Package org.incenp.obofoundry.sssom

Class TSVWriter

java.lang.Object

org.incenp.obofoundry.sssom.SSSOMWriter

org.incenp.obofoundry.sssom.TSVWriter

public class TSVWriter
extends SSSOMWriter

A writer to serialise a SSSOM mapping set into the TSV format.

If the mapping set has a CURIE map (MappingSet.getCurieMap()), it is automatically used to shorten identifiers when they are written to the file.

Usage:

 MappingSet mappingSet = ...;
 try {
     TSVWriter writer = new TSVWriter("my-mappings.sssom.tsv");
     writer.write(mappingSet);
 } catch ( IOException ioe ) {
     // Generic I/O error
 }
 

Field Summary

Fields inherited from class org.incenp.obofoundry.sssom.SSSOMWriter

condensationPolicy, extensionManager, extraPolicy, prefixManager, targetVersion

Constructor Summary

Constructors

Constructor	Description
TSVWriter(File file)	Creates a new instance that will write data to the specified file in embedded mode (metadata block and TSV section in the same file).
TSVWriter(File tsvFile, File metaFile)	Creates a new instance that will write data to the specified files.
TSVWriter(OutputStream stream)	Creates a new instance that will write data to the specified stream in embedded mode.
TSVWriter(OutputStream tsvStream, OutputStream metaStream)	Creates a new instance that will write data to the specified streams.
TSVWriter(String filename)	Creates a new instance that will write data to a file with the specified filename, in embedded mode.
TSVWriter(String tsvFilename, String metaFilename)	Creates a new instance that will write data to files with the specified filenames.

Method Summary

Modifier and Type	Method	Description
protected void	doWrite(MappingSet mappingSet)	Actually serialises a mapping set.
void	enableCSV(boolean csv)	Enables CSV mode.

Methods inherited from class org.incenp.obofoundry.sssom.SSSOMWriter

condenseSet, getUsedPrefixes, getUsedPrefixes, setCondensationEnabled, setCurieMap, setExtraMetadataPolicy, setSortingEnabled, setTargetVersion, write

Methods inherited from class java.lang.Object

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

Constructor Detail

TSVWriter

public TSVWriter(File tsvFile,
                 File metaFile)
          throws IOException

Creates a new instance that will write data to the specified files.

Parameters:

tsvFile - The file to write the TSV section to.

metaFile - The file to write the metadata block to. If null, the metadata block will be embedded in the same file as the TSV section.

Throws:

IOException - If any of the files cannot be opened for any reason.

TSVWriter

public TSVWriter(File file)
          throws IOException

Creates a new instance that will write data to the specified file in embedded mode (metadata block and TSV section in the same file).

Parameters:

file - The file to write to.

Throws:

IOException - If the file cannot be opened for any reason.

TSVWriter

public TSVWriter(OutputStream tsvStream,
                 OutputStream metaStream)

Creates a new instance that will write data to the specified streams.

Parameters:

tsvStream - The stream to write the TSV section to.

metaStream - The stream to write the metadata block to. If null, the metadata block will be embedded in the same stream as the TSV section.

TSVWriter

public TSVWriter(OutputStream stream)

Creates a new instance that will write data to the specified stream in embedded mode.

Parameters:

stream - The stream to write to.

TSVWriter

public TSVWriter(String tsvFilename,
                 String metaFilename)
          throws IOException

Creates a new instance that will write data to files with the specified filenames.

Parameters:

tsvFilename - The name of the file to write the TSV section to.

metaFilename - The name of the file to write the metadata block to. If null, the metadata block will be embedded in the same file as the TSV section.

Throws:

IOException - If any of the files cannot be opened for any reason.

TSVWriter

public TSVWriter(String filename)
          throws IOException

Creates a new instance that will write data to a file with the specified filename, in embedded mode.

Parameters:

filename - The name of the file to write to.

Throws:

IOException - If the file cannot be opened for any reason.

Method Detail

enableCSV

public void enableCSV(boolean csv)

Enables CSV mode. This makes the writer use a comma to separate columns, rather than a tab.

This is not officially supported by the SSSOM specification, which only specifies the tab-separated format. But the comma-separated variant is accepted by SSSOM-Py.

Parameters:

csv - If true, the writer will produce a CSV file.

doWrite

protected void doWrite(MappingSet mappingSet)
                throws IOException

Description copied from class: SSSOMWriter

Actually serialises a mapping set. This method should be overridden by derived classes to implement the serialisation in a specific format.

Specified by:

doWrite in class SSSOMWriter

Parameters:

mappingSet - The mapping set to serialise.

Throws:

IOException - If an I/O error occurs.