uk.ac.ebi.intact.model.util.XrefUtils类的使用及代码示例

x33g5p2x  于2022-02-03 转载在 其他  
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本文整理了Java中uk.ac.ebi.intact.model.util.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：uk.ac.ebi.intact.model.util.XrefUtils
类名称：XrefUtils

XrefUtils介绍

[英]Utils with xrefs
[中]带有外部参照的UTIL

代码示例

代码示例来源：origin: uk.ac.ebi.intact/intact-core

public <X extends Xref> X createIdentityXref(AnnotatedObject<X,?> parent, String primaryId, CvDatabase cvDatabase) {
  return XrefUtils.createIdentityXref(parent, primaryId, getIdentityQualifier(), cvDatabase);
}

代码示例来源：origin: uk.ac.ebi.intact.dataexchange/intact-cvutils

protected CvObjectXref createIdentityXref( CvObject parent, String id ) {
  CvObjectXref idXref = null;
  if (id != null) {
    if (id.startsWith("MI")) {
      idXref = XrefUtils.createIdentityXrefPsiMi(parent, id);
      idXref.prepareParentMi();
    } else if (id.startsWith("IA")) {
      idXref = XrefUtils.createIdentityXref(parent, id, nonMiCvDatabase);
    } else if (id.startsWith("MOD")) {
      idXref = XrefUtils.createIdentityXref(parent, id, psimod);
    } else {
      if (log.isWarnEnabled()) log.warn("Uknown prefix for id: "+id+". Will store as a cross reference to database: "+nonMiCvDatabase.getShortLabel());
      idXref = XrefUtils.createIdentityXref(parent, id, nonMiCvDatabase);
    }
  }
  return idXref;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

/**
   * Returns the Xref with MI number for given CV object
   *
   * @param cvobj the CV to search for MI
   *
   * @return xref with MI or null if no xref found whose primaryid starts with 'MI:'.
   */
  private static Xref getMIXref( CvInteractorType cvobj ) {
    final Collection<CvObjectXref> xrefs = XrefUtils.getIdentityXrefs( cvobj );
    if( xrefs.size() != 1 ) {
      throw new IllegalStateException( "Only a single MI identity expected here, found " + xrefs.size() );
    }

    return xrefs.iterator().next();
  }
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

/**
 * Gets the unique identifier of a CvObject. If it has PSI MI Identifier (miIdentifier) return it,
 * if not, return the 'CvDatabase.intact' identifier; otherwise return the primaryId of the first identity xref found.
 *
 * @param cvObject The object to get the identifier from.
 * @return The identifier. Will be null if no miIdentifier or identity xref is found.
 * @since 1.8.0
 */
public static String getIdentity(CvObject cvObject) {
  if (cvObject == null) return null;
  // try the PSI MI first
  if (cvObject.getIdentifier() != null) {
    return cvObject.getIdentifier();
  }
  // try to get the identity with CvDatabase 'intact'
  CvObjectXref idXref = XrefUtils.getIdentityXref(cvObject, CvDatabase.INTACT);
  // get the first identity, if any
  if (idXref == null) {
    Collection<CvObjectXref> idXrefs = XrefUtils.getIdentityXrefs(cvObject);
    if (!idXrefs.isEmpty()) {
      idXref = idXrefs.iterator().next();
    }
  }
  return (idXref != null) ? idXref.getPrimaryId() : null;
}

代码示例来源：origin: uk.ac.ebi.intact/intact-core

public static CvObjectXref getPsiMiIdentityXref(CvObject cvObject) {
  return XrefUtils.getPsiMiIdentityXref(cvObject);    
}

代码示例来源：origin: uk.ac.ebi.intact/intact-core

public static <T extends CvObject> T createCvObject(Institution institution, Class<T> cvClass, String primaryId, String shortLabel) {
    T cv = ClassUtils.newInstance(cvClass);
    cv.setOwner(institution);
    cv.setShortLabel(shortLabel);

    CvObjectXref idXref = XrefUtils.createIdentityXrefPsiMi(cv, primaryId);
    cv.addXref(idXref);

    return cv;
  }
}

代码示例来源：origin: uk.ac.ebi.intact/intact-core

public static boolean hasIdentity(CvObject cvObject, String psiMi) {
  return XrefUtils.hasIdentity(cvObject, psiMi);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, CvDatabase cvDatabase) {
  String dbMi = cvDatabase.getIdentifier();
  return getIdentityXref(annotatedObject, dbMi);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) {
  X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass());
  xref.setOwner(parent.getOwner());
  xref.setParent(parent);
  xref.setPrimaryId(primaryId);
  xref.setCvXrefQualifier(cvXrefQualifer);
  xref.setCvDatabase(cvDatabase);
  return xref;
}

代码示例来源：origin: uk.ac.ebi.intact/intact-core

public <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X,?> parent, String primaryId) {
  return XrefUtils.createIdentityXrefUniprot(parent, primaryId);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

public <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X,?> parent, String chebiId) {
  return XrefUtils.createIdentityXrefChebi(parent, chebiId);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

/**
 * @deprecated To get the PSI-MI identifier, just invoke CvObject.getMiIdentifier()
 */
@Deprecated
public static CvObjectXref getPsiMiIdentityXref(CvObject cvObject) {
  return XrefUtils.getPsiMiIdentityXref(cvObject);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

/**
 * Gets the unique identifier of a CvObject. If it has PSI MI Identifier (miIdentifier) return it,
 * if not, return the 'CvDatabase.intact' identifier; otherwise return the primaryId of the first identity xref found.
 *
 * @param cvObject The object to get the identifier from.
 * @return The identifier. Will be null if no miIdentifier or identity xref is found.
 * @since 1.8.0
 */
public static String getIdentity(CvObject cvObject) {
  if (cvObject == null) return null;
  // try the PSI MI first
  if (cvObject.getIdentifier() != null) {
    return cvObject.getIdentifier();
  }
  // try to get the identity with CvDatabase 'intact'
  CvObjectXref idXref = XrefUtils.getIdentityXref(cvObject, CvDatabase.INTACT);
  // get the first identity, if any
  if (idXref == null) {
    Collection<CvObjectXref> idXrefs = XrefUtils.getIdentityXrefs(cvObject);
    if (!idXrefs.isEmpty()) {
      idXref = idXrefs.iterator().next();
    }
  }
  return (idXref != null) ? idXref.getPrimaryId() : null;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

public static <T extends CvObject> T createCvObject(Institution institution, Class<T> cvClass, String miIdentifier, String shortLabel) {
  T cv = ClassUtils.newInstance(cvClass);
  cv.setOwner(institution);
  cv.setShortLabel(shortLabel);
  cv.setIdentifier(miIdentifier);
  if (miIdentifier != null) {
    CvObjectXref idXref = XrefUtils.createIdentityXrefPsiMi(cv, miIdentifier);
    cv.addXref(idXref);
    idXref.prepareParentMi();
  }
  return cv;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

public static boolean hasIdentity(CvObject cvObject, String psiMi) {
  if (cvObject.getIdentifier() != null && cvObject.getIdentifier().equals(psiMi)) {
    return true;
  }
  return XrefUtils.hasIdentity(cvObject, psiMi);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, CvDatabase cvDatabase) {
  String dbMi = cvDatabase.getIdentifier();
  return getIdentityXref(annotatedObject, dbMi);
}

代码示例来源：origin: uk.ac.ebi.intact/intact-core

public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) {
  X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass());
  xref.setOwner(parent.getOwner());
  xref.setParent(parent);
  xref.setPrimaryId(primaryId);
  xref.setCvXrefQualifier(cvXrefQualifer);
  xref.setCvDatabase(cvDatabase);
  return xref;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

public <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X,?> parent, String primaryId) {
  return XrefUtils.createIdentityXrefUniprot(parent, primaryId);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

public <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X,?> parent, String chebiId) {
  return XrefUtils.createIdentityXrefChebi(parent, chebiId);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

public <X extends Xref> X createIdentityXref(AnnotatedObject<X,?> parent, String primaryId, CvDatabase cvDatabase) {
  return XrefUtils.createIdentityXref(parent, primaryId, getIdentityQualifier(), cvDatabase);
}

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