Package org.biojava.bio.program.gff

Class GFFWriter

java.lang.Object

org.biojava.bio.program.gff.GFFWriter

All Implemented Interfaces:

GFFDocumentHandler

public class GFFWriter
extends Object
implements GFFDocumentHandler

Listens to a stream of GFF events and writes the lines to a PrintWriter.

This will ignore all exceptions. Perhaps the error-handling needs to move into an error handling interface?

Author:

Matthew Pocock, Keith James (docs)

Constructor Summary

Constructors

Constructor	Description
GFFWriter(PrintWriter out)	Create a new GFFWriter that will write to out.

Method Summary

Modifier and Type	Method	Description
void	commentLine(String comment)	Prints the comment directly to the PrintWriter after adding a leading '#'.
void	endDocument()	Flushes the PrintWriter to make sure that everything is written.
void	invalidEnd(String token, NumberFormatException nfe)
void	invalidFrame(String token, NumberFormatException nfe)
void	invalidScore(String token, NumberFormatException nfe)
void	invalidStart(String token, NumberFormatException nfe)
void	invalidStrand(String token)
void	recordLine(GFFRecord record)	Prints record to the PrintWriter.
void	startDocument(String locator)	Indicates that a new GFF document has been started.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GFFWriter

public GFFWriter(PrintWriter out)

Create a new GFFWriter that will write to out.

Parameters:

out - the PrintWriter to write to

Method Detail

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