gov::lbl::genome::common::features::ChromSegment Class Reference

Inheritance diagram for gov::lbl::genome::common::features::ChromSegment:

[legend]List of all members.

Public Member Functions
	ChromSegment (String inChromosome, long inStart, long inEnd, int rEnd)
	ChromSegment (String inChromosome, long inStart, long inEnd)
	ChromSegment (String inChrom, String inStart, String inEnd)
	ChromSegment (String inChrom, String neg, String inStart, String inEnd)
	ChromSegment (String inName, String inChromosome, long inStart, long inEnd)
void	setRealChrom (boolean realChrom)
boolean	isRealChrom ()
String	getName ()
String	getChromosome ()
String	getChromosome (boolean alter)
void	setChromosome (int chromosome)
void	setChromosome (String chromosome)
String	getChromName ()
long	getStart ()
long	getEnd ()
void	setStart (long start)
void	setEnd (long end)
String	getPos ()
void	add (ChromSegment segment)
boolean	contains (ChromSegment segment)
boolean	contains (ChromPosition position)
boolean	contains (long coordinate)
boolean	touches (ChromSegment segment)
ChromSegment	intersect (ChromSegment segment)
String	toString ()
String	toString (long offset)
int	hashCode ()
int	compareTo (Object obj)
Object	cloneSegment ()
int	getRealEnd ()
Static Public Member Functions
ChromSegment	parsePos (String pos) throws VGBException
long[]	parseSpan (String span)
boolean	positionFormat (String pos)
Package Attributes
String	chromosome
long	start
long	end
int	realEnd = 0
boolean	realChrom = true

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Detailed Description

ChromSegment represents a specific chromosome coordinate span.

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Constructor & Destructor Documentation

gov::lbl::genome::common::features::ChromSegment::ChromSegment (  String  inChromosome, long  inStart, long  inEnd, int  rEnd )  [inline]

ChromSegment Parameters: inChromosome  String inStart  long inEnd  long rEnd  int

gov::lbl::genome::common::features::ChromSegment::ChromSegment (  String  inChromosome, long  inStart, long  inEnd )  [inline]

ChromSegment Parameters: inChromosome  String inStart  long inEnd  long

gov::lbl::genome::common::features::ChromSegment::ChromSegment (  String  inChrom, String  inStart, String  inEnd )  [inline]

ChromSegment Parameters: inChrom  String inStart  String inEnd  String

gov::lbl::genome::common::features::ChromSegment::ChromSegment (  String  inChrom, String  neg, String  inStart, String  inEnd )  [inline]

ChromSegment Parameters: inChrom  String neg  String inStart  String inEnd  String

gov::lbl::genome::common::features::ChromSegment::ChromSegment (  String  inName, String  inChromosome, long  inStart, long  inEnd )  [inline]

ChromSegment Parameters: inName  String inChromosome  String inStart  long inEnd  long

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Member Function Documentation

void gov::lbl::genome::common::features::ChromSegment::add (  ChromSegment  segment  )  [inline]

Merges the specified chromosome segment with this segment

Object gov::lbl::genome::common::features::ChromSegment::cloneSegment (   )  [inline]

clone Segment Returns: Object

int gov::lbl::genome::common::features::ChromSegment::compareTo (  Object  obj  )  [inline]

compare 2 segments Parameters: obj  Object Returns: int

boolean gov::lbl::genome::common::features::ChromSegment::contains (  long  coordinate  )  [inline]

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

boolean gov::lbl::genome::common::features::ChromSegment::contains (  ChromPosition  position  )  [inline]

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

boolean gov::lbl::genome::common::features::ChromSegment::contains (  ChromSegment  segment  )  [inline]

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

String gov::lbl::genome::common::features::ChromSegment::getChromName (   )  [inline]

get Chromosome Name Returns: String

String gov::lbl::genome::common::features::ChromSegment::getChromosome (  boolean  alter  )  [inline]

get Chromosome Parameters: alter  boolean Returns: String

String gov::lbl::genome::common::features::ChromSegment::getChromosome (   )  [inline]

get Chromosome Returns: String

long gov::lbl::genome::common::features::ChromSegment::getEnd (   )  [inline]

get End Returns: long

String gov::lbl::genome::common::features::ChromSegment::getName (   )  [inline]

get Name Returns: String

String gov::lbl::genome::common::features::ChromSegment::getPos (   )  [inline]

get formatted Position string Returns: String

int gov::lbl::genome::common::features::ChromSegment::getRealEnd (   )  [inline]

get Real Segment End Returns: int

long gov::lbl::genome::common::features::ChromSegment::getStart (   )  [inline]

get Start Returns: long

ChromSegment gov::lbl::genome::common::features::ChromSegment::intersect (  ChromSegment  segment  )  [inline]

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

boolean gov::lbl::genome::common::features::ChromSegment::isRealChrom (   )  [inline]

return true if segment is a Real Chromosome Returns: boolean

ChromSegment gov::lbl::genome::common::features::ChromSegment::parsePos (  String  pos  )  throws VGBException [inline, static]

build ChromSegment from the position string Parameters: pos  String Returns: ChromSegment Exceptions: VGBException

long [] gov::lbl::genome::common::features::ChromSegment::parseSpan (  String  span  )  [inline, static]

return array with start and end Parameters: span  String Returns: long[]

boolean gov::lbl::genome::common::features::ChromSegment::positionFormat (  String  pos  )  [inline, static]

return true if position is like chr9:10000-20000 Parameters: pos  String Returns: boolean

void gov::lbl::genome::common::features::ChromSegment::setChromosome (  String  chromosome  )  [inline]

set Chromosome Parameters: chromosome  String

void gov::lbl::genome::common::features::ChromSegment::setChromosome (  int  chromosome  )  [inline]

set Chromosome Parameters: chromosome  int

void gov::lbl::genome::common::features::ChromSegment::setEnd (  long  end  )  [inline]

set End Parameters: end  long

void gov::lbl::genome::common::features::ChromSegment::setRealChrom (  boolean  realChrom  )  [inline]

set Real Chromosome mode Parameters: realChrom  boolean

void gov::lbl::genome::common::features::ChromSegment::setStart (  long  start  )  [inline]

set Start Parameters: start  long

String gov::lbl::genome::common::features::ChromSegment::toString (  long  offset  )  [inline]

return XML formatted summary string Parameters: offset  long Returns: String Reimplemented in gov::lbl::genome::common::features::Contig, gov::lbl::genome::common::features::Gene, gov::lbl::genome::common::features::Repeat, and gov::lbl::genome::common::features::SuperContig.

String gov::lbl::genome::common::features::ChromSegment::toString (   )  [inline]

return XML formatted summary string Returns: String Reimplemented in gov::lbl::genome::common::features::Contig, gov::lbl::genome::common::features::Gene, gov::lbl::genome::common::features::PValue, gov::lbl::genome::common::features::Repeat, and gov::lbl::genome::common::features::SuperContig.

boolean gov::lbl::genome::common::features::ChromSegment::touches (  ChromSegment  segment  )  [inline]

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

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The documentation for this class was generated from the following file:

• /home/teplitski/Projects/vgb2/src/gov/lbl/genome/common/features/ChromSegment.java

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