X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlabelcommand.cpp;h=1c08eb1fab8905674700bdc440a93ebd38b88a4f;hb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;hp=c5a59acae780cc5b404fd7236712de164b3adc88;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index c5a59ac..1c08eb1 100644
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -3,27 +3,46 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 1/30/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "getlabelcommand.h"
 
+//**********************************************************************************************************************
 
-
-GetlabelCommand::GetlabelCommand(){
+GetlabelCommand::GetlabelCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			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";
+}
+//**********************************************************************************************************************
+
+void GetlabelCommand::help(){
+	try {
+		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) {
+		m->errorOut(e, "GetlabelCommand", "help");
 		exit(1);
-	}	
-			
+	}
 }
 
 //**********************************************************************************************************************
@@ -35,34 +54,36 @@ GetlabelCommand::~GetlabelCommand(){
 
 int GetlabelCommand::execute(){
 	try {
+		
+		if (abort == true) { return 0; }
+		
 		filename = globaldata->inputFileName;
 		ifstream in;
 		openInputFile(filename, in);
 		string label;
 		int numBins = 0;
 		int count = -1;
-		while(in.good())
-		{
+		while(in.good()) {
+			
+			if (m->control_pressed) { in.close();  return 0; }
+			
 			if(count > numBins)
 				count = 0;
-			if(count == 0)
-			{
-				cout << label << "\n";
+			if(count == 0) {
+				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);
-	}	
 }