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.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
int selectedRow = -1;
-- JButton fetchDAS = new JButton();
--
-- JButton saveDAS = new JButton();
--
-- JButton cancelDAS = new JButton();
--
boolean resettingTable = false;
/*
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
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
- fetchDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fetchDAS_actionPerformed(e);
- }
- });
- saveDAS.setText(MessageManager.getString("action.save_as_default"));
- saveDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- saveDAS_actionPerformed(e);
- }
- });
-
- JPanel dasButtonPanel = new JPanel();
- dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
- dasSettingsPane.setBorder(null);
- cancelDAS.setEnabled(false);
- cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
- cancelDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancelDAS_actionPerformed(e);
- }
- });
- 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);
this.add(settingsPane);
}
- public void fetchDAS_actionPerformed(ActionEvent e)
- {
- fetchDAS.setEnabled(false);
- cancelDAS.setEnabled(true);
- dassourceBrowser.setGuiEnabled(false);
- Vector<jalviewSourceI> selectedSources = dassourceBrowser
- .getSelectedSources();
- doDasFeatureFetch(selectedSources, true, true);
- }
-
- /**
- * get the features from selectedSources for all or the current selection
- *
- * @param selectedSources
- * @param checkDbRefs
- * @param promptFetchDbRefs
- */
- private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
- boolean checkDbRefs, boolean promptFetchDbRefs)
- {
- SequenceI[] dataset, seqs;
- int iSize;
- AlignmentViewport vp = af.getViewport();
- if (vp.getSelectionGroup() != null
- && vp.getSelectionGroup().getSize() > 0)
- {
- iSize = vp.getSelectionGroup().getSize();
- dataset = new SequenceI[iSize];
- seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
- }
- else
- {
- iSize = vp.getAlignment().getHeight();
- seqs = vp.getAlignment().getSequencesArray();
- }
-
- dataset = new SequenceI[iSize];
- for (int i = 0; i < iSize; i++)
- {
- dataset[i] = seqs[i].getDatasetSequence();
- }
-
- cancelDAS.setEnabled(true);
- dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
- this, selectedSources, checkDbRefs, promptFetchDbRefs);
- af.getViewport().setShowSequenceFeatures(true);
- af.showSeqFeatures.setSelected(true);
- }
-
- /**
- * blocking call to initialise the das source browser
- */
- public void initDasSources()
- {
- dassourceBrowser.initDasSources();
- }
-
- /**
- * examine the current list of das sources and return any matching the given
- * nicknames in sources
- *
- * @param sources
- * Vector of Strings to resolve to DAS source nicknames.
- * @return sources that are present in source list.
- */
- public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
- {
- return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
- }
-
- /**
- * get currently selected das sources. ensure you have called initDasSources
- * before calling this.
- *
- * @return vector of selected das source nicknames
- */
- public Vector<jalviewSourceI> getSelectedSources()
- {
- return dassourceBrowser.getSelectedSources();
- }
-
- /**
- * properly initialise DAS fetcher and then initiate a new thread to fetch
- * features from the named sources (rather than any turned on by default)
- *
- * @param sources
- * @param block
- * if true then runs in same thread, otherwise passes to the Swing
- * executor
- */
- public void fetchDasFeatures(Vector<String> sources, boolean block)
- {
- initDasSources();
- List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
- .resolveSourceNicknames(sources);
- if (resolved.size() == 0)
- {
- resolved = dassourceBrowser.getSelectedSources();
- }
- if (resolved.size() > 0)
- {
- final List<jalviewSourceI> dassources = resolved;
- fetchDAS.setEnabled(false);
- // cancelDAS.setEnabled(true); doDasFetch does this.
- Runnable fetcher = new Runnable()
- {
-
- @Override
- public void run()
- {
- doDasFeatureFetch(dassources, true, false);
-
- }
- };
- if (block)
- {
- fetcher.run();
- }
- else
- {
- SwingUtilities.invokeLater(fetcher);
- }
- }
- }
-
- public void saveDAS_actionPerformed(ActionEvent e)
- {
- dassourceBrowser
- .saveProperties(jalview.bin.Cache.applicationProperties);
- }
-
- public void complete()
- {
- fetchDAS.setEnabled(true);
- cancelDAS.setEnabled(false);
- dassourceBrowser.setGuiEnabled(true);
-
- }
-
- public void cancelDAS_actionPerformed(ActionEvent e)
- {
- if (dasFeatureFetcher != null)
- {
- dasFeatureFetcher.cancel();
- }
- complete();
- }
-
- public void noDasSourceActive()
- {
- complete();
- JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.no_das_sources_selected_warn"),
- MessageManager.getString("label.no_das_sources_selected_title"),
- 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
// ///////////////////////////////////////////////////////////////////////
updateFeatureRenderer(data);
}
+ /**
+ * Sets the visibility of any feature types which are sub-types of the type
+ * in the given row of the table
+ *
+ * @param row
+ * @param value
+ */
+ protected void setSubtypesVisibility(int row, Boolean value)
+ {
+ String type = (String) data[row][TYPE_COLUMN];
+ OntologyI so = SequenceOntologyFactory.getInstance();
+
+ for (int r = 0; r < data.length; r++)
+ {
+ if (r != row)
+ {
+ String type2 = (String) data[r][TYPE_COLUMN];
+ if (so.isA(type2, type))
+ {
+ data[r][SHOW_COLUMN] = value;
+ fireTableCellUpdated(r, SHOW_COLUMN);
+ }
+ }
+ }
+ }
-
}
class ColorRenderer extends JLabel implements TableCellRenderer
{
// bring up graduated chooser.
chooser = new FeatureTypeSettings(me.fr, type);
- /**
- * @j2sNative
- */
- {
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
- }
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
chooser.addActionListener(this);
- chooser.showTab(true);
+ // Make the renderer reappear.
+ fireEditingStopped();
}
- // Make the renderer reappear.
- fireEditingStopped();
}
else
{
*/
private List<FeatureMatcherI> filters;
- // set white normally, black to debug layout
- private Color debugBorderColour = Color.white;
-
private JPanel chooseFiltersPanel;
- private JTabbedPane tabbedPane;
-
+ /*
+ * feature types present in Feature Renderer which are
+ * sub-types of the one this editor is acting on
+ */
+ private final List<String> subTypes;
+
+ /*
+ * if true, filter or colour settings are also applied to
+ * any feature sub-types in the Sequence Ontology
+ */
+ private boolean applyFiltersToSubtypes;
+
+ private boolean applyColourToSubtypes;
+
/**
* Constructor
*
private JPanel initialiseColoursPanel()
{
JPanel colourByPanel = new JPanel();
+ colourByPanel.setBackground(Color.white);
colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
+ JvSwingUtils.createTitledBorder(colourByPanel,
+ MessageManager.getString("action.colour"), true);
/*
+ * option to apply colour to sub-types as well (if there are any)
+ */
+ if (!subTypes.isEmpty())
+ {
+ applyColourToSubtypes = false;
+ colourByPanel.add(initSubtypesPanel(false));
+ }
+
+ /*
* simple colour radio button and colour picker
*/
JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
*/
private JPanel initialiseAndOrPanel()
{
- JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel andOrPanel = new JPanel(new BorderLayout());
andOrPanel.setBackground(Color.white);
- JPanel panel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
- andOrPanel.add(panel1, BorderLayout.WEST);
- panel1.setBackground(Color.white);
- panel1.setBorder(BorderFactory.createLineBorder(debugBorderColour));
++//<<<<<<< HEAD
++// JPanel panel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
++// andOrPanel.add(panel1, BorderLayout.WEST);
++// panel1.setBackground(Color.white);
++// panel1.setBorder(BorderFactory.createLineBorder(debugBorderColour));
++//=======
++//>>>>>>> refs/heads/develop
andFilters = new JRadioButton(MessageManager.getString("label.and"));
orFilters = new JRadioButton(MessageManager.getString("label.or"));
ActionListener actionListener = new ActionListener()
andOr.add(andFilters);
andOr.add(orFilters);
andFilters.setSelected(true);
- panel1.add(
+ andOrPanel.add(
new JLabel(MessageManager.getString("label.join_conditions")));
- panel1.add(andFilters);
- panel1.add(orFilters);
+ andOrPanel.add(andFilters);
+ andOrPanel.add(orFilters);
+
return andOrPanel;
}
git://source.jalview.org / jalview.git / commitdiff