X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.cpp;h=7569a4be3113144a96048f5a4d624d271c15b9f4;hb=f687723a8357916e86a05116978e6869b039ce36;hp=c4ef741f80c22bc784df4e6916f4a214fb2feacd;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index c4ef741..7569a4b 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -50,6 +50,26 @@ string BinSeqCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "fasta"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "BinSeqCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 BinSeqCommand::BinSeqCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -138,6 +158,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 				else { 	m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (fastafile == "not open") { abort = true; }	
+			else { m->setFastaFile(fastafile); }
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not found") { 			
@@ -146,6 +167,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (listfile == "not open") { listfile = ""; abort = true; }	
+			else { m->setListFile(listfile); }
 			
 			//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"){	
@@ -165,12 +187,19 @@ BinSeqCommand::BinSeqCommand(string option) {
 			}
 			
 			namesfile = validParameter.validFile(parameters, "name", true);
-			if (namesfile == "not open") { abort = true; }	
+			if (namesfile == "not open") { namesfile = ""; abort = true; }	
 			else if (namesfile == "not found") { namesfile = ""; }
+			else {  m->setNameFile(namesfile); }
 
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
 			else if (groupfile == "not found") { groupfile = ""; }
+			else { m->setGroupFile(groupfile); }
+			
+			if (namesfile == ""){
+				vector<string> files; files.push_back(fastafile); 
+				parser.getNameFile(files);
+			}
 			
 		}
 	}
@@ -217,12 +246,12 @@ int BinSeqCommand::execute(){
 				
 		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 input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
+			if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
 			
 			if(allLines == 1 || labels.count(list->getLabel()) == 1){
 				
 				error = process(list);	
-				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
+				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
 							
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
@@ -235,7 +264,7 @@ int BinSeqCommand::execute(){
 				list = input->getListVector(lastLabel);
 				
 				error = process(list);	
-				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+				if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 													
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
@@ -250,7 +279,7 @@ int BinSeqCommand::execute(){
 			list = input->getListVector();
 		}
 		
-		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
+		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }	
 
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -271,7 +300,7 @@ int BinSeqCommand::execute(){
 			list = input->getListVector(lastLabel);
 				
 			error = process(list);	
-			if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+			if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		} delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 			
 			delete list;  
 		}
@@ -280,7 +309,7 @@ int BinSeqCommand::execute(){
 		delete fasta; 
 		if (groupfile != "") {  delete groupMap;   } 
 		
-		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		}  return 0; }	
+		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);		}  return 0; }	
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -335,8 +364,8 @@ int BinSeqCommand::process(ListVector* list) {
 	try {
 				string binnames, name, sequence;
 				
-				string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
-				m->openOutputFile(outputFileName, out);
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta");
+        m->openOutputFile(outputFileName, out);
 				
 				//save to output list of output file names
 				outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);