congrats Icon
New! Announcing our next generation AI code completions
Read here
Tabnine Logo
ParticipantEvidence.getIdentificationMethods
Code IndexAdd Tabnine to your IDE (free)

How to use
getIdentificationMethods
method
in
psidev.psi.mi.jami.model.ParticipantEvidence

Best Java code snippets using psidev.psi.mi.jami.model.ParticipantEvidence.getIdentificationMethods (Showing top 10 results out of 315)

  • Add the Codota plugin to your IDE and get smart completions
private void myMethod () {
List l =
  • Codota Iconnew ArrayList()
  • Codota Iconnew LinkedList()
  • Smart code suggestions by Tabnine
}
origin: psidev.psi.mi.jami/jami-mitab

public void writeParticipantIdentificationMethod(ParticipantEvidence participant) throws IOException {
  if (participant != null){
    if (!participant.getIdentificationMethods().isEmpty()){
      Iterator<CvTerm> methodIterator = participant.getIdentificationMethods().iterator();
      while(methodIterator.hasNext()){
        writeCvTerm(methodIterator.next());
        if (methodIterator.hasNext()){
          getWriter().write(MitabUtils.FIELD_SEPARATOR);
        }
      }
    }
    else{
      getWriter().write(MitabUtils.EMPTY_COLUMN);
    }
  }
  else {
    getWriter().write(MitabUtils.EMPTY_COLUMN);
  }
}
origin: psidev.psi.mi/psimi-schema-validator

/**
 * Make sure that a participant evidence has a valid Participant Identification Method that all the participant identification methods are valid.
 *
 * @param participant an interaction to check on.
 * @return a collection of validator messages.
 */
public Collection<ValidatorMessage> check( ParticipantEvidence participant ) throws ValidatorException {
  // list of messages to return
  Collection<ValidatorMessage> messages = Collections.EMPTY_LIST;
  if (participant.getIdentificationMethods().isEmpty()){
    MiContext context = RuleUtils.buildContext(participant, "participant");
    messages=Collections.singleton(new ValidatorMessage(" The participant does not have a participant identification method and it is required for MIMIx",
        MessageLevel.ERROR,
        context,
        this));
  }
  return messages;
}
origin: psidev.psi.mi.jami/jami-core

for (InteractionEvidence interaction : exp.getInteractionEvidences()){
  for (ParticipantEvidence p : interaction.getParticipants()){
    for (CvTerm identification : p.getIdentificationMethods()){
      if (frequencyMap.containsKey(identification)){
        int frequency = frequencyMap.get(identification)+1;
origin: psidev.psi.mi/psimi-schema-validator

/**
 * For each experiment associated with this interaction, collect all respective participants and their identification method and
 * check if the dependencies are correct.
 *
 * @param participant a participant to check on.
 * @return a collection of validator messages.
 *         if we fail to retreive the MI Ontology.
 */
public Collection<ValidatorMessage> check( ParticipantEvidence participant ) throws ValidatorException {
  Collection<ValidatorMessage> messages = Collections.EMPTY_LIST;
  if (participant.getInteraction() != null){
    InteractionEvidence interaction = participant.getInteraction();
    Experiment exp = interaction.getExperiment();
    if (exp != null){
      CvTerm detMethod = exp.getInteractionDetectionMethod();
      if (detMethod != null){
        if (!participant.getIdentificationMethods().isEmpty()){
          messages = new ArrayList<ValidatorMessage>(participant.getIdentificationMethods().size());
          for (CvTerm method : participant.getIdentificationMethods()){
            // build a context in case of error
            MiContext context = RuleUtils.buildContext(participant, "participant");
            context.addAssociatedContext(RuleUtils.buildContext(exp, "experiment"));
            messages.addAll( mapping.check( detMethod, method, context, this ) );
          }
        }
      }
    }
  }
  return messages;
}
origin: psidev.psi.mi.jami/jami-core

target.getParameters().clear();
target.getParameters().addAll(source.getParameters());
target.getIdentificationMethods().clear();
target.getIdentificationMethods().addAll(source.getIdentificationMethods());
origin: psidev.psi.mi.jami/jami-interactionviewer-json

if (!object.getIdentificationMethods().isEmpty()){
  MIJsonUtils.writeSeparator(getWriter());
  MIJsonUtils.writePropertyKey("identificationMethods", getWriter());
  MIJsonUtils.writeOpenArray(getWriter());
  Iterator<CvTerm> methodIterator = object.getIdentificationMethods().iterator();
  while (methodIterator.hasNext()){
    getCvWriter().write(methodIterator.next());
origin: psidev.psi.mi.jami/jami-core

Collection<CvTerm> method1 = experimentalParticipant1.getIdentificationMethods();
Collection<CvTerm> method2 = experimentalParticipant2.getIdentificationMethods();
origin: psidev.psi.mi.jami/jami-core

Collection<CvTerm> method1 = experimentalParticipant1.getIdentificationMethods();
Collection<CvTerm> method2 = experimentalParticipant2.getIdentificationMethods();
origin: psidev.psi.mi.jami/jami-core

Collection<CvTerm> method1 = experimentalParticipant1.getIdentificationMethods();
Collection<CvTerm> method2 = experimentalParticipant2.getIdentificationMethods();
origin: psidev.psi.mi/psimi-schema-validator

for (CvTerm term : p.getIdentificationMethods()){
  checkCv(messages, term, p, "participant");
psidev.psi.mi.jami.modelParticipantEvidencegetIdentificationMethods

Javadoc

The identification methods for this participant. Each identification method is a controlled vocabulary term. The collection cannot be null. If the participant does not have any identification methods, this method should return an empty collection Ex: western blot, immunostaining, ...

Popular methods of ParticipantEvidence

  • getExperimentalRole
    The experimental role of the participant. It is a controlled vocabulary term and cannot be null. It
  • getAnnotations
  • getConfidences
    The confidences for this participant. The Collection cannot be null. If the participant does not hav
  • getExpressedInOrganism
    The organisms in which the participant has been expressed. It can be null if not relevant or same as
  • getInteractor
  • getParameters
    Numerical parameters associated with this participant. The Collection cannot be null. If the partici
  • getAliases
  • getBiologicalRole
  • getExperimentalPreparations
    The experimental preparations for this participant. Each experimental preparation is a controlled vo
  • getFeatures
  • getInteraction
  • getXrefs
  • getInteraction,
  • getXrefs,
  • addFeature,
  • getCausalRelationships,
  • getStoichiometry,
  • setBiologicalRole,
  • setExperimentalRole,
  • setExpressedInOrganism,
  • setInteraction

Popular in Java

  • Updating database using SQL prepared statement
  • onRequestPermissionsResult (Fragment)
  • setContentView (Activity)
  • getContentResolver (Context)
  • Point (java.awt)
    A point representing a location in (x,y) coordinate space, specified in integer precision.
  • InputStreamReader (java.io)
    A class for turning a byte stream into a character stream. Data read from the source input stream is
  • PrintStream (java.io)
    Fake signature of an existing Java class.
  • RandomAccessFile (java.io)
    Allows reading from and writing to a file in a random-access manner. This is different from the uni-
  • Time (java.sql)
    Java representation of an SQL TIME value. Provides utilities to format and parse the time's represen
  • Semaphore (java.util.concurrent)
    A counting semaphore. Conceptually, a semaphore maintains a set of permits. Each #acquire blocks if
  • Top plugins for WebStorm
Tabnine Logo
  • Products

    Search for Java codeSearch for JavaScript code
  • IDE Plugins

    IntelliJ IDEAWebStormVisual StudioAndroid StudioEclipseVisual Studio CodePyCharmSublime TextPhpStormVimAtomGoLandRubyMineEmacsJupyter NotebookJupyter LabRiderDataGripAppCode
  • Company

    About UsContact UsCareers
  • Resources

    FAQBlogTabnine AcademyStudentsTerms of usePrivacy policyJava Code IndexJavascript Code Index
Get Tabnine for your IDE now