X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=homovacommand.cpp;h=9b7ec9fb030becda2b3df217afedcdd40facd4cc;hb=597560b3c23f03d0069082cf096ce65e0c087519;hp=22fd1bff1b0af5ac23532423f7b42471e1b6b3b3;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/homovacommand.cpp b/homovacommand.cpp
index 22fd1bf..9b7ec9f 100644
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -139,11 +139,11 @@ HomovaCommand::HomovaCommand(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); 
 		}
 		
 	}
@@ -178,10 +178,16 @@ int HomovaCommand::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 HOMOVAFile;
 		string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName))  + "homova";