X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=e6364555db3d9811d52efa2c5eceea6fb9ef7b7c;hb=4160e6f1fa6aa45849153cce5794faa93e3a19c4;hp=7b708abb2bdcc9bbbd5024066305f710ea9cc0d4;hpb=58922b9dd9afcf0c284834dd160a08703450f701;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 7b708ab..e636455 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,32 +20,11 @@ */ package jalview.gui; -import jalview.api.FeatureColourI; -import jalview.api.FeatureSettingsControllerI; -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.schemes.FeatureColour; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.util.dialogrunner.RunResponse; -import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; -import jalview.xml.binding.jalview.JalviewUserColours; -import jalview.xml.binding.jalview.JalviewUserColours.Colour; -import jalview.xml.binding.jalview.JalviewUserColours.Filter; -import jalview.xml.binding.jalview.ObjectFactory; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; +import java.awt.FlowLayout; import java.awt.Font; import java.awt.Graphics; import java.awt.GridLayout; @@ -98,8 +77,8 @@ import javax.swing.ToolTipManager; import javax.swing.border.Border; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; -import javax.swing.plaf.TableUI; import javax.swing.table.AbstractTableModel; +import javax.swing.table.JTableHeader; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; import javax.swing.table.TableColumn; @@ -109,8 +88,35 @@ import javax.xml.bind.Marshaller; import javax.xml.stream.XMLInputFactory; import javax.xml.stream.XMLStreamReader; +import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsControllerI; +import jalview.api.SplitContainerI; +import jalview.api.ViewStyleI; +import jalview.controller.FeatureSettingsControllerGuiI; +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.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; + public class FeatureSettings extends JPanel - implements FeatureSettingsControllerI + implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI { private static final String SEQUENCE_FEATURE_COLOURS = MessageManager .getString("label.sequence_feature_colours"); @@ -132,7 +138,8 @@ public class FeatureSettings extends JPanel private static final int MIN_HEIGHT = 400; - private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit"); + private final static String BASE_TOOLTIP = MessageManager + .getString("label.click_to_edit"); final FeatureRenderer fr; @@ -143,9 +150,11 @@ public class FeatureSettings extends JPanel */ Object[][] originalData; - float originalTransparency; + private float originalTransparency; - Map originalFilters; + private ViewStyleI originalViewStyle; + + private Map originalFilters; final JInternalFrame frame; @@ -157,6 +166,10 @@ public class FeatureSettings extends JPanel JSlider transparency = new JSlider(); + private JCheckBox showComplementOnTop; + + private JCheckBox showComplement; + /* * when true, constructor is still executing - so ignore UI events */ @@ -164,24 +177,44 @@ public class FeatureSettings extends JPanel int selectedRow = -1; - JButton fetchDAS = new JButton(); - - JButton saveDAS = new JButton(); - - JButton cancelDAS = new JButton(); - boolean resettingTable = false; /* * true when Feature Settings are updating from feature renderer */ - boolean handlingUpdate = false; + private boolean handlingUpdate = false; + + /* + * a change listener to ensure the dialog is updated if + * FeatureRenderer discovers new features + */ + private PropertyChangeListener change; /* * holds {featureCount, totalExtent} for each feature type */ Map typeWidth = null; + private void storeOriginalSettings() + { + // save transparency for restore on Cancel + originalTransparency = fr.getTransparency(); + + updateTransparencySliderFromFR(); + + originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy + originalViewStyle = new ViewStyle(af.viewport.getViewStyle()); + } + + private void updateTransparencySliderFromFR() + { + boolean incon = inConstruction; + inConstruction = true; + + int transparencyAsPercent = (int) (fr.getTransparency() * 100); + transparency.setValue(100 - transparencyAsPercent); + inConstruction = incon; + } /** * Constructor * @@ -192,12 +225,7 @@ public class FeatureSettings extends JPanel this.af = alignFrame; fr = af.getFeatureRenderer(); - // save transparency for restore on Cancel - originalTransparency = fr.getTransparency(); - int originalTransparencyAsPercent = (int) (originalTransparency * 100); - transparency.setMaximum(100 - originalTransparencyAsPercent); - - originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy + storeOriginalSettings(); try { @@ -231,16 +259,16 @@ 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: break; } - + return tip; } - /** * Position the tooltip near the bottom edge of, and half way across, the @@ -257,27 +285,23 @@ 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)); + JTableHeader tableHeader = table.getTableHeader(); + tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12)); + tableHeader.setReorderingAllowed(false); + table.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); @@ -287,21 +311,23 @@ 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(); } } @@ -314,8 +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()); } } }); @@ -358,7 +383,6 @@ public class FeatureSettings extends JPanel } discoverAllFeatureData(); - final PropertyChangeListener change; final FeatureSettings fs = this; fr.addPropertyChangeListener(change = new PropertyChangeListener() { @@ -376,86 +400,112 @@ public class FeatureSettings extends JPanel }); - frame = new JInternalFrame(); - frame.setContentPane(this); - if (Platform.isAMac()) + SplitContainerI splitframe = af.getSplitViewContainer(); + if (splitframe != null) { - Desktop.addInternalFrame(frame, - MessageManager.getString("label.sequence_feature_settings"), - 600, 480); + frame = null; // keeps eclipse happy + splitframe.addFeatureSettingsUI(this); } else { - Desktop.addInternalFrame(frame, - MessageManager.getString("label.sequence_feature_settings"), - 600, 450); - } - frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + frame = new JInternalFrame(); + frame.setContentPane(this); + Rectangle bounds = af.getFeatureSettingsGeometry(); + String title; + if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels( + af.alignPanel.av.getSequenceSetId()).length > 1) + { + title = MessageManager.formatMessage( + "label.sequence_feature_settings_for_view", + af.alignPanel.getViewName()); + } + else + { + title = MessageManager.getString("label.sequence_feature_settings"); + } + if (bounds == null) + { + if (Platform.isAMacAndNotJS()) + { + Desktop.addInternalFrame(frame, title, 600, 480); + } + else + { + Desktop.addInternalFrame(frame, title, 600, 450); + } + } + else + { + Desktop.addInternalFrame(frame, title, false, bounds.width, + bounds.height); + frame.setBounds(bounds); + frame.setVisible(true); + } + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); - frame.addInternalFrameListener( - new javax.swing.event.InternalFrameAdapter() - { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() { - fr.removePropertyChangeListener(change); - }; - }); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - inConstruction = false; + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + featureSettings_isClosed(); + }; + }); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + } + inConstruction = false; + } + + /** + * Sets the state of buttons to show complement features from viewport + * settings + */ + private void updateComplementButtons() + { + showComplement.setSelected(af.getViewport().isShowComplementFeatures()); + showComplementOnTop + .setSelected(af.getViewport().isShowComplementFeaturesOnTop()); } - protected void popupSort(final int rowSelected, final String type, - final Object typeCol, final Map minmax, int x, - int y) + @Override + public AlignViewControllerGuiI getAlignframe() { - final FeatureColourI featureColour = (FeatureColourI) typeCol; + return af; + } + @Override + public void featureSettings_isClosed() + { + fr.removePropertyChangeListener(change); + change = null; + } + + /** + * 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) + { 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")); variableColourCB.setSelected(!featureColour.isSimpleColour()); men.add(variableColourCB); - + /* * checkbox action listener doubles up as listener to OK * from the variable colour / filters dialog @@ -467,12 +517,15 @@ public class FeatureSettings extends JPanel { if (e.getSource() == variableColourCB) { + // BH 2018 for JavaScript because this is a checkbox + men.setVisible(true); + men.setVisible(false); 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 @@ -480,7 +533,8 @@ 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 @@ -489,15 +543,17 @@ 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) { /* @@ -506,12 +562,38 @@ 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.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) + { + sortByScore(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) + { + sortByDensity(Arrays.asList(new String[] { type })); + } }); + men.add(dens); JMenuItem selCols = new JMenuItem( MessageManager.getString("label.select_columns_containing")); @@ -522,6 +604,7 @@ public class FeatureSettings extends JPanel { fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, false, type); + fr.ap.av.sendSelection(); } }); JMenuItem clearCols = new JMenuItem(MessageManager @@ -533,6 +616,7 @@ public class FeatureSettings extends JPanel { fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, false, type); + fr.ap.av.sendSelection(); } }); JMenuItem hideCols = new JMenuItem( @@ -543,6 +627,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent arg0) { fr.ap.alignFrame.hideFeatureColumns(type, true); + fr.ap.av.sendSelection(); } }); JMenuItem hideOtherCols = new JMenuItem( @@ -553,13 +638,55 @@ 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); + } + + /** + * Sort the sequences in the alignment by the number of features for the given + * feature types (or all features if null) + * + * @param featureTypes + */ + protected void sortByDensity(List featureTypes) + { + af.avc.sortAlignmentByFeatureDensity(featureTypes); + } + + /** + * Sort the sequences in the alignment by average score for the given feature + * types (or all features if null) + * + * @param featureTypes + */ + protected void sortByScore(List featureTypes) + { + af.avc.sortAlignmentByFeatureScore(featureTypes); + } + + /** + * Returns true if at least one feature type is visible. Else shows a warning + * dialog and returns false. + * + * @param title + * @return + */ + private boolean canSortBy(String title) + { + if (fr.getDisplayedFeatureTypes().isEmpty()) + { + JvOptionPane.showMessageDialog(this, + MessageManager.getString("label.no_features_to_sort_by"), + title, JvOptionPane.OK_OPTION); + return false; + } + return true; } @Override @@ -616,7 +743,7 @@ public class FeatureSettings extends JPanel { fr.setGroupVisibility(check.getText(), check.isSelected()); resetTable(new String[] { grp }); - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } }); groupPanel.add(check); @@ -714,7 +841,7 @@ 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); @@ -741,7 +868,7 @@ 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); } @@ -772,8 +899,8 @@ 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)
    • @@ -837,8 +964,8 @@ 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 */ @@ -893,13 +1020,15 @@ 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); } @@ -960,8 +1089,7 @@ 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(); @@ -985,11 +1113,11 @@ public class FeatureSettings extends JPanel 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); - } + if (option == JalviewFileChooser.APPROVE_OPTION) + { + File file = chooser.getSelectedFile(); + save(file); + } } /** @@ -1003,8 +1131,8 @@ 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) @@ -1041,11 +1169,11 @@ 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(); jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML - .marshalFilter(firstMatcher, iterator, - filter.isAnded()); + .marshalFilter(firstMatcher, iterator, filter.isAnded()); Filter filterModel = new Filter(); filterModel.setFeatureType(featureType); filterModel.setMatcherSet(ms); @@ -1127,7 +1255,8 @@ 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) { @@ -1144,11 +1273,38 @@ public class FeatureSettings extends JPanel table.repaint(); } + /** + * close ourselves but leave any existing UI handlers (e.g a CDS/Protein tabbed + * feature settings dialog) intact + */ + public void closeOldSettings() + { + closeDialog(false); + } + + /** + * close the feature settings dialog (and any containing frame) + */ public void close() { + closeDialog(true); + } + + private void closeDialog(boolean closeContainingFrame) + { try { - frame.setClosed(true); + if (frame != null) + { + af.setFeatureSettingsGeometry(frame.getBounds()); + frame.setClosed(true); + } + else + { + SplitContainerI sc = af.getSplitViewContainer(); + sc.closeFeatureSettings(this, closeContainingFrame); + af.featureSettings = null; + } } catch (Exception exe) { } @@ -1161,8 +1317,8 @@ 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 @@ -1173,7 +1329,7 @@ public class FeatureSettings extends JPanel if (fr.setFeaturePriority(rowData, visibleNew)) { - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } } @@ -1199,6 +1355,9 @@ public class FeatureSettings extends JPanel { this.setLayout(new BorderLayout()); + final boolean hasComplement = af.getViewport() + .getCodingComplement() != null; + JPanel settingsPane = new JPanel(); settingsPane.setLayout(new BorderLayout()); @@ -1232,47 +1391,37 @@ public class FeatureSettings extends JPanel } }); - JButton sortByScore = new JButton( - MessageManager.getString("label.seq_sort_by_score")); + final String byScoreLabel = MessageManager.getString("label.seq_sort_by_score"); + JButton sortByScore = new JButton(byScoreLabel); sortByScore.setFont(JvSwingUtils.getLabelFont()); sortByScore.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - af.avc.sortAlignmentByFeatureScore(null); + if (canSortBy(byScoreLabel)) + { + sortByScore(null); + } } }); - JButton sortByDens = new JButton( - MessageManager.getString("label.sequence_sort_by_density")); + final String byDensityLabel = MessageManager.getString("label.sequence_sort_by_density"); + JButton sortByDens = new JButton(byDensityLabel); sortByDens.setFont(JvSwingUtils.getLabelFont()); sortByDens.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - af.avc.sortAlignmentByFeatureDensity(null); - } - }); - - JButton help = new JButton(MessageManager.getString("action.help")); - help.setFont(JvSwingUtils.getLabelFont()); - help.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - try + if (canSortBy(byDensityLabel)) { - Help.showHelpWindow(HelpId.SequenceFeatureSettings); - } catch (HelpSetException e1) - { - e1.printStackTrace(); + sortByDensity(null); } } }); + + JButton help = new JButton(MessageManager.getString("action.help")); help.setFont(JvSwingUtils.getLabelFont()); - help.setText(MessageManager.getString("action.help")); help.addActionListener(new ActionListener() { @Override @@ -1287,29 +1436,48 @@ public class FeatureSettings extends JPanel } } }); - - JButton cancel = new JButton(MessageManager.getString("action.cancel")); + // Cancel for a SplitFrame should just revert changes to the currently displayed + // settings. May want to do this for either or both - so need a splitview + // feature settings cancel/OK. + JButton cancel = new JButton(MessageManager + .getString(hasComplement ? "action.revert" : "action.cancel")); + cancel.setToolTipText(MessageManager.getString(hasComplement + ? "action.undo_changes_to_feature_settings" + : "action.undo_changes_to_feature_settings_and_close_the_dialog")); cancel.setFont(JvSwingUtils.getLabelFont()); + // TODO: disable cancel (and apply!) until current settings are different cancel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - fr.setTransparency(originalTransparency); - fr.setFeatureFilters(originalFilters); - updateFeatureRenderer(originalData); - close(); + revert(); + refreshDisplay(); + if (!hasComplement) + { + close(); + } } }); - - JButton ok = new JButton(MessageManager.getString("action.ok")); + // Cancel for the whole dialog should cancel both CDS and Protein. + // OK for an individual feature settings just applies changes, but dialog + // remains open + JButton ok = new JButton(MessageManager + .getString(hasComplement ? "action.apply" : "action.ok")); ok.setFont(JvSwingUtils.getLabelFont()); ok.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - close(); + if (!hasComplement) + { + close(); + } + else + { + storeOriginalSettings(); + } } }); @@ -1348,7 +1516,7 @@ public class FeatureSettings extends JPanel if (!inConstruction) { fr.setTransparency((100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true, true); + refreshDisplay(); } } }); @@ -1357,8 +1525,41 @@ 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"); + showComplement = new JCheckBox(text); + showComplement.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + af.getViewport() + .setShowComplementFeatures(showComplement.isSelected()); + refreshDisplay(); + } + }); + + showComplementOnTop = new JCheckBox( + MessageManager.getString("label.on_top")); + showComplementOnTop.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + af.getViewport().setShowComplementFeaturesOnTop( + showComplementOnTop.isSelected()); + refreshDisplay(); + } + }); + + updateComplementButtons(); + + JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); + bigPanel.add(lowerPanel, BorderLayout.SOUTH); JPanel transbuttons = new JPanel(new GridLayout(5, 1)); transbuttons.add(optimizeOrder); @@ -1366,8 +1567,20 @@ public class FeatureSettings extends JPanel transbuttons.add(sortByScore); transbuttons.add(sortByDens); transbuttons.add(help); - transPanel.add(transparency); - transPanel.add(transbuttons); + + JPanel transPanelLeft = new JPanel( + new GridLayout(hasComplement ? 4 : 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); @@ -1381,11 +1594,27 @@ public class FeatureSettings extends JPanel } /** + * 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 + * if true include 'click to edit' and similar text * @return */ public static String getColorTooltip(FeatureColourI fcol, @@ -1415,7 +1644,7 @@ public class FeatureSettings extends JPanel { boolean thr = false; StringBuilder tx = new StringBuilder(); - + if (gcol.isColourByAttribute()) { tx.append(FeatureMatcher @@ -1472,7 +1701,7 @@ 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; @@ -1522,13 +1751,22 @@ 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 @@ -1672,11 +1910,10 @@ public class FeatureSettings extends JPanel renderGraduatedColor(comp, gcol, w, h); } + @SuppressWarnings("serial") class ColorEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { - FeatureSettings me; - FeatureColourI currentColor; FeatureTypeSettings chooser; @@ -1689,9 +1926,8 @@ 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, @@ -1716,32 +1952,44 @@ 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); + JalviewColourChooser.showColourChooser(button, ttl, + currentColor.getColour(), listener); } else { /* * variable colour and filters dialog */ - chooser = new FeatureTypeSettings(me.fr, type); + chooser = new FeatureTypeSettings(fr, type); + if (!Platform.isJS()) /** - * @j2sNative + * Java only + * + * @j2sIgnore */ { chooser.setRequestFocusEnabled(true); chooser.requestFocus(); } chooser.addActionListener(this); - // Make the renderer reappear. fireEditingStopped(); } } @@ -1753,7 +2001,7 @@ 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(); @@ -1762,12 +2010,25 @@ 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(); } } + /** + * 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() @@ -1777,14 +2038,14 @@ 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(); @@ -1806,14 +2067,14 @@ 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; @@ -1827,9 +2088,8 @@ 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); @@ -1844,7 +2104,7 @@ 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(); @@ -1866,17 +2126,23 @@ 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(); } } @@ -1887,19 +2153,40 @@ 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.setIcon(null); return button; } } + + public boolean isOpen() + { + if (af.getSplitViewContainer() != null) + { + return af.getSplitViewContainer().isFeatureSettingsOpen(); + } + return frame != null && !frame.isClosed(); + } + + @Override + public void revert() + { + fr.setTransparency(originalTransparency); + fr.setFeatureFilters(originalFilters); + updateFeatureRenderer(originalData); + af.getViewport().setViewStyle(originalViewStyle); + updateTransparencySliderFromFR(); + updateComplementButtons(); + refreshDisplay(); + } } class FeatureIcon implements Icon @@ -1979,7 +2266,8 @@ 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); } } }