Package org.snpeff.interval
Class Gene
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.IntervalAndSubIntervals<Transcript>
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- org.snpeff.interval.Gene
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- 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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Gene.GeneType
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
CIRCULAR_GENE_ID
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addPerGene(Marker marker)
Add a gene dependent markerboolean
adjust()
Adjust start, end and strand valuesvoid
buildPerGene()
Build gene dependent interval treeTranscript
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 clonedouble
cpgExonBias()
Calculate CpG bias: number of CpG / expected[CpG]void
filterTranscriptSupportLevel(TranscriptSupportLevel maxTsl)
Filter transcripts by TSLGene.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 trIdsint
keepTranscriptsProteinCoding()
Keep only protein coding transcriptsMarkers
markers()
A list of all markers in this transcriptvoid
removeNonCanonical(java.lang.String trId)
Remove all non-canonical transcriptsboolean
removeUnverified()
Remove unverified or corrected transcriptsvoid
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setBioType(BioType bioType)
int
sizeof(java.lang.String type)
Size of a genetic region for a given genejava.lang.String
toString()
java.lang.String
toString(boolean showTr)
boolean
variantEffect(Variant variant, VariantEffects variantEffects)
Get some details about the effect on this geneprotected 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
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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
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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
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Field Detail
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CIRCULAR_GENE_ID
public static final java.lang.String CIRCULAR_GENE_ID
- See Also:
- Constant Field Values
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Method Detail
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addPerGene
public void addPerGene(Marker marker)
Add a gene dependent marker
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adjust
public boolean adjust()
Adjust start, end and strand values- Returns:
- true if any adjustment was done
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buildPerGene
public void buildPerGene()
Build gene dependent interval tree
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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.
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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.
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cloneShallow
public Gene cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classIntervalAndSubIntervals<Transcript>
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cpgExonBias
public double cpgExonBias()
Calculate CpG bias: number of CpG / expected[CpG]
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filterTranscriptSupportLevel
public void filterTranscriptSupportLevel(TranscriptSupportLevel maxTsl)
Filter transcripts by TSL
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geneType
public Gene.GeneType geneType()
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getBioType
public BioType getBioType()
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getGeneName
public java.lang.String getGeneName()
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isProteinCoding
public boolean isProteinCoding()
Is any of the transcripts protein coding?
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isShowWarningIfParentDoesNotInclude
protected boolean isShowWarningIfParentDoesNotInclude()
Description copied from class:Marker
Show an error if parent does not include child?- Overrides:
isShowWarningIfParentDoesNotInclude
in classMarker
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keepTranscripts
public int keepTranscripts(java.util.Set<java.lang.String> trIds)
Remove all transcripts in trIds- Returns:
- : Number of transcripts removed
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keepTranscriptsProteinCoding
public int keepTranscriptsProteinCoding()
Keep only protein coding transcripts- Returns:
- : Number of transcripts removed
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markers
public Markers markers()
Description copied from class:IntervalAndSubIntervals
A list of all markers in this transcript- Overrides:
markers
in classIntervalAndSubIntervals<Transcript>
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removeNonCanonical
public void removeNonCanonical(java.lang.String trId)
Remove all non-canonical transcripts
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removeUnverified
public boolean removeUnverified()
Remove unverified or corrected transcripts- Returns:
- : True if ALL transcripts have been removed
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serializeParse
public void serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classIntervalAndSubIntervals<Transcript>
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serializeSave
public java.lang.String serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classIntervalAndSubIntervals<Transcript>
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setBioType
public void setBioType(BioType bioType)
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sizeof
public int sizeof(java.lang.String type)
Size of a genetic region for a given gene
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toString
public java.lang.String toString(boolean showTr)
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Get some details about the effect on this gene- Overrides:
variantEffect
in classMarker
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variantEffectGene
protected void variantEffectGene(Variant variant, VariantEffects variantEffects)
Add gene-specific annotations
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