public SmallMolecule createSmallMoleculeRandom() { return createSmallMolecule(nextString("chebi:"), nextString()); }
public SmallMolecule createSmallMoleculeRandom() { return createSmallMolecule(nextString("chebi:"), nextString()); }
public Protein createPeptideRandom() { return createPeptide(nextString("primId"), nextString(), createBioSourceRandom()); }
public <X extends Xref> X createIdentityXrefPsiMiRandom(AnnotatedObject<X,?> parent) { return createIdentityXrefPsiMi(parent, nextString("primId")); }
public Annotation createAnnotationRandom() { return createAnnotation(nextString("annottext"), CvTopic.COMMENT_MI_REF, CvTopic.COMMENT); }
public Protein createProteinRandom() { return createProtein(nextString("primId"), nextString(), createBioSourceRandom()); }
public Confidence createConfidenceRandom() { CvConfidenceType cvConfidenceType = CvObjectUtils.createIntactCvObject(getInstitution(), CvConfidenceType.class, "IA:"+ new Random().nextInt(1000), nextString( "cv")); Confidence conf = createConfidence(cvConfidenceType, Double.toString( new Random().nextDouble())); return conf; }
public Confidence createConfidenceRandom() { CvConfidenceType cvConfidenceType = CvObjectUtils.createIntactCvObject(getInstitution(), CvConfidenceType.class, "IA:"+ new Random().nextInt(1000), nextString( "cv")); Confidence conf = createConfidence(cvConfidenceType, Double.toString( new Random().nextDouble())); return conf; }
public Feature createFeatureRandom() { CvFeatureType cvFeatureType = createCvObject(CvFeatureType.class, CvFeatureType.EXPERIMENTAL_FEATURE_MI_REF, CvFeatureType.EXPERIMENTAL_FEATURE); return createFeature(nextString("feat"), cvFeatureType); }
public Feature createFeatureRandom() { CvFeatureType cvFeatureType = createCvObject(CvFeatureType.class, CvFeatureType.EXPERIMENTAL_FEATURE_MI_REF, CvFeatureType.EXPERIMENTAL_FEATURE); return createFeature(nextString("feat"), cvFeatureType); }
public BioSource createBioSourceRandom() { return createBioSource(nextId(), nextString("label")); }
public Feature createFeatureRandom() { CvFeatureType cvFeatureType = createCvObject(CvFeatureType.class, CvFeatureType.EXPERIMENTAL_FEATURE_MI_REF, CvFeatureType.EXPERIMENTAL_FEATURE); return createFeature(nextString("feat"), cvFeatureType); }
public BioSource createBioSourceRandom() { return createBioSource(nextId(), nextString("label")); }
public BioSource createBioSourceRandom() { return createBioSource(nextId(), nextString("label")); }
private Interaction createInteractionDirect() { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); return new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, intType, nextString("label"), getInstitution()); }
private Interaction createInteractionDirect() { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); return new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, intType, nextString("label"), getInstitution()); }
public Component createComponentNeutral( Interactor interactor ) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.NEUTRAL_PSI_REF, CvExperimentalRole.NEUTRAL); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, intType, nextString("label"), getInstitution()); Component component = createComponent(interaction, interactor, expRole, bioRole); for (int i=0; i<childRandom(0,2); i++) { component.addBindingDomain(createFeatureRandom()); } return component; }
public Component createComponentNeutral( Interactor interactor ) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.NEUTRAL_PSI_REF, CvExperimentalRole.NEUTRAL); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, intType, nextString("label"), getInstitution()); Component component = createComponent(interaction, interactor, expRole, bioRole); for (int i=0; i<childRandom(0,2); i++) { component.addBindingDomain(createFeatureRandom()); } return component; }
public Interaction createInteractionRandomBinary() { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, null, nextString("label"), getInstitution()); interaction.addComponent(createComponentBait(interaction, createProteinRandom())); interaction.addComponent(createComponentPrey(interaction, createProteinRandom())); String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }
public Interaction createInteraction(String ... interactorShortLabels) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, null, nextString("label"), getInstitution()); for (String interactorShortLabel : interactorShortLabels) { interaction.addComponent(createComponentNeutral(interaction, createProtein("uniprotId", interactorShortLabel))); } if (interactorShortLabels.length == 1) { interaction.addComponent(createComponentNeutral(interaction, createProtein("uniprotId", interactorShortLabels[0]))); } String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }