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## org.biojava.bio.seq.db
Class IndexedSequenceDB

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.seq.db.AbstractSequenceDB
              org.biojava.bio.seq.db.IndexedSequenceDB

All Implemented Interfaces:
  Serializable, SequenceDB, SequenceDBLite, Changeable

    public final class IndexedSequenceDB

extends AbstractSequenceDB
implements SequenceDB, Serializable

This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.

This class is primarily responsible for managing the sequence IO, such as calculating the sequence file offsets, and parsing individual sequences based upon file offsets. The actual persistant storage of all this information is delegated to an instance of `IndexStore`, such as TabIndexStore.

     // create a new index store and populate it
     // this may take some time
     TabIndexStore indexStore = new TabIndexStore(
       storeFile, indexFile, dbName,
       format, sbFactory, symbolParser );
     IndexedSequenceDB seqDB = new IndexedSequenceDB(indexStore);

     for(int i = 0; i < files; i++) {
       seqDB.addFile(files[i]);
     }

     // load an existing index store and fetch a sequence
     // this should be quite quick
     TabIndexStore indexStore = TabIndexStore.open(storeFile);
     SequenceDB seqDB = new IndexedSequenceDB(indexStore);
     Sequence seq = seqDB.getSequence(id);

Note: We may be able to improve the indexing speed further by discarding all feature creation & annotation requests during index parsing.

Author:
  Matthew Pocock, Thomas Down, Keith James
See Also:
  `TabIndexStore`, Serialized Form

Field Summary

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
`SEQUENCES`

Constructor Summary
`IndexedSequenceDB(IDMaker idMaker, IndexStore indexStore)` Create an IndexedSequenceDB by specifying both the IDMaker and IndexStore used.
`IndexedSequenceDB(IndexStore indexStore)` Create an IndexedSequenceDB by specifying IndexStore used.

Method Summary
`void` | `addFile(File seqFile)` Add sequences from a file to the sequence database.
`IndexStore` | `getIndexStore()` Retrieve the IndexStore.
`String` | `getName()` Get the name of this sequence database.
`Sequence` | `getSequence(String id)` Retrieve a single sequence by its id.
`Set` | `ids()` Get an immutable set of all of the IDs in the database.
`SequenceIterator` | `sequenceIterator()` Returns a SequenceIterator over all sequences in the database.

Methods inherited from class org.biojava.bio.seq.db.AbstractSequenceDB
`addSequence, filter, removeSequence`

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.biojava.bio.seq.db.SequenceDB
`filter`

Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
`addSequence, removeSequence`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Constructor Detail

### IndexedSequenceDB

    public IndexedSequenceDB(IDMaker idMaker,
                             IndexStore indexStore)

  Create an IndexedSequenceDB by specifying both the IDMaker and IndexStore used.

  The IDMaker will be used to calculate the ID for each Sequence. It will delegate the storage and retrieval of the sequence offsets to the IndexStore.

  Parameters:
    `idMaker` - the IDMaker used to calculate Sequence IDs
    `indexStore` - the IndexStore delegate

### IndexedSequenceDB

    public IndexedSequenceDB(IndexStore indexStore)

  Create an IndexedSequenceDB by specifying IndexStore used.

  IDMaker.byName will be used to calculate the ID for each Sequence. It will delegate the storage and retrieval of the sequence offsets to the IndexStore.

  Parameters:
    `indexStore` - the IndexStore delegate

Method Detail

### getIndexStore

    public IndexStore getIndexStore()

  Retrieve the IndexStore.

  Returns:
    the IndexStore delegate

### addFile

    public void addFile(File seqFile)
                 throws IllegalIDException,
                        BioException,
                        ChangeVetoException

  Add sequences from a file to the sequence database. This method works on an "all or nothing" principle. If it can successfully interpret the entire file, all the sequences will be read in. However, if it encounters any problems, it will abandon the whole file; an IOException will be thrown. Multiple files may be indexed into a single database. A BioException will be thrown if it has problems understanding the sequences.

  Parameters:
    `seqFile` - the file containing the sequence or set of sequences
  Throws:
    `BioException` - if for any reason the sequences can't be read correctly
    `ChangeVetoException` - if there is a listener that vetoes adding the files
    `IllegalIDException`

### getName

    public String getName()

  Get the name of this sequence database. The name is retrieved from the IndexStore delegate.

  Specified by:
    `getName` in interface `SequenceDBLite`
  Returns:
    the name of the sequence database, which may be null.

### getSequence

    public Sequence getSequence(String id)
                         throws IllegalIDException,
                                BioException

  Description copied from interface: `SequenceDBLite`
  Retrieve a single sequence by its id.

  Specified by:
    `getSequence` in interface `SequenceDBLite`
  Parameters:
    `id` - the id to retrieve by
  Returns:
    the Sequence with that id
  Throws:
    `IllegalIDException` - if the database doesn't know about the id
    `BioException` - if there was a failure in retrieving the sequence

### sequenceIterator

    public SequenceIterator sequenceIterator()

  Description copied from interface: `SequenceDB`
  Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.

  Specified by:
    `sequenceIterator` in interface `SequenceDB`
  Overrides:
    `sequenceIterator` in class `AbstractSequenceDB`
  Returns:
    a SequenceIterator over all sequences

### ids

    public Set ids()

  Description copied from interface: `SequenceDB`
  Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.

  Specified by:
    `ids` in interface `SequenceDB`
  Returns:
    a Set of ids - at the moment, strings

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