psidev.psi.mi.jami.model.Interactor java code examples

Common ways to obtain Interactor

private void myMethod () {
 Interactor i =Participant participant;participant.getInteractor()
Smart code suggestions by Tabnine
}

/***
 * This method will copy properties of interactor source in interactor target and will override all the other properties of Target interactor.
 * @param source
 * @param target
 */
public static void copyAndOverrideBasicInteractorProperties(Interactor source, Interactor target){
  if (source != null && target != null){
    target.setShortName(source.getShortName());
    target.setFullName(source.getFullName());
    target.setInteractorType(source.getInteractorType());
    target.setOrganism(source.getOrganism());
    // copy collections
    target.getAnnotations().clear();
    target.getAnnotations().addAll(source.getAnnotations());
    target.getIdentifiers().clear();
    target.getIdentifiers().addAll(source.getIdentifiers());
    target.getAliases().clear();
    target.getAliases().addAll(source.getAliases());
    target.getXrefs().clear();
    target.getXrefs().addAll(source.getXrefs());
    target.getChecksums().clear();
    target.getChecksums().addAll(source.getChecksums());
  }
}

public void writeUniqueIdentifier(P participant) throws IOException {
  if (participant == null){
    writer.write(MitabUtils.EMPTY_COLUMN);
  }
  else {
    Interactor interactor = participant.getInteractor();
    // write first identifier
    if (!interactor.getIdentifiers().isEmpty()){
      writeIdentifier(interactor.getPreferredIdentifier());
    }
    else{
      writer.write(MitabUtils.EMPTY_COLUMN);
    }
  }
}

if (!interactor1.getIdentifiers().isEmpty() || !interactor2.getIdentifiers().isEmpty()){
  Collection<Xref> identifiers1 = interactor1.getIdentifiers();
  Collection<Xref> identifiers2 = interactor2.getIdentifiers();
  return identifierCollectionComparator.compare(identifiers1, identifiers2);
String shortName1 = interactor1.getShortName();
String shortName2 = interactor2.getShortName();
int comp = shortName1.compareTo(shortName2);
String fullName1 = interactor1.getFullName();
String fullName2 = interactor2.getFullName();
if (fullName1 == null && fullName2 == null){
  comp = 0;
Collection<Alias> aliases1 = interactor1.getAliases();
Collection<Alias> aliases2 = interactor2.getAliases();

if (interactor.getOrganism() != null){
  checkOrganism(messages, interactor.getOrganism(), interactor, "interactor");
checkCv(messages, interactor.getInteractorType(), interactor, "interactor");
for (Alias alias : interactor.getAliases()){
  checkAlias(messages, alias, interactor, "interactor");
for (Xref ref : interactor.getIdentifiers()){
  checkXref(messages, ref, interactor, "interactor");
for (Xref ref : interactor.getXrefs()){
  checkXref(messages, ref, interactor, "interactor");
for (Annotation a : interactor.getAnnotations()){
  checkAnnotation(messages, a, interactor, "interactor");
for (Checksum a : interactor.getChecksums()){
  checkChecksum(messages, a, interactor, "interactor");

private void writeInteractorComponent(Interactor object) throws IOException {
  MIJsonUtils.writeStartObject(writer);
  MIJsonUtils.writeProperty("label", JSONValue.escape(object.getShortName()), writer);
  getCvWriter().write(object.getInteractorType());
  if (object.getOrganism() != null){
    MIJsonUtils.writeSeparator(writer);
    MIJsonUtils.writePropertyKey("organism", writer);
    getOrganismWriter().write(object.getOrganism());
  if (object.getPreferredIdentifier() != null){
    MIJsonUtils.writeSeparator(writer);
    MIJsonUtils.writePropertyKey("identifier", writer);
    getIdentifierWriter().write(object.getPreferredIdentifier());

CvTerm type1 = interactor1.getInteractorType();
CvTerm type2 = interactor2.getInteractorType();
Organism organism1 = interactor1.getOrganism();
Organism organism2 = interactor2.getOrganism();

this.ac = (interactor instanceof IntactInteractor) ? ((IntactInteractor)interactor).getAc() : interactor.getShortName();
this.shortName = interactor.getShortName();
for (Xref xref : interactor.getIdentifiers()) {
  if (XrefUtils.isXrefFromDatabase(xref, Xref.UNIPROTKB_MI, Xref.UNIPROTKB)
      && XrefUtils.doesXrefHaveQualifier(xref, Xref.IDENTITY_MI, Xref.IDENTITY)){
for (Alias alias : interactor.getAliases()) {
  if (AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_MI, Alias.GENE_NAME)){
    this.shortName = alias.getName();

public void onInteractorTypeUpdate(T protein, CvTerm old) {
  interactorChangeLogger.log(Level.INFO, "The interactor type" + old.toString() + " has been replaced with " + protein.getInteractorType().toString()+ " in the interactor " + protein.toString());
}

escapeAndWriteString(interactor.getShortName());
writer.write("(");
writer.write(MitabUtils.DISPLAY_SHORT);
if (interactor.getFullName() != null){
  writer.write("|");
  writer.write(CvTerm.PSI_MI);
  writer.write(":");
  escapeAndWriteString(interactor.getFullName());
  writer.write("(");
  writer.write(MitabUtils.DISPLAY_LONG);
if (!interactor.getAliases().isEmpty()){
  Iterator<Alias> aliasIterator = interactor.getAliases().iterator();

interactor.setFullName(fullName);
  interactor.getIdentifiers().addAll(uniqueId);
interactor.getChecksums().addAll(checksum);
  interactor.getXrefs().addAll(xref);

public void onShortNameUpdate(T protein, String oldShortName) {
  interactorChangeLogger.log(Level.INFO, "The short name " + oldShortName + " has been updated with " + protein.getShortName() + " in the interactor " + protein.toString());
}

if( interactor.getInteractorType() != null && (RuleUtils.isSmallMolecule( ontologyManager, interactor ) || RuleUtils.isPolysaccharide( ontologyManager, interactor ) )) {
  final Set<String> dbRefs = RuleUtils.collectNames( dbs );
  final Collection<Xref> identities = XrefUtils.searchAllXrefsHavingDatabaseAndQualifier(interactor.getIdentifiers(), dbMiRefs, dbRefs, Arrays.asList(Xref.IDENTITY_MI), Arrays.asList(Xref.IDENTITY));
else if( interactor.getInteractorType() != null && RuleUtils.isBiopolymer(ontologyManager, interactor)) {
  final Set<String> dbRefs = RuleUtils.collectNames( dbs );
  final Collection<Xref> identities = XrefUtils.searchAllXrefsHavingDatabaseAndQualifier(interactor.getIdentifiers(), dbMiRefs, dbRefs, Arrays.asList(Xref.IDENTITY_MI), Arrays.asList(Xref.IDENTITY));
  if(identities.isEmpty() ) {

Collection<Xref> identifiers = container.getIdentifiers();
Collection<Xref> databaseReferences = container.getXrefs();

protected void createAliasFromAltId(Interactor interactor, MitabXref ref) {
  // create alias from xref
  MitabAlias alias = new MitabAlias(ref.getDatabase().getShortName(), ref.getQualifier(), ref.getId(), ref.getSourceLocator());
  interactor.getAliases().add(alias);
  if (listener != null){
    listener.onSyntaxWarning(ref, "Found an Alias in the alternative identifiers column. Will load it as a checksum.");
  }
}

public void onOrganismUpdate(T protein, Organism old) {
  if (old == null){
    interactorChangeLogger.log(Level.INFO, "The organism has been initialised for the interactor " + protein.toString());
  }
  else if (protein.getOrganism() == null){
    interactorChangeLogger.log(Level.INFO, "The organism has been reset for the interactor " + protein.toString());
  }
  else {
    interactorChangeLogger.log(Level.INFO, "The organism " + old.toString() + " has been replaced with " + protein.getOrganism() + " in the interactor " + protein.toString());
  }
}

protected void processInteractorPool(Collection<MitabXref> xref, InteractorPool interactor) {
  InteractorPool pool = (InteractorPool)interactor;
  for (Xref ref : xref){
    // we have a component of the interactor pool
    if (XrefUtils.doesXrefHaveQualifier(ref, Xref.INTERACTOR_SET_QUALIFIER_MI, Xref.INTERACTOR_SET_QUALIFIER)){
      Interactor subInteractor = interactorFactory.createInteractorFromDatabase(ref.getDatabase(), ref.getId().toLowerCase());
      if (subInteractor != null){
        subInteractor.getIdentifiers().add(new MitabXref(ref.getDatabase(), ref.getId(), ref.getVersion(), CvTermUtils.createIdentityQualifier()));
        ((MitabInteractor)subInteractor).setSourceLocator(((MitabXref)ref).getSourceLocator());
      }
      // create a default interactor
      else{
        subInteractor = interactorFactory.createInteractor(ref.getId().toLowerCase(), CvTermUtils.createUnknownInteractorType());
        subInteractor.getIdentifiers().add(new MitabXref(ref.getDatabase(), ref.getId(), ref.getVersion(), CvTermUtils.createIdentityQualifier()));
        ((MitabInteractor)subInteractor).setSourceLocator(((MitabXref)ref).getSourceLocator());
      }
      // add the component to the interactor pool
      pool.add(subInteractor);
    }
    // we have a simple xref
    else{
      pool.getXrefs().add(ref);
    }
  }
}

public void writeParticipantAnnotations(P participant) throws IOException {
  if (participant != null){
    if (!participant.getInteractor().getAnnotations().isEmpty()){
      Iterator<Annotation> interactorAnnotationIterator = participant.getInteractor().getAnnotations().iterator();

if (!participant.getInteractor().getXrefs().isEmpty()){
  Iterator<Xref> interactorXrefIterator = participant.getInteractor().getXrefs().iterator();
    while (interactorIterator.hasNext()){
      Interactor subInteractor = interactorIterator.next();
      Xref preferredId = subInteractor.getPreferredIdentifier();
      if (preferredId != null){
        getWriter().write(MitabUtils.FIELD_SEPARATOR);
    while (interactorIterator.hasNext()){
      Interactor subInteractor = interactorIterator.next();
      Xref preferredId = subInteractor.getPreferredIdentifier();
      if (preferredId != null){
        getWriter().write(MitabUtils.FIELD_SEPARATOR);
    while (interactorIterator.hasNext()){
      Interactor subInteractor = interactorIterator.next();
      Xref preferredId = subInteractor.getPreferredIdentifier();
      if (preferredId != null){
        if (!first){

public void writeParticipantChecksums(P participant) throws IOException {
  if (participant != null){
    if (!participant.getInteractor().getChecksums().isEmpty()){
      Iterator<Checksum> checksumIterator = participant.getInteractor().getChecksums().iterator();
      while(checksumIterator.hasNext()){
        writeChecksum(checksumIterator.next());
        if (checksumIterator.hasNext()){
          getWriter().write(MitabUtils.FIELD_SEPARATOR);
        }
      }
    }
    else{
      getWriter().write(MitabUtils.EMPTY_COLUMN);
    }
  }
  else {
    getWriter().write(MitabUtils.EMPTY_COLUMN);
  }
}

Interactor interactor = object.getInteractor();
keyValues = MIJsonUtils.extractInteractionId(interactor.getPreferredIdentifier(), (Complex)interactor);
keyValues = MIJsonUtils.extractInteractorId(interactor.getPreferredIdentifier(), interactor);

Javadoc

Molecule or complex of molecules that interacts with other molecules/complexes

Most used methods

getShortName
The short name of the interactor. It cannot be null or empty. Ex: brca2
getAliases
Collection of aliases for an interactor The Collection cannot be null and if the interactor does not
getAnnotations
Collection of annotations for an interactor. The set cannot be null and if the interactor does not h
getIdentifiers
Set of identifiers for this interactor. The identifiers can be from different databases, can be prim
getInteractorType
The molecule type of this interactor. It is a controlled vocabulary term and cannot be null. Ex: pro
getOrganism
The original source organism for this interactor. It can be null in case of chemical compounds/synth
getChecksums
Set of checksums computed for this interactor. The Collection cannot be null so when an interactor d
getXrefs
Collection of other xrefs that give more information about the interactor. Ex: GO references to give
getFullName
The full name of the interactor. It can be null Ex: Breast cancer type 2 susceptibility protein
getPreferredIdentifier
The identifier in the list of identifiers which is the preferred identifier. If no identifiers is pr
setFullName
Sets the full name of the interactor
setOrganism
Sets the source organism of this interactor

Popular in Java

Making http requests using okhttp
getSystemService (Context)
setRequestProperty (URLConnection)
requestLocationUpdates (LocationManager)
Font (java.awt)
The Font class represents fonts, which are used to render text in a visible way. A font provides the
InputStreamReader (java.io)
A class for turning a byte stream into a character stream. Data read from the source input stream is
BigInteger (java.math)
An immutable arbitrary-precision signed integer.FAST CRYPTOGRAPHY This implementation is efficient f
LinkedHashMap (java.util)
LinkedHashMap is an implementation of Map that guarantees iteration order. All optional operations a
ThreadPoolExecutor (java.util.concurrent)
An ExecutorService that executes each submitted task using one of possibly several pooled threads, n
IOUtils (org.apache.commons.io)
General IO stream manipulation utilities. This class provides static utility methods for input/outpu
PhpStorm for WordPress

How to useInteractor in psidev.psi.mi.jami.model

Best Java code snippets using psidev.psi.mi.jami.model.Interactor (Showing top 20 results out of 315)

How to use
Interactor
in
psidev.psi.mi.jami.model