Uses of Class
org.snpeff.interval.Marker
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Uses of Marker in org.snpeff.binseq
Methods in org.snpeff.binseq with parameters of type Marker Modifier and Type Method Description MarkerSeq
GenomicSequences. queryMarkerSequence(Marker marker)
Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form databasejava.lang.String
GenomicSequences. 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 Marker Modifier and Type Method Description CountByKey<Marker>
CountReads. getCountBases()
CountByKey<Marker>
CountReads. getCountReads()
Methods in org.snpeff.coverage with parameters of type Marker Modifier and Type Method Description void
CountReads. addMarkerType(Marker marker, java.lang.String type)
void
CountReadsOnMarkers. addMarkerType(Marker marker, java.lang.String type)
void
MarkerTypes. addType(Marker marker, java.lang.String type)
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
Coverage. coverage(Marker m)
Calculate total coverage per basejava.lang.String
MarkerTypes. getSubType(Marker marker)
Some markers have sub-typesjava.lang.String
MarkerTypes. getType(Marker marker)
Get marker typejava.lang.String
MarkerTypes. getTypeRank(Marker marker)
Get marker + rank (in case of exon or intron)boolean
MarkerTypes. isType(Marker m, java.lang.String mtype)
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Uses of Marker in org.snpeff.fileIterator
Classes in org.snpeff.fileIterator with type parameters of type Marker Modifier and Type Class Description class
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 Marker Modifier and Type Class Description class
IntervalAndSubIntervals<T extends Marker>
Interval that contains sub intervals.Subclasses of Marker in org.snpeff.interval Modifier and Type Class Description class
Cds
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
Chromosome
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalidclass
Custom
This is a custom interval (i.e.class
Downstream
Interval for a gene, as well as some other information: exons, utrs, cds, etc.class
Exon
Interval for an exonclass
Gene
Interval for a gene, as well as transcriptsclass
GenericMarker
An interval intended as a markclass
Genome
This is just used for the Interval class.class
GffMarker
An interval intended as a markclass
Gtf2Marker
An interval intended as a markclass
Intergenic
Interval for in intergenic regionclass
IntergenicConserved
Interval for a conserved intergenic regionclass
IntervalAndSubIntervals<T extends Marker>
Interval that contains sub intervals.class
Intron
Intronclass
IntronConserved
Interval for a conserved non-coding region in an intronclass
MarkerParentId
This is a marker used as a 'fake' parent during data serializationclass
MarkerSeq
Marker with a DNA sequenceclass
MicroRnaBindingSite
miRna binding site (usually this was predicted by some algorithm)class
Motif
Regulatory elementsclass
NextProt
NextProt annotation markerclass
ProteinInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid.class
ProteinProteinInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.class
ProteinStructuralInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid.class
RareAminoAcid
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.class
Regulation
Regulatory elementsclass
SpliceSite
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.class
SpliceSiteAcceptor
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
SpliceSiteBranch
A (putative) branch site.class
SpliceSiteBranchU12
A (putative) U12 branch site.class
SpliceSiteDonor
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
SpliceSiteRegion
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
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.class
Upstream
Interval for a gene, as well as some other information: exons, utrs, cds, etc.class
Utr
Interval for a UTR (5 prime UTR and 3 prime UTRclass
Utr3prime
Interval for a UTR (5 prime UTR and 3 prime UTRclass
Utr5prime
Interval for a UTR (5 prime UTR and 3 prime UTRclass
Variant
A variant represents a change in a reference sequenceclass
VariantBnd
A 'BND' variant (i.e.class
VariantNonRef
A variant respect to non-reference (e.g.class
VariantWithScore
A variant that has a numeric score.Fields in org.snpeff.interval with type parameters of type Marker Modifier and Type Field Description protected java.util.ArrayList<Marker>
Markers. markers
Methods in org.snpeff.interval that return Marker Modifier and Type Method Description Marker
Marker. apply(Variant variant)
Apply a variant to a marker.protected Marker
Marker. applyDel(Variant variant)
Apply a Variant to a marker.protected Marker
Marker. applyDup(Variant variant)
Apply a Variant to a marker.protected Marker
Marker. applyIns(Variant variant)
Apply a Variant to a marker.protected Marker
Marker. applyMixed(Variant variant)
Apply a mixed variant Note: MIXED variant is interpreted as "MNP + InDel"Marker
Transcript. cdsMarker()
Create a marker of the coding region in this transcriptMarker
Marker. clone()
Marker
Marker. cloneShallow()
Perform a shallow cloneMarker
Markers. get(int i)
Marker
VariantBnd. getEndPoint()
Marker
Marker. getParent()
Marker
Transcript. getTss()
Create a TSS markerMarker
Marker. intersect(Marker marker)
Intersect of two markersMarker[]
Markers. toArray()
Marker
Marker. union(Marker m)
Union of two markersMarker
MarkerSeq. union(Marker m)
Union of two markersMethods in org.snpeff.interval that return types with arguments of type Marker Modifier and Type Method Description static java.util.Map<Marker,Marker>
MarkerUtil. collapseZeroGap(Markers markersOri)
Collapse adjacent intervals (i.e.static java.util.Map<Marker,Marker>
MarkerUtil. collapseZeroGap(Markers markersOri)
Collapse adjacent intervals (i.e.java.util.List<Marker>
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 createdjava.util.List<Marker>
Markers. getMarkers()
java.util.Iterator<java.util.Set<Marker>>
IntervalSetIterator. iterator()
java.util.Iterator<Marker>
Markers. iterator()
java.util.Set<Marker>
IntervalSetIterator. next()
static java.util.Map<Marker,Marker>
MarkerUtil. redundant(java.util.Collection<? extends Marker> markersOri)
Redundant markers in a list: Find intervals that are totally included in other intervals in the liststatic java.util.Map<Marker,Marker>
MarkerUtil. redundant(java.util.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 Marker Modifier and Type Method Description void
CytoBands. add(Marker m)
boolean
Markers. add(Marker marker)
Add an interval to the collectionvoid
Gene. addPerGene(Marker marker)
Add a gene dependent markerprotected void
Marker. adjust(Marker child)
Adjust [start,end] to include childint
IntervalComparatorByEnd. compare(Marker i1, Marker i2)
int
IntervalComparatorByStart. compare(Marker i1, Marker i2)
int
Marker. distance(Marker interval)
How far apart are these intervals?Exon
Transcript. findExon(Marker marker)
Return an exon intersecting 'marker' (first exon found)java.util.List<Utr>
Transcript. findUtrs(Marker marker)
Return the UTR that intersects 'marker' (null if not found)java.lang.String
MarkerSeq. getSequence(Marker marker)
Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.boolean
Marker. includes(Marker marker)
Is 'interval' completely included in 'this'?Marker
Marker. intersect(Marker marker)
Intersect of two markersMarkers
Markers. intersect(Marker marker)
Intersection 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
Transcript. isUtr(Marker marker)
Markers
Marker. minus(Marker interval)
Return the difference between two markersMarkers
Markers. minus(Marker interval)
Calculate 'set minus' using one intervaljava.lang.String
Variant. netChange(Marker marker)
Only the part of the change that overlaps with a marker Return the change (always in positive strand)Markers
CytoBands. query(Marker marker)
Markers
Exon. query(Marker marker)
Query all genomic regions that intersect 'marker'Markers
IntervalAndSubIntervals. query(Marker marker)
Query all genomic regions that intersect 'marker'Markers
Intron. query(Marker marker)
Query all genomic regions that intersect 'marker'Markers
Marker. query(Marker marker)
Query all genomic regions that intersect 'marker' (this makes sense in Gene, Transcript, Exon, etc.)Markers
Transcript. query(Marker marker)
Query all genomic regions that intersect 'marker'Exon
Transcript. queryExon(Marker interval)
Return the first exon that intersects 'interval' (null if not found)Marker
Marker. union(Marker m)
Union of two markersMarker
MarkerSeq. union(Marker m)
Union of two markersMethod parameters in org.snpeff.interval with type arguments of type Marker Modifier and Type Method Description boolean
Markers. addAll(java.util.Collection<? extends Marker> mm)
Add all markers in this collectionint
Marker. distanceBases(java.util.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'static java.util.Map<Marker,Marker>
MarkerUtil. redundant(java.util.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 Marker Constructor Description Custom(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String label)
Gene(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String geneName, BioType bioType)
GenericMarker(Marker parent, int start, int end, java.lang.String id)
GffMarker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
Gtf2Marker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
IntervalAndSubIntervals(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
Marker(Marker parent, int start, int end)
Marker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
MarkerSeq(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
MarkerSeq(Marker parent, int start, int end, java.lang.String seq)
MicroRnaBindingSite(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, double pValue)
Motif(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String pwmName, java.lang.String pwmId)
RareAminoAcid(Marker parent, int start, int end, java.lang.String id)
Regulation(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String name, java.lang.String regulationType)
Variant(Marker parent, int start, int end, java.lang.String id)
This constructor is used when we only have interval data (e.g.Variant(Marker parent, int position, java.lang.String referenceStr, java.lang.String altStr)
Variant(Marker parent, int position, java.lang.String referenceStr, java.lang.String altStr, java.lang.String id)
VariantBnd(Marker parent, int start, java.lang.String ref, java.lang.String alt, Chromosome chrTr, int startTr, boolean left, boolean before)
VariantWithScore(Marker parent, int start, int end, java.lang.String id, double score)
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Uses of Marker in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type Marker Modifier and Type Method Description protected 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)
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Uses of Marker in org.snpeff.interval.tree
Fields in org.snpeff.interval.tree declared as Marker Modifier and Type Field Description protected static 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 Marker Modifier and Type Method Description java.util.Iterator<Marker>
IntervalNodeOri. iterator()
java.util.Iterator<Marker>
IntervalTree. iterator()
java.util.Iterator<Marker>
IntervalTreeArray. iterator()
java.util.Iterator<Marker>
IntervalTreeOri. iterator()
Methods in org.snpeff.interval.tree with parameters of type Marker Modifier and Type Method Description void
IntervalForest. add(Marker interval)
Add an intervalvoid
IntervalTree. add(Marker interval)
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
IntervalTreeArray. add(Marker interval)
void
IntervalTreeOri. add(Marker interval)
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
Itree. add(Marker interval)
Add an interval object to the interval tree's listMarkers
IntervalForest. query(Marker marker)
Query all intervals that intersect with 'interval'Markers
IntervalForest. stab(Marker marker)
Obtain all intervals that intersect with 'marker.start'Method parameters in org.snpeff.interval.tree with type arguments of type Marker Modifier and Type Method Description void
IntervalForest. add(java.util.Collection<? extends Marker> intervals)
Add all intervals -
Uses of Marker in org.snpeff.outputFormatter
Methods in org.snpeff.outputFormatter with parameters of type Marker Modifier and Type Method Description java.lang.String
BedOutputFormatter. endSection(Marker marker)
Finish up sectionjava.lang.String
OutputFormatter. endSection(Marker marker)
Finish up sectionjava.lang.String
VcfOutputFormatter. 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)
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Uses of Marker in org.snpeff.probablility
Methods in org.snpeff.probablility that return Marker Modifier and Type Method Description Marker
RandMarker. rand(int readLen)
Create a random marker of size readLen -
Uses of Marker in org.snpeff.serializer
Methods in org.snpeff.serializer that return Marker Modifier and Type Method Description protected Marker
MarkerSerializer. getMarkerById(int id)
Marker
MarkerSerializer. getNextFieldMarker()
Methods in org.snpeff.serializer with parameters of type Marker Modifier and Type Method Description void
MarkerSerializer. doNotSave(Marker m)
int
MarkerSerializer. getIdByMarker(Marker m)
int
MarkerSerializer. save(Marker m)
Save a markerMethod parameters in org.snpeff.serializer with type arguments of type Marker Modifier and Type Method Description java.lang.String
MarkerSerializer. save(java.lang.Iterable<Marker> markersCollection)
Save all markers -
Uses of Marker in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as Marker Modifier and Type Field Description protected Marker
Hgvs. marker
protected Marker
VariantEffect. marker
Methods in org.snpeff.snpEffect that return Marker Modifier and Type Method Description Marker
VariantEffect. getMarker()
Marker
VariantEffectFusion. getMarker()
Marker
VariantEffectStructural. getMarker()
Methods in org.snpeff.snpEffect with parameters of type Marker Modifier and Type Method Description void
SnpEffectPredictor. add(Marker marker)
Add a markervoid
VariantEffects. add(Variant variant, Marker marker, EffectType effectType, java.lang.String message)
Add an effectvoid
VariantEffects. add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.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
VariantEffectStructural. isGene(Marker m)
protected boolean
VariantEffectStructural. isTranscript(Marker m)
Markers
SnpEffectPredictor. query(Marker marker)
Return a collection of intervals that intersect 'marker'Gene
SnpEffectPredictor. queryClosestGene(Marker inputInterval)
Find closest gene to this markerMarkers
SnpEffectPredictor. queryDeep(Marker marker)
Return a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possiblejava.util.Set<java.lang.String>
SnpEffectPredictor. regions(Marker marker, boolean showGeneDetails, boolean compareTemplate)
Name of the regions hit by a markerjava.util.Set<java.lang.String>
SnpEffectPredictor. regions(Marker marker, boolean showGeneDetails, boolean compareTemplate, java.lang.String id)
Name of the regions hit by a markervoid
VariantEffect. set(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String message)
void
VariantEffect. setMarker(Marker marker)
Set marker.void
VariantEffects. setMarker(Marker marker)
Method parameters in org.snpeff.snpEffect with type arguments of type Marker Modifier and Type Method Description protected int
VariantEffectStructural. countGenes(java.util.List<Marker> features)
Constructors in org.snpeff.snpEffect with parameters of type Marker Constructor Description VariantEffect(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String codonsOld, java.lang.String codonsNew, int codonNum, int codonIndex, int cDnaPos)
VariantEffectFusion(Variant variant, Marker mLeft, Marker mRight)
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Uses of Marker in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return Marker Modifier and Type Method Description protected Marker
SnpEffPredictorFactory. findMarker(java.lang.String id)
Methods in org.snpeff.snpEffect.factory with parameters of type Marker Modifier and Type Method Description protected void
SnpEffPredictorFactory. add(Marker marker)
Add a generic Markerprotected void
SnpEffPredictorFactory. addMarker(Marker marker, boolean unique)
Add a marker to the collection -
Uses of Marker in org.snpeff.snpEffect.testCases.unity
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type Marker Modifier and Type Method Description void
TestGenome. add(Marker marker)
Add markers to SnpEffPredictorprotected int
TestCasesIntervalTree. compareQuery(Marker m, Itree intTree)
Perform a query using 'naive' lookup and interval forest.Markers
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 Modifier and Type Method Description void
PosStats. sample(Marker marker, Marker markerReference)
Use 'num' as a sample -
Uses of Marker in org.snpeff.svg
Methods in org.snpeff.svg with parameters of type Marker Modifier and Type Method Description static Svg
Svg. factory(Marker m, Svg svg)
Constructors in org.snpeff.svg with parameters of type Marker Constructor Description Svg(Marker m, Svg svg)
SvgScale(Marker m, Svg svg)
SvgSpacer(Marker m, Svg svg)
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Uses of Marker in org.snpeff.vcf
Subclasses of Marker in org.snpeff.vcf Modifier and Type Class Description class
VariantVcfEntry
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.class
VcfEntry
A VCF entry (a line) in a VCF fileConstructors in org.snpeff.vcf with parameters of type Marker Constructor Description VcfEntry(VcfFileIterator vcfFileIterator, Marker parent, java.lang.String chromosomeName, int start, java.lang.String id, java.lang.String ref, java.lang.String altsStr, double quality, java.lang.String filterPass, java.lang.String infoStr, java.lang.String format)
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