X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.cpp;h=c4260fb096dd8b0b253f5239f7ce265376d24ed5;hb=957d67f7d8bbadfd2930de061e89fd9b149270fd;hp=af867de3bf4811e00f98904f06935ac95a8313f3;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/amovacommand.cpp b/amovacommand.cpp
index af867de..c4260fb 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -50,7 +50,26 @@ string AmovaCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string AmovaCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string tag = "";
+		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 == "amova") {  tag = "amova"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file.\n");  }
+        }
+        return tag;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AmovaCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 AmovaCommand::AmovaCommand(){	
 	try {
@@ -71,6 +90,7 @@ AmovaCommand::AmovaCommand(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();
@@ -122,25 +142,25 @@ 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) {
@@ -174,13 +194,20 @@ 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";				
+		string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("amova");				
 		m->openOutputFile(AMOVAFileName, AMOVAFile);
 		outputNames.push_back(AMOVAFileName); outputTypes["amova"].push_back(AMOVAFileName);
 		
@@ -282,7 +309,7 @@ double AmovaCommand::runAMOVA(ofstream& AMOVAFile, map<string, vector<int> > gro
 		m->mothurOut("df\t" + toString(dfAmong) + '\t' + toString(dfWithin) + '\t' + toString(dfTotal) + '\n');
 
 		AMOVAFile << "MS\t" << MSAmong << '\t' << MSWithin << endl << endl;
-		m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n");
+		m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n\n");
 
 		AMOVAFile << "Fs:\t" << Fs << endl;
 		m->mothurOut("Fs:\t" + toString(Fs) + '\n');