X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitgroupscommand.cpp;h=af3ca665b5791d0001141f27192b78aab171d71a;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=113439c9220429f4d9466a72a579c5aa2caa10ae;hpb=d0cceb86216f1174afa51582a51490294912b00e;p=mothur.git

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 113439c..af3ca66 100644
--- 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);