function runTrain()
    % The main function, this is what is called first. I use this function to initialize all of our variables and set up the arduino.
    delete(timerfindall);
    clear;
    close all;
    delete(instrfindall);
    clc;

    % Get the speed limits and set up the arduino for either sim or physical
    simulator = input('Run the train on a simulator? (0/1)\nsimulator = ');
    dSpeed = input('What is the speed limit in the departure phase?\ndSpeed = ');
    aSpeed = input('What is the speed limit in the approach phase?\naSpeed = ');
    if(simulator > 0)
        train = arduino_sim('COM3');
    else
        train = arduino('COM3');
    end

    % Set up the LEDs
    train.pinMode(14, 'output');
    train.pinMode(15, 'output');

    % Set up the gates
    train.servoAttach(1);

    % Global allows other functions to edit this variable. This is used to flash the lights.
    global flashState;
    flashState = 1;

    % Set up all the timing functions
    startTimer = timer('StartDelay', 4.5, 'Name', 'startTimer');
    startTimer.TimerFcn = {@startTrain, train, aSpeed};
    stopTimer = timer('StartDelay', 2, 'Name', 'stopTimer');
    stopTimer.TimerFcn = {@stopTrain, train};
    flashTimer = timer('Period', .5, 'TasksToExecute', 4, 'ExecutionMode', 'fixedRate', 'Name', 'flashTimer');
    flashTimer.TimerFcn = {@flashLights, train};
    flashTimer.StopFcn = {@turnOffLights, train};
    gateTimer = timer('StartDelay', .45, 'ExecutionMode', 'fixedRate', 'Period', 1.55, 'TasksToExecute', 2, 'Name', 'gateTimer');
    gateTimer.TimerFcn = {@toggleGate, train};

    % Start the train
    train.motorRun(1, 'forward');
    train.motorSpeed(1, dSpeed);

    % Move into the function that actually runs the train
    manageTrain(train, stopTimer, flashTimer, gateTimer, startTimer, dSpeed, aSpeed);
end

function manageTrain(train, stopTimer, flashTimer, gateTimer, startTimer, dSpeed, aSpeed)
    % Pause execution until the approach sensor is broken
    train.analogRead(2);
    while train.analogRead(2) < 200
    end

    % Once the sensor is broken, the while loop ends and this code runs. The train is slowed, and our timers are started.
    % All timers run at the same time.
    train.motorSpeed(1, aSpeed);
    % Lowers the gate after .45s, then raises it after 1.55s using the toggleGate() function
    start(gateTimer);
    % Alternates the lights every .5 seconds, 4 times = 2 total seconds using flashLights()
    % After the 2 seconds, makes sure both lights are off using turnOffLights()
    start(flashTimer);
    % Stops the train after 2 seconds using stopTrain()
    start(stopTimer);
    % Starts the train after 4.5 seconds using startTrain()
    start(startTimer);

    % Wait for the departure sensor to trip
    train.analogRead(3);
    while train.analogRead(3) < 200
    end

    % Return to normal speed
    train.motorSpeed(1, dSpeed);

    % Call itself to loop
    manageTrain(train, stopTimer, flashTimer, gateTimer, startTimer, dSpeed, aSpeed);
end

function flashLights(~, ~, train)
    global flashState;
    if flashState == 1
        train.digitalWrite(14, 1);
        train.digitalWrite(15, 0);
    else
        train.digitalWrite(14, 0);
        train.digitalWrite(15, 1);
    end
    flashState = ~flashState;
end

function turnOffLights(~, ~, train)
    train.digitalWrite(14, 0);
    train.digitalWrite(15, 0);
end

function stopTrain(~, ~, train)
    train.motorRun(1, 'release');
end

function toggleGate(~, ~, train)
    if train.servoRead(1) == 180;
        train.servoWrite(1, 90);
    else
        train.servoWrite(1, 180);
    end
end

function startTrain(~, ~, train, aSpeed)
    train.motorRun(1, 'forward');
    train.motorSpeed(1, aSpeed);
end