Serialized Form (Jannovar 0.17 API)

Package de.charite.compbio.jannovar
- Class de.charite.compbio.jannovar.JannovarException extends Exception implements Serializable
  
  serialVersionUID:
  
  2L
- Class de.charite.compbio.jannovar.UncheckedJannovarException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  2L
Package de.charite.compbio.jannovar.annotation
- Class de.charite.compbio.jannovar.annotation.AnnotationException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  2L
- Class de.charite.compbio.jannovar.annotation.InvalidGenomeVariant extends AnnotationException implements Serializable
  
  serialVersionUID:
  
  -6983204936815945929L
Package de.charite.compbio.jannovar.cmd
- Class de.charite.compbio.jannovar.cmd.CommandLineParsingException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
- Class de.charite.compbio.jannovar.cmd.HelpRequestedException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.data
- Class de.charite.compbio.jannovar.data.Chromosome extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - refDict
```
ReferenceDictionary refDict
```
      reference dictionary to use
    - chrID
```
int chrID
```
      numeric chromsome ID
    - tmIntervalTree
```
IntervalArray<T> tmIntervalTree
```
      An IntervalArray that contains all of the TranscriptModel objects for transcripts located on this chromosome.
- Class de.charite.compbio.jannovar.data.JannovarData extends Object implements Serializable
  
  serialVersionUID:
  
  3L
  - Serialized Fields
    - chromosomes
```
com.google.common.collect.ImmutableMap<K,V> chromosomes
```
      map from chromosome ID to Chromosome
    - tmByAccession
```
com.google.common.collect.ImmutableMap<K,V> tmByAccession
```
      map from transcript accession to TranscriptModel instance.
    - tmByGeneSymbol
```
com.google.common.collect.ImmutableMultimap<K,V> tmByGeneSymbol
```
      map from transcript accession to TranscriptModel instance.
    - refDict
```
ReferenceDictionary refDict
```
      information about reference lengths and identities
- Class de.charite.compbio.jannovar.data.ReferenceDictionary extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contigID
```
com.google.common.collect.ImmutableMap<K,V> contigID
```
      stores a mapping from the string chromosome/contig name to its numeric id, e.g. from both "chr1" and "1" to (int)1
    - contigName
```
com.google.common.collect.ImmutableMap<K,V> contigName
```
      stores primary name for each numeric chromsomomeID/contigID
    - contigLength
```
com.google.common.collect.ImmutableMap<K,V> contigLength
```
      stores a mapping from numeric chromosomeID/contigID to chromosome/contig length
- Class de.charite.compbio.jannovar.data.SerializationException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.datasource
- Class de.charite.compbio.jannovar.datasource.FileDownloadException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
- Class de.charite.compbio.jannovar.datasource.InvalidDataSourceException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.hgvs.bridge
- Class de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.hgvs.parser
- Class de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.htsjdk
- Class de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - annotationMessage
```
AnnotationMessage annotationMessage
```
Package de.charite.compbio.jannovar.impl.intervals
- Class de.charite.compbio.jannovar.impl.intervals.Interval extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - begin
```
int begin
```
      start point of the interval (inclusive)
    - end
```
int end
```
      end point of the interval (exclusive)
    - value
```
Object value
```
      the value stored for the Interval
    - maxEnd
```
int maxEnd
```
      the maximum of this nodes Interval.end and both of it children's Interval.end
- Class de.charite.compbio.jannovar.impl.intervals.IntervalArray extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - intervals
```
com.google.common.collect.ImmutableList<E> intervals
```
      list of Interval objects, sorted by begin position
    - intervalsEnd
```
com.google.common.collect.ImmutableList<E> intervalsEnd
```
      list of Interval objects, sorted by end position
- Class de.charite.compbio.jannovar.impl.intervals.MutableInterval extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - begin
```
int begin
```
      start point of the interval (inclusive)
    - end
```
int end
```
      end point of the interval (exclusive)
    - value
```
Object value
```
      the value stored for the Interval
    - maxEnd
```
int maxEnd
```
      the maximum of this nodes MutableInterval.end and both of it children's MutableInterval.end
Package de.charite.compbio.jannovar.impl.parse
- Class de.charite.compbio.jannovar.impl.parse.InvalidAttributeException extends IOException implements Serializable
  
  serialVersionUID:
  
  1L
- Class de.charite.compbio.jannovar.impl.parse.TranscriptParseException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  2L
Package de.charite.compbio.jannovar.mendel
- Class de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.mendel.bridge
- Class de.charite.compbio.jannovar.mendel.bridge.CannotAnnotateMendelianInheritance extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.mendel.filter
- Class de.charite.compbio.jannovar.mendel.filter.VariantContextFilterException extends UncheckedJannovarException implements Serializable
  
  serialVersionUID:
  
  1L
Package de.charite.compbio.jannovar.pedigree
- Class de.charite.compbio.jannovar.pedigree.InheritanceVariantContext extends htsjdk.variant.variantcontext.VariantContext implements Serializable
  
  serialVersionUID:
  
  6381923752159274326L
  - Serialized Fields
    - matchedModesOfInheritance
```
Set<E> matchedModesOfInheritance
```
      Set of stored possible modes of inheritances. The set is build by the the InheritanceCompatibilityChecker .
- Class de.charite.compbio.jannovar.pedigree.PedParseException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  2L
Package de.charite.compbio.jannovar.pedigree.compatibilitychecker
- Class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityCheckerException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  -4032184488029441661L
Package de.charite.compbio.jannovar.reference
- Class de.charite.compbio.jannovar.reference.GenomeInterval extends Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - refDict
```
ReferenceDictionary refDict
```
      reference dictionary to use for coordinate translation
    - strand
```
Strand strand
```
      the strand that the position is located on
    - chr
```
int chr
```
      the chromosome number, as index in chromosome dictionary
    - beginPos
```
int beginPos
```
      the begin position on the chromosome
    - endPos
```
int endPos
```
      the end position on the chromosome
- Class de.charite.compbio.jannovar.reference.GenomePosition extends Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - refDict
```
ReferenceDictionary refDict
```
      reference dictionary to use for coordinate translation
    - strand
```
Strand strand
```
      the strand that the position is located on
    - chr
```
int chr
```
      the chromosome number, as index in chromosome dictionary
    - pos
```
int pos
```
      the position on the chromosome
- Class de.charite.compbio.jannovar.reference.InvalidCodonException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
- Class de.charite.compbio.jannovar.reference.InvalidCoordinateException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class de.charite.compbio.jannovar.reference.ProjectionException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L
- Class de.charite.compbio.jannovar.reference.TranscriptModel extends Object implements Serializable
  
  serialVersionUID:
  
  3L
  - Serialized Fields
    - accession
```
String accession
```
      Accession number of the transcript (e.g., the UCSC knownGene id - uc011nca.2). The version number may be included.
    - geneSymbol
```
String geneSymbol
```
      Gene symbol of the known Gene. Can be null for some genes. Note that in annovar, $name2 corresponds to the geneSymbol if available, otherwise the kgID is used.
    - txRegion
```
GenomeInterval txRegion
```
      Genomic interval with transcript begin/end.
    - cdsRegion
```
GenomeInterval cdsRegion
```
      Genomic interval with CDS begin/end. Note that in Jannovar, the CDS region includes the start and stop codon.
    - exonRegions
```
com.google.common.collect.ImmutableList<E> exonRegions
```
      Genomic intervals with the exons, order is dictated by strand of transcript.
    - sequence
```
String sequence
```
      cDNA sequence of the spliced RNA of this known gene transcript.
    - geneID
```
String geneID
```
      The gene ID, from Ensembl ("ENS[MUS]*G0+([0-9]+)"), Entrez ("ENTREZ([0-9]+) "), RefSeq ("gene([0-9]+)"). null for no available gene ID.
    - altGeneIDs
```
com.google.common.collect.ImmutableSortedMap<K,V> altGeneIDs
```
      Alternative gene IDs, as parsed from RefSeq GFF3 file See TranscriptModel.getAltGeneIDs() for more information
    - transcriptSupportLevel
```
int transcriptSupportLevel
```
      The transcript support level of the this transcript (the lower the better).
      
      See Also:
      
      TranscriptSupportLevels, http://www.ensembl.org/Help/Glossary?id=492
Package de.charite.compbio.jannovar.vardbs.base
- Class de.charite.compbio.jannovar.vardbs.base.JannovarVarDBException extends JannovarException implements Serializable
  
  serialVersionUID:
  
  1L

Serialized Form

Package de.charite.compbio.jannovar

Class de.charite.compbio.jannovar.JannovarException extends Exception implements Serializable

Class de.charite.compbio.jannovar.UncheckedJannovarException extends RuntimeException implements Serializable

Package de.charite.compbio.jannovar.annotation

Class de.charite.compbio.jannovar.annotation.AnnotationException extends JannovarException implements Serializable

Class de.charite.compbio.jannovar.annotation.InvalidGenomeVariant extends AnnotationException implements Serializable

Package de.charite.compbio.jannovar.cmd

Class de.charite.compbio.jannovar.cmd.CommandLineParsingException extends JannovarException implements Serializable

Class de.charite.compbio.jannovar.cmd.HelpRequestedException extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.data

Class de.charite.compbio.jannovar.data.Chromosome extends Object implements Serializable

Serialized Fields

refDict

chrID

tmIntervalTree

Class de.charite.compbio.jannovar.data.JannovarData extends Object implements Serializable

Serialized Fields

chromosomes

tmByAccession

tmByGeneSymbol

refDict

Class de.charite.compbio.jannovar.data.ReferenceDictionary extends Object implements Serializable

Serialized Fields

contigID

contigName

contigLength

Class de.charite.compbio.jannovar.data.SerializationException extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.datasource

Class de.charite.compbio.jannovar.datasource.FileDownloadException extends JannovarException implements Serializable

Class de.charite.compbio.jannovar.datasource.InvalidDataSourceException extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.hgvs.bridge

Class de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant extends Exception implements Serializable

Package de.charite.compbio.jannovar.hgvs.parser

Class de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException extends RuntimeException implements Serializable

Package de.charite.compbio.jannovar.htsjdk

Class de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException extends Exception implements Serializable

Serialized Fields

annotationMessage

Package de.charite.compbio.jannovar.impl.intervals

Class de.charite.compbio.jannovar.impl.intervals.Interval extends Object implements Serializable

Serialized Fields

begin

end

value

maxEnd

Class de.charite.compbio.jannovar.impl.intervals.IntervalArray extends Object implements Serializable

Serialized Fields

intervals

intervalsEnd

Class de.charite.compbio.jannovar.impl.intervals.MutableInterval extends Object implements Serializable

Serialized Fields

begin

end

value

maxEnd

Package de.charite.compbio.jannovar.impl.parse

Class de.charite.compbio.jannovar.impl.parse.InvalidAttributeException extends IOException implements Serializable

Class de.charite.compbio.jannovar.impl.parse.TranscriptParseException extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.mendel

Class de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.mendel.bridge

Class de.charite.compbio.jannovar.mendel.bridge.CannotAnnotateMendelianInheritance extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.mendel.filter

Class de.charite.compbio.jannovar.mendel.filter.VariantContextFilterException extends UncheckedJannovarException implements Serializable

Package de.charite.compbio.jannovar.pedigree

Class de.charite.compbio.jannovar.pedigree.InheritanceVariantContext extends htsjdk.variant.variantcontext.VariantContext implements Serializable

Serialized Fields

matchedModesOfInheritance

Class de.charite.compbio.jannovar.pedigree.PedParseException extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.pedigree.compatibilitychecker

Class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityCheckerException extends JannovarException implements Serializable

Package de.charite.compbio.jannovar.reference

Class de.charite.compbio.jannovar.reference.GenomeInterval extends Object implements Serializable

Serialized Fields

refDict

strand

chr

beginPos

endPos