Package org.snpeff.interval

Class MarkerSeq

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.MarkerSeq

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, TxtSerializable

Direct Known Subclasses:

Exon

public class MarkerSeq
extends Marker

Marker with a DNA sequence

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
MarkerSeq()
MarkerSeq(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
MarkerSeq(Marker parent, int start, int end, java.lang.String seq)

Method Summary

Modifier and Type	Method	Description
MarkerSeq	apply(Variant variant)	Apply variant
protected void	applyDel(Variant variant, MarkerSeq markerSeq)	Apply a change type deletion (update sequence)
protected void	applyDup(Variant variant, MarkerSeq markerSeq)	Apply a change type duplication (update sequence)
protected void	applyIns(Variant variant, MarkerSeq markerSeq)	Apply a change type insertion (update sequence)
protected void	applyMnp(Variant variant, MarkerSeq markerSeq)	Apply a change type MNP (update sequence)
protected void	applySnp(Variant variant, MarkerSeq markerSeq)	Apply a change type SNP (update sequence)
java.lang.String	basesAt(int index, int len)	Base in this marker at position 'index' (relative to marker start)
java.lang.String	basesAtPos(int pos, int len)	Base at position 'pos' (genomic coordinates)
MarkerSeq	cloneShallow()	Perform a shallow clone
java.lang.String	getSequence()	Get sequence WARNING: Sequence is always according to coding strand.
java.lang.String	getSequence(Marker marker)	Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.
boolean	hasSequence()	Do we have a sequence for this exon?
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	setSequence(java.lang.String sequence)	Set sequence WARNING: Sequence is always according to coding strand.
java.lang.String	toString()
Marker	union(Marker m)	Union of two markers

Methods inherited from class org.snpeff.interval.Marker

adjust, applyDel, applyDup, applyIns, applyMixed, clone, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, shouldApply, 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, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos

Methods inherited from class java.lang.Object

equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MarkerSeq

public MarkerSeq()

MarkerSeq

public MarkerSeq(Marker parent,
                 int start,
                 int end,
                 boolean strandMinus,
                 java.lang.String id)

MarkerSeq

public MarkerSeq(Marker parent,
                 int start,
                 int end,
                 java.lang.String seq)

Method Detail

apply

public MarkerSeq apply(Variant variant)

Apply variant

Overrides:

apply in class Marker

Returns:

The marker result after applying variant

applyDel

protected void applyDel(Variant variant,
                        MarkerSeq markerSeq)

Apply a change type deletion (update sequence)

applyDup

protected void applyDup(Variant variant,
                        MarkerSeq markerSeq)

Apply a change type duplication (update sequence)

applyIns

protected void applyIns(Variant variant,
                        MarkerSeq markerSeq)

Apply a change type insertion (update sequence)

applyMnp

protected void applyMnp(Variant variant,
                        MarkerSeq markerSeq)

Apply a change type MNP (update sequence)

applySnp

protected void applySnp(Variant variant,
                        MarkerSeq markerSeq)

Apply a change type SNP (update sequence)

basesAt

public java.lang.String basesAt(int index,
                                int len)

Base in this marker at position 'index' (relative to marker start)

basesAtPos

public java.lang.String basesAtPos(int pos,
                                   int len)

Base at position 'pos' (genomic coordinates)

cloneShallow

public MarkerSeq cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

getSequence

public java.lang.String getSequence()

Get sequence WARNING: Sequence is always according to coding strand. E.g. if the strand is negative, the sequence returned by this method is the reverse-WC that you see in the reference genome

getSequence

public java.lang.String getSequence(Marker marker)

Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand. E.g. if the strand is negative, the sequence returned by this method is the reverse-WC that you see in the reference genome

hasSequence

public boolean hasSequence()

Do we have a sequence for this exon?

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

setSequence

public void setSequence(java.lang.String sequence)

Set sequence WARNING: Sequence is always according to coding strand. So use you should use setSequence( GprSeq.reverseWc( seq ) ) if the marker is in negative strand.

toString

public java.lang.String toString()

Overrides:

toString in class Marker

union

public Marker union(Marker m)

Union of two markers

Overrides:

union in class Marker

Returns:

A new marker which is the union of the two