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

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index bcff0fcd820a497da04405bef0ddb42d7d60ded9..951b2008b062c26c5fabb54dfd8ef2d2a858da67 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -51,7 +51,28 @@ string PreClusterCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string PreClusterCommand::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 == "fasta") {  outputFileName =  "precluster" + m->getExtension(inputName); }
+            else if (type == "name") {  outputFileName =  "precluster.names"; }
+            else if (type == "map") {  outputFileName =  "precluster.map"; }
+            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, "PreClusterCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 PreClusterCommand::PreClusterCommand(){        
        try {
@@ -184,9 +205,9 @@ int PreClusterCommand::execute(){
                int start = time(NULL);
                
                string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
-               string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
-               string newNamesFile = fileroot + "precluster.names";
-               string newMapFile = fileroot + "precluster.map"; //add group name if by group
+               string newFastaFile = fileroot + getOutputFileNameTag("fasta", fastafile);
+               string newNamesFile = fileroot + getOutputFileNameTag("name");
+               string newMapFile = fileroot + getOutputFileNameTag("map"); //add group name if by group
                outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
                outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);