X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=7fb3af9fffd4e6a44086fb29a03fd22cb2cc717c;hb=refs%2Fheads%2Fbug%2FJAL-3049colourCellTooltip;hp=811b3770159aff73ce055190acf3b1c70ba50bfb;hpb=ab7590e6d0bbb8764d8df5bfcfa55956d80a4ac9;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 811b377..7fb3af9 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -22,7 +22,6 @@ package jalview.gui; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; -import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.datamodel.features.FeatureMatcher; @@ -32,23 +31,13 @@ import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.Help.HelpId; 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 java.awt.BorderLayout; import java.awt.Color; @@ -75,7 +64,6 @@ 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 +72,6 @@ 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; @@ -106,7 +93,7 @@ import javax.swing.JSlider; import javax.swing.JTable; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; -import javax.swing.SwingUtilities; +import javax.swing.border.Border; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.table.AbstractTableModel; @@ -117,6 +104,9 @@ import javax.swing.table.TableColumn; 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 +124,7 @@ 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 = "Click to edit, right-click for menu"; final FeatureRenderer fr; @@ -189,290 +175,6 @@ 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 @@ -499,19 +201,27 @@ public class FeatureSettings extends JPanel table = new JTable() { + static final String tt = "Click to edit, right-click for menu"; // todo i18n + @Override public String getToolTipText(MouseEvent e) { 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); + break; case FILTER_COLUMN: - int row = table.rowAtPoint(e.getPoint()); FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, column); tip = o.isEmpty() @@ -523,6 +233,21 @@ public class FeatureSettings extends JPanel } return tip; } + + /** + * Position the tooltip at 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); + return loc; + } }; table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); table.setFont(new Font("Verdana", Font.PLAIN, 12)); @@ -616,9 +341,6 @@ 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! @@ -667,7 +389,6 @@ public class FeatureSettings extends JPanel javax.swing.event.InternalFrameEvent evt) { fr.removePropertyChangeListener(change); - dassourceBrowser.fs = null; }; }); frame.setLayer(JLayeredPane.PALETTE_LAYER); @@ -1153,7 +874,7 @@ 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")); @@ -1164,56 +885,67 @@ public class FeatureSettings extends JPanel if (value == JalviewFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); + load(file); + } + } - try - { - InputStreamReader in = new InputStreamReader( - new FileInputStream(file), "UTF-8"); + /** + * Loads feature colours and filters from XML stored in the given file + * + * @param file + */ + void load(File file) + { + try + { + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); - 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.getColourCount() - 1; i >= 0; i--) + { + jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); + FeatureColourI colour = Jalview2XML.unmarshalColour(newcol); + fr.setColour(newcol.getName(), colour); + fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount()); + } - /* - * 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.getFilterCount(); i++) + { + jalview.schemabinding.version2.Filter filterModel = jucs + .getFilter(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(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); } } @@ -1224,7 +956,7 @@ 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")); @@ -1234,77 +966,87 @@ public class FeatureSettings extends JPanel if (value == JalviewFileChooser.APPROVE_OPTION) { - 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")); + save(chooser.getSelectedFile()); + } + } - /* - * 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)); - } - }); + /** + * Saves feature colours and filters to the given file + * + * @param file + */ + void save(File file) + { + JalviewUserColours ucs = new JalviewUserColours(); + ucs.setSchemeName("Sequence Features"); + try + { + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(file), "UTF-8")); - /* - * 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); + jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour( + featureType, fcol); + ucs.addColour(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(); + MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator, + filter.isAnded()); + Filter filterModel = new Filter(); + filterModel.setFeatureType(featureType); + filterModel.setMatcherSet(ms); + ucs.addFilter(filterModel); + } } + + 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() @@ -1428,8 +1170,6 @@ 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 +1284,8 @@ 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 +1298,8 @@ 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 +1324,6 @@ 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 +1343,87 @@ 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 + * @return */ - private void doDasFeatureFetch(List selectedSources, - boolean checkDbRefs, boolean promptFetchDbRefs) + public static String getColorTooltip(FeatureColourI fcol) { - 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()); - } - else + if (fcol == null) { - iSize = vp.getAlignment().getHeight(); - seqs = vp.getAlignment().getSequencesArray(); + return null; } - - dataset = new SequenceI[iSize]; - for (int i = 0; i < iSize; i++) + if (fcol.isSimpleColour()) { - dataset[i] = seqs[i].getDatasetSequence(); + return BASE_TOOLTIP; } - - cancelDAS.setEnabled(true); - dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, - this, selectedSources, checkDbRefs, promptFetchDbRefs); - af.getViewport().setShowSequenceFeatures(true); - af.showSeqFeatures.setSelected(true); + String description = fcol.getDescription(); + description = description.replaceAll("<", "<"); + description = description.replaceAll(">", ">"); + StringBuilder tt = new StringBuilder(description); + tt.append("
").append(BASE_TOOLTIP).append("
"); + return JvSwingUtils.wrapTooltip(true, tt.toString()); } - /** - * 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(); - } - - /** - * 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()); } // /////////////////////////////////////////////////////////////////////// @@ -1882,11 +1511,9 @@ public class FeatureSettings extends JPanel class ColorRenderer extends JLabel implements TableCellRenderer { - javax.swing.border.Border unselectedBorder = null; + Border unselectedBorder = null; - javax.swing.border.Border selectedBorder = null; - - final String baseTT = "Click to edit, right/apple click for menu."; + Border selectedBorder = null; public ColorRenderer() { @@ -1901,7 +1528,6 @@ public class FeatureSettings extends JPanel { FeatureColourI cellColour = (FeatureColourI) color; setOpaque(true); - setToolTipText(baseTT); setBackground(tbl.getBackground()); if (!cellColour.isSimpleColour()) { @@ -2008,77 +1634,6 @@ 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 implements TableCellEditor, ActionListener { @@ -2312,7 +1867,6 @@ public class FeatureSettings extends JPanel button.setOpaque(true); button.setBackground(me.getBackground()); button.setText(currentFilter.toString()); - button.setToolTipText(currentFilter.toString()); button.setIcon(null); return button; }