public final class TranscriptSequenceOntologyDecorator extends Object
TranscriptModel
using genomic positions.Constructor and Description |
---|
TranscriptSequenceOntologyDecorator(TranscriptModel transcript)
Initialize the object with the given
TranscriptModel . |
Modifier and Type | Method and Description |
---|---|
boolean |
containsExon(GenomeInterval interval) |
GenomeInterval |
getDownstreamInterval() |
GenomeInterval |
getFivePrimeUTRInterval()
Returns the genomic 5' UTR interval.
|
GenomeInterval |
getStartCodonInterval() |
GenomeInterval |
getStopCodonInterval() |
GenomeInterval |
getThreePrimeUTRInterval()
Returns the genomic 3' UTR interval.
|
TranscriptModel |
getTranscript() |
GenomeInterval |
getUpstreamInterval() |
boolean |
liesInCDS(GenomePosition pos) |
boolean |
liesInCDSExon(GenomeInterval interval) |
boolean |
liesInCDSExon(GenomePosition pos) |
boolean |
liesInCDSIntron(GenomePosition pos) |
boolean |
liesInDownstreamRegion(GenomePosition pos)
Returns whether the given
pos lies within with the downstream region of the transcript. |
boolean |
liesInExon(GenomeInterval interval) |
boolean |
liesInExon(GenomePosition pos) |
boolean |
liesInFivePrimeUTR(GenomePosition pos) |
boolean |
liesInIntron(GenomeInterval interval) |
boolean |
liesInIntron(GenomePosition pos) |
boolean |
liesInSpliceAcceptorSite(GenomePosition pos)
Returns whether the given
pos lies within a splice acceptor site. |
boolean |
liesInSpliceDonorSite(GenomePosition pos)
Returns whether the given
pos lies within a splice donor site. |
boolean |
liesInSpliceRegion(GenomePosition pos)
Returns whether the given
pos lies within a splice region. |
boolean |
liesInThreePrimeUTR(GenomePosition pos) |
boolean |
liesInTranslationalStartSite(GenomePosition pos) |
boolean |
liesInTranslationalStopSite(GenomePosition pos) |
boolean |
liesInUpstreamRegion(GenomePosition pos)
Returns whether the given
pos lies within with the upstream region of the transcript. |
boolean |
overlapsWithCDS(GenomeInterval interval) |
boolean |
overlapsWithCDSExon(GenomeInterval interval) |
boolean |
overlapsWithCDSIntron(GenomeInterval changeInterval) |
boolean |
overlapsWithDownstreamRegion(GenomeInterval interval)
Returns whether the given
interval overlaps with the downstream region of the transcript. |
boolean |
overlapsWithExon(GenomeInterval interval) |
boolean |
overlapsWithFivePrimeUTR(GenomeInterval interval) |
boolean |
overlapsWithIntron(GenomeInterval changeInterval) |
boolean |
overlapsWithSpliceAcceptorSite(GenomeInterval interval)
Returns whether the given
interval overlaps with a splice acceptor site. |
boolean |
overlapsWithSpliceDonorSite(GenomeInterval interval)
Returns whether the given
interval overlaps with a splice donor site. |
boolean |
overlapsWithSpliceRegion(GenomeInterval interval)
Returns whether the given
interval overlaps with a splice region. |
boolean |
overlapsWithThreePrimeUTR(GenomeInterval interval) |
boolean |
overlapsWithTranslationalStartSite(GenomeInterval interval) |
boolean |
overlapsWithTranslationalStopSite(GenomeInterval interval) |
boolean |
overlapsWithUpstreamRegion(GenomeInterval interval)
Returns whether the given
interval overlaps with the upstream region of the transcript. |
public TranscriptSequenceOntologyDecorator(TranscriptModel transcript)
TranscriptModel
.transcript
- the TranscriptModel
to decoratepublic TranscriptModel getTranscript()
public GenomeInterval getStartCodonInterval()
GenomeInterval
with the start codonpublic GenomeInterval getStopCodonInterval()
GenomeInterval
with the start codonpublic GenomeInterval getFivePrimeUTRInterval()
GenomeInterval
with the 5' UTRpublic GenomeInterval getThreePrimeUTRInterval()
GenomeInterval
with the 3' UTRpublic boolean containsExon(GenomeInterval interval)
interval
- query whether interval
contains an exontrue
if interval
contains a full exon (coding or non-coding).public boolean overlapsWithCDSExon(GenomeInterval interval)
interval
- query whether interval
overlaps with a CDS exon (exon that overlaps with CDS)true
if interval
overlaps with a CDS-overlapping exonpublic boolean liesInCDSExon(GenomeInterval interval)
interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
falls fully into the coding part of an exonpublic boolean liesInCDSExon(GenomePosition pos)
pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
points to a base in the coding part of an exonpublic boolean overlapsWithCDS(GenomeInterval interval)
interval
- query whether interval
overlaps with the CDS regiontrue
if interval
overlaps with the CDS region of the transcriptpublic boolean liesInCDS(GenomePosition pos)
true
if pos
lies within the CDS of transcript
public boolean overlapsWithIntron(GenomeInterval changeInterval)
changeInterval
- the GenomeInterval
to use for the querytrue
if changeInterval
overlaps with an intron of transcript
public boolean liesInIntron(GenomePosition pos)
true
if pos
lies within an intron of transcript
public boolean overlapsWithCDSIntron(GenomeInterval changeInterval)
changeInterval
- the GenomeInterval
to use for the querytrue
if changeInterval
overlaps with an intron of transcript
that
overlaps with the CDSpublic boolean liesInCDSIntron(GenomePosition pos)
true
if the GenomePosition
lies within an intron of transcript
that
overlaps with the CDSpublic boolean overlapsWithTranslationalStartSite(GenomeInterval interval)
interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with the translational start sitepublic boolean liesInTranslationalStartSite(GenomePosition pos)
true
if the GenomePosition
lies within the translational start sitepublic boolean overlapsWithTranslationalStopSite(GenomeInterval interval)
interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with the translational stop sitepublic boolean liesInTranslationalStopSite(GenomePosition pos)
true
if the GenomePosition
lies within the translational stop sitepublic boolean overlapsWithSpliceRegion(GenomeInterval interval)
interval
overlaps with a splice region.
A splice_region_variant is a sequence variant in which a change has occurred within the region of the splice
site, either within 1-3 bases of the exon or 3-8 bases of the intron.interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with a splice region.public boolean liesInSpliceRegion(GenomePosition pos)
pos
lies within a splice region.
A splice_region_variant is a sequence variant in which a change has occurred within the region of the splice
site, either within 1-3 bases of the exon or 3-8 bases of the intron.pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
lies within a splice donor site.public boolean overlapsWithSpliceDonorSite(GenomeInterval interval)
interval
overlaps with a splice donor site.
A splice variant that changes the 2 base pair region at the 5' end of an intron.interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with a splice donor site.public boolean liesInSpliceDonorSite(GenomePosition pos)
pos
lies within a splice donor site.
A splice variant that changes the 2 base pair region at the 5' end of an intron.pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
lies within a splice donor site.public boolean overlapsWithSpliceAcceptorSite(GenomeInterval interval)
interval
overlaps with a splice acceptor site.
A splice variant that changes the 2 base pair region at the 3' end of an intron.interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with a splice acceptor site.public boolean liesInSpliceAcceptorSite(GenomePosition pos)
pos
lies within a splice acceptor site.
A splice variant that changes the 2 base pair region at the 3' end of an intron.pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
lies within a splice acceptor site.public GenomeInterval getUpstreamInterval()
GenomeInterval
that gives the upstream region of the transcript.public boolean overlapsWithUpstreamRegion(GenomeInterval interval)
interval
overlaps with the upstream region of the transcript.
The upstream region of the transcript is up to 1000 bp upstream of the transcript.interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with the upstream region of the transcript.public boolean liesInUpstreamRegion(GenomePosition pos)
pos
lies within with the upstream region of the transcript.
The upstream region of the transcript is up to 1000 bp upstream of the transcript.pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
lies within the upstream region of the transcript.public GenomeInterval getDownstreamInterval()
GenomeInterval
that gives the downstream region of the transcript.public boolean overlapsWithDownstreamRegion(GenomeInterval interval)
interval
overlaps with the downstream region of the transcript.
The upstream region of the transcript is up to 1000 bp upstream of the transcript.interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with the downstream region of the transcript.public boolean liesInDownstreamRegion(GenomePosition pos)
pos
lies within with the downstream region of the transcript.
The upstream region of the transcript is up to 1000 bp downstream of the transcript.pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
lies within the downstream region of the transcript.public boolean overlapsWithFivePrimeUTR(GenomeInterval interval)
interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with the 5' UTRpublic boolean liesInFivePrimeUTR(GenomePosition pos)
pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
lies in the 5' UTRpublic boolean overlapsWithThreePrimeUTR(GenomeInterval interval)
interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
overlaps with the 3' UTRpublic boolean liesInThreePrimeUTR(GenomePosition pos)
pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
lies in the 3' UTRpublic boolean liesInIntron(GenomeInterval interval)
interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
falls fully into an intronpublic boolean liesInExon(GenomeInterval interval)
interval
- the GenomeInterval
to use for queryingtrue
if the GenomeInterval
falls fully into an exonpublic boolean liesInExon(GenomePosition pos)
pos
- the GenomePosition
to use for queryingtrue
if the GenomePosition
points to a base an exonpublic boolean overlapsWithExon(GenomeInterval interval)
interval
- the GenomeInterval
to use for the overlap checkingtrue
if the interval overlaps with an exonCopyright © 2016. All rights reserved.