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.
       
    • Field Detail

      • STRAND_NUMBER_TAG

        protected static final java.lang.String STRAND_NUMBER_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • CIRCULAR_TAG

        protected static final java.lang.String CIRCULAR_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • DIVISION_TAG

        protected static final java.lang.String DIVISION_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • ACCESSION_TAG

        protected static final java.lang.String ACCESSION_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • VERSION_TAG

        protected static final java.lang.String VERSION_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • DEFINITION_TAG

        protected static final java.lang.String DEFINITION_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • KEYWORDS_TAG

        protected static final java.lang.String KEYWORDS_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • SOURCE_TAG

        protected static final java.lang.String SOURCE_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • ORGANISM_TAG

        protected static final java.lang.String ORGANISM_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • ORGANISM_XREF_TAG

        protected static final java.lang.String ORGANISM_XREF_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • REFERENCE_TAG

        protected static final java.lang.String REFERENCE_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • COORDINATE_TAG

        protected static final java.lang.String COORDINATE_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • REF_ACCESSION_TAG

        protected static final java.lang.String REF_ACCESSION_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • AUTHORS_TAG

        protected static final java.lang.String AUTHORS_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • REF_XREF_TAG

        protected static final java.lang.String REF_XREF_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • TITLE_TAG

        protected static final java.lang.String TITLE_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • JOURNAL_TAG

        protected static final java.lang.String JOURNAL_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • COMMENT_TAG

        protected static final java.lang.String COMMENT_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • FEATURE_TAG

        protected static final java.lang.String FEATURE_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • SEPARATOR_TAG

        protected static final java.lang.String SEPARATOR_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • FEATURE_TABLE_TAG

        protected static final java.lang.String FEATURE_TABLE_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • START_SEQUENCE_TAG

        protected static final java.lang.String START_SEQUENCE_TAG
        Deprecated.
        See Also:
        Constant Field Values
      • END_SEQUENCE_TAG

        protected static final java.lang.String END_SEQUENCE_TAG
        Deprecated.
        See Also:
        Constant Field Values
    • Constructor Detail

      • EmblLikeFormat

        public EmblLikeFormat()
        Deprecated.
    • Method Detail

      • setElideSymbols

        public void setElideSymbols​(boolean b)
        Deprecated.

        Specifies whether the symbols (SQ) part of the entry should be ignored. If this property is set to true, the parser will never call addSymbols on the SeqIOListener, but parsing will be faster if you're only interested in header information.

        This property also allows the header to be parsed for files which have invalid sequence data.

      • getElideSymbols

        public boolean getElideSymbols()
        Deprecated.
        Return a flag indicating if symbol data will be skipped when parsing streams.
      • readSequence

        public boolean readSequence​(java.io.BufferedReader reader,
                                    SymbolTokenization symParser,
                                    SeqIOListener listener)
                             throws IllegalSymbolException,
                                    java.io.IOException,
                                    ParseException
        Deprecated.
        Description copied from interface: SequenceFormat
        Read a sequence and pass data on to a SeqIOListener.
        Specified by:
        readSequence in interface SequenceFormat
        Parameters:
        reader - The stream of data to parse.
        symParser - A SymbolParser defining a mapping from character data to Symbols.
        listener - A listener to notify when data is extracted from the stream.
        Returns:
        a boolean indicating whether or not the stream contains any more sequences.
        Throws:
        IllegalSymbolException - if it is not possible to translate character data from the stream into valid BioJava symbols.
        java.io.IOException - if an error occurs while reading from the stream.
        ParseException
      • writeSequence

        public void writeSequence​(Sequence seq,
                                  java.io.PrintStream os)
                           throws java.io.IOException
        Deprecated.
        Description copied from interface: SequenceFormat
        writeSequence writes a sequence to the specified PrintStream, using the default format.
        Specified by:
        writeSequence in interface SequenceFormat
        Parameters:
        seq - the sequence to write out.
        os - the printstream to write to.
        Throws:
        java.io.IOException
      • writeSequence

        public void writeSequence​(Sequence seq,
                                  java.lang.String format,
                                  java.io.PrintStream os)
                           throws java.io.IOException
        Deprecated.
        use writeSequence(Sequence seq, PrintStream os)
        writeSequence writes a sequence to the specified PrintStream, using the specified format.
        Specified by:
        writeSequence in interface SequenceFormat
        Parameters:
        seq - a Sequence to write out.
        format - a String indicating which sub-format of those available from a particular SequenceFormat implemention to use when writing.
        os - a PrintStream object.
        Throws:
        java.io.IOException - if an error occurs.
      • getDefaultFormat

        public java.lang.String getDefaultFormat()
        Deprecated.
        getDefaultFormat returns the String identifier for the default format written by a SequenceFormat implementation.
        Specified by:
        getDefaultFormat in interface SequenceFormat
        Returns:
        a String.
      • BadLineParsed

        public void BadLineParsed​(ParseErrorEvent theEvent)
        Deprecated.

        This method determines the behaviour when a bad line is processed. Some options are to log the error, throw an exception, ignore it completely, or pass the event through.

        This method should be overwritten when different behavior is desired.

        Specified by:
        BadLineParsed in interface ParseErrorListener
        Parameters:
        theEvent - The event that contains the bad line and token.
      • addParseErrorListener

        public void addParseErrorListener​(ParseErrorListener theListener)
        Deprecated.
        Adds a parse error listener to the list of listeners if it isn't already included.
        Specified by:
        addParseErrorListener in interface ParseErrorSource
        Parameters:
        theListener - Listener to be added.
      • removeParseErrorListener

        public void removeParseErrorListener​(ParseErrorListener theListener)
        Deprecated.
        Removes a parse error listener from the list of listeners if it is included.
        Specified by:
        removeParseErrorListener in interface ParseErrorSource
        Parameters:
        theListener - Listener to be removed.
      • notifyParseErrorEvent

        protected void notifyParseErrorEvent​(ParseErrorEvent theEvent)
        Deprecated.
        Passes the event on to all the listeners registered for ParseErrorEvents.
        Parameters:
        theEvent - The event to be handed to the listeners.