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.
- 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
makeSequence
public Sequence makeSequence()
- create the sequence
- Specified by:
makeSequence
in interface SequenceBuilder
- Overrides:
makeSequence
in class SequenceBuilderBase