X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=homovacommand.cpp;h=006f1e4d5ee0b046e3216b0f470ce5d5c6200aa0;hb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;hp=22fd1bff1b0af5ac23532423f7b42471e1b6b3b3;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/homovacommand.cpp b/homovacommand.cpp
index 22fd1bf..006f1e4 100644
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -49,9 +49,27 @@ string HomovaCommand::getHelpString(){
 		exit(1);
 	}
 }
-
 //**********************************************************************************************************************
-
+string HomovaCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "homova")            {   outputFileName =  "homova";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HomovaCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 HomovaCommand::HomovaCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -139,11 +157,11 @@ 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); 
 		}
 		
 	}
@@ -178,13 +196,19 @@ 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";				
+		string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("homova");				
 		m->openOutputFile(HOMOVAFileName, HOMOVAFile);
 		outputNames.push_back(HOMOVAFileName); outputTypes["homova"].push_back(HOMOVAFileName);