X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=57e5943a2fe9821ec91ceb18cdab1de47c91bec0;hb=f0bba4cb65260c4e7f79c30cd442123aeb1b312f;hp=4b0a0bc21222476303b73940f516828b944a9798;hpb=0e7325771ec658d66194b7abab05616681f03a57;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 4b0a0bc..57e5943 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,32 +20,6 @@ */ package jalview.gui; -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.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; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -71,6 +45,7 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; +import java.io.Reader; import java.util.Arrays; import java.util.Comparator; import java.util.HashMap; @@ -78,6 +53,7 @@ import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Set; @@ -87,8 +63,6 @@ import javax.swing.BorderFactory; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; -import javax.swing.JColorChooser; -import javax.swing.JDialog; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JLayeredPane; @@ -100,6 +74,7 @@ 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; @@ -114,6 +89,35 @@ 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.DataSourceType; +import jalview.io.FileParse; +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, FeatureSettingsControllerGuiI { @@ -137,7 +141,8 @@ 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; @@ -164,6 +169,10 @@ 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 */ @@ -179,10 +188,37 @@ public class FeatureSettings extends JPanel 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 * @@ -193,13 +229,7 @@ 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 - originalViewStyle = new ViewStyle(af.viewport.getViewStyle()); + storeOriginalSettings(); try { @@ -240,7 +270,7 @@ public class FeatureSettings extends JPanel default: break; } - + return tip; } @@ -263,19 +293,19 @@ public class FeatureSettings extends JPanel tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12)); tableHeader.setReorderingAllowed(false); table.setFont(new Font("Verdana", Font.PLAIN, 12)); - - 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); @@ -291,8 +321,7 @@ public class FeatureSettings extends JPanel if (evt.isPopupTrigger()) { Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); - popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), - evt.getY()); + showPopupMenu(selectedRow, type, colour, evt.getPoint()); } else if (evt.getClickCount() == 2 && table.columnAtPoint(pt) == TYPE_COLUMN) @@ -315,8 +344,7 @@ 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()); } } }); @@ -375,6 +403,7 @@ public class FeatureSettings extends JPanel } }); + SplitContainerI splitframe = af.getSplitViewContainer(); if (splitframe != null) { @@ -385,6 +414,7 @@ public class FeatureSettings extends JPanel { frame = new JInternalFrame(); frame.setContentPane(this); + frame.setFrameIcon(null); Rectangle bounds = af.getFeatureSettingsGeometry(); String title; if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels( @@ -400,7 +430,7 @@ public class FeatureSettings extends JPanel } if (bounds == null) { - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { Desktop.addInternalFrame(frame, title, 600, 480); } @@ -411,8 +441,8 @@ public class FeatureSettings extends JPanel } else { - Desktop.addInternalFrame(frame, title, - false, bounds.width, bounds.height); + Desktop.addInternalFrame(frame, title, false, bounds.width, + bounds.height); frame.setBounds(bounds); frame.setVisible(true); } @@ -433,7 +463,16 @@ public class FeatureSettings extends JPanel inConstruction = false; } - PropertyChangeListener change; + /** + * 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()); + } @Override public AlignViewControllerGuiI getAlignframe() @@ -448,42 +487,42 @@ public class FeatureSettings extends JPanel change = null; } - 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) { 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 })); + 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) { - me.af.avc - .sortAlignmentByFeatureDensity(Arrays.asList(new String[] - { type })); + sortByDensity(Arrays.asList(new String[] { type })); } - }); men.add(dens); @@ -537,7 +576,48 @@ public class FeatureSettings extends JPanel men.add(clearCols); men.add(hideCols); men.add(hideOtherCols); - men.show(table, x, y); + men.show(table, pt.x, pt.y); + } + + /** + * 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 @@ -750,8 +830,8 @@ 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)
    • @@ -815,8 +895,8 @@ 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 */ @@ -871,14 +951,70 @@ public class FeatureSettings extends JPanel chooser.setDialogTitle( MessageManager.getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); + chooser.setResponseHandler(0, () -> { + File file = chooser.getSelectedFile(); + load(file); + }); + chooser.showOpenDialog(this); + } + + public static boolean loadFeatureSettingsFile(FeatureRenderer fr, + File file) throws Exception + { + InputStreamReader in = new InputStreamReader(new FileInputStream(file), + "UTF-8"); + return loadFeatureSettingsFile(fr, in); + } + + public static void loadFeatureSettingsFile( + FeatureRenderer featureRenderer, Object fileObject, + DataSourceType sourceType) throws Exception + { + FileParse fp = new FileParse(fileObject, sourceType); + loadFeatureSettingsFile(featureRenderer, fp.getReader()); + } - int value = chooser.showOpenDialog(this); + private static boolean loadFeatureSettingsFile(FeatureRenderer fr, + Reader in) throws Exception + { + 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); - if (value == JalviewFileChooser.APPROVE_OPTION) + /* + * load feature colours + */ + for (int i = jucs.getColour().size() - 1; i >= 0; i--) { - File file = chooser.getSelectedFile(); - load(file); + Colour newcol = jucs.getColour().get(i); + FeatureColourI colour = jalview.project.Jalview2XML + .parseColour(newcol); + fr.setColour(newcol.getName(), colour); + fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); + } + + /* + * load feature filters; loaded filters will replace any that are + * currently defined, other defined filters are left unchanged + */ + for (int i = 0; i < jucs.getFilter().size(); i++) + { + Filter filterModel = jucs.getFilter().get(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = jalview.project.Jalview2XML + .parseFilter(featureType, filterModel.getMatcherSet()); + if (!filter.isEmpty()) + { + fr.setFeatureFilter(featureType, filter); + } } + return true; } /** @@ -888,65 +1024,36 @@ public class FeatureSettings extends JPanel */ void load(File file) { + load(file, DataSourceType.FILE); + } + + /** + * Loads feature colours and filters from XML at a specified source + * + * @param file + * - string or file or other object that allows FileParse to be + * created + */ + void load(Object file, DataSourceType sourceType) + { try { - InputStreamReader in = new InputStreamReader( - new FileInputStream(file), "UTF-8"); - - JAXBContext jc = JAXBContext - .newInstance("jalview.xml.binding.jalview"); - javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); - XMLStreamReader streamReader = XMLInputFactory.newInstance() - .createXMLStreamReader(in); - JAXBElement jbe = um.unmarshal(streamReader, - JalviewUserColours.class); - JalviewUserColours jucs = jbe.getValue(); - - // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); - - /* - * load feature colours - */ - for (int i = jucs.getColour().size() - 1; i >= 0; i--) - { - Colour newcol = jucs.getColour().get(i); - FeatureColourI colour = jalview.project.Jalview2XML - .parseColour(newcol); - fr.setColour(newcol.getName(), colour); - fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); - } - - /* - * load feature filters; loaded filters will replace any that are - * currently defined, other defined filters are left unchanged - */ - for (int i = 0; i < jucs.getFilter().size(); i++) - { - Filter filterModel = jucs.getFilter().get(i); - String featureType = filterModel.getFeatureType(); - FeatureMatcherSetI filter = jalview.project.Jalview2XML - .parseFilter(featureType, filterModel.getMatcherSet()); - if (!filter.isEmpty()) - { - fr.setFeatureFilter(featureType, filter); - } - } - + loadFeatureSettingsFile(fr, file, sourceType); /* * update feature settings table */ if (table != null) { resetTable(null); - Object[][] data = ((FeatureTableModel) table.getModel()) - .getData(); + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); ensureOrder(data); updateFeatureRenderer(data, false); table.repaint(); } } catch (Exception ex) { - System.out.println("Error loading User Colour File\n" + ex); + jalview.bin.Console + .outPrintln("Error loading User Colour File\n" + ex); } } @@ -962,12 +1069,11 @@ public class FeatureSettings extends JPanel 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); } } @@ -982,8 +1088,8 @@ 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) @@ -1020,11 +1126,11 @@ 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); @@ -1106,7 +1212,8 @@ 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) { @@ -1123,8 +1230,25 @@ 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 { if (frame != null) @@ -1150,13 +1274,13 @@ 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 */ - private void updateFeatureRenderer(Object[][] data, boolean visibleNew) + void updateFeatureRenderer(Object[][] data, boolean visibleNew) { FeatureSettingsBean[] rowData = getTableAsBeans(data); @@ -1188,6 +1312,9 @@ public class FeatureSettings extends JPanel { this.setLayout(new BorderLayout()); + final boolean hasComplement = af.getViewport() + .getCodingComplement() != null; + JPanel settingsPane = new JPanel(); settingsPane.setLayout(new BorderLayout()); @@ -1221,26 +1348,34 @@ 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); + if (canSortBy(byDensityLabel)) + { + sortByDensity(null); + } } }); @@ -1260,30 +1395,49 @@ 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); - af.getViewport().setViewStyle(originalViewStyle); - 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(); + } } }); @@ -1332,13 +1486,13 @@ public class FeatureSettings extends JPanel MessageManager.getString("label.transparency_tip")); 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()); + String text = MessageManager + .formatMessage("label.show_linked_features", + nucleotide + ? MessageManager.getString("label.protein") + .toLowerCase(Locale.ROOT) + : "CDS"); + showComplement = new JCheckBox(text); showComplement.addActionListener(new ActionListener() { @Override @@ -1350,10 +1504,8 @@ public class FeatureSettings extends JPanel } }); - JCheckBox showComplementOnTop = new JCheckBox( + showComplementOnTop = new JCheckBox( MessageManager.getString("label.on_top")); - showComplementOnTop - .setSelected(af.getViewport().isShowComplementFeaturesOnTop()); showComplementOnTop.addActionListener(new ActionListener() { @Override @@ -1364,38 +1516,9 @@ public class FeatureSettings extends JPanel refreshDisplay(); } }); - // JButton viewComplementSettings = new JButton(MessageManager - // .formatMessage("label.show_linked_feature_settings", - // nucleotide - // ? MessageManager.getString("label.protein") - // .toLowerCase() - // : "CDS")); - // viewComplementSettings.addActionListener(new ActionListener() - // { - // - // @Override - // public void actionPerformed(ActionEvent e) - // { - // AlignViewControllerGuiI complAf = af.getSplitViewContainer() - // .getComplementAlignFrame(af); - // FeatureSettings complFeatureSettings = (FeatureSettings) complAf - // .getFeatureSettingsUI(); - // if (complFeatureSettings != null) - // { - // complFeatureSettings.frame.setVisible(true); - // try - // { - // complFeatureSettings.frame.setSelected(true); - // return; - // } catch (Exception q) - // { - // } - // } - // { - // complAf.showFeatureSettingsUI(); - // } - // } - // }); + + updateComplementButtons(); + JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); bigPanel.add(lowerPanel, BorderLayout.SOUTH); @@ -1406,7 +1529,6 @@ public class FeatureSettings extends JPanel transbuttons.add(sortByDens); transbuttons.add(help); - boolean hasComplement = af.getViewport().getCodingComplement() != null; JPanel transPanelLeft = new JPanel( new GridLayout(hasComplement ? 4 : 2, 1)); transPanelLeft.add(new JLabel(" Colour transparency" + ":")); @@ -1453,7 +1575,7 @@ public class FeatureSettings extends JPanel * * @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, @@ -1483,7 +1605,7 @@ public class FeatureSettings extends JPanel { boolean thr = false; StringBuilder tx = new StringBuilder(); - + if (gcol.isColourByAttribute()) { tx.append(FeatureMatcher @@ -1520,7 +1642,7 @@ public class FeatureSettings extends JPanel { Color newColor = gcol.getMaxColour(); comp.setBackground(newColor); - // System.err.println("Width is " + w / 2); + // jalview.bin.Console.errPrintln("Width is " + w / 2); Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); comp.setIcon(ficon); // tt+="RGB value: Max (" + newColor.getRed() + ", " @@ -1699,11 +1821,15 @@ public class FeatureSettings extends JPanel { FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; setOpaque(true); - String asText = theFilter.toString(); setBackground(tbl.getBackground()); - this.setText(asText); this.setIcon(null); + if (theFilter != null) + { + String asText = theFilter.toString(); + this.setText(asText); + } + if (isSelected) { if (selectedBorder == null) @@ -1749,11 +1875,10 @@ 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; @@ -1762,17 +1887,12 @@ public class FeatureSettings extends JPanel JButton button; - JColorChooser colorChooser; - - JDialog dialog; - protected static final String EDIT = "edit"; int rowSelected = 0; - public ColorEditor(FeatureSettings me) + public ColorEditor() { - this.me = me; // Set up the editor (from the table's point of view), // which is a button. // This button brings up the color chooser dialog, @@ -1781,81 +1901,105 @@ 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())) + if (button == e.getSource()) { - // 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); + /* + * simple colour chooser + */ + String ttl = MessageManager + .formatMessage("label.select_colour_for", type); + Object last=(Boolean)table.getValueAt(selectedRow, SHOW_COLUMN); + table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); + ColourChooserListener listener = new ColourChooserListener() + { + @Override + public void colourSelected(Color c) + { + currentColor = new FeatureColour(c); + table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); + table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); + fireEditingStopped(); + } + + @Override + public void cancel() + { + table.setValueAt(last, selectedRow, SHOW_COLUMN); + fireEditingStopped(); + } + }; + JalviewColourChooser.showColourChooser(button, ttl, + currentColor.getColour(), listener); } else { - // bring up graduated chooser. - chooser = new FeatureTypeSettings(me.fr, type); + /* + * variable colour and filters dialog + */ + boolean last=(Boolean)table.getValueAt(selectedRow, SHOW_COLUMN); + table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); + chooser = new FeatureTypeSettings(fr, type,last); + if (!Platform.isJS()) /** - * @j2sNative + * Java only + * + * @j2sIgnore */ { chooser.setRequestFocusEnabled(true); chooser.requestFocus(); } chooser.addActionListener(this); - // Make the renderer reappear. fireEditingStopped(); } } else { - if (currentColor.isSimpleColour()) - { - /* - * read off colour picked in colour chooser after OK pressed - */ - currentColor = new FeatureColour(colorChooser.getColor()); - me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); - } - 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) { - /* - * 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 = me.fr.getFeatureFilter(type); - if (currentFilter == null) - { - currentFilter = new FeatureMatcherSet(); - } - Object[] data = ((FeatureTableModel) table.getModel()) - .getData()[rowSelected]; - data[COLOUR_COLUMN] = currentColor; - data[FILTER_COLUMN] = currentFilter; + 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() @@ -1865,14 +2009,14 @@ 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(); @@ -1894,14 +2038,14 @@ 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; @@ -1915,9 +2059,8 @@ 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); @@ -1932,7 +2075,9 @@ public class FeatureSettings extends JPanel { if (button == e.getSource()) { - FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type); + boolean last = fr.getFeaturesDisplayed().isVisible(type); + ((FeatureTableModel) table.getModel()).setValueAt(Boolean.TRUE, rowSelected, SHOW_COLUMN); + FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type,last); chooser.addActionListener(this); chooser.setRequestFocusEnabled(true); chooser.requestFocus(); @@ -1954,17 +2099,25 @@ 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; + data[SHOW_COLUMN] = fr.getFeaturesDisplayed().isVisible(type); + 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(); } } @@ -1975,21 +2128,41 @@ 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 { FeatureColourI gcol; @@ -2067,7 +2240,8 @@ 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); } } }