X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mantelcommand.cpp;h=b9e4df93eff8b19bece4740e22c6526736b1faf2;hp=409eae414779acb412abec7aa295b61e82cd0e16;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index 409eae4..b9e4df9 100644
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -14,12 +14,12 @@
 //**********************************************************************************************************************
 vector<string> MantelCommand::setParameters(){	
 	try {
-		CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip1);
-		CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip2);
-		CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
-		CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none","mantel",false,true,true); parameters.push_back(pphylip1);
+		CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none","mantel",false,true,true); parameters.push_back(pphylip2);
+		CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+		CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -50,6 +50,21 @@ string MantelCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string MantelCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "mantel") {  pattern = "[filename],mantel"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MantelCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 MantelCommand::MantelCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -206,7 +221,9 @@ int MantelCommand::execute(){
 		
 		if (m->control_pressed) { return 0; }
 		
-		string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + "mantel";
+        map<string, string> variables; 
+		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile1));
+		string outputFile = getOutputFileName("mantel",variables);
 		outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
 		ofstream out;