/* * 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.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.datamodel.features.FeatureMatcherI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemabinding.version2.Filter; import jalview.schemabinding.version2.JalviewUserColours; import jalview.schemabinding.version2.MatcherSet; import jalview.schemes.FeatureColour; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; 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; 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.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 javax.help.HelpSetException; import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JColorChooser; import javax.swing.JDialog; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JScrollPane; import javax.swing.JSlider; import javax.swing.JTable; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; import javax.swing.table.TableColumn; public class FeatureSettings extends JPanel implements FeatureSettingsControllerI { private static final String SEQUENCE_FEATURE_COLOURS = MessageManager .getString("label.sequence_feature_colours"); /* * column indices of fields in Feature Settings table */ 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; 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; /** * 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 = new HashMap<>(fr.getFeatureFilters()); // shallow copy try { jbInit(); } catch (Exception ex) { ex.printStackTrace(); } table = new JTable() { @Override public String getToolTipText(MouseEvent e) { String tip = null; int column = table.columnAtPoint(e.getPoint()); switch (column) { case TYPE_COLUMN: tip = JvSwingUtils.wrapTooltip(true, MessageManager .getString("label.feature_settings_click_drag")); break; case FILTER_COLUMN: int row = table.rowAtPoint(e.getPoint()); FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, column); tip = o.isEmpty() ? MessageManager .getString("label.configure_feature_tooltip") : o.toString(); break; default: break; } return tip; } }; 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.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() { @Override public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); if (evt.isPopupTrigger()) { Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); popupSort(selectedRow, type, colour, 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, type); } } // isPopupTrigger fires on mouseReleased on Windows @Override public void mouseReleased(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); if (evt.isPopupTrigger()) { String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), evt.getY()); } } }); 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); 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; } protected void popupSort(final int rowSelected, 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); 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); } } } 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()][COLUMN_COUNT]; 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][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); } } /* * process any extra features belonging only to * a group which was just selected */ while (!displayableTypes.isEmpty()) { String type = displayableTypes.iterator().next(); data[dataIndex][TYPE_COLUMN] = type; data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); if (data[dataIndex][COLOUR_COLUMN] == null) { // "Colour has been updated in another view!!" fr.clearRenderOrder(); return; } 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][COLUMN_COUNT]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); } } 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[TYPE_COLUMN]; boolean found = false; for (Object[] current : currentData) { if (type.equals(current[TYPE_COLUMN])) { found = true; /* * currently dependent on object equality here; * really need an equals method on FeatureColour */ if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN])) { /* * feature colour has changed externally - update originalData */ for (Object[] original : originalData) { if (type.equals(original[TYPE_COLUMN])) { original[COLOUR_COLUMN] = row[COLOUR_COLUMN]; break; } } } break; } } if (!found) { /* * new feature detected - add to original data (on top) */ 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, COLUMN_COUNT); } 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); } } /** * 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); 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(); load(file); } } /** * Loads feature colours and filters from XML stored in the given file * * @param file */ void load(File file) { try { InputStreamReader in = new InputStreamReader( new FileInputStream(file), "UTF-8"); JalviewUserColours jucs = JalviewUserColours.unmarshal(in); /* * load feature colours */ for (int i = jucs.getColourCount() - 1; i >= 0; i--) { jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); FeatureColourI colour = Jalview2XML.unmarshalColour(newcol); fr.setColour(newcol.getName(), colour); fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount()); } /* * load feature filters; loaded filters will replace any that are * currently defined, other defined filters are left unchanged */ for (int i = 0; i < jucs.getFilterCount(); i++) { jalview.schemabinding.version2.Filter filterModel = jucs .getFilter(i); String featureType = filterModel.getFeatureType(); FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType, filterModel.getMatcherSet()); if (!filter.isEmpty()) { fr.setFeatureFilter(featureType, filter); } } /* * update feature settings table */ if (table != null) { resetTable(null); Object[][] data = ((FeatureTableModel) table.getModel()) .getData(); ensureOrder(data); updateFeatureRenderer(data, false); table.repaint(); } } catch (Exception ex) { 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); 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) { 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")); /* * sort feature types by colour order, from 0 (highest) * to 1 (lowest) */ Set fr_colours = fr.getAllFeatureColours(); String[] sortedTypes = fr_colours .toArray(new String[fr_colours.size()]); Arrays.sort(sortedTypes, new Comparator() { @Override public int compare(String type1, String type2) { return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); } }); /* * save feature colours */ for (String featureType : sortedTypes) { FeatureColourI fcol = fr.getFeatureStyle(featureType); jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour( featureType, fcol); ucs.addColour(col); } /* * save any feature filters */ for (String featureType : sortedTypes) { FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); if (filter != null && !filter.isEmpty()) { Iterator iterator = filter.getMatchers().iterator(); FeatureMatcherI firstMatcher = iterator.next(); MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator, filter.isAnded()); Filter filterModel = new Filter(); filterModel.setFeatureType(featureType); filterModel.setMatcherSet(ms); ucs.addFilter(filterModel); } } ucs.marshal(out); out.close(); } catch (Exception ex) { ex.printStackTrace(); } } public void invertSelection() { Object[][] data = ((FeatureTableModel) table.getModel()).getData(); for (int i = 0; i < data.length; i++) { data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; } updateFeatureRenderer(data, true); table.repaint(); } 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; for (int i = 0; i < data.length; i++) { 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. } 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][TYPE_COLUMN].toString()); if (width[i] < 0) { width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(), i / data.length); } } else { width[i] /= max; // normalize fr.setOrder(data[i][TYPE_COLUMN].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) { FeatureSettingsBean[] rowData = getTableAsBeans(data); if (fr.setFeaturePriority(rowData, visibleNew)) { af.alignPanel.paintAlignment(true, true); } } /** * 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(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.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.setToolTipText( MessageManager.getString("label.load_colours_tooltip")); 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.setToolTipText( MessageManager.getString("label.save_colours_tooltip")); 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")); 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); settingsPane.add(bigPanel, BorderLayout.CENTER); settingsPane.add(buttonPanel, BorderLayout.SOUTH); this.add(settingsPane); } // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html // /////////////////////////////////////////////////////////////////////// class FeatureTableModel extends AbstractTableModel { private String[] columnNames = { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.configuration"), MessageManager.getString("label.show") }; private Object[][] data; FeatureTableModel(Object[][] data) { this.data = 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]; } /** * Answers the class of the object in column c of the first row of the table */ @Override public Class getColumnClass(int c) { Object v = getValueAt(0, c); return v == null ? null : v.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; } } 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) { 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 ColorEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { FeatureSettings me; FeatureColourI currentColor; FeatureTypeSettings chooser; String type; JButton button; JColorChooser colorChooser; JDialog dialog; protected static final String EDIT = "edit"; int rowSelected = 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_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) { // todo test e.getSource() instead here if (EDIT.equals(e.getActionCommand())) { // The user has clicked the cell, so // bring up the dialog. if (currentColor.isSimpleColour()) { // bring up simple color chooser button.setBackground(currentColor.getColour()); colorChooser.setColor(currentColor.getColour()); dialog.setVisible(true); } else { // bring up graduated chooser. chooser = new FeatureTypeSettings(me.fr, type); /** * @j2sNative */ { chooser.setRequestFocusEnabled(true); chooser.requestFocus(); } chooser.addActionListener(this); // Make the renderer reappear. fireEditingStopped(); } } else { if (currentColor.isSimpleColour()) { /* * read off colour picked in colour chooser after OK pressed */ currentColor = new FeatureColour(colorChooser.getColor()); me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); } else { /* * after OK in variable colour dialog, any changes to colour * (or filters!) are already set in FeatureRenderer, so just * update table data without triggering updateFeatureRenderer */ currentColor = fr.getFeatureColours().get(type); FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type); if (currentFilter == null) { currentFilter = new FeatureMatcherSet(); } Object[] data = ((FeatureTableModel) table.getModel()) .getData()[rowSelected]; data[COLOUR_COLUMN] = currentColor; data[FILTER_COLUMN] = currentFilter; } 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 theTable, Object value, boolean isSelected, int row, int column) { currentColor = (FeatureColourI) value; this.rowSelected = row; type = me.table.getValueAt(row, TYPE_COLUMN).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; } } /** * 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 button; protected static final String EDIT = "edit"; int rowSelected = 0; public FilterEditor(FeatureSettings me) { this.me = me; button = new JButton(); button.setActionCommand(EDIT); button.addActionListener(this); button.setBorderPainted(false); } /** * Handles events from the editor button */ @Override public void actionPerformed(ActionEvent e) { if (button == e.getSource()) { 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 if (e.getSource() instanceof Component) { /* * 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 */ FeatureColourI currentColor = fr.getFeatureColours().get(type); currentFilter = me.fr.getFeatureFilter(type); if (currentFilter == null) { currentFilter = new FeatureMatcherSet(); } Object[] data = ((FeatureTableModel) table.getModel()) .getData()[rowSelected]; data[COLOUR_COLUMN] = currentColor; data[FILTER_COLUMN] = currentFilter; 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(); button.setOpaque(true); button.setBackground(me.getBackground()); button.setText(currentFilter.toString()); button.setToolTipText(currentFilter.toString()); button.setIcon(null); return button; } } } 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); } } }