uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload.<init> java code examples

Common ways to obtain UserSessionDownload

private void myMethod () {
 UserSessionDownload u =Conversion.PsiVersion psiVersion;new UserSessionDownload(psiVersion)
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}

public static Document generatePsiData(Collection<Interaction> interactions, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  return generatePsiData(interactions, session);
}

public static Document generatePsiData(Collection<Interaction> interactions, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  return generatePsiData(interactions, session);
}

public static Document generatePsiData(Collection<Interaction> interactions, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  return generatePsiData(interactions, session);
}

/**
 * Converts a list of experiments to PSI XML, providing the experiment labels
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @return The Document containing the PSI XML
 */
public static Document generatePsiData(ExperimentListItem eli, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Collection<Interaction> interactions = getInteractionsForExperimentListItem(eli);
  return generatePsiData(interactions, session);
}

UserSessionDownload session = new UserSessionDownload( version );
if ( mapping != null ) {
  session.setReverseCvMapping( mapping );

UserSessionDownload session = new UserSessionDownload( version );
if ( mapping != null ) {
  session.setReverseCvMapping( mapping );

/**
 * Converts a list of experiments to PSI XML, providing the experiment labels
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @return The Document containing the PSI XML
 */
public static Document generatePsiData(ExperimentListItem eli, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Collection<Interaction> interactions = getInteractionsForExperimentListItem(eli);
  return generatePsiData(interactions, session);
}

/**
 * Converts a list of experiments to PSI XML, providing the experiment labels
 *
 * @param eli The ExperimentListItem, which contaisn information about the experiment to be fetched, the pagination and files
 * @param psiVersion The version of PSI to use
 * @param cvMapping The cv mapping
 * @return The Document containing the PSI XML
 */
public static Document generatePsiData(ExperimentListItem eli, PsiVersion psiVersion, CvMapping cvMapping)
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Collection<Interaction> interactions = getInteractionsForExperimentListItem(eli);
  return generatePsiData(interactions, session);
}

UserSessionDownload session = new UserSessionDownload( version );
if ( mapping != null ) {
  session.setReverseCvMapping( mapping );

UserSessionDownload session = new UserSessionDownload( version );
if ( mapping != null ) {
  session.setReverseCvMapping( mapping );

UserSessionDownload session = new UserSessionDownload( version );
if ( mapping != null ) {
  session.setReverseCvMapping( mapping );

UserSessionDownload session = new UserSessionDownload( version );
if ( mapping != null ) {
  session.setReverseCvMapping( mapping );

/**
 * Writes a file containing the PSI XML, with the interactions provided
 *
 * @param interactions
 * @param psiVersion
 * @param cvMapping
 * @param xmlTargetFile
 * @param validate
 * @return
 * @throws IOException
 */
public static PsiValidatorReport writePsiData(Collection<Interaction> interactions,
                  PsiVersion psiVersion,
                  CvMapping cvMapping,
                  File xmlTargetFile, boolean validate) throws IOException
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Document doc =  generatePsiData(interactions, session);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlTargetFile, validate);
}

/**
 * Writes a file containing the PSI XML, with the interactions provided
 *
 * @param interactions
 * @param psiVersion
 * @param cvMapping
 * @param xmlTargetFile
 * @param validate
 * @return
 * @throws IOException
 */
public static PsiValidatorReport writePsiData(Collection<Interaction> interactions,
                  PsiVersion psiVersion,
                  CvMapping cvMapping,
                  File xmlTargetFile, boolean validate) throws IOException
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Document doc =  generatePsiData(interactions, session);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlTargetFile, validate);
}

/**
 * Writes a file containing the PSI XML, with the interactions provided
 *
 * @param interactions
 * @param psiVersion
 * @param cvMapping
 * @param xmlTargetFile
 * @param validate
 * @return
 * @throws IOException
 */
public static PsiValidatorReport writePsiData(Collection<Interaction> interactions,
                  PsiVersion psiVersion,
                  CvMapping cvMapping,
                  File xmlTargetFile, boolean validate) throws IOException
{
  UserSessionDownload session = new UserSessionDownload(psiVersion);
  if (cvMapping != null)
  {
    session.setReverseCvMapping(cvMapping);
  }
  Document doc =  generatePsiData(interactions, session);
  if (doc == null)
  {
    return new PsiValidatorReport();
  }
  return writeFile(doc, xmlTargetFile, validate);
}

System.out.println( version );
UserSessionDownload session = new UserSessionDownload( version );
session.filterObsoleteAnnotationTopic();

System.out.println( version );
UserSessionDownload session = new UserSessionDownload( version );
session.filterObsoleteAnnotationTopic();

System.out.println( version );
UserSessionDownload session = new UserSessionDownload( version );
session.filterObsoleteAnnotationTopic();

Popular methods of UserSessionDownload

addMessage
createElement
createTextNode
declareAlreadyDefined
Declare in the session that the given protein has been already converted in XML.
filterObsoleteAnnotationTopic
Load all CvTopic and check which one have been flagged 'obsolete'. Those CvTopic are automatically a
getAvailabilityListElement
Return the availabilityList element under the entry of the PSI document. If the element doesn't exis
getCvObjectCache
getEntryElement
Return the entry element of the PSI document. If the element doesn't exist, it is created.
getExperimentIdentifier
Get a specific identifier for the given experiemnt. If an identifier had already been affected for t
getExperimentListElement
Return the experimentList element under the entry of the PSI document. If the element doesn't exist,
getFeatureIdentifier
Get a specific identifier for the given feature. If an identifier had already been affected for that
getHostOrganismCache

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

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload.<init> (Showing top 18 results out of 315)

How to use
uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload
constructor