Class FastaFormat

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

    public class FastaFormat
    extends java.lang.Object
    implements SequenceFormat, java.io.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
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String DEFAULT
      Deprecated.
       
      protected int lineWidth
      Deprecated.
      The line width for output.
      protected java.util.Vector mListeners
      Deprecated.
       
      static java.lang.String PROPERTY_DESCRIPTIONLINE
      Deprecated.
      Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.
    • Constructor Summary

      Constructors 
      Constructor Description
      FastaFormat()
      Deprecated.
       
    • Field Detail

      • PROPERTY_DESCRIPTIONLINE

        public static final java.lang.String PROPERTY_DESCRIPTIONLINE
        Deprecated.
        Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.
        See Also:
        Constant Field Values
      • mListeners

        protected java.util.Vector mListeners
        Deprecated.
      • lineWidth

        protected int lineWidth
        Deprecated.
        The line width for output.
    • Constructor Detail

      • FastaFormat

        public FastaFormat()
        Deprecated.
    • 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
      • readSequence

        public boolean readSequence​(java.io.BufferedReader reader,
                                    SymbolTokenization symParser,
                                    SeqIOListener siol)
                             throws IllegalSymbolException,
                                    java.io.IOException,
                                    ParseException
        Deprecated.
        Reads information from a flatfile to a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol objects.
        Specified by:
        readSequence in interface SequenceFormat
        Parameters:
        reader - The reader that is the source of the information
        symParser - converts text seqeunce to biojava objects
        siol - The listener that listens for event callbacks from this class. The listener can be a RichSeqIOListener.
        Returns:
        true if there is another unread sequence in the source.
        Throws:
        IllegalSymbolException - if symParser doesn't know how to convert the text sequence into biojava Symbols
        java.io.IOException - if there is a problem reading.
        ParseException - if the source cannot be parsed.
      • describeSequence

        protected java.lang.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,
                                  java.io.PrintStream os)
                           throws java.io.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:
        java.io.IOException - if data cannot be written to os
      • 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.
        Specified by:
        getDefaultFormat in interface SequenceFormat
        Returns:
        a String.
      • 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.
      • 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.