Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

Serialized Form


Package uk.ac.roslin.ensembl.biojava3

Class uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet extends org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet implements Serializable


Package uk.ac.roslin.ensembl.config

Class uk.ac.roslin.ensembl.config.EnsemblComparaDivision extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.EnsemblDBType extends EnsemblType implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException
Ensure Singleton class

Throws:
ObjectStreamException
Serialized Fields

databaseType

uk.ac.roslin.ensembl.config.EnsemblDBType.SpecificDBType databaseType
The SpecificDBType of a given EnsemblDBType Object i.e. CORE, COMPARA etc.


ENSEMBL_TYPE

uk.ac.roslin.ensembl.config.EnsemblDBType.GenericDBType ENSEMBL_TYPE
The GenericDBType of a given EnsemblDBType Object i.e. SINGLE_SPECIES, SPECIES_COMPARISON etc.

Class uk.ac.roslin.ensembl.config.EnsemblType extends Object implements Serializable

Serialized Fields

label

String label

Class uk.ac.roslin.ensembl.config.FeatureType extends EnsemblType implements Serializable


Package uk.ac.roslin.ensembl.exception

Class uk.ac.roslin.ensembl.exception.ConfigurationException extends EnsemblException implements Serializable

serialVersionUID: 1L

Class uk.ac.roslin.ensembl.exception.DAOException extends EnsemblException implements Serializable

serialVersionUID: 1L

Class uk.ac.roslin.ensembl.exception.EnsemblException extends Exception implements Serializable

Class uk.ac.roslin.ensembl.exception.RangeException extends EnsemblException implements Serializable


Package uk.ac.roslin.ensembl.model

Class uk.ac.roslin.ensembl.model.Coordinate extends Object implements Serializable

Serialized Fields

start

Integer start

end

Integer end

strand

Coordinate.Strand strand

strandInt

Integer strandInt

Class uk.ac.roslin.ensembl.model.CoordinateSet extends TreeSet<Coordinate> implements Serializable

Class uk.ac.roslin.ensembl.model.Mapping extends Object implements Serializable

Serialized Fields

source

MappableObject source

target

MappableObject target

sourceCoordinates

Coordinate sourceCoordinates

targetCoordinates

Coordinate targetCoordinates

sourceCoordSystem

CoordinateSystem sourceCoordSystem

targetCoordSystem

CoordinateSystem targetCoordSystem

reverseMapping

Mapping reverseMapping

Class uk.ac.roslin.ensembl.model.MappingSet extends TreeSet<Mapping> implements Serializable


Package uk.ac.roslin.ensembl.model.compara

Class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties extends Object implements Serializable

Serialized Fields

cigarLine

String cigarLine

peptideID

String peptideID

geneID

String geneID

speciesName

String speciesName

cigarStart

Integer cigarStart

cigarEnd

Integer cigarEnd

percentCovered

Integer percentCovered

percentIdentity

Integer percentIdentity

percentSimilar

Integer percentSimilar

coords

Coordinate coords

sequenceName

String sequenceName

Class uk.ac.roslin.ensembl.model.compara.HomologyType extends RelationshipType implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException
Ensure Singleton class

Throws:
ObjectStreamException

Package uk.ac.roslin.ensembl.model.core

Package uk.ac.roslin.ensembl.model.database

Package uk.ac.roslin.ensembl.model.relationship

Class uk.ac.roslin.ensembl.model.relationship.RelationshipType extends EnsemblType implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException
Ensure Singleton class

Throws:
ObjectStreamException


Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3