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.datamodel.AlignmentI;
25 import jalview.datamodel.SequenceFeature;
26 import jalview.schemes.AnnotationColourGradient;
27 import jalview.schemes.GraduatedColor;
28 import jalview.util.MessageManager;
30 import java.awt.BorderLayout;
31 import java.awt.Button;
32 import java.awt.Checkbox;
33 import java.awt.Color;
34 import java.awt.Component;
35 import java.awt.Dimension;
37 import java.awt.FontMetrics;
38 import java.awt.Frame;
39 import java.awt.Graphics;
40 import java.awt.GridLayout;
41 import java.awt.Image;
42 import java.awt.Label;
43 import java.awt.MenuItem;
44 import java.awt.Panel;
45 import java.awt.PopupMenu;
46 import java.awt.ScrollPane;
47 import java.awt.Scrollbar;
48 import java.awt.event.ActionEvent;
49 import java.awt.event.ActionListener;
50 import java.awt.event.AdjustmentEvent;
51 import java.awt.event.AdjustmentListener;
52 import java.awt.event.InputEvent;
53 import java.awt.event.ItemEvent;
54 import java.awt.event.ItemListener;
55 import java.awt.event.MouseEvent;
56 import java.awt.event.MouseListener;
57 import java.awt.event.MouseMotionListener;
58 import java.awt.event.WindowAdapter;
59 import java.awt.event.WindowEvent;
60 import java.util.Enumeration;
61 import java.util.Hashtable;
62 import java.util.List;
63 import java.util.Vector;
65 public class FeatureSettings extends Panel implements ItemListener,
66 MouseListener, MouseMotionListener, ActionListener,
67 AdjustmentListener, FeatureSettingsControllerI
79 Panel featurePanel = new Panel();
81 ScrollPane scrollPane;
85 Scrollbar transparency;
87 public FeatureSettings(final AlignmentPanel ap)
91 ap.av.featureSettings = this;
92 fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
94 transparency = new Scrollbar(Scrollbar.HORIZONTAL,
95 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
97 if (fr.isTransparencyAvailable())
99 transparency.addAdjustmentListener(this);
103 transparency.setEnabled(false);
106 java.net.URL url = getClass().getResource("/images/link.gif");
109 linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
112 if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())
114 fr.findAllFeatures(true); // was default - now true to make all visible
117 discoverAllFeatureData();
119 this.setLayout(new BorderLayout());
120 scrollPane = new ScrollPane();
121 scrollPane.add(featurePanel);
122 if (fr.getAllFeatureColours() != null
123 && fr.getAllFeatureColours().size() > 0)
125 add(scrollPane, BorderLayout.CENTER);
128 Button invert = new Button("Invert Selection");
129 invert.addActionListener(this);
131 Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
132 lowerPanel.add(invert);
134 Panel tPanel = new Panel(new BorderLayout());
136 if (fr.isTransparencyAvailable())
138 tPanel.add(transparency, BorderLayout.CENTER);
139 tPanel.add(new Label("Transparency"), BorderLayout.EAST);
144 new Label("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)
154 groupPanel.setLayout(new GridLayout(
155 (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
156 // scaled on number of
157 // visible groups. seems
159 groupPanel.validate();
161 add(groupPanel, BorderLayout.NORTH);
165 final FeatureSettings me = this;
166 frame.addWindowListener(new WindowAdapter()
169 public void windowClosing(WindowEvent e)
171 if (me.av.featureSettings == me)
173 me.av.featureSettings = null;
179 int height = featurePanel.getComponentCount() * 50 + 60;
181 height = Math.max(200, height);
182 height = Math.min(400, height);
184 jalview.bin.JalviewLite.addFrame(frame,
185 MessageManager.getString("label.sequence_feature_settings"),
190 public void paint(Graphics g)
192 g.setColor(Color.black);
193 g.drawString(MessageManager
194 .getString("label.no_features_added_to_this_alignment"), 10, 20);
195 g.drawString(MessageManager
196 .getString("label.features_can_be_added_from_searches_1"), 10,
198 g.drawString(MessageManager
199 .getString("label.features_can_be_added_from_searches_2"), 10,
203 protected void popupSort(final MyCheckbox check, final Hashtable minmax,
206 final String type = check.type;
207 final Object typeCol = fr.getFeatureStyle(type);
208 java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
209 "label.settings_for_type", new String[] { type }));
210 java.awt.MenuItem scr = new MenuItem(
211 MessageManager.getString("label.sort_by_score"));
213 final FeatureSettings me = this;
214 scr.addActionListener(new ActionListener()
218 public void actionPerformed(ActionEvent e)
221 .sortAlignmentByFeatureScore(new String[] { type });
225 MenuItem dens = new MenuItem(
226 MessageManager.getString("label.sort_by_density"));
227 dens.addActionListener(new ActionListener()
231 public void actionPerformed(ActionEvent e)
234 .sortAlignmentByFeatureDensity(new String[] { type });
241 final Object typeMinMax = minmax.get(type);
243 * final java.awt.CheckboxMenuItem chb = new
244 * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
245 * moment chb.setState(minmax.get(type) != null);
246 * chb.addActionListener(new ActionListener() {
248 * public void actionPerformed(ActionEvent e) {
249 * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
250 * null); } else { minmax.put(type, typeMinMax); } }
254 if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
256 // graduated colourschemes for those where minmax exists for the
257 // positional features
258 MenuItem mxcol = new MenuItem(
259 (typeCol instanceof Color) ? "Graduated Colour"
262 mxcol.addActionListener(new ActionListener()
266 public void actionPerformed(ActionEvent e)
268 if (typeCol instanceof Color)
270 new FeatureColourChooser(me, type);
271 // write back the current colour object to update the table
272 check.updateColor(fr.getFeatureStyle(type));
276 new UserDefinedColours(me, check.type,
277 ((GraduatedColor) typeCol));
284 this.featurePanel.add(men);
285 men.show(this.featurePanel, x, y);
289 public void discoverAllFeatureData()
291 if (fr.getAllFeatureColours() != null
292 && fr.getAllFeatureColours().size() > 0)
301 * rebuilds the group panel
303 public void rebuildGroups()
305 boolean rdrw = false;
306 if (groupPanel == null)
308 groupPanel = new Panel();
313 groupPanel.removeAll();
315 // TODO: JAL-964 - smoothly incorporate new group entries if panel already
316 // displayed and new groups present
317 for (String group : fr.getFeatureGroups())
319 boolean vis = fr.checkGroupVisibility(group, false);
320 Checkbox check = new MyCheckbox(group, vis, false);
321 check.addMouseListener(this);
322 check.setFont(new Font("Serif", Font.BOLD, 12));
323 check.addItemListener(groupItemListener);
324 // note - visibility seems to correlate with displayed. ???wtf ??
325 check.setVisible(vis);
326 groupPanel.add(check);
330 groupPanel.validate();
334 // This routine adds and removes checkboxes depending on
335 // Group selection states
336 void resetTable(boolean groupsChanged)
338 SequenceFeature[] tmpfeatures;
339 String group = null, type;
340 Vector visibleChecks = new Vector();
341 AlignmentI alignment = av.getAlignment();
342 for (int i = 0; i < alignment.getHeight(); i++)
344 if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
349 tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
351 while (index < tmpfeatures.length)
353 group = tmpfeatures[index].featureGroup;
355 if (group == null || fr.checkGroupVisibility(group, true))
357 type = tmpfeatures[index].getType();
358 if (!visibleChecks.contains(type))
360 visibleChecks.addElement(type);
368 int cSize = featurePanel.getComponentCount();
370 // This will remove any checkboxes which shouldn't be
372 for (int i = 0; i < cSize; i++)
374 comps = featurePanel.getComponents();
375 check = (MyCheckbox) comps[i];
376 if (!visibleChecks.contains(check.type))
378 featurePanel.remove(i);
384 if (fr.getRenderOrder() != null)
386 // First add the checks in the previous render order,
387 // in case the window has been closed and reopened
388 List<String> rol = fr.getRenderOrder();
389 for (int ro = rol.size() - 1; ro > -1; ro--)
391 String item = rol.get(ro);
393 if (!visibleChecks.contains(item))
398 visibleChecks.removeElement(item);
400 addCheck(false, item);
404 // now add checkboxes which should be visible,
405 // if they have not already been added
406 Enumeration en = visibleChecks.elements();
408 while (en.hasMoreElements())
410 addCheck(groupsChanged, en.nextElement().toString());
413 featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
415 featurePanel.validate();
417 if (scrollPane != null)
419 scrollPane.validate();
422 itemStateChanged(null);
426 * update the checklist of feature types with the given type
428 * @param groupsChanged
429 * true means if the type is not in the display list then it will be
430 * added and displayed
432 * feature type to be checked for in the list.
434 void addCheck(boolean groupsChanged, String type)
437 Component[] comps = featurePanel.getComponents();
440 for (int i = 0; i < featurePanel.getComponentCount(); i++)
442 check = (MyCheckbox) comps[i];
443 if (check.type.equals(type))
452 boolean selected = false;
453 if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
458 check = new MyCheckbox(type, selected, false,
459 fr.getFeatureStyle(type));
461 check.addMouseListener(this);
462 check.addMouseMotionListener(this);
463 check.addItemListener(this);
466 // add at beginning of stack.
467 featurePanel.add(check, 0);
471 // add at end of stack.
472 featurePanel.add(check);
478 public void actionPerformed(ActionEvent evt)
480 for (int i = 0; i < featurePanel.getComponentCount(); i++)
482 Checkbox check = (Checkbox) featurePanel.getComponent(i);
483 check.setState(!check.getState());
488 private ItemListener groupItemListener = new ItemListener()
491 public void itemStateChanged(ItemEvent evt)
493 Checkbox source = (Checkbox) evt.getSource();
494 fr.setGroupVisibility(source.getLabel(), source.getState());
495 ap.seqPanel.seqCanvas.repaint();
496 if (ap.overviewPanel != null)
498 ap.overviewPanel.updateOverviewImage();
506 public void itemStateChanged(ItemEvent evt)
511 void selectionChanged()
513 Component[] comps = featurePanel.getComponents();
514 int cSize = comps.length;
516 Object[][] tmp = new Object[cSize][3];
518 for (int i = 0; i < cSize; i++)
520 MyCheckbox check = (MyCheckbox) comps[i];
521 tmp[tmpSize][0] = check.type;
522 tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
523 tmp[tmpSize][2] = new Boolean(check.getState());
527 Object[][] data = new Object[tmpSize][3];
528 System.arraycopy(tmp, 0, data, 0, tmpSize);
530 fr.setFeaturePriority(data);
532 ap.paintAlignment(true);
535 MyCheckbox selectedCheck;
537 boolean dragging = false;
540 public void mouseDragged(MouseEvent evt)
542 if (((Component) evt.getSource()).getParent() != featurePanel)
550 public void mouseReleased(MouseEvent evt)
552 if (((Component) evt.getSource()).getParent() != featurePanel)
557 Component comp = null;
558 Checkbox target = null;
560 int height = evt.getY() + evt.getComponent().getLocation().y;
562 if (height > featurePanel.getSize().height)
566 .getComponent(featurePanel.getComponentCount() - 1);
570 comp = featurePanel.getComponent(0);
574 comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
575 + evt.getComponent().getLocation().y);
578 if (comp != null && comp instanceof Checkbox)
580 target = (Checkbox) comp;
583 if (selectedCheck != null && target != null && selectedCheck != target)
585 int targetIndex = -1;
586 for (int i = 0; i < featurePanel.getComponentCount(); i++)
588 if (target == featurePanel.getComponent(i))
595 featurePanel.remove(selectedCheck);
596 featurePanel.add(selectedCheck, targetIndex);
597 featurePanel.validate();
598 itemStateChanged(null);
602 public void setUserColour(String feature, Object originalColour)
604 if (originalColour instanceof Color
605 || originalColour instanceof GraduatedColor)
607 fr.setColour(feature, originalColour);
613 .getString("error.implementation_error_unsupported_feature_colour_object"));
618 public void refreshTable()
620 featurePanel.removeAll();
622 ap.paintAlignment(true);
626 public void mouseEntered(MouseEvent evt)
631 public void mouseExited(MouseEvent evt)
636 public void mouseClicked(MouseEvent evt)
638 MyCheckbox check = (MyCheckbox) evt.getSource();
639 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
641 this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
644 if (check.getParent() != featurePanel)
649 if (evt.getClickCount() > 1)
651 Object fcol = fr.getFeatureStyle(check.type);
652 if (fcol instanceof Color)
654 new UserDefinedColours(this, check.type, (Color) fcol);
658 new FeatureColourChooser(this, check.type);
659 // write back the current colour object to update the table
660 check.updateColor(fr.getFeatureStyle(check.type));
666 public void mouseMoved(MouseEvent evt)
671 public void adjustmentValueChanged(AdjustmentEvent evt)
673 fr.setTransparency((100 - transparency.getValue()) / 100f);
674 ap.seqPanel.seqCanvas.repaint();
678 class MyCheckbox extends Checkbox
682 public int stringWidth;
690 public void updateColor(Object newcol)
692 if (newcol instanceof Color)
694 col = (Color) newcol;
697 else if (newcol instanceof GraduatedColor)
699 gcol = (GraduatedColor) newcol;
706 .getString("error.invalid_colour_for_mycheckbox"));
714 String vlabel = type;
715 if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
718 + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
721 if (gcol.isColourByLabel())
723 setBackground(Color.white);
724 vlabel += " (by Label)";
728 setBackground(gcol.getMinColor());
730 this.setLabel(vlabel);
735 public MyCheckbox(String label, boolean checked, boolean haslink)
737 super(label, checked);
739 FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
740 stringWidth = fm.stringWidth(label);
741 this.hasLink = haslink;
744 public MyCheckbox(String type, boolean selected, boolean b,
747 this(type, selected, b);
748 updateColor(featureStyle);
752 public void paint(Graphics g)
754 Dimension d = getSize();
757 if (gcol.isColourByLabel())
759 g.setColor(Color.white);
760 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
762 * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
765 * // g.setFont(g.getFont().deriveFont( //
766 * AffineTransform.getScaleInstance( //
767 * width/g.getFontMetrics().stringWidth("Label"), //
768 * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
775 Color maxCol = gcol.getMaxColor();
777 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
784 g.drawImage(linkImage, stringWidth + 25,
785 (getSize().height - linkImage.getHeight(this)) / 2, this);
791 public void mousePressed(MouseEvent e)