X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=cdca96a97b2a1b7eb0d47b834fdbc03227c4e3c2;hb=9fcb12165750b20f8a73d0bb976b22be5fda94a2;hp=3f1d9c7f9975dd61c1bf680ba87f1a1c83f27d94;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 3f1d9c7..cdca96a 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -22,20 +22,25 @@ 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; +import jalview.datamodel.features.FeatureMatcherI; +import jalview.datamodel.features.FeatureMatcherSet; +import jalview.datamodel.features.FeatureMatcherSetI; +import jalview.datamodel.ontology.OntologyI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; -import jalview.schemabinding.version2.JalviewUserColours; +import jalview.io.gff.SequenceOntologyFactory; import jalview.schemes.FeatureColour; -import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.util.QuickSort; -import jalview.viewmodel.AlignmentViewport; -import jalview.ws.dbsources.das.api.jalviewSourceI; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; +import jalview.xml.binding.jalview.JalviewUserColours; +import jalview.xml.binding.jalview.JalviewUserColours.Colour; +import jalview.xml.binding.jalview.JalviewUserColours.Filter; +import jalview.xml.binding.jalview.ObjectFactory; import java.awt.BorderLayout; import java.awt.Color; @@ -44,6 +49,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; import java.awt.GridLayout; +import java.awt.Point; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -60,14 +66,16 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; +import java.util.ArrayList; import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; 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; @@ -75,7 +83,6 @@ import javax.swing.BorderFactory; 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; @@ -86,36 +93,65 @@ import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JScrollPane; import javax.swing.JSlider; -import javax.swing.JTabbedPane; import javax.swing.JTable; import javax.swing.ListSelectionModel; +import javax.swing.RowFilter; 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; +import javax.swing.table.JTableHeader; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; +import javax.swing.table.TableRowSorter; +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 { - DasSourceBrowser dassourceBrowser; + private static final Font VERDANA_12 = new Font("Verdana", Font.PLAIN, 12); - jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; + private static final String SEQUENCE_FEATURE_COLOURS = MessageManager + .getString("label.sequence_feature_colours"); - JPanel settingsPane = new JPanel(); + /* + * column indices of fields in Feature Settings table + */ + static final int TYPE_COLUMN = 0; + + static final int COLOUR_COLUMN = 1; + + static final int FILTER_COLUMN = 2; + + static final int SHOW_COLUMN = 3; + + private static final int COLUMN_COUNT = 4; + + private static final int MIN_WIDTH = 400; + + private static final int MIN_HEIGHT = 400; - JPanel dasSettingsPane = new JPanel(); + private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit"); final FeatureRenderer fr; public final AlignFrame af; + /* + * 'original' fields hold settings to restore on Cancel + */ Object[][] originalData; private float originalTransparency; + private Map originalFilters; + final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); @@ -126,29 +162,54 @@ public class FeatureSettings extends JPanel JSlider transparency = new JSlider(); - JPanel transPanel = new JPanel(new GridLayout(1, 2)); - - private static final int MIN_WIDTH = 400; - - private static final int MIN_HEIGHT = 400; - - /** + /* * when true, constructor is still executing - so ignore UI events */ protected volatile boolean inConstruction = true; + int selectedRow = -1; + + boolean resettingTable = false; + + /* + * true when Feature Settings are updating from feature renderer + */ + private boolean handlingUpdate = false; + + /* + * holds {featureCount, totalExtent} for each feature type + */ + Map typeWidth = null; + + /* + * if true, 'child' feature types are not displayed + */ + JCheckBox summaryView; + + /* + * those feature types that do not have a parent feature type present + * (as determined by an Ontology relationship) + */ + List topLevelTypes; + /** * Constructor * * @param af */ - public FeatureSettings(AlignFrame af) + public FeatureSettings(AlignFrame alignFrame) { - this.af = af; + this.af = alignFrame; fr = af.getFeatureRenderer(); - // allow transparency to be recovered - transparency.setMaximum(100 - - (int) ((originalTransparency = fr.getTransparency()) * 100)); + + // 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 + + topLevelTypes = new ArrayList<>(); try { @@ -158,30 +219,143 @@ public class FeatureSettings extends JPanel ex.printStackTrace(); } + initTable(); + + scrollPane.setViewportView(table); + + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) + { + fr.findAllFeatures(true); // display everything! + } + + discoverAllFeatureData(); + final PropertyChangeListener change; + final FeatureSettings fs = this; + fr.addPropertyChangeListener(change = new PropertyChangeListener() + { + @Override + public void propertyChange(PropertyChangeEvent evt) + { + if (!fs.resettingTable && !fs.handlingUpdate) + { + fs.handlingUpdate = true; + fs.resetTable(null); + // new groups may be added with new sequence feature types only + fs.handlingUpdate = false; + } + } + }); + + 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); + } + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + fr.removePropertyChangeListener(change); + }; + }); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + inConstruction = false; + } + + /** + * Constructs and configures the JTable which displays columns of data for + * each feature type + */ + protected void initTable() + { table = new JTable() { @Override public String getToolTipText(MouseEvent e) { - if (table.columnAtPoint(e.getPoint()) == 0) + String tip = null; + int column = table.columnAtPoint(e.getPoint()); + int row = table.rowAtPoint(e.getPoint()); + switch (column) { + case TYPE_COLUMN: /* - * Tooltip for feature name only + * drag to reorder not enabled in Summary View */ - return JvSwingUtils.wrapTooltip(true, MessageManager + tip = summaryView.isSelected() + ? MessageManager.getString( + "label.feature_settings_select_columns") + : 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: + FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, + column); + tip = o.isEmpty() + ? MessageManager + .getString("label.configure_feature_tooltip") + : o.toString(); + break; + default: + break; } - return null; + return tip; + } + + /** + * Position the tooltip near the bottom edge of, and half way across, the + * current cell + */ + @Override + public Point getToolTipLocation(MouseEvent e) + { + Point point = e.getPoint(); + int column = table.columnAtPoint(point); + int row = table.rowAtPoint(point); + Rectangle r = getCellRect(row, column, false); + Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3); + return loc; } }; - table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setDefaultRenderer(Color.class, new ColorRenderer()); - table.setDefaultEditor(Color.class, new ColorEditor(this)); + JTableHeader tableHeader = table.getTableHeader(); + tableHeader.setFont(VERDANA_12); + tableHeader.setReorderingAllowed(false); + table.setFont(VERDANA_12); table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); + + table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this)); + table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer()); + + TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75, + new ColorRenderer(), new ColorEditor(this)); + table.addColumn(colourColumn); + + TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75, + new FilterRenderer(), new FilterEditor(this)); + table.addColumn(filterColumn); + table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() @@ -190,20 +364,19 @@ public class FeatureSettings extends JPanel public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); + String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); if (evt.isPopupTrigger()) { - popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.getMinMax(), - evt.getX(), evt.getY()); + popupMenu(selectedRow, type, evt.getX(), evt.getY()); } else if (evt.getClickCount() == 2) { boolean invertSelection = evt.isAltDown(); boolean toggleSelection = Platform.isControlDown(evt); boolean extendSelection = evt.isShiftDown(); + String[] terms = getTermsInScope(type); fr.ap.alignFrame.avc.markColumnsContainingFeatures( - invertSelection, extendSelection, toggleSelection, - (String) table.getValueAt(selectedRow, 0)); + invertSelection, extendSelection, toggleSelection, terms); } } @@ -214,9 +387,8 @@ public class FeatureSettings extends JPanel selectedRow = table.rowAtPoint(evt.getPoint()); if (evt.isPopupTrigger()) { - popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.getMinMax(), - evt.getX(), evt.getY()); + String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); + popupMenu(selectedRow, type, evt.getX(), evt.getY()); } } }); @@ -227,96 +399,46 @@ public class FeatureSettings extends JPanel public void mouseDragged(MouseEvent evt) { int newRow = table.rowAtPoint(evt.getPoint()); - if (newRow != selectedRow && selectedRow != -1 && newRow != -1) - { - /* - * reposition 'selectedRow' to 'newRow' (the dragged to location) - * this could be more than one row away for a very fast drag action - * so just swap it with adjacent rows until we get it there - */ - Object[][] data = ((FeatureTableModel) table.getModel()) - .getData(); - int direction = newRow < selectedRow ? -1 : 1; - for (int i = selectedRow; i != newRow; i += direction) - { - Object[] temp = data[i]; - data[i] = data[i + direction]; - data[i + direction] = temp; - } - updateFeatureRenderer(data); - table.repaint(); - selectedRow = newRow; - } + dragRow(newRow); } }); - // table.setToolTipText(JvSwingUtils.wrapTooltip(true, - // 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()) + /** + * Answers an array consisting of the given type, and also (if 'Summary View' + * is selected), any feature types which are child terms of it in the Sequence + * Ontology + * + * @param type + * @return + */ + protected String[] getTermsInScope(String type) + { + if (!summaryView.isSelected()) { - fr.findAllFeatures(true); // display everything! + return new String[] { type }; } - discoverAllFeatureData(); - final PropertyChangeListener change; - final FeatureSettings fs = this; - fr.addPropertyChangeListener(change = new PropertyChangeListener() - { - @Override - public void propertyChange(PropertyChangeEvent evt) - { - if (!fs.resettingTable && !fs.handlingUpdate) - { - fs.handlingUpdate = true; - fs.resetTable(null); // new groups may be added with new seuqence - // feature types only - fs.handlingUpdate = false; - } - } + List terms = new ArrayList<>(); + terms.add(type); - }); + OntologyI so = SequenceOntologyFactory.getInstance(); - frame = new JInternalFrame(); - frame.setContentPane(this); - if (Platform.isAMac()) - { - Desktop.addInternalFrame(frame, - MessageManager.getString("label.sequence_feature_settings"), - 475, 480); - } - else + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); + for (Object[] row : data) { - Desktop.addInternalFrame(frame, - MessageManager.getString("label.sequence_feature_settings"), - 400, 450); + String type2 = (String) row[TYPE_COLUMN]; + if (!type2.equals(type) && so.isA(type2, type)) + { + terms.add(type2); + } } - frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); - - frame.addInternalFrameListener( - new javax.swing.event.InternalFrameAdapter() - { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - fr.removePropertyChangeListener(change); - dassourceBrowser.fs = null; - }; - }); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - inConstruction = false; + return terms.toArray(new String[terms.size()]); } - protected void popupSort(final int selectedRow, final String type, - final Object typeCol, final Map minmax, int x, + protected void popupMenu(final int rowSelected, final String type, int x, int y) { - final FeatureColourI featureColour = (FeatureColourI) typeCol; - JPopupMenu men = new JPopupMenu(MessageManager .formatMessage("label.settings_for_param", new String[] { type })); @@ -326,109 +448,26 @@ public class FeatureSettings extends JPanel final FeatureSettings me = this; scr.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent e) { - me.af.avc - .sortAlignmentByFeatureScore(Arrays.asList(new String[] - { type })); + String[] types = getTermsInScope(type); + me.af.avc.sortAlignmentByFeatureScore(Arrays.asList(types)); } - }); 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 })); + String[] types = getTermsInScope(type); + me.af.avc.sortAlignmentByFeatureDensity(Arrays.asList(types)); } - }); men.add(dens); - if (minmax != null) - { - final float[][] typeMinMax = minmax.get(type); - /* - * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); // - * this is broken at the moment and isn't that useful anyway! - * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new - * ActionListener() { - * - * public void actionPerformed(ActionEvent e) { - * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type, - * null); } else { minmax.put(type, typeMinMax); } } - * - * }); - * - * men.add(chb); - */ - if (typeMinMax != null && typeMinMax[0] != null) - { - // if (table.getValueAt(row, column)); - // graduated colourschemes for those where minmax exists for the - // positional features - final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( - "Graduated Colour"); - mxcol.setSelected(!featureColour.isSimpleColour()); - men.add(mxcol); - mxcol.addActionListener(new ActionListener() - { - JColorChooser colorChooser; - - @Override - public void actionPerformed(ActionEvent e) - { - if (e.getSource() == mxcol) - { - if (featureColour.isSimpleColour()) - { - FeatureColourChooser fc = new FeatureColourChooser(me.fr, - type); - fc.addActionListener(this); - } - else - { - // bring up simple color chooser - colorChooser = new JColorChooser(); - JDialog dialog = JColorChooser.createDialog(me, - "Select new Colour", true, // modal - colorChooser, this, // OK button handler - null); // no CANCEL button handler - colorChooser.setColor(featureColour.getMaxColour()); - dialog.setVisible(true); - } - } - else - { - if (e.getSource() instanceof FeatureColourChooser) - { - FeatureColourChooser fc = (FeatureColourChooser) e - .getSource(); - table.setValueAt(fc.getLastColour(), selectedRow, 1); - table.validate(); - } - else - { - // probably the color chooser! - table.setValueAt(new FeatureColour(colorChooser.getColor()), - selectedRow, 1); - table.validate(); - me.updateFeatureRenderer( - ((FeatureTableModel) table.getModel()).getData(), - false); - } - } - } - }); - } - } JMenuItem selCols = new JMenuItem( MessageManager.getString("label.select_columns_containing")); selCols.addActionListener(new ActionListener() @@ -436,8 +475,9 @@ public class FeatureSettings extends JPanel @Override public void actionPerformed(ActionEvent arg0) { + String[] types = getTermsInScope(type); fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, - false, type); + false, types); } }); JMenuItem clearCols = new JMenuItem(MessageManager @@ -447,8 +487,9 @@ public class FeatureSettings extends JPanel @Override public void actionPerformed(ActionEvent arg0) { + String[] types = getTermsInScope(type); fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, - false, type); + false, types); } }); JMenuItem hideCols = new JMenuItem( @@ -458,7 +499,8 @@ public class FeatureSettings extends JPanel @Override public void actionPerformed(ActionEvent arg0) { - fr.ap.alignFrame.hideFeatureColumns(type, true); + String[] types = getTermsInScope(type); + fr.ap.alignFrame.hideFeatureColumns(true, types); } }); JMenuItem hideOtherCols = new JMenuItem( @@ -468,7 +510,8 @@ public class FeatureSettings extends JPanel @Override public void actionPerformed(ActionEvent arg0) { - fr.ap.alignFrame.hideFeatureColumns(type, false); + String[] types = getTermsInScope(type); + fr.ap.alignFrame.hideFeatureColumns(false, types); } }); men.add(selCols); @@ -478,16 +521,6 @@ public class FeatureSettings extends JPanel men.show(table, x, y); } - /** - * true when Feature Settings are updating from feature renderer - */ - private boolean handlingUpdate = false; - - /** - * holds {featureCount, totalExtent} for each feature type - */ - Map typeWidth = null; - @Override synchronized public void discoverAllFeatureData() { @@ -549,8 +582,6 @@ public class FeatureSettings extends JPanel return visible; } - boolean resettingTable = false; - synchronized void resetTable(String[] groupChanged) { if (resettingTable) @@ -595,6 +626,7 @@ public class FeatureSettings extends JPanel */ Set types = seq.getFeatures().getFeatureTypesForGroups(true, visibleGroups.toArray(new String[visibleGroups.size()])); + for (String type : types) { displayableTypes.add(type); @@ -613,7 +645,14 @@ public class FeatureSettings extends JPanel } } - Object[][] data = new Object[displayableTypes.size()][3]; + /* + * enable 'Summary View' if some types are sub-types of others + */ + Set parents = SequenceOntologyFactory.getInstance() + .getParentTerms(displayableTypes); + summaryView.setEnabled(parents.size() < displayableTypes.size()); + + Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; int dataIndex = 0; if (fr.hasRenderOrder()) @@ -635,10 +674,13 @@ public class FeatureSettings extends JPanel { continue; } - - data[dataIndex][0] = type; - data[dataIndex][1] = fr.getFeatureStyle(type); - data[dataIndex][2] = new Boolean( + data[dataIndex][TYPE_COLUMN] = type; + data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new FeatureMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = new Boolean( af.getViewport().getFeaturesDisplayed().isVisible(type)); dataIndex++; displayableTypes.remove(type); @@ -652,27 +694,30 @@ public class FeatureSettings extends JPanel while (!displayableTypes.isEmpty()) { String type = displayableTypes.iterator().next(); - data[dataIndex][0] = type; + data[dataIndex][TYPE_COLUMN] = type; - data[dataIndex][1] = fr.getFeatureStyle(type); - if (data[dataIndex][1] == null) + data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); + if (data[dataIndex][COLOUR_COLUMN] == null) { // "Colour has been updated in another view!!" fr.clearRenderOrder(); return; } - - data[dataIndex][2] = new Boolean(true); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new FeatureMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = new Boolean(true); dataIndex++; displayableTypes.remove(type); } if (originalData == null) { - originalData = new Object[data.length][3]; + originalData = new Object[data.length][COLUMN_COUNT]; for (int i = 0; i < data.length; i++) { - System.arraycopy(data[i], 0, originalData[i], 0, 3); + System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); } } else @@ -680,7 +725,43 @@ public class FeatureSettings extends JPanel updateOriginalData(data); } - table.setModel(new FeatureTableModel(data)); + /* + * recreate the table model + */ + FeatureTableModel dataModel = new FeatureTableModel(data); + table.setModel(dataModel); + + /* + * we want to be able to filter out rows for sub-types, but not to sort + * rows, so have to add a RowFilter to a disabled TableRowSorter (!) + */ + final TableRowSorter sorter = new TableRowSorter<>( + dataModel); + for (int i = 0; i < table.getColumnCount(); i++) + { + sorter.setSortable(i, false); + } + + /* + * filter rows to only top-level Ontology types if requested + */ + sorter.setRowFilter(new RowFilter() + { + @Override + public boolean include( + Entry entry) + { + if (!summaryView.isSelected()) + { + return true; + } + int row = entry.getIdentifier(); // this is model, not view, row number + String featureType = (String) entry.getModel().getData()[row][TYPE_COLUMN]; + return parents.contains(featureType); + } + }); + table.setRowSorter(sorter); + table.getColumnModel().getColumn(0).setPreferredWidth(200); groupPanel.setLayout( @@ -693,8 +774,8 @@ 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)
    • @@ -710,27 +791,27 @@ public class FeatureSettings extends JPanel .getData(); for (Object[] row : foundData) { - String type = (String) row[0]; + String type = (String) row[TYPE_COLUMN]; boolean found = false; for (Object[] current : currentData) { - if (type.equals(current[0])) + if (type.equals(current[TYPE_COLUMN])) { found = true; /* * currently dependent on object equality here; * really need an equals method on FeatureColour */ - if (!row[1].equals(current[1])) + if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN])) { /* * feature colour has changed externally - update originalData */ for (Object[] original : originalData) { - if (type.equals(original[0])) + if (type.equals(original[TYPE_COLUMN])) { - original[1] = row[1]; + original[COLOUR_COLUMN] = row[COLOUR_COLUMN]; break; } } @@ -743,10 +824,12 @@ public class FeatureSettings extends JPanel /* * new feature detected - add to original data (on top) */ - Object[][] newData = new Object[originalData.length + 1][3]; + Object[][] newData = new Object[originalData.length + + 1][COLUMN_COUNT]; for (int i = 0; i < originalData.length; i++) { - System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3); + System.arraycopy(originalData[i], 0, newData[i + 1], 0, + COLUMN_COUNT); } newData[0] = row; originalData = newData; @@ -756,8 +839,8 @@ 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 */ @@ -800,10 +883,14 @@ public class FeatureSettings extends JPanel } } + /** + * Offers a file chooser dialog, and then loads the feature colours and + * filters from file in XML format and unmarshals to Jalview feature settings + */ 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")); @@ -814,88 +901,87 @@ 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"); + + 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.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()); + } - for (int i = jucs.getColourCount() - 1; i >= 0; 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()) { - String name; - jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); - if (newcol.hasMax()) - { - Color mincol = null, maxcol = null; - try - { - mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16)); - maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16)); + fr.setFeatureFilter(featureType, filter); + } + } - } catch (Exception e) - { - Cache.log.warn("Couldn't parse out graduated feature color.", - e); - } - FeatureColourI gcol = new FeatureColour(mincol, maxcol, - newcol.getMin(), newcol.getMax()); - if (newcol.hasAutoScale()) - { - gcol.setAutoScaled(newcol.getAutoScale()); - } - if (newcol.hasColourByLabel()) - { - gcol.setColourByLabel(newcol.getColourByLabel()); - } - if (newcol.hasThreshold()) - { - gcol.setThreshold(newcol.getThreshold()); - } - if (newcol.getThreshType().length() > 0) - { - String ttyp = newcol.getThreshType(); - if (ttyp.equalsIgnoreCase("ABOVE")) - { - gcol.setAboveThreshold(true); - } - if (ttyp.equalsIgnoreCase("BELOW")) - { - gcol.setBelowThreshold(true); - } - } - fr.setColour(name = newcol.getName(), gcol); - } - else - { - Color color = new Color( - Integer.parseInt(jucs.getColour(i).getRGB(), 16)); - fr.setColour(name = jucs.getColour(i).getName(), - new FeatureColour(color)); - } - fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); - } - if (table != null) - { - 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); + /* + * 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) + { + System.out.println("Error loading User Colour File\n" + ex); } } + /** + * Offers a file chooser dialog, and then saves the current feature colours + * and any filters to the selected file in XML format + */ 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")); @@ -905,68 +991,97 @@ public class FeatureSettings extends JPanel if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours(); - ucs.setSchemeName("Sequence Features"); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); + save(chooser.getSelectedFile()); + } + } + + /** + * 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")); - Set fr_colours = fr.getAllFeatureColours(); - Iterator e = fr_colours.iterator(); - float[] sortOrder = new float[fr_colours.size()]; - String[] sortTypes = new String[fr_colours.size()]; - int i = 0; - while (e.hasNext()) + /* + * 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) { - sortTypes[i] = e.next(); - sortOrder[i] = fr.getOrder(sortTypes[i]); - i++; + return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); } - QuickSort.sort(sortOrder, sortTypes); - sortOrder = null; - for (i = 0; i < sortTypes.length; i++) + }); + + /* + * save feature colours + */ + for (String featureType : sortedTypes) + { + FeatureColourI fcol = fr.getFeatureStyle(featureType); + Colour col = jalview.project.Jalview2XML.marshalColour(featureType, + fcol); + ucs.getColour().add(col); + } + + /* + * save any feature filters + */ + for (String featureType : sortedTypes) + { + FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); + if (filter != null && !filter.isEmpty()) { - jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); - col.setName(sortTypes[i]); - FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]); - 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() ? "ABOVE" - : (fcol.isBelowThreshold() ? "BELOW" : "NONE")); - } - ucs.addColour(col); + 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); } - ucs.marshal(out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); } + 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, 2); - - table.setValueAt(new Boolean(!value.booleanValue()), i, 2); + data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; } + updateFeatureRenderer(data, true); + table.repaint(); } public void orderByAvWidth() @@ -979,17 +1094,16 @@ public class FeatureSettings extends JPanel float[] width = new float[data.length]; float[] awidth; float max = 0; - int num = 0; + for (int i = 0; i < data.length; i++) { - awidth = typeWidth.get(data[i][0]); + awidth = typeWidth.get(data[i][TYPE_COLUMN]); if (awidth[0] > 0) { width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better // weight - but have to make per // sequence, too (awidth[2]) // if (width[i]==1) // hack to distinguish single width sequences. - num++; } else { @@ -1006,16 +1120,17 @@ public class FeatureSettings extends JPanel // awidth = (float[]) typeWidth.get(data[i][0]); if (width[i] == 0) { - width[i] = fr.getOrder(data[i][0].toString()); + width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString()); if (width[i] < 0) { - width[i] = fr.setOrder(data[i][0].toString(), i / data.length); + width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(), + i / data.length); } } else { width[i] /= max; // normalize - fr.setOrder(data[i][0].toString(), width[i]); // store for later + fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later } if (i > 0) { @@ -1049,76 +1164,56 @@ 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) { - if (fr.setFeaturePriority(data, visibleNew)) + FeatureSettingsBean[] rowData = getTableAsBeans(data); + + if (fr.setFeaturePriority(rowData, visibleNew)) { af.alignPanel.paintAlignment(true, true); } } - int selectedRow = -1; - - JTabbedPane tabbedPane = new JTabbedPane(); - - BorderLayout borderLayout1 = new BorderLayout(); - - BorderLayout borderLayout2 = new BorderLayout(); - - BorderLayout borderLayout3 = new BorderLayout(); - - JPanel bigPanel = new JPanel(); - - BorderLayout borderLayout4 = new BorderLayout(); - - JButton invert = new JButton(); - - JPanel buttonPanel = new JPanel(); - - JButton cancel = new JButton(); - - JButton ok = new JButton(); - - JButton loadColours = new JButton(); - - JButton saveColours = new JButton(); - - JPanel dasButtonPanel = new JPanel(); - - JButton fetchDAS = new JButton(); - - JButton saveDAS = new JButton(); - - JButton cancelDAS = new JButton(); - - JButton optimizeOrder = new JButton(); - - JButton sortByScore = new JButton(); - - JButton sortByDens = new JButton(); - - JButton help = new JButton(); - - JPanel transbuttons = new JPanel(new GridLayout(5, 1)); + /** + * Converts table data into an array of data beans + */ + private FeatureSettingsBean[] getTableAsBeans(Object[][] data) + { + FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; + for (int i = 0; i < data.length; i++) + { + String type = (String) data[i][TYPE_COLUMN]; + FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN]; + Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; + rowData[i] = new FeatureSettingsBean(type, colour, theFilter, + isShown); + } + return rowData; + } private void jbInit() throws Exception { - this.setLayout(borderLayout1); - settingsPane.setLayout(borderLayout2); - dasSettingsPane.setLayout(borderLayout3); - bigPanel.setLayout(borderLayout4); + this.setLayout(new BorderLayout()); + + JPanel settingsPane = new JPanel(); + settingsPane.setLayout(new BorderLayout()); + + JPanel bigPanel = new JPanel(); + bigPanel.setLayout(new BorderLayout()); groupPanel = new JPanel(); bigPanel.add(groupPanel, BorderLayout.NORTH); + JButton invert = new JButton( + MessageManager.getString("label.invert_selection")); invert.setFont(JvSwingUtils.getLabelFont()); - invert.setText(MessageManager.getString("label.invert_selection")); invert.addActionListener(new ActionListener() { @Override @@ -1127,8 +1222,10 @@ public class FeatureSettings extends JPanel invertSelection(); } }); + + JButton optimizeOrder = new JButton( + MessageManager.getString("label.optimise_order")); optimizeOrder.setFont(JvSwingUtils.getLabelFont()); - optimizeOrder.setText(MessageManager.getString("label.optimise_order")); optimizeOrder.addActionListener(new ActionListener() { @Override @@ -1137,9 +1234,10 @@ public class FeatureSettings extends JPanel orderByAvWidth(); } }); + + JButton sortByScore = new JButton( + MessageManager.getString("label.seq_sort_by_score")); sortByScore.setFont(JvSwingUtils.getLabelFont()); - sortByScore - .setText(MessageManager.getString("label.seq_sort_by_score")); sortByScore.addActionListener(new ActionListener() { @Override @@ -1148,9 +1246,9 @@ public class FeatureSettings extends JPanel af.avc.sortAlignmentByFeatureScore(null); } }); - sortByDens.setFont(JvSwingUtils.getLabelFont()); - sortByDens.setText( + JButton sortByDens = new JButton( MessageManager.getString("label.sequence_sort_by_density")); + sortByDens.setFont(JvSwingUtils.getLabelFont()); sortByDens.addActionListener(new ActionListener() { @Override @@ -1159,24 +1257,9 @@ public class FeatureSettings extends JPanel af.avc.sortAlignmentByFeatureDensity(null); } }); + + JButton help = new JButton(MessageManager.getString("action.help")); help.setFont(JvSwingUtils.getLabelFont()); - help.setText(MessageManager.getString("action.help")); - help.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - try - { - Help.showHelpWindow(HelpId.SequenceFeatureSettings); - } catch (HelpSetException e1) - { - e1.printStackTrace(); - } - } - }); - help.setFont(JvSwingUtils.getLabelFont()); - help.setText(MessageManager.getString("action.help")); help.addActionListener(new ActionListener() { @Override @@ -1191,20 +1274,23 @@ public class FeatureSettings extends JPanel } } }); + + JButton cancel = new JButton(MessageManager.getString("action.cancel")); cancel.setFont(JvSwingUtils.getLabelFont()); - cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { fr.setTransparency(originalTransparency); + fr.setFeatureFilters(originalFilters); updateFeatureRenderer(originalData); close(); } }); + + JButton ok = new JButton(MessageManager.getString("action.ok")); ok.setFont(JvSwingUtils.getLabelFont()); - ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { @Override @@ -1213,8 +1299,12 @@ public class FeatureSettings extends JPanel close(); } }); + + JButton loadColours = new JButton( + MessageManager.getString("label.load_colours")); loadColours.setFont(JvSwingUtils.getLabelFont()); - loadColours.setText(MessageManager.getString("label.load_colours")); + loadColours.setToolTipText( + MessageManager.getString("label.load_colours_tooltip")); loadColours.addActionListener(new ActionListener() { @Override @@ -1223,8 +1313,12 @@ public class FeatureSettings extends JPanel load(); } }); + + JButton saveColours = new JButton( + MessageManager.getString("label.save_colours")); saveColours.setFont(JvSwingUtils.getLabelFont()); - saveColours.setText(MessageManager.getString("label.save_colours")); + saveColours.setToolTipText( + MessageManager.getString("label.save_colours_tooltip")); saveColours.addActionListener(new ActionListener() { @Override @@ -1241,227 +1335,191 @@ public class FeatureSettings extends JPanel if (!inConstruction) { fr.setTransparency((100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true,true); + af.alignPanel.paintAlignment(true, true); } } }); - transparency.setMaximum(70); - transparency.setToolTipText( - MessageManager.getString("label.transparency_tip")); - fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); - fetchDAS.addActionListener(new ActionListener() + summaryView = new JCheckBox( + MessageManager.getString("label.summary_view")); + summaryView + .setToolTipText( + MessageManager.getString("label.summary_view_tip")); + summaryView.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - fetchDAS_actionPerformed(e); + resetTable(null); } }); - saveDAS.setText(MessageManager.getString("action.save_as_default")); - saveDAS.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - saveDAS_actionPerformed(e); - } - }); - 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); - } - }); - this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab(MessageManager.getString("label.feature_settings"), - settingsPane); - tabbedPane.addTab(MessageManager.getString("label.das_settings"), - dasSettingsPane); - bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); + + transparency.setMaximum(70); + transparency.setToolTipText( + MessageManager.getString("label.transparency_tip")); + + JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); + bigPanel.add(lowerPanel, BorderLayout.SOUTH); + + JPanel transbuttons = new JPanel(new GridLayout(5, 1)); transbuttons.add(optimizeOrder); transbuttons.add(invert); transbuttons.add(sortByScore); transbuttons.add(sortByDens); transbuttons.add(help); - JPanel sliderPanel = new JPanel(); - sliderPanel.add(transparency); + JPanel transPanel = new JPanel(new GridLayout(3, 1)); + transPanel.add(summaryView); + transPanel.add(new JLabel(" Colour transparency" + ":")); transPanel.add(transparency); - transPanel.add(transbuttons); + lowerPanel.add(transPanel); + lowerPanel.add(transbuttons); + + JPanel buttonPanel = new JPanel(); buttonPanel.add(ok); buttonPanel.add(cancel); buttonPanel.add(loadColours); buttonPanel.add(saveColours); - bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER); - dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); - dasButtonPanel.add(fetchDAS); - dasButtonPanel.add(cancelDAS); - dasButtonPanel.add(saveDAS); - settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER); - settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); - } - - public void fetchDAS_actionPerformed(ActionEvent e) - { - fetchDAS.setEnabled(false); - cancelDAS.setEnabled(true); - dassourceBrowser.setGuiEnabled(false); - Vector selectedSources = dassourceBrowser - .getSelectedSources(); - doDasFeatureFetch(selectedSources, true, true); + bigPanel.add(scrollPane, BorderLayout.CENTER); + settingsPane.add(bigPanel, BorderLayout.CENTER); + settingsPane.add(buttonPanel, BorderLayout.SOUTH); + this.add(settingsPane); } /** - * get the features from selectedSources for all or the current selection + * Reorders features by 'dragging' selectedRow to 'newRow' * - * @param selectedSources - * @param checkDbRefs - * @param promptFetchDbRefs + * @param newRow */ - private void doDasFeatureFetch(List selectedSources, - boolean checkDbRefs, boolean promptFetchDbRefs) + protected void dragRow(int newRow) { - SequenceI[] dataset, seqs; - int iSize; - AlignmentViewport vp = af.getViewport(); - if (vp.getSelectionGroup() != null - && vp.getSelectionGroup().getSize() > 0) + if (summaryView.isSelected()) { - iSize = vp.getSelectionGroup().getSize(); - dataset = new SequenceI[iSize]; - seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment()); - } - else - { - iSize = vp.getAlignment().getHeight(); - seqs = vp.getAlignment().getSequencesArray(); + // no drag while in summary view + return; } - dataset = new SequenceI[iSize]; - for (int i = 0; i < iSize; i++) + if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { - dataset[i] = seqs[i].getDatasetSequence(); + /* + * reposition 'selectedRow' to 'newRow' (the dragged to location) + * this could be more than one row away for a very fast drag action + * so just swap it with adjacent rows until we get it there + */ + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + int direction = newRow < selectedRow ? -1 : 1; + for (int i = selectedRow; i != newRow; i += direction) + { + Object[] temp = data[i]; + data[i] = data[i + direction]; + data[i + direction] = temp; + } + updateFeatureRenderer(data); + table.repaint(); + selectedRow = newRow; } - - 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) + protected void refreshTable() { - return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); + for (Object[] row : data) + { + String type = (String) row[TYPE_COLUMN]; + FeatureColourI colour = fr.getFeatureColours().get(type); + FeatureMatcherSetI filter = fr.getFeatureFilter(type); + if (filter == null) + { + filter = new FeatureMatcherSet(); + } + row[COLOUR_COLUMN] = colour; + row[FILTER_COLUMN] = filter; + } + repaint(); } - /** - * get currently selected das sources. ensure you have called initDasSources - * before calling this. + /* + * Answers a suitable tooltip to show on the colour cell of the table * - * @return vector of selected das source nicknames + * @param fcol + * @param withHint + * if true include 'click to edit' and similar text + * @return */ - public Vector getSelectedSources() + public static String getColorTooltip(FeatureColourI fcol, + boolean withHint) { - return dassourceBrowser.getSelectedSources(); + if (fcol == null) + { + return null; + } + if (fcol.isSimpleColour()) + { + return withHint ? BASE_TOOLTIP : null; + } + String description = fcol.getDescription(); + description = description.replaceAll("<", "<"); + description = description.replaceAll(">", ">"); + StringBuilder tt = new StringBuilder(description); + if (withHint) + { + tt.append("
    ").append(BASE_TOOLTIP).append("
    "); + } + return JvSwingUtils.wrapTooltip(true, tt.toString()); } - /** - * 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()); } // /////////////////////////////////////////////////////////////////////// @@ -1469,18 +1527,19 @@ public class FeatureSettings extends JPanel // /////////////////////////////////////////////////////////////////////// class FeatureTableModel extends AbstractTableModel { - FeatureTableModel(Object[][] data) - { - this.data = data; - } - private String[] columnNames = { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), - MessageManager.getString("label.display") }; + MessageManager.getString("label.configuration"), + MessageManager.getString("label.show") }; private Object[][] data; + FeatureTableModel(Object[][] data) + { + this.data = data; + } + public Object[][] getData() { return data; @@ -1520,35 +1579,83 @@ public class FeatureSettings extends JPanel return data[row][col]; } + /** + * Answers the class of column c of the table + */ @Override - public Class getColumnClass(int c) - { - return getValueAt(0, c).getClass(); + public Class getColumnClass(int c) + { + switch (c) + { + case TYPE_COLUMN: + return String.class; + case COLOUR_COLUMN: + return FeatureColour.class; + case FILTER_COLUMN: + return FeatureMatcherSet.class; + default: + return Boolean.class; + } } + /** + * Answers true for all columns except Feature Type + */ @Override public boolean isCellEditable(int row, int col) { - return col == 0 ? false : true; + return col != TYPE_COLUMN; } + /** + * Sets the value in the model for a given row and column. If Visibility + * (Show/Hide) is being set, and the table is in Summary View, then it is + * set also on any sub-types of the row's feature type. + */ @Override public void setValueAt(Object value, int row, int col) { data[row][col] = value; fireTableCellUpdated(row, col); + if (summaryView.isSelected() && col == SHOW_COLUMN) + { + setSubtypesVisibility(row, (Boolean) value); + } updateFeatureRenderer(data); } + /** + * Sets the visibility of any feature types which are sub-types of the type + * in the given row of the table + * + * @param row + * @param value + */ + protected void setSubtypesVisibility(int row, Boolean value) + { + String type = (String) data[row][TYPE_COLUMN]; + OntologyI so = SequenceOntologyFactory.getInstance(); + + for (int r = 0; r < data.length; r++) + { + if (r != row) + { + String type2 = (String) data[r][TYPE_COLUMN]; + if (so.isA(type2, type)) + { + data[r][SHOW_COLUMN] = value; + fireTableCellUpdated(r, SHOW_COLUMN); + } + } + } + } } 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() { @@ -1562,28 +1669,68 @@ public class FeatureSettings extends JPanel boolean isSelected, boolean hasFocus, int row, int column) { FeatureColourI cellColour = (FeatureColourI) color; - // JLabel comp = new JLabel(); - // comp. setOpaque(true); - // comp. - // setBounds(getBounds()); - Color newColor; - setToolTipText(baseTT); setBackground(tbl.getBackground()); if (!cellColour.isSimpleColour()) { Rectangle cr = tbl.getCellRect(row, column, false); FeatureSettings.renderGraduatedColor(this, cellColour, (int) cr.getWidth(), (int) cr.getHeight()); - } else { this.setText(""); this.setIcon(null); - newColor = cellColour.getColour(); - setBackground(newColor); + setBackground(cellColour.getColour()); + } + if (isSelected) + { + if (selectedBorder == null) + { + selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getSelectionBackground()); + } + setBorder(selectedBorder); } + else + { + if (unselectedBorder == null) + { + unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getBackground()); + } + setBorder(unselectedBorder); + } + + return this; + } + } + + class FilterRenderer extends JLabel implements TableCellRenderer + { + javax.swing.border.Border unselectedBorder = null; + + javax.swing.border.Border selectedBorder = null; + + public FilterRenderer() + { + setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); + } + + @Override + public Component getTableCellRendererComponent(JTable tbl, + Object filter, boolean isSelected, boolean hasFocus, int row, + int column) + { + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; + setOpaque(true); + String asText = theFilter.toString(); + setBackground(tbl.getBackground()); + this.setText(asText); + this.setIcon(null); + if (isSelected) { if (selectedBorder == null) @@ -1629,64 +1776,228 @@ public class FeatureSettings extends JPanel renderGraduatedColor(comp, gcol, w, h); } - public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, - int w, int h) + class ColorEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener { - boolean thr = false; - String tt = ""; - String tx = ""; - if (gcol.isAboveThreshold()) + FeatureSettings me; + + FeatureColourI currentColor; + + FeatureTypeSettings chooser; + + String type; + + JButton colourButton; + + JColorChooser colorChooser; + + JDialog dialog; + + protected static final String EDIT = "edit"; + + int rowSelected = 0; + + public ColorEditor(FeatureSettings me) { - thr = true; - tx += ">"; - tt += "Thresholded (Above " + gcol.getThreshold() + ") "; + 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, + // which is the editor from the user's point of view. + colourButton = new JButton(); + colourButton.setActionCommand(EDIT); + colourButton.addActionListener(this); + colourButton.setBorderPainted(false); + // Set up the dialog that the button brings up. + colorChooser = new JColorChooser(); + dialog = JColorChooser.createDialog(colourButton, + MessageManager.getString("label.select_colour"), true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler } - if (gcol.isBelowThreshold()) + + /** + * Handles events from the editor button and from the dialog's OK button. + */ + @Override + public void actionPerformed(ActionEvent e) { - thr = true; - tx += "<"; - tt += "Thresholded (Below " + gcol.getThreshold() + ") "; + // 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 + colourButton.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); + // 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 + */ + refreshTable(); + } + fireEditingStopped(); + me.table.validate(); + } } - if (gcol.isColourByLabel()) + + // Implement the one CellEditor method that AbstractCellEditor doesn't. + @Override + public Object getCellEditorValue() { - tt = "Coloured by label text. " + tt; - if (thr) + return currentColor; + } + + // Implement the one method defined by TableCellEditor. + @Override + 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(); + colourButton.setOpaque(true); + colourButton.setBackground(me.getBackground()); + if (!currentColor.isSimpleColour()) + { + JLabel btn = new JLabel(); + btn.setSize(colourButton.getSize()); + FeatureSettings.renderGraduatedColor(btn, currentColor); + colourButton.setBackground(btn.getBackground()); + colourButton.setIcon(btn.getIcon()); + colourButton.setText(btn.getText()); + } + else { - tx += " "; + colourButton.setText(""); + colourButton.setIcon(null); + colourButton.setBackground(currentColor.getColour()); } - tx += "Label"; - comp.setIcon(null); + return colourButton; } - else + } + + /** + * 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. + */ + class FilterEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener + { + FeatureSettings me; + + FeatureMatcherSetI currentFilter; + + Point lastLocation; + + String type; + + JButton filterButton; + + protected static final String EDIT = "edit"; + + int rowSelected = 0; + + public FilterEditor(FeatureSettings me) { - 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() + ")"); + this.me = me; + filterButton = new JButton(); + filterButton.setActionCommand(EDIT); + filterButton.addActionListener(this); + filterButton.setBorderPainted(false); } - comp.setHorizontalAlignment(SwingConstants.CENTER); - comp.setText(tx); - if (tt.length() > 0) + + /** + * Handles events from the editor button + */ + @Override + public void actionPerformed(ActionEvent e) { - if (comp.getToolTipText() == null) + if (filterButton == e.getSource()) { - comp.setToolTipText(tt); + FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type); + chooser.addActionListener(this); + chooser.setRequestFocusEnabled(true); + chooser.requestFocus(); + if (lastLocation != null) + { + // todo open at its last position on screen + chooser.setBounds(lastLocation.x, lastLocation.y, + chooser.getWidth(), chooser.getHeight()); + chooser.validate(); + } + fireEditingStopped(); } - else + else if (e.getSource() instanceof Component) { - comp.setToolTipText(tt + " " + comp.getToolTipText()); + /* + * after OK in variable colour dialog, any changes to filter + * (or colours!) are already set in FeatureRenderer, so just + * update table data without triggering updateFeatureRenderer + */ + refreshTable(); + fireEditingStopped(); + me.table.validate(); } } + + @Override + public Object getCellEditorValue() + { + return currentFilter; + } + + @Override + 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(); + filterButton.setOpaque(true); + filterButton.setBackground(me.getBackground()); + filterButton.setText(currentFilter.toString()); + filterButton.setToolTipText(currentFilter.toString()); + filterButton.setIcon(null); + return filterButton; + } } } class FeatureIcon implements Icon { + private static final Font VERDANA_9 = new Font("Verdana", Font.PLAIN, 9); + FeatureColourI gcol; Color backg; @@ -1741,7 +2052,7 @@ class FeatureIcon implements Icon // need an icon here. g.setColor(gcol.getMaxColour()); - g.setFont(new Font("Verdana", Font.PLAIN, 9)); + g.setFont(VERDANA_9); // g.setFont(g.getFont().deriveFont( // AffineTransform.getScaleInstance( @@ -1766,124 +2077,3 @@ class FeatureIcon implements Icon } } } - -class ColorEditor extends AbstractCellEditor - implements TableCellEditor, ActionListener -{ - FeatureSettings me; - - FeatureColourI currentColor; - - FeatureColourChooser chooser; - - String type; - - JButton button; - - JColorChooser colorChooser; - - JDialog dialog; - - protected static final String EDIT = "edit"; - - int selectedRow = 0; - - public ColorEditor(FeatureSettings me) - { - 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, - // which is the editor from the user's point of view. - button = new JButton(); - 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, "Select new 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. - */ - @Override - public void actionPerformed(ActionEvent e) - { - - 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 FeatureColourChooser(me.fr, type); - chooser.setRequestFocusEnabled(true); - chooser.requestFocus(); - chooser.addActionListener(this); - } - // Make the renderer reappear. - fireEditingStopped(); - - } - else - { // User pressed dialog's "OK" button. - if (currentColor.isSimpleColour()) - { - currentColor = new FeatureColour(colorChooser.getColor()); - } - else - { - currentColor = chooser.getLastColour(); - } - me.table.setValueAt(getCellEditorValue(), selectedRow, 1); - fireEditingStopped(); - me.table.validate(); - } - } - - // Implement the one CellEditor method that AbstractCellEditor doesn't. - @Override - public Object getCellEditorValue() - { - return currentColor; - } - - // Implement the one method defined by TableCellEditor. - @Override - public Component getTableCellEditorComponent(JTable table, Object value, - boolean isSelected, int row, int column) - { - currentColor = (FeatureColourI) value; - this.selectedRow = row; - type = me.table.getValueAt(row, 0).toString(); - button.setOpaque(true); - button.setBackground(me.getBackground()); - if (!currentColor.isSimpleColour()) - { - JLabel btn = new JLabel(); - btn.setSize(button.getSize()); - FeatureSettings.renderGraduatedColor(btn, currentColor); - button.setBackground(btn.getBackground()); - button.setIcon(btn.getIcon()); - button.setText(btn.getText()); - } - else - { - button.setText(""); - button.setIcon(null); - button.setBackground(currentColor.getColour()); - } - return button; - } -}