src/org/gel/mauve/backbone/Backbone.java

Go to the documentation of this file.

package org.gel.mauve.backbone;

import java.awt.Color;

import org.gel.mauve.Genome;
import org.gel.mauve.analysis.Segment;

public class Backbone extends Segment {

        protected int lcb_index;

        protected long left_col;

        protected long length;

        protected boolean seqs[];

        protected Color color;

        public int getLcbIndex () {
                return lcb_index;
        }

        public void setLcbIndex (int lcb_index) {
                this.lcb_index = lcb_index;
        }

        public long getLeftColumn () {
                return left_col;
        }

        public void setLeftColumn (long left_col) {
                this.left_col = left_col;
        }

        public long getLength () {
                return length;
        }

        public void setLength (long length) {
                this.length = length;
        }

        public boolean [] getSeqs () {
                return seqs;
        }

        public void setSeqs (boolean [] seqs) {
                this.seqs = seqs;
        }

        public long getLeftEnd (Genome g) {
                int gi = g.getSourceIndex ();
                return left [gi];
        }

        public void setLeftEnd (long [] left_end) {
                this.left = left_end;
        }

        public long getRightEnd (Genome g) {
                int gi = g.getSourceIndex ();
                return right [gi];
        }

        public void setRightEnd (long [] right_end) {
                this.right = right_end;
        }

        public boolean exists (Genome g) {
                int sI = g.getSourceIndex ();
                return seqs[sI];
        }

        public Color getColor () {
                return color;
        }

        public void setColor (Color color) {
                this.color = color;
        }
}

---