X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=61cb2454b52ee9e05cf1027995906371b5463762;hb=55bbd10379db27def51cec72a8819d775f73e45b;hp=c79eb63c31b576359f8b6bf270bea83ba25028d2;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index c79eb63..61cb245 100644
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> ParseListCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -46,6 +46,21 @@ string ParseListCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ParseListCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "list") {  pattern = "[filename],[group],list"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ParseListCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 ParseListCommand::ParseListCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -66,6 +81,7 @@ 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 +138,7 @@ ParseListCommand::ParseListCommand(string option)  {
 					abort = true;
 						
 				}
-			}	
+			}else { m->setListFile(listfile); }	
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
@@ -136,6 +152,7 @@ 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();
@@ -168,16 +185,19 @@ int ParseListCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//set fileroot
-		string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+		map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
 		
 		//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";
+            variables["[group]"] = gGroups[i];
+			string filename = getOutputFileName("list",variables);
 			outputNames.push_back(filename); outputTypes["list"].push_back(filename);
 			m->openOutputFile(filename, *temp);
 		}
@@ -192,8 +212,9 @@ 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 +222,8 @@ 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 +260,10 @@ 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 +281,10 @@ 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 +308,7 @@ 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;
 		}