Package de.charite.compbio.jannovar.annotation

Class Summary

Class	Description
AllAnnotationListTextGenerator	Deprecated
Annotation	Collect the information for one variant's annotation.
AnnotationLocation	Describes the location of an annotation.
AnnotationLocationBuilder	Builder for the immutable AnnotationLocation class.
AnnotationTextGenerator	Deprecated
BestAnnotationListTextGenerator	Deprecated
VariantAnnotations	A list of priority-sorted Annotation objects.
VariantAnnotationsContentDecorator	Decorator for VariantAnnotations that allows queries on the content.
VariantAnnotationsTextGenerator	Generate annotation text (effect and HGVS description) from VariantAnnotations object.
VariantAnnotator	Main driver class for annotating variants.

Enum Summary

Enum	Description
AnnotationLocation.RankType	Enumeration for rank types, exon, intron, or neither (i.e.
AnnotationMessage	Error messages for encoding problems during the annotation.
OldVariantType	Enumeration of the old Jannovar variant types (i.e.
PutativeImpact	Putative impact of an annotation.
VariantEffect	These codes reflect the possible types of variants that we call for an exome.

Exception Summary

Exception	Description
AnnotationException	Annotation exceptions are thrown when the information provided is not well formed or not sufficient to create a correct annotation.
InvalidGenomeVariant	Thrown when the the given GenomeVariant does not fit the used annotation builder class.