Class SequenceBuilderFilter

Method Details

• getDelegate

  public SequenceBuilder getDelegate()

  Retrieve the delegate that is wrapped.

  Returns:

  the SequenceBuilder delegate

• startSequence

  public void startSequence() throws ParseException

  Description copied from interface: SeqIOListener

  Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.

  Specified by:

  startSequence in interface SeqIOListener

  Throws:

  ParseException

• endSequence

  public void endSequence() throws ParseException

  Description copied from interface: SeqIOListener

  Notify the listener that processing of the sequence is complete.

  Specified by:

  endSequence in interface SeqIOListener

  Throws:

  ParseException

• setName

  public void setName(String name) throws ParseException

  Description copied from interface: SeqIOListener

  Notify the listener that the current sequence is generally known by a particular name.

  Specified by:

  setName in interface SeqIOListener

  Parameters:

  name - the String that should be returned by getName for the sequence being parsed

  Throws:

  ParseException

• setURI

  public void setURI(String uri) throws ParseException

  Description copied from interface: SeqIOListener

  Notify the listener of a URI identifying the current sequence.

  Specified by:

  setURI in interface SeqIOListener

  Throws:

  ParseException

• addSymbols

  public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException

  Description copied from interface: SeqIOListener

  Notify 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:

  addSymbols in interface SeqIOListener

  Parameters:

  alpha - The alphabet of the symbol data

  syms - An array containing symbols

  start - The start offset of valid data within the array

  length - The number of valid symbols in the array

  Throws:

  IllegalAlphabetException - if we can't cope with this alphabet.

• addSequenceProperty

  public void addSequenceProperty(Object key, Object value) throws ParseException

  Description copied from interface: SeqIOListener

  Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.

  Specified by:

  addSequenceProperty in interface SeqIOListener

  Throws:

  ParseException

• startFeature

  public void startFeature(Feature.Template templ) throws ParseException

  Description copied from interface: SeqIOListener

  Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.

  Specified by:

  startFeature in interface SeqIOListener

  Throws:

  ParseException

• endFeature

  public void endFeature() throws ParseException

  Description copied from interface: SeqIOListener

  Mark the end of data associated with one specific feature.

  Specified by:

  endFeature in interface SeqIOListener

  Throws:

  ParseException

• addFeatureProperty

  public void addFeatureProperty(Object key, Object value) throws ParseException

  Description copied from interface: SeqIOListener

  Notify the listener of a feature property.

  Specified by:

  addFeatureProperty in interface SeqIOListener

  Throws:

  ParseException

• makeSequence

  public Sequence makeSequence() throws BioException

  Description copied from interface: SequenceBuilder

  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.

  Specified by:

  makeSequence in interface SequenceBuilder

  Throws:

  BioException