Package org.snpeff.interval

Class Gene

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.IntervalAndSubIntervals<Transcript>

org.snpeff.interval.Gene

All Implemented Interfaces:

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

public class Gene
extends IntervalAndSubIntervals<Transcript>
implements java.io.Serializable

Interval for a gene, as well as transcripts

Author:

pcingola

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Gene.GeneType

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	CIRCULAR_GENE_ID

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
Gene()
Gene(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String geneName, BioType bioType)

Method Summary

Modifier and Type	Method	Description
void	addPerGene(Marker marker)	Add a gene dependent marker
boolean	adjust()	Adjust start, end and strand values
void	buildPerGene()	Build gene dependent interval tree
Transcript	canonical()	Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts.
Gene	circularClone()	In a circular genome, a gene can have negative coordinates or crosses over chromosome end.
Gene	cloneShallow()	Perform a shallow clone
double	cpgExonBias()	Calculate CpG bias: number of CpG / expected[CpG]
void	filterTranscriptSupportLevel(TranscriptSupportLevel maxTsl)	Filter transcripts by TSL
Gene.GeneType	geneType()
BioType	getBioType()
java.lang.String	getGeneName()
boolean	isProteinCoding()	Is any of the transcripts protein coding?
protected boolean	isShowWarningIfParentDoesNotInclude()	Show an error if parent does not include child?
int	keepTranscripts(java.util.Set<java.lang.String> trIds)	Remove all transcripts in trIds
int	keepTranscriptsProteinCoding()	Keep only protein coding transcripts
Markers	markers()	A list of all markers in this transcript
void	removeNonCanonical(java.lang.String trId)	Remove all non-canonical transcripts
boolean	removeUnverified()	Remove unverified or corrected transcripts
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	setBioType(BioType bioType)
int	sizeof(java.lang.String type)	Size of a genetic region for a given gene
java.lang.String	toString()
java.lang.String	toString(boolean showTr)
boolean	variantEffect(Variant variant, VariantEffects variantEffects)	Get some details about the effect on this gene
protected void	variantEffectGene(Variant variant, VariantEffects variantEffects)	Add gene-specific annotations

Methods inherited from class org.snpeff.interval.IntervalAndSubIntervals

add, addAll, addAll, apply, clone, containsId, get, invalidateSorted, iterator, numChilds, query, remove, reset, setStrandMinus, shiftCoordinates, sorted, sortedStrand, subIntervals

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, minus, query, readTxt, shouldApply, union, 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

Field Detail

CIRCULAR_GENE_ID

public static final java.lang.String CIRCULAR_GENE_ID

See Also:

Constant Field Values

Constructor Detail

Gene

public Gene()

Gene

public Gene(Marker parent,
            int start,
            int end,
            boolean strandMinus,
            java.lang.String id,
            java.lang.String geneName,
            BioType bioType)

Method Detail

addPerGene

public void addPerGene(Marker marker)

Add a gene dependent marker

adjust

public boolean adjust()

Adjust start, end and strand values

Returns:

true if any adjustment was done

buildPerGene

public void buildPerGene()

Build gene dependent interval tree

canonical

public Transcript canonical()

Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts. If none of the transcripts is protein coding, then it is the longest cDNA.

circularClone

public Gene circularClone()

In a circular genome, a gene can have negative coordinates or crosses over chromosome end. These genes are mirrored to the opposite end of the chromosome so that they can be referenced by both circular coordinates.

cloneShallow

public Gene cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class IntervalAndSubIntervals<Transcript>

cpgExonBias

public double cpgExonBias()

Calculate CpG bias: number of CpG / expected[CpG]

filterTranscriptSupportLevel

public void filterTranscriptSupportLevel(TranscriptSupportLevel maxTsl)

Filter transcripts by TSL

geneType

public Gene.GeneType geneType()

getBioType

public BioType getBioType()

getGeneName

public java.lang.String getGeneName()

isProteinCoding

public boolean isProteinCoding()

Is any of the transcripts protein coding?

isShowWarningIfParentDoesNotInclude

protected boolean isShowWarningIfParentDoesNotInclude()

Description copied from class: Marker

Show an error if parent does not include child?

Overrides:

isShowWarningIfParentDoesNotInclude in class Marker

keepTranscripts

public int keepTranscripts(java.util.Set<java.lang.String> trIds)

Remove all transcripts in trIds

Returns:

: Number of transcripts removed

keepTranscriptsProteinCoding

public int keepTranscriptsProteinCoding()

Keep only protein coding transcripts

Returns:

: Number of transcripts removed

markers

public Markers markers()

Description copied from class: IntervalAndSubIntervals

A list of all markers in this transcript

Overrides:

markers in class IntervalAndSubIntervals<Transcript>

removeNonCanonical

public void removeNonCanonical(java.lang.String trId)

Remove all non-canonical transcripts

removeUnverified

public boolean removeUnverified()

Remove unverified or corrected transcripts

Returns:

: True if ALL transcripts have been removed

serializeParse

public void serializeParse(MarkerSerializer markerSerializer)

Parse a line from a serialized file

Specified by:

serializeParse in interface TxtSerializable

Overrides:

serializeParse in class IntervalAndSubIntervals<Transcript>

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 IntervalAndSubIntervals<Transcript>

setBioType

public void setBioType(BioType bioType)

sizeof

public int sizeof(java.lang.String type)

Size of a genetic region for a given gene

toString

public java.lang.String toString()

Overrides:

toString in class Marker

toString

public java.lang.String toString(boolean showTr)

variantEffect

public boolean variantEffect(Variant variant,
                             VariantEffects variantEffects)

Get some details about the effect on this gene

Overrides:

variantEffect in class Marker

variantEffectGene

protected void variantEffectGene(Variant variant,
                                 VariantEffects variantEffects)

Add gene-specific annotations