org.opencb.cellbase.core.variant

Class PhasedQueryManager

java.lang.Object

org.opencb.cellbase.core.variant.PhasedQueryManager

Direct Known Subclasses:

AnnotationBasedPhasedQueryManager, CustomAnnotationPhasedQueryManager

public abstract class PhasedQueryManager
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	GENOTYPE_TAG
static String	PHASE_SET_TAG
static String	PHASED_GENOTYPE_SEPARATOR
static String	UNPHASED_GENOTYPE_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
PhasedQueryManager()

Method Summary

Modifier and Type	Method and Description
static String	getSampleAttribute(org.opencb.biodata.models.variant.Variant variant, String attributeName)
static boolean	isMissing(String field)
protected void	reset(CellBaseDataResult<org.opencb.biodata.models.variant.Variant> variantCellBaseDataResult)
protected boolean	sameHaplotype(org.opencb.biodata.models.variant.Variant queryVariant, List<org.opencb.biodata.models.variant.Variant> inputVariantList, List<org.opencb.biodata.models.variant.Variant> databaseHaplotype)

Methods inherited from class java.lang.Object

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

Field Detail

PHASE_SET_TAG

public static final String PHASE_SET_TAG

See Also:

Constant Field Values

GENOTYPE_TAG

public static final String GENOTYPE_TAG

See Also:

Constant Field Values

UNPHASED_GENOTYPE_SEPARATOR

public static final String UNPHASED_GENOTYPE_SEPARATOR

See Also:

Constant Field Values

PHASED_GENOTYPE_SEPARATOR

public static final String PHASED_GENOTYPE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

PhasedQueryManager

public PhasedQueryManager()

Method Detail

sameHaplotype

protected boolean sameHaplotype(org.opencb.biodata.models.variant.Variant queryVariant,
                                List<org.opencb.biodata.models.variant.Variant> inputVariantList,
                                List<org.opencb.biodata.models.variant.Variant> databaseHaplotype)

getSampleAttribute

public static String getSampleAttribute(org.opencb.biodata.models.variant.Variant variant,
                                        String attributeName)

isMissing

public static boolean isMissing(String field)

reset

protected void reset(CellBaseDataResult<org.opencb.biodata.models.variant.Variant> variantCellBaseDataResult)