public final class VariantAnnotations extends Object implements VariantDescription
Annotation
objects.Constructor and Description |
---|
VariantAnnotations(GenomeVariant variant,
Collection<Annotation> entries)
Construct ImmutableAnnotationList from a
Collection of Annotation objects. |
Modifier and Type | Method and Description |
---|---|
static VariantAnnotations |
buildEmptyList(GenomeVariant change) |
int |
compareTo(Annotation other) |
boolean |
equals(Object obj) |
String |
getAlt() |
com.google.common.collect.ImmutableList<Annotation> |
getAnnotations() |
int |
getChr() |
String |
getChrName() |
GenomeVariant |
getGenomeVariant()
Return the
GenomeVariant that this AnnotationList is annotated with. |
Annotation |
getHighestImpactAnnotation() |
VariantEffect |
getHighestImpactEffect()
Convenience method.
|
int |
getPos() |
String |
getRef() |
boolean |
hasAnnotation() |
int |
hashCode() |
String |
toString() |
public VariantAnnotations(GenomeVariant variant, Collection<Annotation> entries)
Collection
of Annotation
objects.
Note that variant
is converted to the forward strand using GenomeVariant.withStrand(de.charite.compbio.jannovar.reference.Strand)
.variant
- GenomeVariant
that this anotation list annotatesentries
- Collection
of Annotation
objectspublic static VariantAnnotations buildEmptyList(GenomeVariant change)
change
- to use for the empty listAnnotationList
with the given GenomeVariant
public GenomeVariant getGenomeVariant()
GenomeVariant
that this AnnotationList is annotated with.
Note that the GenomeVariant
is converted to be on the forward strand on construction of AnnotationList
objects.GenomeVariant
that this AnnotationList
contains entries for.public com.google.common.collect.ImmutableList<Annotation> getAnnotations()
public boolean hasAnnotation()
true
if the result of getAnnotations()
is emptypublic Annotation getHighestImpactAnnotation()
Annotation
with highest predicted impact, or null
if there is none.public VariantEffect getHighestImpactEffect()
VariantEffect
with the highest impact of all in entries or VariantEffect.SEQUENCE_VARIANT
if entries are empty or contain no annotated effects.public String getChrName()
getChrName
in interface VariantDescription
public int getChr()
getChr
in interface VariantDescription
public int getPos()
getPos
in interface VariantDescription
public String getRef()
getRef
in interface VariantDescription
public String getAlt()
getAlt
in interface VariantDescription
public int compareTo(Annotation other)
compareTo
in interface VariantDescription
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