org.opencb.cellbase.core.variant.annotation

Class ConsequenceTypeGenericRegionCalculator

java.lang.Object

org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator

org.opencb.cellbase.core.variant.annotation.ConsequenceTypeGenericRegionCalculator

Direct Known Subclasses:

ConsequenceTypeBNDCalculator, ConsequenceTypeCNVGainCalculator, ConsequenceTypeDeletionCalculator, ConsequenceTypeMNVCalculator

public class ConsequenceTypeGenericRegionCalculator
extends ConsequenceTypeCalculator

Created by fjlopez on 29/03/17.

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	BIG_VARIANT_SIZE_THRESHOLD
protected int	variantEnd
protected int	variantStart

Fields inherited from class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator

CNV_EXTRA_PADDING, cnvExtraPadding, COMPLEMENTARY_START_CODON, consequenceType, DOWN_UP_STREAM_GENE_TAG, gene, genomeDBAdaptor, imprecise, IMPRECISE, logger, MT, NO_EXON_OVERLAP, SoNames, START_CODON, SV_EXTRA_PADDING, svExtraPadding, transcript, variant

Constructor Summary

Constructors

Constructor and Description
ConsequenceTypeGenericRegionCalculator()

Method Summary

Modifier and Type	Method and Description
List<org.opencb.biodata.models.variant.avro.ConsequenceType>	run(org.opencb.biodata.models.variant.Variant inputVariant, List<org.opencb.biodata.models.core.Gene> geneList, boolean[] overlapsRegulatoryRegion, org.opencb.commons.datastore.core.QueryOptions queryOptions)
protected void	solveCodingExonVariantInNegativeTranscript(boolean splicing, String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
protected void	solveCodingExonVariantInPositiveTranscript(boolean splicing, String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
protected void	solveCodingNegativeTranscript()
protected void	solveCodingPositiveTranscript()
protected void	solveExonVariantInNegativeTranscript(boolean splicing, String transcriptSequence, int cdnaVariantStart, int cdnaVariantEnd, int firstCdsPhase)
protected void	solveExonVariantInPositiveTranscript(boolean splicing, String transcriptSequence, int cdnaVariantStart, int cdnaVariantEnd, int firstCdsPhase)
protected void	solveJunction(Integer spliceSite1, Integer spliceSite2, String leftSpliceSiteTag, String rightSpliceSiteTag, boolean[] junctionSolution)
protected void	solveNonCodingNegativeTranscript()
protected void	solveNonCodingPositiveTranscript()
protected void	solveStopCodonNegativeVariant(String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
protected void	solveStopCodonPositiveVariant(String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
protected void	solveTranscriptFlankingRegions(String leftRegionTag, String rightRegionTag)

Methods inherited from class org.opencb.cellbase.core.variant.annotation.ConsequenceTypeCalculator

addNonCodingSOs, decideStopCodonModificationAnnotation, getEnd, getReverseComplementaryCodon, getSequenceOntologyTerms, getStart, parseQueryParam, regionsOverlap, setCdsAndProteinPosition, setInsertionAlleleAminoacidChange, solveIntergenic, solveMiRNA, solveNegativeTranscript, solvePositiveTranscript, solveRegulatoryRegions, updateNegativeInsertionCodonArrays, updatePositiveInsertionCodonArrays

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

variantStart

protected int variantStart

variantEnd

protected int variantEnd

BIG_VARIANT_SIZE_THRESHOLD

protected static final int BIG_VARIANT_SIZE_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

ConsequenceTypeGenericRegionCalculator

public ConsequenceTypeGenericRegionCalculator()

Method Detail

run

public List<org.opencb.biodata.models.variant.avro.ConsequenceType> run(org.opencb.biodata.models.variant.Variant inputVariant,
                                                                        List<org.opencb.biodata.models.core.Gene> geneList,
                                                                        boolean[] overlapsRegulatoryRegion,
                                                                        org.opencb.commons.datastore.core.QueryOptions queryOptions)

Specified by:

run in class ConsequenceTypeCalculator

solveTranscriptFlankingRegions

protected void solveTranscriptFlankingRegions(String leftRegionTag,
                                              String rightRegionTag)

solveNonCodingNegativeTranscript

protected void solveNonCodingNegativeTranscript()

Specified by:

solveNonCodingNegativeTranscript in class ConsequenceTypeCalculator

solveCodingNegativeTranscript

protected void solveCodingNegativeTranscript()

Specified by:

solveCodingNegativeTranscript in class ConsequenceTypeCalculator

solveExonVariantInNegativeTranscript

protected void solveExonVariantInNegativeTranscript(boolean splicing,
                                                    String transcriptSequence,
                                                    int cdnaVariantStart,
                                                    int cdnaVariantEnd,
                                                    int firstCdsPhase)

solveCodingExonVariantInNegativeTranscript

protected void solveCodingExonVariantInNegativeTranscript(boolean splicing,
                                                          String transcriptSequence,
                                                          int cdnaCodingStart,
                                                          int cdnaVariantStart,
                                                          int cdnaVariantEnd)

solveStopCodonNegativeVariant

protected void solveStopCodonNegativeVariant(String transcriptSequence,
                                             int cdnaCodingStart,
                                             int cdnaVariantStart,
                                             int cdnaVariantEnd)

solveJunction

protected void solveJunction(Integer spliceSite1,
                             Integer spliceSite2,
                             String leftSpliceSiteTag,
                             String rightSpliceSiteTag,
                             boolean[] junctionSolution)

solveCodingPositiveTranscript

protected void solveCodingPositiveTranscript()

Specified by:

solveCodingPositiveTranscript in class ConsequenceTypeCalculator

solveExonVariantInPositiveTranscript

protected void solveExonVariantInPositiveTranscript(boolean splicing,
                                                    String transcriptSequence,
                                                    int cdnaVariantStart,
                                                    int cdnaVariantEnd,
                                                    int firstCdsPhase)

solveCodingExonVariantInPositiveTranscript

protected void solveCodingExonVariantInPositiveTranscript(boolean splicing,
                                                          String transcriptSequence,
                                                          int cdnaCodingStart,
                                                          int cdnaVariantStart,
                                                          int cdnaVariantEnd)

solveStopCodonPositiveVariant

protected void solveStopCodonPositiveVariant(String transcriptSequence,
                                             int cdnaCodingStart,
                                             int cdnaVariantStart,
                                             int cdnaVariantEnd)

solveNonCodingPositiveTranscript

protected void solveNonCodingPositiveTranscript()

Specified by:

solveNonCodingPositiveTranscript in class ConsequenceTypeCalculator