fixed bug in hcluster command

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index 50787e984bd2a3c45cbce0af354fea178771a6b0..233b8e13094cf560ef295522a7cd6a8d552dd55a 100644 (file)
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -12,6 +12,7 @@
 /***********************************************************************/
 
 ReadCluster::ReadCluster(string distfile, float c){
+               globaldata = GlobalData::getInstance();
         distFile = distfile;
                cutoff = c;
 }
@@ -185,24 +186,22 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                        }
                }
                else{
-                       
                        for(int i=1;i<nseqs;i++){
                                in >> name;                
                                rowToName[i] = name;
                                matrixNames.push_back(name);
-                               
+               
                                if(nameMap == NULL){
                                        list->set(i, name);
                                        for(int j=0;j<nseqs;j++){
                                                in >> distance;
-                                               
+                                       
                                                if (distance == -1) { distance = 1000000; }
                                                
                                                if(distance < cutoff && j < i){
                                                        out << i << '\t' << j << '\t' << distance << endl;
                                                }
                                        }
-                                       
                                }
                                else{
                                        if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
@@ -226,11 +225,14 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                out.close();
                
                if(nameMap == NULL){
+                       nameMap = new NameAssignment();
                        for(int i=0;i<matrixNames.size();i++){
                                nameMap->push_back(matrixNames[i]);
                        }
+                       globaldata->nameMap = nameMap;
                }
                
+       
                ifstream in2;
                ofstream out2;