X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=a6f4a8415d6682fe14f2c08b13fde981da2def9e;hb=4c132b37c867a60959dae032addd78892d996345;hp=ea3a6677f475593cca49604dbd4f63bbeda389e8;hpb=f20ff42eac30f33cb69635ba3217a6224dbeb555;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index ea3a667..a6f4a84 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -22,6 +22,7 @@ package jalview.gui; 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; @@ -32,14 +33,14 @@ 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; @@ -101,6 +102,11 @@ 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 @@ -202,6 +208,33 @@ public class FeatureSettings extends JPanel 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) { @@ -224,7 +257,8 @@ public class FeatureSettings extends JPanel 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: @@ -233,6 +267,7 @@ public class FeatureSettings extends JPanel return tip; } + /** * Position the tooltip near the bottom edge of, and half way across, the @@ -249,21 +284,27 @@ public class FeatureSettings extends JPanel 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); - 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); @@ -278,8 +319,7 @@ public class FeatureSettings extends JPanel 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) { @@ -300,8 +340,7 @@ public class FeatureSettings extends JPanel { 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()); } } }); @@ -392,50 +431,25 @@ public class FeatureSettings extends JPanel inConstruction = false; } - protected void popupSort(final int rowSelected, final String type, - final Object typeCol, final Map 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 variableColourCB = new JCheckBoxMenuItem( MessageManager.getString("label.variable_colour")); @@ -453,12 +467,14 @@ public class FeatureSettings extends JPanel { 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); + FeatureTypeSettings fc = new FeatureTypeSettings(fr, type); fc.addActionListener(this); } else @@ -466,7 +482,7 @@ public class FeatureSettings extends JPanel /* * 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 @@ -475,15 +491,17 @@ public class FeatureSettings extends JPanel table.setValueAt(new FeatureColour(c), rowSelected, COLOUR_COLUMN); table.validate(); - me.updateFeatureRenderer( + updateFeatureRenderer( ((FeatureTableModel) table.getModel()).getData(), false); } }; - JalviewColourChooser.showColourChooser(me, title, featureColour.getMaxColour(), listener); + JalviewColourChooser.showColourChooser(FeatureSettings.this, title, + featureColour.getMaxColour(), listener); } } - else { + else + { if (e.getSource() instanceof FeatureTypeSettings) { /* @@ -492,12 +510,42 @@ public class FeatureSettings extends JPanel */ FeatureColourI fci = fr.getFeatureColours().get(type); table.setValueAt(fci, rowSelected, COLOUR_COLUMN); - table.validate(); + // 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")); @@ -545,7 +593,7 @@ public class FeatureSettings extends JPanel men.add(clearCols); men.add(hideCols); men.add(hideOtherCols); - men.show(table, x, y); + men.show(table, pt.x, pt.y); } @Override @@ -879,13 +927,15 @@ public class FeatureSettings extends JPanel chooser.setDialogTitle( MessageManager.getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); - chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION){ - - @Override - public void run() { - File file = chooser.getSelectedFile(); - load(file); - }}); + chooser.setResponseHandler(0, new Runnable() + { + @Override + public void run() + { + File file = chooser.getSelectedFile(); + load(file); + } + }); chooser.showOpenDialog(this); } @@ -901,30 +951,39 @@ public class FeatureSettings extends JPanel 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 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); @@ -1005,9 +1064,9 @@ public class FeatureSettings extends JPanel 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); } /* @@ -1020,16 +1079,26 @@ public class FeatureSettings extends JPanel { Iterator 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) { @@ -1439,7 +1508,7 @@ public class FeatureSettings extends JPanel 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; @@ -1639,11 +1708,10 @@ public class FeatureSettings extends JPanel renderGraduatedColor(comp, gcol, w, h); } - class ColorEditor extends AbstractCellEditor + @SuppressWarnings("serial") +class ColorEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { - FeatureSettings me; - FeatureColourI currentColor; FeatureTypeSettings chooser; @@ -1656,9 +1724,8 @@ public class FeatureSettings extends JPanel int rowSelected = 0; - public ColorEditor(FeatureSettings fs) + public ColorEditor() { - 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, @@ -1683,14 +1750,21 @@ public class FeatureSettings extends JPanel /* * 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); + table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); + fireEditingStopped(); } + @Override + public void cancel() + { + fireEditingStopped(); + } }; JalviewColourChooser.showColourChooser(button, ttl, currentColor.getColour(), listener); } @@ -1699,16 +1773,13 @@ public class FeatureSettings extends JPanel /* * variable colour and filters dialog */ - chooser = new FeatureTypeSettings(me.fr, type); - /** - * @j2sNative - */ + chooser = new FeatureTypeSettings(fr, type); + if (!Jalview.isJS()) { chooser.setRequestFocusEnabled(true); chooser.requestFocus(); } chooser.addActionListener(this); - // Make the renderer reappear. fireEditingStopped(); } } @@ -1720,7 +1791,7 @@ public class FeatureSettings extends JPanel * update table data without triggering updateFeatureRenderer */ currentColor = fr.getFeatureColours().get(type); - FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type); + FeatureMatcherSetI currentFilter = fr.getFeatureFilter(type); if (currentFilter == null) { currentFilter = new FeatureMatcherSet(); @@ -1729,13 +1800,26 @@ public class FeatureSettings extends JPanel .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() { @@ -1749,9 +1833,9 @@ public class FeatureSettings extends JPanel { 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(); @@ -1777,10 +1861,10 @@ public class FeatureSettings extends JPanel * 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; @@ -1794,9 +1878,8 @@ public class FeatureSettings extends JPanel int rowSelected = 0; - public FilterEditor(FeatureSettings me) + public FilterEditor() { - this.me = me; button = new JButton(); button.setActionCommand(EDIT); button.addActionListener(this); @@ -1811,7 +1894,7 @@ public class FeatureSettings extends JPanel { 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(); @@ -1833,17 +1916,23 @@ public class FeatureSettings extends JPanel * 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(); } } @@ -1859,9 +1948,9 @@ public class FeatureSettings extends JPanel { 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.setIcon(null); return button; @@ -1946,7 +2035,8 @@ class FeatureIcon implements Icon 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); } } }