Package org.biojavax.bio.db
Interface RichSequenceDB
- All Superinterfaces:
BioEntryDB
,BioEntryDBLite
,Changeable
,RichSequenceDBLite
,SequenceDB
,SequenceDBLite
- All Known Implementing Classes:
AbstractRichSequenceDB
,BioSQLRichSequenceDB
,GenbankRichSequenceDB
,GenpeptRichSequenceDB
,HashRichSequenceDB
A database of RichSequences with accessible keys and iterators over all
sequences.
This may have several implementations with rich behaviour, but basically most of the time you will just use the interface methods to do stuff. A sequence database contains a finite number of sequences stored under unique keys.
- Since:
- 1.5
- Author:
- Matthew Pocock, Gerald Loeffler, Thomas Down, Richard Holland
-
Field Summary
Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite
BIOENTRYS
Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
-
Method Summary
Modifier and TypeMethodDescriptionReturns a RichSequenceIterator over all sequences in the database.Returns a SequenceIterator over all sequences in the database.Methods inherited from interface org.biojavax.bio.db.BioEntryDB
getBioEntryIterator, ids
Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite
addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, getName, removeBioEntry
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite
addRichSequence, getRichSequence, getRichSequences, getRichSequences, removeRichSequence
Methods inherited from interface org.biojava.bio.seq.db.SequenceDB
filter, ids
Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
addSequence, getName, getSequence, removeSequence
-
Method Details
-
sequenceIterator
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 interfaceSequenceDB
- Returns:
- a SequenceIterator over all sequences
-
getRichSequenceIterator
Returns a RichSequenceIterator over all sequences in the database. The order of retrieval is undefined.- Returns:
- a RichSequenceIterator over all sequences
-