@Override public void traverse(IntactObject intactObject, IntactVisitor... visitors) { if (intactObject instanceof Institution) { return; } super.traverse(intactObject, visitors); }
/** * Prints an IntactObject recursively * @param intactObject * @param ps */ public static void printIntactObject(IntactObject intactObject, PrintStream ps) { DefaultTraverser traverser = new DefaultTraverser(); traverser.traverse(intactObject, new PrintVisitor(ps)); }
nextHierarchyLevel(); hierarchyAwareVisitor.setHierarchyLevel(getCurrentHierarchyLevel()); traverseAnnotatedObject((AnnotatedObject)intactObject, visitors); } else if (intactObject instanceof Annotation) { traverseAnnotation((Annotation)intactObject, visitors); } else if (intactObject instanceof Alias) { traverseAlias((Alias)intactObject, visitors); } else if (intactObject instanceof Xref) { traverseXref((Xref)intactObject, visitors); } else if (intactObject instanceof Range) { traverseRange((Range)intactObject, visitors); } else if (intactObject instanceof Confidence){ traverseConfidence((Confidence) intactObject, visitors); } else if (intactObject instanceof InteractionParameter){ traverseParameter((Parameter) intactObject, visitors); } else if (intactObject instanceof ComponentParameter){ traverseParameter((Parameter) intactObject, visitors); } else { throw new IllegalArgumentException("Cannot traverse objects of type: "+intactObject.getClass().getName()); previousHierarchyLevel();
protected void traverse(Collection<? extends IntactObject> objs, IntactVisitor[] visitors) { if (objs == null || objs.isEmpty()) { return; } for (IntactObject obj : objs) { traverse(obj, visitors); } previousHierarchyLevel(); }
protected void traverseAnnotatedObject(AnnotatedObject annotatedObject, IntactVisitor... visitors) { if (annotatedObject == null) return; for (IntactVisitor visitor : visitors) { visitor.visitAnnotatedObject(annotatedObject); } if (annotatedObject instanceof Interaction) { traverseInteraction((Interaction) annotatedObject, visitors); } else if (annotatedObject instanceof Interactor) { traverseInteractor((Interactor) annotatedObject, visitors); } else if (annotatedObject instanceof CvObject) { traverseCvObject((CvObject) annotatedObject, visitors); } else if (annotatedObject instanceof Experiment) { traverseExperiment((Experiment) annotatedObject, visitors); } else if (annotatedObject instanceof Component) { traverseComponent((Component) annotatedObject, visitors); } else if (annotatedObject instanceof BioSource) { traverseBioSource((BioSource) annotatedObject, visitors); } else if (annotatedObject instanceof Feature) { traverseFeature((Feature) annotatedObject, visitors); } else if (annotatedObject instanceof Publication) { traversePublication((Publication) annotatedObject, visitors); } else if (annotatedObject instanceof Institution) { traverseInstitution((Institution) annotatedObject, visitors); } else { throw new IllegalArgumentException("Cannot process annotated object of type: " + annotatedObject.getClass().getName()); } traverseAnnotatedObjectCommon(annotatedObject, visitors); }
protected void traverseAnnotatedObject(AnnotatedObject annotatedObject, IntactVisitor... visitors) { if (annotatedObject == null) return; for (IntactVisitor visitor : visitors) { visitor.visitAnnotatedObject(annotatedObject); } if (annotatedObject instanceof Interaction) { traverseInteraction((Interaction) annotatedObject, visitors); } else if (annotatedObject instanceof Interactor) { traverseInteractor((Interactor) annotatedObject, visitors); } else if (annotatedObject instanceof CvObject) { traverseCvObject((CvObject) annotatedObject, visitors); } else if (annotatedObject instanceof Experiment) { traverseExperiment((Experiment) annotatedObject, visitors); } else if (annotatedObject instanceof Component) { traverseComponent((Component) annotatedObject, visitors); } else if (annotatedObject instanceof BioSource) { traverseBioSource((BioSource) annotatedObject, visitors); } else if (annotatedObject instanceof Feature) { traverseFeature((Feature) annotatedObject, visitors); } else if (annotatedObject instanceof Publication) { traversePublication((Publication) annotatedObject, visitors); } else if (annotatedObject instanceof Institution) { traverseInstitution((Institution) annotatedObject, visitors); } else { throw new IllegalArgumentException("Cannot process annotated object of type: " + annotatedObject.getClass().getName()); } traverseAnnotatedObjectCommon(annotatedObject, visitors); }
protected void traverse(Collection<? extends IntactObject> objs, IntactVisitor[] visitors) { if (objs == null || objs.isEmpty()) { return; } for (IntactObject obj : objs) { traverse(obj, visitors); } previousHierarchyLevel(); }
nextHierarchyLevel(); hierarchyAwareVisitor.setHierarchyLevel(getCurrentHierarchyLevel()); traverseAnnotatedObject((AnnotatedObject)intactObject, visitors); } else if (intactObject instanceof Annotation) { traverseAnnotation((Annotation)intactObject, visitors); } else if (intactObject instanceof Alias) { traverseAlias((Alias)intactObject, visitors); } else if (intactObject instanceof Xref) { traverseXref((Xref)intactObject, visitors); } else if (intactObject instanceof Range) { traverseRange((Range)intactObject, visitors); } else if (intactObject instanceof Confidence){ traverseConfidence((Confidence) intactObject, visitors); } else if (intactObject instanceof InteractionParameter){ traverseParameter((Parameter) intactObject, visitors); } else if (intactObject instanceof ComponentParameter){ traverseParameter((Parameter) intactObject, visitors); } else { throw new IllegalArgumentException("Cannot traverse objects of type: "+intactObject.getClass().getName()); previousHierarchyLevel();
protected void traverseAnnotatedObjectCommon(AnnotatedObject ao, IntactVisitor ... visitors) { traverse(ao.getAnnotations(), visitors); traverse(ao.getAliases(), visitors); traverse(ao.getXrefs(), visitors); // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(ao)) { return; } traverse(ao.getOwner(), visitors); }
/** * Prints an IntactObject recursively * @param intactObject * @param ps */ public static void printIntactObject(IntactObject intactObject, PrintStream ps) { DefaultTraverser traverser = new DefaultTraverser(); traverser.traverse(intactObject, new PrintVisitor(ps)); }
protected void traverseAnnotatedObjectCommon(AnnotatedObject ao, IntactVisitor ... visitors) { traverse(ao.getAnnotations(), visitors); traverse(ao.getAliases(), visitors); traverse(ao.getXrefs(), visitors); // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(ao)) { return; } traverse(ao.getOwner(), visitors); }
/** * Renders a JFrame with the tree for the provided IntactObject * * @param intactObject the object to be rendered */ public static void renderIntactObjectAsTree( IntactObject intactObject, String windowTitle ) { DefaultTraverser traverser = new DefaultTraverser(); final JTreeBuilderVisitor builderVisitor = new JTreeBuilderVisitor(); traverser.traverse( intactObject, builderVisitor ); if ( windowTitle == null ) { builderVisitor.renderTree(); } else { builderVisitor.renderTree( windowTitle ); } }
protected void traverseExperiment(Experiment experiment, IntactVisitor ... visitors) { if (experiment == null) return; for (IntactVisitor visitor : visitors) { visitor.visitExperiment(experiment); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(experiment)) { return; } traverse(experiment.getCvIdentification(), visitors); traverse(experiment.getCvInteraction(), visitors); traverse(experiment.getBioSource(), visitors); traverse(experiment.getPublication(), visitors); traverse(experiment.getInteractions(), visitors); }
/** * Renders a JFrame with the tree for the provided IntactObject * * @param intactObject the object to be rendered */ public static void renderIntactObjectAsTree( IntactObject intactObject, String windowTitle ) { DefaultTraverser traverser = new DefaultTraverser(); final JTreeBuilderVisitor builderVisitor = new JTreeBuilderVisitor(); traverser.traverse( intactObject, builderVisitor ); if ( windowTitle == null ) { builderVisitor.renderTree(); } else { builderVisitor.renderTree( windowTitle ); } }
protected void traverseExperiment(Experiment experiment, IntactVisitor ... visitors) { if (experiment == null) return; for (IntactVisitor visitor : visitors) { visitor.visitExperiment(experiment); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(experiment)) { return; } traverse(experiment.getCvIdentification(), visitors); traverse(experiment.getCvInteraction(), visitors); traverse(experiment.getBioSource(), visitors); traverse(experiment.getPublication(), visitors); traverse(experiment.getInteractions(), visitors); }
protected void traverseInteraction(Interaction interaction, IntactVisitor ... visitors) { if (interaction == null) return; for (IntactVisitor visitor : visitors) { visitor.visitInteraction(interaction); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(interaction)) { return; } traverse(interaction.getCvInteractionType(), visitors); traverse(interaction.getExperiments(), visitors); traverse(interaction.getComponents(), visitors); traverse(interaction.getConfidences(), visitors); traverse(interaction.getParameters(), visitors); }
protected void traverseInteraction(Interaction interaction, IntactVisitor ... visitors) { if (interaction == null) return; for (IntactVisitor visitor : visitors) { visitor.visitInteraction(interaction); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(interaction)) { return; } traverse(interaction.getCvInteractionType(), visitors); traverse(interaction.getExperiments(), visitors); traverse(interaction.getComponents(), visitors); traverse(interaction.getConfidences(), visitors); traverse(interaction.getParameters(), visitors); }
protected void traversePublication(Publication publication, IntactVisitor ... visitors) { if (publication == null) return; for (IntactVisitor visitor : visitors) { visitor.visitPublication(publication); traverse(publication.getExperiments(), visitors); } }
protected void traverseComponent(Component component, IntactVisitor ... visitors) { if (component == null) return; for (IntactVisitor visitor : visitors) { visitor.visitComponent(component); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(component)) { return; } traverse(component.getInteraction(), visitors); traverse(component.getInteractor(), visitors); traverse(component.getCvBiologicalRole(), visitors); traverse(component.getExpressedIn(), visitors); traverse(component.getParameters(), visitors); traverse(component.getParticipantDetectionMethods(), visitors); traverse(component.getExperimentalPreparations(), visitors); traverse(component.getBindingDomains(), visitors); traverse(component.getExperimentalRoles(), visitors); }
protected void traverseXref(Xref xref, IntactVisitor... visitors) { if (xref == null) return; for (IntactVisitor visitor : visitors) { visitor.visitXref(xref); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(xref)) { return; } traverse(xref.getCvXrefQualifier(), visitors); traverse(xref.getCvDatabase(), visitors); traverse(xref.getOwner(), visitors); }