added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / splitgroupscommand.cpp

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 113439c9220429f4d9466a72a579c5aa2caa10ae..af3ca665b5791d0001141f27192b78aab171d71a 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -51,6 +51,27 @@ string SplitGroupCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string SplitGroupCommand::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 =  "fasta";   }
+            else if (type == "name")        {   outputFileName =  "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, "SplitGroupCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 SplitGroupCommand::SplitGroupCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -125,7 +146,7 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
 
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
                        else { m->setNameFile(namefile); }
                
@@ -151,6 +172,11 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
                                                
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(groupfile);      }
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                }
 
        }
@@ -183,8 +209,8 @@ int SplitGroupCommand::execute(){
                        
                        m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
                        
-                       string newFasta = fastafileRoot + Groups[i] + ".fasta";
-                       string newName = namefileRoot + Groups[i] + ".names";
+                       string newFasta = fastafileRoot + Groups[i] + "." + getOutputFileNameTag("fasta");
+                       string newName = namefileRoot + Groups[i] + "." + getOutputFileNameTag("name");
                        
                        parser->getSeqs(Groups[i], newFasta, false);
                        outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);