added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 2d2db08a40ea5e1aa8712902dcd419ddb1ad757a..38d3bdf929f4ffc110f76ab0a55b12d66ef4ad08 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -53,7 +53,28 @@ string PhylotypeCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string PhylotypeCommand::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 == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            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, "PhylotypeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 PhylotypeCommand::PhylotypeCommand(){  
        try {
@@ -198,13 +219,13 @@ int PhylotypeCommand::execute(){
                string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
                
                ofstream outList;
-               string outputListFile = fileroot + "tx.list";
+               string outputListFile = fileroot + "tx." + getOutputFileNameTag("list");
                m->openOutputFile(outputListFile, outList);
                ofstream outSabund;
-               string outputSabundFile = fileroot + "tx.sabund";
+               string outputSabundFile = fileroot + "tx." + getOutputFileNameTag("sabund");
                m->openOutputFile(outputSabundFile, outSabund);
                ofstream outRabund;
-               string outputRabundFile = fileroot + "tx.rabund";
+               string outputRabundFile = fileroot + "tx." + getOutputFileNameTag("rabund");
                m->openOutputFile(outputRabundFile, outRabund);
                
                outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);