added large parameter to mgcluster along with new rabund support

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 06f05192ad1e91a1c85b2de8e986039d82d5c375..508b05f01d432a83d387b9b5b072d59a4b0fdcd5 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -247,8 +247,8 @@ int MGClusterCommand::execute(){
         }
         
                 
-               list = new ListVector(nameMap->getListVector());
-               RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+               //list = new ListVector(nameMap->getListVector());
+               //rabund = new RAbundVector(list->getRAbundVector());
                
                if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
                
@@ -519,8 +519,8 @@ int MGClusterCommand::execute(){
                        m->mothurRemove(overlapFile);
                }
                
-               delete list; 
-               delete rabund;
+               delete list;
+               if (!large) {delete rabund;}
                listFile.close();
                sabundFile.close();
                rabundFile.close();

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 96410bfc39f1a28140357cdf2ee9233fe5e51bc2..ce3ffec189fa50d025a0fa0a1f39ef8faaa6da93 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -47,7 +47,7 @@ private:
        HCluster* hcluster;
        ListVector* list;
        ListVector oldList;
-        RAbundVector rav;
+    RAbundVector rav;
        vector<seqDist> overlapMatrix;
        vector<string> outputNames;
        
@@ -62,7 +62,7 @@ private:
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
-        void createRabund(map<string, int>);
+    void createRabund(map<string, int>);
 
 };