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.Arrays;
61 import java.util.Enumeration;
62 import java.util.List;
64 import java.util.Vector;
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,
192 final String type = check.type;
193 final Object typeCol = fr.getFeatureStyle(type);
194 java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
195 "label.settings_for_type", new String[] { type }));
196 java.awt.MenuItem scr = new MenuItem(
197 MessageManager.getString("label.sort_by_score"));
199 final FeatureSettings me = this;
200 scr.addActionListener(new ActionListener()
204 public void actionPerformed(ActionEvent e)
206 me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
207 .asList(new String[] { type }));
211 MenuItem dens = new MenuItem(
212 MessageManager.getString("label.sort_by_density"));
213 dens.addActionListener(new ActionListener()
217 public void actionPerformed(ActionEvent e)
219 me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
220 .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 instanceof Color) ? "Graduated Colour"
248 mxcol.addActionListener(new ActionListener()
252 public void actionPerformed(ActionEvent e)
254 if (typeCol instanceof Color)
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,
263 ((GraduatedColor) typeCol));
270 this.featurePanel.add(men);
271 men.show(this.featurePanel, x, y);
275 public void discoverAllFeatureData()
277 if (fr.getAllFeatureColours() != null
278 && fr.getAllFeatureColours().size() > 0)
287 * rebuilds the group panel
289 public void rebuildGroups()
291 boolean rdrw = false;
292 if (groupPanel == null)
294 groupPanel = new Panel();
299 groupPanel.removeAll();
301 // TODO: JAL-964 - smoothly incorporate new group entries if panel already
302 // displayed and new groups present
303 for (String group : fr.getFeatureGroups())
305 boolean vis = fr.checkGroupVisibility(group, false);
306 Checkbox check = new MyCheckbox(group, vis, false);
307 check.addMouseListener(this);
308 check.setFont(new Font("Serif", Font.BOLD, 12));
309 check.addItemListener(groupItemListener);
310 // note - visibility seems to correlate with displayed. ???wtf ??
311 check.setVisible(vis);
312 groupPanel.add(check);
316 groupPanel.validate();
320 // This routine adds and removes checkboxes depending on
321 // Group selection states
322 void resetTable(boolean groupsChanged)
324 SequenceFeature[] tmpfeatures;
325 String group = null, type;
326 Vector<String> visibleChecks = new Vector<String>();
327 AlignmentI alignment = av.getAlignment();
328 for (int i = 0; i < alignment.getHeight(); i++)
330 if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
335 tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
337 while (index < tmpfeatures.length)
339 group = tmpfeatures[index].featureGroup;
341 if (group == null || fr.checkGroupVisibility(group, true))
343 type = tmpfeatures[index].getType();
344 if (!visibleChecks.contains(type))
346 visibleChecks.addElement(type);
354 int cSize = featurePanel.getComponentCount();
356 // This will remove any checkboxes which shouldn't be
358 for (int i = 0; i < cSize; i++)
360 comps = featurePanel.getComponents();
361 check = (MyCheckbox) comps[i];
362 if (!visibleChecks.contains(check.type))
364 featurePanel.remove(i);
370 if (fr.getRenderOrder() != null)
372 // First add the checks in the previous render order,
373 // in case the window has been closed and reopened
374 List<String> rol = fr.getRenderOrder();
375 for (int ro = rol.size() - 1; ro > -1; ro--)
377 String item = rol.get(ro);
379 if (!visibleChecks.contains(item))
384 visibleChecks.removeElement(item);
386 addCheck(false, item);
390 // now add checkboxes which should be visible,
391 // if they have not already been added
392 Enumeration<String> en = visibleChecks.elements();
394 while (en.hasMoreElements())
396 addCheck(groupsChanged, en.nextElement().toString());
399 featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
401 featurePanel.validate();
403 if (scrollPane != null)
405 scrollPane.validate();
408 itemStateChanged(null);
412 * update the checklist of feature types with the given type
414 * @param groupsChanged
415 * true means if the type is not in the display list then it will be
416 * added and displayed
418 * feature type to be checked for in the list.
420 void addCheck(boolean groupsChanged, String type)
423 Component[] comps = featurePanel.getComponents();
426 for (int i = 0; i < featurePanel.getComponentCount(); i++)
428 check = (MyCheckbox) comps[i];
429 if (check.type.equals(type))
438 boolean selected = false;
439 if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
444 check = new MyCheckbox(type, selected, false,
445 fr.getFeatureStyle(type));
447 check.addMouseListener(this);
448 check.addMouseMotionListener(this);
449 check.addItemListener(this);
452 // add at beginning of stack.
453 featurePanel.add(check, 0);
457 // add at end of stack.
458 featurePanel.add(check);
464 public void actionPerformed(ActionEvent evt)
466 for (int i = 0; i < featurePanel.getComponentCount(); i++)
468 Checkbox check = (Checkbox) featurePanel.getComponent(i);
469 check.setState(!check.getState());
474 private ItemListener groupItemListener = new ItemListener()
477 public void itemStateChanged(ItemEvent evt)
479 Checkbox source = (Checkbox) evt.getSource();
480 fr.setGroupVisibility(source.getLabel(), source.getState());
481 ap.seqPanel.seqCanvas.repaint();
482 if (ap.overviewPanel != null)
484 ap.overviewPanel.updateOverviewImage();
492 public void itemStateChanged(ItemEvent evt)
497 void selectionChanged()
499 Component[] comps = featurePanel.getComponents();
500 int cSize = comps.length;
502 Object[][] tmp = new Object[cSize][3];
504 for (int i = 0; i < cSize; i++)
506 MyCheckbox check = (MyCheckbox) comps[i];
507 tmp[tmpSize][0] = check.type;
508 tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
509 tmp[tmpSize][2] = new Boolean(check.getState());
513 Object[][] data = new Object[tmpSize][3];
514 System.arraycopy(tmp, 0, data, 0, tmpSize);
516 fr.setFeaturePriority(data);
518 ap.paintAlignment(true);
521 MyCheckbox selectedCheck;
523 boolean dragging = false;
526 public void mouseDragged(MouseEvent evt)
528 if (((Component) evt.getSource()).getParent() != featurePanel)
536 public void mouseReleased(MouseEvent evt)
538 if (((Component) evt.getSource()).getParent() != featurePanel)
543 Component comp = null;
544 Checkbox target = null;
546 int height = evt.getY() + evt.getComponent().getLocation().y;
548 if (height > featurePanel.getSize().height)
552 .getComponent(featurePanel.getComponentCount() - 1);
556 comp = featurePanel.getComponent(0);
560 comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
561 + evt.getComponent().getLocation().y);
564 if (comp != null && comp instanceof Checkbox)
566 target = (Checkbox) comp;
569 if (selectedCheck != null && target != null && selectedCheck != target)
571 int targetIndex = -1;
572 for (int i = 0; i < featurePanel.getComponentCount(); i++)
574 if (target == featurePanel.getComponent(i))
581 featurePanel.remove(selectedCheck);
582 featurePanel.add(selectedCheck, targetIndex);
583 featurePanel.validate();
584 itemStateChanged(null);
588 public void setUserColour(String feature, Object originalColour)
590 if (originalColour instanceof Color
591 || originalColour instanceof GraduatedColor)
593 fr.setColour(feature, originalColour);
599 .getString("error.implementation_error_unsupported_feature_colour_object"));
604 public void refreshTable()
606 featurePanel.removeAll();
608 ap.paintAlignment(true);
612 public void mouseEntered(MouseEvent evt)
617 public void mouseExited(MouseEvent evt)
622 public void mouseClicked(MouseEvent evt)
624 MyCheckbox check = (MyCheckbox) evt.getSource();
625 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
627 this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
630 if (check.getParent() != featurePanel)
635 if (evt.getClickCount() > 1)
637 Object fcol = fr.getFeatureStyle(check.type);
638 if (fcol instanceof Color)
640 new UserDefinedColours(this, check.type, (Color) fcol);
644 new FeatureColourChooser(this, check.type);
645 // write back the current colour object to update the table
646 check.updateColor(fr.getFeatureStyle(check.type));
652 public void mouseMoved(MouseEvent evt)
657 public void adjustmentValueChanged(AdjustmentEvent evt)
659 fr.setTransparency((100 - transparency.getValue()) / 100f);
660 ap.seqPanel.seqCanvas.repaint();
664 class MyCheckbox extends Checkbox
668 public int stringWidth;
676 public void updateColor(Object newcol)
678 if (newcol instanceof Color)
680 col = (Color) newcol;
683 else if (newcol instanceof GraduatedColor)
685 gcol = (GraduatedColor) newcol;
692 .getString("error.invalid_colour_for_mycheckbox"));
700 String vlabel = type;
701 if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
704 + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
707 if (gcol.isColourByLabel())
709 setBackground(Color.white);
710 vlabel += " (by Label)";
714 setBackground(gcol.getMinColor());
716 this.setLabel(vlabel);
721 public MyCheckbox(String label, boolean checked, boolean haslink)
723 super(label, checked);
725 FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
726 stringWidth = fm.stringWidth(label);
727 this.hasLink = haslink;
730 public MyCheckbox(String type, boolean selected, boolean b,
733 this(type, selected, b);
734 updateColor(featureStyle);
738 public void paint(Graphics g)
740 Dimension d = getSize();
743 if (gcol.isColourByLabel())
745 g.setColor(Color.white);
746 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
748 * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
751 * // g.setFont(g.getFont().deriveFont( //
752 * AffineTransform.getScaleInstance( //
753 * width/g.getFontMetrics().stringWidth("Label"), //
754 * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
761 Color maxCol = gcol.getMaxColor();
763 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
770 g.drawImage(linkImage, stringWidth + 25,
771 (getSize().height - linkImage.getHeight(this)) / 2, this);
777 public void mousePressed(MouseEvent e)