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.Marker

type

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

Modifier and Type	Method	Description
void	add(T t)	Add a subinterval
void	addAll(java.lang.Iterable<T> ts)	Add all intervals
void	addAll(Markers markers)	Add all markers
IntervalAndSubIntervals<T>	apply(Variant variant)	Apply a variant.
IntervalAndSubIntervals<T>	clone()
IntervalAndSubIntervals<T>	cloneShallow()	Perform a shallow clone
boolean	containsId(java.lang.String id)	Is 'id' in the subintervals?
T	get(java.lang.String id)	Obtain a subinterval
protected void	invalidateSorted()	Invalidate sorted collections
java.util.Iterator<T>	iterator()
Markers	markers()	A list of all markers in this transcript
int	numChilds()
Markers	query(Marker marker)	Query all genomic regions that intersect 'marker'
void	remove(T t)	Remove a subinterval
void	reset()	Remove all intervals
void	serializeParse(MarkerSerializer markerSerializer)	Parse a line from a serialized file
java.lang.String	serializeSave(MarkerSerializer markerSerializer)	Create a string to serialize to a file
void	setStrandMinus(boolean strandMinus)
void	shiftCoordinates(int shift)
java.util.List<T>	sorted()	Return a collection of sub intervals sorted by natural order
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 strand < 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, 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

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.

Overrides:

apply in class Marker

Returns:

The marker result after applying variant

clone

public IntervalAndSubIntervals<T> clone()

Overrides:

clone in class Marker

cloneShallow

public IntervalAndSubIntervals<T> cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

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()

Specified by:

iterator in interface java.lang.Iterable<T extends Marker>

markers

public Markers markers()

A list of all markers in this transcript

numChilds

public int numChilds()

query

public Markers query(Marker marker)

Query all genomic regions that intersect 'marker'

Overrides:

query in class Marker

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 interface TxtSerializable

Overrides:

serializeParse in class Marker

serializeSave

public java.lang.String serializeSave(MarkerSerializer markerSerializer)

Create a string to serialize to a file

Specified by:

serializeSave in interface TxtSerializable

Overrides:

serializeSave in class Marker

Returns:

setStrandMinus

public void setStrandMinus(boolean strandMinus)

Overrides:

setStrandMinus in class Interval

shiftCoordinates

public void shiftCoordinates(int shift)

Overrides:

shiftCoordinates in class Interval

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 strand < 0)

subIntervals

public java.util.Collection<T> subIntervals()

Return a collection of sub intervals