Class PhredFormat

java.lang.Object
org.biojava.bio.program.phred.PhredFormat
All Implemented Interfaces:
Serializable, EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

Format object representing Phred Quality files. 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). Essentially a rework of FastaFormat to cope with the quirks of Phred Quality data.

Copyright (c) 2001

Company: AgResearch

Since:
1.1
Author:
Mark Schreiber, Greg Cox, Frans Verhoef
See Also:
  • Field Details

  • Constructor Details

  • Method Details

    • getLineWidth

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

      public void setLineWidth(int width)
      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

      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.
      siol - 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.
      IOException - if an error occurs while reading from the stream.
      ParseException
    • describeSequence

      protected String describeSequence(Sequence seq)
      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
      This method will print symbols to the line width followed by a new line etc. NOTE that an integer symbol does not always correspond to one character therefore a line width of sixty will print sixty characters followed by a new line. Not necessarily sixty integers.
      Specified by:
      writeSequence in interface SequenceFormat
      Parameters:
      seq - the sequence to write out.
      os - the printstream to write to.
      Throws:
      IOException
    • 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

      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)
      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)
      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)
      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)
      Passes the event on to all the listeners registered for ParseErrorEvents.
      Parameters:
      theEvent - The event to be handed to the listeners.