X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.cpp;h=3ec14bf7c06af5883e7eb6d9b3b38449ceac83be;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=141673375fb8bb1a37e67980df9708fe6d2da126;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/amovacommand.cpp b/amovacommand.cpp
index 1416733..3ec14bf 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -136,11 +136,11 @@ AmovaCommand::AmovaCommand(string option) {
 
 			string temp = validParameter.validFile(parameters, "iters", false);
 			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "alpha", false);
 			if (temp == "not found") { temp = "0.05"; }
-			convert(temp, experimentwiseAlpha); 
+			m->mothurConvert(temp, experimentwiseAlpha); 
 		}
 	}
 	catch(exception& e) {
@@ -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";