X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=homovacommand.cpp;h=9b7ec9fb030becda2b3df217afedcdd40facd4cc;hb=4c302368ef34f0d897afefc7853edf86fb45b9f3;hp=f9d259d2e817d9d4458dc4b54adc218aea6ab5b3;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/homovacommand.cpp b/homovacommand.cpp
index f9d259d..9b7ec9f 100644
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -72,6 +72,7 @@ HomovaCommand::HomovaCommand(string option) {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -124,7 +125,7 @@ HomovaCommand::HomovaCommand(string option) {
 				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);
@@ -134,15 +135,15 @@ HomovaCommand::HomovaCommand(string option) {
 				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); 
 		}
 		
 	}
@@ -177,10 +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";