X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;h=1d83f3bef00d08574a66d7e5ecf21efa148452a4;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=c90064f190af3421a2f3f6ebc673b1265a1f202a;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index c90064f..1d83f3b 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -65,6 +65,7 @@ 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 +156,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
-						}
+						}else { m->setFastaFile(fastaFileNames[i]); }
 					}
 				}
 				
@@ -196,7 +197,7 @@ int DegapSeqsCommand::execute(){
 			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 +210,7 @@ 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