Interface SequenceBuilder

All Superinterfaces:
SeqIOListener
All Known Subinterfaces:
RichSequenceBuilder
All Known Implementing Classes:
EmblProcessor, FastaDescriptionLineParser, GenbankProcessor, OrganismParser, ProteinRefSeqProcessor, SequenceBuilderBase, SequenceBuilderFilter, SequenceDBSequenceBuilder, SimpleAssemblyBuilder, SimpleRichSequenceBuilder, SimpleSequenceBuilder, SmartSequenceBuilder, SwissprotProcessor

public interface SequenceBuilder extends SeqIOListener
Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.

It is possible to build `transducer' objects which implement this interface and pass on filtered notifications to a second, underlying SequenceBuilder. In this case, they should provide a makeSequence method which delegates to the underlying SequenceBuilder.

Note: These are one-shot objects that can be used just once to make one sequence. After that, they should be discarded. The usual way to get a supply of these is via a SequenceBuilderFactory. More functionality is offered by the RichSequenceBuilder.
Since:
1.1 [newio proposal]
Author:
Thomas Down
See Also:
  • Method Details

    • makeSequence

      Return the Sequence object which has been constructed by this builder. This method is only expected to succeed after the endSequence() notifier has been called.
      Throws:
      BioException