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.datamodel.Sequence;
24 import jalview.datamodel.SequenceFeature;
25 import jalview.datamodel.SequenceGroup;
26 import jalview.datamodel.SequenceI;
27 import jalview.urls.api.UrlProviderFactoryI;
28 import jalview.urls.api.UrlProviderI;
29 import jalview.urls.applet.AppletUrlProviderFactory;
30 import jalview.viewmodel.AlignmentViewport;
32 import java.awt.BorderLayout;
33 import java.awt.Panel;
34 import java.awt.event.InputEvent;
35 import java.awt.event.MouseEvent;
36 import java.awt.event.MouseListener;
37 import java.awt.event.MouseMotionListener;
38 import java.util.ArrayList;
39 import java.util.HashMap;
40 import java.util.List;
42 public class IdPanel extends Panel implements MouseListener,
46 protected IdCanvas idCanvas;
48 protected AlignmentViewport av;
50 protected AlignmentPanel alignPanel;
52 ScrollThread scrollThread = null;
56 boolean mouseDragging = false;
58 UrlProviderI urlProvider = null;
60 public IdPanel(AlignViewport av, AlignmentPanel parent)
64 idCanvas = new IdCanvas(av);
65 setLayout(new BorderLayout());
66 add(idCanvas, BorderLayout.CENTER);
67 idCanvas.addMouseListener(this);
68 idCanvas.addMouseMotionListener(this);
71 // TODO: add in group link parameter
73 // make a list of label,url pairs
74 HashMap<String, String> urlList = new HashMap<String, String>();
75 if (av.applet != null)
77 for (int i = 1; i < 10; i++)
79 label = av.applet.getParameter("linkLabel_" + i);
80 url = av.applet.getParameter("linkURL_" + i);
82 // only add non-null parameters
85 urlList.put(label, url);
89 if (!urlList.isEmpty())
91 // set default as first entry in list
92 String defaultUrl = av.applet.getParameter("linkLabel_1");
93 UrlProviderFactoryI factory = new AppletUrlProviderFactory(
95 urlProvider = factory.createUrlProvider();
103 public void mouseMoved(MouseEvent e)
105 int seq = alignPanel.seqPanel.findSeq(e);
107 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
109 // look for non-pos features
110 StringBuffer tooltiptext = new StringBuffer();
111 if (sequence != null)
113 if (sequence.getDescription() != null)
115 tooltiptext.append(sequence.getDescription());
116 tooltiptext.append("\n");
119 SequenceFeature sf[] = sequence.getSequenceFeatures();
120 for (int sl = 0; sf != null && sl < sf.length; sl++)
122 if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
125 if (sf[sl].getFeatureGroup() != null)
127 tooltiptext.append(sf[sl].getFeatureGroup());
131 if (sf[sl].getType() != null)
133 tooltiptext.append(" ");
134 tooltiptext.append(sf[sl].getType());
138 if (sf[sl].getDescription() != null)
140 tooltiptext.append(" ");
141 tooltiptext.append(sf[sl].getDescription());
145 if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
147 tooltiptext.append(" Score = ");
148 tooltiptext.append(sf[sl].getScore());
152 if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
154 tooltiptext.append(" (");
155 tooltiptext.append(sf[sl].getStatus());
156 tooltiptext.append(")");
162 tooltiptext.append("\n");
167 if (tooltiptext.length() == 0)
169 // nothing to display - so clear tooltip if one is visible
172 tooltip.setVisible(false);
180 tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
181 + tooltiptext.toString(), idCanvas);
185 tooltip.setTip(sequence.getDisplayId(true) + "\n"
186 + tooltiptext.toString());
192 public void mouseDragged(MouseEvent e)
194 mouseDragging = true;
196 int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
200 selectSeqs(lastid - 1, seq);
202 else if (seq > lastid)
204 selectSeqs(lastid + 1, seq);
208 alignPanel.paintAlignment(false);
212 public void mouseClicked(MouseEvent e)
214 if (e.getClickCount() < 2)
219 // get the sequence details
220 int seq = alignPanel.seqPanel.findSeq(e);
221 SequenceI sq = av.getAlignment().getSequenceAt(seq);
226 String id = sq.getName();
228 // get the default url with the sequence details filled in
229 if (urlProvider == null)
233 String url = urlProvider.getPrimaryUrl(id);
234 String target = urlProvider.getPrimaryTarget(id);
237 alignPanel.alignFrame.showURL(url, target);
238 } catch (Exception ex)
240 ex.printStackTrace();
245 public void mouseEntered(MouseEvent e)
247 if (scrollThread != null)
249 scrollThread.running = false;
254 public void mouseExited(MouseEvent e)
256 if (av.getWrapAlignment())
261 if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
263 scrollThread = new ScrollThread(true);
266 if (mouseDragging && e.getY() >= getSize().height
267 && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
269 scrollThread = new ScrollThread(false);
274 public void mousePressed(MouseEvent e)
276 if (e.getClickCount() > 1)
282 if (av.getWrapAlignment())
284 y -= 2 * av.getCharHeight();
287 int seq = alignPanel.seqPanel.findSeq(e);
289 if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
291 Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
293 // build a new links menu based on the current links + any non-positional
296 if (urlProvider != null)
298 nlinks = urlProvider.getLinksForMenu();
302 nlinks = new ArrayList<String>();
304 SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
305 for (int sl = 0; sf != null && sl < sf.length; sl++)
307 if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
309 if (sf[sl].links != null && sf[sl].links.size() > 0)
311 for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
313 nlinks.add(sf[sl].links.elementAt(l));
319 APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
321 popup.show(this, e.getX(), e.getY());
325 if ((av.getSelectionGroup() == null)
326 || ((!jalview.util.Platform.isControlDown(e) && !e
327 .isShiftDown()) && av.getSelectionGroup() != null))
329 av.setSelectionGroup(new SequenceGroup());
330 av.getSelectionGroup().setStartRes(0);
331 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
334 if (e.isShiftDown() && lastid != -1)
336 selectSeqs(lastid, seq);
343 alignPanel.paintAlignment(false);
346 void selectSeq(int seq)
349 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
350 av.getSelectionGroup().addOrRemove(pickedSeq, true);
353 void selectSeqs(int start, int end)
358 if (end >= av.getAlignment().getHeight())
360 end = av.getAlignment().getHeight() - 1;
370 if (av.getSelectionGroup() == null)
372 av.setSelectionGroup(new SequenceGroup());
374 for (int i = start; i <= end; i++)
376 av.getSelectionGroup().addSequence(
377 av.getAlignment().getSequenceAt(i), i == end);
383 public void mouseReleased(MouseEvent e)
385 if (scrollThread != null)
387 scrollThread.running = false;
390 if (av.getSelectionGroup() != null)
392 av.getSelectionGroup().recalcConservation();
395 mouseDragging = false;
396 PaintRefresher.Refresh(this, av.getSequenceSetId());
397 // always send selection message when mouse is released
401 public void highlightSearchResults(List<SequenceI> list)
403 idCanvas.setHighlighted(list);
410 int index = av.getAlignment().findIndex(list.get(0));
412 // do we need to scroll the panel?
413 if (av.getRanges().getStartSeq() > index
414 || av.getRanges().getEndSeq() < index)
416 av.getRanges().setStartSeq(index);
420 // this class allows scrolling off the bottom of the visible alignment
421 class ScrollThread extends Thread
423 boolean running = false;
427 public ScrollThread(boolean up)
433 public void stopScrolling()
444 if (av.getRanges().scrollUp(up))
446 // scroll was ok, so add new sequence to selection
447 int seq = av.getRanges().getStartSeq();
450 seq = av.getRanges().getEndSeq();
455 selectSeqs(lastid - 1, seq);
457 else if (seq > lastid && seq < av.getAlignment().getHeight())
459 selectSeqs(lastid + 1, seq);
469 alignPanel.paintAlignment(true);
473 } catch (Exception ex)