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

Example 36 with CyTable

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

the class AbstractChart method getDataFromColumns.

public Map<String, List<Double>> getDataFromColumns(final CyNetwork network, final CyIdentifiable model, final List<CyColumnIdentifier> columnNames) {
    LinkedHashMap<String, List<Double>> data = new LinkedHashMap<>();
    final CyRow row = network.getRow(model);
    if (row == null)
        return data;
    final CyTable table = row.getTable();
    final List<Double> singleSeriesValues = new ArrayList<>();
    final StringBuilder singleSeriesKey = new StringBuilder();
    int singleSeriesIndex = -1;
    int count = 0;
    for (final CyColumnIdentifier colId : columnNames) {
        final CyColumn column = table.getColumn(colId.getColumnName());
        if (column == null)
            continue;
        final String colName = column.getName();
        final List<Double> values = new ArrayList<Double>();
        if (column.getType() == List.class) {
            // List Column: One column = one data series
            final Class<?> type = column.getListElementType();
            if (type == Double.class) {
                List<Double> list = row.getList(colName, Double.class);
                if (list != null)
                    values.addAll(list);
            } else if (type == Integer.class) {
                List<Integer> list = row.getList(colName, Integer.class);
                if (list != null) {
                    for (Integer i : list) values.add(i.doubleValue());
                }
            } else if (type == Long.class) {
                List<Long> list = row.getList(colName, Long.class);
                if (list != null) {
                    for (Long l : list) values.add(l.doubleValue());
                }
            } else if (type == Float.class) {
                List<Float> list = row.getList(colName, Float.class);
                if (list != null) {
                    for (Float f : list) values.add(f.doubleValue());
                }
            }
            data.put(colName, values);
        } else {
            // Single Column: All single columns together make only one data series
            final Class<?> type = column.getType();
            if (Number.class.isAssignableFrom(type)) {
                if (!row.isSet(colName)) {
                    singleSeriesValues.add(Double.NaN);
                } else if (type == Double.class) {
                    singleSeriesValues.add(row.get(colName, Double.class));
                } else if (type == Integer.class) {
                    Integer i = row.get(colName, Integer.class);
                    singleSeriesValues.add(i.doubleValue());
                } else if (type == Float.class) {
                    Float f = row.get(colName, Float.class);
                    singleSeriesValues.add(f.doubleValue());
                }
                singleSeriesKey.append(colName + ",");
                // The index of this data series is the index of the first single column
                if (singleSeriesIndex == -1)
                    singleSeriesIndex = count;
            }
        }
        count++;
    }
    if (!singleSeriesValues.isEmpty()) {
        singleSeriesKey.deleteCharAt(singleSeriesKey.length() - 1);
        // To add the series of single columns into the correct position, we have to rebuild the data map
        final Set<Entry<String, List<Double>>> entrySet = data.entrySet();
        data = new LinkedHashMap<>();
        int i = 0;
        for (final Entry<String, List<Double>> entry : entrySet) {
            if (i == singleSeriesIndex)
                data.put(singleSeriesKey.toString(), singleSeriesValues);
            data.put(entry.getKey(), entry.getValue());
            i++;
        }
        if (// (entrySet.isEmpty() || i >= entrySet.size())
        !data.containsKey(singleSeriesKey.toString()))
            data.put(singleSeriesKey.toString(), singleSeriesValues);
    }
    return data;
}

Example 37 with CyTable

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

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 38 with CyTable

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

the class PopupMenuHelper method selectElementsFromSelectedRows.

private void selectElementsFromSelectedRows(final JTable table, final Class<? extends CyIdentifiable> tableType) {
    final Thread t = new Thread() {

        @Override
        public void run() {
            final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
            final CyNetwork net = applicationManager.getCurrentNetwork();
            if (net != null) {
                final BrowserTableModel tableModel = (BrowserTableModel) table.getModel();
                final int[] selectedRows = table.getSelectedRows();
                final Set<CyRow> targetRows = new HashSet<CyRow>();
                for (final int rowIndex : selectedRows) {
                    // Getting the row from data table solves the problem with hidden or moved SUID column.
                    // However, since the rows might be sorted we need to convert the index to model.
                    final ValidatedObjectAndEditString selected = (ValidatedObjectAndEditString) tableModel.getValueAt(table.convertRowIndexToModel(rowIndex), CyNetwork.SUID);
                    targetRows.add(tableModel.getRow(selected.getValidatedObject()));
                }
                final CyTable cyTable = tableType == CyNode.class ? net.getDefaultNodeTable() : net.getDefaultEdgeTable();
                for (final CyRow cyRow : cyTable.getAllRows()) cyRow.set(CyNetwork.SELECTED, targetRows.contains(cyRow));
                final CyNetworkView view = applicationManager.getCurrentNetworkView();
                if (view != null) {
                    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
                    eventHelper.flushPayloadEvents();
                    view.updateView();
                }
            }
        }
    };
    t.start();
}

Example 39 with CyTable

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

the class TableBrowserToolBar method updateEnableState.

protected void updateEnableState(final JComponent comp) {
    if (comp == null)
        return;
    boolean enabled = false;
    if (browserTableModel != null) {
        final CyTable attrs = browserTableModel.getDataTable();
        if (comp == deleteTableButton) {
            enabled = browserTableModel.getDataTable().getMutability() == Mutability.MUTABLE;
        } else if (comp == deleteAttributeButton) {
            for (final CyColumn column : attrs.getColumns()) {
                if (!column.isImmutable()) {
                    enabled = true;
                    break;
                }
            }
        } else if (comp == fnBuilderButton) {
            final int row = browserTable.getSelectedRow();
            final int column = browserTable.getSelectedColumn();
            enabled = row >= 0 && column >= 0 && browserTableModel.isCellEditable(row, column);
        } else if (comp == tableChooser) {
            enabled = tableChooser.getItemCount() > 0;
        } else {
            enabled = true;
        }
    }
    comp.setEnabled(enabled);
    // Unfortunately this is necessary on Nimbus!
    if (comp instanceof AbstractButton && LookAndFeelUtil.isNimbusLAF())
        comp.setForeground(UIManager.getColor(enabled ? "Button.foreground" : "Button.disabledForeground"));
}

Example 40 with CyTable

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

the class TableBrowserToolBar method getFnBuilderButton.

private JButton getFnBuilderButton() {
    if (fnBuilderButton == null) {
        fnBuilderButton = new JButton("f(x)");
        fnBuilderButton.setToolTipText("Function Builder");
        Font iconFont = null;
        try {
            iconFont = Font.createFont(Font.TRUETYPE_FONT, getClass().getResourceAsStream("/fonts/jsMath-cmti10.ttf"));
        } catch (Exception e) {
            throw new RuntimeException("Error loading font", e);
        }
        styleButton(fnBuilderButton, iconFont.deriveFont(18.0f));
        final JFrame rootFrame = (JFrame) SwingUtilities.getRoot(this);
        fnBuilderButton.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(final ActionEvent e) {
                // Do not allow opening of the formula builder dialog while a cell is being edited!
                if (browserTableModel == null || browserTable.getCellEditor() != null)
                    return;
                final int cellRow = browserTable.getSelectedRow();
                final int cellColumn = browserTable.getSelectedColumn();
                int colIndex = -1;
                // Map the screen index of column to internal index of the table model
                if (cellRow >= 0 && cellColumn >= 0) {
                    String colName = browserTable.getColumnName(cellColumn);
                    colIndex = browserTableModel.mapColumnNameToColumnIndex(colName);
                }
                if (cellRow == -1 || cellColumn == -1 || !browserTableModel.isCellEditable(cellRow, colIndex)) {
                    JOptionPane.showMessageDialog(rootFrame, "Can't enter a formula w/o a selected cell.", "Information", JOptionPane.INFORMATION_MESSAGE);
                } else {
                    final String attrName = getAttribName(cellRow, cellColumn);
                    final Map<String, Class<?>> attribNameToTypeMap = new HashMap<>();
                    final CyTable dataTable = browserTableModel.getDataTable();
                    initAttribNameToTypeMap(dataTable, attrName, attribNameToTypeMap);
                    final EquationCompiler compiler = serviceRegistrar.getService(EquationCompiler.class);
                    final FormulaBuilderDialog formulaBuilderDialog = new FormulaBuilderDialog(compiler, browserTable, rootFrame, attrName);
                    formulaBuilderDialog.setLocationRelativeTo(rootFrame);
                    formulaBuilderDialog.setVisible(true);
                }
            }

            private void initAttribNameToTypeMap(final CyTable dataTable, final String attrName, final Map<String, Class<?>> attribNameToTypeMap) {
                for (final CyColumn column : dataTable.getColumns()) attribNameToTypeMap.put(column.getName(), column.getType());
                attribNameToTypeMap.remove(attrName);
            }
        });
    }
    return fnBuilderButton;
}