X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=3b03f3694967d6d480ba0dc00153454c7e8b074f;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=b7dd7153609ada80c297d5d51cab70d3cae5ebc4;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index b7dd715..3b03f36 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -10,16 +10,63 @@
 #include "getrabundcommand.h"
 
 //**********************************************************************************************************************
-
+vector<string> GetRAbundCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"label","sorted","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRAbundCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+GetRAbundCommand::GetRAbundCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		vector<string> tempOutNames;
+		outputTypes["rabund"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetRAbundCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRAbundCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetRAbundCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"list"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRAbundCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(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
@@ -42,6 +89,10 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
 				outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it	
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["rabund"] = tempOutNames;
+			
 			//make sure the user has already run the read.otu command
 			if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; }
 			
@@ -106,7 +157,7 @@ GetRAbundCommand::~GetRAbundCommand(){}
 int GetRAbundCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//read first line
 		read = new ReadOTUFile(globaldata->inputFileName);	
@@ -120,7 +171,7 @@ int GetRAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; globaldata->gListVector = NULL;  return 0; }
+		if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str());  delete list; globaldata->gListVector = NULL;  return 0; }
 		
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
@@ -129,7 +180,7 @@ int GetRAbundCommand::execute(){
 					rabund = new RAbundVector();				
 					*rabund = (list->getRAbundVector());
 					
-					if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+					if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 
 					
 					if(sorted)	{   rabund->print(out);				}
@@ -151,7 +202,7 @@ int GetRAbundCommand::execute(){
 					rabund = new RAbundVector();
 					*rabund = (list->getRAbundVector());
 					
-					if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+					if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 					
 					if(sorted)	{   rabund->print(out);				}
 					else		{	rabund->nonSortedPrint(out);	}
@@ -193,7 +244,7 @@ int GetRAbundCommand::execute(){
 			rabund = new RAbundVector();
 			*rabund = (list->getRAbundVector());
 			
-			if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 			
 			if(sorted)	{   rabund->print(out);				}
 			else		{	rabund->nonSortedPrint(out);	}
@@ -204,13 +255,20 @@ int GetRAbundCommand::execute(){
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(filename); m->mothurOutEndLine();	
+		m->mothurOut(filename); m->mothurOutEndLine();	outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
 		m->mothurOutEndLine();
 		
 		out.close(); 
 		
 		globaldata->gListVector = NULL;
 		
+		//set rabund file as new current rabundfile
+		string current = "";
+		itTypes = outputTypes.find("rabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+		}
+		
 		return 0;		
 	}