X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=2ae807c65c7d9f4ec814564fb5823ccd3f925471;hb=7c08fa69c0b89e7a08341af2aa724f206f182075;hp=9260a5c0fea40ce63bf77ed4f20a12f437b9a08a;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 9260a5c..2ae807c 100644
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -10,16 +10,62 @@
 #include "getsabundcommand.h"
 
 //**********************************************************************************************************************
-
+vector<string> GetSAbundCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"label","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetSAbundCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+GetSAbundCommand::GetSAbundCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		vector<string> tempOutNames;
+		outputTypes["sabund"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"list","rabund"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 GetSAbundCommand::GetSAbundCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		labels.clear();
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -36,10 +82,14 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["sabund"] = tempOutNames;
+		
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			string outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
 				outputDir = "";	
-				outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it	
 			}
 
 			//make sure the user has already run the read.otu command
@@ -50,7 +100,7 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; }
 			else { 
-				if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 				else { allLines = 1;  }
 			}
 			
@@ -61,8 +111,8 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
 			}
 				
 			if (abort == false) {
-				filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund";
-				openOutputFile(filename, out);
+				filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
+				m->openOutputFile(filename, out);
 			}
 		}
 
@@ -101,7 +151,7 @@ GetSAbundCommand::~GetSAbundCommand(){
 int GetSAbundCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 	
 		//using order vector so you don't have to distinguish between the list and rabund files
 		read = new ReadOTUFile(globaldata->inputFileName);	
@@ -115,7 +165,7 @@ int GetSAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL;  return 0; }
+		if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
 		
 		while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -127,13 +177,13 @@ int GetSAbundCommand::execute(){
 					sabund->print(out);
 					delete sabund;
 					
-					if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL;  return 0; }
+					if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
 					processedLabels.insert(order->getLabel());
 					userLabels.erase(order->getLabel());
 			}
 			
-			if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+			if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 					string saveLabel = order->getLabel();
 					
 					delete order;		
@@ -145,7 +195,7 @@ int GetSAbundCommand::execute(){
 					sabund->print(out);
 					delete sabund;
 					
-					if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL;  return 0; }
+					if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
 					processedLabels.insert(order->getLabel());
 					userLabels.erase(order->getLabel());
@@ -185,18 +235,17 @@ int GetSAbundCommand::execute(){
 			sabund->print(out);
 			delete sabund;
 			
-			if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL;  return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 			
 			delete order;
 		}
 		globaldata->gorder = NULL;
-		delete read; delete input;
 
 		out.close();
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(filename); m->mothurOutEndLine();	
+		m->mothurOut(filename); m->mothurOutEndLine();	outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
 		m->mothurOutEndLine();
 		
 		return 0;