X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mantelcommand.cpp;h=f3259e6096c3e0c1373e1c091078c9ceac377f82;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=c41cde34e92374d4c21a57f51636d2729d464d13;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index c41cde3..f3259e6 100644
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -41,7 +41,7 @@ string MantelCommand::getHelpString(){
 		helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n";
 		helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n";
 		helpString += "The mantel command outputs a .mantel file.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -50,6 +50,26 @@ string MantelCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string MantelCommand::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 == "mantel")             {   outputFileName =  "mantel";       }
+            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, "MantelCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 MantelCommand::MantelCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -69,6 +89,7 @@ MantelCommand::MantelCommand(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 +145,7 @@ MantelCommand::MantelCommand(string option)  {
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found"){	method = "pearson";		}
 			
 			string temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters);
+			m->mothurConvert(temp, iters);
 			
 			if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
 		}
@@ -205,7 +226,7 @@ int MantelCommand::execute(){
 		
 		if (m->control_pressed) { return 0; }
 		
-		string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + "mantel";
+		string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + getOutputFileNameTag("mantel");
 		outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
 		ofstream out;