2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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25 import jalview.datamodel.*;
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31 * @version $Revision$
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33 public class IdPanel
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34 extends JPanel implements MouseListener,
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35 MouseMotionListener, MouseWheelListener
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37 protected IdCanvas idCanvas;
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38 protected AlignViewport av;
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39 protected AlignmentPanel alignPanel;
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40 ScrollThread scrollThread = null;
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44 boolean mouseDragging = false;
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47 * Creates a new IdPanel object.
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49 * @param av DOCUMENT ME!
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50 * @param parent DOCUMENT ME!
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52 public IdPanel(AlignViewport av, AlignmentPanel parent)
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55 alignPanel = parent;
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56 idCanvas = new IdCanvas(av);
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57 setLayout(new BorderLayout());
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58 add(idCanvas, BorderLayout.CENTER);
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59 addMouseListener(this);
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60 addMouseMotionListener(this);
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61 addMouseWheelListener(this);
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62 ToolTipManager.sharedInstance().registerComponent(this);
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68 * @param e DOCUMENT ME!
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70 public void mouseMoved(MouseEvent e)
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72 int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
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73 if (seq > -1 && seq < av.alignment.getHeight())
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75 SequenceI sequence = av.alignment.getSequenceAt(seq);
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76 StringBuffer tip = new StringBuffer("<html>");
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77 tip.append(sequence.getDisplayId(true));
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78 if (sequence.getDescription() != null)
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80 tip.append("<table width=250 border=0><tr><td><i>");
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81 tip.append(sequence.getDescription());
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83 DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
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87 for (int i = 0; i < dbrefs.length; i++)
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90 tip.append(dbrefs[i].getSource() + " "
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91 + dbrefs[i].getAccessionId());
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96 //ADD NON POSITIONAL SEQUENCE INFO
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97 SequenceFeature[] features = sequence.getDatasetSequence().
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98 getSequenceFeatures();
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99 if (features != null)
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101 for (int i = 0; i < features.length; i++)
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103 if (features[i].begin == 0 && features[i].end == 0)
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105 tip.append("<br>" + features[i].featureGroup
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106 + " " + features[i].getType() + " " +
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107 features[i].description);
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111 tip.append("</i></td></tr></table>");
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115 tip.append("</html>");
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116 setToolTipText(tip.toString());
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123 * @param e DOCUMENT ME!
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125 public void mouseDragged(MouseEvent e)
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127 mouseDragging = true;
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129 int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
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133 selectSeqs(lastid - 1, seq);
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135 else if (seq > lastid)
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137 selectSeqs(lastid + 1, seq);
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141 alignPanel.paintAlignment(true);
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144 public void mouseWheelMoved(MouseWheelEvent e)
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147 if (e.getWheelRotation() > 0)
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149 alignPanel.scrollUp(false);
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153 alignPanel.scrollUp(true);
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160 * @param e DOCUMENT ME!
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162 public void mouseClicked(MouseEvent e)
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164 if (e.getClickCount() < 2)
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169 java.util.Vector links = Preferences.sequenceURLLinks;
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170 if (links == null || links.size() < 1)
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175 int seq = alignPanel.seqPanel.findSeq(e);
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177 //DEFAULT LINK IS FIRST IN THE LINK LIST
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179 String id = av.getAlignment().getSequenceAt(seq).getName();
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180 if (id.indexOf("|") > -1)
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182 id = id.substring(id.lastIndexOf("|") + 1);
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185 String url = links.elementAt(0).toString();
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186 url = url.substring(url.indexOf("|") + 1);
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188 int index = url.indexOf("$SEQUENCE_ID$");
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189 url = url.substring(0, index) + id + url.substring(index + 13);
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193 jalview.util.BrowserLauncher.openURL(url);
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195 catch (Exception ex)
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197 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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198 "Unixers: Couldn't find default web browser."
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200 "\nAdd the full path to your browser in Preferences.",
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201 "Web browser not found",
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202 JOptionPane.WARNING_MESSAGE);
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203 ex.printStackTrace();
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210 * @param e DOCUMENT ME!
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212 public void mouseEntered(MouseEvent e)
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214 if (scrollThread != null)
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216 scrollThread.running = false;
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223 * @param e DOCUMENT ME!
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225 public void mouseExited(MouseEvent e)
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227 if (av.getWrapAlignment())
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232 if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
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234 scrollThread = new ScrollThread(true);
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237 if (mouseDragging && (e.getY() >= getHeight()) &&
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238 (av.alignment.getHeight() > av.getEndSeq()))
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240 scrollThread = new ScrollThread(false);
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247 * @param e DOCUMENT ME!
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249 public void mousePressed(MouseEvent e)
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251 if (e.getClickCount() == 2)
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256 int seq = alignPanel.seqPanel.findSeq(e);
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258 if (javax.swing.SwingUtilities.isRightMouseButton(e))
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260 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
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261 (Sequence) av.getAlignment().getSequenceAt(seq),
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262 Preferences.sequenceURLLinks);
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263 pop.show(this, e.getX(), e.getY());
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268 if ( (av.getSelectionGroup() == null) ||
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269 ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
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271 av.setSelectionGroup(new SequenceGroup());
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272 av.getSelectionGroup().setStartRes(0);
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273 av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
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276 if (e.isShiftDown() && (lastid != -1))
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278 selectSeqs(lastid, seq);
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285 alignPanel.paintAlignment(true);
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291 * @param seq DOCUMENT ME!
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293 void selectSeq(int seq)
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297 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
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298 av.getSelectionGroup().addOrRemove(pickedSeq, true);
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304 * @param start DOCUMENT ME!
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305 * @param end DOCUMENT ME!
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307 void selectSeqs(int start, int end)
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309 if (av.getSelectionGroup() == null)
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314 if (end >= av.getAlignment().getHeight())
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316 end = av.getAlignment().getHeight() - 1;
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329 for (int i = start; i <= end; i++)
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331 av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
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339 * @param e DOCUMENT ME!
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341 public void mouseReleased(MouseEvent e)
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343 if (scrollThread != null)
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345 scrollThread.running = false;
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348 mouseDragging = false;
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349 PaintRefresher.Refresh(this, av.getSequenceSetId());
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355 * @param found DOCUMENT ME!
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357 public void highlightSearchResults(java.util.Vector found)
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359 idCanvas.setHighlighted(found);
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366 int index = av.alignment.findIndex( (SequenceI) found.get(0));
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368 // do we need to scroll the panel?
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369 if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
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371 alignPanel.setScrollValues(av.getStartRes(), index);
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375 // this class allows scrolling off the bottom of the visible alignment
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379 boolean running = false;
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382 public ScrollThread(boolean up)
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388 public void stopScrolling()
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399 if (alignPanel.scrollUp(up))
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401 // scroll was ok, so add new sequence to selection
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402 int seq = av.getStartSeq();
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406 seq = av.getEndSeq();
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411 selectSeqs(lastid - 1, seq);
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413 else if (seq > lastid)
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415 selectSeqs(lastid + 1, seq);
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425 alignPanel.paintAlignment(false);
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431 catch (Exception ex)
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