uk.ac.ebi.arrayexpress2.magetab.renderer

Class SDRFWriter

java.lang.Object

java.io.Writer

uk.ac.ebi.arrayexpress2.magetab.renderer.SDRFWriter

All Implemented Interfaces:

Closeable, Flushable, Appendable, AutoCloseable

public class SDRFWriter
extends Writer

Writes SDRF objects to a character output stream, formatted according to the MAGE-TAB SDRF serialization specification.

The typical strategy for SDRF serialization involves buffering of one line at a time, before sending each line to the underlying writer. There is a considerable precompute step before any output is written in order to evaluate the optimal format for the resulting SDRF given the current graph: the header must first be computed and then written before any of the actual data. It is not possible to specify a buffer at the level of SDRF writing, as each line may be altered many times before it is complete. However, there are no restrictions on wrapping a BufferedWriter with the SDRF writer ensuring buffering at that level.

Closing an SDRFWriter closes the underlying writer, but has no other effect.

Author:

Tony Burdett

Field Summary

Fields inherited from class java.io.Writer

lock

Constructor Summary

Constructors

Constructor and Description
SDRFWriter(Writer writer)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
void	flush()
void	write(char[] cbuf, int off, int len)
void	write(SDRF sdrf) Writes out the SDRF to the underlying writer, without printing any stdout.
void	write(SDRF sdrf, boolean printStdout) Writes out the SDRF to the underlying, specifying whether to convert information about progress to standard out.

Methods inherited from class java.io.Writer

append, append, append, write, write, write, write

Methods inherited from class java.lang.Object

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

Constructor Detail

SDRFWriter

public SDRFWriter(Writer writer)

Method Detail

write

public void write(char[] cbuf,
         int off,
         int len)
           throws IOException

Specified by:

write in class Writer

Throws:

IOException

flush

public void flush()
           throws IOException

Specified by:

flush in interface Flushable

Specified by:

flush in class Writer

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

close in class Writer

Throws:

IOException

write

public void write(SDRF sdrf)
           throws IOException

Writes out the SDRF to the underlying writer, without printing any stdout. This is equivalent to writeSDRF(sdrf, writer, false)

Parameters:

sdrf - the SDRF to convert

Throws:

IOException - if the writer refused to accept bytes, or the SDRF was formatted in such a way as to make writing impossible

write

public void write(SDRF sdrf,
         boolean printStdout)
           throws IOException

Writes out the SDRF to the underlying, specifying whether to convert information about progress to standard out.

Parameters:

sdrf - the SDRF to convert

printStdout - whether or not to print progress information to standard out

Throws:

IOException - if the writer refused to accept bytes, or the SDRF was formatted in such a way as to make writing impossible