Class SimpleRichSequenceBuilder

java.lang.Object
org.biojavax.bio.seq.io.RichSeqIOAdapter
org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
All Implemented Interfaces:
SeqIOListener, SequenceBuilder, RichSeqIOListener, RichSequenceBuilder

Constructs BioEntry objects by listening to events.
Since:
1.5
Author:
Richard Holland, George Waldon
  • Field Summary

    Fields inherited from class org.biojavax.bio.seq.io.RichSeqIOAdapter

    emptyFeature
  • Constructor Summary

    Constructors
    Constructor
    Description
    Creates a new instance of SimpleRichSequenceBuilder using a SimpleSymbolListFactory with a threshold of zero.
    Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold of zero.
    Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold.
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Notify the listener of a feature property.
    void
    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
    Mark the end of data associated with one specific feature.
    void
    Notify the listener that processing of the sequence is complete.
    Gets the feature currently being created.
    Build a RichSequence.
    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
    Notify the listener that the current sequence is generally known by a particular name.
    void
    Call back method so the event emitter can tell the listener the namespace of the record being read.
    void
    Call back method so the event emitter can tell the listener about a cross reference.
    void
    Call back method so the event emitter can tell the listener about a literature reference in the record being read.
    void
    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
    Call back method so the event emitter can tell the listener the Taxon of the record being read.
    void
    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
    Notify the listener that a new feature object is starting.
    void
    Start the processing of a sequence.

    Methods inherited from class java.lang.Object

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