org.biojava.bio.seq.io
Class SequenceDBSequenceBuilder
java.lang.Object
org.biojava.bio.seq.io.SequenceBuilderBase
org.biojava.bio.seq.io.SequenceDBSequenceBuilder
- All Implemented Interfaces:
- SeqIOListener, SequenceBuilder
public class SequenceDBSequenceBuilder
- extends SequenceBuilderBase
This SequenceBuilder has a variety of modes of operation.
It can take a sequence from an existing SequenceDB and
apply annotations to it.
If the SequenceDB has persistence, then it can also create
a sequence in the sequenceDB and apply the annotation to that.
However, performance under those circumstances can vary depending
on how well the persistent SequenceDB handles this.
Following the introduction of biojavax persistence is handled by
Hibernate refer to
BioSQLRichObjectBuilder
- Author:
- David Huen
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ANNOTATE_EXISTING
public static final int ANNOTATE_EXISTING
- See Also:
- Constant Field Values
CREATE_DUMMYSEQ
public static final int CREATE_DUMMYSEQ
- See Also:
- Constant Field Values
CREATE_REALSEQ
public static final int CREATE_REALSEQ
- See Also:
- Constant Field Values
SequenceDBSequenceBuilder
public SequenceDBSequenceBuilder(SequenceDB db,
int mode)
- constructor
addSymbols
public void addSymbols(Alphabet alpha,
Symbol[] syms,
int pos,
int len)
- does nothing for now.
- Specified by:
addSymbols
in interface SeqIOListener
- Specified by:
addSymbols
in class SequenceBuilderBase
- Parameters:
alpha
- The alphabet of the symbol datasyms
- An array containing symbolspos
- The start offset of valid data within the arraylen
- The number of valid symbols in the array
makeSequence
public Sequence makeSequence()
throws BioException
- create the sequence
- Specified by:
makeSequence
in interface SequenceBuilder
- Overrides:
makeSequence
in class SequenceBuilderBase
- Throws:
BioException