本文整理了Java中psidev.psi.mi.jami.utils.XrefUtils类的一些代码示例，展示了XrefUtils类的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。XrefUtils类的具体详情如下：
包路径：psidev.psi.mi.jami.utils.XrefUtils
类名称：XrefUtils

XrefUtils介绍

[英]Utility class for Xrefs
[中]外部参照的实用程序类

代码示例

代码示例来源：origin: psidev.psi.mi.jami/jami-core

public static Xref createRefseqIdentity(String refseq){
  return createIdentityXref(Xref.REFSEQ, Xref.REFSEQ_MI, refseq);
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

public static Xref createSecondaryXref(String databaseName, String id){
  return createXrefWithQualifier(databaseName, null, id, Xref.SECONDARY, Xref.SECONDARY_MI);
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

protected void processAddedXrefEvent(Xref added) {
  // the added identifier is imex and the current imex is not set
  if (imexId == null && XrefUtils.isXrefFromDatabase(added, Xref.IMEX_MI, Xref.IMEX)){
    // the added xref is imex-primary
    if (XrefUtils.doesXrefHaveQualifier(added, Xref.IMEX_PRIMARY_MI, Xref.IMEX_PRIMARY)){
      imexId = added;
    }
  }
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * This method will return the first Xref from this database having :
 * - identity qualifier
 * - secondary identifier if no identity qualifier
 * - first Xref from this database if no identity or secondary qualifier
 * It will return null if there are no Xrefs with this database id/name
 * @param refs : the collection of Xrefs
 * @param dbId : the database id to look for
 * @param dbName : the database name to look for
 * @return the first identifier having this database name/id, null if no Xrefs with this database name/id
 */
public static Xref collectFirstIdentifierWithDatabase(Collection<? extends Xref> refs, String dbId, String dbName){
  if (refs == null || (dbName == null && dbId == null)){
    return null;
  }
  for (Xref xref : refs){
    if (isXrefAnIdentifier(xref) && isXrefFromDatabase(xref, dbId, dbName)){
      return xref;
    }
  }
  return null;
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * This method will return the first Xref from this database having :
 * - identity qualifier
 * - secondary identifier if no identity qualifier
 * - first Xref from this database if no identity or secondary qualifier
 * It will return null if there are no Xrefs with this database id/name
 * @param refs : the collection of Xrefs
 * @param dbId : the database id to look for
 * @param dbName : the database name to look for
 * @param id
 * @return the first identifier having this database name/id, null if no Xrefs with this database name/id
 */
public static Xref collectFirstIdentifierWithDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id){
  if (refs == null || (dbName == null && dbId == null) || id == null){
    return null;
  }
  for (Xref xref : refs){
    if (isXrefAnIdentifier(xref) && doesXrefHaveDatabaseAndId(xref, dbId, dbName, id)){
      return xref;
    }
  }
  return null;
}

代码示例来源：origin: psidev.psi.mi.jami.bridges/jami-imexcentral

private void copyIdentifiersFromDelegate() {
  List<Identifier> imexIdentifiers = this.delegate.getIdentifier();
  for (Identifier identifier : imexIdentifiers){
    if (identifier.getNs() == null || identifier.getAc() == null){
      // nothing to do
    }
    else if (identifier.getNs().equals("pmid")){
      super.getIdentifiers().add(XrefUtils.createPubmedIdentity(identifier.getAc()));
    }
    else if (identifier.getNs().equals("imex") && !identifier.getAc().equals("N/A")){
      super.getXrefs().add(XrefUtils.createXrefWithQualifier(Xref.IMEX, Xref.IMEX_MI, identifier.getAc(), Xref.IMEX_PRIMARY, Xref.IMEX_PRIMARY_MI));
    }
    else if (identifier.getNs().equals("doi")){
      super.getIdentifiers().add(XrefUtils.createDoiIdentity(identifier.getAc()));
    }
    else if (identifier.getNs().equals("jint")){
      super.getIdentifiers().add(XrefUtils.createIdentityXref("jint", identifier.getAc()));
    }
  }
  if (super.getImexId() == null && this.delegate.getImexAccession() != null && !this.delegate.getImexAccession().equals("N/A")){
    super.getXrefs().add(XrefUtils.createXrefWithQualifier(Xref.IMEX, Xref.IMEX_MI, this.delegate.getImexAccession(), Xref.IMEX_PRIMARY, Xref.IMEX_PRIMARY_MI));
  }
}

代码示例来源：origin: psidev.psi.mi.jami/jami-mitab

if (XrefUtils.doesXrefHaveQualifier(xref, null, DISPLAY_SHORT)){
  displayShort = xref;
  break;
else if (XrefUtils.doesXrefHaveQualifier(xref, null, DISPLAY_LONG)){
  if (displayLong == null){
    displayLong = xref;
else if (XrefUtils.doesXrefHaveQualifier(xref, Alias.GENE_NAME_MI, Alias.GENE_NAME)){
  if (geneName == null){
    geneName = xref;
else if (XrefUtils.doesXrefHaveQualifier(xref, null, SHORTLABEL)){
  if (shortLabel == null){
    shortLabel = xref;

代码示例来源：origin: psidev.psi.mi.jami/jami-core

protected void processRemovedXrefEvent(Xref removed) {
  // the removed identifier is pubmed
  if (imexId != null && imexId.equals(removed)){
    Collection<Xref> existingImex = XrefUtils.collectAllXrefsHavingDatabaseAndQualifier(getXrefs(), Xref.IMEX_MI, Xref.IMEX, Xref.IMEX_PRIMARY_MI, Xref.IMEX_PRIMARY);
    if (!existingImex.isEmpty()){
      imexId = existingImex.iterator().next();
    }
  }
}

代码示例来源：origin: psidev.psi.mi/psimi-schema-validator

final Collection<Xref> pubmeds = XrefUtils.collectAllXrefsHavingDatabase(dbReferences, Xref.PUBMED_MI, Xref.PUBMED);
final Collection<Xref> dois = XrefUtils.collectAllXrefsHavingDatabase(dbReferences, Xref.DOI_MI, Xref.DOI);
    boolean hasSeveralPrimary = false;
    for (Xref pubmed : pubmeds){
      if (XrefUtils.doesXrefHaveQualifier(pubmed, Xref.PRIMARY_MI, Xref.PRIMARY) ||
          XrefUtils.doesXrefHaveQualifier(pubmed, Xref.IDENTITY_MI, Xref.IDENTITY)){
        if (hasPrimary){
          hasSeveralPrimary = true;
    boolean hasSeveralPrimary = false;
    for (Xref doi : dois){
      if (XrefUtils.doesXrefHaveQualifier(doi, Xref.PRIMARY_MI, Xref.PRIMARY) ||
          XrefUtils.doesXrefHaveQualifier(doi, Xref.IDENTITY_MI, Xref.IDENTITY)){
        if (hasPrimary){
          hasSeveralPrimary = true;

代码示例来源：origin: psidev.psi.mi.jami.bridges/jami-uniprot

p.getIdentifiers().add(XrefUtils.createUniprotSecondary(id.getValue()));
p.getXrefs().add(XrefUtils.createXrefWithQualifier(Xref.UNIPROTKB , Xref.UNIPROTKB_MI,
    entry.getPrimaryUniProtAccession().getValue() , Xref.ISOFORM_PARENT, Xref.ISOFORM_PARENT_MI));

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * Collect all cross references having a specific database and qualifier
 * @param refs
 * @param dbId
 * @param dbName
 * @param qualifierId
 * @param qualifierName
 * @param id
 * @return
 */
public static Collection<Xref> collectAllXrefsHavingDatabaseQualifierAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id, String qualifierId, String qualifierName){
  if (refs == null || refs.isEmpty()){
    return Collections.EMPTY_LIST;
  }
  Collection<Xref> identifiers = new ArrayList<Xref>(refs.size());
  for (Xref ref : refs){
    if (isXrefFromDatabase(ref, dbId, dbName) && doesXrefHaveQualifierAndId(ref, qualifierId, qualifierName, id)){
      identifiers.add(ref);
    }
  }
  return identifiers;
}

代码示例来源：origin: psidev.psi.mi/psimi-schema-validator

Collection<psidev.psi.mi.jami.model.Xref> cabriReferences = XrefUtils.collectAllXrefsHavingDatabase(cellType.getIdentifiers(), RuleUtils.CABRI_MI_REF, RuleUtils.CABRI);
Collection<psidev.psi.mi.jami.model.Xref> cellReferences = XrefUtils.collectAllXrefsHavingDatabase(cellType.getIdentifiers(), RuleUtils.CELL_ONTOLOGY_MI_REF, RuleUtils.CELL_ONTOLOGY);
Collection<psidev.psi.mi.jami.model.Xref> allPubmeds = XrefUtils.collectAllXrefsHavingDatabaseAndQualifier(cellType.getXrefs(), psidev.psi.mi.jami.model.Xref.PUBMED_MI, psidev.psi.mi.jami.model.Xref.PUBMED, psidev.psi.mi.jami.model.Xref.PRIMARY_MI, psidev.psi.mi.jami.model.Xref.PRIMARY);

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * Remove all Xrefs having this database name/database id from the collection of xrefs
 * @param refs : the collection of Xrefs
 * @param dbId : the database id to look for
 * @param dbName : the database name to look for
 */
public static void removeAllXrefsWithDatabase(Collection<? extends Xref> refs, String dbId, String dbName){
  if (refs != null){
    Iterator<? extends Xref> refIterator = refs.iterator();
    while (refIterator.hasNext()){
      if (isXrefFromDatabase(refIterator.next(), dbId, dbName)){
        refIterator.remove();
      }
    }
  }
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * Remove all Xrefs having this database name/database id from the collection of xrefs
 * @param refs : the collection of Xrefs
 * @param dbId : the database id to look for
 * @param dbName : the database name to look for
 * @param id
 */
public static void removeAllXrefsWithDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id){
  if (refs != null){
    Iterator<? extends Xref> refIterator = refs.iterator();
    while (refIterator.hasNext()){
      if (doesXrefHaveDatabaseAndId(refIterator.next(), dbId, dbName, id)){
        refIterator.remove();
      }
    }
  }
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

public static Publication createPublicationDoi(String doi){
  return new DefaultPublication(XrefUtils.createDoiIdentity(doi));
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * Collect all cross references having a specific qualifier
 * @param refs
 * @param qualifierId
 * @param qualifierName
 * @return
 */
public static Collection<Xref> collectAllXrefsHavingQualifier(Collection<? extends Xref> refs, String qualifierId, String qualifierName){
  if (refs == null || refs.isEmpty()){
    return Collections.EMPTY_LIST;
  }
  Collection<Xref> identifiers = new ArrayList<Xref>(refs.size());
  for (Xref ref : refs){
    if (doesXrefHaveQualifier(ref, qualifierId, qualifierName)){
      identifiers.add(ref);
    }
  }
  return identifiers;
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

protected void processRemovedXrefEvent(Xref removed) {
  // the removed identifier is pubmed
  if (imexId != null && imexId.equals(removed)){
    Collection<Xref> existingImex = XrefUtils.collectAllXrefsHavingDatabaseAndQualifier(getXrefs(), Xref.IMEX_MI, Xref.IMEX, Xref.IMEX_PRIMARY_MI, Xref.IMEX_PRIMARY);
    if (!existingImex.isEmpty()){
      imexId = existingImex.iterator().next();
    }
  }
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * Collect all cross references having a specific database
 * @param refs
 * @param dbId
 * @param dbName
 * @return
 */
public static Collection<Xref> collectAllXrefsHavingDatabase(Collection<? extends Xref> refs, String dbId, String dbName){
  if (refs == null || refs.isEmpty()){
    return Collections.EMPTY_LIST;
  }
  Collection<Xref> identifiers = new ArrayList<Xref>(refs.size());
  for (Xref ref : refs){
    if (isXrefFromDatabase(ref, dbId, dbName)){
      identifiers.add(ref);
    }
  }
  return identifiers;
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

/**
 * Collect all cross references having a specific database
 * @param refs
 * @param dbId
 * @param dbName
 * @param id
 * @return
 */
public static Collection<Xref> collectAllXrefsHavingDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id){
  if (refs == null || refs.isEmpty()){
    return Collections.EMPTY_LIST;
  }
  Collection<Xref> identifiers = new ArrayList<Xref>(refs.size());
  for (Xref ref : refs){
    if (doesXrefHaveDatabaseAndId(ref, dbId, dbName, id)){
      identifiers.add(ref);
    }
  }
  return identifiers;
}

代码示例来源：origin: psidev.psi.mi.jami/jami-core

protected void processAddedXrefEvent(Xref added) {
  // the added identifier is imex and the current imex is not set
  if (imexId == null && XrefUtils.isXrefFromDatabase(added, Xref.IMEX_MI, Xref.IMEX)){
    // the added xref is imex-primary
    if (XrefUtils.doesXrefHaveQualifier(added, Xref.IMEX_PRIMARY_MI, Xref.IMEX_PRIMARY)){
      imexId = added;
    }
  }
}