Interactor interactor1 = participant1.getInteractor(); Interactor interactor2 = participant2.getInteractor(); Stoichiometry stc1 = participant1.getStoichiometry(); Stoichiometry stc2 = participant2.getStoichiometry();
public void setParticipantAndAddFeature(P participant) { if (this.participant != null){ this.participant.removeFeature(this); } if (participant != null){ participant.addFeature(this); } }
public static void copyAndOverrideBasicEntityProperties(Entity source, Entity target, boolean createNewFeature){ if (source != null && target != null){ target.setStoichiometry(source.getStoichiometry()); target.getCausalRelationships().clear(); target.getCausalRelationships().addAll(source.getCausalRelationships()); target.setInteractor(source.getInteractor()); target.getFeatures().clear(); target.addAllFeatures(source.getFeatures()); target.getFeatures().clear(); for (Object f : source.getFeatures()){ Feature clone = new DefaultFeature(); FeatureCloner.copyAndOverrideBasicFeaturesProperties((Feature)f, clone); target.addFeature(clone);
public void onInteractorUpdate(Entity entity, Interactor oldInteractor) { entityChangeLogger.log(Level.INFO, "The interactor " + oldInteractor + " has been updated with " + entity.getInteractor() + " in the entity " + entity.toString()); } }
public void onStoichiometryUpdate(T entity, Stoichiometry oldStoichiometry) { if (oldStoichiometry == null){ entityChangeLogger.log(Level.INFO, "The stoichiometry has been initialised for the entity " + entity.toString()); } else if (entity.getStoichiometry() == null){ entityChangeLogger.log(Level.INFO, "The stoichiometry has been reset for the entity " + entity.toString()); } else { entityChangeLogger.log(Level.INFO, "The stoichiometry " + oldStoichiometry + " has been updated with " + entity.getStoichiometry() + " in the entity " + entity.toString()); } }
public void onInteractorUpdate(Entity entity, Interactor oldInteractor) { entityChangeLogger.log(Level.INFO, "The interactor " + oldInteractor + " has been updated with " + entity.getInteractor() + " in the entity " + entity.toString()); } }
Interactor interactor1 = participant1.getInteractor(); Interactor interactor2 = participant2.getInteractor(); Stoichiometry stc1 = participant1.getStoichiometry(); Stoichiometry stc2 = participant2.getStoichiometry();
/** * Use DefaultExactParticipantInteractorComparator to know if two participants are equals. * @param participant1 * @param participant2 * @return true if the two participants are equal */ public static boolean areEquals(Entity participant1, Entity participant2){ if (participant1 == participant2){ return true; } else if (participant1 == null || participant2 == null){ return false; } else { // first compares interactors Interactor interactor1 = participant1.getInteractor(); Interactor interactor2 = participant2.getInteractor(); return DefaultExactInteractorComparator.areEquals(interactor1, interactor2); } } }
Interactor interactor1 = participant1.getInteractor(); Interactor interactor2 = participant2.getInteractor(); Stoichiometry stc1 = participant1.getStoichiometry(); Stoichiometry stc2 = participant2.getStoichiometry();
/** * Use DefaultParticipantInteractorComparator to know if two participants are equals. * @param participant1 * @param participant2 * @return true if the two participants are equal */ public static boolean areEquals(Entity participant1, Entity participant2){ if (participant1 == participant2){ return true; } else if (participant1 == null || participant2 == null){ return false; } else { // first compares interactors Interactor interactor1 = participant1.getInteractor(); Interactor interactor2 = participant2.getInteractor(); return DefaultInteractorComparator.areEquals(interactor1, interactor2); } } }
/** * * @param participant * @return the hashcode consistent with the equals method for this comparator */ public static int hashCode(Entity participant){ if (unambiguousExactParticipantComparator == null){ unambiguousExactParticipantComparator = new UnambiguousExactEntityBaseComparator(); } if (participant == null){ return 0; } int hashcode = 31; hashcode = 31*hashcode + UnambiguousExactInteractorBaseComparator.hashCode(participant.getInteractor()); hashcode = 31*hashcode + StoichiometryComparator.hashCode(participant.getStoichiometry()); return hashcode; } }
Interactor interactor1 = participant1.getInteractor(); Interactor interactor2 = participant2.getInteractor();
/** * * @param participant * @return the hashcode consistent with the equals method for this comparator */ public static int hashCode(Entity participant){ if (unambiguousParticipantComparator == null){ unambiguousParticipantComparator = new UnambiguousEntityBaseComparator(); } if (participant == null){ return 0; } int hashcode = 31; hashcode = 31*hashcode + UnambiguousInteractorBaseComparator.hashCode(participant.getInteractor()); hashcode = 31*hashcode + StoichiometryComparator.hashCode(participant.getStoichiometry()); return hashcode; } }
public void onInteractorUpdate(Entity entity, Interactor oldInteractor) { // check that the listener still makes sensr if (contains(entity)){ boolean needsToRemoveOldInteractor = true; // check if an interactor is not in another entity that is kept. // remove any interactors that are kept with other entities for (P e : this){ // we want to check if an interactor is the same as old interactor in another entry if (e != entity){ if (oldInteractor.equals(e.getInteractor())){ needsToRemoveOldInteractor = false; } } } if (!needsToRemoveOldInteractor){ getInteractor().remove(oldInteractor); } getInteractor().add(entity.getInteractor()); } }
interactor = participant.getInteractor(); for (Range range : ranges){ if (range.getParticipant() != null){ interactor = range.getParticipant().getInteractor();
if (object.getParticipant() != null && !(object.getParticipant().getInteractor() instanceof Complex)){ interactor = object.getParticipant().getInteractor(); participant = object.getParticipant(); !(parent.getParticipant().getInteractor() instanceof Complex)){ interactor = parent.getParticipant().getInteractor(); participant = parent.getParticipant();