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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74 if (seq > -1 && seq < av.alignment.getHeight())
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76 SequenceI sequence = av.alignment.getSequenceAt(seq);
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77 StringBuffer tip = new StringBuffer();
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81 if (sequence.getDescription() != null)
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83 tmp = sequence.getDescription();
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84 tip.append("<br>"+tmp);
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85 maxWidth = Math.max(maxWidth, tmp.length());
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88 DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
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91 for (int i = 0; i < dbrefs.length; i++)
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94 tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
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96 maxWidth = Math.max(maxWidth, tmp.length());
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101 //ADD NON POSITIONAL SEQUENCE INFO
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102 SequenceFeature[] features = sequence.getDatasetSequence().
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103 getSequenceFeatures();
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104 if (features != null)
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106 for (int i = 0; i < features.length; i++)
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108 if (features[i].begin == 0 && features[i].end == 0)
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110 tmp = features[i].featureGroup
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111 + " " + features[i].getType() + " " +
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112 features[i].description;
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113 tip.append("<br>" + tmp);
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114 maxWidth = Math.max(maxWidth, tmp.length());
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121 tip.insert(0, "<table width=350 border=0><tr><td><i>");
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122 tip.append("</i></td></tr></table>");
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125 tip.append("</html>");
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127 setToolTipText("<html>"+sequence.getDisplayId(true)+tip.toString());
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134 * @param e DOCUMENT ME!
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136 public void mouseDragged(MouseEvent e)
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138 mouseDragging = true;
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140 int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
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144 selectSeqs(lastid - 1, seq);
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146 else if (seq > lastid)
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148 selectSeqs(lastid + 1, seq);
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152 alignPanel.paintAlignment(true);
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155 public void mouseWheelMoved(MouseWheelEvent e)
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158 if (e.getWheelRotation() > 0)
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160 alignPanel.scrollUp(false);
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164 alignPanel.scrollUp(true);
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171 * @param e DOCUMENT ME!
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173 public void mouseClicked(MouseEvent e)
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175 if (e.getClickCount() < 2)
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180 java.util.Vector links = Preferences.sequenceURLLinks;
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181 if (links == null || links.size() < 1)
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186 int seq = alignPanel.seqPanel.findSeq(e);
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188 //DEFAULT LINK IS FIRST IN THE LINK LIST
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190 String id = av.getAlignment().getSequenceAt(seq).getName();
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191 if (id.indexOf("|") > -1)
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193 id = id.substring(id.lastIndexOf("|") + 1);
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196 String url = links.elementAt(0).toString();
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197 url = url.substring(url.indexOf("|") + 1);
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199 int index = url.indexOf("$SEQUENCE_ID$");
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200 url = url.substring(0, index) + id + url.substring(index + 13);
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204 jalview.util.BrowserLauncher.openURL(url);
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206 catch (Exception ex)
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208 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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209 "Unixers: Couldn't find default web browser."
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211 "\nAdd the full path to your browser in Preferences.",
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212 "Web browser not found",
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213 JOptionPane.WARNING_MESSAGE);
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214 ex.printStackTrace();
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221 * @param e DOCUMENT ME!
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223 public void mouseEntered(MouseEvent e)
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225 if (scrollThread != null)
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227 scrollThread.running = false;
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234 * @param e DOCUMENT ME!
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236 public void mouseExited(MouseEvent e)
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238 if (av.getWrapAlignment())
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243 if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
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245 scrollThread = new ScrollThread(true);
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248 if (mouseDragging && (e.getY() >= getHeight()) &&
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249 (av.alignment.getHeight() > av.getEndSeq()))
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251 scrollThread = new ScrollThread(false);
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258 * @param e DOCUMENT ME!
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260 public void mousePressed(MouseEvent e)
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262 if (e.getClickCount() == 2)
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267 int seq = alignPanel.seqPanel.findSeq(e);
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269 if (javax.swing.SwingUtilities.isRightMouseButton(e))
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271 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
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272 (Sequence) av.getAlignment().getSequenceAt(seq),
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273 Preferences.sequenceURLLinks);
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274 pop.show(this, e.getX(), e.getY());
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279 if ( (av.getSelectionGroup() == null) ||
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280 ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
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282 av.setSelectionGroup(new SequenceGroup());
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283 av.getSelectionGroup().setStartRes(0);
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284 av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
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287 if (e.isShiftDown() && (lastid != -1))
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289 selectSeqs(lastid, seq);
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296 alignPanel.paintAlignment(true);
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302 * @param seq DOCUMENT ME!
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304 void selectSeq(int seq)
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308 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
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309 av.getSelectionGroup().addOrRemove(pickedSeq, true);
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315 * @param start DOCUMENT ME!
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316 * @param end DOCUMENT ME!
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318 void selectSeqs(int start, int end)
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320 if (av.getSelectionGroup() == null)
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325 if (end >= av.getAlignment().getHeight())
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327 end = av.getAlignment().getHeight() - 1;
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340 for (int i = start; i <= end; i++)
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342 av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
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350 * @param e DOCUMENT ME!
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352 public void mouseReleased(MouseEvent e)
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354 if (scrollThread != null)
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356 scrollThread.running = false;
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359 mouseDragging = false;
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360 PaintRefresher.Refresh(this, av.getSequenceSetId());
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366 * @param found DOCUMENT ME!
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368 public void highlightSearchResults(java.util.Vector found)
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370 idCanvas.setHighlighted(found);
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377 int index = av.alignment.findIndex( (SequenceI) found.get(0));
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379 // do we need to scroll the panel?
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380 if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
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382 alignPanel.setScrollValues(av.getStartRes(), index);
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386 // this class allows scrolling off the bottom of the visible alignment
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390 boolean running = false;
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393 public ScrollThread(boolean up)
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399 public void stopScrolling()
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410 if (alignPanel.scrollUp(up))
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412 // scroll was ok, so add new sequence to selection
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413 int seq = av.getStartSeq();
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417 seq = av.getEndSeq();
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422 selectSeqs(lastid - 1, seq);
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424 else if (seq > lastid)
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426 selectSeqs(lastid + 1, seq);
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436 alignPanel.paintAlignment(false);
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442 catch (Exception ex)
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