import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemabinding.version2.Filter;
import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemabinding.version2.MatcherSet;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.HashMap;
import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
import javax.swing.SwingConstants;
import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.swing.table.TableRowSorter;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
{
+ private static final Font VERDANA_12 = new Font("Verdana", Font.PLAIN, 12);
+
private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
.getString("label.sequence_feature_colours");
*/
Map<String, float[]> typeWidth = null;
+ /*
+ * if true, 'child' feature types are not displayed
+ */
+ JCheckBox summaryView;
+
+ /*
+ * those feature types that do not have a parent feature type present
+ * (as determined by an Ontology relationship)
+ */
+ List<String> topLevelTypes;
+
/**
* Constructor
*
originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+ topLevelTypes = new ArrayList<>();
+
try
{
jbInit();
ex.printStackTrace();
}
+ initTable();
+
+ scrollPane.setViewportView(table);
+
+ dassourceBrowser = new DasSourceBrowser(this);
+ dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
+
+ if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
+ {
+ fr.findAllFeatures(true); // display everything!
+ }
+
+ discoverAllFeatureData();
+ final PropertyChangeListener change;
+ final FeatureSettings fs = this;
+ fr.addPropertyChangeListener(change = new PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (!fs.resettingTable && !fs.handlingUpdate)
+ {
+ fs.handlingUpdate = true;
+ fs.resetTable(null);
+ // new groups may be added with new sequence feature types only
+ fs.handlingUpdate = false;
+ }
+ }
+ });
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (Platform.isAMac())
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 450);
+ }
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ dassourceBrowser.fs = null;
+ };
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ inConstruction = false;
+ }
+
+ /**
+ * Constructs and configures the JTable which displays columns of data for
+ * each feature type
+ */
+ protected void initTable()
+ {
table = new JTable()
{
@Override
switch (column)
{
case TYPE_COLUMN:
- tip = JvSwingUtils.wrapTooltip(true, MessageManager
+ tip = summaryView.isSelected()
+ ? MessageManager.getString(
+ "label.feature_settings_select_columns")
+ : JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
case FILTER_COLUMN:
return tip;
}
};
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
- table.setFont(new Font("Verdana", Font.PLAIN, 12));
+ table.getTableHeader().setFont(VERDANA_12);
+ table.setFont(VERDANA_12);
- // table.setDefaultRenderer(Color.class, new ColorRenderer());
- // table.setDefaultEditor(Color.class, new ColorEditor(this));
- //
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
if (evt.isPopupTrigger())
{
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ popupMenu(selectedRow, type, colour, evt.getX(), evt.getY());
}
else if (evt.getClickCount() == 2)
{
{
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ popupMenu(selectedRow, type, colour, evt.getX(), evt.getY());
}
}
});
public void mouseDragged(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
- if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
- {
- /*
- * reposition 'selectedRow' to 'newRow' (the dragged to location)
- * this could be more than one row away for a very fast drag action
- * so just swap it with adjacent rows until we get it there
- */
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
- int direction = newRow < selectedRow ? -1 : 1;
- for (int i = selectedRow; i != newRow; i += direction)
- {
- Object[] temp = data[i];
- data[i] = data[i + direction];
- data[i + direction] = temp;
- }
- updateFeatureRenderer(data);
- table.repaint();
- selectedRow = newRow;
- }
- }
- });
- // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
- // MessageManager.getString("label.feature_settings_click_drag")));
- scrollPane.setViewportView(table);
-
- dassourceBrowser = new DasSourceBrowser(this);
- dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
-
- if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
- {
- fr.findAllFeatures(true); // display everything!
- }
-
- discoverAllFeatureData();
- final PropertyChangeListener change;
- final FeatureSettings fs = this;
- fr.addPropertyChangeListener(change = new PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (!fs.resettingTable && !fs.handlingUpdate)
- {
- fs.handlingUpdate = true;
- fs.resetTable(null);
- // new groups may be added with new sequence feature types only
- fs.handlingUpdate = false;
- }
+ dragRow(newRow);
}
-
});
-
- frame = new JInternalFrame();
- frame.setContentPane(this);
- if (Platform.isAMac())
- {
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 480);
- }
- else
- {
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 450);
- }
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
-
- frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- fr.removePropertyChangeListener(change);
- dassourceBrowser.fs = null;
- };
- });
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- inConstruction = false;
}
- protected void popupSort(final int rowSelected, final String type,
- final Object typeCol, final Map<String, float[][]> minmax, int x,
- int y)
+ protected void popupMenu(final int rowSelected, final String type,
+ final Object typeCol, int x, int y)
{
final FeatureColourI featureColour = (FeatureColourI) typeCol;
}
}
}
-
});
JMenuItem selCols = new JMenuItem(
*/
Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
visibleGroups.toArray(new String[visibleGroups.size()]));
+
for (String type : types)
{
displayableTypes.add(type);
}
}
+ /*
+ * enable 'Summary View' if some types are sub-types of others
+ */
+ Set<String> parents = SequenceOntologyFactory.getInstance()
+ .getParentTerms(displayableTypes);
+ summaryView.setEnabled(parents.size() < displayableTypes.size());
+
Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT];
int dataIndex = 0;
{
continue;
}
-
data[dataIndex][TYPE_COLUMN] = type;
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
updateOriginalData(data);
}
- table.setModel(new FeatureTableModel(data));
+ /*
+ * recreate the table model
+ */
+ FeatureTableModel dataModel = new FeatureTableModel(data);
+ table.setModel(dataModel);
+
+ /*
+ * we want to be able to filter out rows for sub-types, but not to sort
+ * rows, so have to add a RowFilter to a disabled TableRowSorter (!)
+ */
+ final TableRowSorter<FeatureTableModel> sorter = new TableRowSorter<>(
+ dataModel);
+ for (int i = 0; i < table.getColumnCount(); i++)
+ {
+ sorter.setSortable(i, false);
+ }
+
+ /*
+ * filter rows to only top-level Ontology types if requested
+ */
+ sorter.setRowFilter(new RowFilter<FeatureTableModel, Integer>()
+ {
+ @Override
+ public boolean include(
+ Entry<? extends FeatureTableModel, ? extends Integer> entry)
+ {
+ if (!summaryView.isSelected())
+ {
+ return true;
+ }
+ int row = entry.getIdentifier(); // this is model, not view, row number
+ String featureType = (String) entry.getModel().getData()[row][TYPE_COLUMN];
+ return parents.contains(featureType);
+ }
+ });
+ table.setRowSorter(sorter);
+
table.getColumnModel().getColumn(0).setPreferredWidth(200);
groupPanel.setLayout(
}
});
+ summaryView = new JCheckBox("Summary view");
+ summaryView.setToolTipText("Show only top level ontology terms");
+ summaryView.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetTable(null);
+ }
+ });
+
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
}
});
- JPanel transPanel = new JPanel(new GridLayout(1, 2));
- bigPanel.add(transPanel, BorderLayout.SOUTH);
+ JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
+ bigPanel.add(lowerPanel, BorderLayout.SOUTH);
JPanel transbuttons = new JPanel(new GridLayout(5, 1));
transbuttons.add(optimizeOrder);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
transbuttons.add(help);
+ JPanel transPanel = new JPanel(new GridLayout(3, 1));
+ transPanel.add(summaryView);
+ transPanel.add(new JLabel(" Colour transparency" + ":"));
transPanel.add(transparency);
- transPanel.add(transbuttons);
+ lowerPanel.add(transPanel);
+ lowerPanel.add(transbuttons);
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
}
+ /**
+ * Reorders features by 'dragging' selectedRow to 'newRow'
+ *
+ * @param newRow
+ */
+ protected void dragRow(int newRow)
+ {
+ if (summaryView.isSelected())
+ {
+ // no drag while in summary view
+ return;
+ }
+
+ if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
+ {
+ /*
+ * reposition 'selectedRow' to 'newRow' (the dragged to location)
+ * this could be more than one row away for a very fast drag action
+ * so just swap it with adjacent rows until we get it there
+ */
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ int direction = newRow < selectedRow ? -1 : 1;
+ for (int i = selectedRow; i != newRow; i += direction)
+ {
+ Object[] temp = data[i];
+ data[i] = data[i + direction];
+ data[i + direction] = temp;
+ }
+ updateFeatureRenderer(data);
+ table.repaint();
+ selectedRow = newRow;
+ }
+ }
+
+ protected void refreshTable()
+ {
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (Object[] row : data)
+ {
+ String type = (String) row[TYPE_COLUMN];
+ FeatureColourI colour = fr.getFeatureColours().get(type);
+ FeatureMatcherSetI filter = fr.getFeatureFilter(type);
+ if (filter == null)
+ {
+ filter = new FeatureMatcherSet();
+ }
+ row[COLOUR_COLUMN] = colour;
+ row[FILTER_COLUMN] = filter;
+ }
+ repaint();
+ }
+
// ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
// ///////////////////////////////////////////////////////////////////////
String type;
- JButton button;
+ JButton colourButton;
JColorChooser colorChooser;
// which is a button.
// This button brings up the color chooser dialog,
// which is the editor from the user's point of view.
- button = new JButton();
- button.setActionCommand(EDIT);
- button.addActionListener(this);
- button.setBorderPainted(false);
+ colourButton = new JButton();
+ colourButton.setActionCommand(EDIT);
+ colourButton.addActionListener(this);
+ colourButton.setBorderPainted(false);
// Set up the dialog that the button brings up.
colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
+ dialog = JColorChooser.createDialog(colourButton,
MessageManager.getString("label.select_colour"), true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
if (currentColor.isSimpleColour())
{
// bring up simple color chooser
- button.setBackground(currentColor.getColour());
+ colourButton.setBackground(currentColor.getColour());
colorChooser.setColor(currentColor.getColour());
dialog.setVisible(true);
}
}
// Make the renderer reappear.
fireEditingStopped();
-
}
else
{
* (or filters!) are already set in FeatureRenderer, so just
* update table data without triggering updateFeatureRenderer
*/
- currentColor = fr.getFeatureColours().get(type);
- FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
- if (currentFilter == null)
- {
- currentFilter = new FeatureMatcherSet();
- }
- Object[] data = ((FeatureTableModel) table.getModel())
- .getData()[rowSelected];
- data[COLOUR_COLUMN] = currentColor;
- data[FILTER_COLUMN] = currentFilter;
+ refreshTable();
}
fireEditingStopped();
me.table.validate();
currentColor = (FeatureColourI) value;
this.rowSelected = row;
type = me.table.getValueAt(row, TYPE_COLUMN).toString();
- button.setOpaque(true);
- button.setBackground(me.getBackground());
+ colourButton.setOpaque(true);
+ colourButton.setBackground(me.getBackground());
if (!currentColor.isSimpleColour())
{
JLabel btn = new JLabel();
- btn.setSize(button.getSize());
+ btn.setSize(colourButton.getSize());
FeatureSettings.renderGraduatedColor(btn, currentColor);
- button.setBackground(btn.getBackground());
- button.setIcon(btn.getIcon());
- button.setText(btn.getText());
+ colourButton.setBackground(btn.getBackground());
+ colourButton.setIcon(btn.getIcon());
+ colourButton.setText(btn.getText());
}
else
{
- button.setText("");
- button.setIcon(null);
- button.setBackground(currentColor.getColour());
+ colourButton.setText("");
+ colourButton.setIcon(null);
+ colourButton.setBackground(currentColor.getColour());
}
- return button;
+ return colourButton;
}
}
String type;
- JButton button;
+ JButton filterButton;
protected static final String EDIT = "edit";
public FilterEditor(FeatureSettings me)
{
this.me = me;
- button = new JButton();
- button.setActionCommand(EDIT);
- button.addActionListener(this);
- button.setBorderPainted(false);
+ filterButton = new JButton();
+ filterButton.setActionCommand(EDIT);
+ filterButton.addActionListener(this);
+ filterButton.setBorderPainted(false);
}
/**
@Override
public void actionPerformed(ActionEvent e)
{
- if (button == e.getSource())
+ if (filterButton == e.getSource())
{
FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
chooser.addActionListener(this);
}
else if (e.getSource() instanceof Component)
{
-
/*
* after OK in variable colour dialog, any changes to filter
* (or colours!) are already set in FeatureRenderer, so just
* update table data without triggering updateFeatureRenderer
*/
- FeatureColourI currentColor = fr.getFeatureColours().get(type);
- currentFilter = me.fr.getFeatureFilter(type);
- if (currentFilter == null)
- {
- currentFilter = new FeatureMatcherSet();
- }
- Object[] data = ((FeatureTableModel) table.getModel())
- .getData()[rowSelected];
- data[COLOUR_COLUMN] = currentColor;
- data[FILTER_COLUMN] = currentFilter;
+ refreshTable();
fireEditingStopped();
me.table.validate();
}
currentFilter = (FeatureMatcherSetI) value;
this.rowSelected = row;
type = me.table.getValueAt(row, TYPE_COLUMN).toString();
- button.setOpaque(true);
- button.setBackground(me.getBackground());
- button.setText(currentFilter.toString());
- button.setToolTipText(currentFilter.toString());
- button.setIcon(null);
- return button;
+ filterButton.setOpaque(true);
+ filterButton.setBackground(me.getBackground());
+ filterButton.setText(currentFilter.toString());
+ filterButton.setToolTipText(currentFilter.toString());
+ filterButton.setIcon(null);
+ return filterButton;
}
}
}
class FeatureIcon implements Icon
{
+ private static final Font VERDANA_9 = new Font("Verdana", Font.PLAIN, 9);
+
FeatureColourI gcol;
Color backg;
// need an icon here.
g.setColor(gcol.getMaxColour());
- g.setFont(new Font("Verdana", Font.PLAIN, 9));
+ g.setFont(VERDANA_9);
// g.setFont(g.getFont().deriveFont(
// AffineTransform.getScaleInstance(
git://source.jalview.org / jalview.git / blobdiff