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

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

Package	Description
de.charite.compbio.jannovar.annotation
de.charite.compbio.jannovar.annotation.builders
de.charite.compbio.jannovar.data
de.charite.compbio.jannovar.datasource
de.charite.compbio.jannovar.impl.parse
de.charite.compbio.jannovar.impl.parse.ensembl
de.charite.compbio.jannovar.impl.parse.flatbed
de.charite.compbio.jannovar.impl.parse.refseq
de.charite.compbio.jannovar.impl.parse.ucsc
de.charite.compbio.jannovar.reference

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

Class and Description
GenomeVariant Denote a change with a "REF" and an "ALT" string using genome coordinates.
PositionType Enum for differentiating between one- and zero-based positions.
TranscriptInterval Interval on a transcript.
TranscriptModel The information representing a transcript model.
VariantDescription Minimal description of a variant as triple (position, ref, alt).

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

Class and Description
GenomeVariant Denote a change with a "REF" and an "ALT" string using genome coordinates.
TranscriptModel The information representing a transcript model.

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

Class and Description
TranscriptModel The information representing a transcript model.

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

Class and Description
TranscriptModelBuilder Class for building immutable TranscriptModel objects field-by-field.

Classes in de.charite.compbio.jannovar.reference used by de.charite.compbio.jannovar.impl.parse

Class and Description
TranscriptModel The information representing a transcript model.
TranscriptModelBuilder Class for building immutable TranscriptModel objects field-by-field.

Classes in de.charite.compbio.jannovar.reference used by de.charite.compbio.jannovar.impl.parse.ensembl

Class and Description
TranscriptModel The information representing a transcript model.

Classes in de.charite.compbio.jannovar.reference used by de.charite.compbio.jannovar.impl.parse.flatbed

Class and Description
TranscriptModel The information representing a transcript model.
TranscriptModelBuilder Class for building immutable TranscriptModel objects field-by-field.

Classes in de.charite.compbio.jannovar.reference used by de.charite.compbio.jannovar.impl.parse.refseq

Class and Description
TranscriptModel The information representing a transcript model.

Classes in de.charite.compbio.jannovar.reference used by de.charite.compbio.jannovar.impl.parse.ucsc

Class and Description
TranscriptModel The information representing a transcript model.
TranscriptModelBuilder Class for building immutable TranscriptModel objects field-by-field.

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

Class and Description
AminoAcidChange Representation of a change in amino acids.
CDSInterval Interval on a transcript.
CDSPosition Position on a transcript.
GenomeInterval Representation of a genomic interval (chromsome, begin, end).
GenomePosition Representation of a position on a genome (chromosome, position).
GenomeVariant Denote a change with a "REF" and an "ALT" string using genome coordinates.
GenomeVariantType Types of genomic variants represented by GenomeVariant.
InvalidCodonException Raised when it is attempted to access an invalid codon
PositionType Enum for differentiating between one- and zero-based positions.
ProjectionException Thrown when a coordinate conversion failed.
Strand Representation for forward/backward strand.
TranscriptInterval Interval on a transcript.
TranscriptModel The information representing a transcript model.
TranscriptPosition Position on a transcript.
VariantDescription Minimal description of a variant as triple (position, ref, alt).