Class GFFWriter

Method Details

• startDocument

  public void startDocument(String locator)

  Description copied from interface: GFFDocumentHandler

  Indicates that a new GFF document has been started. This gives you a hook to set up per-document resources.

  Specified by:

  startDocument in interface GFFDocumentHandler

  Parameters:

  locator - A URI for the stream being parsed.

• endDocument

  public void endDocument()

  Flushes the PrintWriter to make sure that everything is written.

  Specified by:

  endDocument in interface GFFDocumentHandler

• commentLine

  public void commentLine(String comment)

  Prints the comment directly to the PrintWriter after adding a leading '#'.

  Specified by:

  commentLine in interface GFFDocumentHandler

  Parameters:

  comment - the comment String

• recordLine

  public void recordLine(GFFRecord record)

  Prints record to the PrintWriter.

  Specified by:

  recordLine in interface GFFDocumentHandler

  Parameters:

  record - the GFFRecord containing all the info

• invalidStart

  public void invalidStart(String token, NumberFormatException nfe) throws BioException

  Throws:

  BioException

• invalidEnd

  public void invalidEnd(String token, NumberFormatException nfe) throws BioException

  Throws:

  BioException

• invalidScore

  public void invalidScore(String token, NumberFormatException nfe) throws BioException

  Throws:

  BioException

• invalidStrand

  public void invalidStrand(String token) throws BioException

  Throws:

  BioException

• invalidFrame

  public void invalidFrame(String token, NumberFormatException nfe) throws BioException

  Throws:

  BioException