Class SimpleRichSequenceBuilder

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addFeatureProperty​(Object key, Object value)
      Notify the listener of a feature property.
      void addSequenceProperty​(Object key, Object value)
      Notify the listener of a sequence-wide property.
      void addSymbols​(Alphabet alpha, Symbol[] syms, int start, int length)
      Notify the listener of symbol data.
      void endFeature()
      Mark the end of data associated with one specific feature.
      void endSequence()
      Notify the listener that processing of the sequence is complete.
      RichFeature getCurrentFeature()
      Gets the feature currently being created.
      RichSequence makeRichSequence()
      Build a RichSequence.
      Sequence makeSequence()
      Return the Sequence object which has been constructed by this builder.
      void setAccession​(String accession)
      Call back method so the event emitter can tell the listener the accession of the record being read.
      void setCircular​(boolean circular)
      Defined this sequence being parser as circular.
      void setComment​(String comment)
      Call back method so the event emitter can tell the listener about a comment in the record being read.
      void setDescription​(String description)
      Call back method so the event emitter can tell the listener the description of the record being read.
      void setDivision​(String division)
      Call back method so the event emitter can tell the listener the division of the record being read.
      void setIdentifier​(String identifier)
      Call back method so the event emitter can tell the listener the identifier of the record being read.
      void setName​(String name)
      Notify the listener that the current sequence is generally known by a particular name.
      void setNamespace​(Namespace namespace)
      Call back method so the event emitter can tell the listener the namespace of the record being read.
      void setRankedCrossRef​(RankedCrossRef ref)
      Call back method so the event emitter can tell the listener about a cross reference.
      void setRankedDocRef​(RankedDocRef ref)
      Call back method so the event emitter can tell the listener about a literature reference in the record being read.
      void setRelationship​(BioEntryRelationship relationship)
      Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
      void setSeqVersion​(String seqVersion)
      Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
      void setTaxon​(NCBITaxon taxon)
      Call back method so the event emitter can tell the listener the Taxon of the record being read.
      void setURI​(String uri)
      Notify the listener of a URI identifying the current sequence.
      void setVersion​(int version)
      Call back method so the event emitter can tell the listener the version of the record being read.
      void startFeature​(Feature.Template templ)
      Notify the listener that a new feature object is starting.
      void startSequence()
      Start the processing of a sequence.