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

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index e83c6035731aa5509655dcd25a7a45995c1a0004..8a18fc755e66a04d6013ecbf7dd088821088501a 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -46,7 +46,26 @@ string CountSeqsCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string CountSeqsCommand::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 =  "seq.count"; }
+            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, "CountSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 CountSeqsCommand::CountSeqsCommand(){  
        try {
@@ -147,7 +166,7 @@ int CountSeqsCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("summary");
                m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
                out << "Representative_Sequence\ttotal\t";