import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
-import jalview.bin.Cache;
+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.CompoundMatcher;
-import jalview.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatchCondition;
-import jalview.schemabinding.version2.MatcherSet;
-import jalview.schemabinding.version2.types.ColourNoValueColourType;
-import jalview.schemabinding.version2.types.ColourThreshTypeType;
-import jalview.schemabinding.version2.types.FeatureMatcherByType;
import jalview.schemes.FeatureColour;
-import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.util.matcher.Condition;
-import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
-import jalview.ws.DasSequenceFeatureFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+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 java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.Arrays;
-import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.Vector;
import javax.help.HelpSetException;
import javax.swing.AbstractCellEditor;
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.SwingUtilities;
+import javax.swing.ToolTipManager;
+import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
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 String SEQUENCE_FEATURE_COLOURS = MessageManager
+ .getString("label.sequence_feature_colours");
+
/*
* column indices of fields in Feature Settings table
*/
private static final int MIN_HEIGHT = 400;
- DasSourceBrowser dassourceBrowser;
-
- DasSequenceFeatureFetcher dasFeatureFetcher;
-
- JPanel dasSettingsPane = new JPanel();
+ 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
Map<String, float[]> typeWidth = null;
/**
- * Populates an XML model of the feature colour scheme for one feature type
- *
- * @param featureType
- * @param fcol
- * @return
- */
- protected static jalview.schemabinding.version2.Colour marshalColour(
- String featureType, FeatureColourI fcol)
- {
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- if (fcol.isSimpleColour())
- {
- col.setRGB(Format.getHexString(fcol.getColour()));
- }
- else
- {
- col.setRGB(Format.getHexString(fcol.getMaxColour()));
- col.setMin(fcol.getMin());
- col.setMax(fcol.getMax());
- col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
- col.setAutoScale(fcol.isAutoScaled());
- col.setThreshold(fcol.getThreshold());
- col.setColourByLabel(fcol.isColourByLabel());
- col.setThreshType(fcol.isAboveThreshold() ? ColourThreshTypeType.ABOVE
- : (fcol.isBelowThreshold() ? ColourThreshTypeType.BELOW
- : ColourThreshTypeType.NONE));
- if (fcol.isColourByAttribute())
- {
- col.setAttributeName(fcol.getAttributeName());
- }
- Color noColour = fcol.getNoColour();
- if (noColour == null)
- {
- col.setNoValueColour(ColourNoValueColourType.NONE);
- }
- else if (noColour == fcol.getMaxColour())
- {
- col.setNoValueColour(ColourNoValueColourType.MAX);
- }
- else
- {
- col.setNoValueColour(ColourNoValueColourType.MIN);
- }
- }
- col.setName(featureType);
- return col;
- }
-
- /**
- * Populates an XML model of the feature filter(s) for one feature type
- *
- * @param firstMatcher
- * the first (or only) match condition)
- * @param filter
- * remaining match conditions (if any)
- * @param and
- * if true, conditions are and-ed, else or-ed
- */
- protected static MatcherSet marshalFilter(FeatureMatcherI firstMatcher,
- Iterator<FeatureMatcherI> filters, boolean and)
- {
- MatcherSet result = new MatcherSet();
-
- if (filters.hasNext())
- {
- /*
- * compound matcher
- */
- CompoundMatcher compound = new CompoundMatcher();
- compound.setAnd(and);
- MatcherSet matcher1 = marshalFilter(firstMatcher,
- Collections.emptyIterator(), and);
- compound.addMatcherSet(matcher1);
- FeatureMatcherI nextMatcher = filters.next();
- MatcherSet matcher2 = marshalFilter(nextMatcher, filters, and);
- compound.addMatcherSet(matcher2);
- result.setCompoundMatcher(compound);
- }
- else
- {
- /*
- * single condition matcher
- */
- MatchCondition matcherModel = new MatchCondition();
- matcherModel.setCondition(
- firstMatcher.getMatcher().getCondition().getStableName());
- matcherModel.setValue(firstMatcher.getMatcher().getPattern());
- if (firstMatcher.isByAttribute())
- {
- matcherModel.setBy(FeatureMatcherByType.BYATTRIBUTE);
- matcherModel.setAttributeName(firstMatcher.getAttribute());
- }
- else if (firstMatcher.isByLabel())
- {
- matcherModel.setBy(FeatureMatcherByType.BYLABEL);
- }
- else if (firstMatcher.isByScore())
- {
- matcherModel.setBy(FeatureMatcherByType.BYSCORE);
- }
- result.setMatchCondition(matcherModel);
- }
-
- return result;
- }
-
- /**
- * Loads one XML model of a feature filter to a Jalview object
- *
- * @param colourModel
- * @return
- */
- protected static FeatureMatcherSetI unmarshalFilter(Filter filterModel)
- {
- FeatureMatcherSetI result = new FeatureMatcherSet();
- MatcherSet matcherSetModel = filterModel.getMatcherSet();
- try
- {
- unmarshalFilterConditions(result, matcherSetModel, true);
- } catch (IllegalStateException e)
- {
- // mixing AND and OR conditions perhaps
- System.err.println(
- String.format("Error reading filter conditions for '%s': %s",
- filterModel.getFeatureType(), e.getMessage()));
- // return as much as was parsed up to the error
- }
-
- return result;
- }
-
- /**
- * Adds feature match conditions to matcherSet as unmarshalled from XML
- * (possibly recursively for compound conditions)
- *
- * @param matcherSet
- * @param matcherSetModel
- * @param and
- * if true, multiple conditions are AND-ed, else they are OR-ed
- * @throws IllegalStateException
- * if AND and OR conditions are mixed
- */
- protected static void unmarshalFilterConditions(
- FeatureMatcherSetI matcherSet, MatcherSet matcherSetModel,
- boolean and)
- {
- MatchCondition mc = matcherSetModel.getMatchCondition();
- if (mc != null)
- {
- /*
- * single condition
- */
- FeatureMatcherByType filterBy = mc.getBy();
- Condition cond = Condition.fromString(mc.getCondition());
- String pattern = mc.getValue();
- FeatureMatcherI matchCondition = null;
- if (filterBy == FeatureMatcherByType.BYLABEL)
- {
- matchCondition = FeatureMatcher.byLabel(cond, pattern);
- }
- else if (filterBy == FeatureMatcherByType.BYSCORE)
- {
- matchCondition = FeatureMatcher.byScore(cond, pattern);
-
- }
- else if (filterBy == FeatureMatcherByType.BYATTRIBUTE)
- {
- String[] attNames = mc.getAttributeName();
- matchCondition = FeatureMatcher.byAttribute(cond, pattern,
- attNames);
- }
-
- /*
- * note this throws IllegalStateException if AND-ing to a
- * previously OR-ed compound condition, or vice versa
- */
- if (and)
- {
- matcherSet.and(matchCondition);
- }
- else
- {
- matcherSet.or(matchCondition);
- }
- }
- else
- {
- /*
- * compound condition
- */
- MatcherSet[] matchers = matcherSetModel.getCompoundMatcher()
- .getMatcherSet();
- boolean anded = matcherSetModel.getCompoundMatcher().getAnd();
- if (matchers.length == 2)
- {
- unmarshalFilterConditions(matcherSet, matchers[0], anded);
- unmarshalFilterConditions(matcherSet, matchers[1], anded);
- }
- else
- {
- System.err.println("Malformed compound filter condition");
- }
- }
- }
-
- /**
- * Loads one XML model of a feature colour to a Jalview object
- *
- * @param colourModel
- * @return
- */
- protected static FeatureColourI unmarshalColour(
- jalview.schemabinding.version2.Colour colourModel)
- {
- FeatureColourI colour = null;
-
- if (colourModel.hasMax())
- {
- Color mincol = null;
- Color maxcol = null;
- Color noValueColour = null;
-
- try
- {
- mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
- maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
- } catch (Exception e)
- {
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
- }
-
- ColourNoValueColourType noCol = colourModel.getNoValueColour();
- if (noCol == ColourNoValueColourType.MIN)
- {
- noValueColour = mincol;
- }
- else if (noCol == ColourNoValueColourType.MAX)
- {
- noValueColour = maxcol;
- }
-
- colour = new FeatureColour(mincol, maxcol, noValueColour,
- colourModel.getMin(),
- colourModel.getMax());
- String[] attributes = colourModel.getAttributeName();
- if (attributes != null && attributes.length > 0)
- {
- colour.setAttributeName(attributes);
- }
- if (colourModel.hasAutoScale())
- {
- colour.setAutoScaled(colourModel.getAutoScale());
- }
- if (colourModel.hasColourByLabel())
- {
- colour.setColourByLabel(colourModel.getColourByLabel());
- }
- if (colourModel.hasThreshold())
- {
- colour.setThreshold(colourModel.getThreshold());
- }
- ColourThreshTypeType ttyp = colourModel.getThreshType();
- if (ttyp != null)
- {
- if (ttyp == ColourThreshTypeType.ABOVE)
- {
- colour.setAboveThreshold(true);
- }
- else if (ttyp == ColourThreshTypeType.BELOW)
- {
- colour.setBelowThreshold(true);
- }
- }
- }
- else
- {
- Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
- colour = new FeatureColour(color);
- }
-
- return colour;
- }
-
- /**
* Constructor
*
* @param af
table = new JTable()
{
+
+// @Override
+// public void repaint() {
+// System.out.println("FS repaint");
+// super.repaint();
+//
+// }
+//
+// @Override
+// public void repaint(long tm, int x, int y, int width, int height) {
+// System.out.println("FS repaint " + x + " " + y + " " + width + " " + height);
+// super.repaint(tm, x, y, width, height);
+//
+// }
+// @Override
+// public void invalidate() {
+// if (isValid())
+// System.out.println("FS invalidating ");
+// super.invalidate();
+// }
+//
+// @Override
+// public void validate() {
+// System.out.println("FS validating " + isValid());
+// super.validate();
+// }
+
@Override
public String getToolTipText(MouseEvent e)
{
String tip = null;
int column = table.columnAtPoint(e.getPoint());
+ int row = table.rowAtPoint(e.getPoint());
+
switch (column)
{
case TYPE_COLUMN:
tip = JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
+ case COLOUR_COLUMN:
+ FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
+ column);
+ tip = getColorTooltip(colour, true);
+ break;
case FILTER_COLUMN:
- int row = table.rowAtPoint(e.getPoint());
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
- ? MessageManager.getString("label.filters_tooltip")
+ ? MessageManager
+ .getString("label.configure_feature_tooltip")
: o.toString();
break;
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.setDefaultEditor(FeatureColour.class, new ColorEditor());
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
- table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
+ table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor());
table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
-
+
TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
- new ColorRenderer(), new ColorEditor(this));
+ new ColorRenderer(), new ColorEditor());
table.addColumn(colourColumn);
TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
- new FilterRenderer(), new FilterEditor(this));
+ new FilterRenderer(), new FilterEditor());
table.addColumn(filterColumn);
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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());
}
}
});
// 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!
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);
- }
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, Platform.isAMacAndNotJS() ? 480 : 450);
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
frame.addInternalFrameListener(
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)
+ /**
+ * 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;
-
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
- JMenuItem scr = new JMenuItem(
- MessageManager.getString("label.sort_by_score"));
- men.add(scr);
- final FeatureSettings me = this;
- scr.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- me.af.avc
- .sortAlignmentByFeatureScore(Arrays.asList(new String[]
- { type }));
- }
-
- });
- JMenuItem dens = new JMenuItem(
- MessageManager.getString("label.sort_by_density"));
- dens.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- me.af.avc
- .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
- { type }));
- }
-
- });
- men.add(dens);
+ final FeatureColourI featureColour = (FeatureColourI) typeCol;
/*
- * variable colour options include colour by label, by score,
- * by selected attribute text, or attribute value
+ * menu option to select (or deselect) variable colour
*/
- 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())
{
- FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
+ /*
+ * toggle simple colour to variable colour - show dialog
+ */
+ FeatureTypeSettings fc = new FeatureTypeSettings(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();
+ updateFeatureRenderer(
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
+ }
+ };
+ JalviewColourChooser.showColourChooser(FeatureSettings.this, 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();
}
}
}
+ });
+
+ men.addSeparator();
+
+ JMenuItem scr = new JMenuItem(
+ MessageManager.getString("label.sort_by_score"));
+ men.add(scr);
+ scr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.avc.sortAlignmentByFeatureScore(Arrays.asList(new String[]
+ { type }));
+ }
+ });
+ JMenuItem dens = new JMenuItem(
+ MessageManager.getString("label.sort_by_density"));
+ dens.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.avc.sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ { type }));
+ }
});
+ men.add(dens);
JMenuItem selCols = new JMenuItem(
MessageManager.getString("label.select_columns_containing"));
men.add(clearCols);
men.add(hideCols);
men.add(hideOtherCols);
- men.show(table, x, y);
+ men.show(table, pt.x, pt.y);
}
@Override
void load()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
- "Sequence Feature Colours");
+ SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
+ chooser.setResponseHandler(0, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ File file = chooser.getSelectedFile();
+ load(file);
+ }
+ });
+ chooser.showOpenDialog(this);
+ }
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ /**
+ * Loads feature colours and filters from XML stored in the given file
+ *
+ * @param file
+ */
+ void load(File file)
+ {
+ try
{
- File file = chooser.getSelectedFile();
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
- try
- {
- InputStreamReader in = new InputStreamReader(
- new FileInputStream(file), "UTF-8");
+ 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);
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
- /*
- * load feature colours
- */
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
- {
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = unmarshalColour(newcol);
- fr.setColour(newcol.getName(), colour);
- fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
- }
+ /*
+ * load feature colours
+ */
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
+ {
+ 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.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++)
+ /*
+ * load feature filters; loaded filters will replace any that are
+ * currently defined, other defined filters are left unchanged
+ */
+ for (int i = 0; i < jucs.getFilter().size(); i++)
+ {
+ Filter filterModel = jucs.getFilter().get(i);
+ String featureType = filterModel.getFeatureType();
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
+ if (!filter.isEmpty())
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
- FeatureMatcherSetI filter = unmarshalFilter(filterModel);
- if (!filter.isEmpty())
- {
- fr.setFeatureFilter(filterModel.getFeatureType(), filter);
- }
+ fr.setFeatureFilter(featureType, filter);
}
+ }
- /*
- * update feature settings table
- */
- if (table != null)
- {
- resetTable(null);
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
- ensureOrder(data);
- updateFeatureRenderer(data, false);
- table.repaint();
- }
- } catch (Exception ex)
+ /*
+ * update feature settings table
+ */
+ if (table != null)
{
- System.out.println("Error loading User Colour File\n" + ex);
+ resetTable(null);
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ ensureOrder(data);
+ updateFeatureRenderer(data, false);
+ table.repaint();
}
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User Colour File\n" + ex);
}
}
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
- "Sequence Feature Colours");
+ SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ save(file);
+ }
+ }
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ /**
+ * Saves feature colours and filters to the given file
+ *
+ * @param file
+ */
+ void save(File file)
+ {
+ JalviewUserColours ucs = new JalviewUserColours();
+ ucs.setSchemeName("Sequence Features");
+ try
{
- String choice = chooser.getSelectedFile().getPath();
- JalviewUserColours ucs = new JalviewUserColours();
- ucs.setSchemeName("Sequence Features");
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(file), "UTF-8"));
- /*
- * sort feature types by colour order, from 0 (highest)
- * to 1 (lowest)
- */
- Set<String> fr_colours = fr.getAllFeatureColours();
- String[] sortedTypes = fr_colours
- .toArray(new String[fr_colours.size()]);
- Arrays.sort(sortedTypes, new Comparator<String>()
- {
- @Override
- public int compare(String type1, String type2)
- {
- return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
- }
- });
-
- /*
- * save feature colours
- */
- for (String featureType : sortedTypes)
+ /*
+ * sort feature types by colour order, from 0 (highest)
+ * to 1 (lowest)
+ */
+ Set<String> fr_colours = fr.getAllFeatureColours();
+ String[] sortedTypes = fr_colours
+ .toArray(new String[fr_colours.size()]);
+ Arrays.sort(sortedTypes, new Comparator<String>()
+ {
+ @Override
+ public int compare(String type1, String type2)
{
- FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
}
+ });
- /*
- * save any feature filters
- */
- for (String featureType : sortedTypes)
- {
- FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
- if (filter != null && !filter.isEmpty())
- {
- Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
- FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = marshalFilter(firstMatcher, iterator,
- filter.isAnded());
- Filter filterModel = new Filter();
- filterModel.setFeatureType(featureType);
- filterModel.setMatcherSet(ms);
- ucs.addFilter(filterModel);
- }
- }
+ /*
+ * save feature colours
+ */
+ for (String featureType : sortedTypes)
+ {
+ FeatureColourI fcol = fr.getFeatureStyle(featureType);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
+ }
- ucs.marshal(out);
- out.close();
- } catch (Exception ex)
+ /*
+ * save any feature filters
+ */
+ for (String featureType : sortedTypes)
{
- ex.printStackTrace();
+ FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+ if (filter != null && !filter.isEmpty())
+ {
+ Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+ FeatureMatcherI firstMatcher = iterator.next();
+ 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.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);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
}
public void invertSelection()
{
- for (int i = 0; i < table.getRowCount(); i++)
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (int i = 0; i < data.length; i++)
{
- Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
-
- table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
+ data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
}
+ updateFeatureRenderer(data, true);
+ table.repaint();
}
public void orderByAvWidth()
* @param data
* @param visibleNew
*/
- private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+ void updateFeatureRenderer(Object[][] data, boolean visibleNew)
{
FeatureSettingsBean[] rowData = getTableAsBeans(data);
JPanel settingsPane = new JPanel();
settingsPane.setLayout(new BorderLayout());
- dasSettingsPane.setLayout(new BorderLayout());
-
JPanel bigPanel = new JPanel();
bigPanel.setLayout(new BorderLayout());
JButton loadColours = new JButton(
MessageManager.getString("label.load_colours"));
loadColours.setFont(JvSwingUtils.getLabelFont());
+ loadColours.setToolTipText(
+ MessageManager.getString("label.load_colours_tooltip"));
loadColours.addActionListener(new ActionListener()
{
@Override
JButton saveColours = new JButton(
MessageManager.getString("label.save_colours"));
saveColours.setFont(JvSwingUtils.getLabelFont());
+ saveColours.setToolTipText(
+ MessageManager.getString("label.save_colours_tooltip"));
saveColours.addActionListener(new ActionListener()
{
@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);
buttonPanel.add(loadColours);
buttonPanel.add(saveColours);
bigPanel.add(scrollPane, BorderLayout.CENTER);
- dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH);
- dasButtonPanel.add(fetchDAS);
- dasButtonPanel.add(cancelDAS);
- dasButtonPanel.add(saveDAS);
settingsPane.add(bigPanel, BorderLayout.CENTER);
settingsPane.add(buttonPanel, BorderLayout.SOUTH);
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
+ * Answers a suitable tooltip to show on the colour cell of the table
*
- * @param selectedSources
- * @param checkDbRefs
- * @param promptFetchDbRefs
+ * @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
+ * @return
*/
- private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
- boolean checkDbRefs, boolean promptFetchDbRefs)
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
{
- 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());
+ if (fcol == null)
+ {
+ return null;
}
- else
+ if (fcol.isSimpleColour())
{
- iSize = vp.getAlignment().getHeight();
- seqs = vp.getAlignment().getSequencesArray();
+ return withHint ? BASE_TOOLTIP : null;
}
-
- dataset = new SequenceI[iSize];
- for (int i = 0; i < iSize; i++)
+ String description = fcol.getDescription();
+ description = description.replaceAll("<", "<");
+ description = description.replaceAll(">", ">");
+ StringBuilder tt = new StringBuilder(description);
+ if (withHint)
{
- dataset[i] = seqs[i].getDatasetSequence();
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
}
-
- 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();
+ return JvSwingUtils.wrapTooltip(true, tt.toString());
}
- /**
- * 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)
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+ int w, int h)
{
- initDasSources();
- List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
- .resolveSourceNicknames(sources);
- if (resolved.size() == 0)
+ boolean thr = false;
+ StringBuilder tx = new StringBuilder();
+
+ if (gcol.isColourByAttribute())
{
- resolved = dassourceBrowser.getSelectedSources();
+ tx.append(FeatureMatcher
+ .toAttributeDisplayName(gcol.getAttributeName()));
}
- if (resolved.size() > 0)
+ else if (!gcol.isColourByLabel())
{
- 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)
+ tx.append(MessageManager.getString("label.score"));
+ }
+ tx.append(" ");
+ if (gcol.isAboveThreshold())
+ {
+ thr = true;
+ tx.append(">");
+ }
+ if (gcol.isBelowThreshold())
+ {
+ thr = true;
+ tx.append("<");
+ }
+ if (gcol.isColourByLabel())
+ {
+ if (thr)
{
- fetcher.run();
+ tx.append(" ");
}
- else
+ if (!gcol.isColourByAttribute())
{
- SwingUtilities.invokeLater(fetcher);
+ tx.append("Label");
}
+ comp.setIcon(null);
}
- }
-
- 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)
+ else
{
- dasFeatureFetcher.cancel();
+ Color newColor = gcol.getMaxColour();
+ comp.setBackground(newColor);
+ // System.err.println("Width is " + w / 2);
+ Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
+ comp.setIcon(ficon);
+ // tt+="RGB value: Max (" + newColor.getRed() + ", "
+ // + newColor.getGreen() + ", " + newColor.getBlue()
+ // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+ // + ", " + minCol.getBlue() + ")");
}
- 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);
+ comp.setHorizontalAlignment(SwingConstants.CENTER);
+ comp.setText(tx.toString());
}
// ///////////////////////////////////////////////////////////////////////
private String[] columnNames = {
MessageManager.getString("label.feature_type"),
MessageManager.getString("action.colour"),
- MessageManager.getString("label.filter"),
+ MessageManager.getString("label.configuration"),
MessageManager.getString("label.show") };
private Object[][] data;
class ColorRenderer extends JLabel implements TableCellRenderer
{
- javax.swing.border.Border unselectedBorder = null;
-
- javax.swing.border.Border selectedBorder = null;
+ Border unselectedBorder = null;
- final String baseTT = "Click to edit, right/apple click for menu.";
+ Border selectedBorder = null;
public ColorRenderer()
{
{
FeatureColourI cellColour = (FeatureColourI) color;
setOpaque(true);
- setToolTipText(baseTT);
setBackground(tbl.getBackground());
if (!cellColour.isSimpleColour())
{
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
- int w, int h)
- {
- boolean thr = false;
- StringBuilder tt = new StringBuilder();
- StringBuilder tx = new StringBuilder();
-
- if (gcol.isColourByAttribute())
- {
- tx.append(String.join(":", gcol.getAttributeName()));
- }
- else if (!gcol.isColourByLabel())
- {
- tx.append(MessageManager.getString("label.score"));
- }
- tx.append(" ");
- if (gcol.isAboveThreshold())
- {
- thr = true;
- tx.append(">");
- tt.append("Thresholded (Above ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isBelowThreshold())
- {
- thr = true;
- tx.append("<");
- tt.append("Thresholded (Below ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isColourByLabel())
- {
- tt.append("Coloured by label text. ").append(tt);
- if (thr)
- {
- tx.append(" ");
- }
- if (!gcol.isColourByAttribute())
- {
- tx.append("Label");
- }
- comp.setIcon(null);
- }
- else
- {
- Color newColor = gcol.getMaxColour();
- comp.setBackground(newColor);
- // System.err.println("Width is " + w / 2);
- Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
- comp.setIcon(ficon);
- // tt+="RGB value: Max (" + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue()
- // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
- // + ", " + minCol.getBlue() + ")");
- }
- comp.setHorizontalAlignment(SwingConstants.CENTER);
- comp.setText(tx.toString());
- if (tt.length() > 0)
- {
- if (comp.getToolTipText() == null)
- {
- comp.setToolTipText(tt.toString());
- }
- else
- {
- comp.setToolTipText(
- tt.append(" ").append(comp.getToolTipText()).toString());
- }
- }
- }
-
- class ColorEditor extends AbstractCellEditor
+ @SuppressWarnings("serial")
+class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
- FeatureSettings me;
-
FeatureColourI currentColor;
FeatureTypeSettings chooser;
JButton button;
- JColorChooser colorChooser;
-
- JDialog dialog;
-
protected static final String EDIT = "edit";
int rowSelected = 0;
- public ColorEditor(FeatureSettings me)
+ public ColorEditor()
{
- this.me = me;
// 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()))
- {
- // 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);
- }
- else
- {
- // bring up graduated chooser.
- chooser = new FeatureTypeSettings(me.fr, type);
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
- chooser.addActionListener(this);
- chooser.showTab(true);
- }
- // Make the renderer reappear.
- fireEditingStopped();
-
- }
- else
+ if (button == e.getSource())
{
if (currentColor.isSimpleColour())
{
/*
- * read off colour picked in colour chooser after OK pressed
+ * simple colour chooser
*/
- currentColor = new FeatureColour(colorChooser.getColor());
- me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ String ttl = MessageManager.formatMessage("label.select_colour_for", type);
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ currentColor = new FeatureColour(c);
+ table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ fireEditingStopped();
+ }
+ @Override
+ public void cancel()
+ {
+ fireEditingStopped();
+ }
+ };
+ JalviewColourChooser.showColourChooser(button, ttl, currentColor.getColour(), listener);
}
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
+ * variable colour and filters dialog
*/
- currentColor = fr.getFeatureColours().get(type);
- FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
- if (currentFilter == null)
+ chooser = new FeatureTypeSettings(fr, type);
+ if (!Jalview.isJS())
{
- currentFilter = new FeatureMatcherSet();
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
}
- Object[] data = ((FeatureTableModel) table.getModel())
- .getData()[rowSelected];
- data[COLOUR_COLUMN] = currentColor;
- data[FILTER_COLUMN] = currentFilter;
+ chooser.addActionListener(this);
+ fireEditingStopped();
}
+ }
+ 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 = fr.getFeatureFilter(type);
+ if (currentFilter == null)
+ {
+ currentFilter = new FeatureMatcherSet();
+ }
+ Object[] data = ((FeatureTableModel) table.getModel())
+ .getData()[rowSelected];
+ data[COLOUR_COLUMN] = currentColor;
+ data[FILTER_COLUMN] = currentFilter;
fireEditingStopped();
- me.table.validate();
+ // SwingJS needs an explicit repaint() here,
+ // rather than relying upon no validation having
+ // occurred since the stopEditing call was made.
+ // Its laying out has not been stopped by the modal frame
+ table.validate();
+ table.repaint();
}
}
- // Implement the one CellEditor method that AbstractCellEditor doesn't.
+ /**
+ * Override allows access to this method from anonymous inner classes
+ */
+ @Override
+ protected void fireEditingStopped()
+ {
+ super.fireEditingStopped();
+ }
+
+ // Implement the one CellEditor method that AbstractCellEditor doesn't.
@Override
public Object getCellEditorValue()
{
{
currentColor = (FeatureColourI) value;
this.rowSelected = row;
- type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
- button.setBackground(me.getBackground());
+ button.setBackground(FeatureSettings.this.getBackground());
if (!currentColor.isSimpleColour())
{
JLabel btn = new JLabel();
* as display text). On click in the cell, opens the Feature Display Settings
* dialog at the Filters tab.
*/
- class FilterEditor extends AbstractCellEditor
+ @SuppressWarnings("serial")
+class FilterEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
- FeatureSettings me;
FeatureMatcherSetI currentFilter;
int rowSelected = 0;
- public FilterEditor(FeatureSettings me)
+ public FilterEditor()
{
- this.me = me;
button = new JButton();
button.setActionCommand(EDIT);
button.addActionListener(this);
{
if (button == e.getSource())
{
- FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
+ FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type);
chooser.addActionListener(this);
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
chooser.getWidth(), chooser.getHeight());
chooser.validate();
}
- chooser.showTab(false);
fireEditingStopped();
}
else if (e.getSource() instanceof Component)
* update table data without triggering updateFeatureRenderer
*/
FeatureColourI currentColor = fr.getFeatureColours().get(type);
- currentFilter = me.fr.getFeatureFilter(type);
+ currentFilter = fr.getFeatureFilter(type);
if (currentFilter == null)
{
currentFilter = new FeatureMatcherSet();
}
+
Object[] data = ((FeatureTableModel) table.getModel())
.getData()[rowSelected];
data[COLOUR_COLUMN] = currentColor;
data[FILTER_COLUMN] = currentFilter;
fireEditingStopped();
- me.table.validate();
+ // SwingJS needs an explicit repaint() here,
+ // rather than relying upon no validation having
+ // occurred since the stopEditing call was made.
+ // Its laying out has not been stopped by the modal frame
+ table.validate();
+ table.repaint();
}
}
{
currentFilter = (FeatureMatcherSetI) value;
this.rowSelected = row;
- type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
- button.setBackground(me.getBackground());
+ button.setBackground(FeatureSettings.this.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);
}
}
}
git://source.jalview.org / jalview.git / blobdiff