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

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index d3c7fa48128246f8f4cb28ad53727329b3de856c..6a0eb259379df8480341a5542a7456fc674aea74 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -86,7 +86,27 @@ string ClearcutCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string ClearcutCommand::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 == "tree") {  outputFileName =  "tre"; }
+            else if (type == "matrixout") {  outputFileName =  ""; }
+            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, "ClearcutCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ClearcutCommand::ClearcutCommand(){    
        try {
@@ -244,7 +264,7 @@ int ClearcutCommand::execute() {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //prepare filename
-               string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
+               string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + getOutputFileNameTag("tree");
                outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
                
                vector<char*> cPara;