X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniqueseqscommand.cpp;h=7481416f649ddad983877ab02cac08e5668316d1;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=fb02764e93cc8ca2494773aebeccab857e58f378;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index fb02764..7481416 100644
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -36,7 +36,7 @@ string DeUniqueSeqsCommand::getHelpString(){
 		helpString += "The deunique.seqs command should be in the following format: \n";
 		helpString += "deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n";	
 		helpString += "Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -64,6 +64,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(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();
@@ -113,7 +114,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
 				fastaFile = m->getFastaFile(); 
 				if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setFastaFile(fastaFile); }	
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -127,7 +128,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
 				nameFile = m->getNameFile(); 
 				if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setNameFile(nameFile); }
 		}
 
 	}
@@ -154,14 +155,14 @@ int DeUniqueSeqsCommand::execute() {
 		m->openOutputFile(outFastaFile, out);
 		
 		readNamesFile();
-		if (m->control_pressed) {  out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+		if (m->control_pressed) {  out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
 		
 		ifstream in;
 		m->openInputFile(fastaFile, in);
 		
 		while (!in.eof()) {
 		
-			if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+			if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
 			
 			Sequence seq(in); m->gobble(in);
 			
@@ -195,7 +196,7 @@ int DeUniqueSeqsCommand::execute() {
 			}
 		}
 				
-		if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();