Uses of Class
org.snpeff.interval.Marker
Packages that use Marker
Package
Description
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Uses of Marker in org.snpeff.binseq
Methods in org.snpeff.binseq with parameters of type MarkerModifier and TypeMethodDescriptionGenomicSequences.queryMarkerSequence
(Marker marker) Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form databaseGenomicSequences.querySequence
(Marker marker) Get sequence for a marker -
Uses of Marker in org.snpeff.coverage
Methods in org.snpeff.coverage that return types with arguments of type MarkerMethods in org.snpeff.coverage with parameters of type MarkerModifier and TypeMethodDescriptionvoid
CountReads.addMarkerType
(Marker marker, String type) void
CountReadsOnMarkers.addMarkerType
(Marker marker, String type) void
double
CountFragments.avgCoverage
(Marker m) Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)double
Coverage.avgCoverage
(Marker m) Calculate average coverage per baselong
Calculate total coverage per baseMarkerTypes.getSubType
(Marker marker) Some markers have sub-typesGet marker typeMarkerTypes.getTypeRank
(Marker marker) Get marker + rank (in case of exon or intron)boolean
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Uses of Marker in org.snpeff.fileIterator
Classes in org.snpeff.fileIterator with type parameters of type MarkerModifier and TypeClassDescriptionclass
MarkerFileIterator<M extends Marker>
Opens a Marker file and iterates over all markers -
Uses of Marker in org.snpeff.interval
Classes in org.snpeff.interval with type parameters of type MarkerModifier and TypeClassDescriptionclass
IntervalAndSubIntervals<T extends Marker>
Interval that contains sub intervals.Subclasses of Marker in org.snpeff.intervalModifier and TypeClassDescriptionclass
CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein.class
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalidclass
This is a custom interval (i.e.class
Interval for a gene, as well as some other information: exons, utrs, cds, etc.class
Interval for an exonclass
Interval for a gene, as well as transcriptsclass
An interval intended as a markclass
This is just used for the Interval class.class
An interval intended as a markclass
An interval intended as a markclass
Interval for in intergenic regionclass
Interval for a conserved intergenic regionclass
IntervalAndSubIntervals<T extends Marker>
Interval that contains sub intervals.class
Intronclass
Interval for a conserved non-coding region in an intronclass
This is a marker used as a 'fake' parent during data serializationclass
Marker with a DNA sequenceclass
miRna binding site (usually this was predicted by some algorithm)class
Regulatory elementsclass
NextProt annotation markerclass
Protein interaction: An amino acid that is "in contact" with another amino acid.class
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.class
Protein interaction: An amino acid that is "in contact" with another amino acid.class
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.class
Regulatory elementsclass
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.class
Interval for a splice site acceptor Note: Splice sites donnor are defined as the last 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicingclass
A (putative) branch site.class
A (putative) U12 branch site.class
Interval for a splice site donnor Note: Splice sites donnor are defined as the first 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicingclass
Interval for a splice site acceptor From Sequence Ontology: 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.class
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.class
Interval for a gene, as well as some other information: exons, utrs, cds, etc.class
Interval for a UTR (5 prime UTR and 3 prime UTRclass
Interval for a UTR (5 prime UTR and 3 prime UTRclass
Interval for a UTR (5 prime UTR and 3 prime UTRclass
A variant represents a change in a reference sequenceclass
A 'BND' variant (i.e.class
A variant respect to non-reference (e.g.class
A variant that has a numeric score.Fields in org.snpeff.interval with type parameters of type MarkerMethods in org.snpeff.interval that return MarkerModifier and TypeMethodDescriptionApply a variant to a marker.protected Marker
Apply a Variant to a marker.protected Marker
Apply a Variant to a marker.protected Marker
Apply a Variant to a marker.protected Marker
Marker.applyMixed
(Variant variant) Apply a mixed variant Note: MIXED variant is interpreted as "MNP + InDel"Transcript.cdsMarker()
Create a marker of the coding region in this transcriptMarker.clone()
Marker.cloneShallow()
Perform a shallow cloneMarkers.get
(int i) VariantBnd.getEndPoint()
Marker.getParent()
Transcript.getTss()
Create a TSS markerIntersect of two markersMarker[]
Markers.toArray()
Union of two markersUnion of two markersMethods in org.snpeff.interval that return types with arguments of type MarkerModifier and TypeMethodDescriptionMarkerUtil.collapseZeroGap
(Markers markersOri) Collapse adjacent intervals (i.e.MarkerUtil.collapseZeroGap
(Markers markersOri) Collapse adjacent intervals (i.e.Genes.createUpDownStream
(int upDownLength) Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength <=0 no interval is createdMarkers.getMarkers()
IntervalSetIterator.iterator()
Markers.iterator()
IntervalSetIterator.next()
MarkerUtil.redundant
(Collection<? extends Marker> markersOri) Redundant markers in a list: Find intervals that are totally included in other intervals in the listMarkerUtil.redundant
(Collection<? extends Marker> markersOri) Redundant markers in a list: Find intervals that are totally included in other intervals in the listMethods in org.snpeff.interval with parameters of type MarkerModifier and TypeMethodDescriptionvoid
boolean
Add an interval to the collectionvoid
Gene.addPerGene
(Marker marker) Add a gene dependent markerprotected void
Adjust [start,end] to include childint
int
int
How far apart are these intervals?Return an exon intersecting 'marker' (first exon found)Return the UTR that intersects 'marker' (null if not found)MarkerSeq.getSequence
(Marker marker) Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.boolean
Is 'interval' completely included in 'this'?Intersect of two markersIntersection between 'marker' and all sub-intervalsboolean
Interval.intersects
(Marker interval) Do the intervals intersect?abstract boolean
SpliceSite.intersectsCoreSpliceSite
(Marker marker) Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.boolean
SpliceSiteAcceptor.intersectsCoreSpliceSite
(Marker marker) boolean
SpliceSiteBranch.intersectsCoreSpliceSite
(Marker marker) These are NOT core splice sitesboolean
SpliceSiteDonor.intersectsCoreSpliceSite
(Marker marker) boolean
SpliceSiteRegion.intersectsCoreSpliceSite
(Marker marker) int
Interval.intersectSize
(Marker interval) How much do intervals intersect?protected boolean
Exon.isAdjustIfParentDoesNotInclude
(Marker parent) protected boolean
Marker.isAdjustIfParentDoesNotInclude
(Marker parent) Adjust parent if it does not include child?protected boolean
Transcript.isAdjustIfParentDoesNotInclude
(Marker parent) boolean
Interval.isSameChromo
(Marker interval) boolean
Return the difference between two markersCalculate 'set minus' using one intervalOnly the part of the change that overlaps with a marker Return the change (always in positive strand)Query all genomic regions that intersect 'marker'Query all genomic regions that intersect 'marker'Query all genomic regions that intersect 'marker'Query all genomic regions that intersect 'marker' (this makes sense in Gene, Transcript, Exon, etc.)Query all genomic regions that intersect 'marker'Return the first exon that intersects 'interval' (null if not found)Union of two markersUnion of two markersMethod parameters in org.snpeff.interval with type arguments of type MarkerModifier and TypeMethodDescriptionboolean
Markers.addAll
(Collection<? extends Marker> mm) Add all markers in this collectionint
Marker.distanceBases
(List<? extends Marker> markers, boolean fromEnd) Distance from the beginning/end of a list of intervals, until this SNP It count the number of bases in 'markers'MarkerUtil.redundant
(Collection<? extends Marker> markersOri) Redundant markers in a list: Find intervals that are totally included in other intervals in the listConstructors in org.snpeff.interval with parameters of type MarkerModifierConstructorDescriptionGene
(Marker parent, int start, int end, boolean strandMinus, String id, String geneName, BioType bioType) GenericMarker
(Marker parent, int start, int end, String id) Gtf2Marker
(Marker parent, int start, int end, boolean strandMinus, String id) IntervalAndSubIntervals
(Marker parent, int start, int end, boolean strandMinus, String id) MicroRnaBindingSite
(Marker parent, int start, int end, boolean strandMinus, String id, double pValue) Motif
(Marker parent, int start, int end, boolean strandMinus, String id, String pwmName, String pwmId) RareAminoAcid
(Marker parent, int start, int end, String id) Regulation
(Marker parent, int start, int end, boolean strandMinus, String id, String name, String regulationType) This constructor is used when we only have interval data (e.g.VariantBnd
(Marker parent, int start, String ref, String alt, Chromosome chrTr, int startTr, boolean left, boolean before) VariantWithScore
(Marker parent, int start, int end, String id, double score) -
Uses of Marker in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type MarkerModifier and TypeMethodDescriptionprotected VariantEffect
CodonChange.effect
(Marker marker, EffectType effectType, boolean allowReplace) Calculate variant effectprotected VariantEffect
CodonChange.effectNoCodon
(Marker marker, EffectType effectType) protected VariantEffect
CodonChange.effectNoCodon
(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact) -
Uses of Marker in org.snpeff.interval.tree
Fields in org.snpeff.interval.tree declared as MarkerModifier and TypeFieldDescriptionprotected static final Marker[]
IntervalTreeArray.EMPTY_MARKER_ARRAY
protected Marker[][]
IntervalTreeArray.intersectMarkers
protected Marker[]
IntervalNode.intervalsCenter
Methods in org.snpeff.interval.tree that return types with arguments of type MarkerModifier and TypeMethodDescriptionIntervalNodeOri.iterator()
IntervalTree.iterator()
IntervalTreeArray.iterator()
IntervalTreeOri.iterator()
Methods in org.snpeff.interval.tree with parameters of type MarkerModifier and TypeMethodDescriptionvoid
Add an intervalvoid
Add an interval object to the interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to buildvoid
void
Add an interval object to the interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to buildvoid
Add an interval object to the interval tree's listQuery all intervals that intersect with 'interval'Obtain all intervals that intersect with 'marker.start'Method parameters in org.snpeff.interval.tree with type arguments of type MarkerModifier and TypeMethodDescriptionvoid
IntervalForest.add
(Collection<? extends Marker> intervals) Add all intervals -
Uses of Marker in org.snpeff.outputFormatter
Methods in org.snpeff.outputFormatter with parameters of type MarkerModifier and TypeMethodDescriptionBedOutputFormatter.endSection
(Marker marker) Finish up sectionOutputFormatter.endSection
(Marker marker) Finish up sectionVcfOutputFormatter.endSection
(Marker marker) Finish up sectionvoid
OutputFormatter.printSection
(Marker marker) End this section and print resultsvoid
BedOutputFormatter.startSection
(Marker marker) void
OutputFormatter.startSection
(Marker marker) Starts a new sectionvoid
VcfOutputFormatter.startSection
(Marker marker) -
Uses of Marker in org.snpeff.probablility
Methods in org.snpeff.probablility that return Marker -
Uses of Marker in org.snpeff.serializer
Methods in org.snpeff.serializer that return MarkerModifier and TypeMethodDescriptionprotected Marker
MarkerSerializer.getMarkerById
(int id) MarkerSerializer.getNextFieldMarker()
Methods in org.snpeff.serializer with parameters of type MarkerModifier and TypeMethodDescriptionvoid
int
MarkerSerializer.getIdByMarker
(Marker m) int
Save a markerMethod parameters in org.snpeff.serializer with type arguments of type Marker -
Uses of Marker in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as MarkerModifier and TypeFieldDescriptionprotected Marker
Hgvs.marker
protected Marker
VariantEffect.marker
Methods in org.snpeff.snpEffect that return MarkerModifier and TypeMethodDescriptionVariantEffect.getMarker()
VariantEffectFusion.getMarker()
VariantEffectStructural.getMarker()
Methods in org.snpeff.snpEffect with parameters of type MarkerModifier and TypeMethodDescriptionvoid
Add a markervoid
VariantEffects.add
(Variant variant, Marker marker, EffectType effectType, String message) Add an effectvoid
VariantEffects.add
(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) Add an effectvoid
VariantEffects.addEffectType
(Variant variant, Marker marker, EffectType effectType) Add: If possible, only add an effect type (otherwise add the full effect)protected boolean
protected boolean
VariantEffectStructural.isTranscript
(Marker m) Return a collection of intervals that intersect 'marker'SnpEffectPredictor.queryClosestGene
(Marker inputInterval) Find closest gene to this markerReturn a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possibleName of the regions hit by a markerSnpEffectPredictor.regions
(Marker marker, boolean showGeneDetails, boolean compareTemplate, String id) Name of the regions hit by a markervoid
VariantEffect.set
(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) void
Set marker.void
Method parameters in org.snpeff.snpEffect with type arguments of type MarkerModifier and TypeMethodDescriptionprotected int
VariantEffectStructural.countGenes
(List<Marker> features) Constructors in org.snpeff.snpEffect with parameters of type MarkerModifierConstructorDescriptionVariantEffect
(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String codonsOld, String codonsNew, int codonNum, int codonIndex, int cDnaPos) VariantEffectFusion
(Variant variant, Marker mLeft, Marker mRight) -
Uses of Marker in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return MarkerMethods in org.snpeff.snpEffect.factory with parameters of type Marker -
Uses of Marker in org.snpeff.snpEffect.testCases.unity
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type MarkerModifier and TypeMethodDescriptionvoid
Add markers to SnpEffPredictorprotected int
TestCasesIntervalTree.compareQuery
(Marker m, Itree intTree) Perform a query using 'naive' lookup and interval forest.TestCasesIntervals.intersects
(Markers interval1, Marker intervals) protected Markers
TestCasesIntervalTree.queryNaive
(Marker query) Naively find all intervals intersecting 'marker' -
Uses of Marker in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type Marker -
Uses of Marker in org.snpeff.svg
Methods in org.snpeff.svg with parameters of type MarkerConstructors in org.snpeff.svg with parameters of type Marker -
Uses of Marker in org.snpeff.vcf
Subclasses of Marker in org.snpeff.vcfModifier and TypeClassDescriptionclass
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.class
A VCF entry (a line) in a VCF fileConstructors in org.snpeff.vcf with parameters of type Marker