public class SmartSequenceBuilder extends SequenceBuilderBaseBasic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence. This may or may not bit-encode the symbols (using PackedSymbolList), and may or may not store the symbols in multiple fixed-length chunks (using ChunkedSymbolList).
More functionality is offered by
SimpleRichSequenceBuilder, Use of this class is prefered.
- David Huen, Matthew Pocock
All Methods Instance Methods Concrete Methods Modifier and Type Method Description
addSymbols(Alphabet alpha, Symbol syms, int pos, int len)Notify the listener of symbol data.
makeSequence()Return the Sequence object which has been constructed by this builder.
Methods inherited from class org.biojava.bio.seq.io.SequenceBuilderBase
addFeatureProperty, addProperty, addSequenceProperty, endFeature, endSequence, setName, setURI, startFeature, startSequence
public void addSymbols(Alphabet alpha, Symbol syms, int pos, int len) throws IllegalAlphabetExceptionDescription copied from interface:
SeqIOListenerNotify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception
- Specified by:
- Specified by:
alpha- The alphabet of the symbol data
syms- An array containing symbols
pos- The start offset of valid data within the array
len- The number of valid symbols in the array
IllegalAlphabetException- if we can't cope with this alphabet.
public Sequence makeSequence() throws BioExceptionDescription copied from interface:
SequenceBuilderReturn the Sequence object which has been constructed by this builder. This method is only expected to succeed after the endSequence() notifier has been called.