Package org.biojava.bio.seq.io

Class SequenceBuilderBase

java.lang.Object
org.biojava.bio.seq.io.SequenceBuilderBase
All Implemented Interfaces:
SeqIOListener, SequenceBuilder
Direct Known Subclasses:
SequenceDBSequenceBuilder, SimpleAssemblyBuilder, SimpleSequenceBuilder, SmartSequenceBuilder
public abstract class SequenceBuilderBase extends Object implements SequenceBuilder
Basic SequenceBuilder implementation which accumulates all notified information. Subclass this to implement specific Sequence implementations. More functionality is offered by the SimpleRichSequenceBuilder.
Version:
1.2 [newio proposal]
Author:
Thomas Down, David Huen (modified SimpleSequence to make this)

  • Field Details

  • Constructor Details

  • Method Details

    • startSequence

      public void startSequence()
      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

    • endSequence

      public void endSequence()
      Description copied from interface: SeqIOListener
      Notify the listener that processing of the sequence is complete.
      Specified by:
      endSequence in interface SeqIOListener

    • setName

      public void setName(String name)
      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

    • setURI

      public void setURI(String uri)
      Description copied from interface: SeqIOListener
      Notify the listener of a URI identifying the current sequence.
      Specified by:
      setURI in interface SeqIOListener

    • addSymbols

      public abstract void addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) 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
      pos - The start offset of valid data within the array
      len - 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)
      Add an annotation-bundle entry to the sequence. If the annotation key isn't currently defined, the value is added directly. Otherwise:
      • If the current value implements the Collection interface, the new value is added to that collection.
      • Otherwise, the current value is replaced by a List object containing the old value then the new value in that order.
      Specified by:
      addSequenceProperty in interface SeqIOListener

    • startFeature

      public void startFeature(Feature.Template templ)
      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

    • addFeatureProperty

      public void addFeatureProperty(Object key, Object value) throws ParseException
      Add an annotation-bundle entry to the feature. If the annotation key isn't currently defined, the value is added directly. Otherwise:
      • If the current value implements the Collection interface, the new value is added to that collection.
      • Otherwise, the current value is replaced by a List object containing the old value then the new value in that order.
      Specified by:
      addFeatureProperty in interface SeqIOListener
      Throws:
      ParseException

    • endFeature

      public void endFeature()
      Description copied from interface: SeqIOListener
      Mark the end of data associated with one specific feature.
      Specified by:
      endFeature in interface SeqIOListener

    • 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

    • addProperty

      protected void addProperty(Annotation ann, Object key, Object value)