Examples with CyTable org.cytoscape.model.CyTable used on opensource projects

Example 86 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class GraphMLWriter method writeEdges.

private void writeEdges(Document doc, Element parent) {
    final List<CyEdge> edges = network.getEdgeList();
    final CyTable table = network.getDefaultEdgeTable();
    final Collection<CyColumn> edgeColumns = table.getColumns();
    for (final CyEdge edge : edges) {
        final Element edgeElm = doc.createElement(EDGE);
        edgeElm.setAttribute(SOURCE, edge.getSource().getSUID().toString());
        edgeElm.setAttribute(TARGET, edge.getTarget().getSUID().toString());
        final CyRow row = network.getRow(edge);
        appendData(row, edgeColumns, doc, edgeElm, edge);
        parent.appendChild(edgeElm);
    }
}

Example 87 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class PerformanceScaffold method main.

public static void main(String[] args) {
    NetworkTestSupport testSupport = new NetworkTestSupport();
    CyNetwork network = testSupport.getNetwork();
    CyTable nodeTable = network.getDefaultNodeTable();
    nodeTable.createColumn(STRING_COLUMN, String.class, false);
    nodeTable.createColumn(INTEGER_COLUMN, Integer.class, false);
    nodeTable.createListColumn(LIST_STRING_COLUMN, String.class, false);
    // Use a fixed set of string attributes.
    // Worst case performance for trie expected for first entry
    // Best case performance expected for last entry
    Random random = new Random(1);
    String[] values = { "AAAAAAAAAAAAAAA", "AAAAAAAAAAAAAAB", "AAAAAAAAAAAAACA", "AAAAAAAAAAAADAA", "AAAAAAAAAAAEAAA", "AAAAAAAAAAFAAAA", "AAAAAAAAAGAAAAA", "AAAAAAAAHAAAAAA", "AAAAAAAIAAAAAAA", "AAAAAAJAAAAAAAA", "AAAAAKAAAAAAAAA", "AAAALAAAAAAAAAA", "AAAMAAAAAAAAAAA", "AANAAAAAAAAAAAA", "AOAAAAAAAAAAAAA", "PAAAAAAAAAAAAAA" };
    int totalNodes = TOTAL_NODES;
    int totalEdges = totalNodes * AVERAGE_EDGES_PER_NODE;
    long start;
    start = System.currentTimeMillis();
    List<CyNode> nodes = new ArrayList<CyNode>();
    for (int i = 0; i < totalNodes; i++) {
        CyNode node = network.addNode();
        int valueIndex = random.nextInt(values.length);
        network.getRow(node).set(STRING_COLUMN, values[valueIndex]);
        network.getRow(node).set(INTEGER_COLUMN, valueIndex);
        network.getRow(node).set(LIST_STRING_COLUMN, Collections.singletonList(values[valueIndex]));
        nodes.add(node);
    }
    // Construct random graph
    for (int i = 0; i < totalEdges; i++) {
        CyNode source = nodes.get(random.nextInt(totalNodes));
        CyNode target = nodes.get(random.nextInt(totalNodes));
        network.addEdge(source, target, true);
    }
    System.out.printf("Construct\t%d\n", System.currentTimeMillis() - start);
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    Map<String, String> properties = Collections.emptyMap();
    transformerManager.registerTransformerSource(new CyNetworkSource(), properties);
    List<UseCase> useCases = new ArrayList<UseCase>();
    QuickFind quickFind = new QuickFindImpl();
    useCases.add(new NumberAttributeUseCase(quickFind, 0, transformerManager));
    useCases.add(new StringAttributeUseCase(quickFind, values[values.length - 1], transformerManager));
    useCases.add(new DegreeUseCase(3, transformerManager));
    for (UseCase useCase : useCases) {
        useCase.execute(network, ITERATIONS);
    }
}

Example 88 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class GroupDataCollapseHandler method handleEvent.

public void handleEvent(GroupAboutToCollapseEvent e) {
    CyNetwork network = e.getNetwork();
    CyGroup group = e.getSource();
    if (e.collapsing()) {
        // Are we aggregating
        if (!cyGroupSettings.getEnableAttributeAggregation(group))
            return;
        // Yup -- all of our information is in the settings...
        CyTable nodeTable = network.getDefaultNodeTable();
        for (CyColumn column : nodeTable.getColumns()) {
            Class<?> type = column.getType();
            if (column.isPrimaryKey())
                continue;
            // Skip over our own columns
            if (CyGroupSettingsImpl.AGGREGATION_SETTINGS.equals(column.getName()))
                continue;
            if (CyGroupSettingsImpl.AGGREGATION_OVERRIDE_SETTINGS.equals(column.getName()))
                continue;
            if (CyGroupSettingsImpl.VIEW_SETTINGS.equals(column.getName()))
                continue;
            if (CyGroupImpl.CHILDREN_ATTR.equals(column.getName()))
                continue;
            if (CyGroupImpl.DESCENDENTS_ATTR.equals(column.getName()))
                continue;
            // Don't aggregate the name or shared name columns by default
            if (CyNetwork.NAME.equals(column.getName())) {
                if (!haveOverride(group, column))
                    continue;
            }
            if (CyRootNetwork.SHARED_NAME.equals(column.getName())) {
                if (!haveOverride(group, column))
                    continue;
            }
            // Do we have an override for this group and column?
            Aggregator<?> agg = cyGroupSettings.getAggregator(group, column);
            if (agg == null) {
                continue;
            }
            // OK, aggregate
            agg.aggregate(nodeTable, group, column);
        }
    }
}

Example 89 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class VisualStyleTest method setUp.

@Before
@SuppressWarnings("unchecked")
public void setUp() throws Exception {
    NetworkViewTestSupport nvts = new NetworkViewTestSupport();
    network = nvts.getNetworkFactory().createNetwork();
    node1 = network.addNode();
    node2 = network.addNode();
    node3 = network.addNode();
    edge = network.addEdge(node1, node2, true);
    CyTable nodeTable = network.getDefaultNodeTable();
    nodeTable.createColumn(attrName, String.class, true);
    nodeTable.getRow(node1.getSUID()).set(attrName, "red");
    nodeTable.getRow(node2.getSUID()).set(attrName, "green");
    nodeTable.getRow(node3.getSUID()).set(attrName, "foo");
    networkView = nvts.getNetworkViewFactory().createNetworkView(network);
    // Create root node.
    final NullVisualProperty minimalRoot = new NullVisualProperty("MINIMAL_ROOT", "Minimal Root Visual Property");
    final BasicVisualLexicon minimalLex = new BasicVisualLexicon(minimalRoot);
    final Set<VisualLexicon> lexSet = new HashSet<VisualLexicon>();
    lexSet.add(minimalLex);
    final VisualMappingFunctionFactory ptFactory = mock(VisualMappingFunctionFactory.class);
    eventHelper = mock(CyEventHelper.class);
    final RenderingEngineFactory<CyNetwork> reFatory = mock(RenderingEngineFactory.class);
    when(reFatory.getVisualLexicon()).thenReturn(minimalLex);
    final NetworkViewRenderer nvRenderer = mock(NetworkViewRenderer.class);
    when(nvRenderer.getRenderingEngineFactory(NetworkViewRenderer.DEFAULT_CONTEXT)).thenReturn(reFatory);
    final CyApplicationManager appManager = mock(CyApplicationManager.class);
    when(appManager.getCurrentNetworkViewRenderer()).thenReturn(nvRenderer);
    final CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(eventHelper);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(appManager);
    VisualProperty<NullDataType> rootVisualProperty = mock(VisualProperty.class);
    BasicVisualLexicon lexicon = new BasicVisualLexicon(rootVisualProperty);
    vpSet = new HashSet<VisualProperty<Paint>>();
    vpSet.add(BasicVisualLexicon.NODE_BORDER_PAINT);
    vpSet.add(BasicVisualLexicon.NODE_FILL_COLOR);
    dependency = new VisualPropertyDependency<Paint>("dep1", "Dep 1", vpSet, lexicon);
    final VisualStyleFactoryImpl visualStyleFactory = new VisualStyleFactoryImpl(serviceRegistrar, ptFactory);
    originalTitle = "Style 1";
    newTitle = "Style 2";
    style = visualStyleFactory.createVisualStyle(originalTitle);
    style.setDefaultValue(NODE_SIZE, DEF_NODE_SIZE);
    style.setDefaultValue(NODE_FILL_COLOR, DEF_NODE_COLOR);
    reset(eventHelper);
}

Example 90 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class ImportTableDataTask method getColumns.

private ListSingleSelection<String> getColumns(final Collection<? extends CyNetwork> networkList, final TableType tableType, final String namespace) {
    Set<ColumnDescriptor> colDescSet = null;
    // Get set of columns with same name and type that are common to all networks
    for (CyNetwork network : networkList) {
        final CyTable table = getTable(network, tableType, namespace);
        final Set<ColumnDescriptor> subSet = new HashSet<>();
        for (CyColumn col : table.getColumns()) {
            if (isMappableColumn(col))
                subSet.add(new ColumnDescriptor(col.getName(), col.getType()));
        }
        if (colDescSet == null)
            // First network? Just save the mappable columns...
            colDescSet = subSet;
        else
            // From now on just keep the common columns...
            colDescSet.retainAll(subSet);
    }
    final List<String> columnNames = new ArrayList<>();
    if (colDescSet != null) {
        for (ColumnDescriptor cd : colDescSet) columnNames.add(cd.name);
        sort(columnNames);
    }
    final ListSingleSelection<String> columns = new ListSingleSelection<>(columnNames);
    if (columns.getPossibleValues().contains(CyRootNetwork.SHARED_NAME))
        columns.setSelectedValue(CyRootNetwork.SHARED_NAME);
    return columns;
}