Class EmblLikeFormat

  • All Implemented Interfaces:
    java.io.Serializable, java.util.EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

    public class EmblLikeFormat
    extends java.lang.Object
    implements SequenceFormat, java.io.Serializable, ParseErrorSource, ParseErrorListener
    Deprecated.
    Use org.biojavax.bio.seq.io.EMBLFormat instead

    Format processor for handling EMBL records and similar files. This takes a very simple approach: all `normal' attribute lines are passed to the listener as a tag (first two characters) and a value (the rest of the line from the 6th character onwards). Any data between the special `SQ' line and the "//" entry terminator is passed as a SymbolReader.

    This low-level format processor should normally be used in conjunction with one or more `filter' objects, such as EmblProcessor.

    Many ideas borrowed from the old EmblFormat processor by Thomas Down and Thad Welch.

    Since:
    1.1
    Author:
    Thomas Down, Greg Cox, Keith James, Len Trigg, Lorna Morris
    See Also:
    Serialized Form
    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected static java.lang.String ACCESSION_TAG
      Deprecated.
       
      protected static java.lang.String AUTHORS_TAG
      Deprecated.
       
      protected static java.lang.String CIRCULAR_TAG
      Deprecated.
       
      protected static java.lang.String COMMENT_TAG
      Deprecated.
       
      protected static java.lang.String COORDINATE_TAG
      Deprecated.
       
      protected static java.lang.String DATE_TAG
      Deprecated.
       
      static java.lang.String DEFAULT
      Deprecated.
       
      protected static java.lang.String DEFINITION_TAG
      Deprecated.
       
      protected static java.lang.String DIVISION_TAG
      Deprecated.
       
      protected static java.lang.String DR_TAG
      Deprecated.
       
      protected static java.lang.String END_SEQUENCE_TAG
      Deprecated.
       
      protected static java.lang.String FEATURE_TABLE_TAG
      Deprecated.
       
      protected static java.lang.String FEATURE_TAG
      Deprecated.
       
      protected static java.lang.String ID_TAG
      Deprecated.
       
      protected static java.lang.String JOURNAL_TAG
      Deprecated.
       
      protected static java.lang.String KEYWORDS_TAG
      Deprecated.
       
      protected static java.lang.String ORGANISM_TAG
      Deprecated.
       
      protected static java.lang.String ORGANISM_XREF_TAG
      Deprecated.
       
      protected static java.lang.String REF_ACCESSION_TAG
      Deprecated.
       
      protected static java.lang.String REF_XREF_TAG
      Deprecated.
       
      protected static java.lang.String REFERENCE_TAG
      Deprecated.
       
      protected static java.lang.String SEPARATOR_TAG
      Deprecated.
       
      protected static java.lang.String SIZE_TAG
      Deprecated.
       
      protected static java.lang.String SOURCE_TAG
      Deprecated.
       
      protected static java.lang.String START_SEQUENCE_TAG
      Deprecated.
       
      protected static java.lang.String STRAND_NUMBER_TAG
      Deprecated.
       
      protected static java.lang.String TITLE_TAG
      Deprecated.
       
      protected static java.lang.String TYPE_TAG
      Deprecated.
       
      protected static java.lang.String VERSION_TAG
      Deprecated.
       
    • Constructor Summary

      Constructors 
      Constructor Description
      EmblLikeFormat()
      Deprecated.