X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;h=318a05ec0bee7765f835cce4301d2b7a97d16978;hb=3cd964b03f04bc569c4a7d0b99be9908c54c1d44;hp=c90064f190af3421a2f3f6ebc673b1265a1f202a;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index c90064f..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; 
@@ -65,6 +85,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -155,7 +176,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
-						}
+						}else { m->setFastaFile(fastaFileNames[i]); }
 					}
 				}
 				
@@ -192,11 +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() != "") {
@@ -209,7 +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