Package org.biojavax.bio.db
Class AbstractRichSequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojavax.bio.db.AbstractBioEntryDB
org.biojavax.bio.db.AbstractRichSequenceDB
- All Implemented Interfaces:
SequenceDB
,SequenceDBLite
,Changeable
,BioEntryDB
,BioEntryDBLite
,RichSequenceDB
,RichSequenceDBLite
- Direct Known Subclasses:
BioSQLRichSequenceDB
,GenbankRichSequenceDB
,GenpeptRichSequenceDB
,HashRichSequenceDB
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator
method.
- Since:
- 1.5
- Author:
- Matthew Pocock, Thomas Down, Richard Holland
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Field Summary
Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite
BIOENTRYS
Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addBioEntry
(BioEntry seq) Adds a sequence to the database.void
Adds a sequence to the database.void
addSequence
(Sequence seq) Adds a sequence to the database.filter
(FeatureFilter ff) Query features attached to all sequences in this database.getBioEntry
(String id) Retrieve a single BioEntry by its id.Returns a BioEntryIterator over all BioEntrys in the database.getBioEntrys
(Set ids) Retrieve multiple BioEntry by their ids.getBioEntrys
(Set ids, BioEntryDB db) Retrieve multiple BioEntry into a specific sequence database.Returns a RichSequenceIterator over all sequences in the database.getSequence
(String id) Retrieve a single sequence by its id.void
removeBioEntry
(String id) Remove the BioEntry associated with an ID from the database.void
Remove the RichSequence associated with an ID from the database.void
removeSequence
(String id) Remove the sequence associated with an ID from the database.Returns a SequenceIterator over all sequences in 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
getName
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite
getRichSequence, getRichSequences, getRichSequences
Methods inherited from interface org.biojava.bio.seq.db.SequenceDB
ids
Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
getName
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Constructor Details
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AbstractRichSequenceDB
public AbstractRichSequenceDB()
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Method Details
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getSequence
Description copied from interface:SequenceDBLite
Retrieve a single sequence by its id.- Specified by:
getSequence
in interfaceSequenceDBLite
- Parameters:
id
- the id to retrieve by- Returns:
- the Sequence with that id
- Throws:
BioException
- if there was a failure in retrieving the sequenceIllegalIDException
- if the database doesn't know about the id
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getBioEntry
Description copied from interface:BioEntryDBLite
Retrieve a single BioEntry by its id.- Specified by:
getBioEntry
in interfaceBioEntryDBLite
- Parameters:
id
- the id to retrieve by- Returns:
- the BioEntry with that id
- Throws:
BioException
- if there was a failure in retrieving the BioEntryIllegalIDException
- if the database doesn't know about the id
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getBioEntrys
Description copied from interface:BioEntryDBLite
Retrieve multiple BioEntry by their ids.- Specified by:
getBioEntrys
in interfaceBioEntryDBLite
- Parameters:
ids
- a set of ids to retrieve by- Returns:
- the BioEntrys with those ids
- Throws:
IllegalIDException
- if the database doesn't know about the idBioException
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getBioEntrys
Description copied from interface:BioEntryDBLite
Retrieve multiple BioEntry into a specific sequence database. If that database is null, a new HashBioEntryDB is used.- Specified by:
getBioEntrys
in interfaceBioEntryDBLite
- Parameters:
ids
- a set of ids to retrieve bydb
- a database to load the seqs into- Returns:
- the BioEntrys with that id
- Throws:
IllegalIDException
- if the database doesn't know about the idBioException
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addSequence
Description copied from interface:SequenceDBLite
Adds a sequence to the database.- Specified by:
addSequence
in interfaceSequenceDBLite
- Parameters:
seq
- the Sequence to add- Throws:
IllegalIDException
- if a uniqe ID could not be generated for seqBioException
- if something goes wrong with adding the sequenceChangeVetoException
- if either the database does not allow sequences to be added or the modification was vetoed
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removeSequence
Description copied from interface:SequenceDBLite
Remove the sequence associated with an ID from the database.- Specified by:
removeSequence
in interfaceSequenceDBLite
- Parameters:
id
- the ID of the sequence to remove- Throws:
IllegalIDException
- if there is no sequence for the IDBioException
- if something failed while removing the sequence for that IDChangeVetoException
- if either the database does not allow sequences to be removed or the modification was vetoed
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addBioEntry
Description copied from interface:BioEntryDBLite
Adds a sequence to the database.- Specified by:
addBioEntry
in interfaceBioEntryDBLite
- Overrides:
addBioEntry
in classAbstractBioEntryDB
- Parameters:
seq
- the BioEntry to add- Throws:
IllegalIDException
- if a uniqe ID could not be generated for BioEntryBioException
- if something goes wrong with adding the BioEntryChangeVetoException
- if either the database does not allow BioEntrys to be added or the modification was vetoed
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removeBioEntry
Description copied from interface:BioEntryDBLite
Remove the BioEntry associated with an ID from the database.- Specified by:
removeBioEntry
in interfaceBioEntryDBLite
- Overrides:
removeBioEntry
in classAbstractBioEntryDB
- Parameters:
id
- the ID of the BioEntry to remove- Throws:
IllegalIDException
- if there is no BioEntry for the IDBioException
- if something failed while removing the BioEntry for that IDChangeVetoException
- if either the database does not allow BioEntrys to be removed or the modification was vetoed
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addRichSequence
public void addRichSequence(RichSequence seq) throws IllegalIDException, BioException, ChangeVetoException Description copied from interface:RichSequenceDBLite
Adds a sequence to the database.- Specified by:
addRichSequence
in interfaceRichSequenceDBLite
- Parameters:
seq
- the RichSequence to add- Throws:
IllegalIDException
- if a uniqe ID could not be generated for RichSequenceBioException
- if something goes wrong with adding the RichSequenceChangeVetoException
- if either the database does not allow RichSequences to be added or the modification was vetoed
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removeRichSequence
public void removeRichSequence(String id) throws IllegalIDException, BioException, ChangeVetoException Description copied from interface:RichSequenceDBLite
Remove the RichSequence associated with an ID from the database.- Specified by:
removeRichSequence
in interfaceRichSequenceDBLite
- Parameters:
id
- the ID of the RichSequence to remove- Throws:
IllegalIDException
- if there is no RichSequence for the IDBioException
- if something failed while removing the RichSequence for that IDChangeVetoException
- if either the database does not allow RichSequences to be removed or the modification was vetoed
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sequenceIterator
Description copied from interface:RichSequenceDB
Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined. Will always return an instance of RichSequenceIterator.- Specified by:
sequenceIterator
in interfaceRichSequenceDB
- Specified by:
sequenceIterator
in interfaceSequenceDB
- Returns:
- a SequenceIterator over all sequences
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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 interfaceBioEntryDB
- Overrides:
getBioEntryIterator
in classAbstractBioEntryDB
- Returns:
- a BioEntryIterator over all BioEntrys
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getRichSequenceIterator
Description copied from interface:RichSequenceDB
Returns a RichSequenceIterator over all sequences in the database. The order of retrieval is undefined.- Specified by:
getRichSequenceIterator
in interfaceRichSequenceDB
- Returns:
- a RichSequenceIterator over all sequences
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filter
Description copied from interface:SequenceDB
Query features attached to all sequences in this database. This is equivalent to applyingfilter
to all sequences then merging the results.- Specified by:
filter
in interfaceSequenceDB
- Parameters:
ff
- aFeatureFilter
.
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