gov.lbl.genome.common.features
Class Gene

java.lang.Object
  gov.lbl.genome.common.features.ChromSegment
      gov.lbl.genome.common.features.Gene

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable

public class Gene
extends ChromSegment

Gene represents a specific chromosome coordinate span.

Constructor Summary

Gene(long inStart, long inEnd, java.lang.String inName, java.lang.String descr, boolean inForward)
Gene

Gene(java.lang.String inChrom, long inStart, long inEnd)

Gene(java.lang.String inChromosome, long inStart, long inEnd, java.lang.String inName, java.lang.String descr, boolean inForward)
Gene

Method Summary

java.lang.String	getDescr() get Descriprion
java.lang.String	getGeneName() get Gene Name
boolean	isForward() return true if forward
java.lang.String	toString() return XML formatted string
java.lang.String	toString(long offset) return XML formatted string

Methods inherited from class gov.lbl.genome.common.features.ChromSegment

add, cloneSegment, compareTo, contains, contains, contains, getChromName, getChromosome, getChromosome, getEnd, getName, getPos, getRealEnd, getStart, hashCode, intersect, isRealChrom, parsePos, parseSpan, positionFormat, setChromosome, setChromosome, setEnd, setRealChrom, setStart, touches

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Gene

public Gene(java.lang.String inChrom,
            long inStart,
            long inEnd)

Gene

public Gene(long inStart,
            long inEnd,
            java.lang.String inName,
            java.lang.String descr,
            boolean inForward)

Gene

Parameters:

inStart - long

inEnd - long

inName - String

descr - String

inForward - boolean

Gene

public Gene(java.lang.String inChromosome,
            long inStart,
            long inEnd,
            java.lang.String inName,
            java.lang.String descr,
            boolean inForward)

Gene

Parameters:

inChromosome - String

inStart - long

inEnd - long

inName - String

descr - String

inForward - boolean

Method Detail

getGeneName

public java.lang.String getGeneName()

get Gene Name

Returns:

String

isForward

public boolean isForward()

return true if forward

Returns:

boolean

getDescr

public java.lang.String getDescr()

get Descriprion

Returns:

String

toString

public java.lang.String toString()

return XML formatted string

Overrides:

toString in class ChromSegment

Returns:

String

toString

public java.lang.String toString(long offset)

return XML formatted string

Overrides:

toString in class ChromSegment

Parameters:

offset - long

Returns:

String