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.
23 import jalview.datamodel.Sequence;
24 import jalview.datamodel.SequenceFeature;
25 import jalview.datamodel.SequenceGroup;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.SequenceAnnotationReport;
28 import jalview.util.MessageManager;
29 import jalview.util.Platform;
30 import jalview.viewmodel.AlignmentViewport;
31 import jalview.viewmodel.ViewportRanges;
33 import java.awt.BorderLayout;
34 import java.awt.event.MouseEvent;
35 import java.awt.event.MouseListener;
36 import java.awt.event.MouseMotionListener;
37 import java.awt.event.MouseWheelEvent;
38 import java.awt.event.MouseWheelListener;
39 import java.util.List;
41 import javax.swing.JPanel;
42 import javax.swing.SwingUtilities;
43 import javax.swing.ToolTipManager;
46 * This panel hosts alignment sequence ids and responds to mouse clicks on them,
47 * as well as highlighting ids matched by a search from the Find menu.
52 public class IdPanel extends JPanel
53 implements MouseListener, MouseMotionListener, MouseWheelListener
55 private IdCanvas idCanvas;
57 protected AlignmentViewport av;
59 protected AlignmentPanel alignPanel;
61 ScrollThread scrollThread = null;
70 boolean mouseDragging = false;
72 private final SequenceAnnotationReport seqAnnotReport;
75 * Creates a new IdPanel object.
80 public IdPanel(AlignViewport av, AlignmentPanel parent)
84 setIdCanvas(new IdCanvas(av));
85 linkImageURL = getClass().getResource("/images/link.gif").toString();
86 seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
87 setLayout(new BorderLayout());
88 add(getIdCanvas(), BorderLayout.CENTER);
89 addMouseListener(this);
90 addMouseMotionListener(this);
91 addMouseWheelListener(this);
92 ToolTipManager.sharedInstance().registerComponent(this);
96 * Respond to mouse movement by constructing tooltip text for the sequence id
103 public void mouseMoved(MouseEvent e)
105 SeqPanel sp = alignPanel.getSeqPanel();
106 int seq = Math.max(0, sp.findSeq(e));
107 if (seq > -1 && seq < av.getAlignment().getHeight())
109 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
110 StringBuilder tip = new StringBuilder(64);
111 seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
112 av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
113 setToolTipText(JvSwingUtils.wrapTooltip(true,
114 sequence.getDisplayId(true) + " " + tip.toString()));
119 * Responds to a mouse drag by selecting the sequences under the dragged
125 public void mouseDragged(MouseEvent e)
127 mouseDragging = true;
129 int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
133 selectSeqs(lastid - 1, seq);
135 else if (seq > lastid)
137 selectSeqs(lastid + 1, seq);
141 alignPanel.paintAlignment(false, false);
145 * Response to the mouse wheel by scrolling the alignment panel.
148 public void mouseWheelMoved(MouseWheelEvent e)
151 double wheelRotation = e.getPreciseWheelRotation();
152 if (wheelRotation > 0)
156 av.getRanges().scrollRight(true);
160 av.getRanges().scrollUp(false);
163 else if (wheelRotation < 0)
167 av.getRanges().scrollRight(false);
171 av.getRanges().scrollUp(true);
177 * Handle a mouse click event. Currently only responds to a double-click. The
178 * action is to try to open a browser window at a URL that searches for the
179 * selected sequence id. The search URL is configured in Preferences |
180 * Connections | URL link from Sequence ID. For example:
182 * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
187 public void mouseClicked(MouseEvent e)
190 * Ignore single click. Ignore 'left' click followed by 'right' click (user
191 * selects a row then its pop-up menu).
193 if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e))
195 // reinstate isRightMouseButton check to ignore mouse-related popup events
196 // note - this does nothing on default MacBookPro force-trackpad config!
200 int seq = alignPanel.getSeqPanel().findSeq(e);
201 String id = av.getAlignment().getSequenceAt(seq).getName();
202 String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
206 jalview.util.BrowserLauncher.openURL(url);
207 } catch (Exception ex)
209 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
210 MessageManager.getString("label.web_browser_not_found_unix"),
211 MessageManager.getString("label.web_browser_not_found"),
212 JvOptionPane.WARNING_MESSAGE);
213 ex.printStackTrace();
224 public void mouseEntered(MouseEvent e)
226 if (scrollThread != null)
228 scrollThread.stopScrolling();
239 public void mouseExited(MouseEvent e)
241 if (av.getWrapAlignment())
246 if (mouseDragging && (e.getY() < 0)
247 && (av.getRanges().getStartSeq() > 0))
249 scrollThread = new ScrollThread(true);
252 if (mouseDragging && (e.getY() >= getHeight())
253 && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
255 scrollThread = new ScrollThread(false);
260 * Respond to a mouse press. Does nothing for (left) double-click as this is
261 * handled by mouseClicked().
263 * Right mouse down - construct and show context menu.
265 * Ctrl-down or Shift-down - add to or expand current selection group if there
268 * Mouse down - select this sequence.
273 public void mousePressed(MouseEvent e)
275 if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
280 if (e.isPopupTrigger()) // Mac reports this in mousePressed
287 * defer right-mouse click handling to mouseReleased on Windows
288 * (where isPopupTrigger() will answer true)
289 * NB isRightMouseButton is also true for Cmd-click on Mac
291 if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac())
296 if ((av.getSelectionGroup() == null)
297 || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
298 && av.getSelectionGroup() != null))
300 av.setSelectionGroup(new SequenceGroup());
301 av.getSelectionGroup().setStartRes(0);
302 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
305 int seq = alignPanel.getSeqPanel().findSeq(e);
306 if (e.isShiftDown() && (lastid != -1))
308 selectSeqs(lastid, seq);
315 av.isSelectionGroupChanged(true);
317 alignPanel.paintAlignment(false, false);
321 * Build and show the popup-menu at the right-click mouse position
325 void showPopupMenu(MouseEvent e)
327 int seq2 = alignPanel.getSeqPanel().findSeq(e);
328 Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
331 * build a new links menu based on the current links
332 * and any non-positional features
334 List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
335 List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
336 for (SequenceFeature sf : features)
338 if (sf.links != null)
340 for (String link : sf.links)
347 PopupMenu pop = new PopupMenu(alignPanel, sq, features,
348 Preferences.getGroupURLLinks());
349 pop.show(this, e.getX(), e.getY());
353 * Toggle whether the sequence is part of the current selection group.
357 void selectSeq(int seq)
361 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
362 av.getSelectionGroup().addOrRemove(pickedSeq, true);
366 * Add contiguous rows of the alignment to the current selection group. Does
367 * nothing if there is no selection group.
372 void selectSeqs(int start, int end)
374 if (av.getSelectionGroup() == null)
379 if (end >= av.getAlignment().getHeight())
381 end = av.getAlignment().getHeight() - 1;
394 for (int i = start; i <= end; i++)
396 av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
402 * Respond to mouse released. Refreshes the display and triggers broadcast of
403 * the new selection group to any listeners.
408 public void mouseReleased(MouseEvent e)
410 if (scrollThread != null)
412 scrollThread.stopScrolling();
415 mouseDragging = false;
416 PaintRefresher.Refresh(this, av.getSequenceSetId());
417 // always send selection message when mouse is released
420 if (e.isPopupTrigger()) // Windows reports this in mouseReleased
427 * Highlight sequence ids that match the given list, and if necessary scroll
428 * to the start sequence of the list.
432 public void highlightSearchResults(List<SequenceI> list)
434 getIdCanvas().setHighlighted(list);
441 int index = av.getAlignment().findIndex(list.get(0));
443 // do we need to scroll the panel?
444 if ((av.getRanges().getStartSeq() > index)
445 || (av.getRanges().getEndSeq() < index))
447 av.getRanges().setStartSeq(index);
451 public IdCanvas getIdCanvas()
456 public void setIdCanvas(IdCanvas idCanvas)
458 this.idCanvas = idCanvas;
462 * Performs scrolling of the visible alignment up or down, adding newly
463 * visible sequences to the current selection
465 class ScrollThread extends Thread
467 private boolean running = false;
472 * Constructor for a thread that scrolls either up or down
476 public ScrollThread(boolean up)
479 setName("IdPanel$ScrollThread$" + String.valueOf(up));
484 * Sets a flag to stop the scrolling
486 public void stopScrolling()
492 * Scrolls the alignment either up or down, one row at a time, adding newly
493 * visible sequences to the current selection. Speed is limited to a maximum
494 * of ten rows per second. The thread exits when the end of the alignment is
495 * reached or a flag is set to stop it.
504 ViewportRanges ranges = IdPanel.this.av.getRanges();
505 if (ranges.scrollUp(up))
507 int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
508 int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
509 IdPanel.this.selectSeqs(fromSeq, toSeq);
516 * scroll did nothing - reached limit of visible alignment
521 alignPanel.paintAlignment(false, false);
526 } catch (Exception ex)