2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.util.UrlLink;
29 import java.awt.BorderLayout;
30 import java.awt.Panel;
31 import java.awt.event.InputEvent;
32 import java.awt.event.MouseEvent;
33 import java.awt.event.MouseListener;
34 import java.awt.event.MouseMotionListener;
35 import java.util.List;
36 import java.util.Vector;
38 public class IdPanel extends Panel implements MouseListener,
42 protected IdCanvas idCanvas;
44 protected AlignViewport av;
46 protected AlignmentPanel alignPanel;
48 ScrollThread scrollThread = null;
56 boolean mouseDragging = false;
58 java.util.Vector links = new java.util.Vector();
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
72 if (av.applet != null)
74 for (int i = 1; i < 10; i++)
76 label = av.applet.getParameter("linkLabel_" + i);
77 url = av.applet.getParameter("linkURL_" + i);
79 if (label != null && url != null)
81 links.addElement(label + "|" + url);
87 // upgrade old SRS link
89 .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
93 "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
99 links = new java.util.Vector();
100 links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
106 public void mouseMoved(MouseEvent e)
108 int seq = alignPanel.seqPanel.findSeq(e);
110 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
112 // look for non-pos features
113 StringBuffer tooltiptext = new StringBuffer();
114 if (sequence != null)
116 if (sequence.getDescription() != null)
118 tooltiptext.append(sequence.getDescription());
119 tooltiptext.append("\n");
122 SequenceFeature sf[] = sequence.getSequenceFeatures();
123 for (int sl = 0; sf != null && sl < sf.length; sl++)
125 if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
128 if (sf[sl].getFeatureGroup() != null)
130 tooltiptext.append(sf[sl].getFeatureGroup());
134 if (sf[sl].getType() != null)
136 tooltiptext.append(" ");
137 tooltiptext.append(sf[sl].getType());
141 if (sf[sl].getDescription() != null)
143 tooltiptext.append(" ");
144 tooltiptext.append(sf[sl].getDescription());
148 if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
150 tooltiptext.append(" Score = ");
151 tooltiptext.append(sf[sl].getScore());
155 if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
157 tooltiptext.append(" (");
158 tooltiptext.append(sf[sl].getStatus());
159 tooltiptext.append(")");
165 tooltiptext.append("\n");
170 if (tooltiptext.length() == 0)
172 // nothing to display - so clear tooltip if one is visible
175 tooltip.setVisible(false);
183 tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
184 + tooltiptext.toString(), idCanvas);
188 tooltip.setTip(sequence.getDisplayId(true) + "\n"
189 + tooltiptext.toString());
194 public void mouseDragged(MouseEvent e)
196 mouseDragging = true;
198 int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
202 selectSeqs(lastid - 1, seq);
204 else if (seq > lastid)
206 selectSeqs(lastid + 1, seq);
210 alignPanel.paintAlignment(false);
213 public void mouseClicked(MouseEvent e)
215 if (e.getClickCount() < 2)
220 // DEFAULT LINK IS FIRST IN THE LINK LIST
221 int seq = alignPanel.seqPanel.findSeq(e);
222 SequenceI sq = av.getAlignment().getSequenceAt(seq);
227 String id = sq.getName();
229 String target = null;
232 while (url == null && i < links.size())
234 // DEFAULT LINK IS FIRST IN THE LINK LIST
235 // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
236 url = links.elementAt(i++).toString();
237 jalview.util.UrlLink urlLink = null;
240 urlLink = new UrlLink(url);
241 target = urlLink.getTarget();
242 } catch (Exception foo)
244 System.err.println("Exception for URLLink '" + url + "'");
245 foo.printStackTrace();
250 if (!urlLink.isValid())
252 System.err.println(urlLink.getInvalidMessage());
257 String urls[] = urlLink.makeUrls(id, true);
258 if (urls == null || urls[0] == null || urls[0].length() < 1)
263 // just take first URL made from regex
269 alignPanel.alignFrame.showURL(url, target);
270 } catch (Exception ex)
272 ex.printStackTrace();
276 public void mouseEntered(MouseEvent e)
278 if (scrollThread != null)
280 scrollThread.running = false;
284 public void mouseExited(MouseEvent e)
286 if (av.getWrapAlignment())
291 if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
293 scrollThread = new ScrollThread(true);
296 if (mouseDragging && e.getY() >= getSize().height
297 && av.getAlignment().getHeight() > av.getEndSeq())
299 scrollThread = new ScrollThread(false);
303 public void mousePressed(MouseEvent e)
305 if (e.getClickCount() > 1)
311 if (av.getWrapAlignment())
313 y -= 2 * av.getCharHeight();
316 int seq = alignPanel.seqPanel.findSeq(e);
318 if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
320 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();
325 for (int l = 0, lSize = links.size(); l < lSize; l++)
327 nlinks.addElement(links.elementAt(l));
329 SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
330 for (int sl = 0; sf != null && sl < sf.length; sl++)
332 if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
334 if (sf[sl].links != null && sf[sl].links.size() > 0)
336 for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
338 nlinks.addElement(sf[sl].links.elementAt(l));
344 APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
346 popup.show(this, e.getX(), e.getY());
350 if ((av.getSelectionGroup() == null)
351 || ((!e.isControlDown() && !e.isShiftDown()) && av
352 .getSelectionGroup() != null))
354 av.setSelectionGroup(new SequenceGroup());
355 av.getSelectionGroup().setStartRes(0);
356 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
359 if (e.isShiftDown() && lastid != -1)
361 selectSeqs(lastid, seq);
368 alignPanel.paintAlignment(false);
371 void selectSeq(int seq)
374 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
375 av.getSelectionGroup().addOrRemove(pickedSeq, true);
378 void selectSeqs(int start, int end)
383 if (end >= av.getAlignment().getHeight())
385 end = av.getAlignment().getHeight() - 1;
395 if (av.getSelectionGroup() == null)
397 av.setSelectionGroup(new SequenceGroup());
399 for (int i = start; i <= end; i++)
401 av.getSelectionGroup().addSequence(
402 av.getAlignment().getSequenceAt(i), i == end);
407 public void mouseReleased(MouseEvent e)
409 if (scrollThread != null)
411 scrollThread.running = false;
414 if (av.getSelectionGroup() != null)
416 av.getSelectionGroup().recalcConservation();
419 mouseDragging = false;
420 PaintRefresher.Refresh(this, av.getSequenceSetId());
421 // always send selection message when mouse is released
425 public void highlightSearchResults(List<SequenceI> list)
427 idCanvas.setHighlighted(list);
434 int index = av.getAlignment().findIndex(list.get(0));
436 // do we need to scroll the panel?
437 if (av.getStartSeq() > index || av.getEndSeq() < index)
439 alignPanel.setScrollValues(av.getStartRes(), index);
443 // this class allows scrolling off the bottom of the visible alignment
444 class ScrollThread extends Thread
446 boolean running = false;
450 public ScrollThread(boolean up)
456 public void stopScrolling()
466 if (alignPanel.scrollUp(up))
468 // scroll was ok, so add new sequence to selection
469 int seq = av.getStartSeq();
472 seq = av.getEndSeq();
477 selectSeqs(lastid - 1, seq);
479 else if (seq > lastid && seq < av.getAlignment().getHeight())
481 selectSeqs(lastid + 1, seq);
491 alignPanel.paintAlignment(true);
495 } catch (Exception ex)