Class GenbankFormat

Method Details

• readSequence

  public boolean readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IllegalSymbolException, IOException, ParseException

  Deprecated.

  Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. The sequence read in must be in Genbank format.

  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:

  boolean True if there is another sequence in the file; false otherwise

  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

• writeSequence

  public void writeSequence(Sequence seq, PrintStream os) throws 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:

  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

  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.

• getElideSymbols

  public boolean getElideSymbols()

  Deprecated.

• setElideSymbols

  public void setElideSymbols(boolean elideSymbols)

  Deprecated.

  Use this method to toggle reading of sequence data. If you're only interested in header data set to true.

  Parameters:

  elideSymbols - set to true if you don't want the sequence data.