gov.lbl.genome.common.features
Class ChromSegment

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

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable

Direct Known Subclasses:

Cns, Contig, Exon, Gene, PValue, Repeat, SuperContig, Utr

public class ChromSegment
extends java.lang.Object
implements java.lang.Comparable, java.lang.Cloneable

ChromSegment represents a specific chromosome coordinate span.

Constructor Summary

ChromSegment(java.lang.String inChromosome, long inStart, long inEnd)
ChromSegment

ChromSegment(java.lang.String inChromosome, long inStart, long inEnd, int rEnd)
ChromSegment

ChromSegment(java.lang.String inName, java.lang.String inChromosome, long inStart, long inEnd)
ChromSegment

ChromSegment(java.lang.String inChrom, java.lang.String inStart, java.lang.String inEnd)
ChromSegment

ChromSegment(java.lang.String inChrom, java.lang.String neg, java.lang.String inStart, java.lang.String inEnd)
ChromSegment

Method Summary

void	add(ChromSegment segment) Merges the specified chromosome segment with this segment
java.lang.Object	cloneSegment() clone Segment
int	compareTo(java.lang.Object obj) compare 2 segments
boolean	contains(ChromPosition position) Returns true if the specified Chromosome position falls within this segment.
boolean	contains(ChromSegment segment) Returns true if the specified chromosome segment overlaps at all with this segment.
boolean	contains(long coordinate) Returns true if the specified Chromosome position falls within this segment.
java.lang.String	getChromName() get Chromosome Name
java.lang.String	getChromosome() get Chromosome
java.lang.String	getChromosome(boolean alter) get Chromosome
long	getEnd() get End
java.lang.String	getName() get Name
java.lang.String	getPos() get formatted Position string
int	getRealEnd() get Real Segment End
long	getStart() get Start
int	hashCode()
ChromSegment	intersect(ChromSegment segment) Returns a new ChromSegment which is the intersection of this segment and the provided segment.
boolean	isRealChrom() return true if segment is a Real Chromosome
static ChromSegment	parsePos(java.lang.String pos) build ChromSegment from the position string
static long[]	parseSpan(java.lang.String span) return array with start and end
static boolean	positionFormat(java.lang.String pos) return true if position is like chr9:10000-20000
void	setChromosome(int chromosome) set Chromosome
void	setChromosome(java.lang.String chromosome) set Chromosome
void	setEnd(long end) set End
void	setRealChrom(boolean realChrom) set Real Chromosome mode
void	setStart(long start) set Start
java.lang.String	toString() return XML formatted summary string
java.lang.String	toString(long offset) return XML formatted summary string
boolean	touches(ChromSegment segment) Returns true if the specified Chromosome segment either intersects or is adjacent to this Segment.

Methods inherited from class java.lang.Object

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

Constructor Detail

ChromSegment

public ChromSegment(java.lang.String inChromosome,
                    long inStart,
                    long inEnd,
                    int rEnd)

ChromSegment

Parameters:

inChromosome - String

inStart - long

inEnd - long

rEnd - int

ChromSegment

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

ChromSegment

Parameters:

inChromosome - String

inStart - long

inEnd - long

ChromSegment

public ChromSegment(java.lang.String inChrom,
                    java.lang.String inStart,
                    java.lang.String inEnd)

ChromSegment

Parameters:

inChrom - String

inStart - String

inEnd - String

ChromSegment

public ChromSegment(java.lang.String inChrom,
                    java.lang.String neg,
                    java.lang.String inStart,
                    java.lang.String inEnd)

ChromSegment

Parameters:

inChrom - String

neg - String

inStart - String

inEnd - String

ChromSegment

public ChromSegment(java.lang.String inName,
                    java.lang.String inChromosome,
                    long inStart,
                    long inEnd)

ChromSegment

Parameters:

inName - String

inChromosome - String

inStart - long

inEnd - long

Method Detail

setRealChrom

public void setRealChrom(boolean realChrom)

set Real Chromosome mode

Parameters:

realChrom - boolean

isRealChrom

public boolean isRealChrom()

return true if segment is a Real Chromosome

Returns:

boolean

parsePos

public static ChromSegment parsePos(java.lang.String pos)
                             throws VGBException

build ChromSegment from the position string

Parameters:

pos - String

Returns:

ChromSegment

Throws:

VGBException

parseSpan

public static long[] parseSpan(java.lang.String span)

return array with start and end

Parameters:

span - String

Returns:

long[]

getName

public java.lang.String getName()

get Name

Returns:

String

getChromosome

public java.lang.String getChromosome()

get Chromosome

Returns:

String

getChromosome

public java.lang.String getChromosome(boolean alter)

get Chromosome

Parameters:

alter - boolean

Returns:

String

setChromosome

public void setChromosome(int chromosome)

set Chromosome

Parameters:

chromosome - int

setChromosome

public void setChromosome(java.lang.String chromosome)

set Chromosome

Parameters:

chromosome - String

getChromName

public java.lang.String getChromName()

get Chromosome Name

Returns:

String

getStart

public long getStart()

get Start

Returns:

long

getEnd

public long getEnd()

get End

Returns:

long

setStart

public void setStart(long start)

set Start

Parameters:

start - long

setEnd

public void setEnd(long end)

set End

Parameters:

end - long

getPos

public java.lang.String getPos()

get formatted Position string

Returns:

String

positionFormat

public static boolean positionFormat(java.lang.String pos)

return true if position is like chr9:10000-20000

Parameters:

pos - String

Returns:

boolean

add

public void add(ChromSegment segment)

Merges the specified chromosome segment with this segment

contains

public boolean contains(ChromSegment segment)

Returns true if the specified chromosome segment overlaps at all with this segment.

contains

public boolean contains(ChromPosition position)

Returns true if the specified Chromosome position falls within this segment.

contains

public boolean contains(long coordinate)

Returns true if the specified Chromosome position falls within this segment.

touches

public boolean touches(ChromSegment segment)

Returns true if the specified Chromosome segment either intersects or is adjacent to this Segment.

intersect

public ChromSegment intersect(ChromSegment segment)

Returns a new ChromSegment which is the intersection of this segment and the provided segment.

toString

public java.lang.String toString()

return XML formatted summary string

Overrides:

toString in class java.lang.Object

Returns:

String

toString

public java.lang.String toString(long offset)

return XML formatted summary string

Parameters:

offset - long

Returns:

String

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

compareTo

public int compareTo(java.lang.Object obj)

compare 2 segments

Specified by:

compareTo in interface java.lang.Comparable

Parameters:

obj - Object

Returns:

int

cloneSegment

public java.lang.Object cloneSegment()

clone Segment

Returns:

Object

getRealEnd

public int getRealEnd()

get Real Segment End

Returns:

int