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.UrlLink;
30 import jalview.viewmodel.AlignmentViewport;
32 import java.awt.BorderLayout;
33 import java.awt.event.MouseEvent;
34 import java.awt.event.MouseListener;
35 import java.awt.event.MouseMotionListener;
36 import java.awt.event.MouseWheelEvent;
37 import java.awt.event.MouseWheelListener;
38 import java.util.List;
39 import java.util.Vector;
41 import javax.swing.JOptionPane;
42 import javax.swing.JPanel;
43 import javax.swing.SwingUtilities;
44 import javax.swing.ToolTipManager;
47 * This panel hosts alignment sequence ids and responds to mouse clicks on them,
48 * as well as highlighting ids matched by a search from the Find menu.
53 public class IdPanel extends JPanel implements MouseListener,
54 MouseMotionListener, MouseWheelListener
56 private IdCanvas idCanvas;
58 protected AlignmentViewport av;
60 protected AlignmentPanel alignPanel;
62 ScrollThread scrollThread = null;
71 boolean mouseDragging = false;
73 private final SequenceAnnotationReport seqAnnotReport;
76 * Creates a new IdPanel object.
81 public IdPanel(AlignViewport av, AlignmentPanel parent)
85 setIdCanvas(new IdCanvas(av));
86 linkImageURL = getClass().getResource("/images/link.gif").toString();
87 seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
88 setLayout(new BorderLayout());
89 add(getIdCanvas(), BorderLayout.CENTER);
90 addMouseListener(this);
91 addMouseMotionListener(this);
92 addMouseWheelListener(this);
93 ToolTipManager.sharedInstance().registerComponent(this);
97 * Respond to mouse movement by constructing tooltip text for the sequence id
104 public void mouseMoved(MouseEvent e)
106 SeqPanel sp = alignPanel.getSeqPanel();
107 int seq = Math.max(0, sp.findSeq(e));
108 if (seq > -1 && seq < av.getAlignment().getHeight())
110 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
111 StringBuffer tip = new StringBuffer(64);
112 seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
113 av.isShowDBRefs(), av.isShowNPFeats(),
114 sp.seqCanvas.fr.getMinMax());
115 setToolTipText(JvSwingUtils.wrapTooltip(true,
116 sequence.getDisplayId(true) + " " + tip.toString()));
121 * Responds to a mouse drag by selecting the sequences under the dragged
127 public void mouseDragged(MouseEvent e)
129 mouseDragging = true;
131 int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
135 selectSeqs(lastid - 1, seq);
137 else if (seq > lastid)
139 selectSeqs(lastid + 1, seq);
143 alignPanel.paintAlignment(true);
147 * Response to the mouse wheel by scrolling the alignment panel.
150 public void mouseWheelMoved(MouseWheelEvent e)
153 if (e.getWheelRotation() > 0)
157 alignPanel.scrollRight(true);
161 alignPanel.scrollUp(false);
168 alignPanel.scrollRight(false);
172 alignPanel.scrollUp(true);
178 * Handle a mouse click event. Currently only responds to a double-click. The
179 * action is to try to open a browser window at a URL that searches for the
180 * selected sequence id. The search URL is configured in Preferences |
181 * Connections | URL link from Sequence ID. For example:
183 * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
188 public void mouseClicked(MouseEvent e)
191 * Ignore single click. Ignore 'left' click followed by 'right' click (user
192 * selects a row then its pop-up menu).
194 if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e))
196 // reinstate isRightMouseButton check to ignore mouse-related popup events
197 // note - this does nothing on default MacBookPro force-trackpad config!
201 Vector links = Preferences.sequenceURLLinks;
202 if (links == null || links.size() < 1)
207 int seq = alignPanel.getSeqPanel().findSeq(e);
210 String id = av.getAlignment().getSequenceAt(seq).getName();
211 while (url == null && i < links.size())
213 // DEFAULT LINK IS FIRST IN THE LINK LIST
214 // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
215 url = links.elementAt(i++).toString();
216 jalview.util.UrlLink urlLink = null;
219 urlLink = new UrlLink(url);
220 } catch (Exception foo)
222 jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
228 if (!urlLink.isValid())
230 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
235 String urls[] = urlLink.makeUrls(id, true);
236 if (urls == null || urls[0] == null || urls[0].length() < 4)
241 // just take first URL made from regex
246 jalview.util.BrowserLauncher.openURL(url);
247 } catch (Exception ex)
249 JOptionPane.showInternalMessageDialog(Desktop.desktop,
250 MessageManager.getString("label.web_browser_not_found_unix"),
251 MessageManager.getString("label.web_browser_not_found"),
252 JOptionPane.WARNING_MESSAGE);
253 ex.printStackTrace();
264 public void mouseEntered(MouseEvent e)
266 if (scrollThread != null)
268 scrollThread.running = false;
279 public void mouseExited(MouseEvent e)
281 if (av.getWrapAlignment())
286 if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
288 scrollThread = new ScrollThread(true);
291 if (mouseDragging && (e.getY() >= getHeight())
292 && (av.getAlignment().getHeight() > av.getEndSeq()))
294 scrollThread = new ScrollThread(false);
299 * Respond to a mouse press. Does nothing for (left) double-click as this is
300 * handled by mouseClicked().
302 * Right mouse down - construct and show context menu.
304 * Ctrl-down or Shift-down - add to or expand current selection group if there
307 * Mouse down - select this sequence.
312 public void mousePressed(MouseEvent e)
314 if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
319 int seq = alignPanel.getSeqPanel().findSeq(e);
321 if (e.isPopupTrigger())
323 Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
324 // build a new links menu based on the current links + any non-positional
326 Vector<String> nlinks = new Vector<String>(
327 Preferences.sequenceURLLinks);
328 SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
331 for (SequenceFeature sf : sfs)
333 if (sf.begin == sf.end && sf.begin == 0)
335 if (sf.links != null && sf.links.size() > 0)
337 for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
339 nlinks.addElement(sf.links.elementAt(l));
346 PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
347 Preferences.getGroupURLLinks());
348 pop.show(this, e.getX(), e.getY());
353 if ((av.getSelectionGroup() == null)
354 || ((!e.isControlDown() && !e.isShiftDown()) && av
355 .getSelectionGroup() != null))
357 av.setSelectionGroup(new SequenceGroup());
358 av.getSelectionGroup().setStartRes(0);
359 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
362 if (e.isShiftDown() && (lastid != -1))
364 selectSeqs(lastid, seq);
370 // TODO is this addition ok here?
371 av.isSelectionGroupChanged(true);
373 alignPanel.paintAlignment(true);
377 * Toggle whether the sequence is part of the current selection group.
381 void selectSeq(int seq)
385 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
386 av.getSelectionGroup().addOrRemove(pickedSeq, true);
390 * Add contiguous rows of the alignment to the current selection group. Does
391 * nothing if there is no selection group.
396 void selectSeqs(int start, int end)
398 if (av.getSelectionGroup() == null)
403 if (end >= av.getAlignment().getHeight())
405 end = av.getAlignment().getHeight() - 1;
418 for (int i = start; i <= end; i++)
420 av.getSelectionGroup().addSequence(
421 av.getAlignment().getSequenceAt(i), i == end);
426 * Respond to mouse released. Refreshes the display and triggers broadcast of
427 * the new selection group to any listeners.
432 public void mouseReleased(MouseEvent e)
434 if (scrollThread != null)
436 scrollThread.running = false;
439 mouseDragging = false;
440 PaintRefresher.Refresh(this, av.getSequenceSetId());
441 // always send selection message when mouse is released
446 * Highlight sequence ids that match the given list, and if necessary scroll
447 * to the start sequence of the list.
451 public void highlightSearchResults(List<SequenceI> list)
453 getIdCanvas().setHighlighted(list);
460 int index = av.getAlignment().findIndex(list.get(0));
462 // do we need to scroll the panel?
463 if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
465 alignPanel.setScrollValues(av.getStartRes(), index);
469 public IdCanvas getIdCanvas()
474 public void setIdCanvas(IdCanvas idCanvas)
476 this.idCanvas = idCanvas;
479 // this class allows scrolling off the bottom of the visible alignment
480 class ScrollThread extends Thread
482 boolean running = false;
486 public ScrollThread(boolean up)
492 public void stopScrolling()
504 if (alignPanel.scrollUp(up))
506 // scroll was ok, so add new sequence to selection
507 int seq = av.getStartSeq();
511 seq = av.getEndSeq();
516 selectSeqs(lastid - 1, seq);
518 else if (seq > lastid)
520 selectSeqs(lastid + 1, seq);
530 alignPanel.paintAlignment(false);
535 } catch (Exception ex)