AbstractBioEntryDB (BioJava-1.5-beta API)
Keywords: org.biojavax.bio.db.AbstractBioEntryDB class

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## org.biojavax.bio.db
Class AbstractBioEntryDB

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojavax.bio.db.AbstractBioEntryDB

All Implemented Interfaces:
  Changeable, BioEntryDB, BioEntryDBLite

Direct Known Subclasses:
  AbstractRichSequenceDB, BioSQLBioEntryDB, HashBioEntryDB

    public abstract class AbstractBioEntryDB

extends AbstractChangeable
implements BioEntryDB

An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.

Since:
  1.5
Author:
  Matthew Pocock, Thomas Down, Richard Holland

Field Summary

Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite
`BIOENTRYS`

Constructor Summary
`AbstractBioEntryDB()`

Method Summary
`void` | `addBioEntry(BioEntry seq)` Adds a sequence to the database.
`BioEntryIterator` | `getBioEntryIterator()` Returns a BioEntryIterator over all BioEntrys in the database.
`void` | `removeBioEntry(String id)` Remove the BioEntry associated with an ID from the database.

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Methods inherited from interface org.biojavax.bio.db.BioEntryDB
`ids`

Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite
`getBioEntry, getBioEntrys, getBioEntrys, getName`

Constructor Detail

### AbstractBioEntryDB

    public AbstractBioEntryDB()

Method Detail

### addBioEntry

    public void addBioEntry(BioEntry seq)
                     throws IllegalIDException,
                            BioException,
                            ChangeVetoException

  Description copied from interface: `BioEntryDBLite`
  Adds a sequence to the database.

  Specified by:
    `addBioEntry` in interface `BioEntryDBLite`
  Parameters:
    `seq` - the BioEntry to add
  Throws:
    `IllegalIDException` - if a uniqe ID could not be generated for BioEntry
    `BioException` - if something goes wrong with adding the BioEntry
    `ChangeVetoException` - if either the database does not allow BioEntrys to be added or the modification was vetoed

### removeBioEntry

    public void removeBioEntry(String id)
                        throws IllegalIDException,
                               BioException,
                               ChangeVetoException

  Description copied from interface: `BioEntryDBLite`
  Remove the BioEntry associated with an ID from the database.

  Specified by:
    `removeBioEntry` in interface `BioEntryDBLite`
  Parameters:
    `id` - the ID of the BioEntry to remove
  Throws:
    `IllegalIDException` - if there is no BioEntry for the ID
    `BioException` - if something failed while removing the BioEntry for that ID
    `ChangeVetoException` - if either the database does not allow BioEntrys to be removed or the modification was vetoed

### getBioEntryIterator

    public BioEntryIterator getBioEntryIterator()

  Description copied from interface: `BioEntryDB`
  Returns a BioEntryIterator over all BioEntrys in the database. The order of retrieval is undefined.

  Specified by:
    `getBioEntryIterator` in interface `BioEntryDB`
  Returns:
    a BioEntryIterator over all BioEntrys

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