import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.Help.HelpId;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatcherSet;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.BorderLayout;
import java.awt.Color;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
+import javax.swing.ToolTipManager;
import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
+import javax.swing.plaf.TableUI;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
private static final int MIN_HEIGHT = 400;
- private final static String BASE_TOOLTIP = "Click to edit, right-click for menu";
+ private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
final FeatureRenderer fr;
*/
Object[][] originalData;
- private float originalTransparency;
+ float originalTransparency;
- private Map<String, FeatureMatcherSetI> originalFilters;
+ Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
/*
* true when Feature Settings are updating from feature renderer
*/
- private boolean handlingUpdate = false;
+ boolean handlingUpdate = false;
/*
* holds {featureCount, totalExtent} for each feature type
table = new JTable()
{
- static final String tt = "Click to edit, right-click for menu"; // todo i18n
-
@Override
public String getToolTipText(MouseEvent e)
{
case COLOUR_COLUMN:
FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
column);
- tip = getColorTooltip(colour);
+ tip = getColorTooltip(colour, true);
break;
case FILTER_COLUMN:
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
default:
break;
}
+
return tip;
}
+
+
+ /**
+ * Position the tooltip near the bottom edge of, and half way across, the
+ * current cell
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent e)
+ {
+ Point point = e.getPoint();
+ int column = table.columnAtPoint(point);
+ int row = table.rowAtPoint(point);
+ Rectangle r = getCellRect(row, column, false);
+ Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
+ return loc;
+ }
};
+
+ // next line is needed to avoid (quiet) exceptions thrown
+ // when column ordering changes so that the above constants
+ // no longer apply.
+ table.getTableHeader().setReorderingAllowed(false); // BH 2018
+
table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
- table.setFont(new Font("Verdana", Font.PLAIN, 12));
+ ToolTipManager.sharedInstance().registerComponent(table);
- // 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());
table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
-
+
TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
new ColorRenderer(), new ColorEditor(this));
table.addColumn(colourColumn);
if (evt.isPopupTrigger())
{
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
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());
+ showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
}
});
data[i + direction] = temp;
}
updateFeatureRenderer(data);
- table.repaint();
+ repaintTable();
selectedRow = newRow;
}
}
inConstruction = false;
}
- protected void popupSort(final int rowSelected, final String type,
- final Object typeCol, final Map<String, float[][]> minmax, int x,
- int y)
+ /**
+ * Constructs and shows a popup menu of possible actions on the selected row and
+ * feature type
+ *
+ * @param rowSelected
+ * @param type
+ * @param typeCol
+ * @param pt
+ */
+ protected void showPopupMenu(final int rowSelected, final String type,
+ final Object typeCol, final Point pt)
{
final FeatureColourI featureColour = (FeatureColourI) typeCol;
.sortAlignmentByFeatureScore(Arrays.asList(new String[]
{ type }));
}
-
});
JMenuItem dens = new JMenuItem(
MessageManager.getString("label.sort_by_density"));
.sortAlignmentByFeatureDensity(Arrays.asList(new String[]
{ type }));
}
-
});
men.add(dens);
* variable colour options include colour by label, by score,
* by selected attribute text, or attribute value
*/
- final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
+ final JCheckBoxMenuItem variableColourCB = new JCheckBoxMenuItem(
MessageManager.getString("label.variable_colour"));
- mxcol.setSelected(!featureColour.isSimpleColour());
- men.add(mxcol);
- mxcol.addActionListener(new ActionListener()
+ variableColourCB.setSelected(!featureColour.isSimpleColour());
+ men.add(variableColourCB);
+
+ /*
+ * checkbox action listener doubles up as listener to OK
+ * from the variable colour / filters dialog
+ */
+ variableColourCB.addActionListener(new ActionListener()
{
- JColorChooser colorChooser;
-
@Override
public void actionPerformed(ActionEvent e)
{
- if (e.getSource() == mxcol)
+ if (e.getSource() == variableColourCB)
{
+ men.setVisible(true); // BH 2018 for JavaScript because this is a checkbox
+ men.setVisible(false); // BH 2018 for JavaScript because this is a checkbox
if (featureColour.isSimpleColour())
{
+ /*
+ * toggle simple colour to variable colour - show dialog
+ */
FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
fc.addActionListener(this);
}
else
{
- // bring up simple color chooser
- colorChooser = new JColorChooser();
- String title = MessageManager
- .getString("label.select_colour");
- JDialog dialog = JColorChooser.createDialog(me,
- title, true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- colorChooser.setColor(featureColour.getMaxColour());
- dialog.setVisible(true);
+ /*
+ * toggle variable to simple colour - show colour chooser
+ */
+ String title = MessageManager.formatMessage("label.select_colour_for", type);
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ table.setValueAt(new FeatureColour(c), rowSelected,
+ COLOUR_COLUMN);
+ table.validate();
+ me.updateFeatureRenderer(
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
+ }
+ };
+ JalviewColourChooser.showColourChooser(me, title, featureColour.getMaxColour(), listener);
}
}
- else
+ else
{
if (e.getSource() instanceof FeatureTypeSettings)
{
* colour will have already been set in the FeatureRenderer
*/
FeatureColourI fci = fr.getFeatureColours().get(type);
- table.setValueAt(fci, rowSelected, 1);
- table.validate();
- }
- else
- {
- // probably the color chooser!
- table.setValueAt(new FeatureColour(colorChooser.getColor()),
- rowSelected, 1);
- table.validate();
- me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
+ table.setValueAt(fci, rowSelected, COLOUR_COLUMN);
+ // BH 2018 setting a table value does not invalidate it.
+ System.out.println("FeatureSettings is valied" + table.isValid());
+// table.validate();
}
}
}
-
});
JMenuItem selCols = new JMenuItem(
men.add(clearCols);
men.add(hideCols);
men.add(hideOtherCols);
- men.show(table, x, y);
+ men.show(table, pt.x, pt.y);
}
@Override
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- File file = chooser.getSelectedFile();
- load(file);
- }
+ chooser.addResponse(new RunResponse(JalviewFileChooser.APPROVE_OPTION){
+
+ @Override
+ public void run() {
+ File file = chooser.getSelectedFile();
+ load(file);
+ }});
+ chooser.showOpenDialog(this);
}
/**
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
- JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
+
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
/*
* load feature colours
*/
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
{
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
fr.setColour(newcol.getName(), colour);
- fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
}
/*
* load feature filters; loaded filters will replace any that are
* currently defined, other defined filters are left unchanged
*/
- for (int i = 0; i < jucs.getFilterCount(); i++)
+ for (int i = 0; i < jucs.getFilter().size(); i++)
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
+ Filter filterModel = jucs.getFilter().get(i);
String featureType = filterModel.getFeatureType();
- FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
- filterModel.getMatcherSet());
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
.getData();
ensureOrder(data);
updateFeatureRenderer(data, false);
- table.repaint();
+ repaintTable();
}
} catch (Exception ex)
{
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- save(chooser.getSelectedFile());
- }
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ save(file);
+ }
}
/**
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
}
/*
{
Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+ jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+ .marshalFilter(firstMatcher, iterator,
filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
filterModel.setMatcherSet(ms);
- ucs.addFilter(filterModel);
+ ucs.getFilter().add(filterModel);
}
}
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
- ucs.marshal(out);
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
}
updateFeatureRenderer(data, true);
- table.repaint();
+ repaintTable();
}
public void orderByAvWidth()
table.repaint();
}
+ /**
+ * Repaints the table using alternative code for Java and J2S
+ */
+ private void repaintTable()
+ {
+ if (true)
+ return;
+ // BH 2018
+ // Here is a needed intervention
+ // because generally we don't "repaint"
+ // the table. We re-create the HTML divs
+ // that is associated with it. A better
+ // way to do this would be to fire a property change.
+ @SuppressWarnings("unused")
+ TableUI ui = table.getUI();
+ /**
+ * @j2sNative ui.repaintTable$();
+ */
+ {
+ table.repaint();
+ }
+ }
+
public void close()
{
try
* @param data
* @param visibleNew
*/
- private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+ void updateFeatureRenderer(Object[][] data, boolean visibleNew)
{
FeatureSettingsBean[] rowData = getTableAsBeans(data);
/**
* Answers a suitable tooltip to show on the colour cell of the table
*
- * @param gcol
+ * @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
* @return
*/
- public String getColorTooltip(FeatureColourI gcol)
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
{
- if (gcol.isSimpleColour())
- {
- return BASE_TOOLTIP;
- }
- StringBuilder tt = new StringBuilder();
- if (gcol.isAboveThreshold())
+ if (fcol == null)
{
- tt.append("Thresholded (Above ").append(gcol.getThreshold())
- .append(")");
+ return null;
}
- else if (gcol.isBelowThreshold())
+ if (fcol.isSimpleColour())
{
- tt.append("Thresholded (Below ").append(gcol.getThreshold())
- .append(")");
+ return withHint ? BASE_TOOLTIP : null;
}
- else if (gcol.isColourByLabel())
+ String description = fcol.getDescription();
+ description = description.replaceAll("<", "<");
+ description = description.replaceAll(">", ">");
+ StringBuilder tt = new StringBuilder(description);
+ if (withHint)
{
- tt.insert(0, "Coloured by label text ");
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
}
- tt.append("; ").append(BASE_TOOLTIP);
- return tt.toString();
+ return JvSwingUtils.wrapTooltip(true, tt.toString());
}
public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
JButton button;
- JColorChooser colorChooser;
-
- JDialog dialog;
-
protected static final String EDIT = "edit";
int rowSelected = 0;
- public ColorEditor(FeatureSettings me)
+ public ColorEditor(FeatureSettings fs)
{
- this.me = me;
+ this.me = fs;
// Set up the editor (from the table's point of view),
// which is a button.
// This button brings up the color chooser dialog,
button.setActionCommand(EDIT);
button.addActionListener(this);
button.setBorderPainted(false);
- // Set up the dialog that the button brings up.
- colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
- MessageManager.getString("label.select_colour"), true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
}
/**
- * Handles events from the editor button and from the dialog's OK button.
+ * Handles events from the editor button, and from the colour/filters
+ * dialog's OK button
*/
@Override
public void actionPerformed(ActionEvent e)
{
- // todo test e.getSource() instead here
- if (EDIT.equals(e.getActionCommand()))
+ if (button == e.getSource())
{
- // The user has clicked the cell, so
- // bring up the dialog.
if (currentColor.isSimpleColour())
{
- // bring up simple color chooser
- button.setBackground(currentColor.getColour());
- colorChooser.setColor(currentColor.getColour());
- dialog.setVisible(true);
+ /*
+ * simple colour chooser
+ */
+ String ttl = MessageManager.formatMessage("label.select_colour_for", type);
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ currentColor = new FeatureColour(c);
+ me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ fireEditingStopped();
+ }
+ @Override
+ public void cancel()
+ {
+ fireEditingStopped();
+ }
+ };
+ JalviewColourChooser.showColourChooser(button, ttl, currentColor.getColour(), listener);
}
else
{
- // bring up graduated chooser.
+ /*
+ * variable colour and filters dialog
+ */
chooser = new FeatureTypeSettings(me.fr, type);
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
+ if (!Jalview.isJS())
+ {
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ }
chooser.addActionListener(this);
- chooser.showTab(true);
+ fireEditingStopped();
}
- // Make the renderer reappear.
- fireEditingStopped();
-
}
else
{
- if (currentColor.isSimpleColour())
- {
- /*
- * read off colour picked in colour chooser after OK pressed
- */
- currentColor = new FeatureColour(colorChooser.getColor());
- me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
- }
- else
+ /*
+ * after OK in variable colour dialog, any changes to colour
+ * (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)
{
- /*
- * after OK in variable colour dialog, any changes to colour
- * (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;
+ currentFilter = new FeatureMatcherSet();
}
+ Object[] data = ((FeatureTableModel) table.getModel())
+ .getData()[rowSelected];
+ data[COLOUR_COLUMN] = currentColor;
+ data[FILTER_COLUMN] = currentFilter;
+
fireEditingStopped();
me.table.validate();
}
chooser.getWidth(), chooser.getHeight());
chooser.validate();
}
- chooser.showTab(false);
fireEditingStopped();
}
else if (e.getSource() instanceof Component)
button.setOpaque(true);
button.setBackground(me.getBackground());
button.setText(currentFilter.toString());
- button.setToolTipText(currentFilter.toString());
button.setIcon(null);
return button;
}
g.fillRect(s1, 0, e1 - s1, height);
}
g.setColor(gcol.getMaxColour());
- g.fillRect(0, e1, width - e1, height);
+// g.fillRect(0, e1, width - e1, height); // BH 2018
+ g.fillRect(e1, 0, width - e1, height);
}
}
}