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

[mothur.git] / cooccurrencecommand.cpp

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index e4c915d6a14e4a9755a17d64c073fdda1440803b..00de4d6ee612439732207872eba327b8a03f699e 100644 (file)
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -51,6 +51,26 @@ string CooccurrenceCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string CooccurrenceCommand::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 == "summary") {  outputFileName =  "cooccurence.summary"; }
+            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, "CooccurrenceCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 CooccurrenceCommand::CooccurrenceCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -176,7 +196,7 @@ int CooccurrenceCommand::execute(){
                set<string> userLabels = labels;
 
         ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
         m->openOutputFile(outputFileName, out);
         outputNames.push_back(outputFileName);  outputTypes["summary"].push_back(outputFileName);
         out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);