Package org.snpeff.interval
Class IntervalAndSubIntervals<T extends Marker>
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.IntervalAndSubIntervals<T>
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,Iterable<T>
,TxtSerializable
- Direct Known Subclasses:
Gene
,Transcript
Interval that contains sub intervals.
- Author:
- pcingola
- See Also:
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Field Summary
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionIntervalAndSubIntervals
(Marker parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a subintervalvoid
Add all intervalsvoid
Add all markersApply a variant.clone()
Perform a shallow cloneboolean
containsId
(String id) Is 'id' in the subintervals?Obtain a subintervalprotected void
Invalidate sorted collectionsiterator()
markers()
A list of all markers in this transcriptint
Query all genomic regions that intersect 'marker'void
Remove a subintervalvoid
reset()
Remove all intervalsvoid
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filevoid
setStrandMinus
(boolean strandMinus) void
shiftCoordinates
(int shift) sorted()
Return a collection of sub intervals sorted by natural orderReturn a collection of sub intervals sorted by start position (if strand is >= 0) or by reverse end position (if strand < 0)Return a collection of sub intervalsMethods inherited from class org.snpeff.interval.Marker
adjust, applyDel, applyDup, applyIns, applyMixed, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, readTxt, shouldApply, toString, union, variantEffect, variantEffectNonRef
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, size, toStr, toStringAsciiArt, toStrPos
Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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IntervalAndSubIntervals
public IntervalAndSubIntervals() -
IntervalAndSubIntervals
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Method Details
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add
Add a subinterval -
addAll
Add all intervals -
addAll
Add all markers -
apply
Apply a variant. -
clone
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cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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containsId
Is 'id' in the subintervals? -
get
Obtain a subinterval -
invalidateSorted
protected void invalidateSorted()Invalidate sorted collections -
iterator
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markers
A list of all markers in this transcript -
numChilds
public int numChilds() -
query
Query all genomic regions that intersect 'marker' -
remove
Remove a subinterval -
reset
public void reset()Remove all intervals -
serializeParse
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
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serializeSave
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
- Returns:
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setStrandMinus
public void setStrandMinus(boolean strandMinus) - Overrides:
setStrandMinus
in classInterval
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shiftCoordinates
public void shiftCoordinates(int shift) - Overrides:
shiftCoordinates
in classInterval
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sorted
Return a collection of sub intervals sorted by natural order -
sortedStrand
Return a collection of sub intervals sorted by start position (if strand is >= 0) or by reverse end position (if strand < 0) -
subIntervals
Return a collection of sub intervals
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