added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow...

[mothur.git] / mantelcommand.cpp

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index 0c0163b538a747ca5b9b4eb82ef57a06ca302b91..f3259e6096c3e0c1373e1c091078c9ceac377f82 100644 (file)
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -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;