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
 }

  • Constructor Details

    • 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 Details

    • 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.