Issues with LimitSwitch

[Lesafian]

Hey guys!

I'm having troubles with programming limit switches. We're using a limit switch to stop our arms from going too low. The problem I'm having, is that the limit switch stops the motor, but then the entire robot stops working. Obviously that's a problem with the code. I'm not sure what to do though. I'll paste all of our robot code.

package org.usfirst.frc.team6077.robot;

import edu.wpi.first.wpilibj.CameraServer;
import edu.wpi.first.wpilibj.Compressor;
import edu.wpi.first.wpilibj.Counter;
import edu.wpi.first.wpilibj.DigitalInput;
import edu.wpi.first.wpilibj.DoubleSolenoid;
import edu.wpi.first.wpilibj.Joystick;
import edu.wpi.first.wpilibj.RobotDrive;
import edu.wpi.first.wpilibj.SampleRobot;
import edu.wpi.first.wpilibj.Solenoid;
import edu.wpi.first.wpilibj.Timer;
import edu.wpi.first.wpilibj.VictorSP;
import edu.wpi.first.wpilibj.command.Scheduler;
import edu.wpi.first.wpilibj.smartdashboard.SendableChooser;
import edu.wpi.first.wpilibj.smartdashboard.SmartDashboard;

public class Robot extends SampleRobot {

	// RobotDrive Declaration
	RobotDrive drive;

	Compressor compressor;
	DoubleSolenoid doublesolenoid;
	Solenoid solenoid;
	
	DigitalInput limitSwitch;
	Counter counter;
	
	CameraServer server;

	Joystick xboxController;

	VictorSP armMotor, slideMotor, drivemotor1, 
	drivemotor2, drivemotor3, drivemotor4;
	
	final String defaultAuto = "Default";
	final String customAuto = "Autonomous Choice 1";
	final String customAuto2 = "Autonomous Choice 2";
	final String customAuto3 = "Autonomous Choice 3";
	final String customAuto4 = "Autonomous Choice 4";
	final String customAuto5 = "Autonomous Choice 5";

	SendableChooser chooser;

	public void robotInit() {

		drivemotor1 = new VictorSP(0);
		drivemotor2 = new VictorSP(1);
		drivemotor3 = new VictorSP(2);
		drivemotor4 = new VictorSP(3);
		armMotor = new VictorSP(5);
		slideMotor = new VictorSP(6);

		compressor = new Compressor(0);
		compressor.setClosedLoopControl(true);
		
		drive = new RobotDrive(drivemotor1, drivemotor2, drivemotor3, drivemotor4);
		drive.setExpiration(0.1);

		xboxController = new Joystick(0);

		doublesolenoid = new DoubleSolenoid(0, 1);
		//solenoid = new Solenoid(2);

		server = CameraServer.getInstance();
		server.setQuality(100);
		server.startAutomaticCapture("cam1");
		
		chooser = new SendableChooser();

		chooser.addDefault("Default Auto", defaultAuto);
		chooser.addObject("Autonomous Choice 1", customAuto);
		chooser.addObject("Autonomous Choice 2", customAuto2);
		chooser.addObject("Autonomous Choice 3", customAuto3);
		chooser.addObject("Autonomous Choice 4", customAuto4);
		chooser.addObject("Autonomous Choice 5", customAuto5);
		SmartDashboard.putData("Autonomous Chooser", chooser);
	}

	public void autonomous() {
		drive.setSafetyEnabled(false);
		String autoSelected = (String) chooser.getSelected();
		System.out.println("Autonomous Mode selected: " + autoSelected);

		switch (autoSelected) {

		case customAuto5:
			break;
		case customAuto4:
			break;
		case customAuto3:
			break;
		case customAuto2:
			break;
		case customAuto:
			break;
		case defaultAuto:
		default:
			break;
		}
		Scheduler.getInstance().run();
	}

	public void operatorControl() {
		drive.setSafetyEnabled(true);
		while (isOperatorControl() && isEnabled()) {
			while (counter.get() > 0) {
                             armMotor.stopMotor();
		}
			
		//drive.tankDrive(xboxController.getRawAxis(2), xboxController.getRawAxis(5));
		drive.arcadeDrive(xboxController.getRawAxis(1), -xboxController.getRawAxis(0));

		// Lift and lower the arms using the left and right trigger.

		if (Math.abs(xboxController.getRawAxis(3)) > .1) {
			armMotor.set(xboxController.getRawAxis(3));
		} else if (Math.abs(xboxController.getRawAxis(2)) > .1) {
			armMotor.set(-xboxController.getRawAxis(2));
		} else {
			armMotor.stopMotor();
		}
		
		// Move sliding mechanism forwards and backwards

		if (Math.abs(xboxController.getRawAxis(5)) > .1) {
			slideMotor.set(xboxController.getRawAxis(5));
		} else {
			slideMotor.stopMotor();
		}
		
		// Open and close the claw

		if (xboxController.getRawButton(2)) {
			doublesolenoid.set(DoubleSolenoid.Value.kForward);
		} else if (xboxController.getRawButton(1)) {
			doublesolenoid.set(DoubleSolenoid.Value.kReverse);
		}
		
		Timer.delay(0.005); //Wait for a motor update time
		}
	}
	public void test() {

	}
}

I feel like it's a problem with the while loop.

			while (counter.get() > 0) {
                            armMotor.stopMotor();
		}