working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index 141673375fb8bb1a37e67980df9708fe6d2da126..de277ab6edad4828ee5a35f37474cd4a3a8eee55 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -174,10 +174,17 @@ int AmovaCommand::execute(){
                //link designMap to rows/columns in distance matrix
                map<string, vector<int> > origGroupSampleMap;
                for(int i=0;i<sampleNames.size();i++){
-                       origGroupSampleMap[designMap->getGroup(sampleNames[i])].push_back(i);
+                       string group = designMap->getGroup(sampleNames[i]);
+                       
+                       if (group == "not found") {
+                               m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
+                       }else { origGroupSampleMap[group].push_back(i); }
+                       
                }
                int numGroups = origGroupSampleMap.size();
                
+               if (m->control_pressed) { delete designMap; return 0; }
+               
                //create a new filename
                ofstream AMOVAFile;
                string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName))  + "amova";