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# Serialized Form

Package org.ensembl.compara.driver

Class org.ensembl.compara.driver.FatalException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1l

Class org.ensembl.compara.driver.NonFatalException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1l

Package org.ensembl.datamodel

Class org.ensembl.datamodel.AssemblyException extends org.ensembl.datamodel.impl.BaseFeatureImpl implements Serializable

serialVersionUID: 1l

Serialized Fields

### target

    Location target

### type

    java.lang.String type

Class org.ensembl.datamodel.AssemblyLocation extends Location implements Serializable

serialVersionUID: 1l

Serialized Fields

### next

    AssemblyLocation next

  Deprecated.

### chromosome

    java.lang.String chromosome

  Deprecated.

### chromosomeAsInt

    int chromosomeAsInt

  Deprecated.
  Cached int representation of chromosome.

Class org.ensembl.datamodel.AttributeException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1l

Class org.ensembl.datamodel.CloneFragmentLocation extends Location implements Serializable

serialVersionUID: 1l

Serialized Fields

### cloneFragmentInternalID

    long cloneFragmentInternalID

### next

    CloneFragmentLocation next

Class org.ensembl.datamodel.CoordinateSystem extends org.ensembl.datamodel.impl.PersistentImpl implements Serializable

serialVersionUID: 1l

Serialized Fields

### name

    java.lang.String name

### version

    java.lang.String version

### rank

    int rank

### defaultStatus

    boolean defaultStatus

### sequenceLevel

    boolean sequenceLevel

### hash

    int hash

### complete

    boolean complete

Class org.ensembl.datamodel.InvalidLocationException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1l

Class org.ensembl.datamodel.Location extends java.lang.Object implements Serializable

serialVersionUID: 1l

Serialized Fields

### cs

    CoordinateSystem cs

### start

    int start

### end

    int end

### strand

    int strand

### gap

    boolean gap

### next

    Location next

### seqRegionName

    java.lang.String seqRegionName

### segRegionID

    long segRegionID

### sequenceRegion

    SequenceRegion sequenceRegion

Class org.ensembl.datamodel.Query extends java.lang.Object implements Serializable

serialVersionUID: 1l

Serialized Fields

### location

    Location location

  Deprecated.

### internalID

    long internalID

  Deprecated.

### internalIDs

    long[] internalIDs

  Deprecated.

### accessionID

    java.lang.String accessionID

  Deprecated.

### type

    java.lang.String type

  Deprecated.

### includeSequence

    boolean includeSequence

  Deprecated.

### loadChildren

    boolean loadChildren

  Deprecated.

Package org.ensembl.driver

Class org.ensembl.driver.AdaptorException extends java.rmi.RemoteException implements Serializable

serialVersionUID: 1l

Class org.ensembl.driver.ConfigurationException extends AdaptorException implements Serializable

serialVersionUID: 1l

Class org.ensembl.driver.RuntimeAdaptorException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1l

Package org.ensembl.util

Class org.ensembl.util.FrequencyCounter extends java.util.HashMap implements Serializable

serialVersionUID: 1l

Class org.ensembl.util.IDMap extends java.util.HashMap implements Serializable

serialVersionUID: 1l

Class org.ensembl.util.IDSet extends LongSet implements Serializable

serialVersionUID: 1l

Class org.ensembl.util.LocatableList extends java.util.LinkedList implements Serializable

serialVersionUID: 1l

Serialized Fields

### result

    long[] result

Class org.ensembl.util.LongSet extends java.util.HashSet implements Serializable

serialVersionUID: 1l

Serialized Fields

### arrayCache

    long[] arrayCache

### sorted

    boolean sorted

Class org.ensembl.util.MethodNotSupportedException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1l

Class org.ensembl.util.NotImplementedYetException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1l

Class org.ensembl.util.PersistentSet extends java.lang.Object implements Serializable

serialVersionUID: 1l

Serialized Fields

### map

    IDMap map

Class org.ensembl.util.Timer extends java.lang.Object implements Serializable

serialVersionUID: 1l

Serialized Fields

### running

    boolean running

### duration

    long duration

### startTime

    long startTime

### paranoid

    boolean paranoid

Package org.ensembl.variation.datamodel

Class org.ensembl.variation.datamodel.AlleleConsequence extends org.ensembl.datamodel.impl.LocatableImpl implements Serializable

serialVersionUID: 1l

Serialized Fields

### type

    java.lang.String type

### spliceSite

    java.lang.String spliceSite

### location

    Location location

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