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:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,java.lang.Iterable<T>
,TxtSerializable
- Direct Known Subclasses:
Gene
,Transcript
public class IntervalAndSubIntervals<T extends Marker> extends Marker implements java.lang.Iterable<T>
Interval that contains sub intervals.- Author:
- pcingola
- See Also:
- Serialized Form
-
-
Field Summary
-
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
-
-
Constructor Summary
Constructors Constructor Description IntervalAndSubIntervals()
IntervalAndSubIntervals(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(T t)
Add a subintervalvoid
addAll(java.lang.Iterable<T> ts)
Add all intervalsvoid
addAll(Markers markers)
Add all markersIntervalAndSubIntervals<T>
apply(Variant variant)
Apply a variant.IntervalAndSubIntervals<T>
clone()
IntervalAndSubIntervals<T>
cloneShallow()
Perform a shallow cloneboolean
containsId(java.lang.String id)
Is 'id' in the subintervals?T
get(java.lang.String id)
Obtain a subintervalprotected void
invalidateSorted()
Invalidate sorted collectionsjava.util.Iterator<T>
iterator()
Markers
markers()
A list of all markers in this transcriptint
numChilds()
Markers
query(Marker marker)
Query all genomic regions that intersect 'marker'void
remove(T t)
Remove a subintervalvoid
reset()
Remove all intervalsvoid
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setStrandMinus(boolean strandMinus)
void
shiftCoordinates(int shift)
java.util.List<T>
sorted()
Return a collection of sub intervals sorted by natural orderjava.util.List<T>
sortedStrand()
Return a collection of sub intervals sorted by start position (if strand is >= 0) or by reverse end position (if strans < 0)java.util.Collection<T>
subIntervals()
Return a collection of sub intervals-
Methods 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, 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
-
-
-
-
Constructor Detail
-
IntervalAndSubIntervals
public IntervalAndSubIntervals()
-
IntervalAndSubIntervals
public IntervalAndSubIntervals(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
-
-
Method Detail
-
add
public void add(T t)
Add a subinterval
-
addAll
public void addAll(java.lang.Iterable<T> ts)
Add all intervals
-
addAll
public void addAll(Markers markers)
Add all markers
-
apply
public IntervalAndSubIntervals<T> apply(Variant variant)
Apply a variant.
-
clone
public IntervalAndSubIntervals<T> clone()
-
cloneShallow
public IntervalAndSubIntervals<T> cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
-
containsId
public boolean containsId(java.lang.String id)
Is 'id' in the subintervals?
-
get
public T get(java.lang.String id)
Obtain a subinterval
-
invalidateSorted
protected void invalidateSorted()
Invalidate sorted collections
-
iterator
public java.util.Iterator<T> iterator()
-
markers
public Markers markers()
A list of all markers in this transcript
-
numChilds
public int numChilds()
-
remove
public void remove(T t)
Remove a subinterval
-
reset
public void reset()
Remove all intervals
-
serializeParse
public void serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
-
serializeSave
public java.lang.String serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
- Returns:
-
setStrandMinus
public void setStrandMinus(boolean strandMinus)
- Overrides:
setStrandMinus
in classInterval
-
shiftCoordinates
public void shiftCoordinates(int shift)
- Overrides:
shiftCoordinates
in classInterval
-
sorted
public java.util.List<T> sorted()
Return a collection of sub intervals sorted by natural order
-
sortedStrand
public java.util.List<T> sortedStrand()
Return a collection of sub intervals sorted by start position (if strand is >= 0) or by reverse end position (if strans < 0)
-
subIntervals
public java.util.Collection<T> subIntervals()
Return a collection of sub intervals
-
-