X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlabelcommand.cpp;h=3191d5dda80670b8490203032e35170cf7642044;hb=c3396974063d6efc5e5850ddf4ed8ab65cc94bb9;hp=e0c17204e7c732ed180fd134a1a7c0d05a105c40;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index e0c1720..3191d5d 100644
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -9,51 +9,75 @@
 
 #include "getlabelcommand.h"
 
+//**********************************************************************************************************************
+vector<string> GetlabelCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetlabelCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetlabelCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetlabelCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetlabelCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"list","rabund","sabund", "or"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetlabelCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
-GetlabelCommand::GetlabelCommand(string option){
+GetlabelCommand::GetlabelCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
-			if (option != "") { cout << "There are no valid parameters for the get.label command." << endl; abort = true; }
-			
-			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label command." << endl; abort = true; }				
+			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); m->mothurOutEndLine(); abort = true; }				
 		}
 
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function GetlabelCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GetlabelCommand class function GetlabelCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-			
 }
 //**********************************************************************************************************************
 
 void GetlabelCommand::help(){
 	try {
-		cout << "The get.label command can only be executed after a successful read.otu command." << "\n";
-		cout << "You may not use any parameters with the get.label command." << "\n";
-		cout << "The get.label command should be in the following format: " << "\n";
-		cout << "get.label()" << "\n";
-		cout << "Example get.label()." << "\n";
+		m->mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
+		m->mothurOut("You may not use any parameters with the get.label command.\n");
+		m->mothurOut("The get.label command should be in the following format: \n");
+		m->mothurOut("get.label()\n");
+		m->mothurOut("Example get.label().\n");
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GetlabelCommand", "help");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GetlabelCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 //**********************************************************************************************************************
@@ -66,34 +90,35 @@ GetlabelCommand::~GetlabelCommand(){
 int GetlabelCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		filename = globaldata->inputFileName;
 		ifstream in;
-		openInputFile(filename, in);
+		m->openInputFile(filename, in);
 		string label;
 		int numBins = 0;
 		int count = -1;
 		while(in.good()) {
+			
+			if (m->control_pressed) { in.close();  return 0; }
+			
 			if(count > numBins)
 				count = 0;
 			if(count == 0) {
-				cout << label << "\n";
+				m->mothurOut(label); m->mothurOutEndLine();
 				in >> numBins;
 			}
 			in >> label;
 			count++;
 		}	
+		
+		in.close();
 		return 0;	
 	}
 
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GetlabelCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GetlabelCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }