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

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 35437e760ac636e51cf9f960d8c36e8a6dfce47e..4ebde29f912f6e9a02d88dbee301488b52d4a082 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -95,6 +95,27 @@ string GetOTURepCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string GetOTURepCommand::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 =  "rep.fasta";   }
+            else if (type == "name")        {   outputFileName =  "rep.names";   }
+            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, "GetOTURepCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetOTURepCommand::GetOTURepCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -771,7 +792,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                map<string, ofstream*> filehandles;
                
                if (Groups.size() == 0) { //you don't want to use groups
-                       outputNamesFile  = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
+                       outputNamesFile  = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + getOutputFileNameTag("name");
                        m->openOutputFile(outputNamesFile, newNamesOutput);
                        outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); 
                        outputNameFiles[outputNamesFile] = processList->getLabel();
@@ -780,7 +801,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                        for (int i=0; i<Groups.size(); i++) {
                                temp = new ofstream;
                                filehandles[Groups[i]] = temp;
-                               outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
+                               outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + "." + getOutputFileNameTag("name");
                                
                                m->openOutputFile(outputNamesFile, *(temp));
                                outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile);
@@ -868,7 +889,7 @@ int GetOTURepCommand::processFastaNames(string filename, string label) {
 
                //create output file
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + ".rep.fasta";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("fasta");
                m->openOutputFile(outputFileName, out);
                vector<repStruct> reps;
                outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);