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java.lang.Objectorg.biojava.utils.Unchangeable
org.biojava.bio.program.das.DASSequenceDB
public class DASSequenceDB
Collection of sequences retrieved from the DAS network.
The DAS-specific parts of this API are still subject to change.
Field Summary |
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Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite |
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SEQUENCES |
Constructor Summary | |
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DASSequenceDB(URL dataSourceURL)
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Method Summary | |
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void |
addSequence(Sequence seq)
Adds a sequence to the database. |
SequenceDBLite |
allEntryPointsDB()
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FeatureHolder |
filter(FeatureFilter ff)
Query features attached to all sequences in this database. |
String |
getName()
Get the name of this sequence database. |
Sequence |
getSequence(String id)
Retrieve a single sequence by its id. |
URL |
getURL()
Return the URL of the reference server for this database. |
Set |
ids()
Get an immutable set of all of the IDs in the database. |
void |
removeSequence(String id)
Remove the sequence associated with an ID from the database. |
SequenceIterator |
sequenceIterator()
Returns a SequenceIterator over all sequences in the database. |
Methods inherited from class org.biojava.utils.Unchangeable |
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addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
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public DASSequenceDB(URL dataSourceURL) throws BioException
BioException
Method Detail |
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public FeatureHolder filter(FeatureFilter ff)
SequenceDB
filter
to all
sequences then merging the results.
filter
in interface SequenceDB
ff
- a FeatureFilter
.public SequenceDBLite allEntryPointsDB()
public URL getURL()
public String getName()
SequenceDBLite
getName
in interface SequenceDBLite
public Sequence getSequence(String id) throws BioException, IllegalIDException
SequenceDBLite
getSequence
in interface SequenceDBLite
id
- the id to retrieve by
IllegalIDException
- if the database doesn't know about the id
BioException
- if there was a failure in retrieving the sequencepublic Set ids()
SequenceDB
ids
in interface SequenceDB
public void addSequence(Sequence seq) throws ChangeVetoException
SequenceDBLite
addSequence
in interface SequenceDBLite
seq
- the Sequence to add
ChangeVetoException
- if either the database does not allow
sequences to be added or the modification was vetoedpublic void removeSequence(String id) throws ChangeVetoException
SequenceDBLite
removeSequence
in interface SequenceDBLite
id
- the ID of the sequence to remove
ChangeVetoException
- if either the database does not allow
sequences to be removed or the modification was vetoedpublic SequenceIterator sequenceIterator()
SequenceDB
sequenceIterator
in interface SequenceDB
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