X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.cpp;h=902ac87286e302977d2fe555754a632487e6e43b;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=21cb4c7f622e95bc4a44689ce8ef605703444ec2;hpb=55ec7cde88d5512e177fe9488d5ee13793853bad;p=mothur.git

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 21cb4c7..902ac87 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -71,7 +71,7 @@ ListSeqsCommand::ListSeqsCommand(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();
 			
@@ -257,11 +257,11 @@ int ListSeqsCommand::readFasta(){
 		m->openInputFile(fastafile, in);
 		string name;
 		
-		ofstream out;
-		string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
-		m->openOutputFile(newFastaName, out);
-		int count = 1;
-		string lastName = "";
+		//ofstream out;
+		//string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+		//m->openOutputFile(newFastaName, out);
+		//int count = 1;
+		//string lastName = "";
 		
 		while(!in.eof()){
 			
@@ -269,20 +269,20 @@ int ListSeqsCommand::readFasta(){
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
-			if (lastName == "") { lastName = name; }
-			if (name != lastName) { count = 1; }
-			lastName = name;
+			//if (lastName == "") { lastName = name; }
+			//if (name != lastName) { count = 1; }
+		//	lastName = name;
 			
-			Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
-			newSeq.printSequence(out);
+			//Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
+			//newSeq.printSequence(out);
 			
 			if (name != "") {  names.push_back(name);  }
 			
 			m->gobble(in);
-			count++;
+			//count++;
 		}
 		in.close();	
-		out.close();
+		//out.close();
 		
 		return 0;