X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=bb096d8646873f74c42bd8970b9eef9693a3252e;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=6e4082e0c139b76435aa073cd1f0c7013b85dca3;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 6e4082e..bb096d8 100644
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -37,7 +37,7 @@ string ParseListCommand::getHelpString(){
 		helpString += "The label parameter is used to read specific labels in your input you want to use.\n";
 		helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n";
 		helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -66,6 +66,7 @@ ParseListCommand::ParseListCommand(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();
@@ -122,7 +123,7 @@ ParseListCommand::ParseListCommand(string option)  {
 					abort = true;
 						
 				}
-			}	
+			}else { m->setListFile(listfile); }	
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
@@ -136,6 +137,7 @@ ParseListCommand::ParseListCommand(string option)  {
 					if (error == 1) { abort = true; }
 				}else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();  abort = true; } 
 			}else {  
+				m->setGroupFile(groupfile);
 				groupMap = new GroupMap(groupfile);
 				
 				int error = groupMap->readMap();
@@ -173,11 +175,12 @@ int ParseListCommand::execute(){
 		//fill filehandles with neccessary ofstreams
 		int i;
 		ofstream* temp;
-		for (i=0; i<groupMap->namesOfGroups.size(); i++) {
+		vector<string> gGroups = groupMap->getNamesOfGroups();
+		for (i=0; i<gGroups.size(); i++) {
 			temp = new ofstream;
-			filehandles[groupMap->namesOfGroups[i]] = temp;
+			filehandles[gGroups[i]] = temp;
 			
-			string filename = fileroot +  groupMap->namesOfGroups[i] + ".list";
+			string filename = fileroot +  gGroups[i] + ".list";
 			outputNames.push_back(filename); outputTypes["list"].push_back(filename);
 			m->openOutputFile(filename, *temp);
 		}
@@ -192,8 +195,9 @@ int ParseListCommand::execute(){
 		
 		if (m->control_pressed) { 
 			delete input; delete list; delete groupMap;
-			for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+			vector<string> gGroups = groupMap->getNamesOfGroups();
+			for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 			return 0;
 		}
 		
@@ -201,8 +205,8 @@ int ParseListCommand::execute(){
 		
 			if (m->control_pressed) { 
 				delete input; delete list; delete groupMap;
-				for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+				for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 				return 0;
 			}
 			
@@ -239,10 +243,10 @@ int ParseListCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-				delete input; delete groupMap;
-				for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-				return 0;
+			delete input; delete groupMap;
+			for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+			return 0;
 		}
 		
 		//output error messages about any remaining user labels
@@ -260,10 +264,10 @@ int ParseListCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-				delete input; delete groupMap;
-				for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-				return 0;
+			delete input; delete groupMap;
+			for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+			return 0;
 		}
 		
 		//run last label if you need to
@@ -287,7 +291,7 @@ int ParseListCommand::execute(){
 		delete input;
 		
 		if (m->control_pressed) { 
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 			return 0;
 		}