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.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.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
return tip;
}
+
/**
* Position the tooltip near the bottom edge of, and half way across, the
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));
ToolTipManager.sharedInstance().registerComponent(table);
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);
/*
* toggle variable to simple colour - show colour chooser
*/
- String title = MessageManager.getString("label.select_colour");
+ String title = MessageManager.formatMessage("label.select_colour_for", type);
ColourChooserListener listener = new ColourChooserListener()
{
@Override
JalviewColourChooser.showColourChooser(me, title, featureColour.getMaxColour(), listener);
}
}
- else {
+ else
+ {
if (e.getSource() instanceof FeatureTypeSettings)
{
/*
}
}
}
-
});
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
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)
{
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);
- ucs.marshal(out);
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
+
+ // 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()
}
updateFeatureRenderer(data, false);
- table.repaint();
+ repaintTable();
+ }
+
+ /**
+ * Repaints the table using alternative code for Java and J2S
+ */
+ private void repaintTable()
+ {
+ // 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()
/*
* simple colour chooser
*/
- String ttl = MessageManager.getString("label.select_colour");
- ColourChooserListener listener = new ColourChooserListener() {
+ 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);
}
* variable colour and filters dialog
*/
chooser = new FeatureTypeSettings(me.fr, type);
- /**
- * @j2sNative
- */
+ if (!Jalview.isJS())
{
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
}
chooser.addActionListener(this);
- // Make the renderer reappear.
fireEditingStopped();
}
}
git://source.jalview.org / jalview.git / blobdiff