2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.api.FeatureSettingsControllerI;
24 import jalview.bin.JalviewLite;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.SequenceFeature;
27 import jalview.schemes.AnnotationColourGradient;
28 import jalview.schemes.GraduatedColor;
29 import jalview.util.MessageManager;
31 import java.awt.BorderLayout;
32 import javax.swing.JButton;
33 import javax.swing.JCheckBox;
34 import java.awt.Color;
35 import java.awt.Component;
36 import java.awt.Dimension;
38 import java.awt.FontMetrics;
39 import javax.swing.JFrame;
40 import java.awt.Graphics;
41 import java.awt.GridLayout;
42 import java.awt.Image;
43 import javax.swing.JLabel;
44 import javax.swing.JMenuItem;
45 import javax.swing.JPanel;
46 import javax.swing.JPopupMenu;
47 import javax.swing.JScrollPane;
48 import javax.swing.JScrollBar;
49 import java.awt.event.ActionEvent;
50 import java.awt.event.ActionListener;
51 import java.awt.event.AdjustmentEvent;
52 import java.awt.event.AdjustmentListener;
53 import java.awt.event.InputEvent;
54 import java.awt.event.ItemEvent;
55 import java.awt.event.ItemListener;
56 import java.awt.event.MouseEvent;
57 import java.awt.event.MouseListener;
58 import java.awt.event.MouseMotionListener;
59 import java.awt.event.WindowAdapter;
60 import java.awt.event.WindowEvent;
61 import java.util.Enumeration;
62 import java.util.Hashtable;
63 import java.util.List;
64 import java.util.Vector;
66 public class FeatureSettings extends JPanel implements ItemListener,
67 MouseListener, MouseMotionListener, ActionListener,
68 AdjustmentListener, FeatureSettingsControllerI
80 JPanel featurePanel = new JPanel();
82 JScrollPane scrollPane;
86 JScrollBar transparency;
88 public FeatureSettings(final AlignmentPanel ap)
92 ap.av.featureSettings = this;
93 fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
95 transparency = new JScrollBar(JScrollBar.HORIZONTAL,
96 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
98 if (fr.isTransparencyAvailable())
100 transparency.addAdjustmentListener(this);
104 transparency.setEnabled(false);
107 java.net.URL url = getClass().getResource("/images/link.gif");
110 linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
113 if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())
115 fr.findAllFeatures(true); // was default - now true to make all visible
118 discoverAllFeatureData();
120 this.setLayout(new BorderLayout());
121 scrollPane = new JScrollPane();
122 scrollPane.add(featurePanel);
123 if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
125 add(scrollPane, BorderLayout.CENTER);
128 JButton invert = new JButton("Invert Selection");
129 invert.addActionListener(this);
131 JPanel lowerPanel = new JPanel(new GridLayout(2, 1, 5, 10));
132 lowerPanel.add(invert);
134 JPanel tPanel = new JPanel(new BorderLayout());
136 if (fr.isTransparencyAvailable())
138 tPanel.add(transparency, BorderLayout.CENTER);
139 tPanel.add(new JLabel("Transparency"), BorderLayout.EAST);
144 new JLabel("Transparency not available in this web browser"),
145 BorderLayout.CENTER);
148 lowerPanel.add(tPanel, BorderLayout.SOUTH);
150 add(lowerPanel, BorderLayout.SOUTH);
152 if (groupPanel != null)
155 .setLayout(new GridLayout(
156 (fr.getFeatureGroupsSize()) / 4 + 1,
157 4)); // JBPNote - this was scaled on number of visible groups. seems broken
158 groupPanel.validate();
160 add(groupPanel, BorderLayout.NORTH);
162 frame = new JFrame();
164 final FeatureSettings me = this;
165 frame.addWindowListener(new WindowAdapter()
167 public void windowClosing(WindowEvent e)
169 if (me.av.featureSettings == me)
171 me.av.featureSettings = null;
177 int height = featurePanel.getComponentCount() * 50 + 60;
179 height = Math.max(200, height);
180 height = Math.min(400, height);
182 JalviewLite.addFrame(frame,
183 MessageManager.getString("label.feature_settings"), width,
187 public void paint(Graphics g)
189 g.setColor(Color.black);
190 g.drawString(MessageManager
191 .getString("label.no_features_added_to_this_alignment"), 10, 20);
192 g.drawString(MessageManager
193 .getString("label.features_can_be_added_from_searches_1"), 10,
195 g.drawString(MessageManager
196 .getString("label.features_can_be_added_from_searches_2"), 10,
200 protected void popupSort(final MyCheckbox check, final Hashtable minmax,
203 final String type = check.type;
204 final Object typeCol = fr.getFeatureStyle(type);
205 JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
206 "label.settings_for_type", new String[]
208 JMenuItem scr = new JMenuItem(
209 MessageManager.getString("label.sort_by_score"));
211 final FeatureSettings me = this;
212 scr.addActionListener(new ActionListener()
215 public void actionPerformed(ActionEvent e)
217 me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
222 JMenuItem dens = new JMenuItem(
223 MessageManager.getString("label.sort_by_density"));
224 dens.addActionListener(new ActionListener()
227 public void actionPerformed(ActionEvent e)
229 me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
237 final Object typeMinMax = minmax.get(type);
239 * final java.awt.CheckboxMenuItem chb = new
240 * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
241 * moment chb.setState(minmax.get(type) != null);
242 * chb.addActionListener(new ActionListener() {
244 * public void actionPerformed(ActionEvent e) {
245 * chb.setState(chb.isSelected()); if (chb.isSelected()) { minmax.put(type,
246 * null); } else { minmax.put(type, typeMinMax); } }
250 if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
252 // graduated colourschemes for those where minmax exists for the
253 // positional features
254 JMenuItem mxcol = new JMenuItem(
255 (typeCol instanceof Color) ? "Graduated Colour"
258 mxcol.addActionListener(new ActionListener()
261 public void actionPerformed(ActionEvent e)
263 if (typeCol instanceof Color)
265 new FeatureColourChooser(me, type);
266 // write back the current colour object to update the table
267 check.updateColor(fr.getFeatureStyle(type));
271 new UserDefinedColours(me, check.type,
272 ((GraduatedColor) typeCol));
279 this.featurePanel.add(men);
280 men.show(this.featurePanel, x, y);
284 public void discoverAllFeatureData()
286 if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
295 * rebuilds the group panel
297 public void rebuildGroups()
299 boolean rdrw = false;
300 if (groupPanel == null)
302 groupPanel = new JPanel();
307 groupPanel.removeAll();
309 // TODO: JAL-964 - smoothly incorporate new group entries if panel already
310 // displayed and new groups present
311 for (String group:fr.getFeatureGroups())
313 boolean vis = fr.checkGroupVisibility(group, false);
314 JCheckBox check = new MyCheckbox(group, vis,
315 (fr.featureLinks != null && fr.featureLinks
316 .containsKey(group)));
317 check.addMouseListener(this);
318 check.setFont(new Font("Serif", Font.BOLD, 12));
319 check.addItemListener(groupItemListener);
320 // note - visibility seems to correlate with displayed. ???wtf ??
321 check.setVisible(vis);
322 groupPanel.add(check);
326 groupPanel.validate();
329 // This routine adds and removes checkboxes depending on
330 // Group selection states
331 void resetTable(boolean groupsChanged)
333 SequenceFeature[] tmpfeatures;
334 String group = null, type;
335 Vector visibleChecks = new Vector();
336 AlignmentI alignment = av.getAlignment();
337 for (int i = 0; i < alignment.getHeight(); i++)
339 if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
344 tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
346 while (index < tmpfeatures.length)
348 group = tmpfeatures[index].featureGroup;
350 if (group == null || fr.checkGroupVisibility(group, true))
352 type = tmpfeatures[index].getType();
353 if (!visibleChecks.contains(type))
355 visibleChecks.addElement(type);
363 int cSize = featurePanel.getComponentCount();
365 // This will remove any checkboxes which shouldn't be
367 for (int i = 0; i < cSize; i++)
369 comps = featurePanel.getComponents();
370 check = (MyCheckbox) comps[i];
371 if (!visibleChecks.contains(check.type))
373 featurePanel.remove(i);
379 if (fr.getRenderOrder() != null)
381 // First add the checks in the previous render order,
382 // in case the window has been closed and reopened
383 List<String> rol = fr.getRenderOrder();
384 for (int ro = rol.size() - 1; ro > -1; ro--)
386 String item = rol.get(ro);
388 if (!visibleChecks.contains(item))
393 visibleChecks.removeElement(item);
395 addCheck(false, item);
399 // now add checkboxes which should be visible,
400 // if they have not already been added
401 Enumeration en = visibleChecks.elements();
403 while (en.hasMoreElements())
405 addCheck(groupsChanged, en.nextElement().toString());
408 featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
410 featurePanel.validate();
412 if (scrollPane != null)
414 scrollPane.validate();
417 itemStateChanged(null);
421 * update the checklist of feature types with the given type
423 * @param groupsChanged
424 * true means if the type is not in the display list then it will be
425 * added and displayed
427 * feature type to be checked for in the list.
429 void addCheck(boolean groupsChanged, String type)
432 Component[] comps = featurePanel.getComponents();
435 for (int i = 0; i < featurePanel.getComponentCount(); i++)
437 check = (MyCheckbox) comps[i];
438 if (check.type.equals(type))
447 boolean selected = false;
448 if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
453 check = new MyCheckbox(
456 (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
457 fr.getFeatureStyle(type));
459 check.addMouseListener(this);
460 check.addMouseMotionListener(this);
461 check.addItemListener(this);
464 // add at beginning of stack.
465 featurePanel.add(check, 0);
469 // add at end of stack.
470 featurePanel.add(check);
475 public void actionPerformed(ActionEvent evt)
477 for (int i = 0; i < featurePanel.getComponentCount(); i++)
479 JCheckBox check = (JCheckBox) featurePanel.getComponent(i);
480 check.setSelected(!check.isSelected());
485 private ItemListener groupItemListener = new ItemListener() {
486 public void itemStateChanged(ItemEvent evt) {
487 JCheckBox source = (JCheckBox) evt.getSource();
488 fr.setGroupVisibility(source.getLabel(),
489 source.isSelected());
490 ap.seqPanel.seqCanvas.repaint();
491 if (ap.overviewPanel != null)
493 ap.overviewPanel.updateOverviewImage();
499 public void itemStateChanged(ItemEvent evt)
504 void selectionChanged()
506 Component[] comps = featurePanel.getComponents();
507 int cSize = comps.length;
509 Object[][] tmp = new Object[cSize][3];
511 for (int i = 0; i < cSize; i++)
513 MyCheckbox check = (MyCheckbox) comps[i];
514 tmp[tmpSize][0] = check.type;
515 tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
516 tmp[tmpSize][2] = new Boolean(check.isSelected());
520 Object[][] data = new Object[tmpSize][3];
521 System.arraycopy(tmp, 0, data, 0, tmpSize);
523 fr.setFeaturePriority(data);
525 ap.paintAlignment(true);
528 MyCheckbox selectedCheck;
530 boolean dragging = false;
532 public void mousePressed(MouseEvent evt)
535 selectedCheck = (MyCheckbox) evt.getSource();
537 if (fr.featureLinks != null
538 && fr.featureLinks.containsKey(selectedCheck.type))
540 if (evt.getX() > selectedCheck.stringWidth + 20)
548 public void mouseDragged(MouseEvent evt)
550 if (((Component) evt.getSource()).getParent() != featurePanel)
557 public void mouseReleased(MouseEvent evt)
559 if (((Component) evt.getSource()).getParent() != featurePanel)
564 Component comp = null;
565 JCheckBox target = null;
567 int height = evt.getY() + evt.getComponent().getLocation().y;
569 if (height > featurePanel.getSize().height)
573 .getComponent(featurePanel.getComponentCount() - 1);
577 comp = featurePanel.getComponent(0);
581 comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
582 + evt.getComponent().getLocation().y);
585 if (comp != null && comp instanceof JCheckBox)
587 target = (JCheckBox) comp;
590 if (selectedCheck != null && target != null && selectedCheck != target)
592 int targetIndex = -1;
593 for (int i = 0; i < featurePanel.getComponentCount(); i++)
595 if (target == featurePanel.getComponent(i))
602 featurePanel.remove(selectedCheck);
603 featurePanel.add(selectedCheck, targetIndex);
604 featurePanel.validate();
605 itemStateChanged(null);
609 public void setUserColour(String feature, Object originalColour)
611 if (originalColour instanceof Color
612 || originalColour instanceof GraduatedColor)
614 fr.setColour(feature, originalColour);
618 throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
623 public void refreshTable()
625 featurePanel.removeAll();
627 ap.paintAlignment(true);
630 public void mouseEntered(MouseEvent evt)
634 public void mouseExited(MouseEvent evt)
638 public void mouseClicked(MouseEvent evt)
640 MyCheckbox check = (MyCheckbox) evt.getSource();
641 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
643 this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
645 if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
647 if (evt.getX() > check.stringWidth + 20)
650 String link = fr.featureLinks.get(check.type).toString();
651 ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
652 link.substring(0, link.indexOf("|")));
656 if (check.getParent() != featurePanel)
661 if (evt.getClickCount() > 1)
663 Object fcol = fr.getFeatureStyle(check.type);
664 if (fcol instanceof Color)
666 new UserDefinedColours(this, check.type, (Color) fcol);
670 new FeatureColourChooser(this, check.type);
671 // write back the current colour object to update the table
672 check.updateColor(fr.getFeatureStyle(check.type));
677 public void mouseMoved(MouseEvent evt)
681 public void adjustmentValueChanged(AdjustmentEvent evt)
683 fr.setTransparency((100 - transparency.getValue()) / 100f);
684 ap.seqPanel.seqCanvas.repaint();
688 class MyCheckbox extends JCheckBox
692 public int stringWidth;
700 public void updateColor(Object newcol)
702 if (newcol instanceof Color)
704 col = (Color) newcol;
707 else if (newcol instanceof GraduatedColor)
709 gcol = (GraduatedColor) newcol;
714 throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
722 String vlabel = type;
723 if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
726 + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
729 if (gcol.isColourByLabel())
731 setBackground(Color.white);
732 vlabel += " (by Label)";
736 setBackground(gcol.getMinColor());
738 this.setLabel(vlabel);
743 public MyCheckbox(String label, boolean checked, boolean haslink)
745 super(label, checked);
747 FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
748 stringWidth = fm.stringWidth(label);
749 this.hasLink = haslink;
752 public MyCheckbox(String type, boolean selected, boolean b,
755 this(type, selected, b);
756 updateColor(featureStyle);
759 public void paint(Graphics g)
761 Dimension d = getSize();
764 if (gcol.isColourByLabel())
766 g.setColor(Color.white);
767 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
769 * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
772 * // g.setFont(g.getFont().deriveFont( //
773 * AffineTransform.getScaleInstance( //
774 * width/g.getFontMetrics().stringWidth("Label"), //
775 * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
782 Color maxCol = gcol.getMaxColor();
784 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
791 g.drawImage(linkImage, stringWidth + 25,
792 (getSize().height - linkImage.getHeight(this)) / 2, this);