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.FeatureColourI;
24 import jalview.api.FeatureSettingsControllerI;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.SequenceI;
27 import jalview.util.MessageManager;
29 import java.awt.BorderLayout;
30 import java.awt.Button;
31 import java.awt.Checkbox;
32 import java.awt.Color;
33 import java.awt.Component;
34 import java.awt.Dimension;
36 import java.awt.FontMetrics;
37 import java.awt.Frame;
38 import java.awt.Graphics;
39 import java.awt.GridLayout;
40 import java.awt.Image;
41 import java.awt.Label;
42 import java.awt.MenuItem;
43 import java.awt.Panel;
44 import java.awt.PopupMenu;
45 import java.awt.ScrollPane;
46 import java.awt.Scrollbar;
47 import java.awt.event.ActionEvent;
48 import java.awt.event.ActionListener;
49 import java.awt.event.AdjustmentEvent;
50 import java.awt.event.AdjustmentListener;
51 import java.awt.event.InputEvent;
52 import java.awt.event.ItemEvent;
53 import java.awt.event.ItemListener;
54 import java.awt.event.MouseEvent;
55 import java.awt.event.MouseListener;
56 import java.awt.event.MouseMotionListener;
57 import java.awt.event.WindowAdapter;
58 import java.awt.event.WindowEvent;
59 import java.util.ArrayList;
60 import java.util.Arrays;
61 import java.util.HashSet;
62 import java.util.List;
66 public class FeatureSettings extends Panel implements ItemListener,
67 MouseListener, MouseMotionListener, ActionListener,
68 AdjustmentListener, FeatureSettingsControllerI
80 Panel featurePanel = new Panel();
82 ScrollPane scrollPane;
86 Scrollbar transparency;
88 public FeatureSettings(final AlignmentPanel ap)
92 ap.av.featureSettings = this;
93 fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
95 transparency = new Scrollbar(Scrollbar.HORIZONTAL,
96 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
98 transparency.addAdjustmentListener(this);
100 java.net.URL url = getClass().getResource("/images/link.gif");
103 linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
106 if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())
108 fr.findAllFeatures(true); // was default - now true to make all visible
111 discoverAllFeatureData();
113 this.setLayout(new BorderLayout());
114 scrollPane = new ScrollPane();
115 scrollPane.add(featurePanel);
116 if (fr.getAllFeatureColours() != null
117 && fr.getAllFeatureColours().size() > 0)
119 add(scrollPane, BorderLayout.CENTER);
122 Button invert = new Button("Invert Selection");
123 invert.addActionListener(this);
125 Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
126 lowerPanel.add(invert);
128 Panel tPanel = new Panel(new BorderLayout());
130 tPanel.add(transparency, BorderLayout.CENTER);
131 tPanel.add(new Label("Transparency"), BorderLayout.EAST);
133 lowerPanel.add(tPanel, BorderLayout.SOUTH);
135 add(lowerPanel, BorderLayout.SOUTH);
137 if (groupPanel != null)
139 groupPanel.setLayout(new GridLayout(
140 (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
141 // scaled on number of
142 // visible groups. seems
144 groupPanel.validate();
146 add(groupPanel, BorderLayout.NORTH);
150 final FeatureSettings me = this;
151 frame.addWindowListener(new WindowAdapter()
154 public void windowClosing(WindowEvent e)
156 if (me.av.featureSettings == me)
158 me.av.featureSettings = null;
164 int height = featurePanel.getComponentCount() * 50 + 60;
166 height = Math.max(200, height);
167 height = Math.min(400, height);
169 jalview.bin.JalviewLite.addFrame(frame,
170 MessageManager.getString("label.sequence_feature_settings"),
175 public void paint(Graphics g)
177 g.setColor(Color.black);
178 g.drawString(MessageManager
179 .getString("label.no_features_added_to_this_alignment"), 10, 20);
180 g.drawString(MessageManager
181 .getString("label.features_can_be_added_from_searches_1"), 10,
183 g.drawString(MessageManager
184 .getString("label.features_can_be_added_from_searches_2"), 10,
188 protected void popupSort(final MyCheckbox check,
189 final Map<String, float[][]> minmax, int x, int y)
191 final String type = check.type;
192 final FeatureColourI typeCol = fr.getFeatureStyle(type);
193 PopupMenu men = new PopupMenu(MessageManager.formatMessage(
194 "label.settings_for_type", new String[] { type }));
195 java.awt.MenuItem scr = new MenuItem(
196 MessageManager.getString("label.sort_by_score"));
198 final FeatureSettings me = this;
199 scr.addActionListener(new ActionListener()
203 public void actionPerformed(ActionEvent e)
205 me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
206 .asList(new String[] { type }));
210 MenuItem dens = new MenuItem(
211 MessageManager.getString("label.sort_by_density"));
212 dens.addActionListener(new ActionListener()
216 public void actionPerformed(ActionEvent e)
218 me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
219 .asList(new String[] { type }));
227 final float[][] typeMinMax = minmax.get(type);
229 * final java.awt.CheckboxMenuItem chb = new
230 * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
231 * moment chb.setState(minmax.get(type) != null);
232 * chb.addActionListener(new ActionListener() {
234 * public void actionPerformed(ActionEvent e) {
235 * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
236 * null); } else { minmax.put(type, typeMinMax); } }
240 if (typeMinMax != null && typeMinMax[0] != null)
242 // graduated colourschemes for those where minmax exists for the
243 // positional features
244 MenuItem mxcol = new MenuItem(
245 (typeCol.isSimpleColour()) ? "Graduated Colour"
248 mxcol.addActionListener(new ActionListener()
252 public void actionPerformed(ActionEvent e)
254 if (typeCol.isSimpleColour())
256 new FeatureColourChooser(me, type);
257 // write back the current colour object to update the table
258 check.updateColor(fr.getFeatureStyle(type));
262 new UserDefinedColours(me, check.type, typeCol);
270 MenuItem selectContaining = new MenuItem(
271 MessageManager.getString("label.select_columns_containing"));
272 selectContaining.addActionListener(new ActionListener()
275 public void actionPerformed(ActionEvent e)
277 me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
281 men.add(selectContaining);
283 MenuItem selectNotContaining = new MenuItem(
284 MessageManager.getString("label.select_columns_not_containing"));
285 selectNotContaining.addActionListener(new ActionListener()
288 public void actionPerformed(ActionEvent e)
290 me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
294 men.add(selectNotContaining);
296 MenuItem hideContaining = new MenuItem(
297 MessageManager.getString("label.hide_columns_containing"));
298 hideContaining.addActionListener(new ActionListener()
301 public void actionPerformed(ActionEvent e)
303 hideFeatureColumns(type, true);
306 men.add(hideContaining);
308 MenuItem hideNotContaining = new MenuItem(
309 MessageManager.getString("label.hide_columns_not_containing"));
310 hideNotContaining.addActionListener(new ActionListener()
313 public void actionPerformed(ActionEvent e)
315 hideFeatureColumns(type, false);
318 men.add(hideNotContaining);
320 this.featurePanel.add(men);
321 men.show(this.featurePanel, x, y);
325 public void discoverAllFeatureData()
327 if (fr.getAllFeatureColours() != null
328 && fr.getAllFeatureColours().size() > 0)
337 * rebuilds the group panel
339 public void rebuildGroups()
341 boolean rdrw = false;
342 if (groupPanel == null)
344 groupPanel = new Panel();
349 groupPanel.removeAll();
351 // TODO: JAL-964 - smoothly incorporate new group entries if panel already
352 // displayed and new groups present
353 for (String group : fr.getFeatureGroups())
355 boolean vis = fr.checkGroupVisibility(group, false);
356 Checkbox check = new MyCheckbox(group, vis, false);
357 check.addMouseListener(this);
358 check.setFont(new Font("Serif", Font.BOLD, 12));
359 check.addItemListener(groupItemListener);
360 // note - visibility seems to correlate with displayed. ???wtf ??
361 check.setVisible(vis);
362 groupPanel.add(check);
366 groupPanel.validate();
370 // This routine adds and removes checkboxes depending on
371 // Group selection states
372 void resetTable(boolean groupsChanged)
374 List<String> displayableTypes = new ArrayList<String>();
375 AlignmentI alignment = av.getAlignment();
376 for (int i = 0; i < alignment.getHeight(); i++)
378 SequenceI seq = alignment.getSequenceAt(i);
381 * get the sequence's groups for positional features
382 * and keep track of which groups are visible
384 Set<String> groups = seq.getFeatures().getFeatureGroups(true);
385 Set<String> visibleGroups = new HashSet<String>();
386 for (String group : groups)
388 if (group == null || fr.checkGroupVisibility(group, true))
390 visibleGroups.add(group);
395 * get distinct feature types for visible groups
396 * record distinct visible types
398 Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
399 visibleGroups.toArray(new String[visibleGroups.size()]));
400 displayableTypes.addAll(types);
404 int cSize = featurePanel.getComponentCount();
406 // This will remove any checkboxes which shouldn't be
408 for (int i = 0; i < cSize; i++)
410 comps = featurePanel.getComponents();
411 check = (MyCheckbox) comps[i];
412 if (!displayableTypes.contains(check.type))
414 featurePanel.remove(i);
420 if (fr.getRenderOrder() != null)
422 // First add the checks in the previous render order,
423 // in case the window has been closed and reopened
424 List<String> rol = fr.getRenderOrder();
425 for (int ro = rol.size() - 1; ro > -1; ro--)
427 String item = rol.get(ro);
429 if (!displayableTypes.contains(item))
434 displayableTypes.remove(item);
436 addCheck(false, item);
441 * now add checkboxes which should be visible,
442 * if they have not already been added
444 for (String type : displayableTypes)
446 addCheck(groupsChanged, type);
449 featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
451 featurePanel.validate();
453 if (scrollPane != null)
455 scrollPane.validate();
458 itemStateChanged(null);
462 * update the checklist of feature types with the given type
464 * @param groupsChanged
465 * true means if the type is not in the display list then it will be
466 * added and displayed
468 * feature type to be checked for in the list.
470 void addCheck(boolean groupsChanged, String type)
473 Component[] comps = featurePanel.getComponents();
476 for (int i = 0; i < featurePanel.getComponentCount(); i++)
478 check = (MyCheckbox) comps[i];
479 if (check.type.equals(type))
488 boolean selected = false;
489 if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
494 check = new MyCheckbox(type, selected, false,
495 fr.getFeatureStyle(type));
497 check.addMouseListener(this);
498 check.addMouseMotionListener(this);
499 check.addItemListener(this);
502 // add at beginning of stack.
503 featurePanel.add(check, 0);
507 // add at end of stack.
508 featurePanel.add(check);
514 public void actionPerformed(ActionEvent evt)
516 for (int i = 0; i < featurePanel.getComponentCount(); i++)
518 Checkbox check = (Checkbox) featurePanel.getComponent(i);
519 check.setState(!check.getState());
524 private ItemListener groupItemListener = new ItemListener()
527 public void itemStateChanged(ItemEvent evt)
529 Checkbox source = (Checkbox) evt.getSource();
530 fr.setGroupVisibility(source.getLabel(), source.getState());
531 ap.seqPanel.seqCanvas.repaint();
532 if (ap.overviewPanel != null)
534 ap.overviewPanel.updateOverviewImage();
542 public void itemStateChanged(ItemEvent evt)
547 void selectionChanged()
549 Component[] comps = featurePanel.getComponents();
550 int cSize = comps.length;
552 Object[][] tmp = new Object[cSize][3];
554 for (int i = 0; i < cSize; i++)
556 MyCheckbox check = (MyCheckbox) comps[i];
557 tmp[tmpSize][0] = check.type;
558 tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
559 tmp[tmpSize][2] = new Boolean(check.getState());
563 Object[][] data = new Object[tmpSize][3];
564 System.arraycopy(tmp, 0, data, 0, tmpSize);
566 fr.setFeaturePriority(data);
568 ap.paintAlignment(true);
571 MyCheckbox selectedCheck;
573 boolean dragging = false;
576 public void mouseDragged(MouseEvent evt)
578 if (((Component) evt.getSource()).getParent() != featurePanel)
586 public void mouseReleased(MouseEvent evt)
588 if (((Component) evt.getSource()).getParent() != featurePanel)
593 Component comp = null;
594 Checkbox target = null;
596 int height = evt.getY() + evt.getComponent().getLocation().y;
598 if (height > featurePanel.getSize().height)
602 .getComponent(featurePanel.getComponentCount() - 1);
606 comp = featurePanel.getComponent(0);
610 comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
611 + evt.getComponent().getLocation().y);
614 if (comp != null && comp instanceof Checkbox)
616 target = (Checkbox) comp;
619 if (selectedCheck != null && target != null && selectedCheck != target)
621 int targetIndex = -1;
622 for (int i = 0; i < featurePanel.getComponentCount(); i++)
624 if (target == featurePanel.getComponent(i))
631 featurePanel.remove(selectedCheck);
632 featurePanel.add(selectedCheck, targetIndex);
633 featurePanel.validate();
634 itemStateChanged(null);
638 public void setUserColour(String feature, FeatureColourI originalColour)
640 fr.setColour(feature, originalColour);
644 public void refreshTable()
646 featurePanel.removeAll();
648 ap.paintAlignment(true);
652 public void mouseEntered(MouseEvent evt)
657 public void mouseExited(MouseEvent evt)
662 public void mouseClicked(MouseEvent evt)
664 MyCheckbox check = (MyCheckbox) evt.getSource();
665 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
667 this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
670 if (check.getParent() != featurePanel)
675 if (evt.getClickCount() > 1)
677 FeatureColourI fcol = fr.getFeatureStyle(check.type);
678 if (fcol.isSimpleColour())
680 new UserDefinedColours(this, check.type, fcol.getColour());
684 new FeatureColourChooser(this, check.type);
685 // write back the current colour object to update the table
686 check.updateColor(fr.getFeatureStyle(check.type));
692 public void mouseMoved(MouseEvent evt)
697 public void adjustmentValueChanged(AdjustmentEvent evt)
699 fr.setTransparency((100 - transparency.getValue()) / 100f);
700 ap.paintAlignment(true);
703 class MyCheckbox extends Checkbox
707 public int stringWidth;
713 public void updateColor(FeatureColourI newcol)
716 if (col.isSimpleColour())
718 setBackground(col.getColour());
722 String vlabel = type;
723 if (col.isAboveThreshold())
727 else if (col.isBelowThreshold())
731 if (col.isColourByLabel())
733 setBackground(Color.white);
734 vlabel += " (by Label)";
738 setBackground(col.getMinColour());
740 this.setLabel(vlabel);
745 public MyCheckbox(String label, boolean checked, boolean haslink)
747 super(label, checked);
749 FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
750 stringWidth = fm.stringWidth(label);
751 this.hasLink = haslink;
754 public MyCheckbox(String type, boolean selected, boolean b,
755 FeatureColourI featureStyle)
757 this(type, selected, b);
758 updateColor(featureStyle);
762 public void paint(Graphics g)
764 Dimension d = getSize();
767 if (col.isColourByLabel())
769 g.setColor(Color.white);
770 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
772 * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
775 * // g.setFont(g.getFont().deriveFont( //
776 * AffineTransform.getScaleInstance( //
777 * width/g.getFontMetrics().stringWidth("Label"), //
778 * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
783 else if (col.isGraduatedColour())
785 Color maxCol = col.getMaxColour();
787 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
794 g.drawImage(linkImage, stringWidth + 25,
795 (getSize().height - linkImage.getHeight(this)) / 2, this);
801 * Hide columns containing (or not containing) a given feature type
804 * @param columnsContaining
806 void hideFeatureColumns(final String type, boolean columnsContaining)
808 if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
811 if (ap.alignFrame.avc.markColumnsContainingFeatures(
812 !columnsContaining, false, false, type))
814 ap.alignFrame.viewport.hideSelectedColumns();
820 public void mousePressed(MouseEvent e)
822 // TODO Auto-generated method stub