X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=5aa9499c209c59089820124a63ad09bb02811498;hb=09020de409b5dce834dc59fc1b94e24c653eac0f;hp=cc58e2c67b7e8d84f2de4993b48f010bf13059c2;hpb=cf8a8bbf603e6a5b91a0e85d1039b9580b0fb7e4;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index cc58e2c..5aa9499 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,28 +20,35 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; +import jalview.api.ViewStyleI; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureMatcher; import jalview.datamodel.features.FeatureMatcherI; 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.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; +import jalview.viewmodel.styles.ViewStyle; +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.awt.Component; import java.awt.Dimension; +import java.awt.FlowLayout; import java.awt.Font; import java.awt.Graphics; import java.awt.GridLayout; @@ -79,8 +86,6 @@ 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; import javax.swing.JLabel; import javax.swing.JLayeredPane; @@ -92,12 +97,20 @@ import javax.swing.JSlider; 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.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 @@ -122,6 +135,9 @@ public class FeatureSettings extends JPanel private static final int MIN_HEIGHT = 400; + private final static String BASE_TOOLTIP = MessageManager + .getString("label.click_to_edit"); + final FeatureRenderer fr; public final AlignFrame af; @@ -133,7 +149,9 @@ public class FeatureSettings extends JPanel float originalTransparency; - Map originalFilters; + private ViewStyleI originalViewStyle; + + private Map originalFilters; final JInternalFrame frame; @@ -152,12 +170,6 @@ public class FeatureSettings extends JPanel int selectedRow = -1; - JButton fetchDAS = new JButton(); - - JButton saveDAS = new JButton(); - - JButton cancelDAS = new JButton(); - boolean resettingTable = false; /* @@ -186,6 +198,7 @@ public class FeatureSettings extends JPanel transparency.setMaximum(100 - originalTransparencyAsPercent); originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy + originalViewStyle = new ViewStyle(af.viewport.getViewStyle()); try { @@ -202,44 +215,66 @@ public class FeatureSettings extends JPanel { 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; + } }; - 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)); + ToolTipManager.sharedInstance().registerComponent(table); + 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); @@ -249,21 +284,23 @@ public class FeatureSettings extends JPanel @Override public void mousePressed(MouseEvent evt) { - selectedRow = table.rowAtPoint(evt.getPoint()); + Point pt = evt.getPoint(); + selectedRow = table.rowAtPoint(pt); String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); 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) + else if (evt.getClickCount() == 2 + && table.columnAtPoint(pt) == TYPE_COLUMN) { boolean invertSelection = evt.isAltDown(); boolean toggleSelection = Platform.isControlDown(evt); boolean extendSelection = evt.isShiftDown(); fr.ap.alignFrame.avc.markColumnsContainingFeatures( invertSelection, extendSelection, toggleSelection, type); + fr.ap.av.sendSelection(); } } @@ -276,8 +313,7 @@ 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()); } } }); @@ -340,18 +376,9 @@ public class FeatureSettings extends JPanel 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( @@ -362,87 +389,82 @@ public class FeatureSettings extends JPanel javax.swing.event.InternalFrameEvent evt) { fr.removePropertyChangeListener(change); - }; + } }); frame.setLayer(JLayeredPane.PALETTE_LAYER); 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 mxcol = new JCheckBoxMenuItem( + final JCheckBoxMenuItem variableColourCB = new JCheckBoxMenuItem( MessageManager.getString("label.variable_colour")); - mxcol.setSelected(!featureColour.isSimpleColour()); - men.add(mxcol); - mxcol.addActionListener(new ActionListener() - { - JColorChooser colorChooser; + 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() + { @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(); + /* + * toggle variable to simple colour - show colour chooser + */ 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); + .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 @@ -455,22 +477,42 @@ public class FeatureSettings extends JPanel */ FeatureColourI fci = fr.getFeatureColours().get(type); table.setValueAt(fci, rowSelected, COLOUR_COLUMN); - table.validate(); - } - else - { - // probably the color chooser! - table.setValueAt(new FeatureColour(colorChooser.getColor()), - rowSelected, COLOUR_COLUMN); - table.validate(); - me.updateFeatureRenderer( - ((FeatureTableModel) table.getModel()).getData(), - false); + // BH 2018 setting a table value does not invalidate it. + // System.out.println("FeatureSettings is valied" + + // 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")); @@ -481,6 +523,7 @@ public class FeatureSettings extends JPanel { fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, false, type); + fr.ap.av.sendSelection(); } }); JMenuItem clearCols = new JMenuItem(MessageManager @@ -492,6 +535,7 @@ public class FeatureSettings extends JPanel { fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, false, type); + fr.ap.av.sendSelection(); } }); JMenuItem hideCols = new JMenuItem( @@ -502,6 +546,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent arg0) { fr.ap.alignFrame.hideFeatureColumns(type, true); + fr.ap.av.sendSelection(); } }); JMenuItem hideOtherCols = new JMenuItem( @@ -512,13 +557,14 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent arg0) { fr.ap.alignFrame.hideFeatureColumns(type, false); + fr.ap.av.sendSelection(); } }); men.add(selCols); men.add(clearCols); men.add(hideCols); men.add(hideOtherCols); - men.show(table, x, y); + men.show(table, pt.x, pt.y); } @Override @@ -575,7 +621,7 @@ public class FeatureSettings extends JPanel { fr.setGroupVisibility(check.getText(), check.isSelected()); resetTable(new String[] { grp }); - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } }); groupPanel.add(check); @@ -673,7 +719,7 @@ 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); @@ -700,7 +746,7 @@ 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); } @@ -731,8 +777,8 @@ public class FeatureSettings extends JPanel } /** - * Updates 'originalData' (used for restore on Cancel) if we detect that changes - * have been made outwith this dialog + * Updates 'originalData' (used for restore on Cancel) if we detect that + * changes have been made outwith this dialog *
    *
  • a new feature type added (and made visible)
    • *
  • a feature colour changed (in the Amend Features dialog)
    • @@ -796,8 +842,8 @@ public class FeatureSettings extends JPanel /** * Remove from the groups panel any checkboxes for groups that are not in the - * foundGroups set. This enables removing a group from the display when the last - * feature in that group is deleted. + * foundGroups set. This enables removing a group from the display when the + * last feature in that group is deleted. * * @param foundGroups */ @@ -846,23 +892,22 @@ public class FeatureSettings extends JPanel */ void load() { - // TODO: JAL-3048 relies on Castor XML parsing: not needed for JS-jalview core - // functionalty - JalviewFileChooser chooser = new JalviewFileChooser("fc", SEQUENCE_FEATURE_COLOURS); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { - File file = chooser.getSelectedFile(); - load(file); - } + @Override + public void run() + { + File file = chooser.getSelectedFile(); + load(file); + } + }); + chooser.showOpenDialog(this); } /** @@ -877,30 +922,39 @@ 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); @@ -913,8 +967,7 @@ public class FeatureSettings extends JPanel if (table != null) { resetTable(null); - Object[][] data = ((FeatureTableModel) table.getModel()) - .getData(); + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); ensureOrder(data); updateFeatureRenderer(data, false); table.repaint(); @@ -931,19 +984,17 @@ public class FeatureSettings extends JPanel */ void save() { - // TODO: JAL-3048 not needed for Jalview-JS - save colours JalviewFileChooser chooser = new JalviewFileChooser("fc", SEQUENCE_FEATURE_COLOURS); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.save_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + int option = chooser.showSaveDialog(this); + if (option == JalviewFileChooser.APPROVE_OPTION) { - save(chooser.getSelectedFile()); + File file = chooser.getSelectedFile(); + save(file); } } @@ -958,8 +1009,8 @@ public class FeatureSettings extends JPanel ucs.setSchemeName("Sequence Features"); try { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(file), "UTF-8")); + PrintWriter out = new PrintWriter( + new OutputStreamWriter(new FileOutputStream(file), "UTF-8")); /* * sort feature types by colour order, from 0 (highest) @@ -983,9 +1034,9 @@ 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); } /* @@ -996,18 +1047,28 @@ public class FeatureSettings extends JPanel FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); if (filter != null && !filter.isEmpty()) { - Iterator iterator = filter.getMatchers().iterator(); + Iterator iterator = filter.getMatchers() + .iterator(); FeatureMatcherI firstMatcher = iterator.next(); - MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator, - filter.isAnded()); + 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) { @@ -1072,7 +1133,8 @@ public class FeatureSettings extends JPanel else { width[i] /= max; // normalize - fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later + fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for + // later } if (i > 0) { @@ -1106,8 +1168,8 @@ public class FeatureSettings extends JPanel } /** - * Update the priority order of features; only repaint if this changed the order - * of visible features + * Update the priority order of features; only repaint if this changed the + * order of visible features * * @param data * @param visibleNew @@ -1118,7 +1180,7 @@ public class FeatureSettings extends JPanel if (fr.setFeaturePriority(rowData, visibleNew)) { - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } } @@ -1216,22 +1278,6 @@ 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()); @@ -1243,6 +1289,7 @@ public class FeatureSettings extends JPanel fr.setTransparency(originalTransparency); fr.setFeatureFilters(originalFilters); updateFeatureRenderer(originalData); + af.getViewport().setViewStyle(originalViewStyle); close(); } }); @@ -1293,7 +1340,7 @@ public class FeatureSettings extends JPanel if (!inConstruction) { fr.setTransparency((100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } } }); @@ -1302,8 +1349,42 @@ public class FeatureSettings extends JPanel transparency.setToolTipText( MessageManager.getString("label.transparency_tip")); - JPanel transPanel = new JPanel(new GridLayout(1, 2)); - bigPanel.add(transPanel, BorderLayout.SOUTH); + boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); + String text = MessageManager.formatMessage("label.show_linked_features", + nucleotide + ? MessageManager.getString("label.protein") + .toLowerCase() + : "CDS"); + JCheckBox showComplement = new JCheckBox(text); + showComplement.setSelected(af.getViewport().isShowComplementFeatures()); + showComplement.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + af.getViewport() + .setShowComplementFeatures(showComplement.isSelected()); + refreshDisplay(); + } + }); + + JCheckBox showComplementOnTop = new JCheckBox( + MessageManager.getString("label.on_top")); + showComplementOnTop + .setSelected(af.getViewport().isShowComplementFeaturesOnTop()); + showComplementOnTop.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + af.getViewport().setShowComplementFeaturesOnTop( + showComplementOnTop.isSelected()); + refreshDisplay(); + } + }); + + JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); + bigPanel.add(lowerPanel, BorderLayout.SOUTH); JPanel transbuttons = new JPanel(new GridLayout(5, 1)); transbuttons.add(optimizeOrder); @@ -1311,8 +1392,21 @@ public class FeatureSettings extends JPanel transbuttons.add(sortByScore); transbuttons.add(sortByDens); transbuttons.add(help); - transPanel.add(transparency); - transPanel.add(transbuttons); + + boolean hasComplement = af.getViewport().getCodingComplement() != null; + JPanel transPanelLeft = new JPanel( + new GridLayout(hasComplement ? 3 : 2, 1)); + transPanelLeft.add(new JLabel(" Colour transparency" + ":")); + transPanelLeft.add(transparency); + if (hasComplement) + { + JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT)); + cp.add(showComplement); + cp.add(showComplementOnTop); + transPanelLeft.add(cp); + } + lowerPanel.add(transPanelLeft); + lowerPanel.add(transbuttons); JPanel buttonPanel = new JPanel(); buttonPanel.add(ok); @@ -1325,6 +1419,106 @@ public class FeatureSettings extends JPanel this.add(settingsPane); } + /** + * Repaints alignment, structure and overview (if shown). If there is a + * complementary view which is showing this view's features, then also + * repaints that. + */ + void refreshDisplay() + { + af.alignPanel.paintAlignment(true, true); + AlignViewportI complement = af.getViewport().getCodingComplement(); + if (complement != null && complement.isShowComplementFeatures()) + { + AlignFrame af2 = Desktop.getAlignFrameFor(complement); + af2.alignPanel.paintAlignment(true, true); + } + } + + /** + * Answers a suitable tooltip to show on the colour cell of the table + * + * @param fcol + * @param withHint + * if true include 'click to edit' and similar text + * @return + */ + public static String getColorTooltip(FeatureColourI fcol, + boolean withHint) + { + if (fcol == null) + { + return null; + } + if (fcol.isSimpleColour()) + { + return withHint ? BASE_TOOLTIP : null; + } + String description = fcol.getDescription(); + description = description.replaceAll("<", "<"); + description = description.replaceAll(">", ">"); + StringBuilder tt = new StringBuilder(description); + if (withHint) + { + tt.append("
    ").append(BASE_TOOLTIP).append("
    "); + } + return JvSwingUtils.wrapTooltip(true, tt.toString()); + } + + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, + int w, int h) + { + boolean thr = false; + StringBuilder tx = new StringBuilder(); + + if (gcol.isColourByAttribute()) + { + tx.append(FeatureMatcher + .toAttributeDisplayName(gcol.getAttributeName())); + } + else if (!gcol.isColourByLabel()) + { + 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) + { + 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()); + } + // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html // /////////////////////////////////////////////////////////////////////// @@ -1333,7 +1527,7 @@ 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; @@ -1383,13 +1577,22 @@ public class FeatureSettings extends JPanel } /** - * Answers the class of the object in column c of the first row of the table + * Answers the class of column c of the table */ @Override public Class getColumnClass(int c) { - Object v = getValueAt(0, c); - return v == null ? null : v.getClass(); + switch (c) + { + case TYPE_COLUMN: + return String.class; + case COLOUR_COLUMN: + return FeatureColour.class; + case FILTER_COLUMN: + return FeatureMatcherSet.class; + default: + return Boolean.class; + } } @Override @@ -1410,11 +1613,9 @@ public class FeatureSettings extends JPanel class ColorRenderer extends JLabel implements TableCellRenderer { - javax.swing.border.Border unselectedBorder = null; + Border unselectedBorder = null; - javax.swing.border.Border selectedBorder = null; - - final String baseTT = "Click to edit, right/apple click for menu."; + Border selectedBorder = null; public ColorRenderer() { @@ -1429,7 +1630,6 @@ public class FeatureSettings extends JPanel { FeatureColourI cellColour = (FeatureColourI) color; setOpaque(true); - setToolTipText(baseTT); setBackground(tbl.getBackground()); if (!cellColour.isSimpleColour()) { @@ -1536,82 +1736,10 @@ public class FeatureSettings extends JPanel 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()); - } - } - } - + @SuppressWarnings("serial") class ColorEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { - FeatureSettings me; - FeatureColourI currentColor; FeatureTypeSettings chooser; @@ -1620,17 +1748,12 @@ public class FeatureSettings extends JPanel JButton button; - JColorChooser colorChooser; - - JDialog dialog; - protected static final String EDIT = "edit"; 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, @@ -1639,78 +1762,99 @@ public class FeatureSettings extends JPanel 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 + */ + chooser = new FeatureTypeSettings(fr, type); + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore */ - currentColor = fr.getFeatureColours().get(type); - FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type); - if (currentFilter == null) { - 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(); } } + /** + * 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() @@ -1720,14 +1864,14 @@ public class FeatureSettings extends JPanel // Implement the one method defined by TableCellEditor. @Override - public Component getTableCellEditorComponent(JTable theTable, Object value, - boolean isSelected, int row, int column) + public Component getTableCellEditorComponent(JTable theTable, + Object value, boolean isSelected, int row, int column) { 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(); @@ -1749,14 +1893,14 @@ public class FeatureSettings extends JPanel /** * The cell editor for the Filter column. It displays the text of any filters - * for the feature type in that row (in full as a tooltip, possible abbreviated - * as display text). On click in the cell, opens the Feature Display Settings - * dialog at the Filters tab. + * for the feature type in that row (in full as a tooltip, possible + * abbreviated as display text). On click in the cell, opens the Feature + * Display Settings dialog at the Filters tab. */ + @SuppressWarnings("serial") class FilterEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { - FeatureSettings me; FeatureMatcherSetI currentFilter; @@ -1770,9 +1914,8 @@ 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); @@ -1787,7 +1930,7 @@ 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(); @@ -1798,7 +1941,6 @@ public class FeatureSettings extends JPanel chooser.getWidth(), chooser.getHeight()); chooser.validate(); } - chooser.showTab(false); fireEditingStopped(); } else if (e.getSource() instanceof Component) @@ -1810,17 +1952,23 @@ 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(); } } @@ -1831,16 +1979,15 @@ public class FeatureSettings extends JPanel } @Override - public Component getTableCellEditorComponent(JTable theTable, Object value, - boolean isSelected, int row, int column) + public Component getTableCellEditorComponent(JTable theTable, + Object value, boolean isSelected, int row, int column) { 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; } @@ -1924,7 +2071,8 @@ 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); } } }