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

Example 11 with VirtualColumnInfo

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

the class CloneNetworkTask method addColumns.

private void addColumns(final CyNetwork origNet, final CyNetwork newNet, final Class<? extends CyIdentifiable> tableType, final String namespace) {
    final CyTable from = origNet.getTable(tableType, namespace);
    final CyTable to = newNet.getTable(tableType, namespace);
    final CyRootNetwork origRoot = rootNetMgr.getRootNetwork(origNet);
    final CyRootNetwork newRoot = rootNetMgr.getRootNetwork(newNet);
    final Map<String, CyTable> origRootTables = netTableMgr.getTables(origRoot, tableType);
    for (final CyColumn col : from.getColumns()) {
        final String name = col.getName();
        if (to.getColumn(name) == null) {
            final VirtualColumnInfo info = col.getVirtualColumnInfo();
            if (info.isVirtual()) {
                if (origRootTables.containsValue(info.getSourceTable())) {
                    // If the virtual column is from a root-network table, do NOT set this virtual column directly to
                    // the new table:
                    // Get the original column (not the virtual one!)
                    final CyColumn origCol = info.getSourceTable().getColumn(info.getSourceColumn());
                    // Copy the original column to the root-network's table first
                    String sourceNamespace = netTableMgr.getTableNamespace(info.getSourceTable());
                    final CyTable newRootTable = newRoot.getTable(tableType, sourceNamespace);
                    if (newRootTable.getColumn(origCol.getName()) == null)
                        copyColumn(origCol, newRootTable);
                    // Now we can add the new "root" column as a virtual one to the new network's table
                    to.addVirtualColumn(name, origCol.getName(), newRootTable, CyIdentifiable.SUID, col.isImmutable());
                } else {
                    // Otherwise (e.g. virtual column from a global table) just add the virtual column directly
                    addVirtualColumn(col, to);
                }
            } else {
                // Not a virtual column, so just copy it to the new network's table
                copyColumn(col, to);
            }
        }
    }
}

Example 12 with VirtualColumnInfo

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

the class ClipboardImpl method copyRows.

private void copyRows(Map<CyRow, CyRow> rowMap) {
    if (rowMap == null || rowMap.size() == 0)
        return;
    for (CyRow sourceRow : rowMap.keySet()) {
        CyRow targetRow = rowMap.get(sourceRow);
        CyTable destTable = targetRow.getTable();
        CyTable sourceTable = sourceRow.getTable();
        Map<String, Object> oldDataMap;
        if (oldValueMap.containsKey(sourceRow))
            oldDataMap = oldValueMap.get(sourceRow);
        else
            oldDataMap = sourceRow.getAllValues();
        for (String colName : oldDataMap.keySet()) {
            CyColumn column = destTable.getColumn(colName);
            if (column == null) {
                CyColumn sourceColumn = sourceTable.getColumn(colName);
                if (sourceColumn.getType() == List.class) {
                    destTable.createListColumn(colName, sourceColumn.getListElementType(), sourceColumn.isImmutable());
                } else {
                    destTable.createColumn(colName, sourceColumn.getType(), sourceColumn.isImmutable());
                }
            } else if (column.isPrimaryKey()) {
                continue;
            } else {
                // Column already exists.  We need to check for virtual columns that don't join
                // on SUID (since that's the only thing we're changing).  If they don't, we need to skip them.
                VirtualColumnInfo virtualInfo = column.getVirtualColumnInfo();
                if (virtualInfo.isVirtual() && !virtualInfo.getTargetJoinKey().equals(CyNetwork.SUID))
                    continue;
            }
            // want to copy it.
            try {
                targetRow.set(colName, oldDataMap.get(colName));
            } catch (IllegalArgumentException e) {
                // Log a warning
                System.out.println("Set failed!  " + e);
            }
        }
    }
}

Example 13 with VirtualColumnInfo

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

the class CyTablesXMLWriter method buildModel.

private CyTables buildModel() {
    CyTables model = new CyTables();
    VirtualColumns virtualColumns = new VirtualColumns();
    model.setVirtualColumns(virtualColumns);
    List<VirtualColumn> columns = virtualColumns.getVirtualColumn();
    for (CyTableMetadata metadata : tables) {
        CyTable table = metadata.getTable();
        String targetTable = tableFileNamesBySUID.get(table.getSUID());
        if (targetTable == null) {
            continue;
        }
        for (CyColumn cyColumn : table.getColumns()) {
            VirtualColumnInfo info = cyColumn.getVirtualColumnInfo();
            if (!info.isVirtual()) {
                continue;
            }
            String sourceTable = tableFileNamesBySUID.get(info.getSourceTable().getSUID());
            if (sourceTable == null) {
                // log this
                continue;
            }
            VirtualColumn column = new VirtualColumn();
            column.setName(cyColumn.getName());
            column.setSourceColumn(info.getSourceColumn());
            column.setSourceTable(sourceTable);
            column.setSourceJoinKey(info.getSourceJoinKey());
            column.setTargetTable(targetTable);
            column.setTargetJoinKey(info.getTargetJoinKey());
            columns.add(column);
        }
    }
    return model;
}