Uses of Class
org.snpeff.interval.Markers

Packages that use Markers

Package	Description
org.snpeff
org.snpeff.fileIterator
org.snpeff.interval
org.snpeff.interval.tree
org.snpeff.nextProt
org.snpeff.serializer
org.snpeff.snpEffect
org.snpeff.snpEffect.testCases.unity
org.snpeff.stats
org.snpeff.svg

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()

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 intervals
Markers	Markers.intersect()	Perform the intersection of all overlapping sub-intervals
Markers	Markers.intersect(Marker marker)	Intersection between 'marker' and all sub-intervals
Markers	Gene.markers()
Markers	IntervalAndSubIntervals.markers()	A list of all markers in this transcript
Markers	Transcript.markers()	A list of all markers in this transcript
Markers	Markers.merge()	Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficient
Markers	Marker.minus(Marker interval)	Return the difference between two markers
Markers	Markers.minus(Marker interval)	Calculate 'set minus' using one interval
Markers	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 marker
Markers	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 variant
static Markers	Markers.readMarkers(java.lang.String fileName)	Read markers from a file Supported formats: BED, BigBed, VCF, TXT
static 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 positions
Markers	Markers.sort()	Sort intervals
Markers	Markers.sort(boolean byEnd, boolean reverse)	Sort intervals
Markers	Markers.union()	Perform the union of all overlapping intervals
Markers	Markers.unique()	Remove duplicated markers

Methods in org.snpeff.interval with parameters of type Markers

Modifier and Type	Method	Description
Markers	Markers.add(Markers markersToAdd)	Add all intervals
void	IntervalAndSubIntervals.addAll(Markers markers)	Add all markers
static 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)

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 node
Markers	IntervalNodeOri.query(Interval target)	Perform an interval intersection query on the node
Markers	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 node
Markers	IntervalNodeOri.stab(java.lang.Integer point)	Perform a stabbing query on the node
Markers	IntervalTree.stab(int point)	Perform a stabbing query, returning the interval objects
Markers	IntervalTreeArray.stab(int point)
Markers	IntervalTreeOri.stab(int point)	Perform a stabbing query, returning the interval objects
Markers	Itree.stab(int point)	Perform a stabbing query, returning the interval objects

Methods in org.snpeff.interval.tree with parameters of type Markers

Modifier and Type	Method	Description
void	IntervalForest.add(Markers intervals)	Add all intervals
void	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 build
void	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 build
void	Itree.add(Markers markers)	Add all intervals to interval tree's list
protected void	IntervalNode.build(Markers markers)	Build interval tree
protected 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 node
Markers	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 intervals
IntervalTreeArray(Markers markers)	Instantiate an interval tree with a list of intervals
IntervalTreeOri(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 them
Markers	NextProtMarkerFactory.getMarkers()
Markers	NextProtMarkerFactory.nextProt(Transcript tr, java.lang.String accession, java.lang.String name, int aaStart, int aaEnd)	Create a single NextProt marker
Markers	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 file

Methods 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, etc
Markers	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 possible

Methods in org.snpeff.snpEffect with parameters of type Markers

Modifier and Type	Method	Description
void	SnpEffectPredictor.addAll(Markers markersToAdd)	Add a set of markers
protected 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)

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 intervals

Methods 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)

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)

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)