Package org.biojava.bio.seq.io

Class FastaFormat

java.lang.Object
org.biojava.bio.seq.io.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:

  • Field Details

  • Constructor Details

  • Method Details

    • 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(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) throws IllegalSymbolException, 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
      IOException - if there is a problem reading.
      ParseException - if the source cannot be parsed.

    • 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.

    • getDefaultFormat

      public 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.