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

[mothur.git] / summaryqualcommand.cpp

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 5c175106ecb2584d07ca15a06c71f27284a3571c..5d7971349656d4400e5d41a24c15e576ccdf57f7 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -45,7 +45,26 @@ string SummaryQualCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string SummaryQualCommand::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 =  "qual.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, "SummaryQualCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 SummaryQualCommand::SummaryQualCommand(){      
        try {
@@ -189,7 +208,7 @@ int SummaryQualCommand::execute(){
                if (m->control_pressed) {  return 0; }
                
                //print summary file
-               string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary";
+               string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
                printQual(summaryFile, position, averageQ, scores);
                
                if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }