A B C D E F G H I J L M N O P Q R S T U V W X Y Z _
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All Classes All Packages
All Classes All Packages
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
- ACCESSION_FORMAT - de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- 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.
- AFFECTED - de.charite.compbio.jannovar.pedigree.Disease
-
corresponds to 2 = affected in the PED file.
- Alignment - Class in de.charite.compbio.jannovar.reference
-
An anchor-based alignment, optimized for small-ish alignments where linear search in the gap anchor is fast or even faster than binary search.
- Alignment(List<Anchor>, List<Anchor>) - Constructor for class de.charite.compbio.jannovar.reference.Alignment
-
Construct new
Alignment
. - AlignmentPart(int, int, int, int, String) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModelBuilder.AlignmentPart
-
Construct new alignment part.
- AllAnnotationListTextGenerator - Class in de.charite.compbio.jannovar.annotation
-
Decorator for
VariantAnnotations
for generating variant annotation strings for all variants - AllAnnotationListTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.AllAnnotationListTextGenerator
- 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.
- Anchor - Class in de.charite.compbio.jannovar.reference
-
An anchor in an
Alignment
. - Anchor(int, int) - Constructor for class de.charite.compbio.jannovar.reference.Anchor
-
Construct new anchor.
- Anchors - Class in de.charite.compbio.jannovar.reference
-
Helper class for working with
Anchor
-based alignments. - Anchors() - Constructor for class de.charite.compbio.jannovar.reference.Anchors
- Annotation - Class in de.charite.compbio.jannovar.annotation
-
Collect the information for one variant's annotation.
- 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. - Annotation(Collection<AnnotationMessage>) - Constructor for class de.charite.compbio.jannovar.annotation.Annotation
-
Initialize object with messages only.
- 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, 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.
- ANY - de.charite.compbio.jannovar.mendel.ModeOfInheritance
-
value for encoding uninitialized values
- ANY - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
value for encoding uninitialized values
- AUTOSOMAL - de.charite.compbio.jannovar.mendel.ChromosomeType
-
Autosomal chromosomes
- AUTOSOMAL_DOMINANT - de.charite.compbio.jannovar.mendel.ModeOfInheritance
-
autosomal dominant inheritance
- AUTOSOMAL_DOMINANT - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
autosomal dominant inheritance
- AUTOSOMAL_RECESSIVE - de.charite.compbio.jannovar.mendel.ModeOfInheritance
-
autosomal recessive inheritance
- AUTOSOMAL_RECESSIVE_COMP_HET - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
autosomal recessive inheritance, compound het
- AUTOSOMAL_RECESSIVE_HOM_ALT - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
autosomal recessive inheritance, hom alt
B
- BestAnnotationListTextGenerator - Class in de.charite.compbio.jannovar.annotation
-
Decorator for
VariantAnnotations
for generating variant annotation strings for the best variant - BestAnnotationListTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.BestAnnotationListTextGenerator
- BLOCK_SUBSTITUTION - de.charite.compbio.jannovar.reference.GenomeVariantType
-
block substitution
- BlockSubstitutionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
- BlockSubstitutionAnnotationBuilder(TranscriptModel, GenomeVariant, AnnotationBuilderOptions) - Constructor for class de.charite.compbio.jannovar.annotation.builders.BlockSubstitutionAnnotationBuilder
- BND - de.charite.compbio.jannovar.reference.SVDescription.Type
-
breakend
- 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
andStructuralVariantAnnotationBuilder.change
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVAnnotationBuilderDispatcher
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVBreakendAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVCopyNumberVariantAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVDeletionAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVDuplicationAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVInsertionAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVInversionAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVMobileElementDeletionAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVMobileElementInsertionAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.annotation.builders.SVTandemDuplicationAnnotationBuilder
- build() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder
- 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
- build(String, boolean, List<String>) - Method in class de.charite.compbio.jannovar.datasource.JannovarDataFactory
- 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.
- buildAnnotations(SVGenomeVariant) - Method in class de.charite.compbio.jannovar.annotation.SVAnnotator
-
Main entry point to getting Annovar-type annotations for a
SVGenomeVariant
. - buildEffectText() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator
- buildEmptyList(GenomeVariant) - Static method in class de.charite.compbio.jannovar.annotation.VariantAnnotations
- buildEmptyList(SVGenomeVariant) - Static method in class de.charite.compbio.jannovar.annotation.SVAnnotations
- buildHGVSText(AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator
- buildMessages() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator
- buildSiblings() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator
C
- CCDS_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
CCDS ids
- 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
- checkMendelianInheritance(Collection<GenotypeCalls>, Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker
-
Perform checking for compatible mode of inheritance
- checkMendelianInheritanceSub(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker
- checkMendelianInheritanceSub(Collection<GenotypeCalls>, Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker
-
Perform checking for compatible sub 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.
- CHROMOSOME - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0000340 Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (is a: replicon).
- CHROMOSOME_NUMBER_VARIATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:1000182 A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number (is a chromosome_variation).
- 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
- CNV - de.charite.compbio.jannovar.reference.SVDescription.Type
-
copy number variant
- CODING_SEQUENCE_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001580 A sequence variant that changes the coding sequence (is a:
VariantEffect.CODING_TRANSCRIPT_VARIANT
,VariantEffect.EXON_VARIANT
). - CODING_TRANSCRIPT_INTRON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001969 A sequence variant that changes non-coding intro sequence in a non-coding transcript (is a:
VariantEffect.CODING_TRANSCRIPT_VARIANT
,VariantEffect.INTRON_VARIANT
). - CODING_TRANSCRIPT_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001968 A transcript variant of a protein coding transcript (is a:
VariantEffect.TRANSCRIPT_VARIANT
). - codonWithUpdatedBase(String, int, char) - Static method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator
-
Update the base given by
frameShift
in the given codon stringtranscriptCodon
totargetNC
and return updated codon. - compare(String, String) - Method in class de.charite.compbio.jannovar.data.impl.VersionComparator
- compareTo(Annotation) - Method in class de.charite.compbio.jannovar.annotation.Annotation
- compareTo(Annotation) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations
- compareTo(Annotation) - Method in class de.charite.compbio.jannovar.reference.GenomeVariant
- compareTo(Annotation) - Method in interface de.charite.compbio.jannovar.reference.VariantDescription
- compareTo(SVAnnotation) - Method in class de.charite.compbio.jannovar.annotation.SVAnnotation
- 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(TranscriptModel) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- COMPLEX_SUBSTITUTION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:1000005 When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used.
- concatenate(Object...) - Static method in class de.charite.compbio.jannovar.impl.util.StringUtil
-
Concatenate values.toString() using a StringBuilder.
- CONSERVED_INTERGENIC_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002017 A sequence variant located in a conserved intergenic region, between genes (is a:
VariantEffect.INTERGENIC_VARIANT
). - CONSERVED_INTRON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002018 A transcript variant occurring within a conserved region of an intron (is a:
VariantEffect.INTRON_VARIANT
). - 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(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval
- contains(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval
- containsExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
- COPY_NUMBER_CHANGE - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001563 A sequence variant where copies of a feature (CNV) are either increased or decreased.
- COSMIC_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
COSMIC id
- countLeadingGaps(List<Anchor>) - Static method in class de.charite.compbio.jannovar.reference.Anchors
-
Compute number of leading gaps in anchors.
- countTrailingGaps(List<Anchor>) - Static method in class de.charite.compbio.jannovar.reference.Anchors
-
Compute number of leading gaps in anchors.
- createUngappedAlignment(int) - Static method in class de.charite.compbio.jannovar.reference.Alignment
-
Create ungapped alignment for the given sequence.
- CUSTOM - de.charite.compbio.jannovar.annotation.VariantEffect
-
Variant in a user-specified custom region.
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.data.impl - package de.charite.compbio.jannovar.data.impl
- 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
- DEL - de.charite.compbio.jannovar.reference.SVDescription.Type
-
generic deletion
- DEL_ME - de.charite.compbio.jannovar.reference.SVDescription.Type
-
mobile element deletion
- DELETION - de.charite.compbio.jannovar.reference.GenomeVariantType
-
deletion
- DeletionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
- detect(String) - Static method in enum de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- differenceTo(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomePosition
- differenceTo(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition
- DIRECT_TANDEM_DUPLICATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:1000039 A tandem duplication where the individual regions are in the same orientation (is a: tandem_duplication).
- Disease - Enum in de.charite.compbio.jannovar.pedigree
-
Codes used to denote affection status of a person in a pedigree.
- DISRUPTIVE_INFRAME_DELETION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001826 An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon (is a:
VariantEffect.INFRAME_DELETION
). - DISRUPTIVE_INFRAME_INSERTION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001824 An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon (is a:
VariantEffect.INFRAME_INSERTION
). - 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
- DOWNSTREAM - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is downstream of a gene
- DOWNSTREAM_GENE_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001632 A sequence variant located 3' of a gene (is a:
VariantEffect.INTERGENIC_VARIANT
). - DOWNSTREAM_LENGTH - Static variable in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
-
Length of downstream interval around a transcript.
- DUP - de.charite.compbio.jannovar.reference.SVDescription.Type
-
generic duplication
- DUP_TANDEM - de.charite.compbio.jannovar.reference.SVDescription.Type
-
tandem duplication
- 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
- ENA_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
ENA id
- ENSEMBL_GENE_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
ENSEMBL gene id
- EnsemblParser - Class in de.charite.compbio.jannovar.impl.parse.ensembl
-
Parsing of ENSEMBL GTF files
- EnsemblParser(ReferenceDictionary, String, List<String>, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser
- ENTREZ_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
Entrez ID
- 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.SVAnnotations
- 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.Alignment
- equals(Object) - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange
- equals(Object) - Method in class de.charite.compbio.jannovar.reference.Anchor
- 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
- ERROR - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant assessed as probably erroneous (may indicate an error in the VCF file)
- ERROR_CHROMOSOME_NOT_FOUND - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(E1) Chromosome does not exists in reference genome database.
- ERROR_OUT_OF_CHROMOSOME_RANGE - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(E2) The variant's genomic coordinate is greater than chromosome's length.
- ERROR_PROBLEM_DURING_ANNOTATION - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(non-standard) There was a problem with the annotation problem, if you see this in the output of the program then this indicates a bug.
- EXON - de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType
- EXON_LOSS_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001572 A sequence variant whereby an exon is lost from the transcript (is a (is a:
VariantEffect.SPLICING_VARIANT
),VariantEffect.TRANSCRIPT_VARIANT
). - EXON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001791 A sequence variant that changes exon sequence (is a:
VariantEffect.TRANSCRIPT_VARIANT
). - exonIDInReferenceOrder(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator
-
Returns the index of the (0-based) exon in the reference (forward) order.
- extractAccession(String) - Static method in enum de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
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
- FEATURE_TRUNCATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001906 A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence (is a: feature_variant).
- 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
- FEMALE - de.charite.compbio.jannovar.pedigree.Sex
-
individual is female
- 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.InheritanceCheckerMT
- 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
- filterCompatibleRecords(Collection<GenotypeCalls>, ModeOfInheritance) - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker
-
Filters records in
calls
for compatibility withmode
- filterCompatibleRecordsSub(Collection<GenotypeCalls>, SubModeOfInheritance) - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker
-
Filters records in
calls
for compatibility withsubMode
- 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
. - FIVE_PRIME_UTR_EXON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002092 A UTR variant of the 5' UTR (is a: 5_prime_UTR_variant; is a: UTR_variant).
- FIVE_PRIME_UTR_INTRON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002091 A UTR variant between 5' UTRs (is a: 5_prime_UTR_variant; is a: UTR_variant).
- FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001983 A 5' UTR variant where a premature start codon is introduced, moved or lost (is a:
VariantEffect.FIVE_PRIME_UTR_EXON_VARIANT
orVariantEffect.FIVE_PRIME_UTR_INTRON_VARIANT
). - FIVE_PRIME_UTR_TRUNCATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002013 A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence (is a:
VariantEffect.FIVE_PRIME_UTR_EXON_VARIANT
orVariantEffect.FIVE_PRIME_UTR_INTRON_VARIANT
) - 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
- FORWARD - de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand
-
Record is on forward strand
- FRAMESHIFT_ELONGATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001909 A frameshift variant that causes the translational reading frame to be extended relative to the reference feature (is a
VariantEffect.FRAMESHIFT_VARIANT
, internal_feature_elongation). - FRAMESHIFT_TRUNCATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001910 A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature (is a
VariantEffect.FRAMESHIFT_VARIANT
, internal_feature_truncation). - FRAMESHIFT_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001589A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of threee (is a: protein_altering_variant).
- FS_DELETION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Deletion resulting in a frameshift.
- FS_DUPLICATION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Nucleotide duplication that results in a frameshift.
- FS_INSERTION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Insertion resulting in a frameshift.
- FS_SUBSTITUTION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Nucleotide substitution that results in a frameshift.
- FWD - de.charite.compbio.jannovar.reference.Strand
-
forward strand
G
- gap - Variable in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder.AlignmentPart
-
Description from gaps, as in RefSeq "Gap" tag.
- gapLength(List<Anchor>) - Static method in class de.charite.compbio.jannovar.reference.Anchors
-
Return length of gaps.
- GENE_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001564 A sequence variant where the structure of the gene is changed (is a: feature_variant).
- 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(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.
- GenomeVariantNormalizer - Class in de.charite.compbio.jannovar.reference
-
Helper code for the normalization of
GenomeVariant
s. - 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 aGenomeVariant
. - 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
- Genotype - Enum in de.charite.compbio.jannovar.pedigree
-
Enumeration of genotype kinds.
- Genotype(Collection<Integer>) - Constructor for class de.charite.compbio.jannovar.mendel.Genotype
-
Construct
Genotype
with list of allele numbers - 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
- 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
- getAbbreviation() - Method in enum de.charite.compbio.jannovar.mendel.SubModeOfInheritance
- getAccession() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- getAccession() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- getAcdcessionIndex() - Method in enum de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- 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
- getAlignmentParts() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- 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
- 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.SVAnnotations
- 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() - 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
- getBegin(T) - Method in interface de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor
- 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.SVAnnotations
- 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 interface de.charite.compbio.jannovar.reference.SVDescription
- getChr() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
- getChr() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- getChr() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription
- getChr2() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotations
- getChr2() - Method in interface de.charite.compbio.jannovar.reference.SVDescription
- getChr2() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
- getChr2Name() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotations
- getChr2Name() - Method in interface de.charite.compbio.jannovar.reference.SVDescription
- getChr2Name() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
- 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.SVAnnotations
- 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.SVDescription
- getChrName() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
- 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) - 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 attxPos
/cdsPos
. - 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 attxPos
/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
- getEffects() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotation
-
Return the effects the variant is annotated with for the transcript.
- getEnaID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord
- getEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval
- 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
- getEnd(T) - Method in interface de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor
- 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
- getFivePrimeUTRExonIntervals() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
-
Returns the genomic intervals of the exonic 5' UTR regions.
- 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
- getGapPos() - Method in class de.charite.compbio.jannovar.reference.Anchor
- 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
- getGeneVersion() - 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
- getGenomeInterval() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return genome interval (from mid points, ignoring confidence interval).
- getGenomePos() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant
- getGenomePos() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return genomic start/first position.
- getGenomePos2() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return genomic end/second position.
- getGenomeVariant() - Method in class de.charite.compbio.jannovar.annotation.Annotation
- getGenomeVariant() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotations
-
Return the
SVGenomeVariant
that this AnnotationList is annotated with. - 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.SVAnnotations
-
Return the highest impact annotation for each gene.
- getHighestImpactAnnotation() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations
- getHighestImpactEffect() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotations
-
Convenience method.
- 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
- getIDElementCount() - Method in enum de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- 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
- getMostPathogenicVariantEffect() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotation
- 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. - getNumber() - Method in class de.charite.compbio.jannovar.data.impl.VersionTokenizer
- 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.SVAnnotations
- 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 interface de.charite.compbio.jannovar.reference.SVDescription
- getPos() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
- getPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition
- getPos() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription
- getPos2() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotations
- getPos2() - Method in interface de.charite.compbio.jannovar.reference.SVDescription
- getPos2() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
- getPos2CILowerBound() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return lower bound of confidence interval around
SVGenomeVariant.genomePos2
. - getPos2CIUpperBound() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return upper bound of confidence interval around
SVGenomeVariant.genomePos2
. - getPosCILowerBound() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return lower bound of confidence interval around
SVGenomeVariant.genomePos
. - getPosCIUpperBound() - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return upper bound of confidence interval around
SVGenomeVariant.genomePos
. - getPrefix() - Method in enum de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- 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() - Method in class de.charite.compbio.jannovar.annotation.Annotation
- getProteinChangeStr(AminoAcidCode) - 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
- getPutativeImpact() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotation
- getQryAnchors() - Method in class de.charite.compbio.jannovar.reference.Alignment
- 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
- getRefAnchors() - Method in class de.charite.compbio.jannovar.reference.Alignment
- 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
- getSeqAlignment() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- getSeqAlignment() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- getSeqID() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord
- getSeqPos() - Method in class de.charite.compbio.jannovar.reference.Anchor
- 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
- getSuffix() - Method in class de.charite.compbio.jannovar.data.impl.VersionTokenizer
- 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.
- getThreePrimeUTRExonIntervals() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
-
Returns the genomic intervals of the exonic 3' UTR regions
- 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.annotation.SVAnnotation
-
Return the annotated transcript model.
- 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.
- getTrimmedSequence() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- 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
- getTxVersion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- getType() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotations
- getType() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord
- getType() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant
- getType() - Method in class de.charite.compbio.jannovar.reference.SVBreakend
- getType() - Method in class de.charite.compbio.jannovar.reference.SVCopyNumberVariant
- getType() - Method in class de.charite.compbio.jannovar.reference.SVDeletion
- getType() - Method in interface de.charite.compbio.jannovar.reference.SVDescription
- getType() - Method in class de.charite.compbio.jannovar.reference.SVDuplication
- getType() - Method in class de.charite.compbio.jannovar.reference.SVInsertion
- getType() - Method in class de.charite.compbio.jannovar.reference.SVInversion
- getType() - Method in class de.charite.compbio.jannovar.reference.SVMobileElementDeletion
- getType() - Method in class de.charite.compbio.jannovar.reference.SVMobileElementInsertion
- getType() - Method in class de.charite.compbio.jannovar.reference.SVTandemDuplication
- getType() - Method in class de.charite.compbio.jannovar.reference.SVUnknown
- 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
- getVariant() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotation
-
Return the annotated variant.
- getVariantType() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator
- getVegaID() - Method in class de.charite.compbio.jannovar.hgnc.HGNCRecord
- getVersion() - Static method in class de.charite.compbio.jannovar.data.JannovarDataSerializer
- GFF3 - de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion
-
Value for GFF3
- 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
- GI_REF_FORMAT - de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- GTF - de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion
-
Value for GTF ("GFF2")
- 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.SVAnnotations
- 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.SVAnnotations
- 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.Alignment
- hashCode() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange
- hashCode() - Method in class de.charite.compbio.jannovar.reference.Anchor
- 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
- hasValue() - Method in class de.charite.compbio.jannovar.data.impl.VersionTokenizer
- HETEROZYGOUS - de.charite.compbio.jannovar.pedigree.Genotype
-
0/1 in the VCF genotype field, heterozygous sequence.
- 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
- HGNC_ALIAS - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
HGNC aliases
- HGNC_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
Official HGNC identifier
- HGNC_PREVIOUS - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
Previously used HGNC ids
- HGNC_SYMBOL - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
Official HGNC symbol
- 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
- HIGH - de.charite.compbio.jannovar.annotation.PutativeImpact
-
high impact
- HOMOZYGOUS_ALT - de.charite.compbio.jannovar.pedigree.Genotype
-
1/1 in the VCF genotype field, homozygous alternate sequence
- HOMOZYGOUS_REF - de.charite.compbio.jannovar.pedigree.Genotype
-
0/0 in the VCF genotype field, homozygous reference sequence.
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) - Constructor for exception de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException
- IncompatiblePedigreeException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException
- IndexedFASTAReader - Class in de.charite.compbio.jannovar.impl.util
-
Helper class for reading FAI-indexed FASTA files.
- IndexedFASTAReader(ReferenceDictionary, String) - Constructor for class de.charite.compbio.jannovar.impl.util.IndexedFASTAReader
-
Construct with default FAI path (
fastaPath + ".fai"
. - IndexedFASTAReader(ReferenceDictionary, String, String) - Constructor for class de.charite.compbio.jannovar.impl.util.IndexedFASTAReader
-
Construct with explicit FAI path.
- IndexedPerson(int, Person) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson
- INFO_COMPOUND_ANNOTATION - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W7) This effect is a result of combining more than one variants (e.g.
- 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.
- INFO_NON_REFERENCE_ANNOTATION - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W8) An alternative reference sequence was used to calculate this annotation (e.g.
- INFO_REALIGN_3_PRIME - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W6) Variant has been realigned to the most 3Āprime position within the transcript.
- INFRAME_DELETION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001822 An inframe non synonymous variant that deletes bases from the coding sequence (is a: inframe_indel, feature_truncation).
- INFRAME_INSERTION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001821 An inframe non synonymous variant that inserts bases into in the coding sequence (is a: inframe_indel, internal_feature_elongation).
- InheritanceCheckerMT - Class in de.charite.compbio.jannovar.mendel.impl
-
Helper class for checking a
GenotypeCalls
for compatibility with a pedigree and mitochondrial inheritance - InheritanceCheckerMT(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.InheritanceCheckerMT
- INITIATOR_CODON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001582 A codon variant that changes at least one base of the first codon of a transcript (is a:
VariantEffect.CODING_SEQUENCE_VARIANT
, children: start_retained_variant, start_lost). - INS - de.charite.compbio.jannovar.reference.SVDescription.Type
-
insertion
- INS_ME - de.charite.compbio.jannovar.reference.SVDescription.Type
-
mobile element insertion
- INSERTION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0000667 The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
- INSERTION - de.charite.compbio.jannovar.reference.GenomeVariantType
-
insertion
- InsertionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
- INTERGENIC - de.charite.compbio.jannovar.annotation.OldVariantType
-
variant located between two genes (far enough away not to qualify as upstream/downstream)
- INTERGENIC_REGION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0000605 A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome (is a: biological_region).
- INTERGENIC_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001628 A sequence variant located in the intergenic region, between genes (is a: feature_variant).
- INTERNAL_FEATURE_ELONGATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001908 A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence.
- 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(int, int, T, int) - Constructor for class de.charite.compbio.jannovar.impl.intervals.Interval
- Interval(MutableInterval<T>) - 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.
- INTRAGENIC_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002011 A variant that occurs within a gene but falls outside of all transcript features.
- INTRON - de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType
- INTRON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001627 A transcript variant occurring within an intron (is a:
VariantEffect.TRANSCRIPT_VARIANT
). - INTRONIC - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant located in an intron.
- intronRegion(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- INV - de.charite.compbio.jannovar.reference.SVDescription.Type
-
inversion
- 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) - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCodonException
- InvalidCodonException(String, Throwable) - 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
- INVERSION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:1000036 A continuous nucleotide sequence is inverted in the same position.
- IS_INTRONIC - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect
-
Predicate
for testing whether aVariantEffect
is intronic. - IS_SPLICING - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect
-
Predicate
for testing whether aVariantEffect
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
- isDominant() - Method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance
- isDominant() - Method in enum de.charite.compbio.jannovar.mendel.SubModeOfInheritance
- 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
- isHasIndels() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- isHasIndels() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- isHasSubstitutions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel
- isHasSubstitutions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- 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
- isOffExome(boolean, boolean) - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect
-
Variant of
isOffExome()
that allows to specify whether UTR and non-consensus intronic splice variants count as off-exome or not. - isOffTranscript() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect
- isOverrideTxSeqWithGenomeVariantRef() - Method in class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions
- isParentOfAffected(Person) - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator
- isRecessive() - Method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance
- isRecessive() - Method in enum de.charite.compbio.jannovar.mendel.SubModeOfInheritance
- 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
- 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 fromDataSource
s. - 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
- LEFT_END - de.charite.compbio.jannovar.reference.SVBreakend.Side
-
Left breakend
- 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(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
- liesInIntron(GenomePosition) - 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 - de.charite.compbio.jannovar.annotation.PutativeImpact
-
low impact
- 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
- MALE - de.charite.compbio.jannovar.pedigree.Sex
-
individual is male
- 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
ofGenotypeCalls
for compatibility with aPedigree
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
ofGenotypeCalls
for compatibility with aPedigree
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 aPedigree
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 aPedigree
and XR 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
- MGD_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
MGD id
- MIRNA - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0000276 Variant affects a miRNA (is a: miRNA_primary_transcript, small_regulatory_ncRNA).
- MISSENSE - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant that leads to the subsitution of one amino acid (note this was earlier "NONYSYNONYMOUS" but the term name was changed to conform with the terminology od Sequence Ontology).
- MISSENSE_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001583 A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.
- MITOCHONDRIAL - de.charite.compbio.jannovar.mendel.ChromosomeType
-
Mitochondrium chromosome
- MITOCHONDRIAL - de.charite.compbio.jannovar.mendel.ModeOfInheritance
-
Mitochondrial inheritance
- MITOCHONDRIAL - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
mitochondrial inheritance
- MNV - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002007 An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence (is a: substitution).
- MOBILE_ELEMENT_DELETION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002066 A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element).
- MOBILE_ELEMENT_INSERTION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001837 A kind of insertion where the inserted sequence is a mobile element.
- ModeOfInheritance - Enum in de.charite.compbio.jannovar.mendel
-
An enumeration of the main Mendelian modes of inheritance for prioritizing exome data
- MODERATE - de.charite.compbio.jannovar.annotation.PutativeImpact
-
moderate impact
- MODIFIER - de.charite.compbio.jannovar.annotation.PutativeImpact
-
modifier of other
PutativeImpact
values - MoveNext() - Method in class de.charite.compbio.jannovar.data.impl.VersionTokenizer
- 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) - 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
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 ofpedigree
. - ncRNA_EXONIC - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant located in an exon of a noncoding RNA gene
- ncRNA_INTRONIC - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant located in an intron of a noncoding RNA gene
- ncRNA_SPLICING - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant located in a splice site of a noncoding RNA gene
- 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
- NON_CODING_TRANSCRIPT_EXON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001792 A sequence variant that changes non-coding exon sequence in a non-coding transcript (is a:
VariantEffect.NON_CODING_TRANSCRIPT_VARIANT
,VariantEffect.EXON_VARIANT
). - NON_CODING_TRANSCRIPT_INTRON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001970 A sequence variant that changes non-coding intro sequence in a non-coding transcript (is a:
VariantEffect.NON_CODING_TRANSCRIPT_VARIANT
,VariantEffect.INTRON_VARIANT
). - NON_CODING_TRANSCRIPT_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
- NON_FS_DELETION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Deletion that does not result in a frameshift.
- NON_FS_DUPLICATION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Nucleotide duplication that does not result in a frameshift.
- NON_FS_INSERTION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Insertion that does not result in a frameshift.
- NON_FS_SUBSTITUTION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Nucleotide substitution that does not result in a frameshift.
- 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)
- NOT_OBSERVED - de.charite.compbio.jannovar.pedigree.Genotype
-
./. in the VCF genotype field (not observed, this is usually encoutered in multisample VCF files).
- NucleotidePointLocationBuilder - Class in de.charite.compbio.jannovar.reference
-
Helper class that allows easy building of
NucleotidePointLocation
s. - 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 byframeShift
in the given codon stringtranscriptCodon
totargetNC
and return the updated nucleic string.
O
- OldVariantType - Enum in de.charite.compbio.jannovar.annotation
-
Enumeration of the old Jannovar variant types (i.e.
- OMIM_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
OMIM id
- ONE_BASED - de.charite.compbio.jannovar.reference.PositionType
-
positions start at zero and intervals are closed [begin, end].
- OTHER - de.charite.compbio.jannovar.reference.GenomeVariantType
-
other, e.g., structural variant from symbolic allele
- OTHER_MESSAGE - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
AnnotationMessage not encoded in enum.
- 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
- overlapsWithFivePrimeUTRExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
-
Query whether interval overlaps with exonic 5' UTR sequence.
- 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
- overlapsWithThreePrimeUTRExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
-
Query whether interval overlaps with exonic 3' UTR sequence.
- 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
- 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
- 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(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 topedigreeName
. - Pedigree(String, Collection<Person>) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree
-
Initialize the object with the given values
- 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) - Constructor for class de.charite.compbio.jannovar.pedigree.PedPerson
-
Initialize object with the given data.
- PedPerson(String, String, String, String, Sex, Disease, Collection<String>) - 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) - Constructor for class de.charite.compbio.jannovar.pedigree.Person
-
Initialize object with the given values and empty extra fields list.
- Person(String, Person, Person, Sex, Disease, Collection<String>) - Constructor for class de.charite.compbio.jannovar.pedigree.Person
-
Initialize object with the given values.
- PositionType - Enum in de.charite.compbio.jannovar.reference
-
Enum for differentiating between one- and zero-based positions.
- print(long) - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar
-
print progress up to position
pos
, ifProgressBar.doPrint
- print(PrintStream) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary
-
Print dictionary to
System.err
for debugging purposes. - 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
- projectGapToSeqPos(List<Anchor>, int) - Static method in class de.charite.compbio.jannovar.reference.Anchors
-
Project from gaps position to sequence position.
- projectGenomeToCDSInterval(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator
- projectGenomeToCDSPosition(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator
- projectGenomeToTXInterval(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator
- projectGenomeToTXPosition(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator
- 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
- projectQryToRef(int) - Method in class de.charite.compbio.jannovar.reference.Alignment
-
Project query to reference position.
- projectRefToQry(int) - Method in class de.charite.compbio.jannovar.reference.Alignment
-
Project reference to query position.
- projectSeqToGapPos(List<Anchor>, int) - Static method in class de.charite.compbio.jannovar.reference.Anchors
-
Project from sequence position to gaps position.
- PUBMED_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
PubMed ids
- 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.
Q
- qryLeadingGapLength() - Method in class de.charite.compbio.jannovar.reference.Alignment
- qryTrailingGapLength() - Method in class de.charite.compbio.jannovar.reference.Alignment
R
- rank - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder
-
AnnotationLocation.rank
of next buildAnnotationLocation
. - rankType - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder
-
AnnotationLocation.rankType
of next buildAnnotationLocation
. - RARE_AMINO_ACID_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002008 A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid (children: selenocysteine_loss, pyrrolysine_loss).
- 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. - readBases(String, int, int) - Method in class de.charite.compbio.jannovar.impl.util.IndexedFASTAReader
-
Read the bases from contig
contigName
between 0-basedbeginPos
andendPos
. - REF_CALL - Static variable in class de.charite.compbio.jannovar.mendel.Genotype
- REF_FORMAT - de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- refBeginPos - Variable in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder.AlignmentPart
-
0-based begin position on reference.
- refEndPos - Variable in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder.AlignmentPart
-
0-based begin position on reference.
- 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.
- refLeadingGapLength() - Method in class de.charite.compbio.jannovar.reference.Alignment
- REFSEQ_ACCESSION - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
RefSeq accession
- RefSeqFastaRecordIdFormat - Enum in de.charite.compbio.jannovar.impl.parse.refseq
-
RefSeq import files may have different formats in their FASTA record IDs.
- RefSeqParser - Class in de.charite.compbio.jannovar.impl.parse.refseq
-
Parsing of RefSeq GFF3 files
- RefSeqParser(ReferenceDictionary, String, List<String>, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.refseq.RefSeqParser
- refTrailingGapLength() - Method in class de.charite.compbio.jannovar.reference.Alignment
- REGULATORY_REGION_ABLATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001894 A feature ablation whereby the deleted region includes a regulatory region.
- REGULATORY_REGION_AMPLIFICATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001891 Amplification of a region containing a regulatory region.
- REGULATORY_REGION_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001566 A sequence variant located within a regulatory region (is a: feature_variant).
- reset() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
-
Reset the builder into the state after initialization.
- REV - de.charite.compbio.jannovar.reference.Strand
-
reverse strand
- REVERSE - de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand
-
Record is on reverse strand
- 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.
- RGD_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
RGD id
- RIGHT_END - de.charite.compbio.jannovar.reference.SVBreakend.Side
-
Right breakend
- 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() - 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. - run(Collection<TranscriptModelBuilder>) - Static method in class de.charite.compbio.jannovar.impl.parse.TranscriptSupportLevelsSetterFromLengths
- run(Map<String, TranscriptModelBuilder>) - Method in class de.charite.compbio.jannovar.datasource.TranscriptModelBuilderHGNCExtender
-
Augment the
TranscriptModelBuilder
s with HGNC information
S
- save(JannovarData) - Method in class de.charite.compbio.jannovar.data.JannovarDataSerializer
-
Serialize a
JannovarData
object to a file. - seqLength(List<Anchor>) - Static method in class de.charite.compbio.jannovar.reference.Anchors
-
Return length of sequence.
- SEQUENCE_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001060 Top level term for variants, can be used for marking "uknown effect".
- 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
- 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
- setGeneVersion(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- setHasIndels(boolean) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
-
Set "has indels flag"
- setHasSubstitutions(boolean) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
-
Set "has mismatches flag"
- 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
- setSeqAlignment(Alignment) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- setSeqAlignment(ArrayList<TranscriptModelBuilder.AlignmentPart>) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder
- 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
- setTxVersion(String) - 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.
- shiftLeft() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange
- shiftRight() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange
- shiftSynonymousChange(AminoAcidChange, String, String) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer
-
This shifts the amino acid and its position to be reported in the
proteinChange
HGVS annotation to the first position where the amino acids actually differ. - size() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray
- SNV - de.charite.compbio.jannovar.reference.GenomeVariantType
-
single nucleotide variant
- SNVAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
- SPLICE_ACCEPTOR_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001574 A splice variant that changes the 2 base region at the 3' end of an intron (is a
VariantEffect.SPLICE_REGION_VARIANT
). - SPLICE_DONOR_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001575 A splice variant that changes the 2 base pair region at the 5' end of an intron (is a
VariantEffect.SPLICE_REGION_VARIANT
). - SPLICE_REGION_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001630 A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron (is a:
VariantEffect.SPLICING_VARIANT
). - SPLICING - de.charite.compbio.jannovar.annotation.OldVariantType
-
variant located in a splice site
- SPLICING_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001568 A sequence variant that changes the process of splicing (is a:
VariantEffect.GENE_VARIANT
). - START_LOSS - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variation leads to the loss of the start codon
- START_LOST - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002012 A codon variant that changes at least one base of the canonical start codon (is a: initiator_codon_variant).
- STOP_GAINED - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001587 A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (is a: nonsynonymous_variant, feature_truncation).
- STOP_LOST - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001578 A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (is a: nonsynonymous variant, terminator_codon_variant, feature_elongation)
- STOP_RETAINED_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001567 A sequence variant where at least one base in the terminator codon is changed, but the terminator remains (is a:
VariantEffect.SYNONYMOUS_VARIANT
, terminator_codon_variant). - STOPGAIN - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant that induces a new stop codon (i.e., nonsense)
- STOPLOSS - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant that alters and removes a wildtype stop codon
- 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
- STRUCTURAL_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001537 A sequence variant that changes one or more sequence features (is a: sequence variant).
- 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 givenTranscriptModel
. - SubModeOfInheritance - Enum in de.charite.compbio.jannovar.mendel
-
Enum for refined representation of
ModeOfInheritance
- subsetOfMembers(Collection<String>) - Method in class de.charite.compbio.jannovar.pedigree.Pedigree
-
Obtain subset of members in a pedigree or change order.
- SV_DELETION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is a structual deletion variant 1000bp+
- SV_INSERTION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is a structual insertion variant 1000bp+
- SV_INVERSION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is a structual inversion variant 1000bp+
- SV_SUBSTITUTION - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is a structual substitution variant 1000bp+
- SVAnnotation - Class in de.charite.compbio.jannovar.annotation
-
Annotation information of a
SVGenomeVariant
- SVAnnotation(SVGenomeVariant, TranscriptModel, Collection<VariantEffect>) - Constructor for class de.charite.compbio.jannovar.annotation.SVAnnotation
-
Initialize all fields.
- SVAnnotation(Collection<AnnotationMessage>) - Constructor for class de.charite.compbio.jannovar.annotation.SVAnnotation
-
Initialize object with messages only.
- SVAnnotationBuilderDispatcher - Class in de.charite.compbio.jannovar.annotation.builders
-
Dispatches annotation building for SVs to the specific classes, depending on their
SVDescription.getType()
. - SVAnnotationBuilderDispatcher(TranscriptModel, SVGenomeVariant) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVAnnotationBuilderDispatcher
- SVAnnotations - Class in de.charite.compbio.jannovar.annotation
-
A list of priority-sorted
SVAnnotation
objects. - SVAnnotations(SVGenomeVariant, Collection<SVAnnotation>) - Constructor for class de.charite.compbio.jannovar.annotation.SVAnnotations
-
Construct ImmutableAnnotationList from a
Collection
ofSVAnnotation
objects. - SVAnnotator - Class in de.charite.compbio.jannovar.annotation
-
Main driver class for annotating structural variants.
- SVAnnotator(ReferenceDictionary, ImmutableMap<Integer, Chromosome>) - Constructor for class de.charite.compbio.jannovar.annotation.SVAnnotator
-
Construct new VariantAnnotator, given a chromosome map.
- SVBreakend - Class in de.charite.compbio.jannovar.reference
-
Breakend.
- SVBreakend(GenomePosition, GenomePosition, int, int, int, int, String, String, SVBreakend.Side) - Constructor for class de.charite.compbio.jannovar.reference.SVBreakend
-
Initialize all fields.
- SVBreakend.Side - Enum in de.charite.compbio.jannovar.reference
-
Describe the end point of the breakend.
- SVBreakendAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVBreakend
. - SVBreakendAnnotationBuilder(TranscriptModel, SVBreakend) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVBreakendAnnotationBuilder
-
Construct the builder.
- SVCopyNumberVariant - Class in de.charite.compbio.jannovar.reference
-
Represents an SV deletion.
- SVCopyNumberVariant(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVCopyNumberVariant
-
Initialize all fields.
- SVCopyNumberVariantAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVCopyNumberVariant
. - SVCopyNumberVariantAnnotationBuilder(TranscriptModel, SVCopyNumberVariant) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVCopyNumberVariantAnnotationBuilder
-
Construct the builder.
- SVDeletion - Class in de.charite.compbio.jannovar.reference
-
Deletion relative to the reference.
- SVDeletion(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVDeletion
-
Initialize all fields.
- SVDeletionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVDeletion
. - SVDeletionAnnotationBuilder(TranscriptModel, SVDeletion) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVDeletionAnnotationBuilder
-
Construct the builder.
- SVDescription - Interface in de.charite.compbio.jannovar.reference
-
Minimal description of a variant as tuple
(position, position2, type)
. - SVDescription.Type - Enum in de.charite.compbio.jannovar.reference
-
Enumeration for the type of the structural variant.
- SVDuplication - Class in de.charite.compbio.jannovar.reference
-
Region of elevated copy number relative to the reference.
- SVDuplication(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVDuplication
-
Initialize all fields.
- SVDuplicationAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVDuplication
. - SVDuplicationAnnotationBuilder(TranscriptModel, SVDuplication) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVDuplicationAnnotationBuilder
-
Construct the builder.
- SVGenomeVariant - Class in de.charite.compbio.jannovar.reference
-
Representation of a structural variant on the genome level as defined in VCF.
- SVGenomeVariant(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Initialize all fields.
- SVInsertion - Class in de.charite.compbio.jannovar.reference
-
Insertion of novel sequence relative to the reference.
- SVInsertion(GenomePosition, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVInsertion
-
Initialize all fields.
- SVInsertionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVInsertion
. - SVInsertionAnnotationBuilder(TranscriptModel, SVInsertion) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVInsertionAnnotationBuilder
-
Construct the builder.
- SVInversion - Class in de.charite.compbio.jannovar.reference
-
Inversion of reference sequence
- SVInversion(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVInversion
-
Initialize all fields.
- SVInversionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVInversion
. - SVInversionAnnotationBuilder(TranscriptModel, SVInversion) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVInversionAnnotationBuilder
-
Construct the builder.
- SVMobileElementDeletion - Class in de.charite.compbio.jannovar.reference
-
Deletion of mobile element relative to the reference.
- SVMobileElementDeletion(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVMobileElementDeletion
-
Initialize all fields.
- SVMobileElementDeletionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVMobileElementDeletion
. - SVMobileElementDeletionAnnotationBuilder(TranscriptModel, SVMobileElementDeletion) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVMobileElementDeletionAnnotationBuilder
-
Construct the builder.
- SVMobileElementInsertion - Class in de.charite.compbio.jannovar.reference
-
Insertion of mobile element relative to the reference.
- SVMobileElementInsertion(GenomePosition, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVMobileElementInsertion
-
Initialize all fields.
- SVMobileElementInsertionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVMobileElementDeletion
. - SVMobileElementInsertionAnnotationBuilder(TranscriptModel, SVMobileElementInsertion) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVMobileElementInsertionAnnotationBuilder
-
Construct the builder.
- SVTandemDuplication - Class in de.charite.compbio.jannovar.reference
-
Tandem duplication.
- SVTandemDuplication(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVTandemDuplication
-
Initialize all fields.
- SVTandemDuplicationAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders
-
Build annotation for
SVTandemDuplication
. - SVTandemDuplicationAnnotationBuilder(TranscriptModel, SVTandemDuplication) - Constructor for class de.charite.compbio.jannovar.annotation.builders.SVTandemDuplicationAnnotationBuilder
-
Construct the builder.
- SVUnknown - Class in de.charite.compbio.jannovar.reference
-
Unknown structural variant.
- SVUnknown(GenomePosition, GenomePosition, int, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.SVUnknown
-
Initialize all fields.
- SYNONYMOUS - de.charite.compbio.jannovar.annotation.OldVariantType
-
Nucleotide substitution that does not alter the encoded amino acid of the affected codon.
- SYNONYMOUS_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001819 A sequence variant where there is no resulting change to the encoded amino acid (is a:
VariantEffect.CODING_SEQUENCE_VARIANT
, children: start_retained_variant, stop_retained_variant).
T
- TF_BINDING_SITE_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001782 A sequence variant located within a transcription factor binding site (is a:
VariantEffect.REGULATORY_REGION_VARIANT
). - TFBS_ABLATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001895 An ablation whereby the deleted region includes a transcription factor binding site.
- TFBS_AMPLIFICATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001892 An amplification of a region containing a transcription factor binding site.
- THREE_PRIME_UTR_EXON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002089 A UTR variant of the 3' UTR (is a: 3_prime_UTR_variant; is a: UTR_variant).
- THREE_PRIME_UTR_INTRON_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002090 A UTR variant between 3' UTRs (is a: 3_prime_UTR_variant; is a: UTR_variant).
- THREE_PRIME_UTR_TRUNCATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0002015 A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence (is a:
VariantEffect.FIVE_PRIME_UTR_EXON_VARIANT
orVariantEffect.FIVE_PRIME_UTR_INTRON_VARIANT
). - TO_LEGACY_NAME - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect
-
Function
for converting fromVariantEffect
to legacy term. - TO_SO_TERM - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect
-
Function
for converting fromVariantEffect
to SO term String. - toDisease(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Disease
-
Parse
String
into aDisease
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(char) - Method in class de.charite.compbio.jannovar.impl.util.Translator
- toLong(String) - Method in class de.charite.compbio.jannovar.impl.util.Translator
- toModeOfInheritance() - Method in enum de.charite.compbio.jannovar.mendel.SubModeOfInheritance
- 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 aSex
value. - toString() - Method in class de.charite.compbio.jannovar.annotation.Annotation
- toString() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation
- toString() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotation
- toString() - Method in class de.charite.compbio.jannovar.annotation.SVAnnotations
- 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.Alignment
- toString() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange
- toString() - Method in class de.charite.compbio.jannovar.reference.Anchor
- 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.SVBreakend
- toString() - Method in class de.charite.compbio.jannovar.reference.SVCopyNumberVariant
- toString() - Method in class de.charite.compbio.jannovar.reference.SVDeletion
- toString() - Method in class de.charite.compbio.jannovar.reference.SVDuplication
- toString() - Method in class de.charite.compbio.jannovar.reference.SVInsertion
- toString() - Method in class de.charite.compbio.jannovar.reference.SVInversion
- toString() - Method in class de.charite.compbio.jannovar.reference.SVMobileElementDeletion
- toString() - Method in class de.charite.compbio.jannovar.reference.SVMobileElementInsertion
- toString() - Method in class de.charite.compbio.jannovar.reference.SVTandemDuplication
- toString() - Method in class de.charite.compbio.jannovar.reference.SVUnknown
- 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.TranscriptModelBuilder.AlignmentPart
- toString() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition
- toVCFAnnoString(String, boolean, AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.Annotation
-
Return the standardized VCF variant string for the given
ALT
allele. - toVCFAnnoString(String, AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.Annotation
-
Forward to
toVCFAnnoString(alt, true, code)
. - toVCFSVAnnoString(boolean) - Method in class de.charite.compbio.jannovar.annotation.SVAnnotation
-
Return string for
SVANNO
entry of theINFO
VCF field. - transcript - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder
-
AnnotationLocation.transcript
of next buildAnnotationLocation
. - TRANSCRIPT_ABLATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001893 A feature ablation whereby the deleted region includes a transcript feature (is a: feature_ablation)
- TRANSCRIPT_AMPLIFICATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001880 A feature amplification of a region containing a transcript.
- TRANSCRIPT_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001576 A sequence variant that changes the structure of the transcript (is a:
VariantEffect.GENE_VARIANT
). - 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, boolean, boolean) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModel
-
Initialize the
TranscriptModel
object from the given parameters. - TranscriptModel(String, String, GenomeInterval, GenomeInterval, ImmutableList<GenomeInterval>, String, String, int, boolean, boolean, Map<String, String>, Alignment) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModel
-
Initialize the
TranscriptModel
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
- TranscriptModelBuilder.AlignmentPart - Class in de.charite.compbio.jannovar.reference
-
Describe a part of an alignment, e.g., as parsed from RefSeq.
- TranscriptModelBuilderHGNCExtender - Class in de.charite.compbio.jannovar.datasource
-
Helper class for extending
TranscriptModelBuilder
objects with HGNC information - TranscriptModelBuilderHGNCExtender(String, Function<HGNCRecord, List<String>>, Function<TranscriptModelBuilder, 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.
- TRANSLOCATION - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0000199 A region of nucleotide sequence that has translocated to a new position.
- truncateAltAfterStopCodon(AminoAcidChange) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer
-
Search for stop codon in
change.alt
and truncate afterwards. - 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.
- txBeginPos - Variable in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder.AlignmentPart
-
0-based begin position on transcript.
- txEndPos - Variable in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder.AlignmentPart
-
0-based begin position on transcript.
- txLocation - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder
-
AnnotationLocation.txLocation
of next buildAnnotationLocation
.
U
- UCSC_CANONICAL - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels
-
Annotated as canonical transcript by UCSC (used in absence of TSL).
- UCSC_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
UCSC id
- UCSCParser - Class in de.charite.compbio.jannovar.impl.parse.ucsc
-
Parser for the UCCSC knownGene and related files.
- UCSCParser(ReferenceDictionary, String, List<String>, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser
- UNAFFECTED - de.charite.compbio.jannovar.pedigree.Disease
-
corresponds to 1 = unaffected in the PED file.
- 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
- UNDEFINED - de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType
- union(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval
- UNIPROT_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
Uniprot ids
- UNKNOWN - de.charite.compbio.jannovar.pedigree.Disease
-
corresponds to 0 = unknown disease status in the PED file.
- UNKNOWN - de.charite.compbio.jannovar.pedigree.Sex
-
sex is unknown
- UNKNOWN - de.charite.compbio.jannovar.reference.SVDescription.Type
-
unknown type
- UNKNOWN_FORMAT - de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- UPSTREAM - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is upstream of a gene
- UPSTREAM_GENE_VARIANT - de.charite.compbio.jannovar.annotation.VariantEffect
-
SO:0001631 A sequence variant located 5' of a gene (is a:
VariantEffect.INTERGENIC_VARIANT
). - UPSTREAM_LENGTH - Static variable in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
-
Length of upstream interval around a transcript.
- UTR3 - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is located in the 3' untranslated region
- UTR5 - de.charite.compbio.jannovar.annotation.OldVariantType
-
Variant is located in the 5' untranslated region
V
- valueOf(char) - Method in enum de.charite.compbio.jannovar.reference.Strand
-
Returns the enum constant of this type with the specified name.
- 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.impl.parse.refseq.RefSeqFastaRecordIdFormat
-
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.mendel.SubModeOfInheritance
-
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(String) - Static method in enum de.charite.compbio.jannovar.reference.SVBreakend.Side
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.charite.compbio.jannovar.reference.SVDescription.Type
-
Returns the enum constant of this type with the specified name.
- 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.impl.parse.refseq.RefSeqFastaRecordIdFormat
-
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.mendel.SubModeOfInheritance
-
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.
- values() - Static method in enum de.charite.compbio.jannovar.reference.SVBreakend.Side
-
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.SVDescription.Type
-
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
ofAnnotation
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
- VCF_SVANN_DESCRIPTION_STRING - Static variable in class de.charite.compbio.jannovar.annotation.SVAnnotation
-
The DESCRIPTION string to use in the VCF header for VCFVariantAnnotation objects
- VEGA_ID - de.charite.compbio.jannovar.hgnc.AltGeneIDType
-
VEGA id
- VersionComparator - Class in de.charite.compbio.jannovar.data.impl
-
Taken from http://stackoverflow.com/a/10034633/84349
- VersionComparator() - Constructor for class de.charite.compbio.jannovar.data.impl.VersionComparator
- VersionTokenizer - Class in de.charite.compbio.jannovar.data.impl
-
Taken from http://stackoverflow.com/a/10034633/84349
- VersionTokenizer(String) - Constructor for class de.charite.compbio.jannovar.data.impl.VersionTokenizer
W
- WARNING_REF_DOES_NOT_MATCH_GENOME - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W1) This means that the "REF" field in the input VCF file does not match the reference genome.
- WARNING_REF_DOES_NOT_MATCH_TRANSCRIPT - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(Additional warning) This means that the "REF" field in the input VCF file does not match the reference genome.
- WARNING_SEQUENCE_NOT_AVAILABLE - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W2) Reference sequence is not available, thus no inference could be performed.
- WARNING_TRANSCRIPT_INCOMPLETE - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W3) A protein coding transcript having a nonĀmultiple of 3 length.
- WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W4) A protein coding transcript has two or more STOP codons in the middle of the coding sequence (CDS).
- WARNING_TRANSCRIPT_NO_START_CODON - de.charite.compbio.jannovar.annotation.AnnotationMessage
-
(W5) A protein coding transcript does not have a proper START codon.
- withDeltas(int, int) - Method in class de.charite.compbio.jannovar.reference.Anchor
- 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
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVBreakend
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVCopyNumberVariant
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVDeletion
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVDuplication
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVGenomeVariant
-
Return this variant projected to the given
Strand
, at least at the start position. - withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVInsertion
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVInversion
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVMobileElementDeletion
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVMobileElementInsertion
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVTandemDuplication
- withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.SVUnknown
- wouldBeSymbolicAllele(String) - Static method in class de.charite.compbio.jannovar.reference.GenomeVariant
-
Check whether the given allele string would be interpreted as a symbolic one.
- 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 aOutputStream
.
X
- X_CHROMOSOMAL - de.charite.compbio.jannovar.mendel.ChromosomeType
-
X chromosome
- X_DOMINANT - de.charite.compbio.jannovar.mendel.ModeOfInheritance
-
dominant inheritance on X chromosome
- X_DOMINANT - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
dominant inheritance on X chromosome
- X_RECESSIVE - de.charite.compbio.jannovar.mendel.ModeOfInheritance
-
recessive inheritance on X chromosome
- X_RECESSIVE_COMP_HET - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
recessive inheritance on X chromosome, compound het
- X_RECESSIVE_HOM_ALT - de.charite.compbio.jannovar.mendel.SubModeOfInheritance
-
recessive inheritance on X chromosome, hom alt
Y
- Y_CHROMOSOMAL - de.charite.compbio.jannovar.mendel.ChromosomeType
-
Y chromosome
Z
- ZERO_BASED - de.charite.compbio.jannovar.reference.PositionType
-
positions start at zero and intervals are half-opened [begin, end).
_
- _SMALLEST_HIGH_IMPACT - de.charite.compbio.jannovar.annotation.VariantEffect
-
Marker for smallest
VariantEffect
withPutativeImpact.HIGH
impact. - _SMALLEST_LOW_IMPACT - de.charite.compbio.jannovar.annotation.VariantEffect
-
Marker for smallest
VariantEffect
withPutativeImpact.LOW
impact. - _SMALLEST_MODERATE_IMPACT - de.charite.compbio.jannovar.annotation.VariantEffect
-
Marker for smallest
VariantEffect
withPutativeImpact.MODERATE
impact.
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