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))
199 Vector links = Preferences.sequenceURLLinks;
200 if (links == null || links.size() < 1)
205 int seq = alignPanel.getSeqPanel().findSeq(e);
208 String id = av.getAlignment().getSequenceAt(seq).getName();
209 while (url == null && i < links.size())
211 // DEFAULT LINK IS FIRST IN THE LINK LIST
212 // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
213 url = links.elementAt(i++).toString();
214 jalview.util.UrlLink urlLink = null;
217 urlLink = new UrlLink(url);
218 } catch (Exception foo)
220 jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
226 if (!urlLink.isValid())
228 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
233 String urls[] = urlLink.makeUrls(id, true);
234 if (urls == null || urls[0] == null || urls[0].length() < 4)
239 // just take first URL made from regex
244 jalview.util.BrowserLauncher.openURL(url);
245 } catch (Exception ex)
247 JOptionPane.showInternalMessageDialog(Desktop.desktop,
248 MessageManager.getString("label.web_browser_not_found_unix"),
249 MessageManager.getString("label.web_browser_not_found"),
250 JOptionPane.WARNING_MESSAGE);
251 ex.printStackTrace();
262 public void mouseEntered(MouseEvent e)
264 if (scrollThread != null)
266 scrollThread.running = false;
277 public void mouseExited(MouseEvent e)
279 if (av.getWrapAlignment())
284 if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
286 scrollThread = new ScrollThread(true);
289 if (mouseDragging && (e.getY() >= getHeight())
290 && (av.getAlignment().getHeight() > av.getEndSeq()))
292 scrollThread = new ScrollThread(false);
297 * Respond to a mouse press. Does nothing for (left) double-click as this is
298 * handled by mouseClicked().
300 * Right mouse down - construct and show context menu.
302 * Ctrl-down or Shift-down - add to or expand current selection group if there
305 * Mouse down - select this sequence.
310 public void mousePressed(MouseEvent e)
312 if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
317 int seq = alignPanel.getSeqPanel().findSeq(e);
319 if (SwingUtilities.isRightMouseButton(e))
321 Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
322 // build a new links menu based on the current links + any non-positional
324 Vector nlinks = new Vector(Preferences.sequenceURLLinks);
325 SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
326 for (int sl = 0; sf != null && sl < sf.length; sl++)
328 if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
330 if (sf[sl].links != null && sf[sl].links.size() > 0)
332 for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
334 nlinks.addElement(sf[sl].links.elementAt(l));
340 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
341 nlinks, new Vector(Preferences.getGroupURLLinks()));
342 pop.show(this, e.getX(), e.getY());
347 if ((av.getSelectionGroup() == null)
348 || ((!e.isControlDown() && !e.isShiftDown()) && av
349 .getSelectionGroup() != null))
351 av.setSelectionGroup(new SequenceGroup());
352 av.getSelectionGroup().setStartRes(0);
353 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
356 if (e.isShiftDown() && (lastid != -1))
358 selectSeqs(lastid, seq);
364 // TODO is this addition ok here?
365 av.isSelectionGroupChanged(true);
367 alignPanel.paintAlignment(true);
371 * Toggle whether the sequence is part of the current selection group.
375 void selectSeq(int seq)
379 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
380 av.getSelectionGroup().addOrRemove(pickedSeq, true);
384 * Add contiguous rows of the alignment to the current selection group. Does
385 * nothing if there is no selection group.
390 void selectSeqs(int start, int end)
392 if (av.getSelectionGroup() == null)
397 if (end >= av.getAlignment().getHeight())
399 end = av.getAlignment().getHeight() - 1;
412 for (int i = start; i <= end; i++)
414 av.getSelectionGroup().addSequence(
415 av.getAlignment().getSequenceAt(i), i == end);
420 * Respond to mouse released. Refreshes the display and triggers broadcast of
421 * the new selection group to any listeners.
426 public void mouseReleased(MouseEvent e)
428 if (scrollThread != null)
430 scrollThread.running = false;
433 mouseDragging = false;
434 PaintRefresher.Refresh(this, av.getSequenceSetId());
435 // always send selection message when mouse is released
440 * Highlight sequence ids that match the given list, and if necessary scroll
441 * to the start sequence of the list.
445 public void highlightSearchResults(List<SequenceI> list)
447 getIdCanvas().setHighlighted(list);
454 int index = av.getAlignment().findIndex(list.get(0));
456 // do we need to scroll the panel?
457 if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
459 alignPanel.setScrollValues(av.getStartRes(), index);
463 public IdCanvas getIdCanvas()
468 public void setIdCanvas(IdCanvas idCanvas)
470 this.idCanvas = idCanvas;
473 // this class allows scrolling off the bottom of the visible alignment
474 class ScrollThread extends Thread
476 boolean running = false;
480 public ScrollThread(boolean up)
486 public void stopScrolling()
498 if (alignPanel.scrollUp(up))
500 // scroll was ok, so add new sequence to selection
501 int seq = av.getStartSeq();
505 seq = av.getEndSeq();
510 selectSeqs(lastid - 1, seq);
512 else if (seq > lastid)
514 selectSeqs(lastid + 1, seq);
524 alignPanel.paintAlignment(false);
529 } catch (Exception ex)