X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.cpp;h=c4260fb096dd8b0b253f5239f7ce265376d24ed5;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=8e3edd573b40706458c0b4c8a5803b6ed2265b14;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/amovacommand.cpp b/amovacommand.cpp
index 8e3edd5..c4260fb 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -35,14 +35,14 @@ vector<string> AmovaCommand::setParameters(){
 string AmovaCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\n";
-		helpString += "The amova command outputs a .amova file. \n";
-		helpString += "The amova command parameters are phylip, iters, and alpha.  The phylip and design parameters are required, unless you have valid current files.\n";
-		helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required. \n";
-		helpString += "The design file looks like the group file.  It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.\n";
-		helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n";
-		helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n\n";
+		helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.";
+		helpString += "The amova command outputs a .amova file.";
+		helpString += "The amova command parameters are phylip, iters, and alpha.  The phylip and design parameters are required, unless you have valid current files.";
+		helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required.";
+		helpString += "The design file looks like the group file.  It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.";
+		helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000.";
+		helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).";
+		helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -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);