X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.cpp;h=223e5dbb86600907fafaafdf5af48ee665adfc5b;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=9172819bd78f39dfee97b94c4c4b24c79bd080ae;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 9172819..223e5db 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -142,7 +142,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 			}else { m->setFastaFile(fastafile); }	
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
 			
@@ -159,11 +159,15 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 			}
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);  if (temp == "not found") { temp = "100"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			//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"){	outputDir = m->hasPath(fastafile);	}
-
+			
+			if (namefile == ""){
+				vector<string> files; files.push_back(fastafile); 
+				parser.getNameFile(files);
+			}
 		}
 	}
 	catch(exception& e) {
@@ -206,7 +210,7 @@ int ConsensusSeqsCommand::execute(){
 			int seqLength = 0;
 			for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
 				
-				if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+				if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 				
 				string seq = fastaMap[it->second];
 				seqs.push_back(seq);
@@ -223,7 +227,7 @@ int ConsensusSeqsCommand::execute(){
 			//get counts
 			for (int j = 0; j < seqLength; j++) {
 				
-				if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+				if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 				
 				vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
 				int numDots = 0;
@@ -276,7 +280,7 @@ int ConsensusSeqsCommand::execute(){
 			//as long as you are not at the end of the file or done wih the lines you want
 			while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				
-				if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } delete list; delete input;  return 0;  }
+				if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } delete list; delete input;  return 0;  }
 				
 				if(allLines == 1 || labels.count(list->getLabel()) == 1){			
 					
@@ -314,7 +318,7 @@ int ConsensusSeqsCommand::execute(){
 			}
 			
 			
-			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0;  }
+			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } if (list != NULL) { delete list; } delete input; return 0;  }
 			
 			//output error messages about any remaining user labels
 			set<string>::iterator it;