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

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00001 package org.gel.mauve.backbone;
00002 
00003 import java.awt.Color;
00004 
00005 import org.gel.mauve.Genome;
00006 import org.gel.mauve.analysis.Segment;
00007 
00008 public class Backbone extends Segment {
00009 
00010         protected int lcb_index;
00011 
00012         protected long left_col;
00013 
00014         protected long length;
00015 
00016         protected boolean seqs[];
00017 
00018         protected Color color;
00019 
00020         public int getLcbIndex () {
00021                 return lcb_index;
00022         }
00023 
00024         public void setLcbIndex (int lcb_index) {
00025                 this.lcb_index = lcb_index;
00026         }
00027 
00028         public long getLeftColumn () {
00029                 return left_col;
00030         }
00031 
00032         public void setLeftColumn (long left_col) {
00033                 this.left_col = left_col;
00034         }
00035 
00036         public long getLength () {
00037                 return length;
00038         }
00039 
00040         public void setLength (long length) {
00041                 this.length = length;
00042         }
00043 
00044         public boolean [] getSeqs () {
00045                 return seqs;
00046         }
00047 
00048         public void setSeqs (boolean [] seqs) {
00049                 this.seqs = seqs;
00050         }
00051 
00052         public long getLeftEnd (Genome g) {
00053                 int gi = g.getSourceIndex ();
00054                 return left [gi];
00055         }
00056 
00057         public void setLeftEnd (long [] left_end) {
00058                 this.left = left_end;
00059         }
00060 
00061         public long getRightEnd (Genome g) {
00062                 int gi = g.getSourceIndex ();
00063                 return right [gi];
00064         }
00065 
00066         public void setRightEnd (long [] right_end) {
00067                 this.right = right_end;
00068         }
00069 
00070         public boolean exists (Genome g) {
00071                 int sI = g.getSourceIndex ();
00072                 return seqs[sI];
00073         }
00074 
00075         public Color getColor () {
00076                 return color;
00077         }
00078 
00079         public void setColor (Color color) {
00080                 this.color = color;
00081         }
00082 }

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