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## Deprecated API

Deprecated Classes
org.ensembl.datamodel.AssemblyLocation Create instances of Location directly. The specific location types such as AssemblyLocation have been superseded by the more generic Location class.
org.ensembl.datamodel.Query since version 27.0

Deprecated Interfaces
org.ensembl.driver.Driver Deprecated in version 29.2, use org.ensembl.driver.CoreDriver instead.

Deprecated Methods
org.ensembl.driver.TranscriptAdaptor.fetch(Query) use more specific fetch methods
org.ensembl.driver.ExonAdaptor.fetch(Query) since version 27.0 use other fetch(...) methods.
org.ensembl.driver.GeneAdaptor.fetch(Query) since version 27.0. Use other fetch(...) methods instead.
org.ensembl.datamodel.Gene.getConfidence() since version 34.1. Use getStatus() instead.
org.ensembl.datamodel.Transcript.getConfidence() since version 34.1. Use getStatus() instead.
org.ensembl.datamodel.Location.getGap() Since ensj28.3. Use getLength() instead.
org.ensembl.datamodel.Gene.getType() since ensj34.2 use getBioType() instead.
org.ensembl.driver.EnsemblDriver.isConnected() Since ensj 30.3. Use testConnection() instead.
org.ensembl.datamodel.CloneFragmentLocation.reverse() use complement, reverse is not biological meaningful
org.ensembl.datamodel.CoordinateSystem.setDefault(boolean) set this value in the appropriate constructor instead
org.ensembl.datamodel.CoordinateSystem.setName(String) set this value in the appropriate constructor instead
org.ensembl.datamodel.CoordinateSystem.setRank(int) set this value in the appropriate constructor instead
org.ensembl.datamodel.CoordinateSystem.setSequenceLevel(boolean) set this value in the appropriate constructor instead
org.ensembl.datamodel.CoordinateSystem.setVersion(String) set this value in the appropriate constructor instead

Deprecated Constructors
org.ensembl.datamodel.CoordinateSystem() use another constructor.
org.ensembl.datamodel.CoordinateSystem(String, String, boolean) use another constructor.
org.ensembl.datamodel.CoordinateSystem(String, String, boolean, long) use another constructor.

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