Uses of Package
de.charite.compbio.jannovar.annotation

Packages that use de.charite.compbio.jannovar.annotation

Package	Description
de.charite.compbio.jannovar.annotation
de.charite.compbio.jannovar.annotation.builders
de.charite.compbio.jannovar.cmd.annotate_vcf
de.charite.compbio.jannovar.htsjdk
de.charite.compbio.jannovar.reference

Classes in de.charite.compbio.jannovar.annotation used by de.charite.compbio.jannovar.annotation

Class and Description
Annotation Collect the information for one variant's annotation.
AnnotationException Annotation exceptions are thrown when the information provided is not well formed or not sufficient to create a correct annotation.
AnnotationLocation Describes the location of an annotation.
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.
VariantAnnotations A list of priority-sorted Annotation objects.
VariantAnnotationsTextGenerator Generate annotation text (effect and HGVS description) from VariantAnnotations object.
VariantEffect These codes reflect the possible types of variants that we call for an exome.

Classes in de.charite.compbio.jannovar.annotation used by de.charite.compbio.jannovar.annotation.builders

Class and Description
Annotation Collect the information for one variant's annotation.
InvalidGenomeVariant Thrown when the the given GenomeVariant does not fit the used annotation builder class.

Classes in de.charite.compbio.jannovar.annotation used by de.charite.compbio.jannovar.cmd.annotate_vcf

Class and Description
AnnotationException Annotation exceptions are thrown when the information provided is not well formed or not sufficient to create a correct annotation.

Classes in de.charite.compbio.jannovar.annotation used by de.charite.compbio.jannovar.htsjdk

Class and Description
AnnotationMessage Error messages for encoding problems during the annotation.
VariantAnnotations A list of priority-sorted Annotation objects.
VariantAnnotator Main driver class for annotating variants.

Classes in de.charite.compbio.jannovar.annotation used by de.charite.compbio.jannovar.reference

Class and Description
Annotation Collect the information for one variant's annotation.