| Interface | Description |
|---|---|
| TranscriptSupportLevels |
Container for constants of transcript support levels.
|
| VariantDescription |
Minimal description of a variant as triple (position, ref, alt).
|
| Class | Description |
|---|---|
| AminoAcidChange |
Representation of a change in amino acids.
|
| AminoAcidChangeNormalizer |
Helper for normalizing changes in amino acid sequences.
|
| CDSInterval |
Interval on a transcript.
|
| CDSPosition |
Position on a transcript.
|
| DuplicationChecker |
Helper class for checking whether an insertion in a string is a duplication.
|
| 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.
|
| GenomeVariantNormalizer |
Helper code for the normalization of
GenomeVariants. |
| HG19RefDictBuilder |
Builds a
ReferenceDictionary for the hg19 release. |
| NucleotidePointLocationBuilder |
Helper class that allows easy building of
NucleotidePointLocations. |
| TranscriptInterval |
Interval on a transcript.
|
| TranscriptIntervalEndExtractor |
Extraction of interval end points for
TranscriptModel. |
| TranscriptModel |
The information representing a transcript model.
|
| TranscriptModelBuilder |
Class for building immutable
TranscriptModel objects field-by-field. |
| TranscriptPosition |
Position on a transcript.
|
| TranscriptProjectionDecorator |
Wraps a
TranscriptModel object and allow the coordinate conversion. |
| TranscriptSequenceChangeHelper |
Helper class for getting updated transcript sequence for deletions and block substitutions.
|
| TranscriptSequenceDecorator |
Decorator for
TranscriptModel that helps with operations on its sequence |
| TranscriptSequenceOntologyDecorator |
Functionality for finding out about certain points/regions of
TranscriptModel using genomic positions. |
| Enum | Description |
|---|---|
| GenomeVariantType |
Types of genomic variants represented by
GenomeVariant. |
| PositionType |
Enum for differentiating between one- and zero-based positions.
|
| Strand |
Representation for forward/backward strand.
|
| Exception | Description |
|---|---|
| InvalidCodonException |
Raised when it is attempted to access an invalid codon
|
| InvalidCoordinateException |
Thrown if two coordinates were on different chromosomes.
|
| ProjectionException |
Thrown when a coordinate conversion failed.
|
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