/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package MCview;

import java.awt.*;


public class Bond {
    float[] start;
    float[] end;
    Color startCol;
    Color endCol;
    public myAtom at1;
    public myAtom at2;

    public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {
        this.start = start;
        this.end = end;
        this.startCol = at1.color;
        this.endCol = at2.color;
        this.at1 = at1;
        this.at2 = at2;
    }

    public Bond(Bond bond) {
        this.start = new float[3];

        this.start[0] = bond.start[0];
        this.start[1] = bond.start[1];
        this.start[2] = bond.start[2];

        this.end = new float[3];

        this.end[0] = bond.end[0];
        this.end[1] = bond.end[1];
        this.end[2] = bond.end[2];

        this.startCol = bond.startCol;
        this.endCol = bond.endCol;
    }

    public void print() {
        System.out.println("Start " + start[0] + " " + start[1] + " " +
            start[2]);
        System.out.println("End   " + end[0] + " " + end[1] + " " + end[2]);
    }

    public float length() {
        float len = ((end[0] - start[0]) * (end[0] - start[0])) +
            ((end[1] - start[1]) * (end[1] - start[1])) +
            ((end[2] - start[2]) * (end[2] - start[2]));

        len = (float) (Math.sqrt(len));

        return len;
    }

    public void translate(float x, float y, float z) {
        start[0] = (start[0] + x);
        end[0] = (end[0] + x);

        start[1] = (start[1] + y);
        end[1] = (end[1] + y);

        start[2] = (start[2] + z);
        end[2] = (end[2] + z);
    }
}