Package org.ensembl.datamodel

Data types that appear in the core ensembl databases such as Genes, Exons and Karyotypes and various support classes such as Location.

See:
Description

Interface Summary

Accessioned	Object is capable of having an accession (stable id) which is stable across Ensembl data releases and a version.
AffyArray	An Affymetrix oligo microarray chip which contains probes.
AffyFeature	The location where an Affymetrix Probe hits the genome.
AffyProbe	An oligo spot from one or more Affymetric micro arrays.
Analysis	Represents a process used to create features such as genes.
ArchiveStableID	Represents a single immutable archive stable ID.
AssemblyElement
AssemblyMapper
Attribute	A generic attribute that can be associatted with a features such as MiscFeature.
Chromosome
ChromosomeBand
DnaDnaAlignFeature
DnaDnaAlignment	An alignment between part of a genome and a dna hit
DnaProteinAlignment	An alignment between part of a genome and a protein.
Exon	Exon.
ExternalDatabase
ExternalRef	Reference to object outside ensembl database.
Feature	Simple genomic feature.
FeaturePair	Feature hit.
Gene	Gene.
GeneSnapShot	Represents part of the state of a gene at some point in time.
KaryotypeBand
Locatable	Genome feature with a location on genome.
MappingSession
Marker	Marker.
MarkerFeature	Represents a marker feature in the EnsEMBL database.
MiscFeature	MiscFeatures are extremely general features with a location and an arbitrary group of attributes.
MiscSet	MiscSets represent classsifications or groupings of MiscFeatures.
Persistent	Capable of storing in persistent storage.
Population
PredictionExon	Predicted exon which lacks a gene and UTRs.
PredictionTranscript	Transcript consisting of PredictionExons.
ProteinFeature	An alignment between a part of the genome and a peptide.
Qtl	Represents a quantitative trait locus (Qtl) in the EnsEMBL database.
QtlFeature	A QtlFeature represent a region where the Qtl appears in the Ensembl database.
QtlSynonym	Synonym for a Qtl.
RepeatConsensus	Repeat sequence.
RepeatFeature	Repetitive sequence on genome.
Sequence	Genomic DNA sequence.
SequenceEdit	A sequence modification action.
SequenceRegion	Represents a region of sequence, which could be from any co-ordinate system.
SimpleFeature
SnapShot	A partial representation of a data element's state at some point in time.
StableIDEvent
SubmittedVariation
Transcript	Transcript.
TranscriptSnapShot	Represents part of the state of a transcript at some point in time.
Translation	Translation.
TranslationSnapShot	Represents part of the state of a translation at some point in time.
UngappedAlignment	Alignment to external reference.
Variation	A variation such as a SNP.
VariationFrequency

Class Summary

AssemblyException	Defines how some semi-virtual sequence regions (PAR/Haplotypes) are partially constructed from other sequence regions.
AssemblyLocation	Deprecated. Create instances of Location directly.
ChainedAssemblyMapper
CloneFragmentLocation	Location on a Contig (Clone Fragment).
CoordinateSystem	A genomic co-ordinate system.
CoordinateSystemMapping	Store information about the mapping between a pair of co-ordinate systems.
Location	A Location is an 'address' of regions on sequences.
Query	Deprecated. since version 27.0
SimpleAssemblyMapper
TranscriptAlleleHelper	Denormalised representation of the transcript optimised for answering questions about variations.

Exception Summary

AttributeException
InvalidLocationException	Represents the fact that an attempt was made to create or use an invalid location.

Package org.ensembl.datamodel Description

Data types that appear in the core ensembl databases such as Genes, Exons and Karyotypes and various support classes such as Location.

Most of the types are defined as interfaces in this package with implementing classes in org.ensembl.datamodel.impl.

Biological objects such as Exons are Locatable because they have locations on sequences.

Ensj supports one type of Location which can specify part or all of a region in a coordinate system. This replaces the AssemblyLocation and CloneFragmentLocation classes which are deprecated.