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

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 115e930969323ba4655e0b5ba5c2a8e1166a1397..c34f25de509c78b9e1b97b7c303142864e3c7e01 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -802,7 +802,7 @@ string ShhherCommand::createNamesFile(){
                        duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
                }
                
-               string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName) + getOutputFileNameTag("name");
+               string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
                
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
@@ -2309,7 +2309,7 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 if (m->control_pressed) { break; }
                 
                 vector<int> otuCounts(numOTUs, 0);
-                for(int i=0;i<numSeqs;i++)     {       otuCounts[otuData[i]]++;        }
+                for(int j=0;j<numSeqs;j++)     {       otuCounts[otuData[j]]++;        }
                 
                 calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);        
                 
@@ -2632,7 +2632,7 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil
                read->read(clusterNameMap);
         
                ListVector* list = read->getListVector();
-               SparseMatrix* matrix = read->getMatrix();
+               SparseDistanceMatrix* matrix = read->getDMatrix();
                
                delete read; 
                delete clusterNameMap;