owltools.gaf.io

Class AbstractGafWriter

java.lang.Object

owltools.gaf.io.AbstractGafWriter

Direct Known Subclasses:

GafWriter, GafWriter.BufferedGafWriter

public abstract class AbstractGafWriter
extends Object

General utility to write a GafDocument or GeneAnnotation.

Constructor Summary

Constructors

Constructor and Description
AbstractGafWriter()

Method Summary

Methods

Modifier and Type	Method and Description
protected abstract void	end() Called after the writing of a GafDocument has been finished.
protected void	nl() Append the separator between rows.
protected abstract void	print(String s) Append an arbitrary string.
protected void	sep() Append a the separator between columns.
void	write(GafDocument gdoc) Write a full GAF.
void	write(GeneAnnotation ann) Write a single GeneAnnotation.
void	writeHeader(GafDocument gdoc) Write a header of a GAF, use the comments from the GafDocument.
void	writeHeader(List<String> comments) Write a header for a GAF, header comments are optional.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractGafWriter

public AbstractGafWriter()

Method Detail

write

public void write(GafDocument gdoc)

Write a full GAF.

Parameters:

gdoc -

writeHeader

public void writeHeader(GafDocument gdoc)

Write a header of a GAF, use the comments from the GafDocument.

Parameters:

gdoc -

writeHeader

public void writeHeader(List<String> comments)

Write a header for a GAF, header comments are optional.

Parameters:

comments -

write

public void write(GeneAnnotation ann)

Write a single GeneAnnotation.

Parameters:

ann -

print

protected abstract void print(String s)

Append an arbitrary string.

Parameters:

s -

end

protected abstract void end()

Called after the writing of a GafDocument has been finished.

sep

protected void sep()

Append a the separator between columns.

nl

protected void nl()

Append the separator between rows.