/* * 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.FeatureSettingsControllerI; import jalview.bin.Cache; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.ws.dbsources.das.api.jalviewSourceI; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Font; import java.awt.Graphics; import java.awt.GridLayout; 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.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Set; import java.util.Vector; 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.JCheckBoxMenuItem; 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.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JScrollPane; import javax.swing.JSlider; import javax.swing.JTabbedPane; import javax.swing.JTable; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; import javax.swing.SwingUtilities; 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; public class FeatureSettings extends JPanel implements FeatureSettingsControllerI { DasSourceBrowser dassourceBrowser; jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; JPanel settingsPane = new JPanel(); JPanel dasSettingsPane = new JPanel(); final FeatureRenderer fr; public final AlignFrame af; Object[][] originalData; private float originalTransparency; final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); JTable table; JPanel groupPanel; JSlider transparency = new JSlider(); JPanel transPanel = new JPanel(new GridLayout(1, 2)); public FeatureSettings(AlignFrame af) { this.af = af; fr = af.getFeatureRenderer(); // allow transparency to be recovered transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100)); 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(GraduatedColor.class, new ColorEditor(this)); table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer()); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); if (SwingUtilities.isRightMouseButton(evt)) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), table.getValueAt(selectedRow, 1), fr.getMinMax(), evt.getX(), evt.getY()); } else if (evt.getClickCount() == 2) { fr.ap.alignFrame.avc.markColumnsContainingFeatures( evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(), evt.isMetaDown(), (String) table.getValueAt(selectedRow, 0)); } } // isPopupTrigger fires on mouseReleased on Mac @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() { public void mouseDragged(MouseEvent evt) { int newRow = table.rowAtPoint(evt.getPoint()); if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { Object[] temp = new Object[3]; temp[0] = table.getValueAt(selectedRow, 0); temp[1] = table.getValueAt(selectedRow, 1); temp[2] = table.getValueAt(selectedRow, 2); table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); table.setValueAt(temp[0], newRow, 0); table.setValueAt(temp[1], newRow, 1); table.setValueAt(temp[2], newRow, 2); 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() { 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 (new jalview.util.Platform().isAMac()) { Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 475, 480); } else { Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 400, 450); } frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { fr.removePropertyChangeListener(change); dassourceBrowser.fs = null; }; }); frame.setLayer(JLayeredPane.PALETTE_LAYER); } protected void popupSort(final int selectedRow, final String type, final Object typeCol, final Hashtable minmax, int x, int y) { 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() { public void actionPerformed(ActionEvent e) { me.af.avc.sortAlignmentByFeatureScore(new String[] { type }); } }); JMenuItem dens = new JMenuItem( MessageManager.getString("label.sort_by_density")); dens.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { me.af.avc.sortAlignmentByFeatureDensity(new String[] { type }); } }); men.add(dens); if (minmax != null) { final Object typeMinMax = minmax.get(type); /* * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); // * this is broken at the moment and isn't that useful anyway! * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new * ActionListener() { * * public void actionPerformed(ActionEvent e) { * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type, * null); } else { minmax.put(type, typeMinMax); } } * * }); * * men.add(chb); */ if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null) { // if (table.getValueAt(row, column)); // graduated colourschemes for those where minmax exists for the // positional features final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( "Graduated Colour"); mxcol.setSelected(!(typeCol instanceof Color)); men.add(mxcol); mxcol.addActionListener(new ActionListener() { JColorChooser colorChooser; public void actionPerformed(ActionEvent e) { if (e.getSource() == mxcol) { if (typeCol instanceof Color) { 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(((GraduatedColor) typeCol) .getMaxColor()); 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(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); } }); men.add(selCols); men.add(clearCols); men.show(table, x, y); } /** * true when Feature Settings are updating from feature renderer */ private boolean handlingUpdate = false; /** * contains a float[3] for each feature type string. created by setTableData */ Hashtable typeWidth = null; @Override synchronized public void discoverAllFeatureData() { Vector allFeatures = new Vector(); Vector allGroups = new Vector(); SequenceFeature[] tmpfeatures; String group; for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) .getSequenceFeatures(); if (tmpfeatures == null) { continue; } int index = 0; while (index < tmpfeatures.length) { if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) { index++; continue; } if (tmpfeatures[index].getFeatureGroup() != null) { group = tmpfeatures[index].featureGroup; if (!allGroups.contains(group)) { allGroups.addElement(group); checkGroupState(group); } } if (!allFeatures.contains(tmpfeatures[index].getType())) { allFeatures.addElement(tmpfeatures[index].getType()); } index++; } } 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); if (groupPanel == null) { groupPanel = new JPanel(); } boolean alreadyAdded = false; for (int g = 0; g < groupPanel.getComponentCount(); g++) { if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) { alreadyAdded = true; ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); break; } } if (alreadyAdded) { return visible; } final String grp = group; final JCheckBox check = new JCheckBox(group, visible); check.setFont(new Font("Serif", Font.BOLD, 12)); check.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent evt) { fr.setGroupVisibility(check.getText(), check.isSelected()); af.alignPanel.getSeqPanel().seqCanvas.repaint(); if (af.alignPanel.overviewPanel != null) { af.alignPanel.overviewPanel.updateOverviewImage(); } resetTable(new String[] { grp }); } }); groupPanel.add(check); return visible; } boolean resettingTable = false; synchronized void resetTable(String[] groupChanged) { if (resettingTable == true) { return; } resettingTable = true; typeWidth = new Hashtable(); // TODO: change avWidth calculation to 'per-sequence' average and use long // rather than float float[] avWidth = null; SequenceFeature[] tmpfeatures; String group = null, type; Vector visibleChecks = new Vector(); // Find out which features should be visible depending on which groups // are selected / deselected // and recompute average width ordering for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) .getSequenceFeatures(); if (tmpfeatures == null) { continue; } int index = 0; while (index < tmpfeatures.length) { group = tmpfeatures[index].featureGroup; if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) { index++; continue; } if (group == null || checkGroupState(group)) { type = tmpfeatures[index].getType(); if (!visibleChecks.contains(type)) { visibleChecks.addElement(type); } } if (!typeWidth.containsKey(tmpfeatures[index].getType())) { typeWidth.put(tmpfeatures[index].getType(), avWidth = new float[3]); } else { avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); } avWidth[0]++; if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) { avWidth[1] += 1 + tmpfeatures[index].getBegin() - tmpfeatures[index].getEnd(); } else { avWidth[1] += 1 + tmpfeatures[index].getEnd() - tmpfeatures[index].getBegin(); } index++; } } int fSize = visibleChecks.size(); Object[][] data = new Object[fSize][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--) { type = frl.get(ro); if (!visibleChecks.contains(type)) { continue; } data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); data[dataIndex][2] = new Boolean(af.getViewport() .getFeaturesDisplayed().isVisible(type)); dataIndex++; visibleChecks.removeElement(type); } } fSize = visibleChecks.size(); for (int i = 0; i < fSize; i++) { // These must be extra features belonging to the group // which was just selected type = visibleChecks.elementAt(i).toString(); 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++; } 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); } } table.setModel(new FeatureTableModel(data)); table.getColumnModel().getColumn(0).setPreferredWidth(200); if (groupPanel != null) { groupPanel.setLayout(new GridLayout( fr.getFeatureGroupsSize() / 4 + 1, 4)); groupPanel.validate(); bigPanel.add(groupPanel, BorderLayout.NORTH); } updateFeatureRenderer(data, groupChanged != null); resettingTable = false; } /** * 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( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "fc" }, new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours"); chooser.setFileView(new jalview.io.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"); jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); jucs = jucs .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); } GraduatedColor gcol = new GraduatedColor(mincol, maxcol, newcol.getMin(), newcol.getMax()); if (newcol.hasAutoScale()) { gcol.setAutoScaled(newcol.getAutoScale()); } if (newcol.hasColourByLabel()) { gcol.setColourByLabel(newcol.getColourByLabel()); } if (newcol.hasThreshold()) { gcol.setThresh(newcol.getThreshold()); gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default } if (newcol.getThreshType().length() > 0) { String ttyp = newcol.getThreshType(); if (ttyp.equalsIgnoreCase("NONE")) { gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); } if (ttyp.equalsIgnoreCase("ABOVE")) { gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); } if (ttyp.equalsIgnoreCase("BELOW")) { gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); } } fr.setColour(name = newcol.getName(), gcol); } else { fr.setColour(name = jucs.getColour(i).getName(), new Color( Integer.parseInt(jucs.getColour(i).getRGB(), 16))); } 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( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "fc" }, new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours"); chooser.setFileView(new jalview.io.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().toString(); sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } jalview.util.QuickSort.sort(sortOrder, sortTypes); sortOrder = null; Object fcol; GraduatedColor gcol; for (i = 0; i < sortTypes.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(sortTypes[i]); col.setRGB(jalview.util.Format.getHexString(fr.getColour(col .getName()))); fcol = fr.getFeatureStyle(sortTypes[i]); if (fcol instanceof GraduatedColor) { gcol = (GraduatedColor) fcol; col.setMin(gcol.getMin()); col.setMax(gcol.getMax()); col.setMinRGB(jalview.util.Format.getHexString(gcol .getMinColor())); col.setAutoScale(gcol.isAutoScale()); col.setThreshold(gcol.getThresh()); col.setColourByLabel(gcol.isColourByLabel()); switch (gcol.getThreshType()) { case AnnotationColourGradient.NO_THRESHOLD: col.setThreshType("NONE"); break; case AnnotationColourGradient.ABOVE_THRESHOLD: col.setThreshType("ABOVE"); break; case AnnotationColourGradient.BELOW_THRESHOLD: col.setThreshType("BELOW"); break; } } 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 = (float[]) 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); } private void updateFeatureRenderer(Object[][] data, boolean visibleNew) { fr.setFeaturePriority(data, visibleNew); af.alignPanel.paintAlignment(true); } int selectedRow = -1; JTabbedPane tabbedPane = new JTabbedPane(); BorderLayout borderLayout1 = new BorderLayout(); BorderLayout borderLayout2 = new BorderLayout(); BorderLayout borderLayout3 = new BorderLayout(); JPanel bigPanel = new JPanel(); BorderLayout borderLayout4 = new BorderLayout(); JButton invert = new JButton(); JPanel buttonPanel = new JPanel(); JButton cancel = new JButton(); JButton ok = new JButton(); JButton loadColours = new JButton(); JButton saveColours = new JButton(); JPanel dasButtonPanel = new JPanel(); JButton fetchDAS = new JButton(); JButton saveDAS = new JButton(); JButton cancelDAS = new JButton(); JButton optimizeOrder = new JButton(); JButton sortByScore = new JButton(); JButton sortByDens = new JButton(); JButton help = new JButton(); JPanel transbuttons = new JPanel(new GridLayout(5, 1)); private void jbInit() throws Exception { this.setLayout(borderLayout1); settingsPane.setLayout(borderLayout2); dasSettingsPane.setLayout(borderLayout3); bigPanel.setLayout(borderLayout4); invert.setFont(JvSwingUtils.getLabelFont()); invert.setText(MessageManager.getString("label.invert_selection")); invert.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { invertSelection(); } }); optimizeOrder.setFont(JvSwingUtils.getLabelFont()); optimizeOrder.setText(MessageManager.getString("label.optimise_order")); optimizeOrder.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { orderByAvWidth(); } }); sortByScore.setFont(JvSwingUtils.getLabelFont()); sortByScore .setText(MessageManager.getString("label.seq_sort_by_score")); sortByScore.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureScore(null); } }); sortByDens.setFont(JvSwingUtils.getLabelFont()); sortByDens.setText(MessageManager .getString("label.sequence_sort_by_density")); sortByDens.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureDensity(null); } }); help.setFont(JvSwingUtils.getLabelFont()); help.setText(MessageManager.getString("action.help")); help.addActionListener(new ActionListener() { 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() { public void actionPerformed(ActionEvent e) { try { Help.showHelpWindow(HelpId.SequenceFeatureSettings); } catch (HelpSetException e1) { e1.printStackTrace(); } } }); cancel.setFont(JvSwingUtils.getLabelFont()); cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { fr.setTransparency(originalTransparency); updateFeatureRenderer(originalData); close(); } }); ok.setFont(JvSwingUtils.getLabelFont()); ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { close(); } }); loadColours.setFont(JvSwingUtils.getLabelFont()); loadColours.setText(MessageManager.getString("label.load_colours")); loadColours.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { load(); } }); saveColours.setFont(JvSwingUtils.getLabelFont()); saveColours.setText(MessageManager.getString("label.save_colours")); saveColours.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { save(); } }); transparency.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent evt) { fr.setTransparency((100 - transparency.getValue()) / 100f); af.alignPanel.paintAlignment(true); } }); transparency.setMaximum(70); transparency.setToolTipText(MessageManager .getString("label.transparency_tip")); fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); fetchDAS.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { fetchDAS_actionPerformed(e); } }); saveDAS.setText(MessageManager.getString("action.save_as_default")); saveDAS.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { saveDAS_actionPerformed(e); } }); dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); dasSettingsPane.setBorder(null); cancelDAS.setEnabled(false); cancelDAS.setText(MessageManager.getString("action.cancel_fetch")); cancelDAS.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { cancelDAS_actionPerformed(e); } }); this.add(tabbedPane, java.awt.BorderLayout.CENTER); tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane); tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane); bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); transbuttons.add(optimizeOrder); transbuttons.add(invert); transbuttons.add(sortByScore); transbuttons.add(sortByDens); transbuttons.add(help); JPanel sliderPanel = new JPanel(); sliderPanel.add(transparency); transPanel.add(transparency); transPanel.add(transbuttons); buttonPanel.add(ok); buttonPanel.add(cancel); buttonPanel.add(loadColours); buttonPanel.add(saveColours); bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER); dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); dasButtonPanel.add(fetchDAS); dasButtonPanel.add(cancelDAS); dasButtonPanel.add(saveDAS); settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER); settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); } public void fetchDAS_actionPerformed(ActionEvent e) { fetchDAS.setEnabled(false); cancelDAS.setEnabled(true); dassourceBrowser.setGuiEnabled(false); Vector selectedSources = dassourceBrowser.getSelectedSources(); doDasFeatureFetch(selectedSources, true, true); } /** * 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() { 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(); JOptionPane .showInternalConfirmDialog( Desktop.desktop, MessageManager .getString("label.no_das_sources_selected_warn"), MessageManager .getString("label.no_das_sources_selected_title"), JOptionPane.DEFAULT_OPTION, JOptionPane.INFORMATION_MESSAGE); } // /////////////////////////////////////////////////////////////////////// // 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; } public int getColumnCount() { return columnNames.length; } public Object[] getRow(int row) { return data[row]; } public int getRowCount() { return data.length; } public String getColumnName(int col) { return columnNames[col]; } public Object getValueAt(int row, int col) { return data[row][col]; } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } public boolean isCellEditable(int row, int col) { return col == 0 ? false : true; } 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); } public Component getTableCellRendererComponent(JTable table, Object color, boolean isSelected, boolean hasFocus, int row, int column) { // JLabel comp = new JLabel(); // comp. setOpaque(true); // comp. // setBounds(getBounds()); Color newColor; setToolTipText(baseTT); setBackground(table.getBackground()); if (color instanceof GraduatedColor) { Rectangle cr = table.getCellRect(row, column, false); FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color, (int) cr.getWidth(), (int) cr.getHeight()); } else { this.setText(""); this.setIcon(null); newColor = (Color) color; // comp. setBackground(newColor); // comp.setToolTipText("RGB value: " + newColor.getRed() + ", " // + newColor.getGreen() + ", " + newColor.getBlue()); } if (isSelected) { if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, table.getSelectionBackground()); } // comp. setBorder(selectedBorder); } else { if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, table.getBackground()); } // comp. setBorder(unselectedBorder); } return this; } } /** * update comp using rendering settings from gcol * * @param comp * @param gcol */ public static void renderGraduatedColor(JLabel comp, GraduatedColor 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, GraduatedColor gcol, int w, int h) { boolean thr = false; String tt = ""; String tx = ""; if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) { thr = true; tx += ">"; tt += "Thresholded (Above " + gcol.getThresh() + ") "; } if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) { thr = true; tx += "<"; tt += "Thresholded (Below " + gcol.getThresh() + ") "; } if (gcol.isColourByLabel()) { tt = "Coloured by label text. " + tt; if (thr) { tx += " "; } tx += "Label"; comp.setIcon(null); } else { Color newColor = gcol.getMaxColor(); 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); if (tt.length() > 0) { if (comp.getToolTipText() == null) { comp.setToolTipText(tt); } else { comp.setToolTipText(tt + " " + comp.getToolTipText()); } } } } class FeatureIcon implements Icon { GraduatedColor 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(GraduatedColor 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; } } public int getIconWidth() { return width; } public int getIconHeight() { return height; } 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.getMaxColor()); 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.getMinColor(); 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.getMaxColor()); g.fillRect(0, e1, width - e1, height); } } } class ColorEditor extends AbstractCellEditor implements TableCellEditor, ActionListener { FeatureSettings me; GraduatedColor currentGColor; FeatureColourChooser chooser; String type; Color currentColor; JButton button; JColorChooser colorChooser; JDialog dialog; protected static final String EDIT = "edit"; int selectedRow = 0; public ColorEditor(FeatureSettings me) { this.me = me; // Set up the editor (from the table's point of view), // which is a button. // This button brings up the color chooser dialog, // which is the editor from the user's point of view. button = new JButton(); button.setActionCommand(EDIT); button.addActionListener(this); button.setBorderPainted(false); // Set up the dialog that the button brings up. colorChooser = new JColorChooser(); dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal colorChooser, this, // OK button handler null); // no CANCEL button handler } /** * Handles events from the editor button and from the dialog's OK button. */ public void actionPerformed(ActionEvent e) { if (EDIT.equals(e.getActionCommand())) { // The user has clicked the cell, so // bring up the dialog. if (currentColor != null) { // bring up simple color chooser button.setBackground(currentColor); colorChooser.setColor(currentColor); 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 != null) { currentColor = colorChooser.getColor(); } else { // class cast exceptions may be raised if the chooser created on a // non-graduated color currentGColor = (GraduatedColor) chooser.getLastColour(); } me.table.setValueAt(getCellEditorValue(), selectedRow, 1); fireEditingStopped(); me.table.validate(); } } // Implement the one CellEditor method that AbstractCellEditor doesn't. public Object getCellEditorValue() { if (currentColor == null) { return currentGColor; } return currentColor; } // Implement the one method defined by TableCellEditor. public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) { currentGColor = null; currentColor = null; this.selectedRow = row; type = me.table.getValueAt(row, 0).toString(); button.setOpaque(true); button.setBackground(me.getBackground()); if (value instanceof GraduatedColor) { currentGColor = (GraduatedColor) value; JLabel btn = new JLabel(); btn.setSize(button.getSize()); FeatureSettings.renderGraduatedColor(btn, currentGColor); button.setBackground(btn.getBackground()); button.setIcon(btn.getIcon()); button.setText(btn.getText()); } else { button.setText(""); button.setIcon(null); currentColor = (Color) value; button.setBackground(currentColor); } return button; } }