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.SequenceFeature;
24 import jalview.datamodel.SequenceGroup;
25 import jalview.datamodel.SequenceI;
26 import jalview.urls.api.UrlProviderFactoryI;
27 import jalview.urls.api.UrlProviderI;
28 import jalview.urls.applet.AppletUrlProviderFactory;
29 import jalview.viewmodel.AlignmentViewport;
31 import java.awt.BorderLayout;
32 import java.awt.Panel;
33 import java.awt.event.InputEvent;
34 import java.awt.event.MouseEvent;
35 import java.awt.event.MouseListener;
36 import java.awt.event.MouseMotionListener;
37 import java.util.ArrayList;
38 import java.util.HashMap;
39 import java.util.List;
41 public class IdPanel extends Panel implements MouseListener,
45 protected IdCanvas idCanvas;
47 protected AlignmentViewport av;
49 protected AlignmentPanel alignPanel;
51 ScrollThread scrollThread = null;
55 boolean mouseDragging = false;
57 UrlProviderI urlProvider = null;
59 public IdPanel(AlignViewport viewport, AlignmentPanel parent)
63 idCanvas = new IdCanvas(viewport);
64 setLayout(new BorderLayout());
65 add(idCanvas, BorderLayout.CENTER);
66 idCanvas.addMouseListener(this);
67 idCanvas.addMouseMotionListener(this);
70 // TODO: add in group link parameter
72 // make a list of label,url pairs
73 HashMap<String, String> urlList = new HashMap<String, String>();
74 if (viewport.applet != null)
76 for (int i = 1; i < 10; i++)
78 label = viewport.applet.getParameter("linkLabel_" + i);
79 url = viewport.applet.getParameter("linkURL_" + i);
81 // only add non-null parameters
84 urlList.put(label, url);
88 if (!urlList.isEmpty())
90 // set default as first entry in list
91 String defaultUrl = viewport.applet.getParameter("linkLabel_1");
92 UrlProviderFactoryI factory = new AppletUrlProviderFactory(
94 urlProvider = factory.createUrlProvider();
102 public void mouseMoved(MouseEvent e)
104 int seq = alignPanel.seqPanel.findSeq(e);
106 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
108 StringBuffer tooltiptext = new StringBuffer();
109 if (sequence == null)
113 if (sequence.getDescription() != null)
115 tooltiptext.append(sequence.getDescription());
116 tooltiptext.append("\n");
119 for (SequenceFeature sf : sequence.getFeatures()
120 .getNonPositionalFeatures())
123 if (sf.getFeatureGroup() != null)
125 tooltiptext.append(sf.getFeatureGroup());
128 if (sf.getType() != null)
130 tooltiptext.append(" ");
131 tooltiptext.append(sf.getType());
134 if (sf.getDescription() != null)
136 tooltiptext.append(" ");
137 tooltiptext.append(sf.getDescription());
140 if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
142 tooltiptext.append(" Score = ");
143 tooltiptext.append(sf.getScore());
146 if (sf.getStatus() != null && sf.getStatus().length() > 0)
148 tooltiptext.append(" (");
149 tooltiptext.append(sf.getStatus());
150 tooltiptext.append(")");
155 tooltiptext.append("\n");
159 if (tooltiptext.length() == 0)
161 // nothing to display - so clear tooltip if one is visible
164 tooltip.setVisible(false);
172 tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
173 + tooltiptext.toString(), idCanvas);
177 tooltip.setTip(sequence.getDisplayId(true) + "\n"
178 + tooltiptext.toString());
184 public void mouseDragged(MouseEvent e)
186 mouseDragging = true;
188 int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
192 selectSeqs(lastid - 1, seq);
194 else if (seq > lastid)
196 selectSeqs(lastid + 1, seq);
200 alignPanel.paintAlignment(false);
204 public void mouseClicked(MouseEvent e)
206 if (e.getClickCount() < 2)
211 // get the sequence details
212 int seq = alignPanel.seqPanel.findSeq(e);
213 SequenceI sq = av.getAlignment().getSequenceAt(seq);
218 String id = sq.getName();
220 // get the default url with the sequence details filled in
221 if (urlProvider == null)
225 String url = urlProvider.getPrimaryUrl(id);
226 String target = urlProvider.getPrimaryTarget(id);
229 alignPanel.alignFrame.showURL(url, target);
230 } catch (Exception ex)
232 ex.printStackTrace();
237 public void mouseEntered(MouseEvent e)
239 if (scrollThread != null)
241 scrollThread.running = false;
246 public void mouseExited(MouseEvent e)
248 if (av.getWrapAlignment())
253 if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
255 scrollThread = new ScrollThread(true);
258 if (mouseDragging && e.getY() >= getSize().height
259 && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
261 scrollThread = new ScrollThread(false);
266 public void mousePressed(MouseEvent e)
268 if (e.getClickCount() > 1)
274 if (av.getWrapAlignment())
276 y -= 2 * av.getCharHeight();
279 int seq = alignPanel.seqPanel.findSeq(e);
281 if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
283 SequenceI sq = av.getAlignment().getSequenceAt(seq);
286 * build a new links menu based on the current links
287 * and any non-positional features
290 if (urlProvider != null)
292 nlinks = urlProvider.getLinksForMenu();
296 nlinks = new ArrayList<String>();
299 for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
301 if (sf.links != null)
303 for (String link : sf.links)
310 APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
312 popup.show(this, e.getX(), e.getY());
316 if ((av.getSelectionGroup() == null)
317 || ((!jalview.util.Platform.isControlDown(e) && !e
318 .isShiftDown()) && av.getSelectionGroup() != null))
320 av.setSelectionGroup(new SequenceGroup());
321 av.getSelectionGroup().setStartRes(0);
322 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
325 if (e.isShiftDown() && lastid != -1)
327 selectSeqs(lastid, seq);
334 alignPanel.paintAlignment(false);
337 void selectSeq(int seq)
340 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
341 av.getSelectionGroup().addOrRemove(pickedSeq, true);
344 void selectSeqs(int start, int end)
349 if (end >= av.getAlignment().getHeight())
351 end = av.getAlignment().getHeight() - 1;
361 if (av.getSelectionGroup() == null)
363 av.setSelectionGroup(new SequenceGroup());
365 for (int i = start; i <= end; i++)
367 av.getSelectionGroup().addSequence(
368 av.getAlignment().getSequenceAt(i), i == end);
374 public void mouseReleased(MouseEvent e)
376 if (scrollThread != null)
378 scrollThread.running = false;
381 if (av.getSelectionGroup() != null)
383 av.getSelectionGroup().recalcConservation();
386 mouseDragging = false;
387 PaintRefresher.Refresh(this, av.getSequenceSetId());
388 // always send selection message when mouse is released
392 public void highlightSearchResults(List<SequenceI> list)
394 idCanvas.setHighlighted(list);
401 int index = av.getAlignment().findIndex(list.get(0));
403 // do we need to scroll the panel?
404 if (av.getRanges().getStartSeq() > index
405 || av.getRanges().getEndSeq() < index)
407 alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
411 // this class allows scrolling off the bottom of the visible alignment
412 class ScrollThread extends Thread
414 boolean running = false;
418 public ScrollThread(boolean isUp)
424 public void stopScrolling()
435 if (alignPanel.scrollUp(up))
437 // scroll was ok, so add new sequence to selection
438 int seq = av.getRanges().getStartSeq();
441 seq = av.getRanges().getEndSeq();
446 selectSeqs(lastid - 1, seq);
448 else if (seq > lastid && seq < av.getAlignment().getHeight())
450 selectSeqs(lastid + 1, seq);
460 alignPanel.paintAlignment(true);
464 } catch (Exception ex)