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

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 9beca6aa96f75a58891b5326b5cbd94209701656..1b69a25d4af7e638dbf48a64baec2390f37dcfec 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -417,10 +417,11 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                        
                        vector<string> namesOfSeqsInThisBin;
                        
-                       string names = shared->get(i);  
-                       while ((names.find_first_of(',') != -1)) { 
-                               string name = names.substr(0,names.find_first_of(','));
-                               names = names.substr(names.find_first_of(',')+1, names.length());
+                       string names = shared->get(i); 
+            vector<string> binNames;
+            m->splitAtComma(names, binNames);
+                       for(int j = 0; j < binNames.size(); j++) {
+                               string name = binNames[j];
                                
                                //find group
                                string seqGroup = groupMap->getGroup(name);
@@ -436,20 +437,6 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                                else {  atLeastOne[seqGroup]++;  }
                        }
                        
-                       //get last name
-                       string seqGroup = groupMap->getGroup(names);
-                       if (output != "accnos") {
-                               namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
-                       }else {  namesOfSeqsInThisBin.push_back(names); }
-                       
-                       if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
-                       
-                       //is this seq in one of hte groups we care about
-                       it = groupFinder.find(seqGroup);
-                       if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
-                       else {  atLeastOne[seqGroup]++;  }
-                       
-                       
                        //make sure you have at least one seq from each group you want
                        bool sharedByAll = true;
                        map<string, int>::iterator it2;