Uses of Class
org.snpeff.interval.Markers
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Uses of Markers in org.snpeff
Methods in org.snpeff that return Markers Modifier and Type Method Description protected Markers
SnpEff. loadMarkers(java.lang.String fileName)
Read markers file Supported formats: BED, TXT, BigBed, GFF -
Uses of Markers in org.snpeff.fileIterator
Methods in org.snpeff.fileIterator that return Markers Modifier and Type Method Description static Markers
BedFileIterator. load(java.lang.String bedFileName, boolean verbose)
Markers
MarkerFileIterator. loadMarkers()
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Uses of Markers in org.snpeff.interval
Methods in org.snpeff.interval that return Markers Modifier and Type Method Description Markers
Markers. add(Markers markersToAdd)
Add all intervalsMarkers
Markers. intersect()
Perform the intersection of all overlapping sub-intervalsMarkers
Markers. intersect(Marker marker)
Intersection between 'marker' and all sub-intervalsMarkers
Gene. markers()
Markers
IntervalAndSubIntervals. markers()
A list of all markers in this transcriptMarkers
Transcript. markers()
A list of all markers in this transcriptMarkers
Markers. merge()
Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficientMarkers
Marker. minus(Marker interval)
Return the difference between two markersMarkers
Markers. minus(Marker interval)
Calculate 'set minus' using one intervalMarkers
Markers. minus(Markers intervals)
Returns the result of this set minus 'intervals'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
Marker. query(IntervalForest intervalForest)
Return a collection of intervals that intersect this markerMarkers
Transcript. query(Marker marker)
Query all genomic regions that intersect 'marker'Markers
VariantBnd. query(IntervalForest intervalForest)
Return a collection of intervals that intersect both ends of this variantstatic Markers
Markers. readMarkers(java.lang.String fileName)
Read markers from a file Supported formats: BED, BigBed, VCF, TXTstatic Markers
MarkerUtil. readTxt(java.lang.String fileName, Genome genome, int positionBase)
Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positionsMarkers
Markers. sort()
Sort intervalsMarkers
Markers. sort(boolean byEnd, boolean reverse)
Sort intervalsMarkers
Markers. union()
Perform the union of all overlapping intervalsMarkers
Markers. unique()
Remove duplicated markersMethods in org.snpeff.interval with parameters of type Markers Modifier and Type Method Description Markers
Markers. add(Markers markersToAdd)
Add all intervalsvoid
IntervalAndSubIntervals. addAll(Markers markers)
Add all markersstatic java.util.Map<Marker,Marker>
MarkerUtil. collapseZeroGap(Markers markersOri)
Collapse adjacent intervals (i.e.boolean
Markers. equals(Markers intervals)
Are all intervals equal?Markers
Markers. minus(Markers intervals)
Returns the result of this set minus 'intervals'Constructors in org.snpeff.interval with parameters of type Markers Constructor Description IntervalSetIterator(Markers intervals)
Markers(Markers otherMarkers)
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Uses of Markers in org.snpeff.interval.tree
Fields in org.snpeff.interval.tree declared as Markers Modifier and Type Field Description protected Markers
IntervalTree. intervals
protected Markers
IntervalTreeOri. intervals
protected Markers
IntervalTreeArray. markers
Methods in org.snpeff.interval.tree that return Markers Modifier and Type Method Description Markers
IntervalTree. getIntervals()
Markers
IntervalTreeArray. getIntervals()
Markers
IntervalTreeOri. getIntervals()
Markers
Itree. getIntervals()
Markers
IntervalForest. intersect(Markers markers)
Return the intersection of 'markers' and this IntervalForest For each marker 'm' in 'markers' - query the tree to get all markers intersecting 'm' - create a new interval which is the intersection of 'm' with all the resutls from the previous query.Markers
IntervalForest. query(Marker marker)
Query all intervals that intersect with 'interval'Markers
IntervalForest. query(Markers marker)
Query all intervals that intersect with any interval in 'intervals'Markers
IntervalNode. query(Interval queryInterval)
Perform an interval intersection query on the nodeMarkers
IntervalNodeOri. query(Interval target)
Perform an interval intersection query on the nodeMarkers
IntervalTree. query(Interval interval)
Perform an interval query, returning the intervals that intersect with 'interval'Markers
IntervalTreeArray. query(Interval marker)
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'Markers
IntervalTreeOri. query(Interval interval)
Perform an interval query, returning the intervals that intersect with 'interval'Markers
Itree. query(Interval interval)
Perform an interval query, returning the intervals that intersect with 'interval'Markers
IntervalForest. queryUnique(Markers markers)
Query unique intervals that intersect with any interval in 'markers' I.e.: Return a set of intervals that intersects (at least once) with any interval in 'markers'Markers
IntervalForest. stab(java.lang.String chromo, int point)
Obtain all intervals that intersect with 'point'Markers
IntervalForest. stab(Marker marker)
Obtain all intervals that intersect with 'marker.start'Markers
IntervalNode. stab(java.lang.Integer point)
Perform a stabbing query on the nodeMarkers
IntervalNodeOri. stab(java.lang.Integer point)
Perform a stabbing query on the nodeMarkers
IntervalTree. stab(int point)
Perform a stabbing query, returning the interval objectsMarkers
IntervalTreeArray. stab(int point)
Markers
IntervalTreeOri. stab(int point)
Perform a stabbing query, returning the interval objectsMarkers
Itree. stab(int point)
Perform a stabbing query, returning the interval objectsMethods in org.snpeff.interval.tree with parameters of type Markers Modifier and Type Method Description void
IntervalForest. add(Markers intervals)
Add all intervalsvoid
IntervalTree. add(Markers markers)
Add all intervals to 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(Markers markers)
void
IntervalTreeOri. add(Markers markers)
Add all intervals to 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(Markers markers)
Add all intervals to interval tree's listprotected void
IntervalNode. build(Markers markers)
Build interval treeprotected int
IntervalTreeArray. build(Markers markers)
Index intervals from 'start' to 'end' (index in 'markers')Markers
IntervalForest. intersect(Markers markers)
Return the intersection of 'markers' and this IntervalForest For each marker 'm' in 'markers' - query the tree to get all markers intersecting 'm' - create a new interval which is the intersection of 'm' with all the resutls from the previous query.protected IntervalNode
IntervalNode. newNode(Markers markers)
Create a new nodeMarkers
IntervalForest. query(Markers marker)
Query all intervals that intersect with any interval in 'intervals'protected void
IntervalTreeArray. query(Interval marker, int idx, Markers results)
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'protected void
IntervalTreeArray. queryIntersects(Interval marker, int idx, Markers results)
Query entries intersecting 'marker' at node 'idx'Markers
IntervalForest. queryUnique(Markers markers)
Query unique intervals that intersect with any interval in 'markers' I.e.: Return a set of intervals that intersects (at least once) with any interval in 'markers'protected void
IntervalTreeArray. stab(int point, int idx, Markers results)
protected void
IntervalTreeArray. stabIntersects(int point, int idx, Markers results)
Stab entries intersecting 'point' at node 'idx'Constructors in org.snpeff.interval.tree with parameters of type Markers Constructor Description IntervalForest(Markers markers)
IntervalNode(Markers markers)
IntervalNodeOri(Markers markers)
IntervalTree(Markers intervals)
Instantiate an interval tree with a list of intervalsIntervalTreeArray(Markers markers)
Instantiate an interval tree with a list of intervalsIntervalTreeOri(Markers intervals)
Instantiate an interval tree with a list of intervals -
Uses of Markers in org.snpeff.nextProt
Methods in org.snpeff.nextProt that return Markers Modifier and Type Method Description Markers
NextProtMarkerFactory. addMarkers(NextProtXmlEntry entry, NextProtXmlIsoform isoform, NextProtXmlAnnotation annotation, Location location, java.lang.String trId)
Create markers and add themMarkers
NextProtMarkerFactory. getMarkers()
Markers
NextProtMarkerFactory. nextProt(Transcript tr, java.lang.String accession, java.lang.String name, int aaStart, int aaEnd)
Create a single NextProt markerMarkers
NextProtMarkerFactory. nextProt(Transcript tr, NextProtXmlAnnotation annotation, Location location)
Create a list of NextProt markers according to this annotation -
Uses of Markers in org.snpeff.serializer
Methods in org.snpeff.serializer that return Markers Modifier and Type Method Description Markers
MarkerSerializer. getNextFieldMarkers()
Markers
MarkerSerializer. load(java.lang.String fileName)
Load data from fileMethods in org.snpeff.serializer with parameters of type Markers Modifier and Type Method Description void
MarkerSerializer. save(java.lang.String fileName, Markers markers)
Save data to file -
Uses of Markers in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return Markers Modifier and Type Method Description Markers
SnpEffectPredictor. createGenomicRegions()
Create (and add) up-down stream, splice sites, intergenic, etcMarkers
SnpEffectPredictor. getMarkers()
Markers
SnpEffectPredictor. query(Marker marker)
Return a collection of intervals that intersect 'marker'Markers
SnpEffectPredictor. queryDeep(Marker marker)
Return a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possibleMethods in org.snpeff.snpEffect with parameters of type Markers Modifier and Type Method Description void
SnpEffectPredictor. addAll(Markers markersToAdd)
Add a set of markersprotected void
SnpEffectPredictor. variantEffect(Variant variant, VariantEffects variantEffects, Markers intersects)
Calculate variant effect for each marker in 'intersect'Constructors in org.snpeff.snpEffect with parameters of type Markers Constructor Description VariantEffectStructural(Variant variant, Markers intersects)
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Uses of Markers in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as Markers Modifier and Type Field Description protected Markers
TestCasesIntervalTree. markers
Markers
TestGenome. markers
Methods in org.snpeff.snpEffect.testCases.unity that return Markers Modifier and Type Method Description protected Markers
TestCasesIntervalTree. createRandomLargeMarkers(Chromosome chr, int num)
protected Markers
TestCasesIntervalTree. createRandomMarkers()
protected Markers
TestCasesIntervalTree. createRandomSmallMarkers(Chromosome chr, int num)
Markers
TestCasesIntervals. intersects(Markers interval1, Marker intervals)
protected Markers
TestCasesIntervalTree. queryNaive(Marker query)
Naively find all intervals intersecting 'marker'Markers
TestCasesIntervals. randomIntervals(int numIntervals, int maxStart, int maxLength, int numChromo)
Create a random set of intervalsMethods in org.snpeff.snpEffect.testCases.unity with parameters of type Markers Modifier and Type Method Description Markers
TestCasesIntervals. intersects(Markers interval1, Marker intervals)
protected Itree
TestCasesIntervalTree. newItree(Markers markers)
protected Itree
TestCasesIntervalTreeArray. newItree(Markers markers)
protected Itree
TestCasesIntervalTreeOri. newItree(Markers markers)
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Uses of Markers in org.snpeff.stats
Constructors in org.snpeff.stats with parameters of type Markers Constructor Description MineMarkerIntervals(Markers markers)
MineTwoMarkerIntervals(Markers markersA, Markers markersB)
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Uses of Markers in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type Markers Constructor Description SvgNextProt(Transcript tr, Svg svg, Markers nextprotMarkers)
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