A B C D E F G H I J L M N O P R S T U V W

A

AbstractMendelianChecker - Class in de.charite.compbio.jannovar.mendel.impl

Abstract base class for mendelian checkers

AbstractMendelianChecker(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker

addExonRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

addGenotypes(ImmutableList<Genotype>) - Method in class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

Adds new list of genotypes, one for each individual.

AllAnnotationListTextGenerator - Class in de.charite.compbio.jannovar.annotation

Deprecated.

AllAnnotationListTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.AllAnnotationListTextGenerator

Deprecated.

allLeftOf(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

AltGeneIDType - Enum in de.charite.compbio.jannovar.hgnc

Enum for describing an alternative gene ID type

AminoAcidChange - Class in de.charite.compbio.jannovar.reference

Representation of a change in amino acids.

AminoAcidChange(int, String, String) - Constructor for class de.charite.compbio.jannovar.reference.AminoAcidChange

Construct object with given values.

AminoAcidChangeNormalizer - Class in de.charite.compbio.jannovar.reference

Helper for normalizing changes in amino acid sequences.

AminoAcidChangeNormalizer() - Constructor for class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Annotation - Class in de.charite.compbio.jannovar.annotation

Collect the information for one variant's annotation.

Annotation(Collection<AnnotationMessage>) - Constructor for class de.charite.compbio.jannovar.annotation.Annotation

Initialize object with messages only.

Annotation(TranscriptModel, GenomeVariant, Collection<VariantEffect>, AnnotationLocation, NucleotideChange, NucleotideChange, ProteinChange) - Constructor for class de.charite.compbio.jannovar.annotation.Annotation

Initialize the Annotation with the given values.

Annotation(TranscriptModel, GenomeVariant, Collection<VariantEffect>, AnnotationLocation, NucleotideChange, NucleotideChange, ProteinChange, Collection<AnnotationMessage>) - Constructor for class de.charite.compbio.jannovar.annotation.Annotation

Initialize the Annotation with the given values.

AnnotationBuilderDispatcher - Class in de.charite.compbio.jannovar.annotation.builders

Dispatches annotation building to the specific classes, depending on their GenomeVariant.getType().

AnnotationBuilderDispatcher(TranscriptModel, GenomeVariant, AnnotationBuilderOptions) - Constructor for class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher

AnnotationBuilderOptions - Class in de.charite.compbio.jannovar.annotation.builders

Configuration for the AnnotationBuilder subclasses.

AnnotationBuilderOptions() - Constructor for class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions

AnnotationBuilderOptions(boolean) - Constructor for class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions

AnnotationException - Exception in de.charite.compbio.jannovar.annotation

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

AnnotationException() - Constructor for exception de.charite.compbio.jannovar.annotation.AnnotationException

AnnotationException(String) - Constructor for exception de.charite.compbio.jannovar.annotation.AnnotationException

AnnotationException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.annotation.AnnotationException

AnnotationLocation - Class in de.charite.compbio.jannovar.annotation

Describes the location of an annotation.

AnnotationLocation(TranscriptModel, AnnotationLocation.RankType, int, int, TranscriptInterval) - Constructor for class de.charite.compbio.jannovar.annotation.AnnotationLocation

AnnotationLocation.RankType - Enum in de.charite.compbio.jannovar.annotation

Enumeration for rank types, exon, intron, or neither (i.e.

AnnotationLocationBuilder - Class in de.charite.compbio.jannovar.annotation

Builder for the immutable AnnotationLocation class.

AnnotationLocationBuilder() - Constructor for class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationMessage - Enum in de.charite.compbio.jannovar.annotation

Error messages for encoding problems during the annotation.

B

BestAnnotationListTextGenerator - Class in de.charite.compbio.jannovar.annotation

Deprecated.

BestAnnotationListTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.BestAnnotationListTextGenerator

Deprecated.

BlockSubstitutionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the block substitution GenomeVariant in the given TranscriptModel .

BlockSubstitutionAnnotationBuilder(TranscriptModel, GenomeVariant, AnnotationBuilderOptions) - Constructor for class de.charite.compbio.jannovar.annotation.builders.BlockSubstitutionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher

build() - Method in class de.charite.compbio.jannovar.annotation.builders.BlockSubstitutionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.DeletionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.InsertionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.StructuralVariantAnnotationBuilder

Build annotation for StructuralVariantAnnotationBuilder.transcript and StructuralVariantAnnotationBuilder.change

build() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

build(String, boolean) - Method in class de.charite.compbio.jannovar.datasource.JannovarDataFactory

build() - Method in class de.charite.compbio.jannovar.mendel.GenotypeBuilder

build() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

build() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

build() - Static method in class de.charite.compbio.jannovar.reference.HG19RefDictBuilder

build() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

buildAnnotations(int, int, String, String, PositionType) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotator

Convenience function for obtaining an VariantAnnotations from genome change in primitive types.

buildAnnotations(GenomeVariant) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotator

Main entry point to getting Annovar-type annotations for a variant identified by chromosomal coordinates.

buildEffectText() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

buildEmptyList(GenomeVariant) - Static method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

buildHGVSText(AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

buildSiblings() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

C

CDSInterval - Class in de.charite.compbio.jannovar.reference

Interval on a transcript.

CDSInterval(TranscriptModel, int, int) - Constructor for class de.charite.compbio.jannovar.reference.CDSInterval

construct transcript interval with one-based coordinate system

CDSInterval(TranscriptModel, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.CDSInterval

construct transcript interval with selected coordinate system

CDSPosition - Class in de.charite.compbio.jannovar.reference

Position on a transcript.

CDSPosition(TranscriptModel, int) - Constructor for class de.charite.compbio.jannovar.reference.CDSPosition

construct transcript position with one-based coordinate system

CDSPosition(TranscriptModel, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.CDSPosition

construct transcript position with selected coordinate system

cdsToGenomePos(CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from CDS to genome position.

cdsToTranscriptPos(CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from CDS to transcript position.

cdsTranscriptLength() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

checkMendelianInheritance(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker

Perform checking for compatible mode of inheritance

Chromosome - Class in de.charite.compbio.jannovar.data

This class encapsulates a chromosome and all of the genes its contains.

Chromosome(ReferenceDictionary, int, IntervalArray<TranscriptModel>) - Constructor for class de.charite.compbio.jannovar.data.Chromosome

Initialize object.

ChromosomeType - Enum in de.charite.compbio.jannovar.mendel

Describe the chromosome type, for use in mendelian inheritance filtering

clearAltGeneIDs() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

Clear alternative geneIDs map

clearExonRegions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

Clear exon regions list

codonWithUpdatedBase(String, int, char) - Static method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Update the base given by frameShift in the given codon string transcriptCodon to targetNC and return updated codon.

compareTo(Annotation) - Method in class de.charite.compbio.jannovar.annotation.Annotation

compareTo(Annotation) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

compareTo(Interval<T>) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

compareTo(MutableInterval<T>) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

compareTo(FeatureRecord) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

compareTo(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

compareTo(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

compareTo(Annotation) - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

compareTo(TranscriptModel) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

compareTo(Annotation) - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

concatenate(Object...) - Static method in class de.charite.compbio.jannovar.impl.util.StringUtil

Concatenate values.toString() using a StringBuilder.

constructSingleSamplePedigree(String) - Static method in class de.charite.compbio.jannovar.pedigree.Pedigree

contains(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

contains(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

contains(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

containsExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

D

DataSource - Class in de.charite.compbio.jannovar.datasource

Base class for all data sources.

DataSourceFactory - Class in de.charite.compbio.jannovar.datasource

Factory class that allows the construction of DataSource objects as configured in INI files.

DataSourceFactory(DatasourceOptions, List<String>) - Constructor for class de.charite.compbio.jannovar.datasource.DataSourceFactory

DatasourceOptions - Class in de.charite.compbio.jannovar.datasource

Configuration for data sources.

DatasourceOptions() - Constructor for class de.charite.compbio.jannovar.datasource.DatasourceOptions

Initialize with default settings.

DatasourceOptions(URL, URL, URL, boolean) - Constructor for class de.charite.compbio.jannovar.datasource.DatasourceOptions

de.charite.compbio.jannovar - package de.charite.compbio.jannovar

de.charite.compbio.jannovar.annotation - package de.charite.compbio.jannovar.annotation

de.charite.compbio.jannovar.annotation.builders - package de.charite.compbio.jannovar.annotation.builders

de.charite.compbio.jannovar.data - package de.charite.compbio.jannovar.data

de.charite.compbio.jannovar.datasource - package de.charite.compbio.jannovar.datasource

de.charite.compbio.jannovar.hgnc - package de.charite.compbio.jannovar.hgnc

de.charite.compbio.jannovar.impl.intervals - package de.charite.compbio.jannovar.impl.intervals

de.charite.compbio.jannovar.impl.parse - package de.charite.compbio.jannovar.impl.parse

de.charite.compbio.jannovar.impl.parse.ensembl - package de.charite.compbio.jannovar.impl.parse.ensembl

de.charite.compbio.jannovar.impl.parse.flatbed - package de.charite.compbio.jannovar.impl.parse.flatbed

de.charite.compbio.jannovar.impl.parse.gtfgff - package de.charite.compbio.jannovar.impl.parse.gtfgff

de.charite.compbio.jannovar.impl.parse.refseq - package de.charite.compbio.jannovar.impl.parse.refseq

de.charite.compbio.jannovar.impl.parse.ucsc - package de.charite.compbio.jannovar.impl.parse.ucsc

de.charite.compbio.jannovar.impl.util - package de.charite.compbio.jannovar.impl.util

de.charite.compbio.jannovar.mendel - package de.charite.compbio.jannovar.mendel

de.charite.compbio.jannovar.mendel.impl - package de.charite.compbio.jannovar.mendel.impl

de.charite.compbio.jannovar.pedigree - package de.charite.compbio.jannovar.pedigree

de.charite.compbio.jannovar.reference - package de.charite.compbio.jannovar.reference

DeletionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the deletion GenomeVariants in the given TranscriptModel.

differenceTo(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

differenceTo(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

Disease - Enum in de.charite.compbio.jannovar.pedigree

Codes used to denote affection status of a person in a pedigree.

DNAUtils - Class in de.charite.compbio.jannovar.impl.util

Utility class for DNA string manipulation.

DNAUtils() - Constructor for class de.charite.compbio.jannovar.impl.util.DNAUtils

doPrint() - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

doPrintProgressBars() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

DOWNLOAD_URL - Static variable in class de.charite.compbio.jannovar.hgnc.HGNCParser

Download URL for the HGNC complete set TSV file

DuplicationChecker - Class in de.charite.compbio.jannovar.reference

Helper class for checking whether an insertion in a string is a duplication.

DuplicationChecker() - Constructor for class de.charite.compbio.jannovar.reference.DuplicationChecker

E

EnsemblParser - Class in de.charite.compbio.jannovar.impl.parse.ensembl

Parsing of ENSEMBL GTF files

EnsemblParser(ReferenceDictionary, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser

equals(Object) - Method in class de.charite.compbio.jannovar.annotation.Annotation

equals(Object) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

equals(Object) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

equals(Object) - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

equals(Object) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

equals(Object) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

equals(Object) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

equals(Object) - Method in class de.charite.compbio.jannovar.mendel.Genotype

equals(Object) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

equals(Object) - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

equals(Object) - Method in class de.charite.compbio.jannovar.pedigree.Person

equals(Object) - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

equals(Object) - Method in class de.charite.compbio.jannovar.reference.CDSInterval

equals(Object) - Method in class de.charite.compbio.jannovar.reference.CDSPosition

equals(Object) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

equals(Object) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

equals(Object) - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

equals(Object) - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

equals(Object) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

equals(Object) - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

exonIDInReferenceOrder(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns the index of the (0-based) exon in the reference (forward) order.

F

FASTAParser - Class in de.charite.compbio.jannovar.impl.parse

Generic FASTA parser that allow record-wise loading of FASTA files

FASTAParser(File) - Constructor for class de.charite.compbio.jannovar.impl.parse.FASTAParser

Initialize with a file, gzip compression is automatically recognized.

FASTAParser(InputStream) - Constructor for class de.charite.compbio.jannovar.impl.parse.FASTAParser

Initialize from a InputStream, gzip compression is automatically recognized.

FASTARecord - Class in de.charite.compbio.jannovar.impl.parse

Representation of a FASTA record

FASTARecord(String, String, String) - Constructor for class de.charite.compbio.jannovar.impl.parse.FASTARecord

FeatureRecord - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Immutable class for describing a record from a GFF or GTF file.

FeatureRecord(String, String, String, int, int, String, FeatureRecord.Strand, int, Map<String, String>) - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

Initialize the GFFRecord

FeatureRecord.Strand - Enum in de.charite.compbio.jannovar.impl.parse.gtfgff

Type for describing record strand

FeatureRecordParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Abstract base class for GTF/GFF record parsers.

FeatureRecordParser() - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecordParser

FileDownloadException - Exception in de.charite.compbio.jannovar.datasource

Exception that can be called if something went wrong while downloading the transcript files.

FileDownloadException() - Constructor for exception de.charite.compbio.jannovar.datasource.FileDownloadException

FileDownloadException(String) - Constructor for exception de.charite.compbio.jannovar.datasource.FileDownloadException

FileDownloadException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.datasource.FileDownloadException

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker

Filter list of GenotypeCalls for fitting to mode

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAD

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAR

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARCompoundHet

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARHom

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXD

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXR

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRCompoundHet

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRHom

findOverlappingWithInterval(int, int) - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

Query the encoded interval tree for all values with intervals overlapping with a given interval.

findOverlappingWithPoint(int) - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

Query the encoded interval tree for all values with intervals overlapping with a given point.

FlatBEDDataSource - Class in de.charite.compbio.jannovar.datasource

A DataSource that reads regions from a BED file.

FlatBEDFastaParser - Class in de.charite.compbio.jannovar.impl.parse.flatbed

Parser for the FASTA formated files from flat BED files.

FlatBEDFastaParser(String, ArrayList<TranscriptModelBuilder>, boolean) - Constructor for class de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDFastaParser

FlatBEDJannovarDataFactory - Class in de.charite.compbio.jannovar.datasource

JannovarDataFactory for flat BED files.

FlatBEDJannovarDataFactory(DatasourceOptions, DataSource, Profile.Section) - Constructor for class de.charite.compbio.jannovar.datasource.FlatBEDJannovarDataFactory

Construct the factory with the given EnsemblDataSource.

FlatBEDParser - Class in de.charite.compbio.jannovar.impl.parse.flatbed

Class for parsing flat BED data.

FlatBEDParser(ReferenceDictionary, String, Profile.Section, boolean) - Constructor for class de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDParser

G

GenomeInterval - Class in de.charite.compbio.jannovar.reference

Representation of a genomic interval (chromsome, begin, end).

GenomeInterval(ReferenceDictionary, Strand, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval with zero-based coordinate system

GenomeInterval(ReferenceDictionary, Strand, int, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval with selected coordinate system

GenomeInterval(GenomeInterval) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval from other with selected coordinate system

GenomeInterval(GenomeInterval, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval from other with selected strand

GenomeInterval(GenomePosition, int) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval from GenomePosition with a length towards 3' of pos' coordinate system

GenomePosition - Class in de.charite.compbio.jannovar.reference

Representation of a position on a genome (chromosome, position).

GenomePosition(ReferenceDictionary, Strand, int, int) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position with zero-based coordinate system

GenomePosition(ReferenceDictionary, Strand, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position with selected coordinate system

GenomePosition(GenomePosition) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position from other with selected coordinate system

GenomePosition(GenomePosition, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position from other with the selected strand

genomeToCDSPos(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from genome position to CDS position.

genomeToTranscriptPos(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from genome position to transcript position.

GenomeVariant - Class in de.charite.compbio.jannovar.reference

Denote a change with a "REF" and an "ALT" string using genome coordinates.

GenomeVariant(GenomePosition, String, String) - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariant

Construct object given the position, reference, and alternative nucleic acid string.

GenomeVariant(GenomePosition, String, String, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariant

Construct object given the position, reference, alternative nucleic acid string, and strand.

GenomeVariant(GenomeVariant, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariant

Construct object and enforce strand.

GenomeVariantNormalizer - Class in de.charite.compbio.jannovar.reference

Helper code for the normalization of GenomeVariants.

GenomeVariantNormalizer() - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

GenomeVariantType - Enum in de.charite.compbio.jannovar.reference

Types of genomic variants represented by GenomeVariant.

GenomicNucleotideChangeBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Build NucleotideChange for a GenomeVariant.

GenomicNucleotideChangeBuilder(GenomeVariant) - Constructor for class de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder

Initialize with the given variant.

Genotype - Class in de.charite.compbio.jannovar.mendel

Representation of a genotype in an individual Genotypes are represented by lists of integers identifying alleles from a GenotypeCalls.

Genotype(Collection<Integer>) - Constructor for class de.charite.compbio.jannovar.mendel.Genotype

Construct Genotype with list of allele numbers

Genotype - Enum in de.charite.compbio.jannovar.pedigree

Enumeration of genotype kinds.

GenotypeBuilder - Class in de.charite.compbio.jannovar.mendel

Helper class for building Genotype objects

GenotypeBuilder() - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeBuilder

GenotypeCalls - Class in de.charite.compbio.jannovar.mendel

A list of genotypes (at an implicitely assumed site) in multiple individuals This list contains the core information for the filtration of variants by mendelian inheritance.

GenotypeCalls(ChromosomeType, Iterable<? extends Map.Entry<String, Genotype>>) - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeCalls

Initialize GenotypeCalls with mapping from sample to genotype

GenotypeCalls(ChromosomeType, Iterable<? extends Map.Entry<String, Genotype>>, Object) - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeCalls

Initialize GenotypeCalls with mapping from sample to genotype and an additional "payload" object

GenotypeCallsBuilder - Class in de.charite.compbio.jannovar.mendel

Helper class for building GenotypeCalls objects

GenotypeCallsBuilder() - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

GenotypeList - Class in de.charite.compbio.jannovar.pedigree

Deprecated.

GenotypeList(String, List<String>, boolean, ImmutableList<ImmutableList<Genotype>>) - Constructor for class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

Construct and initialize object.

GenotypeListBuilder - Class in de.charite.compbio.jannovar.pedigree

Deprecated.

GenotypeListBuilder(String, List<String>) - Constructor for class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

GenotypeListBuilder(String, List<String>, boolean) - Constructor for class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

getAbbreviation() - Method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance

getAccession() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getAccession() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getAffectedFemaleParentNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getAffectedMaleParentNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getAliasSymbols() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getAlleleID() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

getAlleleNumbers() - Method in class de.charite.compbio.jannovar.mendel.Genotype

getAlleleNumbers() - Method in class de.charite.compbio.jannovar.mendel.GenotypeBuilder

getAlt() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getAlt() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getAlt() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getAlt() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getAlt() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getAltCount() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

getAltGeneIDs() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

Return mapping containing alternative gene IDs, as parsed from RefSeq GFF3 file The alternative identifiers used are the values of AltGeneIDType converted to strings.

getAltGeneIDs() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getAnnoLoc() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getAnnotations() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getAnnotations() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getAttributes() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getBegin() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getBegin(T) - Method in interface de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor

getBegin() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getBegin() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getBegin(TranscriptModel) - Method in class de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor

getBeginPos() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

getBeginPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getBeginPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getCalls() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

the lists of genotype calls, each contains one entry for each individual

getCCDSIDs() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getCDSNTChange() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getCDSNTChangeStr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getCDSRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getCDSRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getCDSTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

getCDSWithGenomeVariant(GenomeVariant) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper

Similar to TranscriptSequenceChangeHelper.getTranscriptWithChange(de.charite.compbio.jannovar.reference.GenomeVariant) but starting at the CDS begin position.

getChr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getChr() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getChr() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getChr() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getChr() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getChr() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getChr() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getChrID() - Method in class de.charite.compbio.jannovar.data.Chromosome

getChrName() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getChrName() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getChrName() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getChrName() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getChromosomeName() - Method in class de.charite.compbio.jannovar.data.Chromosome

getChromosomes() - Method in class de.charite.compbio.jannovar.data.JannovarData

getChromType() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getChromType() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

getCodonAt(TranscriptPosition, CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Returns the codon (String of length 3) for a change at a given position

getCodonsStartingFrom(TranscriptPosition, CDSPosition, int) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Returns a number of codons (String of length 3 * len) starting from the affected one by the change at txPos/cdsPos.

getCodonsStartingFrom(TranscriptPosition, CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Returns all codons (String of length 3 * len) starting from the affected one by the change at txPos/cdsPos.

getComment() - Method in class de.charite.compbio.jannovar.impl.parse.FASTARecord

getContigID(String) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Allows contig name to numeric ID translation before final construction of the ReferenceDictionary.

getContigIDToLength() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

getContigIDToName() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

getContigLength(int) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Allows contig length retrieval before final construction of the ReferenceDictionary.

getContigName(Integer) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Allows get contig name from a contig id.

getContigNameToID() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

getCosmicID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getDataFactory() - Method in class de.charite.compbio.jannovar.datasource.DataSource

getDataFactory() - Method in class de.charite.compbio.jannovar.datasource.FlatBEDDataSource

getDataSource(String) - Method in class de.charite.compbio.jannovar.datasource.DataSourceFactory

Construct DataSource

getDisease() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getDisease() - Method in class de.charite.compbio.jannovar.pedigree.Person

getDownloadURLs() - Method in class de.charite.compbio.jannovar.datasource.DataSource

getDownstreamInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getEffects() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getEnaID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getEnd(T) - Method in interface de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor

getEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getEnd() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getEnd(TranscriptModel) - Method in class de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor

getEndPos() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

getEndPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getEndPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getEnsemblGeneID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getEntrezID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getEntries() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult

getExonRegions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getExonRegions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getExtraColumnHeaders() - Method in class de.charite.compbio.jannovar.pedigree.PedFileContents

getExtraFields() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getExtraFields() - Method in class de.charite.compbio.jannovar.pedigree.Person

getFather() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getFather() - Method in class de.charite.compbio.jannovar.pedigree.Person

getFileName(String) - Method in class de.charite.compbio.jannovar.datasource.DataSource

getFivePrimeUTRInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns the genomic 5' UTR interval.

getFrameshift() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

getFTPProxy() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

getGeneID() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getGeneID() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getGeneID() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getGeneName() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

the name of the gene for this genotype call list

getGeneSymbol() - Method in class de.charite.compbio.jannovar.annotation.Annotation

Return the gene annotation or "." if it has no transcript.

getGeneSymbol() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getGeneSymbol() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getGeneSymbol() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getGenomeBeginPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

return the genome begin position

getGenomeEndPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

return the genome end position

getGenomeInterval() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getGenomePos() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getGenomeVariant() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getGenomeVariant() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

Return the GenomeVariant that this AnnotationList is annotated with.

getGenomicNTChange() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getGenomicNTChangeStr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getGenotypeBySampleNo(int) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getGenotypeForSample(String) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getGFFVersion() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

getHgncID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getHighestImpactAnnotation() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getHighestImpactEffect() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

Convenience method.

getHTTPProxy() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

getHTTPSProxy() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

getID() - Method in class de.charite.compbio.jannovar.impl.parse.FASTARecord

getIdx() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson

getImpact() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getIndividuals() - Method in class de.charite.compbio.jannovar.pedigree.PedFileContents

getIntervals() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

getIntervalsEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

getLastPos() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getLeft() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult

getLegacyTerm() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getMax() - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

getMaxEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getMaxEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getMembers() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getMessages() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getMGDID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getMin() - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

getMostPathogenicVarType() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getMother() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getMother() - Method in class de.charite.compbio.jannovar.pedigree.Person

getName() - Method in class de.charite.compbio.jannovar.datasource.DataSource

getName() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getName() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getName() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getName() - Method in class de.charite.compbio.jannovar.pedigree.Person

getNames() - Method in class de.charite.compbio.jannovar.datasource.DataSourceFactory

getNames() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

the list of individual names

getNames() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getNameToMember() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getNameToPerson() - Method in class de.charite.compbio.jannovar.pedigree.PedFileContents

getNMembers() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getNSamples() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getNucleotidePointLocation(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.NucleotidePointLocationBuilder

getNumber() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

Forward to ordinal() member function.

getNumberOfAffecteds() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getNumberOfGenes() - Method in class de.charite.compbio.jannovar.data.Chromosome

getNumberOfParents() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getNumberOfUnaffecteds() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getOmimID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getParentNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getParents() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getPayload() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getPayload() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

getPedigree() - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker

getPedigree() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getPedigree() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getPerson() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson

getPhase() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getPloidy() - Method in class de.charite.compbio.jannovar.mendel.Genotype

getPos() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getPos() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getPos() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getPos() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

getPos() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getPos() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

getPos() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getPrevSymbol() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getPrioritySortedList() - Static method in enum de.charite.compbio.jannovar.annotation.OldVariantType

This returns an array with the VariantTypes arranged according to their priority.

getProteinChange() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getProteinChangeStr(AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.Annotation

getProteinChangeStr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getPubmedIDs() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getPutativeImpact() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getRank() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getRank() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getRankType() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getRankType() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getRef() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getRef() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getRef() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getRef() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getRef() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getRefDict() - Method in class de.charite.compbio.jannovar.data.Chromosome

getRefDict() - Method in class de.charite.compbio.jannovar.data.JannovarData

getRefDict() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getRefDict() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getRefseqAccession() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getRGDID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getRight() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult

getSampleNames() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getSampleToGenotype() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getSampleToGenotype() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

getScore() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getSeparator() - Method in enum de.charite.compbio.jannovar.hgnc.AltGeneIDType

getSeqID() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getSequence() - Method in class de.charite.compbio.jannovar.impl.parse.FASTARecord

getSequence() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getSequence() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getSequenceOID() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getSequenceOntologyTerm() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getSex() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getSex() - Method in class de.charite.compbio.jannovar.pedigree.Person

getSource() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getStartCodonInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getStopCodonInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getStrand() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getStrand() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getStrand() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getStrand() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getStrand() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getSymbol() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getSymbolAndAnnotation(AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.Annotation

Return the full annotation with the gene symbol.

getThreePrimeUTRInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns the genomic 3' UTR interval.

getTmByAccession() - Method in class de.charite.compbio.jannovar.data.JannovarData

getTmByGeneSymbol() - Method in class de.charite.compbio.jannovar.data.JannovarData

getTMIntervalTree() - Method in class de.charite.compbio.jannovar.data.Chromosome

getTotalRank() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getTranscript() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getTranscript() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getTranscript() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getTranscript() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

getTranscript() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getTranscriptBeginPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getTranscriptEndPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getTranscriptStartingAtCDS() - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

getTranscriptSupportLevel() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getTranscriptSupportLevel() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getTranscriptWithChange(GenomeVariant) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper

Return modified transcript after applying a GenomeVariant.

getTranslator() - Static method in class de.charite.compbio.jannovar.impl.util.Translator

Factory method to get reference to Translator.

getTXLocation() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getTXLocation() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getTXRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getTXRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getType() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getType() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getUCSCID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getUnaffectedNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getUniprotIDs() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

getUpstreamInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getValue() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getValue() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getVariant() - Method in class de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder

getVariantType() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getVegaID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

GFFParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

A class for parsing a stream of GFFRecord objects from a GTF or GFF file.

GFFParser(File) - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

Initialize with a file, gzip compression is automatically recognized.

GFFParser(InputStream) - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

Initialize from a InputStream, gzip compression is automatically recognized.

GFFParser.GFFVersion - Enum in de.charite.compbio.jannovar.impl.parse.gtfgff

Enum type for describing the GFF version

GFFRecordParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Parse a line of GFF and return a FeatureRecord from this

GFFRecordParser() - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFRecordParser

GTFRecordParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Parse a line of GTF and return a FeatureRecord from this

GTFRecordParser() - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GTFRecordParser

H

hasAnnotation() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

hashCode() - Method in class de.charite.compbio.jannovar.annotation.Annotation

hashCode() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

hashCode() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

hashCode() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

hashCode() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

hashCode() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

hashCode() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

hashCode() - Method in class de.charite.compbio.jannovar.mendel.Genotype

hashCode() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

hashCode() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

hashCode() - Method in class de.charite.compbio.jannovar.pedigree.Person

hashCode() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

hashCode() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

hashCode() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

hashCode() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

hashCode() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

hashCode() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

hashCode() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

hashCode() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

hashCode() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

hasMultipleGeneSymbols() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

hasPerson(String) - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

hasStructuralVariant() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

HG19RefDictBuilder - Class in de.charite.compbio.jannovar.reference

Builds a ReferenceDictionary for the hg19 release.

HG19RefDictBuilder() - Constructor for class de.charite.compbio.jannovar.reference.HG19RefDictBuilder

HGNCParser - Class in de.charite.compbio.jannovar.hgnc

Parser for hgnc_complete_set.txt

HGNCParser(String) - Constructor for class de.charite.compbio.jannovar.hgnc.HGNCParser

HGNCRecord - Class in de.charite.compbio.jannovar.hgnc

Representation of the relevant entries from one record from the hgnc_complete_set.txt file.

HGNCRecord(String, String, String, Collection<String>, Collection<String>, String, String, String, String, String, String, Collection<String>, Collection<String>, Collection<String>, String, String, String, String) - Constructor for class de.charite.compbio.jannovar.hgnc.HGNCRecord

I

Immutable - Annotation Type in de.charite.compbio.jannovar

Annotation for marking a class as immutable.

IncompatiblePedigreeException - Exception in de.charite.compbio.jannovar.mendel

Thrown when the pedigree does not fit to the GenotypeCalls

IncompatiblePedigreeException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException

IncompatiblePedigreeException(String) - Constructor for exception de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException

IndexedPerson(int, Person) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson

INFO_EFFECT - Static variable in class de.charite.compbio.jannovar.annotation.Annotation

This line is added to the output of a VCF file annotated by Jannovar and describes the new field for the INFO section entitled EFFECT, which decribes the effects of variants (splicing,missense,stoploss, etc).

INFO_HGVS - Static variable in class de.charite.compbio.jannovar.annotation.Annotation

This line is added to the output of a VCF file annotated by Jannovar and describes the new field for the INFO section entitled HGVS, which provides the HGVS encoded variant corresponding to the chromosomal variant in the original VCF file.

InsertionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the insertion GenomeVariant in the given TranscriptModel

intersection(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

Interval<T> - Class in de.charite.compbio.jannovar.impl.intervals

Half-open interval for serialization of an IntervalArray.

Interval(MutableInterval<T>) - Constructor for class de.charite.compbio.jannovar.impl.intervals.Interval

Interval(int, int, T, int) - Constructor for class de.charite.compbio.jannovar.impl.intervals.Interval

IntervalArray<T> - Class in de.charite.compbio.jannovar.impl.intervals

Sorted array of Interval objects representing an immutable interval tree.

IntervalArray(Collection<T>, IntervalEndExtractor<T>) - Constructor for class de.charite.compbio.jannovar.impl.intervals.IntervalArray

Construct object with the given values.

IntervalArray.QueryResult - Class in de.charite.compbio.jannovar.impl.intervals

Type for storing the query result.

IntervalEndExtractor<T> - Interface in de.charite.compbio.jannovar.impl.intervals

Allows extraction of begin and end position for a type.

intronRegion(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

INVALID_EXON_ID - Static variable in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

constant for invalid exon index

INVALID_INTRON_ID - Static variable in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

constant for invalid intron index

INVALID_RANK - Static variable in class de.charite.compbio.jannovar.annotation.AnnotationLocation

Sentinel value for "invalid rank".

InvalidAttributeException - Exception in de.charite.compbio.jannovar.impl.parse

InvalidAttributeException are thrown if a attribute given to a method is invalid and can not be processed.

InvalidAttributeException(String) - Constructor for exception de.charite.compbio.jannovar.impl.parse.InvalidAttributeException

InvalidCodonException - Exception in de.charite.compbio.jannovar.reference

Raised when it is attempted to access an invalid codon

InvalidCodonException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCodonException

InvalidCodonException(String) - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCodonException

InvalidCoordinateException - Exception in de.charite.compbio.jannovar.reference

Thrown if two coordinates were on different chromosomes.

InvalidCoordinateException() - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCoordinateException

InvalidCoordinateException(String) - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCoordinateException

InvalidDataSourceException - Exception in de.charite.compbio.jannovar.datasource

Thrown on problems with data source configuration files.

InvalidDataSourceException() - Constructor for exception de.charite.compbio.jannovar.datasource.InvalidDataSourceException

InvalidDataSourceException(String) - Constructor for exception de.charite.compbio.jannovar.datasource.InvalidDataSourceException

InvalidDataSourceException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.datasource.InvalidDataSourceException

InvalidGenomeVariant - Exception in de.charite.compbio.jannovar.annotation

Thrown when the the given GenomeVariant does not fit the used annotation builder class.

InvalidGenomeVariant() - Constructor for exception de.charite.compbio.jannovar.annotation.InvalidGenomeVariant

InvalidGenomeVariant(String) - Constructor for exception de.charite.compbio.jannovar.annotation.InvalidGenomeVariant

IS_INTRONIC - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Predicate for testing whether a VariantEffect is intronic.

IS_SPLICING - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Predicate for testing whether a VariantEffect is related to splicing.

isAffected() - Method in class de.charite.compbio.jannovar.pedigree.Person

isCoding() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

isDiploid() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isDuplication(String, String, int) - Static method in class de.charite.compbio.jannovar.reference.DuplicationChecker

isEq(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isFemale() - Method in class de.charite.compbio.jannovar.pedigree.Person

isForward() - Method in enum de.charite.compbio.jannovar.reference.Strand

isFounder() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

isFounder() - Method in class de.charite.compbio.jannovar.pedigree.Person

isGeq(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isGt(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isHet() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isHomAlt() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isHomRef() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isIntronic() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isLeftOf(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

isLeftOf(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isLeftOfGap(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isLeq(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isLt(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isMale() - Method in class de.charite.compbio.jannovar.pedigree.Person

isMonoploid() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isMulti() - Method in enum de.charite.compbio.jannovar.hgnc.AltGeneIDType

isNop() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

isNotObserved() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isNt3PrimeShifting() - Method in class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions

isOffExome() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isOffTranscript() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isParentOfAffected(Person) - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

isReverse() - Method in enum de.charite.compbio.jannovar.reference.Strand

isRightOf(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

isRightOf(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isRightOfGap(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isSplicing() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isStructural() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isSymbolic() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

isTopPriorityVariant() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

We do not know, actually, whether any given variant is pathogenic if we just judge its pathogenicity class.

isTransition() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

A transition is between purine and purine or between pyrimidine and pyrimidine.

isTransversion() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

A transversion is purine <-> pyrimidine.

isUnaffected() - Method in class de.charite.compbio.jannovar.pedigree.Person

isXChromosomal() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

whether or not the variants are on the X chromsome

iterator() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

J

JannovarData - Class in de.charite.compbio.jannovar.data

This data type is used for serialization after downloading.

JannovarData(ReferenceDictionary, ImmutableList<TranscriptModel>) - Constructor for class de.charite.compbio.jannovar.data.JannovarData

Initialize the object with the given values.

JannovarDataFactory - Class in de.charite.compbio.jannovar.datasource

Interface for data factories, allowing to create JannovarData objects from DataSources.

JannovarDataFactory(DatasourceOptions, DataSource, Profile.Section) - Constructor for class de.charite.compbio.jannovar.datasource.JannovarDataFactory

Construct the factory with the given DataSource.

JannovarDataSerializer - Class in de.charite.compbio.jannovar.data

Manager for serializing and deserializing JannovarData objects.

JannovarDataSerializer(String) - Constructor for class de.charite.compbio.jannovar.data.JannovarDataSerializer

Initialize the (de)serializer with the path to the file to load/save.

JannovarException - Exception in de.charite.compbio.jannovar

Base class for exceptions in Jannovar.

JannovarException() - Constructor for exception de.charite.compbio.jannovar.JannovarException

JannovarException(String) - Constructor for exception de.charite.compbio.jannovar.JannovarException

JannovarException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.JannovarException

join(String...) - Static method in class de.charite.compbio.jannovar.impl.util.PathUtil

Join file name components.

L

length() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

returns length of the interval

length() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

returns length of the interval

length() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

liesInCDS(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInCDSExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInCDSExon(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInCDSIntron(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInDownstreamRegion(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within with the downstream region of the transcript.

liesInExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInExon(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInFivePrimeUTR(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInIntron(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInIntron(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInSpliceAcceptorSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within a splice acceptor site.

liesInSpliceDonorSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within a splice donor site.

liesInSpliceRegion(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within a splice region.

liesInThreePrimeUTR(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInTranslationalStartSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInTranslationalStopSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInUpstreamRegion(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within with the upstream region of the transcript.

load() - Method in class de.charite.compbio.jannovar.data.JannovarDataSerializer

Deserialize a JannovarData object from a file.

locateExon(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns (0-based) index of the exon (in the order determined by the transcript's strand).

locateExon(TranscriptPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns (0-based) index of the exon (in the order determined by the transcript's strand).

locateIntron(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns (0-based) index of the intron (in the order determined by the transcript's strand).

LONGEST_TRANSCRIPT - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

Longest transcript of a gene (used in absence of any TSL annotation and UCSC annotation of this transcript).

LOW_PRIORITY - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

Lowest available priority (used in absence of any TSL and UCSC annotation of this transcript).

M

MendelianCheckerAD - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal dominant case

MendelianCheckerAD(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAD

MendelianCheckerAR - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal recessive case

MendelianCheckerAR(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAR

MendelianCheckerARCompoundHet - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a Collection of GenotypeCalls for compatibility with a Pedigree and autosomal recessive compound het mode of inheritance.

MendelianCheckerARCompoundHet(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARCompoundHet

MendelianCheckerARHom - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a Collection of GenotypeCalls for compatibility with a Pedigree and autosomal recessive homozygous mode of inheritance.

MendelianCheckerARHom(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARHom

MendelianCheckerXD - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal dominant case

MendelianCheckerXD(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXD

MendelianCheckerXR - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal recessive case

MendelianCheckerXR(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXR

MendelianCheckerXRCompoundHet - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a GenotypeCalls for compatibility with a Pedigree and X recessive compound het.

MendelianCheckerXRCompoundHet(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRCompoundHet

MendelianCheckerXRHom - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a GenotypeCalls for compatibility with a Pedigree and AR homozygous mode

MendelianCheckerXRHom(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRHom

MendelianInheritanceChecker - Class in de.charite.compbio.jannovar.mendel

Facade class for checking lists of GenotypeCalls for compatibility with mendelian inheritance

MendelianInheritanceChecker(Pedigree) - Constructor for class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker

Construct checker with the pedigree to use

ModeOfInheritance - Enum in de.charite.compbio.jannovar.mendel

An enumeration of the four main Mendelian modes of inheritance for prioritizing exome data

MutableInterval<T> - Class in de.charite.compbio.jannovar.impl.intervals

Mutable half-open interval, for incremental building of Interval objects.

MutableInterval() - Constructor for class de.charite.compbio.jannovar.impl.intervals.MutableInterval

MutableInterval(int, int, T, int) - Constructor for class de.charite.compbio.jannovar.impl.intervals.MutableInterval

MutableInterval(int, int, T) - Constructor for class de.charite.compbio.jannovar.impl.intervals.MutableInterval

N

namesEqual(Pedigree) - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

Check whether the GenotypeList.names of this GenotypeCalls are the same as the names of the members of pedigree.

next() - Method in class de.charite.compbio.jannovar.impl.parse.FASTAParser

Reads next record from the GFF file and return it, null when the file is at its end.

next() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

Reads next record from the GFF file and return it, null when the file is at its end.

NO_CALL - Static variable in class de.charite.compbio.jannovar.mendel.Genotype

normalizeDeletion(String, AminoAcidChange) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Normalize deletion AminoAcidChange for amino acid string Return change if it is not a clean deletion.

normalizeDeletion(TranscriptModel, GenomeVariant, TranscriptPosition) - Static method in class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

Transform a deletion GenomeVariant into its HGVS-normalized representation.

normalizeGenomeChange(TranscriptModel, GenomeVariant, TranscriptPosition) - Static method in class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

Transform a GenomeVariant to its HGVS-normalized representation.

normalizeInsertion(TranscriptModel, GenomeVariant, TranscriptPosition) - Static method in class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

Transform an insertion GenomeVariant to its HGVS-normalized representation.

NOT_AVAILABLE - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version)

NucleotidePointLocationBuilder - Class in de.charite.compbio.jannovar.reference

Helper class that allows easy building of NucleotidePointLocations.

NucleotidePointLocationBuilder(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.NucleotidePointLocationBuilder

Construct the position builder with the given transcript

nucleotidesWithInsertion(String, int, String) - Static method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Insert the string in insertion at the position given by frameShift in the given codon string transcriptCodon to targetNC and return the updated nucleic string.

O

OldVariantType - Enum in de.charite.compbio.jannovar.annotation

Enumeration of the old Jannovar variant types (i.e.

overlapsWith(int, int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

overlapsWith(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

overlapsWithCDS(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithCDSExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithCDSIntron(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithDownstreamRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with the downstream region of the transcript.

overlapsWithExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithFivePrimeUTR(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithIntron(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithSpliceAcceptorSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with a splice acceptor site.

overlapsWithSpliceDonorSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with a splice donor site.

overlapsWithSpliceRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with a splice region.

overlapsWithThreePrimeUTR(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithTranslationalStartSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithTranslationalStopSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithUpstreamRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with the upstream region of the transcript.

P

parse() - Method in class de.charite.compbio.jannovar.impl.parse.ReferenceDictParser

Load accessions and chromInfo file and return resulting ReferenceDictionary.

parseLine(String) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecordParser

Parse the line and return the corresponding FeatureRecord

parseTranscriptModelFromLine(String) - Method in class de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser

The function parses a single line of the knownGene.txt file.

PathUtil - Class in de.charite.compbio.jannovar.impl.util

Utility class with static methods for path manipulation.

PathUtil() - Constructor for class de.charite.compbio.jannovar.impl.util.PathUtil

PedFileContents - Class in de.charite.compbio.jannovar.pedigree

Represents the contents of a pedigree file.

PedFileContents(ImmutableList<String>, ImmutableList<PedPerson>) - Constructor for class de.charite.compbio.jannovar.pedigree.PedFileContents

PedFileReader - Class in de.charite.compbio.jannovar.pedigree

Allows reading of PedFileContents from a InputStream or File.

PedFileReader(File) - Constructor for class de.charite.compbio.jannovar.pedigree.PedFileReader

Initialize object with the given file.

PedFileWriter - Class in de.charite.compbio.jannovar.pedigree

Allows writing of PedFileContents to a OutputStream or File.

PedFileWriter(File) - Constructor for class de.charite.compbio.jannovar.pedigree.PedFileWriter

Pedigree - Class in de.charite.compbio.jannovar.pedigree

Represent one pedigree from a PED file.

Pedigree(String, Collection<Person>) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree

Initialize the object with the given values

Pedigree(PedFileContents, String) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree

Initialize the object with the members of contents that have the pedigree name equal to pedigreeName.

Pedigree.IndexedPerson - Class in de.charite.compbio.jannovar.pedigree

Helper class, used in the name to member map.

PedigreeExtractor - Class in de.charite.compbio.jannovar.pedigree

Helper class for extracting one family from a PedFileContents object.

PedigreeExtractor(String, PedFileContents) - Constructor for class de.charite.compbio.jannovar.pedigree.PedigreeExtractor

PedigreeQueryDecorator - Class in de.charite.compbio.jannovar.pedigree

Decorator of Pedigree that allows for the easy querying.

PedigreeQueryDecorator(Pedigree) - Constructor for class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

Initialize decorator.

PedParseException - Exception in de.charite.compbio.jannovar.pedigree

Exception that occurs during parsing of PEDfiles.

PedParseException() - Constructor for exception de.charite.compbio.jannovar.pedigree.PedParseException

PedParseException(String) - Constructor for exception de.charite.compbio.jannovar.pedigree.PedParseException

PedParseException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.pedigree.PedParseException

PedPerson - Class in de.charite.compbio.jannovar.pedigree

Representation of a line from a pedigree (.ped) file.

PedPerson(String, String, String, String, Sex, Disease, Collection<String>) - Constructor for class de.charite.compbio.jannovar.pedigree.PedPerson

Initialize object with the given data.

PedPerson(String, String, String, String, Sex, Disease) - Constructor for class de.charite.compbio.jannovar.pedigree.PedPerson

Initialize object with the given data.

Person - Class in de.charite.compbio.jannovar.pedigree

An individual from a pedigree file, Java programmer friendly version.

Person(String, Person, Person, Sex, Disease, Collection<String>) - Constructor for class de.charite.compbio.jannovar.pedigree.Person

Initialize object with the given values.

Person(String, Person, Person, Sex, Disease) - Constructor for class de.charite.compbio.jannovar.pedigree.Person

Initialize object with the given values and empty extra fields list.

PositionType - Enum in de.charite.compbio.jannovar.reference

Enum for differentiating between one- and zero-based positions.

print(PrintStream) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

Print dictionary to System.err for debugging purposes.

print(long) - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

print progress up to position pos, if ProgressBar.doPrint

priorityLevel() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

The preference level for annotations is exonic (1): FS_DELETION, FS_INSERTION, NON_FS_SUBSTITUTION, FS_SUBSTITUTION, MISSENSE, NON_FS_DELETION, NON_FS_INSERTION, STOPGAIN, STOPLOSS, FS_DUPLICATION, NON_FS_DUPLICATION, START_LOSS, START_GAIN.

ProgressBar - Class in de.charite.compbio.jannovar.impl.util

A simple status bar that only work on terminals where "\r" has an affect.

ProgressBar(long, long) - Constructor for class de.charite.compbio.jannovar.impl.util.ProgressBar

Initialize progress bar with the given settings

ProgressBar(long, long, boolean) - Constructor for class de.charite.compbio.jannovar.impl.util.ProgressBar

Initialize progress bar with the given settings

projectGenomeToCDSInterval(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomeInterval to CDSInterval for TranscriptProjectionDecorator.transcript.

projectGenomeToCDSPosition(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomePosition to CDSPosition for TranscriptProjectionDecorator.transcript.

projectGenomeToTXInterval(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomeInterval to TranscriptInterval for TranscriptProjectionDecorator.transcript.

projectGenomeToTXPosition(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomePosition to TranscriptPosition for TranscriptProjectionDecorator.transcript.

ProjectionException - Exception in de.charite.compbio.jannovar.reference

Thrown when a coordinate conversion failed.

ProjectionException(String) - Constructor for exception de.charite.compbio.jannovar.reference.ProjectionException

PutativeImpact - Enum in de.charite.compbio.jannovar.annotation

Putative impact of an annotation.

putContigID(String, int) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Add a contig name to numeric ID mapping to builder.

putContigLength(int, int) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Add a contig id to length mapping.

putContigName(int, String) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Set primary contig ID to name mapping.

R

rank - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.rank of next build AnnotationLocation.

rankType - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.rankType of next build AnnotationLocation.

read() - Method in class de.charite.compbio.jannovar.pedigree.PedFileReader

Read in the pedigree file in PedFileReader.file.

read(InputStream) - Static method in class de.charite.compbio.jannovar.pedigree.PedFileReader

Static method for parsing a PED file into a PedFileContents object.

REF_CALL - Static variable in class de.charite.compbio.jannovar.mendel.Genotype

ReferenceDictionary - Class in de.charite.compbio.jannovar.data

Stores lengths of contigs/chromosomes and a mapping from string to numeric IDs.

ReferenceDictionaryBuilder - Class in de.charite.compbio.jannovar.data

Builder class for incremental building of immutable ReferenceDictionary objects.

ReferenceDictionaryBuilder() - Constructor for class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

ReferenceDictParser - Class in de.charite.compbio.jannovar.impl.parse

Allows loading of ReferenceDictParser from UCSC and RefSeq data.

ReferenceDictParser(String, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ReferenceDictParser

Initialize the parser with the paths to the file to parse.

RefSeqParser - Class in de.charite.compbio.jannovar.impl.parse.refseq

Parsing of RefSeq GFF3 files

RefSeqParser(ReferenceDictionary, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.refseq.RefSeqParser

reset() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

Reset the builder into the state after initialization.

reverseComplement(String) - Static method in class de.charite.compbio.jannovar.impl.util.DNAUtils

Return the reverse complement version of a DNA string in upper case.

run(Map<String, TranscriptModelBuilder>) - Method in class de.charite.compbio.jannovar.datasource.TranscriptModelBuilderHGNCExtender

Augment the TranscriptModelBuilders with HGNC information

run() - Method in class de.charite.compbio.jannovar.hgnc.HGNCParser

run() - Method in class de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser

run() - Method in class de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDParser

run() - Method in class de.charite.compbio.jannovar.impl.parse.refseq.RefSeqParser

run() - Method in interface de.charite.compbio.jannovar.impl.parse.TranscriptParser

run(Collection<TranscriptModelBuilder>) - Static method in class de.charite.compbio.jannovar.impl.parse.TranscriptSupportLevelsSetterFromLengths

run() - Method in class de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser

run() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeExtractor

Invoke extraction of the given pedigree from contents used in construction.

S

save(JannovarData) - Method in class de.charite.compbio.jannovar.data.JannovarDataSerializer

Serialize a JannovarData object to a file.

SerializationException - Exception in de.charite.compbio.jannovar.data

Exception thrown on problems with serialization or deserialization.

SerializationException(String) - Constructor for exception de.charite.compbio.jannovar.data.SerializationException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.annotation.AnnotationException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.JannovarException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.pedigree.PedParseException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.reference.ProjectionException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.UncheckedJannovarException

setAccession(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setAttributes(ImmutableMap<String, String>) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

setBegin(int) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

setCDSRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setChromType(ChromosomeType) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

setEnd(int) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

setFTPProxy(URL) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set FTP proxy URL

setGeneID(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setGeneSymbol(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setHTTPProxy(URL) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set HTTP proxy URL

setHTTPSProxy(URL) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set HTTPS proxy URL

setIsXChromosomal(boolean) - Method in class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

Set "is X chromosomal" flag of next build GenotypeCalls.

setMaxEnd(int) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

setPayload(Object) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

setPrintProgressBars(boolean) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set whether to print progress bars or not

setRank(int) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setRankType(AnnotationLocation.RankType) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setSampleToGenotype(TreeMap<String, Genotype>) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

setSequence(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setTranscript(TranscriptModel) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setTranscriptSupportLevel(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setTXLocation(TranscriptInterval) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setTXRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setValue(T) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

Sex - Enum in de.charite.compbio.jannovar.pedigree

Representation of an individual's sex.

shifted(int) - Method in class de.charite.compbio.jannovar.reference.CDSPosition

Return shifted CDSPosition.

shifted(int) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

Return shifted GenomePosition.

shifted(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

Return shifted TranscriptPosition.

shiftInsertion(AminoAcidChange, String) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Shift insertion AminoAcidChange to the right in WT AA sequence.

shiftLeft() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

shiftRight() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

size() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

SNVAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the SNV GenomeVariants in the given TranscriptModel

Strand - Enum in de.charite.compbio.jannovar.reference

Representation for forward/backward strand.

StringUtil - Class in de.charite.compbio.jannovar.impl.util

StringUtil() - Constructor for class de.charite.compbio.jannovar.impl.util.StringUtil

StructuralVariantAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Class providing static functions for creating Annotation objects for SVs.

StructuralVariantAnnotationBuilder(TranscriptModel, GenomeVariant) - Constructor for class de.charite.compbio.jannovar.annotation.builders.StructuralVariantAnnotationBuilder

Initialize the builder for the structural variant GenomeVariant in the given TranscriptModel.

subsetOfMembers(Collection<String>) - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

Obtain subset of members in a pedigree or change order.

T

TO_LEGACY_NAME - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Function for converting from VariantEffect to legacy term.

TO_SO_TERM - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Function for converting from VariantEffect to SO term String.

toDisease(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Disease

Parse String into a Disease value.

toDisplayString() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

A string representing the variant type (e.g., missense_variant, stop_gained,...)

toHGVSChunk() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

toInt() - Method in enum de.charite.compbio.jannovar.pedigree.Disease

toInt() - Method in enum de.charite.compbio.jannovar.pedigree.Sex

toLong(String) - Method in class de.charite.compbio.jannovar.impl.util.Translator

toLong(char) - Method in class de.charite.compbio.jannovar.impl.util.Translator

toSequenceOntologyID() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

Return the sequence ontology accession number for the variant class if available, otherwise return the name.

toSequenceOntologyTerm() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

A Sequence Ontology (SO) term string representing the variant type (e.g., missense_variant, stop_gained,...)

toSex(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Sex

Parse String into a Sex value.

toString() - Method in class de.charite.compbio.jannovar.annotation.Annotation

toString() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

toString() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord

toString() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

toString() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

toString() - Method in class de.charite.compbio.jannovar.mendel.Genotype

toString() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

toString() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

toString() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

toString() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

toString() - Method in class de.charite.compbio.jannovar.pedigree.Person

toString() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

toString() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

toString() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

toString() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

toString() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

toString() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

toString() - Method in enum de.charite.compbio.jannovar.reference.Strand

toString() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

toString() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

toString() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

toVCFAnnoString(String, boolean) - Method in class de.charite.compbio.jannovar.annotation.Annotation

Return the standardized VCF variant string for the given ALT allele.

toVCFAnnoString(String) - Method in class de.charite.compbio.jannovar.annotation.Annotation

Forward to toVCFAnnoString(alt, true).

transcript - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.transcript of next build AnnotationLocation.

TranscriptInterval - Class in de.charite.compbio.jannovar.reference

Interval on a transcript.

TranscriptInterval(TranscriptModel, int, int) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptInterval

construct transcript interval with one-based coordinate system

TranscriptInterval(TranscriptModel, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptInterval

construct transcript interval with selected coordinate system

TranscriptIntervalEndExtractor - Class in de.charite.compbio.jannovar.reference

Extraction of interval end points for TranscriptModel.

TranscriptIntervalEndExtractor() - Constructor for class de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor

transcriptLength() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

TranscriptModel - Class in de.charite.compbio.jannovar.reference

The information representing a transcript model.

TranscriptModel(String, String, GenomeInterval, GenomeInterval, ImmutableList<GenomeInterval>, String, String, int) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModel

Initialize the TranscriptInfo object from the given parameters.

TranscriptModel(String, String, GenomeInterval, GenomeInterval, ImmutableList<GenomeInterval>, String, String, int, Map<String, String>) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModel

Initialize the TranscriptInfo object from the given parameters.

TranscriptModelBuilder - Class in de.charite.compbio.jannovar.reference

Class for building immutable TranscriptModel objects field-by-field.

TranscriptModelBuilder() - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

TranscriptModelBuilderHGNCExtender - Class in de.charite.compbio.jannovar.datasource

Helper class for extending TranscriptModelBuilder objects with HGNC information

TranscriptModelBuilderHGNCExtender(String, Function<HGNCRecord, String>) - Constructor for class de.charite.compbio.jannovar.datasource.TranscriptModelBuilderHGNCExtender

TranscriptParseException - Exception in de.charite.compbio.jannovar.impl.parse

Exception that occurs during parsing of transcript database files.

TranscriptParseException() - Constructor for exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

TranscriptParseException(String) - Constructor for exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

TranscriptParseException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

TranscriptParser - Interface in de.charite.compbio.jannovar.impl.parse

General interface for transcript parsers.

TranscriptPosition - Class in de.charite.compbio.jannovar.reference

Position on a transcript.

TranscriptPosition(TranscriptModel, int) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptPosition

construct transcript position with one-based coordinate system

TranscriptPosition(TranscriptModel, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptPosition

construct transcript position with selected coordinate system

TranscriptProjectionDecorator - Class in de.charite.compbio.jannovar.reference

Wraps a TranscriptModel object and allow the coordinate conversion.

TranscriptProjectionDecorator(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Initialize the object with the given TranscriptModel

TranscriptSequenceChangeHelper - Class in de.charite.compbio.jannovar.reference

Helper class for getting updated transcript sequence for deletions and block substitutions.

TranscriptSequenceChangeHelper(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper

Construct helper with the given TranscriptModel

TranscriptSequenceDecorator - Class in de.charite.compbio.jannovar.reference

Decorator for TranscriptModel that helps with operations on its sequence

TranscriptSequenceDecorator(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

TranscriptSequenceOntologyDecorator - Class in de.charite.compbio.jannovar.reference

Functionality for finding out about certain points/regions of TranscriptModel using genomic positions.

TranscriptSequenceOntologyDecorator(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Initialize the object with the given TranscriptModel.

TranscriptSupportLevels - Interface in de.charite.compbio.jannovar.reference

Container for constants of transcript support levels.

TranscriptSupportLevelsSetterFromLengths - Class in de.charite.compbio.jannovar.impl.parse

Set the transcript support level from transcript lengths.

TranscriptSupportLevelsSetterFromLengths() - Constructor for class de.charite.compbio.jannovar.impl.parse.TranscriptSupportLevelsSetterFromLengths

transcriptToGenomePos(TranscriptPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from transcript to genome position.

translateDNA(String) - Method in class de.charite.compbio.jannovar.impl.util.Translator

Translates a DNA sequence.

translateDNA3(String) - Method in class de.charite.compbio.jannovar.impl.util.Translator

Translator - Class in de.charite.compbio.jannovar.impl.util

This singleton class helps to translate DNA sequences.

truncateAltAfterStopCodon(AminoAcidChange) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Search for stop codon in change.alt and truncate afterwards.

truncateBothSides(AminoAcidChange) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Truncate AminoAcidChange from both sides for matching ref/alt prefixes/suffixes.

TSL1 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

All splice junctions of the transcript are supported by at least one non-suspect mRNA.

TSL2 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

The best supporting mRNA is flagged as suspect or the support is from multiple ESTs.

TSL3 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

The only support is from a single EST.

TSL4 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

The best supporting EST is flagged as suspect.

TSL5 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

No single transcript supports the model structure.

txLocation - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.txLocation of next build AnnotationLocation.

U

UCSC_CANONICAL - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

Annotated as canonical transcript by UCSC (used in absence of TSL).

UCSCParser - Class in de.charite.compbio.jannovar.impl.parse.ucsc

Parser for the UCCSC knownGene and related files.

UCSCParser(ReferenceDictionary, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser

UncheckedJannovarException - Exception in de.charite.compbio.jannovar

Base class for unchecked exceptions in Jannovar

UncheckedJannovarException() - Constructor for exception de.charite.compbio.jannovar.UncheckedJannovarException

UncheckedJannovarException(String) - Constructor for exception de.charite.compbio.jannovar.UncheckedJannovarException

UncheckedJannovarException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.UncheckedJannovarException

union(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

V

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationMessage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.OldVariantType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.PutativeImpact

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.VariantEffect

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.hgnc.AltGeneIDType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.mendel.ChromosomeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Disease

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Genotype

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Sex

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.reference.GenomeVariantType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.reference.PositionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.reference.Strand

Returns the enum constant of this type with the specified name.

valueOf(char) - Method in enum de.charite.compbio.jannovar.reference.Strand

values() - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationMessage

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.OldVariantType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.PutativeImpact

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.VariantEffect

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.hgnc.AltGeneIDType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.mendel.ChromosomeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.pedigree.Disease

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.pedigree.Genotype

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.pedigree.Sex

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.reference.GenomeVariantType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.reference.PositionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.reference.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

VariantAnnotations - Class in de.charite.compbio.jannovar.annotation

A list of priority-sorted Annotation objects.

VariantAnnotations(GenomeVariant, Collection<Annotation>) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotations

Construct ImmutableAnnotationList from a Collection of Annotation objects.

VariantAnnotationsContentDecorator - Class in de.charite.compbio.jannovar.annotation

Decorator for VariantAnnotations that allows queries on the content.

VariantAnnotationsContentDecorator(VariantAnnotations) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

Initialize the decorator.

VariantAnnotationsTextGenerator - Class in de.charite.compbio.jannovar.annotation

Generate annotation text (effect and HGVS description) from VariantAnnotations object.

VariantAnnotationsTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

Initialize the decorator.

VariantAnnotator - Class in de.charite.compbio.jannovar.annotation

Main driver class for annotating variants.

VariantAnnotator(ReferenceDictionary, ImmutableMap<Integer, Chromosome>, AnnotationBuilderOptions) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotator

Construct new VariantAnnotator, given a chromosome map.

VariantDescription - Interface in de.charite.compbio.jannovar.reference

Minimal description of a variant as triple (position, ref, alt).

VariantEffect - Enum in de.charite.compbio.jannovar.annotation

These codes reflect the possible types of variants that we call for an exome.

VCF_ANN_DESCRIPTION_STRING - Static variable in class de.charite.compbio.jannovar.annotation.Annotation

The DESCRIPTION string to use in the VCF header for VCFVariantAnnotation objects

W

withMorePadding(int) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

withMorePadding(int, int) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

convert into GenomeInterval of the given strand

withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

convert into GenomePosition of the given strand

withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

write(PedFileContents) - Method in class de.charite.compbio.jannovar.pedigree.PedFileWriter

Write out the PedFileContents object to the output.

write(PedFileContents, OutputStream) - Static method in class de.charite.compbio.jannovar.pedigree.PedFileWriter

Static method for writing a PedFileContents file to a OutputStream.

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