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

[mothur.git] / getcoremicrobiomecommand.cpp

diff --git a/getcoremicrobiomecommand.cpp b/getcoremicrobiomecommand.cpp
index 47dc963f1bf657ce334326d90d28068df1be44d7..63af3abb3a595cff133a2caac91dea1aa1e420c1 100644 (file)
--- a/getcoremicrobiomecommand.cpp
+++ b/getcoremicrobiomecommand.cpp
@@ -51,6 +51,27 @@ string GetCoreMicroBiomeCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string GetCoreMicroBiomeCommand::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 == "coremicrobiome") {  outputFileName =  "core.microbiome"; }
+            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, "GetCoreMicroBiomeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){  
        try {
@@ -287,7 +308,7 @@ int GetCoreMicroBiomeCommand::execute(){
 int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
        try {
         
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiome";
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + getOutputFileNameTag("coremicrobiome");
         outputNames.push_back(outputFileName);  outputTypes["coremicrobiome"].push_back(outputFileName);
                ofstream out;
                m->openOutputFile(outputFileName, out);