  globaldata->gListVector = NULL;
-               
+       
                //saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list
                if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
                else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
@@ -221,7 +222,7 @@ int ClusterCommand::execute(){
                sabundFile.close();
                rabundFile.close();
                listFile.close();
-               
+       
                if (saveCutoff != cutoff) { m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();  }
                
                m->mothurOutEndLine();