picard.annotation

Class Gene

java.lang.Object

htsjdk.samtools.util.Interval

picard.annotation.Gene

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, java.lang.Cloneable, java.lang.Comparable<htsjdk.samtools.util.Interval>, java.lang.Iterable<Gene.Transcript>

public class Gene
extends htsjdk.samtools.util.Interval
implements java.lang.Iterable<Gene.Transcript>

Holds annotation of a gene for storage in an OverlapDetector. May hold multiple transcripts for the same gene. The transcripts must all be relative to the same strand.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Gene.Transcript A single transcript of a gene.

Constructor Summary

Constructors

Constructor and Description
Gene(java.lang.String sequence, int start, int end, boolean negative, java.lang.String name)

Method Summary

Methods

Modifier and Type	Method and Description
Gene.Transcript	addTranscript(java.lang.String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)
java.util.Iterator<Gene.Transcript>	iterator()

Methods inherited from class htsjdk.samtools.util.Interval

abuts, clone, compareTo, countBases, equals, getContig, getEnd, getIntersectionLength, getName, getSequence, getStart, hashCode, intersect, intersects, isNegativeStrand, isPositiveStrand, length, pad, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Gene

public Gene(java.lang.String sequence,
    int start,
    int end,
    boolean negative,
    java.lang.String name)

Method Detail

addTranscript

public Gene.Transcript addTranscript(java.lang.String name,
                            int transcriptionStart,
                            int transcriptionEnd,
                            int codingStart,
                            int codingEnd,
                            int numExons)

iterator

public java.util.Iterator<Gene.Transcript> iterator()

Specified by:

iterator in interface java.lang.Iterable<Gene.Transcript>