X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=3a04b8864c413ac13ba98c53b52fed82521e771f;hb=b35271fb7c5b9cb0a07aeefca9e2e5b5d5bdaa8d;hp=01a73109c9efa8f35343d68c9d13cc2d86c1e95e;hpb=00ec8073218a0788e62cc2aa22de9a1a14d81952;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 01a7310..3a04b88 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -31,13 +31,14 @@ import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.Help.HelpId; 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.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; @@ -79,7 +80,6 @@ import javax.swing.BorderFactory; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JDialog; import javax.swing.JInternalFrame; @@ -97,9 +97,15 @@ import javax.swing.border.Border; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.table.AbstractTableModel; +import javax.swing.table.JTableHeader; 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 @@ -124,7 +130,7 @@ public class FeatureSettings extends JPanel 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; @@ -147,7 +153,7 @@ public class FeatureSettings extends JPanel JPanel groupPanel; - JSlider transparency = new JSlider(); + JSlider transparency; /* * when true, constructor is still executing - so ignore UI events @@ -156,12 +162,6 @@ public class FeatureSettings extends JPanel int selectedRow = -1; - JButton fetchDAS = new JButton(); - - JButton saveDAS = new JButton(); - - JButton cancelDAS = new JButton(); - boolean resettingTable = false; /* @@ -187,7 +187,7 @@ public class FeatureSettings extends JPanel // save transparency for restore on Cancel originalTransparency = fr.getTransparency(); int originalTransparencyAsPercent = (int) (originalTransparency * 100); - transparency.setMaximum(100 - originalTransparencyAsPercent); + transparency = new JSlider(0, 70, 100 - originalTransparencyAsPercent); originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy @@ -201,8 +201,6 @@ public class FeatureSettings extends JPanel table = new JTable() { - static final String tt = "Click to edit, right-click for menu"; // todo i18n - @Override public String getToolTipText(MouseEvent e) { @@ -219,27 +217,43 @@ public class FeatureSettings extends JPanel 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, 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; + } }; - table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); + JTableHeader tableHeader = table.getTableHeader(); + tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12)); + tableHeader.setReorderingAllowed(false); table.setFont(new Font("Verdana", Font.PLAIN, 12)); - // 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()); @@ -421,69 +435,6 @@ public class FeatureSettings extends JPanel }); men.add(dens); - /* - * variable colour options include colour by label, by score, - * by selected attribute text, or attribute value - */ - final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( - MessageManager.getString("label.variable_colour")); - mxcol.setSelected(!featureColour.isSimpleColour()); - men.add(mxcol); - mxcol.addActionListener(new ActionListener() - { - JColorChooser colorChooser; - - @Override - public void actionPerformed(ActionEvent e) - { - if (e.getSource() == mxcol) - { - if (featureColour.isSimpleColour()) - { - 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); - } - } - else - { - if (e.getSource() instanceof FeatureTypeSettings) - { - /* - * update after OK in feature colour dialog; the updated - * 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); - } - } - } - - }); - JMenuItem selCols = new JMenuItem( MessageManager.getString("label.select_columns_containing")); selCols.addActionListener(new ActionListener() @@ -685,7 +636,7 @@ public class FeatureSettings extends JPanel data[dataIndex][FILTER_COLUMN] = featureFilter == null ? new FeatureMatcherSet() : featureFilter; - data[dataIndex][SHOW_COLUMN] = new Boolean( + data[dataIndex][SHOW_COLUMN] = Boolean.valueOf( af.getViewport().getFeaturesDisplayed().isVisible(type)); dataIndex++; displayableTypes.remove(type); @@ -712,7 +663,7 @@ public class FeatureSettings extends JPanel data[dataIndex][FILTER_COLUMN] = featureFilter == null ? new FeatureMatcherSet() : featureFilter; - data[dataIndex][SHOW_COLUMN] = new Boolean(true); + data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true); dataIndex++; displayableTypes.remove(type); } @@ -886,30 +837,39 @@ 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); @@ -991,9 +951,9 @@ 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); } /* @@ -1006,16 +966,26 @@ 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) { @@ -1224,22 +1194,6 @@ public class FeatureSettings extends JPanel } } }); - help.setFont(JvSwingUtils.getLabelFont()); - help.setText(MessageManager.getString("action.help")); - help.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - try - { - Help.showHelpWindow(HelpId.SequenceFeatureSettings); - } catch (HelpSetException e1) - { - e1.printStackTrace(); - } - } - }); JButton cancel = new JButton(MessageManager.getString("action.cancel")); cancel.setFont(JvSwingUtils.getLabelFont()); @@ -1306,7 +1260,6 @@ public class FeatureSettings extends JPanel } }); - transparency.setMaximum(70); transparency.setToolTipText( MessageManager.getString("label.transparency_tip")); @@ -1336,32 +1289,31 @@ public class FeatureSettings extends JPanel /** * 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()) + if (fcol == null) { - return BASE_TOOLTIP; + return null; } - StringBuilder tt = new StringBuilder(); - if (gcol.isAboveThreshold()) + if (fcol.isSimpleColour()) { - tt.append("Thresholded (Above ").append(gcol.getThreshold()) - .append(")"); + return withHint ? BASE_TOOLTIP : null; } - else if (gcol.isBelowThreshold()) + String description = fcol.getDescription(); + description = description.replaceAll("<", "<"); + description = description.replaceAll(">", ">"); + StringBuilder tt = new StringBuilder(description); + if (withHint) { - tt.append("Thresholded (Below ").append(gcol.getThreshold()) - .append(")"); + tt.append("
").append(BASE_TOOLTIP).append("
"); } - else if (gcol.isColourByLabel()) - { - tt.insert(0, "Coloured by label text "); - } - tt.append("; ").append(BASE_TOOLTIP); - return tt.toString(); + return JvSwingUtils.wrapTooltip(true, tt.toString()); } public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, @@ -1426,7 +1378,7 @@ 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; @@ -1688,14 +1640,17 @@ public class FeatureSettings extends JPanel { // bring up graduated chooser. chooser = new FeatureTypeSettings(me.fr, type); - chooser.setRequestFocusEnabled(true); - chooser.requestFocus(); + /** + * @j2sNative + */ + { + chooser.setRequestFocusEnabled(true); + chooser.requestFocus(); + } chooser.addActionListener(this); - chooser.showTab(true); + // Make the renderer reappear. + fireEditingStopped(); } - // Make the renderer reappear. - fireEditingStopped(); - } else { @@ -1817,7 +1772,6 @@ public class FeatureSettings extends JPanel chooser.getWidth(), chooser.getHeight()); chooser.validate(); } - chooser.showTab(false); fireEditingStopped(); } else if (e.getSource() instanceof Component) @@ -1859,7 +1813,6 @@ public class FeatureSettings extends JPanel button.setOpaque(true); button.setBackground(me.getBackground()); button.setText(currentFilter.toString()); - button.setToolTipText(currentFilter.toString()); button.setIcon(null); return button; }