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How to use
Participant
in
psidev.psi.mi.xml.model

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

origin: psidev.psi.mi/psi25-xml

jParticipant.setId( mParticipant.getId() );
if ( mParticipant.hasInteractor() || mParticipant.hasInteractorRef() ) {
    if ( mParticipant.hasInteractorRef() )
      jParticipant.setInteractorRef( mParticipant.getInteractorRef().getRef() );
    else
      jParticipant.setInteractorRef( mParticipant.getInteractor().getId() );
    jParticipant.setInteractor( interactorConverter.toJaxb( mParticipant.getInteractor() ) );
} else if ( mParticipant.hasInteraction() ) {
  jParticipant.setInteractionRef( mParticipant.getInteraction().getId() );
} else {
  throw new ConverterException( "Neither an interactor or an interaction was present in participant " + mParticipant.getId() );
if ( mParticipant.hasBiologicalRole() ) {
  jParticipant.setBiologicalRole( cvTypeConverter.toJaxb( mParticipant.getBiologicalRole() ) );
if ( mParticipant.hasNames() ) {
  jParticipant.setNames( namesConverter.toJaxb( mParticipant.getNames() ) );
if ( mParticipant.hasXref() ) {
  jParticipant.setXref( xrefConverter.toJaxb( mParticipant.getXref() ) );
if ( mParticipant.hasConfidences() ) {
  if ( jParticipant.getConfidenceList() == null ) {
    jParticipant.setConfidenceList( new ConfidenceListType() );
origin: psidev.psi.mi/psi25-xml

public static Participant createParticipant(Interactor interactor, BiologicalRole biologicalRole, ExperimentalRole experimentalRole) {
  Participant participant = new Participant();
  assignNextId(participant);
  participant.setInteractor(interactor);
  participant.setBiologicalRole(biologicalRole);
  participant.getExperimentalRoles().add(experimentalRole);
  return participant;
}
origin: psidev.psi.mi/psimitab

protected boolean isBait(Participant participant) {
  if (participant == null) {
    throw new IllegalArgumentException("Participant must not be null.");
  }
  if (participant.hasExperimentalRoles()) {
    for (ExperimentalRole role : participant.getExperimentalRoles()) {
      // search for bait
      log.debug("Checking if participant (id:" + participant.getId() + ") is a bait.");
      if (XrefUtils.hasPsiId(role.getXref(), BAIT_MI_REF)) {
        log.debug("Yes it is.");
        return true;
      }
      log.debug("No it is not.");
    }
  }
  return false;
}
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

public static Collection<Object> nonRedundantInteractorsFromPsiEntry(Entry psiEntry) {
  Map<Integer, Object> nonRedundantInteractors = new HashMap<Integer, Object>();
  if( ConverterContext.getInstance().isGenerateExpandedXml() ) {
    // iterate to get the unique experiments/interactors
    for (psidev.psi.mi.xml.model.Interaction interaction : psiEntry.getInteractions()) {
      for (Participant participant : interaction.getParticipants()) {
        if (participant.getInteractor() != null){
          nonRedundantInteractors.put(participant.getInteractor().getId(), participant.getInteractor());
        }
        else if (participant.getInteraction() != null){
          nonRedundantInteractors.put(participant.getInteraction().getId(), participant.getInteraction());
        }
      }
    }
  } else {
    for ( psidev.psi.mi.xml.model.Interactor interactor : psiEntry.getInteractors() ) {
      nonRedundantInteractors.put( interactor.getId(), interactor );
    }
  }
  return nonRedundantInteractors.values();
}
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

IntactConverterUtils.populateNames(participant.getNames(), component);
IntactConverterUtils.populateXref(participant.getXref(), component, new XrefConverter<ComponentXref>(getInstitution(), ComponentXref.class));
IntactConverterUtils.populateAnnotations(participant.getAttributes(), component, getInstitution());
if (participant.getInteractor() != null){
  interactor = this.interactorConverter.psiToIntact(participant.getInteractor());
else if (participant.getInteraction() != null){
  interactor = this.interactionConverter.psiToIntact(participant.getInteraction());
BiologicalRole psiBioRole = participant.getBiologicalRole();
if (psiBioRole == null) {
  psiBioRole = PsiConverterUtils.createUnspecifiedBiologicalRole();
if (participant.getExperimentalRoles().size() > 1) {
  throw new UnsupportedConversionException("Cannot convert participants with more than one experimental role: "+participant);
if (participant.getExperimentalRoles().isEmpty()) {
  if (log.isWarnEnabled()) log.warn("Participant without experimental roles: " + participant);
  roles = participant.getExperimentalRoles();
for (psidev.psi.mi.xml.model.Feature psiFeature : participant.getFeatures()) {
  Feature feature = featureConverter.psiToIntact(psiFeature);
  component.addFeature(feature);
for (ParticipantIdentificationMethod pim : participant.getParticipantIdentificationMethods()) {
  CvIdentification cvIdentification = pimConverter.psiToIntact(pim);
  component.getParticipantDetectionMethods().add(cvIdentification);
origin: psidev.psi.mi/psi25-xml

Participant mParticipant = new Participant();
mParticipant.setId( jParticipant.getId() );
  mInteractor = factory.getInteractorDAO().retreive( jParticipant.getInteractorRef() );
  if ( mInteractor == null ) {
    mParticipant.setInteractorRef( new InteractorRef( jParticipant.getInteractorRef() ) );
  } else {
    mParticipant.setInteractor( mInteractor );
  mParticipant.setInteractor( mInteractor );
  mInteraction = factory.getInteractionDAO().retreive( jParticipant.getInteractionRef() );
  if ( mInteraction == null ) {
    mParticipant.setInteractionRef( new InteractionRef( jParticipant.getInteractionRef() ) );
    mParticipant.setInteraction( mInteraction);
  mParticipant.setBiologicalRole( cvTypeConverter.fromJaxb( jParticipant.getBiologicalRole(), BiologicalRole.class ) );
  mParticipant.setNames( namesConverter.fromJaxb( jParticipant.getNames() ) );
  mParticipant.setXref( xrefConverter.fromJaxb( jParticipant.getXref() ) );
    mParticipant.getConfidenceList().add( confidenceConverter.fromJaxb( jConfidence ) );
  for ( psidev.psi.mi.xml254.jaxb.ExperimentalInteractor jExperimentalInteractor :
      jParticipant.getExperimentalInteractorList().getExperimentalInteractors() ) {
    mParticipant.getExperimentalInteractors().add( experimentalInteractorConverter.fromJaxb( jExperimentalInteractor ) );
origin: psidev.psi.mi/psi25-xml

if ( participant.hasInteractionRef() ) {
  InteractionRef ref = participant.getInteractionRef();
  participant.setInteractionRef( null );
      throw new PsimiXmlReaderException("The interaction " + ref.getRef() + " has a participant ("+participant.getId()+") which is an interaction and this interaction is referring to itself." +
          " It is not a valid participant.");
      throw new PsimiXmlReaderException("The participant "+participant.getId()+" refers to the interaction " + ref.getRef() + " but this interaction cannot be found by the parser. Please check that this interaction is described somewhere in the list of interactions.");
    participant.setInteraction(i); // recursive call !!
    throw new PsimiXmlReaderException("The  participant ("+participant.getId()+") doesn't have any interactions attached to it.");
if ( participant.hasInteractorRef() ) {
  InteractorRef ref = participant.getInteractorRef();
  InputStreamRange irange = index.getInteractorPosition( ref.getRef() );
  InputStream iis = null;
    throw new PsimiXmlReaderException("The participant "+participant.getId()+" refers to the interactor " + ref.getRef() + " but this interactior cannot be found by the parser. " +
        "Please check that you are not mixing the expanded PSI xml schema and the compact PSI xml schema together. Either all the interactors are described at the beginning of the file and" +
        " all the participants then use references to pre-declared interactors or all the interactors are only described at the level of the participants and no interactor reference can be used.");
  participant.setInteractorRef( null );
  participant.setInteractor( interactor );
if ( participant.hasParticipantIdentificationMethods() ) {
  for ( ParticipantIdentificationMethod pim : participant.getParticipantIdentificationMethods() ) {
    if ( pim.hasExperimentRefs() ) {
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

  participant.getExperimentalRoles().add( expRole );
participant.setBiologicalRole(bioRole);
  psidev.psi.mi.xml.model.Interaction interactor = interactionConverter.intactToPsi((InteractionImpl) intactObject.getInteractor());
  if( ConverterContext.getInstance().isGenerateExpandedXml() ) {
    participant.setInteraction(interactor);
  } else {
    participant.setInteractionRef(new InteractionRef(interactor.getId()));
  psidev.psi.mi.xml.model.Interactor interactor = interactorConverter.intactToPsi(intactObject.getInteractor());
  if( ConverterContext.getInstance().isGenerateExpandedXml() ) {
    participant.setInteractor(interactor);
  } else {
    participant.setInteractorRef(new InteractorRef(interactor.getId()));
  participant.getParticipantIdentificationMethods().add(participantIdentificationMethod);
  participant.getExperimentalPreparations().add(expPrep);
    participant.getFeatures().add(psiFeature);
    participant.getHostOrganisms().add(hostOrganism);
  participant.getConfidenceList().add( confidence);
    if (!participant.getAttributes().contains(authConf)){
      participant.getAttributes().add(authConf);
origin: psidev.psi.mi/psimitab

Interactor xmlInteractor = xmlParticipant.getInteractor();
if (xmlParticipant.hasBiologicalRole()) {
  BiologicalRole xmlBioRole = xmlParticipant.getBiologicalRole();
  CrossReference cr = cvConverter.toMitab(xmlBioRole);
if (xmlParticipant.hasExperimentalRoles()) {
  Collection<ExperimentalRole> xmlExpRoles = xmlParticipant.getExperimentalRoles();
if (xmlParticipant.getAttributes() != null) {
  Collection<Attribute> xmlParticipantAttributes = xmlParticipant.getAttributes();
  for (Attribute xmlParticipantAttribute : xmlParticipantAttributes) {
    String name = xmlParticipantAttribute.getName();
if (xmlParticipant.getFeatures() != null) {
  Collection<Feature> xmlFeatures = xmlParticipant.getFeatures();
  List<psidev.psi.mi.tab.model.Feature> tabFeatures
      = new ArrayList<psidev.psi.mi.tab.model.Feature>();
if (xmlParticipant.getAttributes() != null) {
  Collection<Attribute> attributes = xmlParticipant.getAttributes();
if (xmlParticipant.getParticipantIdentificationMethods() != null) {
  Collection<ParticipantIdentificationMethod> xmlPartIdentMethodsRoles = xmlParticipant.getParticipantIdentificationMethods();
origin: org.biopax.paxtools/psimi-converter

private Entity createBiopaxEntity(Participant participant, Set<String> avail, Provenance pro) 
  LOG.debug("createBiopaxEntity, processing participant: " + participant.getId());
  if (participant.hasInteractor()) {
    entity = createParticipant(participant, participant.getInteractor(), avail, pro, false);
  } else if(participant.hasInteraction()) {
    entity = (Complex) processInteraction(participant.getInteraction(), avail, pro, true);
    .create(Evidence.class, genUri(Evidence.class, "p",participant.getId()));
  if(participant.hasExperimentalRoles() 
    || participant.hasExperimentalInteractors() 
      || participant.hasFeatures()) 
    if(participant.hasExperimentalInteractors()) {
      for(ExperimentalInteractor experimentalInteractor : participant.getExperimentalInteractors()) {
        Interactor interactor = experimentalInteractor.getInteractor();
        LOG.debug("createBiopaxEntity, participant: " + participant.getId() 
            + ", exp. interactor: " + interactor.getId());
        Entity expEntity = createParticipant(participant, interactor, avail, pro, true);
      LOG.debug("createBiopaxEntity, participant: " + participant.getId() 
          + " doesn't have any exp. interactors");
      createAddExperimentalForm(participant, participantEvidence, null, null);
origin: psidev.psi.mi/psimitab

participant = new Participant();
participant.setId(IdentifierGenerator.getInstance().nextId());
participant.setInteractor(interactor);
participant.setBiologicalRole(biologicalRole);
participant.getExperimentalRoles().add(experimentalRole);
      xmlfeature.getAttributes().add(attribute);
    participant.getFeatures().add(xmlfeature);
    if (!participant.getAttributes().contains(attribute)) {
      participant.getAttributes().add(attribute);
    participant.getParticipantIdentificationMethods().add(xmlParticipantIdMethod);
origin: psidev.psi.mi/psi25-xml

for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) {
  if (!participantIds.contains(mParticipant.getId())) {
    mEntry.getInteractors().add(mParticipant.getInteractor());
    participantIds.add(mParticipant.getInteractor().getId());
origin: psidev.psi.mi/psimitab

  public int compare(Participant p1, Participant p2) {
    Interactor i1 = p1.getInteractor();
    if( i1 == null ) {
      throw new IllegalArgumentException( "Both participant should hold a valid interactor." );
    }
    Interactor i2 = p2.getInteractor();
    if( i2 == null ) {
      throw new IllegalArgumentException( "Both participant should hold a valid interactor." );
    }
    String name1 = getName( i1 );
    String name2 = getName( i2 );
    int result;
    if ( name1 == null ) {
      result = -1;
    } else if ( name2 == null ) {
      result = 1;
    } else {
      result = name1.compareTo( name2 );
    }
    return result;
  }
} );
origin: psidev.psi.mi/psimitab

protected String displayParticipant(Participant p) {
  // fetch role
  String role = "";
  for (ExperimentalRole aRole : p.getExperimentalRoles()) {
    if (role.length() > 0) {
      role += "&";
    }
    if (aRole.hasNames()) {
      role += aRole.getNames().getShortLabel();
    } else {
      role += "?";
    }
  }
  // fetch interactor
  String interactor = p.getInteractor().getNames().getShortLabel();
  return interactor + ":" + role;
}
origin: org.biopax.paxtools/psimi-converter

for(Feature f : participant.getFeatures()) {
  if(exp==null || f.getExperiments().contains(exp) || f.getExperiments().isEmpty()) {
    EntityFeature feature = getFeature(ModificationFeature.class, f);			
if (participant.hasExperimentalRoles()) {
  for (ExperimentalRole role : participant.getExperimentalRoles()) {
    if(exp==null || role.getExperiments().contains(exp) || role.getExperiments().isEmpty()) {
origin: psidev.psi.mi/psi25-xml

Interactor interactor = participant.getInteractor();
String name = interactor.getNames().getShortLabel();
String type = interactor.getInteractorType().getNames().getShortLabel();
if ( participant.hasBiologicalRole() ) {
  role = participant.getBiologicalRole().getNames().getShortLabel();
origin: org.biopax.paxtools/psimi-converter

if(p.hasInteractor()) {
  String type = getName(p.getInteractor().getInteractorType().getNames());
  if(type==null) type = "protein"; //default type (if unspecified)
  participantTypes.add(type.toLowerCase());
} else if (p.hasInteraction()) {
  participantTypes.add("complex"); //hierarchical complex build up
    + "; so we'll replace 'gene' with 'dna' (a quick fix)");
for(Participant p : interaction.getParticipants()) {
  if(p.hasInteractor() && p.getInteractor().getInteractorType().hasNames()) {
    String type = getName(p.getInteractor().getInteractorType().getNames());
    if("gene".equalsIgnoreCase(type)) {
      p.getInteractor().getInteractorType().getNames().setShortLabel("dna");
origin: psidev.psi.mi/psi25-xml

private void removeInteractorRedundancy( EntrySet mEntrySet ) {
  if( ConverterContext.getInstance().getConverterConfig().getXmlForm() == PsimiXmlForm.FORM_COMPACT ) {
    for ( Entry entry : mEntrySet.getEntries() ) {
      Map<Interactor, Interactor> uniqueInteractors = new HashMap<Interactor, Interactor>();
      for ( Interaction interaction : entry.getInteractions() ) {
        for ( Participant participant : interaction.getParticipants() ) {
          if( participant.getInteractor() != null ) {
            final Interactor myInteractor = participant.getInteractor();
            if( uniqueInteractors.containsKey( myInteractor ) ) {
              final Interactor uniq = uniqueInteractors.get( myInteractor );
              participant.setInteractor( uniq );
            } else {
              uniqueInteractors.put( myInteractor, myInteractor );
            }
          }
        } // participants
      } // interactions
      // if we had a compact format, we cannot remove interactor redundancy without changing the interactions
      // and update the interactor xref
      if (!uniqueInteractors.isEmpty()){
        entry.getInteractors().clear();
        entry.getInteractors().addAll( uniqueInteractors.keySet() );
      }
    } // entries
  } // model is compact
}
origin: psidev.psi.mi/psi25-xml

psiIndex.addParticipant( participant.getId(), isr );
origin: org.biopax.paxtools/psimi-converter

if(participant.hasInteraction()) {
  participantInteractions.add(participant.getInteraction());
psidev.psi.mi.xml.modelParticipant

Javadoc

A molecule participating in an interaction.

Java class for participantType complex type.

The following schema fragment specifies the expected content contained within this class.

 
<complexType name="participantType"> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="names" type="{net:sf:psidev:mi}namesType" minOccurs="0"/> 
<element name="xref" type="{net:sf:psidev:mi}xrefType" minOccurs="0"/> 
<choice> 
<element name="interactorRef" type="{http://www.w3.org/2001/XMLSchema}int"/> 
<element name="interactor" type="{net:sf:psidev:mi}interactorElementType"/> 
<element name="interactionRef" type="{http://www.w3.org/2001/XMLSchema}int"/> 
</choice> 
<element name="participantIdentificationMethodList" minOccurs="0"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="participantIdentificationMethod" maxOccurs="unbounded"> 
<complexType> 
<complexContent> 
<extension base="{net:sf:psidev:mi}cvType"> 
<sequence minOccurs="0"> 
<element name="experimentRefList" type="{net:sf:psidev:mi}experimentRefListType" 
minOccurs="0"/> 
</sequence> 
</extension> 
</complexContent> 
</complexType> 
</element> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
<element name="biologicalRole" type="{net:sf:psidev:mi}cvType" minOccurs="0"/> 
<element name="experimentalRoleList" minOccurs="0"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="experimentalRole" maxOccurs="unbounded"> 
<complexType> 
<complexContent> 
<extension base="{net:sf:psidev:mi}cvType"> 
<sequence minOccurs="0"> 
<element name="experimentRefList" type="{net:sf:psidev:mi}experimentRefListType" 
minOccurs="0"/> 
</sequence> 
</extension> 
</complexContent> 
</complexType> 
</element> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
<element name="experimentalPreparationList" minOccurs="0"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="experimentalPreparation" maxOccurs="unbounded"> 
<complexType> 
<complexContent> 
<extension base="{net:sf:psidev:mi}cvType"> 
<sequence minOccurs="0"> 
<element name="experimentRefList" type="{net:sf:psidev:mi}experimentRefListType" 
minOccurs="0"/> 
</sequence> 
</extension> 
</complexContent> 
</complexType> 
</element> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
<element name="experimentalInteractorList" minOccurs="0"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="experimentalInteractor" maxOccurs="unbounded"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<choice> 
<element name="interactorRef" type="{http://www.w3.org/2001/XMLSchema}int"/> 
<element name="interactor" type="{net:sf:psidev:mi}interactorElementType"/> 
</choice> 
<element name="experimentRefList" type="{net:sf:psidev:mi}experimentRefListType" 
minOccurs="0"/> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
<element name="featureList" minOccurs="0"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="feature" type="{net:sf:psidev:mi}featureElementType" maxOccurs="unbounded"/> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
<element name="hostOrganismList" minOccurs="0"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="hostOrganism" maxOccurs="unbounded" minOccurs="0"> 
<complexType> 
<complexContent> 
<extension base="{net:sf:psidev:mi}bioSourceType"> 
<sequence minOccurs="0"> 
<element name="experimentRefList" type="{net:sf:psidev:mi}experimentRefListType" 
minOccurs="0"/> 
</sequence> 
</extension> 
</complexContent> 
</complexType> 
</element> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
<element name="confidenceList" type="{net:sf:psidev:mi}confidenceListType" minOccurs="0"/> 
<element name="parameterList" minOccurs="0"> 
<complexType> 
<complexContent> 
<restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> 
<sequence> 
<element name="parameter" maxOccurs="unbounded"> 
<complexType> 
<complexContent> 
<extension base="{net:sf:psidev:mi}parameterType"> 
<sequence> 
<element name="experimentRef" type="{http://www.w3.org/2001/XMLSchema}int"/> 
</sequence> 
<attribute name="uncertainty" type="{http://www.w3.org/2001/XMLSchema}decimal" /> 
</extension> 
</complexContent> 
</complexType> 
</element> 
</sequence> 
</restriction> 
</complexContent> 
</complexType> 
</element> 
<element name="attributeList" type="{net:sf:psidev:mi}attributeListType" minOccurs="0"/> 
</sequence> 
<attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> 
</restriction> 
</complexContent> 
</complexType> 

Most used methods

  • getInteractor
    Gets the value of the interactor property.
  • getExperimentalRoles
    Gets the value of the experimentalRoleList property.
  • getFeatures
    Gets the value of the featureList property.
  • getAttributes
    Gets the value of the attributeList property.
  • getBiologicalRole
    Gets the value of the biologicalRole property.
  • getExperimentalInteractors
    Gets the value of the experimentalInteractorList property.
  • getId
    Gets the value of the id property.
  • getInteraction
  • getParticipantIdentificationMethods
    Gets the value of the participantIdentificationMethodList property.
  • hasExperimentalRoles
    Check if the optional experimentalRoles is defined.
  • setBiologicalRole
    Sets the value of the biologicalRole property.
  • setInteractor
    Sets the value of the interactor property.
  • setBiologicalRole,
  • setInteractor,
  • <init>,
  • getConfidenceList,
  • getExperimentalPreparations,
  • getHostOrganisms,
  • getNames,
  • getParameters,
  • getXref,
  • hasAttributes

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