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

Example 51 with CyTable

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

the class CySubNetworkImpl method removeNodes.

@Override
public boolean removeNodes(final Collection<CyNode> nodes) {
    if (nodes == null || nodes.isEmpty())
        return false;
    eventHelper.fireEvent(new AboutToRemoveNodesEvent(this, nodes));
    CyTable nodeHiddenTable = getTable(CyNode.class, CyNetwork.HIDDEN_ATTRS);
    CyTable nodeDefaultTable = getTable(CyNode.class, CyNetwork.DEFAULT_ATTRS);
    CyTable edgeHiddenTable = getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS);
    CyTable edgeDefaultTable = getTable(CyEdge.class, CyNetwork.DEFAULT_ATTRS);
    List<Long> nodeSuids = new ArrayList<>();
    Set<Long> edgeSuids = new HashSet<>();
    for (CyNode node : nodes) {
        if (this.containsNode(node)) {
            Long nodeSuid = node.getSUID();
            if (nodeDefaultTable.rowExists(nodeSuid))
                nodeSuids.add(nodeSuid);
            for (CyEdge edge : getAdjacentEdgeIterable(node, Type.ANY)) {
                Long edgeSuid = edge.getSUID();
                if (edgeDefaultTable.rowExists(edgeSuid)) {
                    edgeSuids.add(edgeSuid);
                }
            }
        }
    }
    boolean ret = removeNodesInternal(nodes);
    nodeHiddenTable.deleteRows(nodeSuids);
    nodeDefaultTable.deleteRows(nodeSuids);
    edgeHiddenTable.deleteRows(edgeSuids);
    edgeDefaultTable.deleteRows(edgeSuids);
    if (ret) {
        parent.subnetworkNodesRemoved(nodes);
    }
    if (ret) {
        eventHelper.fireEvent(new RemovedNodesEvent(this));
    }
    return ret;
}

Example 52 with CyTable

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

the class CyTableManagerImpl method getLocalTables.

@Override
public Set<CyTable> getLocalTables(final Class<? extends CyIdentifiable> type) {
    final Set<CyTable> localTables = new HashSet<CyTable>();
    final Set<CyNetwork> networks = networkManager.getNetworkSet();
    for (final CyNetwork network : networks) {
        final Map<String, CyTable> objTables = networkTableManager.getTables(network, type);
        if (network instanceof CySubNetwork) {
            final CyTable shared = networkTableManager.getTable(((CySubNetwork) network).getRootNetwork(), type, CyRootNetwork.SHARED_ATTRS);
            localTables.add(shared);
        }
        localTables.addAll(objTables.values());
    }
    return localTables;
}

Example 53 with CyTable

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

the class CyTableManagerImpl method getGlobalTables.

@Override
public Set<CyTable> getGlobalTables() {
    final Set<CyTable> nonGlobalTables = new HashSet<CyTable>();
    final Set<CyTable> globalTables = new HashSet<CyTable>();
    final Set<CyNetwork> networks = networkTableManager.getNetworkSet();
    for (final CyNetwork network : networks) {
        for (final Class<? extends CyIdentifiable> type : COMPATIBLE_TYPES) {
            final Map<String, CyTable> objTables = networkTableManager.getTables(network, type);
            nonGlobalTables.addAll(objTables.values());
        }
    }
    for (final CyTable table : tables.values()) if (nonGlobalTables.contains(table) == false)
        globalTables.add(table);
    return globalTables;
}

Example 54 with CyTable

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

the class CyTableManagerImpl method refreshTableEquations.

private void refreshTableEquations() {
    final EquationCompiler compiler = serviceRegistrar.getService(EquationCompiler.class);
    Set<CyTable> tables = getAllTables(true);
    for (CyTable table : tables) {
        EquationUtil.refreshEquations(table, compiler);
    }
}

Example 55 with CyTable

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

the class DefaultTablesNetwork method getRow.

public CyRow getRow(final CyIdentifiable entry, final String tableName) {
    if (entry == null)
        throw new NullPointerException("null entry");
    if (tableName == null)
        throw new NullPointerException("null table name");
    CyTable table;
    // The table returned should be immutable.
    if (entry instanceof CyNode && containsNode((CyNode) entry))
        table = networkTableManager.getTable(networkRef.get(), CyNode.class, tableName);
    else if (entry instanceof CyEdge && containsEdge((CyEdge) entry))
        table = networkTableManager.getTable(networkRef.get(), CyEdge.class, tableName);
    else if (entry instanceof CyNetwork && entry.equals(this)) {
        if (networkRef == null)
            throw new IllegalArgumentException("Network reference is null.  This should not be null.");
        final CyNetwork n = networkRef.get();
        table = networkTableManager.getTable(n, CyNetwork.class, tableName);
    } else
        throw new IllegalArgumentException("unrecognized (table entry): " + entry.toString() + "  (table name): " + tableName);
    if (table == null)
        throw new NullPointerException("Table does not exist: " + tableName);
    return table.getRow(entry.getSUID());
}