How to use

Xml2Tab

in

psidev.psi.mi.tab.converter.xml2tab

/**
 * Converts a given entrySet into a Collection of BinaryInteractionImpl. <br/> If a ExpansionStrategy was set, every
 * interaction in the given entrySet will be expanded prior to conversion to MITAB25. Should the expansion result in
 * multiple interaction, they are converted iteratively.
 *
 * @param entrySet the entrySet to convert in MITAB25.
 * @return a non null collection of BinaryInteractionImpl.
 */
public Collection<BinaryInteraction> convert(EntrySet entrySet) throws TabConversionException {
  return convert(entrySet, false);
}

Xml2Tab x2t = new Xml2Tab();
x2t.addOverrideSourceDatabase(new CrossReference("MI", "0469", "intact"));
x2t.setExpansionStrategy(expansionStragegy);
  x2t.setPostProcessor(new ClusterInteractorPairProcessor());
} else {
  x2t.setPostProcessor(null);
Collection<BinaryInteraction> interactions = x2t.convert(xmlFilesToConvert);

Xml2Tab x2t = new Xml2Tab();
x2t.setPostProcessor(new ClusterInteractorPairProcessor());
System.out.println("Applying Spoke model expansion wherever appropriate.");
Collection<BinaryInteraction> interactions = x2t.convert(dir);

Xml2Tab x2t = new Xml2Tab();
x2t.setPostProcessor(postProcessorStrategy);
    Collection<BinaryInteraction> interactions = x2t.convert(inputFiles);
    fileWriter.write(interactions, outputWriter);
      singleFile.add(inputFile);
      Collection<BinaryInteraction> interactions = x2t.convert(singleFile);
      fileWriter.write(interactions, outputWriter);

/**
 * Convert a collection of files into a collection of PSIMITAB BinaryInteractionImpl.
 *
 * @param inputFiles Collection of files to convert.
 * @return a non null collection of PSIMITAB BinaryInteractionImpl.
 * @throws TabConversionException if an error occur during the processing.
 */
public Collection<BinaryInteraction> convert(Collection<File> inputFiles) throws TabConversionException {
  return convert(inputFiles, false);
}

/**
 * Convert a file into a collection of PSIMITAB BinaryInteractionImpl. Post processing will be applied if requested.
 *
 * @param file the file to convert.
 * @return a non null collection of PSIMITAB BinaryInteractionImpl.
 * @throws TabConversionException if an error occur during the processing.
 */
public Collection<BinaryInteraction> convert(File file) throws TabConversionException {
  return convert(file, false);
}

  /**
   * Convert a collection of files into a collection of PSIMITAB BinaryInteractionImpl. The postprocessing can be
   * enabled/disabled by using the skipPostProcessing variable. The postprocessing can be enabled/disabled by using
   * the skipPostProcessing variable.
   *
   * @param inputFiles Collection of files to convert.
   * @return a non null collection of PSIMITAB BinaryInteractionImpl.
   * @throws TabConversionException if an error occur during the processing.
   */
  public Collection<BinaryInteraction> convert(Collection<File> inputFiles, boolean skipPostProcessing) throws TabConversionException {
    Collection<BinaryInteraction> interactions = new ArrayList<BinaryInteraction>(128);

    for (File file : inputFiles) {
      interactions.addAll(convert(file));
    }

//        if ( false == skipPostProcessing ) {
//            interactions = doPostProcessing( interactions );
//        }

    return interactions;
  }

  interactions.addAll(convert(entrySet, true)); // skip post processing, we'll do it later.
interactions.addAll(convert(entrySet, true)); // skip post processing, we'll do it later.