org.opencb.cellbase.core.variant

Class ClinicalPhasedQueryManager

java.lang.Object

org.opencb.cellbase.core.variant.PhasedQueryManager

org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager<org.opencb.biodata.models.variant.avro.EvidenceEntry>

org.opencb.cellbase.core.variant.ClinicalPhasedQueryManager

public class ClinicalPhasedQueryManager
extends AnnotationBasedPhasedQueryManager<org.opencb.biodata.models.variant.avro.EvidenceEntry>

Field Summary

Fields inherited from class org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager

logger

Fields inherited from class org.opencb.cellbase.core.variant.PhasedQueryManager

GENOTYPE_TAG, PHASE_SET_TAG, PHASED_GENOTYPE_SEPARATOR, UNPHASED_GENOTYPE_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
ClinicalPhasedQueryManager()

Method Summary

Modifier and Type	Method and Description
protected List<org.opencb.biodata.models.variant.avro.EvidenceEntry>	getAnnotationObjectList(org.opencb.biodata.models.variant.Variant variant)
protected List<org.opencb.biodata.models.variant.Variant>	getHaplotype(org.opencb.biodata.models.variant.avro.EvidenceEntry evidenceEntry, org.opencb.biodata.models.variant.Variant variant)

Methods inherited from class org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager

run

Methods inherited from class org.opencb.cellbase.core.variant.PhasedQueryManager

getSampleAttribute, isMissing, reset, sameHaplotype

Methods inherited from class java.lang.Object

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

Constructor Detail

ClinicalPhasedQueryManager

public ClinicalPhasedQueryManager()

Method Detail

getHaplotype

protected List<org.opencb.biodata.models.variant.Variant> getHaplotype(org.opencb.biodata.models.variant.avro.EvidenceEntry evidenceEntry,
                                                                       org.opencb.biodata.models.variant.Variant variant)

Specified by:

getHaplotype in class AnnotationBasedPhasedQueryManager<org.opencb.biodata.models.variant.avro.EvidenceEntry>

getAnnotationObjectList

protected List<org.opencb.biodata.models.variant.avro.EvidenceEntry> getAnnotationObjectList(org.opencb.biodata.models.variant.Variant variant)

Specified by:

getAnnotationObjectList in class AnnotationBasedPhasedQueryManager<org.opencb.biodata.models.variant.avro.EvidenceEntry>