X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.cpp;h=223e5dbb86600907fafaafdf5af48ee665adfc5b;hb=8e3e7b1e124f45cb1f2ca9d764ff67fa9b2e532b;hp=9d817a212cc2ad2ee3a330b982d96cffe251bdce;hpb=7ecb96ba54980d303fa066b4c29dae1e5a5be5b9;p=mothur.git

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 9d817a2..223e5db 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -139,15 +139,17 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(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); }	
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
-			else if (namefile == "not found") { namefile = ""; }	
+			if (namefile == "not open") { namefile = ""; abort = true; }
+			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
 			else if (listfile == "not found") { listfile = "";  }	
+			else { m->setListFile(listfile); }
 			
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; }
@@ -157,11 +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) {
@@ -204,7 +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);
@@ -221,7 +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;
@@ -274,7 +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){			
 					
@@ -312,7 +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;