X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=26cb104678f71f0809349512c469a87e3f9ef456;hb=96026e673c3629afa54a0d03be4b0022c7b42869;hp=811b3770159aff73ce055190acf3b1c70ba50bfb;hpb=ab7590e6d0bbb8764d8df5bfcfa55956d80a4ac9;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 811b377..26cb104 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -22,7 +22,7 @@ package jalview.gui; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; -import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.datamodel.features.FeatureMatcher; @@ -30,25 +30,17 @@ 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.CompoundMatcher; -import jalview.schemabinding.version2.Filter; -import jalview.schemabinding.version2.JalviewUserColours; -import jalview.schemabinding.version2.MatchCondition; -import jalview.schemabinding.version2.MatcherSet; -import jalview.schemabinding.version2.types.ColourNoValueColourType; -import jalview.schemabinding.version2.types.ColourThreshTypeType; -import jalview.schemabinding.version2.types.FeatureMatcherByType; import jalview.schemes.FeatureColour; -import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.util.matcher.Condition; -import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; -import jalview.ws.DasSequenceFeatureFetcher; -import jalview.ws.dbsources.das.api.jalviewSourceI; +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; @@ -75,7 +67,6 @@ import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.util.Arrays; -import java.util.Collections; import java.util.Comparator; import java.util.HashMap; import java.util.HashSet; @@ -84,7 +75,6 @@ import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; -import java.util.Vector; import javax.help.HelpSetException; import javax.swing.AbstractCellEditor; @@ -93,8 +83,6 @@ 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; @@ -106,17 +94,26 @@ import javax.swing.JSlider; import javax.swing.JTable; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; -import javax.swing.SwingUtilities; +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.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 { + private static final String SEQUENCE_FEATURE_COLOURS = MessageManager + .getString("label.sequence_feature_colours"); + /* * column indices of fields in Feature Settings table */ @@ -134,11 +131,7 @@ public class FeatureSettings extends JPanel private static final int MIN_HEIGHT = 400; - DasSourceBrowser dassourceBrowser; - - DasSequenceFeatureFetcher dasFeatureFetcher; - - JPanel dasSettingsPane = new JPanel(); + private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit"); final FeatureRenderer fr; @@ -149,9 +142,9 @@ public class FeatureSettings extends JPanel */ Object[][] originalData; - private float originalTransparency; + float originalTransparency; - private Map originalFilters; + Map originalFilters; final JInternalFrame frame; @@ -181,7 +174,7 @@ public class FeatureSettings extends JPanel /* * true when Feature Settings are updating from feature renderer */ - private boolean handlingUpdate = false; + boolean handlingUpdate = false; /* * holds {featureCount, totalExtent} for each feature type @@ -189,290 +182,6 @@ public class FeatureSettings extends JPanel Map typeWidth = null; /** - * Populates an XML model of the feature colour scheme for one feature type - * - * @param featureType - * @param fcol - * @return - */ - protected static jalview.schemabinding.version2.Colour marshalColour( - String featureType, FeatureColourI fcol) - { - jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); - if (fcol.isSimpleColour()) - { - col.setRGB(Format.getHexString(fcol.getColour())); - } - else - { - col.setRGB(Format.getHexString(fcol.getMaxColour())); - col.setMin(fcol.getMin()); - col.setMax(fcol.getMax()); - col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour())); - col.setAutoScale(fcol.isAutoScaled()); - col.setThreshold(fcol.getThreshold()); - col.setColourByLabel(fcol.isColourByLabel()); - col.setThreshType(fcol.isAboveThreshold() ? ColourThreshTypeType.ABOVE - : (fcol.isBelowThreshold() ? ColourThreshTypeType.BELOW - : ColourThreshTypeType.NONE)); - if (fcol.isColourByAttribute()) - { - col.setAttributeName(fcol.getAttributeName()); - } - Color noColour = fcol.getNoColour(); - if (noColour == null) - { - col.setNoValueColour(ColourNoValueColourType.NONE); - } - else if (noColour == fcol.getMaxColour()) - { - col.setNoValueColour(ColourNoValueColourType.MAX); - } - else - { - col.setNoValueColour(ColourNoValueColourType.MIN); - } - } - col.setName(featureType); - return col; - } - - /** - * Populates an XML model of the feature filter(s) for one feature type - * - * @param firstMatcher - * the first (or only) match condition) - * @param filter - * remaining match conditions (if any) - * @param and - * if true, conditions are and-ed, else or-ed - */ - protected static MatcherSet marshalFilter(FeatureMatcherI firstMatcher, - Iterator filters, boolean and) - { - MatcherSet result = new MatcherSet(); - - if (filters.hasNext()) - { - /* - * compound matcher - */ - CompoundMatcher compound = new CompoundMatcher(); - compound.setAnd(and); - MatcherSet matcher1 = marshalFilter(firstMatcher, - Collections.emptyIterator(), and); - compound.addMatcherSet(matcher1); - FeatureMatcherI nextMatcher = filters.next(); - MatcherSet matcher2 = marshalFilter(nextMatcher, filters, and); - compound.addMatcherSet(matcher2); - result.setCompoundMatcher(compound); - } - else - { - /* - * single condition matcher - */ - MatchCondition matcherModel = new MatchCondition(); - matcherModel.setCondition( - firstMatcher.getMatcher().getCondition().getStableName()); - matcherModel.setValue(firstMatcher.getMatcher().getPattern()); - if (firstMatcher.isByAttribute()) - { - matcherModel.setBy(FeatureMatcherByType.BYATTRIBUTE); - matcherModel.setAttributeName(firstMatcher.getAttribute()); - } - else if (firstMatcher.isByLabel()) - { - matcherModel.setBy(FeatureMatcherByType.BYLABEL); - } - else if (firstMatcher.isByScore()) - { - matcherModel.setBy(FeatureMatcherByType.BYSCORE); - } - result.setMatchCondition(matcherModel); - } - - return result; - } - - /** - * Loads one XML model of a feature filter to a Jalview object - * - * @param colourModel - * @return - */ - protected static FeatureMatcherSetI unmarshalFilter(Filter filterModel) - { - FeatureMatcherSetI result = new FeatureMatcherSet(); - MatcherSet matcherSetModel = filterModel.getMatcherSet(); - try - { - unmarshalFilterConditions(result, matcherSetModel, true); - } catch (IllegalStateException e) - { - // mixing AND and OR conditions perhaps - System.err.println( - String.format("Error reading filter conditions for '%s': %s", - filterModel.getFeatureType(), e.getMessage())); - // return as much as was parsed up to the error - } - - return result; - } - - /** - * Adds feature match conditions to matcherSet as unmarshalled from XML - * (possibly recursively for compound conditions) - * - * @param matcherSet - * @param matcherSetModel - * @param and - * if true, multiple conditions are AND-ed, else they are OR-ed - * @throws IllegalStateException - * if AND and OR conditions are mixed - */ - protected static void unmarshalFilterConditions( - FeatureMatcherSetI matcherSet, MatcherSet matcherSetModel, - boolean and) - { - MatchCondition mc = matcherSetModel.getMatchCondition(); - if (mc != null) - { - /* - * single condition - */ - FeatureMatcherByType filterBy = mc.getBy(); - Condition cond = Condition.fromString(mc.getCondition()); - String pattern = mc.getValue(); - FeatureMatcherI matchCondition = null; - if (filterBy == FeatureMatcherByType.BYLABEL) - { - matchCondition = FeatureMatcher.byLabel(cond, pattern); - } - else if (filterBy == FeatureMatcherByType.BYSCORE) - { - matchCondition = FeatureMatcher.byScore(cond, pattern); - - } - else if (filterBy == FeatureMatcherByType.BYATTRIBUTE) - { - String[] attNames = mc.getAttributeName(); - matchCondition = FeatureMatcher.byAttribute(cond, pattern, - attNames); - } - - /* - * note this throws IllegalStateException if AND-ing to a - * previously OR-ed compound condition, or vice versa - */ - if (and) - { - matcherSet.and(matchCondition); - } - else - { - matcherSet.or(matchCondition); - } - } - else - { - /* - * compound condition - */ - MatcherSet[] matchers = matcherSetModel.getCompoundMatcher() - .getMatcherSet(); - boolean anded = matcherSetModel.getCompoundMatcher().getAnd(); - if (matchers.length == 2) - { - unmarshalFilterConditions(matcherSet, matchers[0], anded); - unmarshalFilterConditions(matcherSet, matchers[1], anded); - } - else - { - System.err.println("Malformed compound filter condition"); - } - } - } - - /** - * Loads one XML model of a feature colour to a Jalview object - * - * @param colourModel - * @return - */ - protected static FeatureColourI unmarshalColour( - jalview.schemabinding.version2.Colour colourModel) - { - FeatureColourI colour = null; - - if (colourModel.hasMax()) - { - Color mincol = null; - Color maxcol = null; - Color noValueColour = null; - - try - { - mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16)); - maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16)); - } catch (Exception e) - { - Cache.log.warn("Couldn't parse out graduated feature color.", e); - } - - ColourNoValueColourType noCol = colourModel.getNoValueColour(); - if (noCol == ColourNoValueColourType.MIN) - { - noValueColour = mincol; - } - else if (noCol == ColourNoValueColourType.MAX) - { - noValueColour = maxcol; - } - - colour = new FeatureColour(mincol, maxcol, noValueColour, - colourModel.getMin(), - colourModel.getMax()); - String[] attributes = colourModel.getAttributeName(); - if (attributes != null && attributes.length > 0) - { - colour.setAttributeName(attributes); - } - if (colourModel.hasAutoScale()) - { - colour.setAutoScaled(colourModel.getAutoScale()); - } - if (colourModel.hasColourByLabel()) - { - colour.setColourByLabel(colourModel.getColourByLabel()); - } - if (colourModel.hasThreshold()) - { - colour.setThreshold(colourModel.getThreshold()); - } - ColourThreshTypeType ttyp = colourModel.getThreshType(); - if (ttyp != null) - { - if (ttyp == ColourThreshTypeType.ABOVE) - { - colour.setAboveThreshold(true); - } - else if (ttyp == ColourThreshTypeType.BELOW) - { - colour.setBelowThreshold(true); - } - } - } - else - { - Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16)); - colour = new FeatureColour(color); - } - - return colour; - } - - /** * Constructor * * @param af @@ -499,49 +208,103 @@ public class FeatureSettings extends JPanel table = new JTable() { + +// @Override +// public void repaint() { +// System.out.println("FS repaint"); +// super.repaint(); +// +// } +// +// @Override +// public void repaint(long tm, int x, int y, int width, int height) { +// System.out.println("FS repaint " + x + " " + y + " " + width + " " + height); +// super.repaint(tm, x, y, width, height); +// +// } +// @Override +// public void invalidate() { +// if (isValid()) +// System.out.println("FS invalidating "); +// super.invalidate(); +// } +// +// @Override +// public void validate() { +// System.out.println("FS validating " + isValid()); +// super.validate(); +// } + @Override public String getToolTipText(MouseEvent e) { 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; + } }; + + // 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)); - table.setFont(new Font("Verdana", Font.PLAIN, 12)); + ToolTipManager.sharedInstance().registerComponent(table); - // table.setDefaultRenderer(Color.class, new ColorRenderer()); - // table.setDefaultEditor(Color.class, new ColorEditor(this)); - // - 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); @@ -556,8 +319,7 @@ public class FeatureSettings extends JPanel if (evt.isPopupTrigger()) { Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); - popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), - evt.getY()); + showPopupMenu(selectedRow, type, colour, evt.getPoint()); } else if (evt.getClickCount() == 2) { @@ -578,8 +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()); } } }); @@ -616,9 +377,6 @@ public class FeatureSettings extends JPanel // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); - dassourceBrowser = new DasSourceBrowser(this); - dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! @@ -645,18 +403,9 @@ 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( @@ -667,91 +416,82 @@ public class FeatureSettings extends JPanel javax.swing.event.InternalFrameEvent evt) { fr.removePropertyChangeListener(change); - dassourceBrowser.fs = null; }; }); 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() + 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() { - JColorChooser colorChooser; - @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(); - 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); + /* + * toggle variable to simple colour - show colour chooser + */ + String title = MessageManager.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 + else { if (e.getSource() instanceof FeatureTypeSettings) { @@ -760,23 +500,43 @@ public class FeatureSettings extends JPanel * colour will have already been set in the FeatureRenderer */ FeatureColourI fci = fr.getFeatureColours().get(type); - table.setValueAt(fci, rowSelected, 1); - table.validate(); - } - else - { - // probably the color chooser! - table.setValueAt(new FeatureColour(colorChooser.getColor()), - rowSelected, 1); - table.validate(); - me.updateFeatureRenderer( - ((FeatureTableModel) table.getModel()).getData(), - false); + table.setValueAt(fci, rowSelected, COLOUR_COLUMN); + // BH 2018 setting a table value does not invalidate it. +// System.out.println("FeatureSettings is valied" + table.isValid()); +// table.validate(); } } } + }); + + men.addSeparator(); + + JMenuItem scr = new JMenuItem( + MessageManager.getString("label.sort_by_score")); + men.add(scr); + scr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + af.avc.sortAlignmentByFeatureScore(Arrays.asList(new String[] + { type })); + } + }); + JMenuItem dens = new JMenuItem( + MessageManager.getString("label.sort_by_density")); + dens.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + af.avc.sortAlignmentByFeatureDensity(Arrays.asList(new String[] + { type })); + } }); + men.add(dens); JMenuItem selCols = new JMenuItem( MessageManager.getString("label.select_columns_containing")); @@ -824,7 +584,7 @@ public class FeatureSettings extends JPanel men.add(clearCols); men.add(hideCols); men.add(hideOtherCols); - men.show(table, x, y); + men.show(table, pt.x, pt.y); } @Override @@ -1153,67 +913,89 @@ public class FeatureSettings extends JPanel void load() { JalviewFileChooser chooser = new JalviewFileChooser("fc", - "Sequence Feature Colours"); + SEQUENCE_FEATURE_COLOURS); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); + chooser.setResponseHandler(0, new Runnable() + { + @Override + public void run() + { + File file = chooser.getSelectedFile(); + load(file); + } + }); + chooser.showOpenDialog(this); + } - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + /** + * Loads feature colours and filters from XML stored in the given file + * + * @param file + */ + void load(File file) + { + try { - File file = chooser.getSelectedFile(); + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); - 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); + // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); - /* - * load feature colours - */ - for (int i = jucs.getColourCount() - 1; i >= 0; i--) - { - jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); - FeatureColourI colour = unmarshalColour(newcol); - fr.setColour(newcol.getName(), colour); - fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount()); - } + /* + * 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.getFilterCount(); i++) + /* + * 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()) { - jalview.schemabinding.version2.Filter filterModel = jucs - .getFilter(i); - FeatureMatcherSetI filter = unmarshalFilter(filterModel); - if (!filter.isEmpty()) - { - fr.setFeatureFilter(filterModel.getFeatureType(), filter); - } + fr.setFeatureFilter(featureType, filter); } + } - /* - * update feature settings table - */ - if (table != null) - { - resetTable(null); - Object[][] data = ((FeatureTableModel) table.getModel()) - .getData(); - ensureOrder(data); - updateFeatureRenderer(data, false); - table.repaint(); - } - } catch (Exception ex) + /* + * update feature settings table + */ + if (table != null) { - System.out.println("Error loading User Colour File\n" + ex); + resetTable(null); + 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); } } @@ -1224,87 +1006,106 @@ public class FeatureSettings extends JPanel void save() { JalviewFileChooser chooser = new JalviewFileChooser("fc", - "Sequence Feature Colours"); + SEQUENCE_FEATURE_COLOURS); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( 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); + } + } - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + /** + * Saves feature colours and filters to the given file + * + * @param file + */ + void save(File file) + { + JalviewUserColours ucs = new JalviewUserColours(); + ucs.setSchemeName("Sequence Features"); + try { - String choice = chooser.getSelectedFile().getPath(); - JalviewUserColours ucs = new JalviewUserColours(); - ucs.setSchemeName("Sequence Features"); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(file), "UTF-8")); - /* - * sort feature types by colour order, from 0 (highest) - * to 1 (lowest) - */ - Set fr_colours = fr.getAllFeatureColours(); - String[] sortedTypes = fr_colours - .toArray(new String[fr_colours.size()]); - Arrays.sort(sortedTypes, new Comparator() - { - @Override - public int compare(String type1, String type2) - { - return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); - } - }); - - /* - * save feature colours - */ - for (String featureType : sortedTypes) + /* + * sort feature types by colour order, from 0 (highest) + * to 1 (lowest) + */ + Set fr_colours = fr.getAllFeatureColours(); + String[] sortedTypes = fr_colours + .toArray(new String[fr_colours.size()]); + Arrays.sort(sortedTypes, new Comparator() + { + @Override + public int compare(String type1, String type2) { - FeatureColourI fcol = fr.getFeatureStyle(featureType); - jalview.schemabinding.version2.Colour col = marshalColour( - featureType, fcol); - ucs.addColour(col); + return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); } + }); - /* - * save any feature filters - */ - for (String featureType : sortedTypes) - { - FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); - if (filter != null && !filter.isEmpty()) - { - Iterator iterator = filter.getMatchers().iterator(); - FeatureMatcherI firstMatcher = iterator.next(); - MatcherSet ms = marshalFilter(firstMatcher, iterator, - filter.isAnded()); - Filter filterModel = new Filter(); - filterModel.setFeatureType(featureType); - filterModel.setMatcherSet(ms); - ucs.addFilter(filterModel); - } - } + /* + * save feature colours + */ + for (String featureType : sortedTypes) + { + FeatureColourI fcol = fr.getFeatureStyle(featureType); + Colour col = jalview.project.Jalview2XML.marshalColour(featureType, + fcol); + ucs.getColour().add(col); + } - ucs.marshal(out); - out.close(); - } catch (Exception ex) + /* + * save any feature filters + */ + for (String featureType : sortedTypes) { - ex.printStackTrace(); + FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); + if (filter != null && !filter.isEmpty()) + { + Iterator iterator = filter.getMatchers().iterator(); + FeatureMatcherI firstMatcher = iterator.next(); + 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.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); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); } } public void invertSelection() { - for (int i = 0; i < table.getRowCount(); i++) + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); + for (int i = 0; i < data.length; i++) { - Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN); - - table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN); + data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; } + updateFeatureRenderer(data, true); + table.repaint(); } public void orderByAvWidth() @@ -1393,7 +1194,7 @@ public class FeatureSettings extends JPanel * @param data * @param visibleNew */ - private void updateFeatureRenderer(Object[][] data, boolean visibleNew) + void updateFeatureRenderer(Object[][] data, boolean visibleNew) { FeatureSettingsBean[] rowData = getTableAsBeans(data); @@ -1428,8 +1229,6 @@ public class FeatureSettings extends JPanel JPanel settingsPane = new JPanel(); settingsPane.setLayout(new BorderLayout()); - dasSettingsPane.setLayout(new BorderLayout()); - JPanel bigPanel = new JPanel(); bigPanel.setLayout(new BorderLayout()); @@ -1544,6 +1343,8 @@ public class FeatureSettings extends JPanel JButton loadColours = new JButton( MessageManager.getString("label.load_colours")); loadColours.setFont(JvSwingUtils.getLabelFont()); + loadColours.setToolTipText( + MessageManager.getString("label.load_colours_tooltip")); loadColours.addActionListener(new ActionListener() { @Override @@ -1556,6 +1357,8 @@ public class FeatureSettings extends JPanel JButton saveColours = new JButton( MessageManager.getString("label.save_colours")); saveColours.setFont(JvSwingUtils.getLabelFont()); + saveColours.setToolTipText( + MessageManager.getString("label.save_colours_tooltip")); saveColours.addActionListener(new ActionListener() { @Override @@ -1580,38 +1383,6 @@ public class FeatureSettings extends JPanel transparency.setMaximum(70); transparency.setToolTipText( MessageManager.getString("label.transparency_tip")); - fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); - fetchDAS.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - fetchDAS_actionPerformed(e); - } - }); - saveDAS.setText(MessageManager.getString("action.save_as_default")); - saveDAS.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - saveDAS_actionPerformed(e); - } - }); - - JPanel dasButtonPanel = new JPanel(); - dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); - dasSettingsPane.setBorder(null); - cancelDAS.setEnabled(false); - cancelDAS.setText(MessageManager.getString("action.cancel_fetch")); - cancelDAS.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - cancelDAS_actionPerformed(e); - } - }); JPanel transPanel = new JPanel(new GridLayout(1, 2)); bigPanel.add(transPanel, BorderLayout.SOUTH); @@ -1631,170 +1402,93 @@ public class FeatureSettings extends JPanel buttonPanel.add(loadColours); buttonPanel.add(saveColours); bigPanel.add(scrollPane, BorderLayout.CENTER); - dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH); - dasButtonPanel.add(fetchDAS); - dasButtonPanel.add(cancelDAS); - dasButtonPanel.add(saveDAS); settingsPane.add(bigPanel, BorderLayout.CENTER); settingsPane.add(buttonPanel, BorderLayout.SOUTH); this.add(settingsPane); } - public void fetchDAS_actionPerformed(ActionEvent e) - { - fetchDAS.setEnabled(false); - cancelDAS.setEnabled(true); - dassourceBrowser.setGuiEnabled(false); - Vector selectedSources = dassourceBrowser - .getSelectedSources(); - doDasFeatureFetch(selectedSources, true, true); - } - /** - * get the features from selectedSources for all or the current selection + * Answers a suitable tooltip to show on the colour cell of the table * - * @param selectedSources - * @param checkDbRefs - * @param promptFetchDbRefs + * @param fcol + * @param withHint + * if true include 'click to edit' and similar text + * @return */ - private void doDasFeatureFetch(List selectedSources, - boolean checkDbRefs, boolean promptFetchDbRefs) + public static String getColorTooltip(FeatureColourI fcol, + boolean withHint) { - SequenceI[] dataset, seqs; - int iSize; - AlignmentViewport vp = af.getViewport(); - if (vp.getSelectionGroup() != null - && vp.getSelectionGroup().getSize() > 0) - { - iSize = vp.getSelectionGroup().getSize(); - dataset = new SequenceI[iSize]; - seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment()); + if (fcol == null) + { + return null; } - else + if (fcol.isSimpleColour()) { - iSize = vp.getAlignment().getHeight(); - seqs = vp.getAlignment().getSequencesArray(); + return withHint ? BASE_TOOLTIP : null; } - - dataset = new SequenceI[iSize]; - for (int i = 0; i < iSize; i++) + String description = fcol.getDescription(); + description = description.replaceAll("<", "<"); + description = description.replaceAll(">", ">"); + StringBuilder tt = new StringBuilder(description); + if (withHint) { - dataset[i] = seqs[i].getDatasetSequence(); + tt.append("
").append(BASE_TOOLTIP).append("
"); } - - cancelDAS.setEnabled(true); - dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, - this, selectedSources, checkDbRefs, promptFetchDbRefs); - af.getViewport().setShowSequenceFeatures(true); - af.showSeqFeatures.setSelected(true); - } - - /** - * blocking call to initialise the das source browser - */ - public void initDasSources() - { - dassourceBrowser.initDasSources(); - } - - /** - * examine the current list of das sources and return any matching the given - * nicknames in sources - * - * @param sources - * Vector of Strings to resolve to DAS source nicknames. - * @return sources that are present in source list. - */ - public List resolveSourceNicknames(Vector sources) - { - return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); - } - - /** - * get currently selected das sources. ensure you have called initDasSources - * before calling this. - * - * @return vector of selected das source nicknames - */ - public Vector getSelectedSources() - { - return dassourceBrowser.getSelectedSources(); + return JvSwingUtils.wrapTooltip(true, tt.toString()); } - /** - * properly initialise DAS fetcher and then initiate a new thread to fetch - * features from the named sources (rather than any turned on by default) - * - * @param sources - * @param block - * if true then runs in same thread, otherwise passes to the Swing - * executor - */ - public void fetchDasFeatures(Vector sources, boolean block) + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, + int w, int h) { - initDasSources(); - List resolved = dassourceBrowser.sourceRegistry - .resolveSourceNicknames(sources); - if (resolved.size() == 0) + boolean thr = false; + StringBuilder tx = new StringBuilder(); + + if (gcol.isColourByAttribute()) { - resolved = dassourceBrowser.getSelectedSources(); + tx.append(FeatureMatcher + .toAttributeDisplayName(gcol.getAttributeName())); } - if (resolved.size() > 0) + else if (!gcol.isColourByLabel()) { - final List dassources = resolved; - fetchDAS.setEnabled(false); - // cancelDAS.setEnabled(true); doDasFetch does this. - Runnable fetcher = new Runnable() - { - - @Override - public void run() - { - doDasFeatureFetch(dassources, true, false); - - } - }; - if (block) + 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) { - fetcher.run(); + tx.append(" "); } - else + if (!gcol.isColourByAttribute()) { - SwingUtilities.invokeLater(fetcher); + tx.append("Label"); } + comp.setIcon(null); } - } - - public void saveDAS_actionPerformed(ActionEvent e) - { - dassourceBrowser - .saveProperties(jalview.bin.Cache.applicationProperties); - } - - public void complete() - { - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - dassourceBrowser.setGuiEnabled(true); - - } - - public void cancelDAS_actionPerformed(ActionEvent e) - { - if (dasFeatureFetcher != null) + else { - dasFeatureFetcher.cancel(); + 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() + ")"); } - complete(); - } - - public void noDasSourceActive() - { - complete(); - JvOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.getString("label.no_das_sources_selected_warn"), - MessageManager.getString("label.no_das_sources_selected_title"), - JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE); + comp.setHorizontalAlignment(SwingConstants.CENTER); + comp.setText(tx.toString()); } // /////////////////////////////////////////////////////////////////////// @@ -1805,7 +1499,7 @@ 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; @@ -1882,11 +1576,9 @@ public class FeatureSettings extends JPanel class ColorRenderer extends JLabel implements TableCellRenderer { - javax.swing.border.Border unselectedBorder = null; - - javax.swing.border.Border selectedBorder = null; + Border unselectedBorder = null; - final String baseTT = "Click to edit, right/apple click for menu."; + Border selectedBorder = null; public ColorRenderer() { @@ -1901,7 +1593,6 @@ public class FeatureSettings extends JPanel { FeatureColourI cellColour = (FeatureColourI) color; setOpaque(true); - setToolTipText(baseTT); setBackground(tbl.getBackground()); if (!cellColour.isSimpleColour()) { @@ -2008,82 +1699,10 @@ 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()); - } - } - } - - class ColorEditor extends AbstractCellEditor + @SuppressWarnings("serial") +class ColorEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { - FeatureSettings me; - FeatureColourI currentColor; FeatureTypeSettings chooser; @@ -2092,17 +1711,12 @@ 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, @@ -2111,79 +1725,92 @@ 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 */ - currentColor = fr.getFeatureColours().get(type); - FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type); - if (currentFilter == null) + chooser = new FeatureTypeSettings(fr, type); + if (!Jalview.isJS()) { - 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(); } } - // Implement the one CellEditor method that AbstractCellEditor doesn't. + /** + * Override allows access to this method from anonymous inner classes + */ + @Override + protected void fireEditingStopped() + { + super.fireEditingStopped(); + } + + // Implement the one CellEditor method that AbstractCellEditor doesn't. @Override public Object getCellEditorValue() { @@ -2197,9 +1824,9 @@ public class FeatureSettings extends JPanel { currentColor = (FeatureColourI) value; this.rowSelected = row; - type = me.table.getValueAt(row, TYPE_COLUMN).toString(); + type = table.getValueAt(row, TYPE_COLUMN).toString(); button.setOpaque(true); - button.setBackground(me.getBackground()); + button.setBackground(FeatureSettings.this.getBackground()); if (!currentColor.isSimpleColour()) { JLabel btn = new JLabel(); @@ -2225,10 +1852,10 @@ public class FeatureSettings extends JPanel * as display text). On click in the cell, opens the Feature Display Settings * dialog at the Filters tab. */ - class FilterEditor extends AbstractCellEditor + @SuppressWarnings("serial") +class FilterEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { - FeatureSettings me; FeatureMatcherSetI currentFilter; @@ -2242,9 +1869,8 @@ 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); @@ -2259,7 +1885,7 @@ 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(); @@ -2270,7 +1896,6 @@ public class FeatureSettings extends JPanel chooser.getWidth(), chooser.getHeight()); chooser.validate(); } - chooser.showTab(false); fireEditingStopped(); } else if (e.getSource() instanceof Component) @@ -2282,17 +1907,23 @@ 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(); } } @@ -2308,11 +1939,10 @@ public class FeatureSettings extends JPanel { currentFilter = (FeatureMatcherSetI) value; this.rowSelected = row; - type = me.table.getValueAt(row, TYPE_COLUMN).toString(); + type = table.getValueAt(row, TYPE_COLUMN).toString(); button.setOpaque(true); - button.setBackground(me.getBackground()); + button.setBackground(FeatureSettings.this.getBackground()); button.setText(currentFilter.toString()); - button.setToolTipText(currentFilter.toString()); button.setIcon(null); return button; } @@ -2396,7 +2026,8 @@ 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); } } }