gov.lbl.genome.common.features
Class Contig

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

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable

public class Contig
extends ChromSegment

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 Summary

Contig(java.lang.String chrom, long start, long end)
Contig

Contig(java.lang.String chrom, long start, long end, boolean dir, int align, int base, int ds, int ctgId, java.lang.String name, java.lang.String dsChrom, long dsStart, long dsEnd, boolean dsStrand)
Contig

Method Summary

int	getAlign() get Align
int	getBase()
java.lang.String	getContigName() get Contig Name
int	getContigNum() get Contig Number
boolean	getDir() get Dir
int	getDs() get DataSet
java.lang.String	getDsChrom() get DataSet Chromosome
long	getDsEnd() get DataSet End
long	getDsStart() get DataSet Start
boolean	getDsStrand() get DataSet Strand
boolean	getStrand() get Strand
void	setDsEnd(long dsEnd) set DataSet End
void	setDsStart(long dsStart) set DataSet Start
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

Contig

public Contig(java.lang.String chrom,
              long start,
              long end)

Contig

Parameters:

chrom - String

start - long

end - long

Contig

public Contig(java.lang.String chrom,
              long start,
              long end,
              boolean dir,
              int align,
              int base,
              int ds,
              int ctgId,
              java.lang.String name,
              java.lang.String dsChrom,
              long dsStart,
              long dsEnd,
              boolean dsStrand)

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

Method Detail

getBase

public int getBase()

getDir

public boolean getDir()

get Dir

Returns:

boolean

getStrand

public boolean getStrand()

get Strand

Returns:

boolean

getAlign

public int getAlign()

get Align

Returns:

int

getDs

public int getDs()

get DataSet

Returns:

int

getContigNum

public int getContigNum()

get Contig Number

Returns:

int

getContigName

public java.lang.String getContigName()

get Contig Name

Returns:

String

getDsChrom

public java.lang.String getDsChrom()

get DataSet Chromosome

Returns:

String

getDsStart

public long getDsStart()

get DataSet Start

Returns:

long

getDsEnd

public long getDsEnd()

get DataSet End

Returns:

long

getDsStrand

public boolean getDsStrand()

get DataSet Strand

Returns:

boolean

setDsStart

public void setDsStart(long dsStart)

set DataSet Start

Parameters:

dsStart - long

setDsEnd

public void setDsEnd(long dsEnd)

set DataSet End

Parameters:

dsEnd - long

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