org.biojava.bio.program.gff
Class GFFWriter

java.lang.Object
  extended byorg.biojava.bio.program.gff.GFFWriter
All Implemented Interfaces:
GFFDocumentHandler

public class GFFWriter
extends java.lang.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
GFFWriter(java.io.PrintWriter out)
          Create a new GFFWriter that will write to out.
 
Method Summary
 void commentLine(java.lang.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(java.lang.String token, java.lang.NumberFormatException nfe)
           
 void invalidFrame(java.lang.String token, java.lang.NumberFormatException nfe)
           
 void invalidScore(java.lang.String token, java.lang.NumberFormatException nfe)
           
 void invalidStart(java.lang.String token, java.lang.NumberFormatException nfe)
           
 void invalidStrand(java.lang.String token)
           
 void recordLine(GFFRecord record)
          Prints record to the PrintWriter.
 void startDocument(java.lang.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(java.io.PrintWriter out)
Create a new GFFWriter that will write to out.

Parameters:
out - the PrintWriter to write to
Method Detail

startDocument

public void startDocument(java.lang.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(java.lang.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(java.lang.String token,
                         java.lang.NumberFormatException nfe)
                  throws BioException
Throws:
BioException

invalidEnd

public void invalidEnd(java.lang.String token,
                       java.lang.NumberFormatException nfe)
                throws BioException
Throws:
BioException

invalidScore

public void invalidScore(java.lang.String token,
                         java.lang.NumberFormatException nfe)
                  throws BioException
Throws:
BioException

invalidStrand

public void invalidStrand(java.lang.String token)
                   throws BioException
Throws:
BioException

invalidFrame

public void invalidFrame(java.lang.String token,
                         java.lang.NumberFormatException nfe)
                  throws BioException
Throws:
BioException