How to use uk.ac.ebi.intact.application.dataConversion

public Map<String, String> getExperimentWithErrors() {
  if ( !experimentsClassified ) {
    classifyExperiments();
  }
  return experimentsWithErrors;
}

public ExperimentListItem(Collection<String> experimentLabels, String name, String parentFolders, boolean negative, Integer chunkNumber, Integer largeScaleSize)
{
  this.experimentLabels = experimentLabels;
  this.name = name;
  this.negative = negative;
  this.chunkNumber = chunkNumber;
  this.largeScaleChunkSize = largeScaleSize;
  this.parentFolders = removeTrailingSlash(parentFolders);
}

public Set<Experiment> getNegativeExperiments() {
  if ( negativeExperiments == null ) {
    classifyNegatives();
  }
  return negativeExperiments;
}

@Override
public void error( SAXParseException e ) throws SAXException {
  log.error(e.getMessage());
  report.setValid(false);
  PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.ERROR, e);
  report.addMessage(msg);
}

@Override
public String toString() {
  return getAc() + " " + getShortLabel();
}

public void createItemClassificationBySpecies() {
  for ( SimplifiedAnnotatedObject<BioSource> bioSource : species2experimentSet.keySet() ) {
    Collection<SimplifiedAnnotatedObject<Experiment>> smallScaleExp = species2experimentSet.get( bioSource );
    // split the set into subset of size under SMALL_SCALE_LIMIT
    String filePrefixGlobal = bioSource.getShortLabel().replace( ' ', '-' );
    createExpListItems( smallScaleExp,
              filePrefixGlobal + "_" + SMALL, // small scale
              filePrefixGlobal,              // large scale
              Classification.SPECIES );
  }
}

@Override
public void warning( SAXParseException e ) throws SAXException {
  log.warn(e.getMessage());
  PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.WARN, e);
  report.addMessage(msg);
}

@Override
public void error( SAXParseException e ) throws SAXException {
  log.error(e.getMessage());
  report.setValid(false);
  PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.ERROR, e);
  report.addMessage(msg);
}

@Override
public String toString() {
  return getAc() + " " + getShortLabel();
}

public void createItemClassificationBySpecies() {
  for ( SimplifiedAnnotatedObject<BioSource> bioSource : species2experimentSet.keySet() ) {
    Collection<SimplifiedAnnotatedObject<Experiment>> smallScaleExp = species2experimentSet.get( bioSource );
    // split the set into subset of size under SMALL_SCALE_LIMIT
    String filePrefixGlobal = bioSource.getShortLabel().replace( ' ', '-' );
    createExpListItems( smallScaleExp,
              filePrefixGlobal + "_" + SMALL, // small scale
              filePrefixGlobal,              // large scale
              Classification.SPECIES );
  }
}

@Override
public void warning( SAXParseException e ) throws SAXException {
  log.warn(e.getMessage());
  PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.WARN, e);
  report.addMessage(msg);
}

public Map<String, String> getExperimentWithErrors() {
  if ( !experimentsClassified ) {
    classifyExperiments();
  }
  return experimentsWithErrors;
}

public ExperimentListItem(Collection<String> experimentLabels, String name, String parentFolders, boolean negative, Integer chunkNumber, Integer largeScaleSize)
{
  this.experimentLabels = experimentLabels;
  this.name = name;
  this.negative = negative;
  this.chunkNumber = chunkNumber;
  this.largeScaleChunkSize = largeScaleSize;
  this.parentFolders = removeTrailingSlash(parentFolders);
}

public Set<Experiment> getNegativeExperiments() {
  if ( negativeExperiments == null ) {
    classifyNegatives();
  }
  return negativeExperiments;
}

@Override
public String toString() {
  return getAc() + " " + getShortLabel();
}

public void createItemClassificationBySpecies() {
  for ( SimplifiedAnnotatedObject<BioSource> bioSource : species2experimentSet.keySet() ) {
    Collection<SimplifiedAnnotatedObject<Experiment>> smallScaleExp = species2experimentSet.get( bioSource );
    // split the set into subset of size under SMALL_SCALE_LIMIT
    String filePrefixGlobal = bioSource.getShortLabel().replace( ' ', '-' );
    createExpListItems( smallScaleExp,
              filePrefixGlobal + "_" + SMALL, // small scale
              filePrefixGlobal,              // large scale
              Classification.SPECIES );
  }
}

@Override
public void warning( SAXParseException e ) throws SAXException {
  log.warn(e.getMessage());
  PsiValidatorMessage msg = new PsiValidatorMessage(PsiValidatorMessage.Level.WARN, e);
  report.addMessage(msg);
}

public Map<String, String> getExperimentWithErrors() {
  if ( !experimentsClassified ) {
    classifyExperiments();
  }
  return experimentsWithErrors;
}

public ExperimentListItem(Collection<String> experimentLabels, String name, String parentFolders, boolean negative, Integer chunkNumber, Integer largeScaleSize)
{
  this.experimentLabels = experimentLabels;
  this.name = name;
  this.negative = negative;
  this.chunkNumber = chunkNumber;
  this.largeScaleChunkSize = largeScaleSize;
  this.parentFolders = removeTrailingSlash(parentFolders);
}

public Set<Experiment> getNegativeExperiments() {
  if ( negativeExperiments == null ) {
    classifyNegatives();
  }
  return negativeExperiments;
}