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## org.ensembl.driver
Interface DnaDnaAlignmentAdaptor

All Superinterfaces:
  Adaptor, FeatureAdaptor, java.rmi.Remote

public interface DnaDnaAlignmentAdaptor
extends FeatureAdaptor

Provides access to DnaDnaAlignments in a datasource.

Field Summary
`static java.lang.String` | `TYPE` Name of the default DnaDnaAlignmentAdaptor available from a driver.

Method Summary
`void` | `delete(DnaDnaAlignment alignment)`
`void` | `delete(long internalID)`
`java.util.List` | `fetch(Location location)` Fetches features that overlap with location.
`java.util.List` | `fetch(Location location, Analysis analysis)`
`java.util.List` | `fetch(Location location, Analysis[] analyses)`
`java.util.List` | `fetch(Location location, java.lang.String logicalName)`
`java.util.List` | `fetch(Location location, java.lang.String[] logicalNames)`
`DnaDnaAlignment` | `fetch(long internalID)`
`java.util.List` | `fetch(java.lang.String logicalName)`
`long` | `store(DnaDnaAlignment feature)` Stores the feature in the approriate data source.

Methods inherited from interface org.ensembl.driver.FeatureAdaptor
`convertLocations, fetch, fetch, fetch, fetchAll, fetchAll, fetchCount, fetchInternalIDs, fetchInternalIDs, fetchIterator, fetchIterator, fetchIterator, fetchIterator, fetchIterator, fetchIterator, fetchIterator, fetchIterator, fetchIterator`

Methods inherited from interface org.ensembl.driver.Adaptor
`clearCache, closeAllConnections, getType`

Field Detail

### TYPE

    public static final java.lang.String TYPE

  Name of the default DnaDnaAlignmentAdaptor available from a driver.

  See Also:
    Constant Field Values

Method Detail

### store

    public long store(DnaDnaAlignment feature)
               throws AdaptorException

  Stores the feature in the approriate data source.

  Throws:
    `AdaptorException`

### fetch

    public DnaDnaAlignment fetch(long internalID)
                          throws AdaptorException

  Returns:
    A feature matching the internalID, or null if non found.
  Throws:
    `AdaptorException`

### fetch

    public java.util.List fetch(Location location)
                         throws AdaptorException

  Description copied from interface: `FeatureAdaptor`
  Fetches features that overlap with location.

  Specified by:
    `fetch` in interface `FeatureAdaptor`
  Parameters:
    `location` - location filter.
  Returns:
    A list of features inside the Location. An empty List is returned if non found.
  Throws:
    `AdaptorException`
  See Also:
    `if you want to include child data.`

### fetch

    public java.util.List fetch(Location location,
                                Analysis analysis)
                         throws AdaptorException

  Returns:
    A list of features inside the Location, and filtered by the Analysis. An empty List is returned if non found.
  Throws:
    `AdaptorException`

### fetch

    public java.util.List fetch(Location location,
                                Analysis[] analyses)
                         throws AdaptorException

  Returns:
    A list of features inside the Location, and filtered by the Analyses. An empty List is returned if non found.
  Throws:
    `AdaptorException`

### fetch

    public java.util.List fetch(Location location,
                                java.lang.String logicalName)
                         throws AdaptorException

  Returns:
    A list of features inside the Location of type "logicName". An empty List is returned if non found.
  Throws:
    `AdaptorException`

### fetch

    public java.util.List fetch(java.lang.String logicalName)
                         throws AdaptorException

  Returns:
    A feature matching the logicalName, or null if non found.
  Throws:
    `AdaptorException`

### fetch

    public java.util.List fetch(Location location,
                                java.lang.String[] logicalNames)
                         throws AdaptorException

  Returns:
    A list of features inside the Location with a type specified in "locicNames". An empty List is returned if non found.
  Throws:
    `AdaptorException`

### delete

    public void delete(long internalID)
                throws AdaptorException

  Parameters:
    `internalID` - internalID of alignmet to be deleted from database.
  Throws:
    `AdaptorException` - if an adaptor error occurs

### delete

    public void delete(DnaDnaAlignment alignment)
                throws AdaptorException

  Parameters:
    `alignment` - alignment to be deleted.
  Throws:
    `AdaptorException` - if an adaptor error occurs

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