All Classes Interface Summary Class Summary Enum Summary Exception Summary
Class |
Description |
AminoAcidCode |
Representation of the two possible amino acid codes, 1-letter and 3-letter.
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Antlr4HGVSLexer |
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Antlr4HGVSParser |
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Antlr4HGVSParser.Aa_change_deletionContext |
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Antlr4HGVSParser.Aa_change_duplicationContext |
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Antlr4HGVSParser.Aa_change_extensionContext |
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Antlr4HGVSParser.Aa_change_frameshiftContext |
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Antlr4HGVSParser.Aa_change_indelContext |
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Antlr4HGVSParser.Aa_change_innerContext |
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Antlr4HGVSParser.Aa_change_insertionContext |
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Antlr4HGVSParser.Aa_change_miscContext |
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Antlr4HGVSParser.Aa_change_ssrContext |
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Antlr4HGVSParser.Aa_change_substitutionContext |
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Antlr4HGVSParser.Aa_change_unchangedContext |
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Antlr4HGVSParser.Aa_changeContext |
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Antlr4HGVSParser.Aa_charContext |
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Antlr4HGVSParser.Aa_multi_allele_varContext |
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Antlr4HGVSParser.Aa_multi_change_allele_innerContext |
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Antlr4HGVSParser.Aa_multi_change_alleleContext |
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Antlr4HGVSParser.Aa_point_locationContext |
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Antlr4HGVSParser.Aa_rangeContext |
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Antlr4HGVSParser.Aa_single_allele_multi_change_varContext |
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Antlr4HGVSParser.Aa_single_allele_single_change_varContext |
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Antlr4HGVSParser.Aa_single_allele_varContext |
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Antlr4HGVSParser.Aa_stringContext |
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Antlr4HGVSParser.Aa_var_sepContext |
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Antlr4HGVSParser.Hgvs_variantContext |
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Antlr4HGVSParser.Legacy_change_deletionContext |
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Antlr4HGVSParser.Legacy_change_indelContext |
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Antlr4HGVSParser.Legacy_change_insertionContext |
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Antlr4HGVSParser.Legacy_change_substitutionContext |
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Antlr4HGVSParser.Legacy_changeContext |
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Antlr4HGVSParser.Legacy_point_locationContext |
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Antlr4HGVSParser.Legacy_variantContext |
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Antlr4HGVSParser.Nt_base_locationContext |
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Antlr4HGVSParser.Nt_change_deletionContext |
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Antlr4HGVSParser.Nt_change_duplicationContext |
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Antlr4HGVSParser.Nt_change_indelContext |
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Antlr4HGVSParser.Nt_change_innerContext |
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Antlr4HGVSParser.Nt_change_insertionContext |
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Antlr4HGVSParser.Nt_change_inversionContext |
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Antlr4HGVSParser.Nt_change_miscContext |
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Antlr4HGVSParser.Nt_change_not_sequenced_repeatContext |
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Antlr4HGVSParser.Nt_change_repeat_sequenceContext |
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Antlr4HGVSParser.Nt_change_sequenced_repeatContext |
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Antlr4HGVSParser.Nt_change_ssrContext |
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Antlr4HGVSParser.Nt_change_substitutionContext |
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Antlr4HGVSParser.Nt_change_unchangedContext |
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Antlr4HGVSParser.Nt_changeContext |
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Antlr4HGVSParser.Nt_multi_allele_varContext |
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Antlr4HGVSParser.Nt_multi_change_allele_innerContext |
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Antlr4HGVSParser.Nt_multi_change_alleleContext |
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Antlr4HGVSParser.Nt_numberContext |
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Antlr4HGVSParser.Nt_offsetContext |
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Antlr4HGVSParser.Nt_point_locationContext |
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Antlr4HGVSParser.Nt_rangeContext |
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Antlr4HGVSParser.Nt_single_allele_multi_change_varContext |
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Antlr4HGVSParser.Nt_single_allele_single_change_varContext |
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Antlr4HGVSParser.Nt_single_allele_varContext |
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Antlr4HGVSParser.Nt_stringContext |
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Antlr4HGVSParser.Nt_var_sepContext |
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Antlr4HGVSParser.ReferenceContext |
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Antlr4HGVSParserBaseListener |
This class provides an empty implementation of Antlr4HGVSParserListener ,
which can be extended to create a listener which only needs to handle a subset
of the available methods.
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Antlr4HGVSParserListener |
This interface defines a complete listener for a parse tree produced by
Antlr4HGVSParser .
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ConvertibleToHGVSString |
Provide HGVS string representation of an element.
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HGVSErrorStrategy |
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HGVSLexer |
Extends the generated Antlr4HGVSLexer to bail out at the first lexing error.
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HGVSParser |
Driver code for parsing HGVS strings into HGVSVariant objects.
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HGVSParsingException |
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HGVSVariant |
Base class for nucleotide and protein variants.
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LegacyChange |
Base class for legacy changes.
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LegacyChangeParser |
Parser for legacy change syntax (starting with "IVS", "EX", or "E").
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LegacyDeletion |
Representation of a legacy notation deletion.
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LegacyIndel |
Representation of a legacy notation substitution.
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LegacyInsertion |
Representation of a legacy notation insertion.
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LegacyLocation |
Exonic location for legacy variants, e.g.
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LegacyLocationType |
Enum describing either intronic or exonic locations.
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LegacySubstitution |
Representation of a legacy notation substitution.
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LegacyVariant |
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MultiAlleleNucleotideVariant |
Nucleotide variant having multiple alleles.
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MultiAlleleProteinVariant |
Protein variant having multiple alleles.
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NucleotideChange |
Base class for nucleotide changes.
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NucleotideChangeAllele |
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NucleotideDeletion |
Deletion in a nucleotide sequence.
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NucleotideDuplication |
Representation of a duplication on the nucleotide level.
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NucleotideIndel |
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NucleotideInsertion |
Insertion into a Nucleotide sequence.
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NucleotideInversion |
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NucleotideMiscChange |
Represents a silent protein-level change, i.e., "p.=".
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NucleotideMiscChangeType |
Enumeration of the miscellaneous nucleotide change types (for RNA).
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NucleotideNotSequencedRepeat |
A repeat that is not completely sequenced (i.e.
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NucleotideNotSequencedRepeat.InDelType |
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NucleotidePointLocation |
Position in a nucleotide string.
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NucleotideRange |
Range in a nucleotide sequence.
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NucleotideRepeatSequence |
A repeated sequence.
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NucleotideSeqDescription |
Specification for a nucleotide sequence, e.g.
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NucleotideSequencedRepeat |
A repeat that has been sequenced.
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NucleotideShortSequenceRepeatVariability |
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NucleotideSubstitution |
Substitution of one nucleotide.
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NucleotideUnchanged |
Unchanged in a nucleotide sequence.
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NucleotideVariant |
Base class for nucleotide changes.
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ProteinChange |
Base class for protein changes.
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ProteinChangeAllele |
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ProteinDeletion |
In-frame deletion of a protein (i.e., without frameshift, but can destroy codons).
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ProteinDuplication |
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ProteinExtension |
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ProteinFrameshift |
Protein frame shift change.
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ProteinIndel |
In-frame substitution on the protein level with more than one base.
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ProteinInsertion |
Insertion into a protein sequence.
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ProteinMiscChange |
Represents a silent protein-level change, i.e., "p.=".
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ProteinMiscChangeType |
Enum with for the miscellaneous protein changes.
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ProteinPointLocation |
Represent one position in a protein.
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ProteinRange |
Represent a range in a protein.
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ProteinSeqDescription |
Specification for inserted protein sequence, e.g.
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ProteinShortSequenceRepeatVariability |
Describes short sequence repeat (SSR) variability.
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ProteinSubstitution |
Represents a missense protein substitution, for example "Trp2Ala" or "T2A".
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ProteinUnchanged |
Unchanged mark inside protein.
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ProteinVariant |
Base class for protein changes.
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SequenceType |
Type of the sequence that the variant is on.
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SingleAlleleNucleotideVariant |
Nucleotide change with one allele only.
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SingleAlleleProteinVariant |
Protein change with one allele only.
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Translator |
This singleton class helps to translate DNA sequences.
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VariantConfiguration |
Variant configuration of changes in the same gene.
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