gov.lbl.genome.common.features
Class Repeat

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

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable

public class Repeat
extends ChromSegment

Repeat represents a segment of a DNA sequence that is a repeated portion.

Field Summary

static java.lang.String	DNA
static java.lang.String	LINE
static java.lang.String	LTR
static java.lang.String	NAME
static java.lang.String	OTHER
static java.lang.String	RNA
static java.lang.String	SINE
static java.lang.String[]	TYPES

Constructor Summary

Repeat(java.lang.String inChromosome, long inStart, long inEnd, java.lang.String inType)
Repeat

Method Summary

java.lang.String	getType() get Type
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

Field Detail

NAME

public static final java.lang.String NAME

See Also:

Constant Field Values

LINE

public static final java.lang.String LINE

See Also:

Constant Field Values

LTR

public static final java.lang.String LTR

See Also:

Constant Field Values

SINE

public static final java.lang.String SINE

See Also:

Constant Field Values

RNA

public static final java.lang.String RNA

See Also:

Constant Field Values

DNA

public static final java.lang.String DNA

See Also:

Constant Field Values

OTHER

public static final java.lang.String OTHER

See Also:

Constant Field Values

TYPES

public static final java.lang.String[] TYPES

Constructor Detail

Repeat

public Repeat(java.lang.String inChromosome,
              long inStart,
              long inEnd,
              java.lang.String inType)

Repeat

Parameters:

inChromosome - String

inStart - long

inEnd - long

inType - String

Method Detail

getType

public java.lang.String getType()

get Type

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