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Make my circles randomly disappear and after random seconds again appear

So I'm making very simple game. Game is about some guy who jumps on rocks(circles) and rocks sometimes get covered by water and when they are, you cant stand on them otherwise you'll fall into water and drown. I'm stuck in part where i need to make those rocks disappear(be covered by water). So I need at randomized time make them disappear, for random seconds(not too long) make them "invisible" and then again they need to show up. I'm still kinda beginner and I would appreciate any kind of answer but if you could explain it to me I'd be thrilled. Here is my code: My main class

package com.pitcher654.main;

import java.awt.Canvas;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.event.KeyListener;
import java.awt.image.BufferStrategy;
import java.util.Random;

import com.pitcher654.main.Game.STATE;

public class Game extends Canvas implements Runnable{

private static final long serialVersionUID = -7800496711589684767L;

public static final int WIDTH = 640, HEIGHT = WIDTH / 12 * 9;

private Thread thread;
private boolean running = false;

private Random r;
private Handler handler;
//private HUD hud;
private Menu menu;

public enum STATE {
    Menu,
    Help,
    Game
};

public STATE gameState = STATE.Menu;

public Game() {
    handler = new Handler();
    menu = new Menu(this, handler);
    this.addKeyListener(new KeyInput(handler));
    this.addMouseListener(menu);
    new Window(WIDTH, HEIGHT, "My game", this);

    //hud = new HUD();
    r = new Random();

    if(gameState == STATE.Game) {
        //handler.addObject(new Player(100, 200, ID.Player));
    }

    //handler.addObject(new Player(100, 200, ID.Player));
    //handler.addObject(new BasicEnemy(100, 200, ID.BasicEnemy));

}

public synchronized void start() {
    thread = new Thread(this);
    thread.start();
    running = true;
}

public synchronized void stop() {
    try {
        thread.join();
        running = false;
    }catch(Exception ex) { ex.printStackTrace(); }
}

public void run()
{
    this.requestFocus();
    long lastTime = System.nanoTime();
    double amountOfTicks = 60.0;
    double ns = 1000000000 / amountOfTicks;
    double delta = 0;
    long timer = System.currentTimeMillis();
    int frames = 0;
    while(running)
    {
                long now = System.nanoTime();
                delta += (now - lastTime) / ns;
                lastTime = now;
                while(delta >=1)
                        {
                            tick();
                            delta--;
                        }
                        if(running)
                            render();
                        frames++;

                        if(System.currentTimeMillis() - timer > 1000)
                        {
                            timer += 1000;
                            //System.out.println("FPS: "+ frames);
                            frames = 0;
                        }
    }
            stop();
 }  

private void tick() {
    handler.tick();
    //hud.tick();
    if(gameState == STATE.Game) {

    }else if(gameState == STATE.Menu) {
        menu.tick();
    }
}

private void render() {
    BufferStrategy bs = this.getBufferStrategy();
    if(bs == null) {
        this.createBufferStrategy(3);
        return;
    }

    Graphics g = bs.getDrawGraphics();

    g.setColor(new Color(87, 124, 212));
    g.fillRect(0, 0, WIDTH, HEIGHT);
    if(gameState == STATE.Game) {
        g.setColor(new Color(209, 155, 29));
        for(int i = 0; i < 5; i++) {
            g.fillOval(80 + (100 * i), 325, 70, 20);
        }
    }else if(gameState == STATE.Menu || gameState == STATE.Help){
        menu.render(g);
    }

    handler.render(g);

    if(gameState == STATE.Game) {

    }
    //hud.render(g);

    g.dispose();
    bs.show();
}

public static int clamp(int var, int min, int max) {
    if(var >= max)
        return var = max;
    else if(var <= max)
        return var = min;
    else 
        return var;
}

public static void main(String[] args) {
    new Game();
}
}

My Player class where I create my player:

package com.pitcher654.main;

import java.awt.Color;
import java.awt.Graphics;
import java.util.Random;

import com.pitcher654.main.Game.STATE;

public class Player extends GameObject {

    Random r = new Random();

public Player(int x, int y, ID id) {
    super(x, y, id);
    //velX = r.nextInt(5) + 1;
    //velY = r.nextInt(5);
}

public void tick() {
    x += velX;
    y += velY;
    //System.out.println(x);
    if(x == 500) x = 500;
}

public void render(Graphics g) {
    if(id == ID.Player) g.setColor(Color.white);
    if(id == ID.Player2) g.setColor(Color.blue);
    g.fillRect(x, y, 32, 32);
    g.drawLine(x + 15, y, x + 15, y + 100);
    g.drawLine(x + 15, y + 100, x, y + 135);
    g.drawLine(x + 15, y + 100, x + 33, y + 135);
    g.drawLine(x + 15, y + 70, x - 35, y + 30);
    g.drawLine(x + 15, y + 70, x + 65, y + 30);
    /*if(game.gameState == STATE.Menu) {
        g.setColor(new Color(87, 124, 212));
        g.fillRect(0, 0, Game.WIDTH, Game.HEIGHT);
    }*/
}


}

And my game Object class:

package com.pitcher654.main;

import java.awt.Graphics;

public abstract class GameObject {

protected static int x, y;
protected ID id;
protected int velX, velY;

public GameObject(int x, int y, ID id) {
    this.x = x;
    this.y = y;
    this.id = id;
}

public abstract void tick();
public abstract void render(Graphics g);

public void setX(int x) {
    this.x = x;
}
public void setY(int y) {
    this.y = y;
}
public int getX() {
    return x;
}
public int getY() {
    return y;
}
public void setID(ID id) {
    this.id = id;
}
public ID getID() {
    return id;
}
public void setVelX(int velX) {
    this.velX = velX;
}
public void setVelY(int velY) {
    this.velY = velY;
}
public int getVelX() {
    return velX;
}
public int getVelY() {
    return velY;
}
}

If you need any other class, just tell me I'll post it.

You should store a status of every stone in the game.

So if you have given number of stones (5), create a constant field with this number. Then create an array of ### boolean values where you'll save status of each stone. Then create an array of "times" when the stones will change their visibility.

private static final int NUM_STONES = 5; // you can change the # of the stones here
private boolean[] visible = new int[NUM_STONES];
private long[] changeTimes = new long[NUM_STONES];

In your game's init method initialize the values.

for(int i=0; i<NUM_STONES; i++){
    visible[i] = true; // each stone will be visible
    changeTimes[i] = System.currentTimeMillis() + r.nextInt(10000); // every stone will disappear in less than 10 seconds
}

In your update method (I suppose tick() ) update visibility statuses.

long now = System.currentTimeMillis();
for(int i=0; i<NUM_STONES; i++){
    if(now < changeTimes[i]){ // if the time has come
        if(visible[i]) changeTimes[i] = now + r.nextInt(5000); // every stone will be invisible up to five seconds
        else changeTimes[i] = now + r.nextInt(10000); // every stone will be visible again up to 10 seconds
        visible[i] = !visible[i]; // switch the visibility state
   }
}

And finally add the condition to the render method:

if(gameState == STATE.Game) {

    for(int i = 0; i < NUM_STONES; i++) {
        if(visible[i] g.setColor(new Color(209, 155, 29));
        else g.setColor(new Color(107, 155, 170));
        g.fillOval(80 + (100 * i), 325, 70, 20);
    }
}

That should be it. Next thing you should do is extracting magic numbers into constants, like I showed you with the NUM_STONES. And also don't create a new instance of the Color class every time you render a stone and create instances of the colors just like I've written before.

Also notice that some stones will disappear (and appear again) for a very short time - you can add few seconds to the changeTimes[i] in your update method to ensure that each stone will be (in)visible at least for this amount of time.

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