X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=5425c41a917f4b02d67c5b4dfcb63e1b2fc6159b;hb=fdfbfe59134dd7dd3e49d90609d129128ba2d370;hp=98bdcb2cba6cb726f9d793baca1c78f785a04c00;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 98bdcb2..5425c41 100644
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -37,7 +37,7 @@ string GetSAbundCommand::getHelpString(){
 		helpString += "Example get.sabund().\n";
 		helpString += "The default value for label is all labels in your inputfile.\n";
 		helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -45,7 +45,26 @@ string GetSAbundCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string GetSAbundCommand::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 == "sabund")            {   outputFileName = "sabund";  }
+            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, "GetSAbundCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 GetSAbundCommand::GetSAbundCommand(){	
 	try {
@@ -67,6 +86,7 @@ GetSAbundCommand::GetSAbundCommand(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();
@@ -113,12 +133,12 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else {  format = "list"; inputfile = listfile; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
-			else {  format = "rabund"; inputfile = rabundfile; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 		
 						//check for optional parameter and set defaults
@@ -165,7 +185,7 @@ int GetSAbundCommand::execute(){
 	try {
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-		filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund";
+		filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("sabund");
 		m->openOutputFile(filename, out);
 		
 		input = new InputData(inputfile, format);
@@ -177,7 +197,7 @@ int GetSAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input; return 0; }
+		if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input; return 0; }
 
 		
 		while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -186,9 +206,8 @@ int GetSAbundCommand::execute(){
 					m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 					
 					sabund->print(out);
-					delete sabund;
 					
-				if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+				if (m->control_pressed) { outputTypes.clear();  out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
 					processedLabels.insert(sabund->getLabel());
 					userLabels.erase(sabund->getLabel());
@@ -202,9 +221,8 @@ int GetSAbundCommand::execute(){
 					
 					m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 					sabund->print(out);
-					delete sabund;
 					
-					if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+					if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
 					processedLabels.insert(sabund->getLabel());
 					userLabels.erase(sabund->getLabel());
@@ -242,7 +260,7 @@ int GetSAbundCommand::execute(){
 			sabund->print(out);
 			delete sabund;
 			
-			if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; return 0; }
 			
 		}