RichSequenceDB (biojava-legacy 1.9.5 API)

All Superinterfaces:

BioEntryDB, BioEntryDBLite, Changeable, RichSequenceDBLite, SequenceDB, SequenceDBLite

All Known Implementing Classes:

AbstractRichSequenceDB, BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB
```
public interface RichSequenceDB
extends SequenceDB, BioEntryDB, RichSequenceDBLite
```
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

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`RichSequenceIterator`	`getRichSequenceIterator()`	Returns a RichSequenceIterator over all sequences in the database.
`SequenceIterator`	`sequenceIterator()`	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 Detail
  - sequenceIterator
```
SequenceIterator 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 interface SequenceDB
    
    Returns:
    
    a SequenceIterator over all sequences
  - getRichSequenceIterator
```
RichSequenceIterator getRichSequenceIterator()
```
    Returns a RichSequenceIterator over all sequences in the database. The order of retrieval is undefined.
    
    Returns:
    
    a RichSequenceIterator over all sequences