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()
168 public void windowClosing(WindowEvent e)
170 if (me.av.featureSettings == me)
172 me.av.featureSettings = null;
178 int height = featurePanel.getComponentCount() * 50 + 60;
180 height = Math.max(200, height);
181 height = Math.min(400, height);
183 jalview.bin.JalviewLite.addFrame(frame,
184 MessageManager.getString("label.sequence_feature_settings"),
188 public void paint(Graphics g)
190 g.setColor(Color.black);
191 g.drawString(MessageManager
192 .getString("label.no_features_added_to_this_alignment"), 10, 20);
193 g.drawString(MessageManager
194 .getString("label.features_can_be_added_from_searches_1"), 10,
196 g.drawString(MessageManager
197 .getString("label.features_can_be_added_from_searches_2"), 10,
201 protected void popupSort(final MyCheckbox check, final Hashtable minmax,
204 final String type = check.type;
205 final Object typeCol = fr.getFeatureStyle(type);
206 java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
207 "label.settings_for_type", new String[] { type }));
208 java.awt.MenuItem scr = new MenuItem(
209 MessageManager.getString("label.sort_by_score"));
211 final FeatureSettings me = this;
212 scr.addActionListener(new ActionListener()
215 public void actionPerformed(ActionEvent e)
218 .sortAlignmentByFeatureScore(new String[] { type });
222 MenuItem dens = new MenuItem(
223 MessageManager.getString("label.sort_by_density"));
224 dens.addActionListener(new ActionListener()
227 public void actionPerformed(ActionEvent e)
230 .sortAlignmentByFeatureDensity(new String[] { type });
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.getState()); if (chb.getState()) { 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 MenuItem mxcol = new MenuItem(
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
287 && fr.getAllFeatureColours().size() > 0)
296 * rebuilds the group panel
298 public void rebuildGroups()
300 boolean rdrw = false;
301 if (groupPanel == null)
303 groupPanel = new Panel();
308 groupPanel.removeAll();
310 // TODO: JAL-964 - smoothly incorporate new group entries if panel already
311 // displayed and new groups present
312 for (String group : fr.getFeatureGroups())
314 boolean vis = fr.checkGroupVisibility(group, false);
315 Checkbox check = new MyCheckbox(group, vis,
316 (fr.featureLinks != null && fr.featureLinks
317 .containsKey(group)));
318 check.addMouseListener(this);
319 check.setFont(new Font("Serif", Font.BOLD, 12));
320 check.addItemListener(groupItemListener);
321 // note - visibility seems to correlate with displayed. ???wtf ??
322 check.setVisible(vis);
323 groupPanel.add(check);
327 groupPanel.validate();
331 // This routine adds and removes checkboxes depending on
332 // Group selection states
333 void resetTable(boolean groupsChanged)
335 SequenceFeature[] tmpfeatures;
336 String group = null, type;
337 Vector visibleChecks = new Vector();
338 AlignmentI alignment = av.getAlignment();
339 for (int i = 0; i < alignment.getHeight(); i++)
341 if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
346 tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
348 while (index < tmpfeatures.length)
350 group = tmpfeatures[index].featureGroup;
352 if (group == null || fr.checkGroupVisibility(group, true))
354 type = tmpfeatures[index].getType();
355 if (!visibleChecks.contains(type))
357 visibleChecks.addElement(type);
365 int cSize = featurePanel.getComponentCount();
367 // This will remove any checkboxes which shouldn't be
369 for (int i = 0; i < cSize; i++)
371 comps = featurePanel.getComponents();
372 check = (MyCheckbox) comps[i];
373 if (!visibleChecks.contains(check.type))
375 featurePanel.remove(i);
381 if (fr.getRenderOrder() != null)
383 // First add the checks in the previous render order,
384 // in case the window has been closed and reopened
385 List<String> rol = fr.getRenderOrder();
386 for (int ro = rol.size() - 1; ro > -1; ro--)
388 String item = rol.get(ro);
390 if (!visibleChecks.contains(item))
395 visibleChecks.removeElement(item);
397 addCheck(false, item);
401 // now add checkboxes which should be visible,
402 // if they have not already been added
403 Enumeration en = visibleChecks.elements();
405 while (en.hasMoreElements())
407 addCheck(groupsChanged, en.nextElement().toString());
410 featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
412 featurePanel.validate();
414 if (scrollPane != null)
416 scrollPane.validate();
419 itemStateChanged(null);
423 * update the checklist of feature types with the given type
425 * @param groupsChanged
426 * true means if the type is not in the display list then it will be
427 * added and displayed
429 * feature type to be checked for in the list.
431 void addCheck(boolean groupsChanged, String type)
434 Component[] comps = featurePanel.getComponents();
437 for (int i = 0; i < featurePanel.getComponentCount(); i++)
439 check = (MyCheckbox) comps[i];
440 if (check.type.equals(type))
449 boolean selected = false;
450 if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
455 check = new MyCheckbox(
458 (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
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);
477 public void actionPerformed(ActionEvent evt)
479 for (int i = 0; i < featurePanel.getComponentCount(); i++)
481 Checkbox check = (Checkbox) featurePanel.getComponent(i);
482 check.setState(!check.getState());
487 private ItemListener groupItemListener = new ItemListener()
489 public void itemStateChanged(ItemEvent evt)
491 Checkbox source = (Checkbox) evt.getSource();
492 fr.setGroupVisibility(source.getLabel(), source.getState());
493 ap.seqPanel.seqCanvas.repaint();
494 if (ap.overviewPanel != null)
496 ap.overviewPanel.updateOverviewImage();
503 public void itemStateChanged(ItemEvent evt)
508 void selectionChanged()
510 Component[] comps = featurePanel.getComponents();
511 int cSize = comps.length;
513 Object[][] tmp = new Object[cSize][3];
515 for (int i = 0; i < cSize; i++)
517 MyCheckbox check = (MyCheckbox) comps[i];
518 tmp[tmpSize][0] = check.type;
519 tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
520 tmp[tmpSize][2] = new Boolean(check.getState());
524 Object[][] data = new Object[tmpSize][3];
525 System.arraycopy(tmp, 0, data, 0, tmpSize);
527 fr.setFeaturePriority(data);
529 ap.paintAlignment(true);
532 MyCheckbox selectedCheck;
534 boolean dragging = false;
536 public void mousePressed(MouseEvent evt)
539 selectedCheck = (MyCheckbox) evt.getSource();
541 if (fr.featureLinks != null
542 && fr.featureLinks.containsKey(selectedCheck.type))
544 if (evt.getX() > selectedCheck.stringWidth + 20)
552 public void mouseDragged(MouseEvent evt)
554 if (((Component) evt.getSource()).getParent() != featurePanel)
561 public void mouseReleased(MouseEvent evt)
563 if (((Component) evt.getSource()).getParent() != featurePanel)
568 Component comp = null;
569 Checkbox target = null;
571 int height = evt.getY() + evt.getComponent().getLocation().y;
573 if (height > featurePanel.getSize().height)
577 .getComponent(featurePanel.getComponentCount() - 1);
581 comp = featurePanel.getComponent(0);
585 comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
586 + evt.getComponent().getLocation().y);
589 if (comp != null && comp instanceof Checkbox)
591 target = (Checkbox) comp;
594 if (selectedCheck != null && target != null && selectedCheck != target)
596 int targetIndex = -1;
597 for (int i = 0; i < featurePanel.getComponentCount(); i++)
599 if (target == featurePanel.getComponent(i))
606 featurePanel.remove(selectedCheck);
607 featurePanel.add(selectedCheck, targetIndex);
608 featurePanel.validate();
609 itemStateChanged(null);
613 public void setUserColour(String feature, Object originalColour)
615 if (originalColour instanceof Color
616 || originalColour instanceof GraduatedColor)
618 fr.setColour(feature, originalColour);
624 .getString("error.implementation_error_unsupported_feature_colour_object"));
629 public void refreshTable()
631 featurePanel.removeAll();
633 ap.paintAlignment(true);
636 public void mouseEntered(MouseEvent evt)
640 public void mouseExited(MouseEvent evt)
644 public void mouseClicked(MouseEvent evt)
646 MyCheckbox check = (MyCheckbox) evt.getSource();
647 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
649 this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
651 if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
653 if (evt.getX() > check.stringWidth + 20)
656 String link = fr.featureLinks.get(check.type).toString();
657 ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
658 link.substring(0, link.indexOf("|")));
662 if (check.getParent() != featurePanel)
667 if (evt.getClickCount() > 1)
669 Object fcol = fr.getFeatureStyle(check.type);
670 if (fcol instanceof Color)
672 new UserDefinedColours(this, check.type, (Color) fcol);
676 new FeatureColourChooser(this, check.type);
677 // write back the current colour object to update the table
678 check.updateColor(fr.getFeatureStyle(check.type));
683 public void mouseMoved(MouseEvent evt)
687 public void adjustmentValueChanged(AdjustmentEvent evt)
689 fr.setTransparency((100 - transparency.getValue()) / 100f);
690 ap.seqPanel.seqCanvas.repaint();
694 class MyCheckbox extends Checkbox
698 public int stringWidth;
706 public void updateColor(Object newcol)
708 if (newcol instanceof Color)
710 col = (Color) newcol;
713 else if (newcol instanceof GraduatedColor)
715 gcol = (GraduatedColor) newcol;
722 .getString("error.invalid_colour_for_mycheckbox"));
730 String vlabel = type;
731 if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
734 + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
737 if (gcol.isColourByLabel())
739 setBackground(Color.white);
740 vlabel += " (by Label)";
744 setBackground(gcol.getMinColor());
746 this.setLabel(vlabel);
751 public MyCheckbox(String label, boolean checked, boolean haslink)
753 super(label, checked);
755 FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
756 stringWidth = fm.stringWidth(label);
757 this.hasLink = haslink;
760 public MyCheckbox(String type, boolean selected, boolean b,
763 this(type, selected, b);
764 updateColor(featureStyle);
767 public void paint(Graphics g)
769 Dimension d = getSize();
772 if (gcol.isColourByLabel())
774 g.setColor(Color.white);
775 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
777 * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
780 * // g.setFont(g.getFont().deriveFont( //
781 * AffineTransform.getScaleInstance( //
782 * width/g.getFontMetrics().stringWidth("Label"), //
783 * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
790 Color maxCol = gcol.getMaxColor();
792 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
799 g.drawImage(linkImage, stringWidth + 25,
800 (getSize().height - linkImage.getHeight(this)) / 2, this);