2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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21 import jalview.datamodel.*;
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24 import java.awt.event.*;
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26 import javax.swing.*;
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33 * @version $Revision$
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35 public class IdPanel extends JPanel implements MouseListener,
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38 protected IdCanvas idCanvas;
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39 protected AlignViewport av;
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40 protected AlignmentPanel alignPanel;
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41 ScrollThread scrollThread = null;
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45 boolean mouseDragging = false;
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48 * Creates a new IdPanel object.
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50 * @param av DOCUMENT ME!
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51 * @param parent DOCUMENT ME!
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53 public IdPanel(AlignViewport av, AlignmentPanel parent)
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56 alignPanel = parent;
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57 idCanvas = new IdCanvas(av);
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58 setLayout(new BorderLayout());
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59 add(idCanvas, BorderLayout.CENTER);
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60 addMouseListener(this);
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61 addMouseMotionListener(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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74 if (av.getWrapAlignment())
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79 final int seq = av.getIndex(y);
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82 SequenceI sequence = av.alignment.getSequenceAt(seq);
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83 StringBuffer tip = new StringBuffer("<html>");
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84 tip.append(sequence.getDisplayId(true));
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85 if (av.alignment.getSequenceAt(seq).getDescription() != null)
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87 tip.append("<table width=250 border=0><tr><td><i>");
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88 tip.append(av.alignment.getSequenceAt(seq).getDescription());
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90 //ADD NON POSITIONAL SEQUENCE INFO
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91 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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94 for(int i=0; i<features.length; i++)
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96 if(features[i].begin == 0 && features[i].end ==0)
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98 tip.append("<br>"+features[i].featureGroup
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99 +" "+ features[i].getType()+" "+features[i].description);
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104 tip.append("</i></td></tr></table>");
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106 tip.append("</html>");
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107 setToolTipText(tip.toString());
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110 if(av.hasHiddenRows)
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112 if(av.adjustForHiddenSeqs(seq) -
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113 av.adjustForHiddenSeqs(seq-1)>1)
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115 JPopupMenu pop = new JPopupMenu();
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116 JMenuItem item = new JMenuItem("Reveal");
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117 item.addActionListener(new ActionListener()
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119 public void actionPerformed(ActionEvent e)
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121 av.showSequence(seq);
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122 alignPanel.repaint();
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123 if(alignPanel.overviewPanel!=null)
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124 alignPanel.overviewPanel.updateOverviewImage();
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128 pop.show(this, e.getX(), e.getY());
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134 int getWrappedY(int y)
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136 int hgap = av.charHeight;
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137 if (av.scaleAboveWrapped)
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138 hgap += av.charHeight;
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147 * @param e DOCUMENT ME!
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149 public void mouseDragged(MouseEvent e)
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151 mouseDragging = true;
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155 if (av.getWrapAlignment())
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157 y = getWrappedY(y);
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160 int seq = av.getIndex(y);
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169 selectSeqs(lastid - 1, seq);
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171 else if (seq > lastid)
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173 selectSeqs(lastid + 1, seq);
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177 alignPanel.repaint();
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184 * @param e DOCUMENT ME!
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186 public void mouseClicked(MouseEvent e)
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188 if (e.getClickCount() < 2)
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191 java.util.Vector links = Preferences.sequenceURLLinks;
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192 if (links == null || links.size() < 1)
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197 if (av.getWrapAlignment())
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199 y = getWrappedY(y);
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202 //DEFAULT LINK IS FIRST IN THE LINK LIST
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203 int seq = av.getIndex(y);
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207 String id = av.getAlignment().getSequenceAt(seq).getName();
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208 if (id.indexOf("|") > -1)
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209 id = id.substring(id.lastIndexOf("|") + 1);
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212 String url = links.elementAt(0).toString();
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213 url = url.substring(url.indexOf("|")+1);
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215 int index = url.indexOf("$SEQUENCE_ID$");
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216 url = url.substring(0, index)+ id + url.substring(index+13);
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220 jalview.util.BrowserLauncher.openURL(url);
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222 catch (Exception ex)
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224 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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225 "Unixers: Couldn't find default web browser."
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226 +"\nAdd the full path to your browser in Preferences.",
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227 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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228 ex.printStackTrace();
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235 * @param e DOCUMENT ME!
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237 public void mouseEntered(MouseEvent e)
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239 if (scrollThread != null)
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241 scrollThread.running = false;
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248 * @param e DOCUMENT ME!
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250 public void mouseExited(MouseEvent e)
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252 if (av.getWrapAlignment())
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257 if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
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259 scrollThread = new ScrollThread(true);
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262 if (mouseDragging && (e.getY() >= getHeight()) &&
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263 (av.alignment.getHeight() > av.getEndSeq()))
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265 scrollThread = new ScrollThread(false);
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272 * @param e DOCUMENT ME!
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274 public void mousePressed(MouseEvent e)
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276 if (e.getClickCount() == 2)
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283 if (av.getWrapAlignment())
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285 y = getWrappedY(y);
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288 int seq = av.getIndex(y);
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295 if (javax.swing.SwingUtilities.isRightMouseButton(e))
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297 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
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298 (Sequence) av.getAlignment().getSequenceAt(seq),
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299 Preferences.sequenceURLLinks);
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300 pop.show(this, e.getX(), y);
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305 /* if (!e.isControlDown() && !e.isShiftDown() &&
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306 (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))
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308 System.out.println("no modifiers");
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309 SequenceGroup selection = new SequenceGroup();
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310 SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(
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312 selection.setStartRes(0);
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313 selection.setEndRes(av.alignment.getWidth() - 1);
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315 for (int i = 0; i < sg.getSize(); i++)
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317 selection.addSequence(sg.getSequenceAt(i), true);
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320 av.setSelectionGroup(selection);
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325 if ((av.getSelectionGroup() == null) ||
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326 ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
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328 av.setSelectionGroup(new SequenceGroup());
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329 av.getSelectionGroup().setStartRes(0);
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330 av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
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335 if (e.isShiftDown() && (lastid != -1))
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337 selectSeqs(lastid, seq);
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344 alignPanel.repaint();
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350 * @param seq DOCUMENT ME!
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352 void selectSeq(int seq)
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356 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
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357 av.getSelectionGroup().addOrRemove(pickedSeq, true);
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363 * @param start DOCUMENT ME!
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364 * @param end DOCUMENT ME!
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366 void selectSeqs(int start, int end)
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368 if(av.getSelectionGroup()==null)
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381 for (int i = start; i <= end; i++)
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383 av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
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391 * @param e DOCUMENT ME!
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393 public void mouseReleased(MouseEvent e)
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395 if (scrollThread != null)
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397 scrollThread.running = false;
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400 mouseDragging = false;
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401 PaintRefresher.Refresh(av.alignment);
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407 * @param found DOCUMENT ME!
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409 public void highlightSearchResults(java.util.Vector found)
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411 idCanvas.setHighlighted(found);
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418 int index = av.alignment.findIndex((SequenceI) found.get(0));
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420 // do we need to scroll the panel?
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421 if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
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423 alignPanel.setScrollValues(av.getStartRes(), index);
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427 // this class allows scrolling off the bottom of the visible alignment
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428 class ScrollThread extends Thread
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430 boolean running = false;
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433 public ScrollThread(boolean up)
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439 public void stopScrolling()
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450 if (alignPanel.scrollUp(up))
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452 // scroll was ok, so add new sequence to selection
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453 int seq = av.getStartSeq();
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457 seq = av.getEndSeq();
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462 selectSeqs(lastid - 1, seq);
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464 else if (seq > lastid)
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466 selectSeqs(lastid + 1, seq);
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476 alignPanel.repaint();
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482 catch (Exception ex)
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