X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;h=318a05ec0bee7765f835cce4301d2b7a97d16978;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=f590d8b3baaf67091f59a741a87a23e09c8873b0;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index f590d8b..318a05e 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -46,6 +46,26 @@ string DegapSeqsCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string DegapSeqsCommand::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 =  "ng.fasta"; }
+            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, "DegapSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -193,11 +213,11 @@ int DegapSeqsCommand::execute(){
 			ofstream outFASTA;
 			string tempOutputDir = outputDir;
 			if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
-			string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+			string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("fasta");
 			m->openOutputFile(degapFile, outFASTA);
 			
 			while(!inFASTA.eof()){
-				if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
+				if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} return 0; }
 				 
 				Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 				if (currSeq.getName() != "") {
@@ -210,7 +230,7 @@ int DegapSeqsCommand::execute(){
 			
 			outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
 			
-			if (m->control_pressed) {  outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} return 0; }
 		}
 		
 		//set fasta file as new current fastafile