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SimpleAssemblyBuilder (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.bio.seq.io.SequenceBuilderBase
      • org.biojava.bio.seq.io.SimpleAssemblyBuilder
  • All Implemented Interfaces:
    SeqIOListener, SequenceBuilder
    public class SimpleAssemblyBuilder
extends SequenceBuilderBase

    Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.

    Version:
    1.2
    Author:
    David Huen

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static SequenceBuilderFactory FACTORY  

      • Fields inherited from class org.biojava.bio.seq.io.SequenceBuilderBase

        annotation, ERROR_FEATURES_PROPERTY, name, seq, uri

    • Constructor Summary

      Constructors 
      Constructor Description
      SimpleAssemblyBuilder()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      ComponentFeature addComponentSequence​(ComponentFeature.Template cft)  
      void addSymbols​(Alphabet alpha, Symbol[] syms, int pos, int len)

      Notify the listener of symbol data.
      Sequence 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

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • FACTORY

        public static final SequenceBuilderFactory FACTORY

    • Constructor Detail

      • SimpleAssemblyBuilder

        public SimpleAssemblyBuilder()

    • Method Detail

      • addSymbols

        public void addSymbols​(Alphabet alpha,
                       Symbol[] syms,
                       int pos,
                       int len)
                throws IllegalAlphabetException

        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
        Specified by:
        addSymbols in class SequenceBuilderBase
        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.

      • addComponentSequence

        public ComponentFeature addComponentSequence​(ComponentFeature.Template cft)
                                      throws BioException,
                                             ChangeVetoException
        Throws:
        BioException
        ChangeVetoException

      • makeSequence

        public Sequence makeSequence()
                      throws BioException

        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
        Overrides:
        makeSequence in class SequenceBuilderBase
        Throws:
        BioException