/** * Gets the value of the attributeList property. * * @return possible object is {@link Attribute } */ @Deprecated public Collection<Attribute> getAttributeList() { return getAttributes(); }
/** * Build a new Interaction with no participants but holding a copy of all other attributes of the given interaction. * <br/> WARNING: all attributes of the newly created interaction are the same as the source's (that is same object * instance). This is not an object clone. * * @param source the source interaction. * @return a target interaction which is a copy of the source interaction but the participants or * inferredInteractions. */ protected Interaction copyInteraction(Interaction source) { Interaction target = new Interaction(); // clone inner attributes target.setId(source.getId()); target.setImexId(source.getImexId()); // objects target.setNames(source.getNames()); target.setXref(source.getXref()); // collections target.getConfidences().addAll(source.getConfidences()); target.getExperiments().addAll(source.getExperiments()); target.getInteractionTypes().addAll(source.getInteractionTypes()); // added with mitab 27 target.setModelled(source.isModelled()); target.setIntraMolecular(source.isIntraMolecular()); target.setNegative(source.isNegative()); target.getParameters().addAll(source.getParameters()); target.getAttributes().addAll(source.getAttributes()); target.setAvailability(source.getAvailability()); return target; }
for (Attribute attr : interaction.getAttributes()) { if ("source reference:label".equals(attr.getName())) { text = attr.getValue(); List<Checksum> iChecksums = new ArrayList<Checksum>(); for (Attribute attribute : interaction.getAttributes()) { String name = attribute.getName(); String text = attribute.getValue();
for (Annotation annotation : annotations) { Attribute attribute = new Attribute(annotation.getTopic(), annotation.getText()); interaction.getAttributes().add(attribute); for (Checksum checksum : checksums) { Attribute attribute = new Attribute(checksum.getMethodName(), checksum.getChecksum()); interaction.getAttributes().add(attribute);
for (Attribute attribute : interaction.getAttributes()) {
Attribute authConf = new Attribute(IntactConverterUtils.AUTH_CONF_MI, IntactConverterUtils.AUTH_CONF, conf.getValue()); if (!interaction.getAttributes().contains(authConf)){ interaction.getAttributes().add(authConf);
private void processEdge(final Participant source, final Participant target, final Interaction interaction, final Collection<Participant> nodes, CyTable nodeTable, CyTable edgeTable) { Interactor sourceInteractor = source.getInteractor(); Interactor targetInteractor = target.getInteractor(); if (sourceInteractor == null || targetInteractor == null) { return; } final CyNode sourceCyNode = id2NodeMap.get(sourceInteractor.getId()); final CyNode targetCyNode = id2NodeMap.get(targetInteractor.getId()); // PPI does not have directinarity final CyEdge edge = network.addEdge(sourceCyNode, targetCyNode, false); // TODO: what's the best value for interaction? edgeTable.getRow(edge.getSUID()).set(CyEdge.INTERACTION, "pp"); final String sourceName = nodeTable.getRow(sourceCyNode.getSUID()).get(CyNetwork.NAME, String.class); final String targetName = nodeTable.getRow(targetCyNode.getSUID()).get(CyNetwork.NAME, String.class); edgeTable.getRow(edge.getSUID()).set(CyNetwork.NAME, sourceName + " (pp) " + targetName); mapNames(edgeTable, edge.getSUID(), interaction.getNames(), null); mapAttributes(interaction.getAttributes(), edgeTable, edge.getSUID()); final Collection<InteractionType> types = interaction.getInteractionTypes(); mapInteractionType(types, edgeTable, edge.getSUID()); }
mInteraction.getAttributes().add( attributeConverter.fromJaxb( jAttribute ) );
mInteraction.getAttributes().add( attributeConverter.fromJaxb( jAttribute ) );
for ( Attribute mAttribute : mInteraction.getAttributes() ) { jInteraction.getAttributeList().getAttributes().add( attributeConverter.toJaxb( mAttribute ) );
for ( Attribute mAttribute : mInteraction.getAttributes() ) { jInteraction.getAttributeList().getAttributes().add( attributeConverter.toJaxb( mAttribute ) );