94 lines
2.6 KiB
Java
94 lines
2.6 KiB
Java
|
package edu.mit.broad.sting.utils;
|
||
|
|
|
||
|
|
import java.util.HashMap;
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Created by IntelliJ IDEA.
|
||
|
|
* User: mdepristo
|
||
|
|
* Date: Feb 27, 2009
|
||
|
|
* Time: 10:49:47 AM
|
||
|
|
* To change this template use File | Settings | File Templates.
|
||
|
|
*/
|
||
|
|
public class ReferenceOrderedDatum {
|
||
|
|
private String contig, source, feature, strand, frame;
|
||
|
|
private long start, stop;
|
||
|
|
private double score;
|
||
|
|
private HashMap<String, String> attributes;
|
||
|
|
|
||
|
|
// ----------------------------------------------------------------------
|
||
|
|
//
|
||
|
|
// Constructors
|
||
|
|
//
|
||
|
|
// ----------------------------------------------------------------------
|
||
|
|
public ReferenceOrderedDatum(final String contig, final String source, final String feature,
|
||
|
|
final long start, final long stop, final double score,
|
||
|
|
final String strand, final String frame, HashMap<String, String> attributes) {
|
||
|
|
this.contig = contig;
|
||
|
|
this.source = source;
|
||
|
|
this.feature = feature;
|
||
|
|
this.start = start;
|
||
|
|
this.stop= stop;
|
||
|
|
this.score = score;
|
||
|
|
this.strand = strand;
|
||
|
|
this.frame = frame;
|
||
|
|
this.attributes = attributes;
|
||
|
|
}
|
||
|
|
|
||
|
|
// public ReferenceOrderedDatum(final String contig, final String source, final String feature,
|
||
|
|
// final long start, final long stop, final double score,
|
||
|
|
// final String strand, final String frame) {
|
||
|
|
// ReferenceOrderedDatum(contig, source, feature, start, stop, score, strand, frame, null);
|
||
|
|
// }
|
||
|
|
|
||
|
|
// ----------------------------------------------------------------------
|
||
|
|
//
|
||
|
|
// Accessors
|
||
|
|
//
|
||
|
|
// ----------------------------------------------------------------------
|
||
|
|
public String getContig() {
|
||
|
|
return this.contig;
|
||
|
|
}
|
||
|
|
|
||
|
|
public String getSource() {
|
||
|
|
return source;
|
||
|
|
}
|
||
|
|
|
||
|
|
public String getFeature() {
|
||
|
|
return feature;
|
||
|
|
}
|
||
|
|
|
||
|
|
public String getStrand() {
|
||
|
|
return strand;
|
||
|
|
}
|
||
|
|
|
||
|
|
public String getFrame() {
|
||
|
|
return frame;
|
||
|
|
}
|
||
|
|
|
||
|
|
public long getStart() {
|
||
|
|
return start;
|
||
|
|
}
|
||
|
|
|
||
|
|
public long getStop() {
|
||
|
|
return stop;
|
||
|
|
}
|
||
|
|
|
||
|
|
public double getScore() {
|
||
|
|
return score;
|
||
|
|
}
|
||
|
|
|
||
|
|
public String getAttribute(final String key) {
|
||
|
|
return attributes.get(key);
|
||
|
|
}
|
||
|
|
|
||
|
|
// ----------------------------------------------------------------------
|
||
|
|
//
|
||
|
|
// formatting
|
||
|
|
//
|
||
|
|
// ----------------------------------------------------------------------
|
||
|
|
public String toString() {
|
||
|
|
return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s", contig, source, feature, start, stop, score, strand, frame);
|
||
|
|
}
|
||
|
|
|
||
|
|
}
|