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

Constructors

Constructor and Description
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

Methods

Modifier and Type	Method and Description
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