Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## Uses of Package
org.ensembl.datamodel

Packages that use org.ensembl.datamodel
org.ensembl | Java library for accessing Ensembl core, compara and variation (SNP) databases.
org.ensembl.compara.datamodel | Data types that are unique to ensembl compara databases such as Homology and GenomicAlign.
org.ensembl.compara.driver | Compara adaptors.
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.driver | Driver and adaptors for accessing ensembl core databases.
org.ensembl.util | Utility classes.
org.ensembl.variation.datamodel | Data types that are unique to ensembl variation databases such as Variation, Allele and Genotype.
org.ensembl.variation.driver | Driver and adaptors for accessing ensembl variation databases.

Classes in org.ensembl.datamodel used by org.ensembl
CoordinateSystem A genomic co-ordinate system.
Location A Location is an 'address' of regions on sequences.

Classes in org.ensembl.datamodel used by org.ensembl.compara.datamodel
DnaDnaAlignFeature
FeaturePair Feature hit.
Location A Location is an 'address' of regions on sequences.
Persistent Capable of storing in persistent storage.

Classes in org.ensembl.datamodel used by org.ensembl.compara.driver
Location A Location is an 'address' of regions on sequences.

Classes in org.ensembl.datamodel used by org.ensembl.datamodel
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.
Analysis Represents a process used to create features such as genes.
ArchiveStableID Represents a single immutable archive stable ID.
AssemblyLocation Deprecated. Create instances of Location directly. The specific location types such as AssemblyLocation have been superseded by the more generic Location class.
AssemblyMapper
Attribute A generic attribute that can be associatted with a features such as MiscFeature.
CloneFragmentLocation Location on a Contig (Clone Fragment).
CoordinateSystem A genomic co-ordinate system.
Exon Exon.
ExternalDatabase
ExternalRef Reference to object outside ensembl database.
Feature Simple genomic feature.
FeaturePair Feature hit.
Gene Gene.
InvalidLocationException Represents the fact that an attempt was made to create or use an invalid location.
Locatable Genome feature with a location on genome.
Location A Location is an 'address' of regions on sequences.
MappingSession
Marker Marker.
MiscSet MiscSets represent classsifications or groupings of MiscFeatures.
OligoArray An microarray chip which contains probes.
OligoProbe An oligo spot from one or more microarrays.
Persistent Capable of storing in persistent storage.
PredictionTranscript Transcript consisting of PredictionExons.
Qtl Represents a quantitative trait locus (Qtl) in the EnsEMBL database.
RepeatConsensus Repeat sequence.
Sequence Genomic DNA sequence.
SequenceRegion Represents a region of sequence, which could be from any co-ordinate system.
SnapShot A partial representation of a data element's state at some point in time.
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.

Classes in org.ensembl.datamodel used by org.ensembl.datamodel.impl
Feature Simple genomic feature.
Locatable Genome feature with a location on genome.
Persistent Capable of storing in persistent storage.

Classes in org.ensembl.datamodel used by org.ensembl.driver
Analysis Represents a process used to create features such as genes.
AssemblyException Defines how some semi-virtual sequence regions (PAR/Haplotypes) are partially constructed from other sequence regions.
AssemblyMapper
ChainedAssemblyMapper
CoordinateSystem A genomic co-ordinate system.
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.
Gene Gene.
GeneSnapShot Represents part of the state of a gene at some point in time.
Location A Location is an 'address' of regions on sequences.
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.
OligoArray An microarray chip which contains probes.
OligoFeature The location where an OligoProbe hits the genome.
OligoProbe An oligo spot from one or more microarrays.
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.
Query Deprecated. since version 27.0
RepeatConsensus Repeat sequence.
RepeatFeature Repetitive sequence on genome.
Sequence Genomic DNA sequence.
SequenceRegion Represents a region of sequence, which could be from any co-ordinate system.
SimpleAssemblyMapper
SimpleFeature
StableIDEvent
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.

Classes in org.ensembl.datamodel used by org.ensembl.util
Location A Location is an 'address' of regions on sequences.
Persistent Capable of storing in persistent storage.

Classes in org.ensembl.datamodel used by org.ensembl.variation.datamodel
Feature Simple genomic feature.
Locatable Genome feature with a location on genome.
Location A Location is an 'address' of regions on sequences.
Persistent Capable of storing in persistent storage.
Transcript Transcript.

Classes in org.ensembl.datamodel used by org.ensembl.variation.driver
Location A Location is an 'address' of regions on sequences.
Transcript Transcript.

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES