X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makegroupcommand.cpp;h=77c2a2911468fe8c0cd123eddce3346b02a4c54c;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=e7704642874d050a3de7625a28ed3fae390fe653;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index e770464..77c2a29 100644
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -16,6 +16,7 @@ vector<string> MakeGroupCommand::setParameters(){
 	try {
 		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+		CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 		
@@ -47,6 +48,26 @@ string MakeGroupCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string MakeGroupCommand::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 == "group")             {   outputFileName =  "groups";         }
+            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, "MakeGroupCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 MakeGroupCommand::MakeGroupCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -159,13 +180,13 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
-						}else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
+						}else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  m->setFastaFile(fastaFileNames[i]); }
 					}
 				}
 				
 				//prevent giantic file name
-				if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
-				else {  filename += "groups";  }
+				if (fastaFileNames.size() > 3) { filename = outputDir + "merge." + getOutputFileNameTag("group"); }
+				else {  filename += getOutputFileNameTag("group");  }
 				
 				//make sure there is at least one valid file left
 				if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
@@ -205,7 +226,7 @@ int MakeGroupCommand::execute(){
 		
 		for (int i = 0; i < fastaFileNames.size(); i++) {
 		
-			if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
 			
 			ifstream in;
 			m->openInputFile(fastaFileNames[i], in);
@@ -214,7 +235,7 @@ int MakeGroupCommand::execute(){
 				
 				Sequence seq(in, "no align"); m->gobble(in);
 				
-				if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); remove(filename.c_str()); return 0; }
+				if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); m->mothurRemove(filename); return 0; }
 				
 				if (seq.getName() != "") {	out << seq.getName() << '\t' << groupsNames[i] << endl;		}
 			}