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

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

[legend]Collaboration diagram for gov::lbl::genome::common::features::Contig:

[legend]List of all members.

Public Member Functions
	Contig (String chrom, long start, long end)
	Contig (String chrom, long start, long end, boolean dir, int align, int base, int ds, int ctgId, String name, String dsChrom, long dsStart, long dsEnd, boolean dsStrand)
int	getBase ()
boolean	getDir ()
boolean	getStrand ()
int	getAlign ()
int	getDs ()
int	getContigNum ()
String	getContigName ()
String	getDsChrom ()
long	getDsStart ()
long	getDsEnd ()
boolean	getDsStrand ()
void	setDsStart (long dsStart)
void	setDsEnd (long dsEnd)
String	toString ()
String	toString (long offset)

---

Detailed Description

A data set contig mapped onto a base genome. If the contig came from another genome. its location on that genome is recorded as well

---

Constructor & Destructor Documentation

gov::lbl::genome::common::features::Contig::Contig (  String  chrom, long  start, long  end )  [inline]

Contig Parameters: chrom  String start  long end  long

gov::lbl::genome::common::features::Contig::Contig (  String  chrom, long  start, long  end, boolean  dir, int  align, int  base, int  ds, int  ctgId, String  name, String  dsChrom, long  dsStart, long  dsEnd, boolean  dsStrand )  [inline]

Contig Parameters: chrom  String start  long end  long dir  boolean align  int base  int ds  int ctgId  int name  String dsChrom  String dsStart  long dsEnd  long dsStrand  boolean

---

Member Function Documentation

int gov::lbl::genome::common::features::Contig::getAlign (   )  [inline]

get Align Returns: int

String gov::lbl::genome::common::features::Contig::getContigName (   )  [inline]

get Contig Name Returns: String

int gov::lbl::genome::common::features::Contig::getContigNum (   )  [inline]

get Contig Number Returns: int

boolean gov::lbl::genome::common::features::Contig::getDir (   )  [inline]

get Dir Returns: boolean

int gov::lbl::genome::common::features::Contig::getDs (   )  [inline]

get DataSet Returns: int

String gov::lbl::genome::common::features::Contig::getDsChrom (   )  [inline]

get DataSet Chromosome Returns: String

long gov::lbl::genome::common::features::Contig::getDsEnd (   )  [inline]

get DataSet End Returns: long

long gov::lbl::genome::common::features::Contig::getDsStart (   )  [inline]

get DataSet Start Returns: long

boolean gov::lbl::genome::common::features::Contig::getDsStrand (   )  [inline]

get DataSet Strand Returns: boolean

boolean gov::lbl::genome::common::features::Contig::getStrand (   )  [inline]

get Strand Returns: boolean

void gov::lbl::genome::common::features::Contig::setDsEnd (  long  dsEnd  )  [inline]

set DataSet End Parameters: dsEnd  long

void gov::lbl::genome::common::features::Contig::setDsStart (  long  dsStart  )  [inline]

set DataSet Start Parameters: dsStart  long

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

return XML formatted string Parameters: offset  long Returns: String Reimplemented from gov::lbl::genome::common::features::ChromSegment.

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

return XML formatted string Returns: String Reimplemented from gov::lbl::genome::common::features::ChromSegment.

---

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

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

---