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

Example 6 with VirtualColumnInfo

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

the class RowsSetViewUpdater method updateView.

private final void updateView(final RowsSetEvent e) {
    boolean refreshView = false;
    boolean refreshOtherViews = false;
    // Acquire services once to avoid performance overhead of repeated lookup
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    final CyColumnIdentifierFactory columnIdentifierFactory = serviceRegistrar.getService(CyColumnIdentifierFactory.class);
    final CyNetworkViewManager networkViewManager = serviceRegistrar.getService(CyNetworkViewManager.class);
    final VisualMappingManager visualMappingManager = serviceRegistrar.getService(VisualMappingManager.class);
    final RenderingEngine<CyNetwork> renderer = applicationManager.getCurrentRenderingEngine();
    final CyNetwork network = applicationManager.getCurrentNetwork();
    if (network == null)
        return;
    // 1: Update current network view
    final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(network);
    CyNetworkView networkView = null;
    if (views.isEmpty())
        return;
    else
        networkView = views.iterator().next();
    final VisualStyle vs = visualMappingManager.getVisualStyle(networkView);
    Map<CyRow, View<? extends CyIdentifiable>> rowViewMap = tracker.getRowViewMap(networkView);
    for (final RowSetRecord record : e.getPayloadCollection()) {
        final CyRow row = record.getRow();
        final String columnName = record.getColumn();
        final CyColumn column = row.getTable().getColumn(columnName);
        if (column == null)
            continue;
        final VirtualColumnInfo virtualColInfo = column.getVirtualColumnInfo();
        final boolean virtual = virtualColInfo.isVirtual();
        final View<? extends CyIdentifiable> v = rowViewMap.get(row);
        if (v == null)
            continue;
        if (v.getModel() instanceof CyNode) {
            final CyNode node = (CyNode) v.getModel();
            if (network.containsNode(node) && isStyleAffected(vs, columnName, renderer, columnIdentifierFactory)) {
                vs.apply(row, v);
                refreshView = false;
            }
        } else if (v.getModel() instanceof CyEdge) {
            final CyEdge edge = (CyEdge) v.getModel();
            if (network.containsEdge(edge) && isStyleAffected(vs, columnName, renderer, columnIdentifierFactory)) {
                vs.apply(row, v);
                refreshView = false;
            }
        }
        // If virtual, it may be used in other networks.
        if (refreshView && virtual)
            refreshOtherViews = true;
    // if (refreshView)
    // vs.apply(record.getRow(), (View<? extends CyIdentifiable>) v);
    }
    if (refreshView) {
        vs.apply(networkView);
        networkView.updateView();
        if (refreshOtherViews) {
            // Check other views. If update is required, set the flag.
            for (final CyNetworkView view : networkViewManager.getNetworkViewSet()) {
                if (view == networkView)
                    continue;
                final VisualStyle style = visualMappingManager.getVisualStyle(view);
                if (style == vs) {
                    // Same style is in use. Need to apply.
                    netViewMediator.setUpdateFlag(view);
                }
            }
        }
    }
}

Example 7 with VirtualColumnInfo

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

the class AttributeValueUtil method handleAttribute.

@SuppressWarnings({ "unchecked", "rawtypes" })
protected ParseState handleAttribute(Attributes atts) throws SAXParseException {
    ParseState parseState = ParseState.NONE;
    final String name = atts.getValue("name");
    String type = atts.getValue("type");
    String cyType = atts.getValue("cy:type");
    if ("has_nested_network".equals(name))
        type = ObjectType.BOOLEAN.getXgmmlValue();
    final boolean isEquation = ObjectTypeMap.fromXGMMLBoolean(atts.getValue("cy:equation"));
    final boolean isHidden = ObjectTypeMap.fromXGMMLBoolean(atts.getValue("cy:hidden"));
    final CyIdentifiable curElement = manager.getCurrentElement();
    CyNetwork curNet = manager.getCurrentNetwork();
    // under the group subgraph, but the edge will be created on the root-network only,
    if (curElement instanceof CyNode || curElement instanceof CyEdge) {
        boolean containsElement = (curElement instanceof CyNode && curNet.containsNode((CyNode) curElement));
        containsElement |= (curElement instanceof CyEdge && curNet.containsEdge((CyEdge) curElement));
        // So if the current network does not contain this element, the CyRootNetwork should contain it
        if (!containsElement)
            curNet = manager.getRootNetwork();
    }
    CyRow row = null;
    if (isHidden) {
        row = curNet.getRow(curElement, CyNetwork.HIDDEN_ATTRS);
    } else {
        // Network name must be local, right? What about other network attributes?
        if (CyNetwork.SELECTED.equals(name) || (curElement instanceof CyNetwork))
            row = curNet.getRow(curElement, CyNetwork.LOCAL_ATTRS);
        else
            // Will be created in the shared table
            row = curNet.getRow(curElement, CyNetwork.DEFAULT_ATTRS);
    }
    CyTable table = row.getTable();
    CyColumn column = table.getColumn(name);
    if (column != null) {
        // Check if it's a virtual column
        // It's necessary because the source row may not exist yet, which would throw an exception
        // when the value is set. Doing this forces the creation of the source row.
        final VirtualColumnInfo info = column.getVirtualColumnInfo();
        if (info.isVirtual()) {
            final CyTable srcTable = info.getSourceTable();
            final CyColumn srcColumn = srcTable.getColumn(info.getSourceColumn());
            final Class<?> jkColType = table.getColumn(info.getTargetJoinKey()).getType();
            final Object jkValue = row.get(info.getTargetJoinKey(), jkColType);
            final Collection<CyRow> srcRowList = srcTable.getMatchingRows(info.getSourceJoinKey(), jkValue);
            final CyRow srcRow;
            if (srcRowList == null || srcRowList.isEmpty()) {
                if (info.getTargetJoinKey().equals(CyIdentifiable.SUID)) {
                    // Try to create the row
                    srcRow = srcTable.getRow(jkValue);
                } else {
                    logger.error("Unable to import virtual column \"" + name + "\": The source table \"" + srcTable.getTitle() + "\" does not have any matching rows for join key \"" + info.getSourceJoinKey() + "=" + jkValue + "\".");
                    return parseState;
                }
            } else {
                srcRow = srcRowList.iterator().next();
            }
            // Use the source table instead
            table = srcTable;
            column = srcColumn;
            row = srcRow;
        }
    } else {
        // Also check if the column exists in a network's local table
        final Class<? extends CyIdentifiable> tableType;
        if (curElement instanceof CyNode)
            tableType = CyNode.class;
        else if (curElement instanceof CyEdge)
            tableType = CyEdge.class;
        else
            tableType = CyNetwork.class;
        if (existsInLocalTable(name, tableType, manager.getRootNetwork()))
            row = curNet.getRow(curElement, CyNetwork.LOCAL_ATTRS);
    }
    Object value = null;
    final ObjectType objType = typeMap.fromXgmml(cyType, type);
    if (isEquation) {
        // It is an equation...
        String formula = atts.getValue("value");
        if (name != null && formula != null) {
            manager.addEquationString(row, name, formula);
        }
    } else {
        // Regular attribute value...
        value = getTypedAttributeValue(objType, atts, name);
    }
    switch(objType) {
        case BOOLEAN:
            if (name != null)
                setAttribute(row, name, Boolean.class, (Boolean) value);
            break;
        case REAL:
            if (name != null) {
                if (SUIDUpdater.isUpdatable(name))
                    setAttribute(row, name, Long.class, (Long) value);
                else
                    setAttribute(row, name, Double.class, (Double) value);
            }
            break;
        case INTEGER:
            if (name != null) {
                if (SUIDUpdater.isUpdatable(name))
                    setAttribute(row, name, Long.class, (Long) value);
                else
                    setAttribute(row, name, Integer.class, (Integer) value);
            }
            break;
        case LONG:
            if (name != null)
                setAttribute(row, name, Long.class, (Long) value);
            break;
        case STRING:
            if (name != null)
                setAttribute(row, name, String.class, (String) value);
            break;
        // must make sure to clear out any existing values before we parse.
        case LIST:
            manager.currentAttributeID = name;
            manager.setCurrentRow(row);
            if (column != null && List.class.isAssignableFrom(column.getType()))
                row.set(name, null);
            if (column == null) {
                // Since Cytoscape v3.3
                final String elementType = atts.getValue("cy:elementType");
                if (elementType != null) {
                    final ObjectType elementObjType = typeMap.fromXgmml(elementType, null);
                    final Class<?> clazz = typeMap.getClass(elementObjType, name);
                    table.createListColumn(name, clazz, false, new ArrayList());
                    column = row.getTable().getColumn(name);
                    manager.listAttrHolder = new ArrayList<Object>();
                }
            }
            return ParseState.LIST_ATT;
    }
    return parseState;
}

Example 8 with VirtualColumnInfo

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

the class CyTableImpl method removeAllVirtColumns.

// Warning: This method is only to be used by CyTableManagerImpl!!!  That's also the reason
// why no ColumnDeletedEvent events are being fired by it!  Also this deletes
// (intentionally!) immutable columns!
void removeAllVirtColumns() {
    synchronized (lock) {
        if (getDependentCount() > 0)
            return;
        for (final String columnName : virtualColumnMap.keySet()) {
            final CyColumn column = types.get(columnName);
            types.remove(columnName);
            colList.remove(column);
            VirtualColumnInfo info = column.getVirtualColumnInfo();
            ((CyTableImpl) info.getSourceTable()).removeDependent(info.getSourceColumn(), column);
        }
        virtualColumnMap.clear();
    }
}

Example 9 with VirtualColumnInfo

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

the class CyTableImpl method deleteColumn.

@Override
public void deleteColumn(final String columnName) {
    synchronized (lock) {
        if (columnName == null)
            throw new NullPointerException("\"columnName\" must not be null.");
        final String normalizedColName = normalizeColumnName(columnName);
        final CyColumn column = types.get(normalizedColName);
        if (column == null)
            return;
        if (column.isImmutable())
            throw new IllegalArgumentException("cannot delete immutable column \"" + columnName + "\".");
        final VirtualColumn virtColumn = virtualColumnMap.get(normalizedColName);
        if (attributes.containsKey(normalizedColName) || virtColumn != null) {
            if (virtColumn != null) {
                final CyColumn cyColumn = types.get(normalizedColName);
                virtualColumnMap.remove(normalizedColName);
                attributes.remove(normalizedColName);
                types.remove(normalizedColName);
                colList.remove(cyColumn);
                VirtualColumnInfo info = cyColumn.getVirtualColumnInfo();
                ((CyTableImpl) info.getSourceTable()).removeDependent(info.getSourceColumn(), cyColumn);
            } else {
                attributes.remove(normalizedColName);
                colList.remove(types.get(normalizedColName));
                types.remove(normalizedColName);
            }
        }
    }
    // This event must be synchronous!
    eventHelper.fireEvent(new ColumnDeletedEvent(this, columnName));
}

Example 10 with VirtualColumnInfo

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

the class CloneNetworkTask method cloneRow.

private void cloneRow(final CyNetwork newNet, final Class<? extends CyIdentifiable> tableType, final CyRow from, final CyRow to) {
    final CyRootNetwork newRoot = rootNetMgr.getRootNetwork(newNet);
    Map<String, CyTable> rootTables = netTableMgr.getTables(newRoot, tableType);
    for (final CyColumn col : to.getTable().getColumns()) {
        final String name = col.getName();
        if (name.equals(CyIdentifiable.SUID))
            continue;
        final VirtualColumnInfo info = col.getVirtualColumnInfo();
        // then we have to set the value, because the rows of the new root table may not have been copied yet
        if (!info.isVirtual() || rootTables.containsValue(info.getSourceTable()))
            to.set(name, from.getRaw(name));
    }
}