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

Example 1 with CyTable

use of org.cytoscape.model.CyTable in project EnrichmentMapApp by BaderLab.

the class CreateEMNetworkTask method createEdgeColumns.

private CyTable createEdgeColumns(CyNetwork network) {
    CyTable table = network.getDefaultEdgeTable();
    Columns.EDGE_SIMILARITY_COEFF.createColumn(table, prefix, null);
    Columns.EDGE_OVERLAP_SIZE.createColumn(table, prefix, null);
    Columns.EDGE_DATASET.createColumn(table, prefix, null);
    Columns.EDGE_OVERLAP_GENES.createColumn(table, prefix, null);
    map.getParams().addSimilarityCutoffColumnName(Columns.EDGE_SIMILARITY_COEFF.with(prefix, null));
    return table;
}

Example 2 with CyTable

use of org.cytoscape.model.CyTable in project EnrichmentMapApp by BaderLab.

the class CreateEMNetworkTask method createNodeColumns.

private CyTable createNodeColumns(CyNetwork network) {
    CyTable table = network.getDefaultNodeTable();
    // !
    Columns.NODE_NAME.createColumn(table, prefix, null);
    // !
    Columns.NODE_GS_DESCR.createColumn(table, prefix, null);
    // !
    Columns.NODE_GS_TYPE.createColumn(table, prefix, null);
    // !
    Columns.NODE_FORMATTED_NAME.createColumn(table, prefix, null);
    // Union of geneset genes across all datasets // !
    Columns.NODE_GENES.createColumn(table, prefix, null);
    // Size of the union // !
    Columns.NODE_GS_SIZE.createColumn(table, prefix, null);
    EMCreationParameters params = map.getParams();
    for (String datasetName : map.getDataSetNames()) {
        Columns.NODE_PVALUE.createColumn(table, prefix, datasetName);
        Columns.NODE_FDR_QVALUE.createColumn(table, prefix, datasetName);
        Columns.NODE_FWER_QVALUE.createColumn(table, prefix, datasetName);
        // MKTODO only create these if method is GSEA?
        Columns.NODE_ES.createColumn(table, prefix, datasetName);
        Columns.NODE_NES.createColumn(table, prefix, datasetName);
        Columns.NODE_COLOURING.createColumn(table, prefix, datasetName);
        params.addPValueColumnName(Columns.NODE_PVALUE.with(prefix, datasetName));
        params.addQValueColumnName(Columns.NODE_FDR_QVALUE.with(prefix, datasetName));
    }
    return table;
}

Example 3 with CyTable

use of org.cytoscape.model.CyTable in project EnrichmentMapApp by BaderLab.

the class WidthFunction method createColumns.

private void createColumns(CyNetwork network, String prefix) {
    CyTable networkTable = network.getDefaultNetworkTable();
    NETWORK_EDGE_WIDTH_PARAMETERS_COLUMN.createColumnIfAbsent(networkTable, null, null);
    CyTable edgeTable = network.getDefaultEdgeTable();
    EDGE_WIDTH_FORMULA_COLUMN.createColumnIfAbsent(edgeTable, prefix, null);
}

Example 4 with CyTable

use of org.cytoscape.model.CyTable in project EnrichmentMapApp by BaderLab.

the class AbstractChart method getLabelsFromColumn.

@SuppressWarnings("unchecked")
public List<String> getLabelsFromColumn(final CyNetwork network, final CyIdentifiable model, final CyColumnIdentifier columnId) {
    final List<String> labels = new ArrayList<>();
    final CyRow row = network.getRow(model);
    if (row != null && columnId != null) {
        final CyTable table = row.getTable();
        final CyColumn column = table.getColumn(columnId.getColumnName());
        if (column != null && column.getType() == List.class) {
            final Class<?> type = column.getListElementType();
            final List<?> values = row.getList(columnId.getColumnName(), type);
            if (type == String.class) {
                labels.addAll((List<String>) values);
            } else {
                for (Object obj : values) labels.add(obj.toString());
            }
        }
    }
    return labels;
}

Example 5 with CyTable

use of org.cytoscape.model.CyTable in project EnrichmentMapApp by BaderLab.

the class AbstractChart method getSingleValueColumnNames.

/**
	 * @return The names of the data columns or an empty list if any of the data columns is of type List.
	 */
protected List<String> getSingleValueColumnNames(final CyNetwork network, final CyIdentifiable model) {
    final List<String> names = new ArrayList<>();
    final CyRow row = network.getRow(model);
    if (row == null)
        return names;
    final List<CyColumnIdentifier> dataColumns = getList(DATA_COLUMNS, CyColumnIdentifier.class);
    final CyTable table = row.getTable();
    boolean invalid = false;
    for (final CyColumnIdentifier colId : dataColumns) {
        final CyColumn column = table.getColumn(colId.getColumnName());
        if (column == null || column.getType() == List.class) {
            // Not a single value column!
            invalid = true;
            break;
        }
        names.add(colId.getColumnName());
    }
    if (invalid)
        names.clear();
    return names;
}