Lissajous pattern simulator
About point (1)
If it's obviously copied from somewhere without changing anything then it's perfectly fine to not change anything to the code itself. Given that you also have the link to the (pseudo-)code. In this case I wouldn't even add comments other than: look at this page to know how it works.

If however you want to integrate it better into your own code to treat it like it's actually part of it then there's no reason to keep the code as close to the original as possible.
Instead you should refactor it until it fits the general java standards. Meaning making variables private, making constants final (static), following naming conventions (both for variables and methods), ...

question (2)
(see above if you want to stick to the structure from the source without changing anything. If you start refactoring following coding standards read on)

If like you say there are a number of variables and methods that are forming a coherent group then you should put them into their own class.

For your new class you'll have to find out what to put in the class and what methods to provide.

My first thought is something like this:

public class LissajousPointCalculator{
    private static final int HORIZONTAL_FACTOR = 300;
    private static final int VERTICAL_FACTOR = 300;
    private float xTimeScale;
    private float yTimeScale;
    private float xTimeOffset;

    public LissajousPointCalculator(float xTimeScale, yTimeScale, xTimeOffset){
        this.xTimeScale = xTimeScale;
        this.yTimeScale = yTimeScale;
        this.xTimeOffset = xTimeOffset;
    }

    public Point getPointAt(float time) {
        int x = (int) ( HORIZONTAL_FACTOR  * Math.sin(xTimeScale*time + xTimeOffset) );
        int y = (int) ( VERTICAL_FACTOR  * Math.sin(yTimeScale*time) );

        return new Point(x + HORIZONTAL_FACTOR , y + VERTICAL_FACTOR ); 
    }
}


Note that I did not include any timetracking inside this class. My reasoning is that the other class that uses this one is responsible for deciding which points to draw. So that class is responsible for staring over, deciding the step size, deciding how many points to add before drawing it on the screen etc...

I also made the horizontal and vertical scaling factors constant inside the class. This was just as an example. If you want to be able to change the size of the figure as well it's obvious that you want these as variables that you can pass through constructor or setters instead.