/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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.FeatureAttributes; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemabinding.version2.JalviewUserColours; import jalview.schemes.FeatureColour; import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.QuickSort; import jalview.util.ReverseListIterator; import jalview.util.matcher.Condition; import jalview.util.matcher.KeyedMatcher; import jalview.util.matcher.KeyedMatcherI; import jalview.util.matcher.KeyedMatcherSet; import jalview.util.matcher.KeyedMatcherSetI; import jalview.viewmodel.AlignmentViewport; import jalview.ws.DasSequenceFeatureFetcher; import jalview.ws.dbsources.das.api.jalviewSourceI; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.Font; import java.awt.Graphics; import java.awt.GridLayout; import java.awt.LayoutManager; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.MouseMotionAdapter; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileInputStream; 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.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; import javax.swing.BorderFactory; import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JDialog; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.JSlider; import javax.swing.JTabbedPane; import javax.swing.JTable; import javax.swing.JTextArea; import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; import javax.swing.SwingUtilities; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.plaf.basic.BasicArrowButton; import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; public class FeatureSettings extends JPanel implements FeatureSettingsControllerI { private static final String COLON = ":"; private static final int MIN_WIDTH = 400; private static final int MIN_HEIGHT = 400; private static final int MAX_TOOLTIP_LENGTH = 50; DasSourceBrowser dassourceBrowser; DasSequenceFeatureFetcher dasFeatureFetcher; JPanel dasSettingsPane = new JPanel(); 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(); JTable table; JPanel groupPanel; JSlider transparency = new JSlider(); /* * when true, constructor is still executing - so ignore UI events */ protected volatile boolean inConstruction = true; int selectedRow = -1; JButton fetchDAS = new JButton(); JButton saveDAS = new JButton(); JButton cancelDAS = new JButton(); boolean resettingTable = false; /* * true when Feature Settings are updating from feature renderer */ private boolean handlingUpdate = false; /* * holds {featureCount, totalExtent} for each feature type */ Map typeWidth = null; /* * fields of the feature filters tab */ private JPanel filtersPane; private JPanel chooseFiltersPanel; private JComboBox filteredFeatureChoice; private JRadioButton andFilters; private JRadioButton orFilters; /* * filters for the currently selected feature type */ private List filters; private JTextArea filtersAsText; // set white normally, black to debug layout private Color debugBorderColour = Color.white; /** * Constructor * * @param af */ public FeatureSettings(AlignFrame alignFrame) { this.af = alignFrame; fr = af.getFeatureRenderer(); // save transparency for restore on Cancel originalTransparency = fr.getTransparency(); int originalTransparencyAsPercent = (int) (originalTransparency * 100); transparency.setMaximum(100 - originalTransparencyAsPercent); originalFilters = fr.getFeatureFilters(); try { jbInit(); } catch (Exception ex) { ex.printStackTrace(); } table = new JTable() { @Override public String getToolTipText(MouseEvent e) { if (table.columnAtPoint(e.getPoint()) == 0) { /* * Tooltip for feature name only */ return JvSwingUtils.wrapTooltip(true, MessageManager .getString("label.feature_settings_click_drag")); } return null; } }; 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)); table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent evt) { 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()); } else if (evt.getClickCount() == 2) { boolean invertSelection = evt.isAltDown(); boolean toggleSelection = Platform.isControlDown(evt); boolean extendSelection = evt.isShiftDown(); fr.ap.alignFrame.avc.markColumnsContainingFeatures( invertSelection, extendSelection, toggleSelection, (String) table.getValueAt(selectedRow, 0)); } } // isPopupTrigger fires on mouseReleased on Windows @Override public void mouseReleased(MouseEvent evt) { 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()); } } }); table.addMouseMotionListener(new MouseMotionAdapter() { @Override 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; } } }); // 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()) { 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 seuqence // 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); dassourceBrowser.fs = null; }; }); frame.setLayer(JLayeredPane.PALETTE_LAYER); inConstruction = false; } protected void popupSort(final int selectedRow, final String type, final Object typeCol, final Map minmax, int x, int y) { final FeatureColourI featureColour = (FeatureColourI) typeCol; JPopupMenu men = new JPopupMenu(MessageManager .formatMessage("label.settings_for_param", new String[] { type })); JMenuItem scr = new JMenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); final FeatureSettings me = this; scr.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { me.af.avc .sortAlignmentByFeatureScore(Arrays.asList(new String[] { type })); } }); JMenuItem dens = new JMenuItem( MessageManager.getString("label.sort_by_density")); dens.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { me.af.avc .sortAlignmentByFeatureDensity(Arrays.asList(new String[] { type })); } }); men.add(dens); /* * variable colour options include colour by label, by score, * by selected attribute text, or attribute value */ final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( MessageManager.getString("label.variable_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() { @Override public void actionPerformed(ActionEvent arg0) { fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, false, type); } }); JMenuItem clearCols = new JMenuItem(MessageManager .getString("label.select_columns_not_containing")); clearCols.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, false, type); } }); JMenuItem hideCols = new JMenuItem( MessageManager.getString("label.hide_columns_containing")); hideCols.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { fr.ap.alignFrame.hideFeatureColumns(type, true); } }); JMenuItem hideOtherCols = new JMenuItem( MessageManager.getString("label.hide_columns_not_containing")); hideOtherCols.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { fr.ap.alignFrame.hideFeatureColumns(type, false); } }); men.add(selCols); men.add(clearCols); men.add(hideCols); men.add(hideOtherCols); men.show(table, x, y); } @Override synchronized public void discoverAllFeatureData() { Set allGroups = new HashSet<>(); AlignmentI alignment = af.getViewport().getAlignment(); for (int i = 0; i < alignment.getHeight(); i++) { SequenceI seq = alignment.getSequenceAt(i); for (String group : seq.getFeatures().getFeatureGroups(true)) { if (group != null && !allGroups.contains(group)) { allGroups.add(group); checkGroupState(group); } } } populateFilterableFeatures(); resetTable(null); validate(); } /** * Synchronise gui group list and check visibility of group * * @param group * @return true if group is visible */ private boolean checkGroupState(String group) { boolean visible = fr.checkGroupVisibility(group, true); for (int g = 0; g < groupPanel.getComponentCount(); g++) { if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) { ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); return visible; } } final String grp = group; final JCheckBox check = new JCheckBox(group, visible); check.setFont(new Font("Serif", Font.BOLD, 12)); check.setToolTipText(group); check.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent evt) { fr.setGroupVisibility(check.getText(), check.isSelected()); resetTable(new String[] { grp }); af.alignPanel.paintAlignment(true, true); } }); groupPanel.add(check); return visible; } synchronized void resetTable(String[] groupChanged) { if (resettingTable) { return; } resettingTable = true; typeWidth = new Hashtable<>(); // TODO: change avWidth calculation to 'per-sequence' average and use long // rather than float Set displayableTypes = new HashSet<>(); Set foundGroups = new HashSet<>(); /* * determine which feature types may be visible depending on * which groups are selected, and recompute average width data */ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); /* * get the sequence's groups for positional features * and keep track of which groups are visible */ Set groups = seq.getFeatures().getFeatureGroups(true); Set visibleGroups = new HashSet<>(); for (String group : groups) { if (group == null || checkGroupState(group)) { visibleGroups.add(group); } } foundGroups.addAll(groups); /* * get distinct feature types for visible groups * record distinct visible types, and their count and total length */ Set types = seq.getFeatures().getFeatureTypesForGroups(true, visibleGroups.toArray(new String[visibleGroups.size()])); for (String type : types) { displayableTypes.add(type); float[] avWidth = typeWidth.get(type); if (avWidth == null) { avWidth = new float[2]; typeWidth.put(type, avWidth); } // todo this could include features with a non-visible group // - do we greatly care? // todo should we include non-displayable features here, and only // update when features are added? avWidth[0] += seq.getFeatures().getFeatureCount(true, type); avWidth[1] += seq.getFeatures().getTotalFeatureLength(type); } } Object[][] data = new Object[displayableTypes.size()][3]; int dataIndex = 0; if (fr.hasRenderOrder()) { if (!handlingUpdate) { fr.findAllFeatures(groupChanged != null); // prod to update // colourschemes. but don't // affect display // First add the checks in the previous render order, // in case the window has been closed and reopened } List frl = fr.getRenderOrder(); for (int ro = frl.size() - 1; ro > -1; ro--) { String type = frl.get(ro); if (!displayableTypes.contains(type)) { continue; } data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); data[dataIndex][2] = new Boolean( af.getViewport().getFeaturesDisplayed().isVisible(type)); dataIndex++; displayableTypes.remove(type); } } /* * process any extra features belonging only to * a group which was just selected */ while (!displayableTypes.isEmpty()) { String type = displayableTypes.iterator().next(); data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); if (data[dataIndex][1] == null) { // "Colour has been updated in another view!!" fr.clearRenderOrder(); return; } data[dataIndex][2] = new Boolean(true); dataIndex++; displayableTypes.remove(type); } if (originalData == null) { originalData = new Object[data.length][3]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, originalData[i], 0, 3); } } else { updateOriginalData(data); } table.setModel(new FeatureTableModel(data)); table.getColumnModel().getColumn(0).setPreferredWidth(200); groupPanel.setLayout( new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); pruneGroups(foundGroups); groupPanel.validate(); updateFeatureRenderer(data, groupChanged != null); resettingTable = false; } /** * 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)
  • *
* * @param foundData */ protected void updateOriginalData(Object[][] foundData) { // todo LinkedHashMap instead of Object[][] would be nice Object[][] currentData = ((FeatureTableModel) table.getModel()) .getData(); for (Object[] row : foundData) { String type = (String) row[0]; boolean found = false; for (Object[] current : currentData) { if (type.equals(current[0])) { found = true; /* * currently dependent on object equality here; * really need an equals method on FeatureColour */ if (!row[1].equals(current[1])) { /* * feature colour has changed externally - update originalData */ for (Object[] original : originalData) { if (type.equals(original[0])) { original[1] = row[1]; break; } } } break; } } if (!found) { /* * new feature detected - add to original data (on top) */ Object[][] newData = new Object[originalData.length + 1][3]; for (int i = 0; i < originalData.length; i++) { System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3); } newData[0] = row; originalData = newData; } } } /** * 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. * * @param foundGroups */ protected void pruneGroups(Set foundGroups) { for (int g = 0; g < groupPanel.getComponentCount(); g++) { JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); if (!foundGroups.contains(checkbox.getText())) { groupPanel.remove(checkbox); } } } /** * reorder data based on the featureRenderers global priority list. * * @param data */ private void ensureOrder(Object[][] data) { boolean sort = false; float[] order = new float[data.length]; for (int i = 0; i < order.length; i++) { order[i] = fr.getOrder(data[i][0].toString()); if (order[i] < 0) { order[i] = fr.setOrder(data[i][0].toString(), i / order.length); } if (i > 1) { sort = sort || order[i - 1] > order[i]; } } if (sort) { jalview.util.QuickSort.sort(order, data); } } void load() { JalviewFileChooser chooser = new JalviewFileChooser("fc", "Sequence Feature Colours"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); try { InputStreamReader in = new InputStreamReader( new FileInputStream(file), "UTF-8"); JalviewUserColours jucs = JalviewUserColours.unmarshal(in); for (int i = jucs.getColourCount() - 1; i >= 0; i--) { 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)); } 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); } } } void save() { JalviewFileChooser chooser = new JalviewFileChooser("fc", "Sequence Feature Colours"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.save_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); 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")); 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()) { sortTypes[i] = e.next(); sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } QuickSort.sort(sortOrder, sortTypes); sortOrder = null; for (i = 0; i < sortTypes.length; i++) { 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); } ucs.marshal(out); out.close(); } catch (Exception ex) { ex.printStackTrace(); } } } public void invertSelection() { for (int i = 0; i < table.getRowCount(); i++) { Boolean value = (Boolean) table.getValueAt(i, 2); table.setValueAt(new Boolean(!value.booleanValue()), i, 2); } } public void orderByAvWidth() { if (table == null || table.getModel() == null) { return; } Object[][] data = ((FeatureTableModel) table.getModel()).getData(); 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]); 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 { width[i] = 0; } if (max < width[i]) { max = width[i]; } } boolean sort = false; for (int i = 0; i < width.length; i++) { // awidth = (float[]) typeWidth.get(data[i][0]); if (width[i] == 0) { width[i] = fr.getOrder(data[i][0].toString()); if (width[i] < 0) { width[i] = fr.setOrder(data[i][0].toString(), i / data.length); } } else { width[i] /= max; // normalize fr.setOrder(data[i][0].toString(), width[i]); // store for later } if (i > 0) { sort = sort || width[i - 1] > width[i]; } } if (sort) { jalview.util.QuickSort.sort(width, data); // update global priority order } updateFeatureRenderer(data, false); table.repaint(); } public void close() { try { frame.setClosed(true); } catch (Exception exe) { } } public void updateFeatureRenderer(Object[][] data) { updateFeatureRenderer(data, true); } /** * 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)) { af.alignPanel.paintAlignment(true, true); } } private void jbInit() throws Exception { this.setLayout(new BorderLayout()); JPanel settingsPane = new JPanel(); settingsPane.setLayout(new BorderLayout()); filtersPane = new JPanel(); dasSettingsPane.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.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { invertSelection(); } }); JButton optimizeOrder = new JButton( MessageManager.getString("label.optimise_order")); optimizeOrder.setFont(JvSwingUtils.getLabelFont()); optimizeOrder.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { orderByAvWidth(); } }); JButton sortByScore = new JButton( MessageManager.getString("label.seq_sort_by_score")); sortByScore.setFont(JvSwingUtils.getLabelFont()); sortByScore.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureScore(null); } }); JButton sortByDens = new JButton( MessageManager.getString("label.sequence_sort_by_density")); sortByDens.setFont(JvSwingUtils.getLabelFont()); sortByDens.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureDensity(null); } }); JButton help = new JButton(MessageManager.getString("action.help")); help.setFont(JvSwingUtils.getLabelFont()); help.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { try { Help.showHelpWindow(HelpId.SequenceFeatureSettings); } catch (HelpSetException e1) { e1.printStackTrace(); } } }); 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(); } } }); JButton cancel = new JButton(MessageManager.getString("action.cancel")); cancel.setFont(JvSwingUtils.getLabelFont()); 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.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { close(); } }); JButton loadColours = new JButton( MessageManager.getString("label.load_colours")); loadColours.setFont(JvSwingUtils.getLabelFont()); loadColours.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { load(); } }); JButton saveColours = new JButton( MessageManager.getString("label.save_colours")); saveColours.setFont(JvSwingUtils.getLabelFont()); saveColours.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { save(); } }); transparency.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { if (!inConstruction) { fr.setTransparency((100 - transparency.getValue()) / 100f); 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() { @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); } }); JTabbedPane tabbedPane = new JTabbedPane(); this.add(tabbedPane, BorderLayout.CENTER); tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane); tabbedPane.addTab(MessageManager.getString("label.filters"), filtersPane); // tabbedPane.addTab(MessageManager.getString("label.das_settings"), // dasSettingsPane); JPanel transPanel = new JPanel(new GridLayout(1, 2)); bigPanel.add(transPanel, 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); transPanel.add(transparency); transPanel.add(transbuttons); JPanel buttonPanel = new JPanel(); buttonPanel.add(ok); buttonPanel.add(cancel); 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); initFiltersTab(); } /** * Populates initial layout of the feature attribute filters panel */ protected void initFiltersTab() { filters = new ArrayList<>(); /* * choose feature type */ JPanel chooseTypePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); chooseTypePanel.setBackground(Color.white); JvSwingUtils.createItalicTitledBorder(chooseTypePanel, MessageManager.getString("label.feature_type"), true); filteredFeatureChoice = new JComboBox<>(); filteredFeatureChoice.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { refreshFiltersDisplay(); } }); chooseTypePanel.add(new JLabel(MessageManager .getString("label.feature_to_filter"))); chooseTypePanel.add(filteredFeatureChoice); populateFilterableFeatures(); /* * the panel with the filters for the selected feature type */ JPanel filtersPanel = new JPanel(); filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS)); filtersPanel.setBackground(Color.white); JvSwingUtils.createItalicTitledBorder(filtersPanel, MessageManager.getString("label.filters"), true); /* * add AND or OR radio buttons */ JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); andOrPanel.setBackground(Color.white); andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour)); andFilters = new JRadioButton("And"); orFilters = new JRadioButton("Or"); ActionListener actionListener = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { filtersChanged(); } }; andFilters.addActionListener(actionListener); orFilters.addActionListener(actionListener); ButtonGroup andOr = new ButtonGroup(); andOr.add(andFilters); andOr.add(orFilters); andFilters.setSelected(true); andOrPanel.add(new JLabel(MessageManager .getString("label.join_conditions"))); andOrPanel.add(andFilters); andOrPanel.add(orFilters); filtersPanel.add(andOrPanel); /* * panel with filters - populated by refreshFiltersDisplay */ chooseFiltersPanel = new JPanel(); LayoutManager box = new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS); chooseFiltersPanel.setLayout(box); filtersPanel.add(chooseFiltersPanel); /* * a read-only text view of the current filters */ JPanel showFiltersPanel = new JPanel(new BorderLayout(5, 5)); showFiltersPanel.setBackground(Color.white); JvSwingUtils.createItalicTitledBorder(showFiltersPanel, MessageManager.getString("label.match_condition"), true); filtersAsText = new JTextArea(); filtersAsText.setLineWrap(true); filtersAsText.setWrapStyleWord(true); filtersAsText.setEnabled(false); // for display only showFiltersPanel.add(filtersAsText); filtersPane.setLayout(new BorderLayout()); filtersPane.add(chooseTypePanel, BorderLayout.NORTH); filtersPane.add(filtersPanel, BorderLayout.CENTER); filtersPane.add(showFiltersPanel, BorderLayout.SOUTH); /* * update display for initial feature type selection */ refreshFiltersDisplay(); } /** * Adds entries to the 'choose feature to filter' drop-down choice. Only * feature types which have known attributes (so can be filtered) are * included, so recall this method to update the list (check for newly added * attributes). */ protected void populateFilterableFeatures() { /* * suppress action handler while updating the list */ ItemListener listener = filteredFeatureChoice.getItemListeners()[0]; filteredFeatureChoice.removeItemListener(listener); filteredFeatureChoice.removeAllItems(); ReverseListIterator types = new ReverseListIterator<>( fr.getRenderOrder()); boolean found = false; while (types.hasNext()) { String type = types.next(); if (FeatureAttributes.getInstance().hasAttributes(type)) { filteredFeatureChoice.addItem(type); found = true; } } if (!found) { filteredFeatureChoice.addItem(MessageManager .getString("label.no_feature_attributes")); filteredFeatureChoice.setEnabled(false); } filteredFeatureChoice.addItemListener(listener); } /** * Refreshes the display to show any filters currently configured for the * selected feature type (editable, with 'remove' option), plus one extra row * for adding a condition. This should be called on change of selected feature * type, or after a filter has been removed, added or amended. */ protected void refreshFiltersDisplay() { /* * clear the panel and list of filter conditions */ chooseFiltersPanel.removeAll(); filters.clear(); /* * look up attributes known for feature type */ String selectedType = (String) filteredFeatureChoice.getSelectedItem(); List attNames = FeatureAttributes.getInstance() .getAttributes(selectedType); /* * if this feature type has filters set, load them first */ KeyedMatcherSetI featureFilters = fr.getFeatureFilter(selectedType); filtersAsText.setText(""); if (featureFilters != null) { filtersAsText.setText(featureFilters.toString()); if (!featureFilters.isAnded()) { orFilters.setSelected(true); } featureFilters.getMatchers().forEach(matcher -> filters.add(matcher)); } /* * and an empty filter for the user to populate (add) */ KeyedMatcherI noFilter = new KeyedMatcher(Condition.values()[0], "", (String) null); filters.add(noFilter); /* * render the conditions in rows, each in its own JPanel */ int filterIndex = 0; for (KeyedMatcherI filter : filters) { String[] attName = filter.getKey(); Condition condition = filter.getMatcher() .getCondition(); String pattern = filter.getMatcher().getPattern(); JPanel row = addFilter(attName, attNames, condition, pattern, filterIndex); row.setBorder(BorderFactory.createLineBorder(debugBorderColour)); chooseFiltersPanel.add(row); filterIndex++; } // chooseFiltersPanel.add(Box.createVerticalGlue()); filtersPane.validate(); filtersPane.repaint(); } /** * A helper method that constructs a panel with one filter condition: *
    *
  • a drop-down list of attribute names to choose from
  • *
  • a drop-down list of conditions to choose from
  • *
  • a text field for input of a match pattern
  • *
  • optionally, a 'remove' button
  • *
* If attribute, condition or pattern are not null, they are set as defaults for * the input fields. The 'remove' button is added unless the pattern is null or * empty (incomplete filter condition). * * @param attName * @param attNames * @param cond * @param pattern * @param filterIndex * @return */ protected JPanel addFilter(String[] attName, List attNames, Condition cond, String pattern, int filterIndex) { JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT)); filterRow.setBackground(Color.white); /* * drop-down choice of attribute, with description as a tooltip * if we can obtain it */ String featureType = (String) filteredFeatureChoice.getSelectedItem(); final JComboBox attCombo = populateAttributesDropdown( featureType, attNames); JComboBox condCombo = new JComboBox<>(); JTextField patternField = new JTextField(8); /* * action handlers that validate and (if valid) apply changes */ ActionListener actionListener = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (attCombo.getSelectedItem() != null) { if (validateFilter(patternField, condCombo)) { updateFilter(attCombo, condCombo, patternField, filterIndex); filtersChanged(); } } } }; ItemListener itemListener = new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { actionListener.actionPerformed(null); } }; if (attName == null) // the 'add a condition' row { attCombo.setSelectedItem(null); } else { attCombo.setSelectedItem(String.join(COLON, attName)); } attCombo.addItemListener(itemListener); filterRow.add(attCombo); /* * drop-down choice of test condition */ for (Condition c : Condition.values()) { condCombo.addItem(c); } if (cond != null) { condCombo.setSelectedItem(cond); } condCombo.addItemListener(itemListener); filterRow.add(condCombo); /* * pattern to match against */ patternField.setText(pattern); patternField.addActionListener(actionListener); patternField.addFocusListener(new FocusAdapter() { @Override public void focusLost(FocusEvent e) { actionListener.actionPerformed(null); } }); filterRow.add(patternField); /* * add remove button if filter is populated (non-empty pattern) */ if (pattern != null && pattern.trim().length() > 0) { // todo: gif for button drawing '-' or 'x' JButton removeCondition = new BasicArrowButton(SwingConstants.WEST); removeCondition.setToolTipText(MessageManager .getString("label.delete_row")); removeCondition.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { filters.remove(filterIndex); filtersChanged(); } }); filterRow.add(removeCondition); } return filterRow; } /** * A helper method to build the drop-down choice of attributes for a feature. * Where metadata is available with a description for an attribute, that is * added as a tooltip. * * @param featureType * @param attNames */ protected JComboBox populateAttributesDropdown( String featureType, List attNames) { List displayNames = new ArrayList<>(); List tooltips = new ArrayList<>(); FeatureAttributes fa = FeatureAttributes.getInstance(); for (String[] attName : attNames) { String desc = fa.getDescription(featureType, attName); if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH) { desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "..."; } displayNames.add(String.join(COLON, attName)); tooltips.add(desc == null ? "" : desc); } JComboBox attCombo = JvSwingUtils.buildComboWithTooltips( displayNames, tooltips); if (attNames.isEmpty()) { attCombo.setToolTipText(MessageManager .getString("label.no_attributes")); } return attCombo; } /** * Action on any change to feature filtering, namely *
    *
  • change of selected attribute
  • *
  • change of selected condition
  • *
  • change of match pattern
  • *
  • removal of a condition
  • *
* The action should be to *
    *
  • parse and validate the filters
  • *
  • if valid, update the filter text box
  • *
  • and apply the filters to the viewport
  • *
*/ protected void filtersChanged() { /* * update the filter conditions for the feature type */ String featureType = (String) filteredFeatureChoice.getSelectedItem(); boolean anded = andFilters.isSelected(); KeyedMatcherSetI combined = new KeyedMatcherSet(); for (KeyedMatcherI filter : filters) { String pattern = filter.getMatcher().getPattern(); if (pattern.trim().length() > 0) { if (anded) { combined.and(filter); } else { combined.or(filter); } } } /* * save the filter conditions in the FeatureRenderer * (note this might now be an empty filter with no conditions) */ fr.setFeatureFilter(featureType, combined); filtersAsText.setText(combined.toString()); refreshFiltersDisplay(); af.alignPanel.paintAlignment(true, true); } /** * Constructs a filter condition from the given input fields, and replaces the * condition at filterIndex with the new one * * @param attCombo * @param condCombo * @param valueField * @param filterIndex */ protected void updateFilter(JComboBox attCombo, JComboBox condCombo, JTextField valueField, int filterIndex) { String attName = (String) attCombo.getSelectedItem(); Condition cond = (Condition) condCombo.getSelectedItem(); String pattern = valueField.getText(); KeyedMatcherI km = new KeyedMatcher(cond, pattern, attName.split(COLON)); filters.set(filterIndex, km); } 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 * * @param selectedSources * @param checkDbRefs * @param promptFetchDbRefs */ private void doDasFeatureFetch(List selectedSources, boolean checkDbRefs, boolean promptFetchDbRefs) { 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 { iSize = vp.getAlignment().getHeight(); seqs = vp.getAlignment().getSequencesArray(); } dataset = new SequenceI[iSize]; for (int i = 0; i < iSize; i++) { dataset[i] = seqs[i].getDatasetSequence(); } cancelDAS.setEnabled(true); dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, this, selectedSources, checkDbRefs, promptFetchDbRefs); af.getViewport().setShowSequenceFeatures(true); af.showSeqFeatures.setSelected(true); } /** * blocking call to initialise the das source browser */ public void initDasSources() { dassourceBrowser.initDasSources(); } /** * examine the current list of das sources and return any matching the given * nicknames in sources * * @param sources * Vector of Strings to resolve to DAS source nicknames. * @return sources that are present in source list. */ public List resolveSourceNicknames(Vector sources) { return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); } /** * get currently selected das sources. ensure you have called initDasSources * before calling this. * * @return vector of selected das source nicknames */ public Vector getSelectedSources() { return dassourceBrowser.getSelectedSources(); } /** * 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) { initDasSources(); List resolved = dassourceBrowser.sourceRegistry .resolveSourceNicknames(sources); if (resolved.size() == 0) { resolved = dassourceBrowser.getSelectedSources(); } if (resolved.size() > 0) { 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) { fetcher.run(); } else { SwingUtilities.invokeLater(fetcher); } } } 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) { dasFeatureFetcher.cancel(); } 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); } /** * Answers true unless a numeric condition has been selected with a * non-numeric value. Sets the value field to RED with a tooltip if in error. *

* If the pattern entered is empty, this method returns false, but does not * mark the field as invalid. This supports selecting an attribute for a new * condition before a match pattern has been entered. * * @param value * @param condCombo */ protected boolean validateFilter(JTextField value, JComboBox condCombo) { if (value == null || condCombo == null) { return true; // fields not populated } Condition cond = (Condition) condCombo.getSelectedItem(); value.setBackground(Color.white); value.setToolTipText(""); String v1 = value.getText().trim(); if (v1.length() == 0) { return false; } if (cond.isNumeric()) { try { Float.valueOf(v1); } catch (NumberFormatException e) { value.setBackground(Color.red); value.setToolTipText(MessageManager .getString("label.numeric_required")); return false; } } return true; } // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html // /////////////////////////////////////////////////////////////////////// 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") }; private Object[][] data; public Object[][] getData() { return data; } public void setData(Object[][] data) { this.data = data; } @Override public int getColumnCount() { return columnNames.length; } public Object[] getRow(int row) { return data[row]; } @Override public int getRowCount() { return data.length; } @Override public String getColumnName(int col) { return columnNames[col]; } @Override public Object getValueAt(int row, int col) { return data[row][col]; } @Override public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } @Override public boolean isCellEditable(int row, int col) { return col == 0 ? false : true; } @Override public void setValueAt(Object value, int row, int col) { data[row][col] = value; fireTableCellUpdated(row, col); updateFeatureRenderer(data); } } class ColorRenderer extends JLabel implements TableCellRenderer { javax.swing.border.Border unselectedBorder = null; javax.swing.border.Border selectedBorder = null; final String baseTT = "Click to edit, right/apple click for menu."; public ColorRenderer() { setOpaque(true); // MUST do this for background to show up. setHorizontalTextPosition(SwingConstants.CENTER); setVerticalTextPosition(SwingConstants.CENTER); } @Override public Component getTableCellRendererComponent(JTable tbl, Object color, boolean isSelected, boolean hasFocus, int row, int column) { FeatureColourI cellColour = (FeatureColourI) color; setOpaque(true); 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); 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; } } /** * update comp using rendering settings from gcol * * @param comp * @param gcol */ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol) { int w = comp.getWidth(), h = comp.getHeight(); if (w < 20) { w = (int) comp.getPreferredSize().getWidth(); h = (int) comp.getPreferredSize().getHeight(); if (w < 20) { w = 80; h = 12; } } 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 FeatureIcon implements Icon { FeatureColourI gcol; Color backg; boolean midspace = false; int width = 50, height = 20; int s1, e1; // start and end of midpoint band for thresholded symbol Color mpcolour = Color.white; FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace) { gcol = gfc; backg = bg; width = w; height = h; midspace = mspace; if (midspace) { s1 = width / 3; e1 = s1 * 2; } else { s1 = width / 2; e1 = s1; } } @Override public int getIconWidth() { return width; } @Override public int getIconHeight() { return height; } @Override public void paintIcon(Component c, Graphics g, int x, int y) { if (gcol.isColourByLabel()) { g.setColor(backg); g.fillRect(0, 0, width, height); // need an icon here. g.setColor(gcol.getMaxColour()); g.setFont(new Font("Verdana", Font.PLAIN, 9)); // g.setFont(g.getFont().deriveFont( // AffineTransform.getScaleInstance( // width/g.getFontMetrics().stringWidth("Label"), // height/g.getFontMetrics().getHeight()))); g.drawString(MessageManager.getString("label.label"), 0, 0); } else { Color minCol = gcol.getMinColour(); g.setColor(minCol); g.fillRect(0, 0, s1, height); if (midspace) { g.setColor(Color.white); g.fillRect(s1, 0, e1 - s1, height); } g.setColor(gcol.getMaxColour()); g.fillRect(0, e1, width - e1, height); } } } 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, MessageManager.getString("label.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; } }