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## Uses of Interface
org.ensembl.datamodel.Persistent

Packages that use Persistent
org.ensembl.compara.datamodel | Data types that are unique to ensembl compara databases such as Homology and GenomicAlign.
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.
org.ensembl.datamodel.impl | Implementation of core ensembl data types.
org.ensembl.util | Utility classes.
org.ensembl.variation.datamodel | Data types that are unique to ensembl variation databases such as Variation, Allele and Genotype.

Uses of Persistent in org.ensembl.compara.datamodel

Subinterfaces of Persistent in org.ensembl.compara.datamodel
`interface` | `DnaFragment` I am a part of the compara- analysis.
`interface` | `Domain` I represent a single species which is part of the compara- analyses.
`interface` | `Family` I represent a single species which is part of the compara- analyses.
`interface` | `GenomeDB` I represent a single species which is part of the compara- analyses.
`interface` | `GenomicAlign` I am part of the compara-analysis.
`interface` | `GenomicAlignBlock` I am part of the compara-analysis.
`interface` | `Homology` I represent a single species which is part of the compara- analyses.
`interface` | `Member` I represent a single species which is part of the compara- analyses.
`interface` | `MethodLink` I represent a type of dna-dna alignment
`interface` | `MethodLinkSpeciesSet` I represent a type of analysis which could be applied between the elements of a set of genomes and the actual set which had it applied.

Uses of Persistent in org.ensembl.datamodel

Subinterfaces of Persistent in org.ensembl.datamodel
`interface` | `Accessioned` Object is capable of having an accession (stable id) which is stable across Ensembl data releases and has a version, creation and last modified date.
`interface` | `Analysis` Represents a process used to create features such as genes.
`interface` | `Chromosome`
`interface` | `ChromosomeBand`
`interface` | `DnaDnaAlignFeature`
`interface` | `DnaDnaAlignment` An alignment between part of a genome and a dna hit
`interface` | `DnaProteinAlignment` An alignment between part of a genome and a protein.
`interface` | `Exon` Exon.
`interface` | `ExternalDatabase`
`interface` | `ExternalRef` Reference to object outside ensembl database.
`interface` | `Feature` Simple genomic feature.
`interface` | `FeaturePair` Feature hit.
`interface` | `Gene` Gene.
`interface` | `KaryotypeBand`
`interface` | `Locatable` Genome feature with a location on genome.
`interface` | `MappingSession`
`interface` | `Marker` Marker.
`interface` | `MarkerFeature` Represents a marker feature in the EnsEMBL database.
`interface` | `MiscFeature` MiscFeatures are extremely general features with a location and an arbitrary group of attributes.
`interface` | `MiscSet` MiscSets represent classsifications or groupings of MiscFeatures.
`interface` | `OligoArray` An microarray chip which contains probes.
`interface` | `OligoFeature` The location where an OligoProbe hits the genome.
`interface` | `OligoProbe` An oligo spot from one or more microarrays.
`interface` | `Population`
`interface` | `PredictionExon` Predicted exon which lacks a gene and UTRs.
`interface` | `PredictionTranscript` Transcript consisting of PredictionExons.
`interface` | `ProteinFeature` An alignment between a part of the genome and a peptide.
`interface` | `Qtl` Represents a quantitative trait locus (Qtl) in the EnsEMBL database.
`interface` | `QtlFeature` A QtlFeature represent a region where the Qtl appears in the Ensembl database.
`interface` | `RepeatConsensus` Repeat sequence.
`interface` | `RepeatFeature` Repetitive sequence on genome.
`interface` | `Sequence` Genomic DNA sequence.
`interface` | `SequenceRegion` Represents a region of sequence, which could be from any co-ordinate system.
`interface` | `SimpleFeature`
`interface` | `StableIDEvent`
`interface` | `Transcript` Transcript.
`interface` | `Translation` Translation.

Classes in org.ensembl.datamodel that implement Persistent
`class` | `AssemblyException` Defines how some semi-virtual sequence regions (PAR/Haplotypes) are partially constructed from other sequence regions.
`class` | `CoordinateSystem` A genomic co-ordinate system.

Methods in org.ensembl.datamodel with parameters of type Persistent
`boolean` | `Persistent.sameInternalID(Persistent other)`

Uses of Persistent in org.ensembl.datamodel.impl

Classes in org.ensembl.datamodel.impl that implement Persistent
`class` | `org.ensembl.datamodel.impl.BaseFeatureImpl` All locatable classes have locations and have sequences.
`class` | `org.ensembl.datamodel.impl.LocatableImpl`
`class` | `org.ensembl.datamodel.impl.PersistentImpl`

Uses of Persistent in org.ensembl.util

Methods in org.ensembl.util with parameters of type Persistent
`boolean` | `IDSet.add(Persistent persistent)`
`boolean` | `IDSet.contains(Persistent persistent)`
`boolean` | `PersistentSet.add(Persistent persistent)`
`void` | `IDList.addInternalID(Persistent persistent)`
`boolean` | `IDMap.put(Persistent value)` Stores the persistent object using it's internalID as the key.
`void` | `IDMap.putAll(Persistent[] values)` Adds all the persistent objects using their internalIDs as the keys.

Constructors in org.ensembl.util with parameters of type Persistent
`IDMap(Persistent[] values)` Creates a map conainting all the persistent objects keyed on their internalIDs.

Uses of Persistent in org.ensembl.variation.datamodel

Subinterfaces of Persistent in org.ensembl.variation.datamodel
`interface` | `Allele` A single allele of a nucleotide variation.
`interface` | `AlleleFeature` An allele located on a genome.
`interface` | `AlleleGroup` Ensembl representation of a grouping of alleles (aka haplotype).
`interface` | `Genotype` Genotype.
`interface` | `Individual` This is a class representing a single individual.
`interface` | `IndividualGenotype` The genotype of a single diploid individual at a specific locus.
`interface` | `LDFeature` A linkage disequilibrium between two VariationFeatures.
`interface` | `PopulationGenotype` A genotype that is present in a population.
`interface` | `TranscriptVariation` A TranscriptVariation object represents a variation feature which is in close proximity to an Ensembl transcript.
`interface` | `Variation` A nucleotide variation such as a SNP.
`interface` | `VariationFeature` This is a an occurrence of a nucleotide variation in the genome.
`interface` | `VariationGroup` Grouping of variations (aka haplotype set).
`interface` | `VariationGroupFeature` The point of this class is....

Classes in org.ensembl.variation.datamodel that implement Persistent
`class` | `AlleleConsequence` Represents part or all of the effect of a single allele on a transcript.

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