/*
* 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 jalview.datamodel;

import java.awt.*;


public class SequenceNode extends BinaryNode {
    public float dist;
    public int count;
    public float height;
    public float ycount;
    public Color color = Color.black;
    public boolean dummy = false;
    private boolean placeholder = false;

    public SequenceNode() {
        super();
    }

    public SequenceNode(Object val, SequenceNode parent, float dist, String name) {
        super(val, parent, name);
        this.dist = dist;
    }

    public SequenceNode(Object val, SequenceNode parent, String name,
        float dist, int bootstrap, boolean dummy) {
        super(val, parent, name);
        this.dist = dist;
        this.bootstrap = bootstrap;
        this.dummy = dummy;
    }

    /**
     * @param dummy true if node is created for the representation of polytomous trees
     */
    public boolean isDummy() {
        return dummy;
    }

    /* @param placeholder is true if the sequence refered to in the
     *  element node is not actually present in the associated alignment
     */
    public boolean isPlaceholder() {
        return placeholder;
    }

    public boolean setDummy(boolean newstate) {
        boolean oldstate = dummy;
        dummy = newstate;

        return oldstate;
    }

    public void setPlaceholder(boolean Placeholder) {
        this.placeholder = Placeholder;
    }

    /**
     * ascends the tree but doesn't stop until a non-dummy node is discovered.
     * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.
     */
    public SequenceNode AscendTree() {
        SequenceNode c = this;

        do {
            c = (SequenceNode) c.parent();
        } while ((c != null) && c.dummy);

        return c;
    }
}