X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.cpp;h=3ec14bf7c06af5883e7eb6d9b3b38449ceac83be;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=ad5823b15e108396ee1b0e0977167c8e4f1fbb22;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/amovacommand.cpp b/amovacommand.cpp
index ad5823b..3ec14bf 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -122,25 +122,25 @@ AmovaCommand::AmovaCommand(string option) {
 				phylipFileName = m->getPhylipFile(); 
 				if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setPhylipFile(phylipFileName); }
 			
 			//check for required parameters
 			designFileName = validParameter.validFile(parameters, "design", true);
-			if (designFileName == "not open") { abort = true; }
+			if (designFileName == "not open") { designFileName = ""; abort = true; }
 			else if (designFileName == "not found") {
 				//if there is a current design file, use it
 				designFileName = m->getDesignFile(); 
 				if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }				
-			}	
+			}else { m->setDesignFile(designFileName); }	
 
 			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";