Class FastaFormat

  • All Implemented Interfaces:
    Serializable, EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

    public class FastaFormat
    extends Object
    implements SequenceFormat, Serializable, ParseErrorListener, ParseErrorSource
    Deprecated.
    Use org.biojavax.bio.seq.io.FastaFormat
    Format object representing FASTA files. These files are almost pure sequence data. The only `sequence property' reported by this parser is PROPERTY_DESCRIPTIONLINE, which is the contents of the sequence's description line (the line starting with a '>' character). Normally, the first word of this is a sequence ID. If you wish it to be interpreted as such, you should use FastaDescriptionLineParser as a SeqIO filter. If you pass it a RichSeqIOListener, you'll get RichSequence objects in return. Likewise, if you write RichSequence objects, you'll get absolutely correct FASTA formatted output.
    Author:
    Thomas Down, Matthew Pocock, Greg Cox, Lukas Kall, Richard Holland, Mark Schreiber
    See Also:
    Serialized Form
    • Constructor Detail

    • Method Detail

      • getLineWidth

        public int getLineWidth()
        Deprecated.
        Retrive the current line width.
        Returns:
        the line width
      • setLineWidth

        public void setLineWidth​(int width)
        Deprecated.
        Set the line width.

        When writing, the lines of sequence will never be longer than the line width.

        Parameters:
        width - the new line width
      • describeSequence

        protected String describeSequence​(Sequence seq)
        Deprecated.
        Return a suitable description line for a Sequence. If the sequence's annotation bundle contains PROPERTY_DESCRIPTIONLINE, this is used verbatim. Otherwise, the sequence's name is used.
      • writeSequence

        public void writeSequence​(Sequence seq,
                                  PrintStream os)
                           throws IOException
        Deprecated.
        Writes a Sequence or RichSequence to a PrintStream in FASTA format. If the sequence is a RichSequence the format of the header will be in line with the NCBI standard.
        Specified by:
        writeSequence in interface SequenceFormat
        Parameters:
        seq - the sequence to format
        os - the stream to write the sequence to. To print to screen use System.out
        Throws:
        IOException - if data cannot be written to os
      • writeSequence

        public void writeSequence​(Sequence seq,
                                  String format,
                                  PrintStream os)
                           throws 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:
        IOException - if an error occurs.
      • 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.
      • 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.