public final class GenomeInterval extends Object implements Serializable, Comparable<GenomeInterval>
GenomeInterval
.Constructor and Description |
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GenomeInterval(GenomeInterval other)
construct genome interval from other with selected coordinate system
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GenomeInterval(GenomeInterval other,
Strand strand)
construct genome interval from other with selected strand
|
GenomeInterval(GenomePosition pos,
int length)
construct genome interval from
GenomePosition with a length towards 3' of pos' coordinate system |
GenomeInterval(ReferenceDictionary refDict,
Strand strand,
int chr,
int beginPos,
int endPos)
construct genome interval with zero-based coordinate system
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GenomeInterval(ReferenceDictionary refDict,
Strand strand,
int chr,
int beginPos,
int endPos,
PositionType positionType)
construct genome interval with selected coordinate system
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public GenomeInterval(ReferenceDictionary refDict, Strand strand, int chr, int beginPos, int endPos)
public GenomeInterval(ReferenceDictionary refDict, Strand strand, int chr, int beginPos, int endPos, PositionType positionType)
public GenomeInterval(GenomeInterval other)
public GenomeInterval(GenomeInterval other, Strand strand)
public GenomeInterval(GenomePosition pos, int length)
GenomePosition
with a length towards 3' of pos' coordinate systempublic ReferenceDictionary getRefDict()
ReferenceDictionary
to usepublic Strand getStrand()
Strand
of this GenomeInterval
public int getChr()
public int getBeginPos()
public int getEndPos()
public GenomeInterval withStrand(Strand strand)
public GenomePosition getGenomeBeginPos()
public GenomePosition getGenomeEndPos()
public int length()
public GenomeInterval intersection(GenomeInterval other)
this
and other
public GenomeInterval union(GenomeInterval other)
this
and other
and everything in between,
this
if on different chromosomes. Result will be on the same strand as this
.public boolean isLeftOf(GenomePosition pos)
pos
- query positionpublic boolean isRightOf(GenomePosition pos)
pos
- query positionpublic boolean isLeftOfGap(GenomePosition pos)
pos
- query positionpos
points atpublic boolean isRightOfGap(GenomePosition pos)
pos
- query positionpos
points atpublic boolean contains(GenomePosition pos)
pos
- query positionpublic boolean contains(GenomeInterval other)
other
- other GenomeInterval
to use for queryingother
public GenomeInterval withMorePadding(int padding)
GenomeInterval
that has padding
more bases towards each side as paddingpublic GenomeInterval withMorePadding(int paddingUpstream, int paddingDownstream)
GenomeInterval
that has padding
more bases towards either side as padding.public boolean overlapsWith(GenomeInterval other)
other
- other GenomeInterval
to check with overlap forother
overlaps with this
public int compareTo(GenomeInterval other)
compareTo
in interface Comparable<GenomeInterval>
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