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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20 package jalview.appletgui;
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25 import java.awt.event.*;
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27 import jalview.datamodel.*;
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28 import jalview.schemes.*;
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30 public class SeqPanel
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34 public SeqCanvas seqCanvas;
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35 public AlignmentPanel ap;
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37 protected int lastres;
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38 protected int startseq;
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42 protected AlignViewport av;
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44 // if character is inserted or deleted, we will need to recalculate the conservation
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45 int seqEditOccurred = -1;
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47 ScrollThread scrollThread = null;
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48 boolean mouseDragging = false;
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50 boolean editingSeqs = false;
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51 boolean groupEditing = false;
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53 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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57 seqCanvas = new SeqCanvas(avp);
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58 setLayout(new BorderLayout());
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63 seqCanvas.addMouseMotionListener(new MouseMotionAdapter()
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65 public void mouseMoved(MouseEvent evt)
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67 if (av.getWrapAlignment())
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74 public void mouseDragged(MouseEvent evt)
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76 if (av.getWrapAlignment())
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82 doMouseDragged(evt);
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86 doMouseDraggedDefineMode(evt);
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91 seqCanvas.addMouseListener(new MouseAdapter()
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93 public void mouseReleased(MouseEvent evt)
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95 if (av.getWrapAlignment())
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101 doMouseReleased(evt);
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105 doMouseReleasedDefineMode(evt);
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110 public void mousePressed(MouseEvent evt)
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112 if (av.getWrapAlignment())
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116 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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118 if (evt.isAltDown() || evt.isControlDown())
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120 groupEditing = true;
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123 editingSeqs = true;
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124 doMousePressed(evt);
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128 doMousePressedDefineMode(evt);
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132 public void mouseExited(MouseEvent evt)
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134 if (av.getWrapAlignment() || editingSeqs)
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138 doMouseExitedDefineMode(evt);
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142 public void mouseEntered(MouseEvent evt)
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144 if (av.getWrapAlignment() || editingSeqs)
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148 doMouseEnteredDefineMode(evt);
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152 seqCanvas.repaint();
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155 public void doMouseReleased(MouseEvent evt)
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158 if (seqEditOccurred > -1)
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160 editOccurred(seqEditOccurred);
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165 seqEditOccurred = -1;
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166 editingSeqs = false;
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167 groupEditing = false;
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171 public void doMousePressed(MouseEvent evt)
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173 ap.alignFrame.addHistoryItem(new HistoryItem(
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174 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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178 int x = evt.getX();
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179 int y = evt.getY();
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181 res = x / av.getCharWidth() + av.getStartRes();
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182 seq = y / av.getCharHeight() + av.getStartSeq();
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184 if (seq < av.getAlignment().getHeight() &&
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185 res < av.getAlignment().getSequenceAt(seq).getLength())
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187 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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188 // Find the residue's position in the sequence (res is the position
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189 // in the alignment
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203 public void doMouseMoved(MouseEvent evt)
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205 int res = 0, seq = 0;
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206 int x = evt.getX();
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207 int y = evt.getY();
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208 if (av.wrapAlignment)
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210 y -= 2 * av.charHeight;
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211 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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213 res = (int) ( (y / chunkHeight) * (getSize().width / av.charWidth)) +
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214 x / av.getCharWidth() + av.getStartRes();
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217 seq = y / av.getCharHeight() + av.getStartSeq();
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222 res = x / av.getCharWidth() + av.getStartRes();
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223 seq = y / av.getCharHeight() + av.getStartSeq();
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226 if (seq >= av.getAlignment().getHeight())
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231 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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232 if (res > sequence.getLength())
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237 Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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241 aa = obj.toString();
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244 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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245 sequence.getName());
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248 text.append(" Residue: " + aa + " (" +
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249 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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252 ap.alignFrame.statusBar.setText(text.toString());
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254 // use aa to see if the mouse pointer is on a
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255 if (av.showSequenceFeatures)
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257 Vector features = sequence.getSequenceFeatures();
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258 Enumeration e = features.elements();
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259 StringBuffer sbuffer = new StringBuffer();
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261 while (e.hasMoreElements())
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263 SequenceFeature sf = (SequenceFeature) e.nextElement();
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264 if (sf.getStart() <= sequence.findPosition(res) &&
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265 sf.getEnd() >= sequence.findPosition(res))
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267 if (sbuffer.length() > 0)
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269 sbuffer.append("; ");
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271 sbuffer.append(sf.getType() + " " + sf.getDescription());
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272 if (sf.getStatus().length() > 0)
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274 sbuffer.append(" (" + sf.getStatus() + ")");
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283 public void doMouseDragged(MouseEvent evt)
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286 // If we're dragging we're editing
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287 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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293 if (lastres == -1 || lastres == res)
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298 boolean dragRight = true;
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299 if (res < av.getAlignment().getWidth() && res < lastres)
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304 if (res != lastres)
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309 SequenceGroup sg = av.getSelectionGroup();
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319 sg.setEndRes(sg.getEndRes() + (res - lastres));
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325 /// Are we able to delete?
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326 // ie are all columns blank?
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327 boolean deleteAllowed = false;
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328 for (int s = 0; s < sg.getSize(); s++)
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330 SequenceI seq = sg.getSequenceAt(s);
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331 for (int j = res; j < lastres; j++)
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333 if (seq.getSequence().length() <= j)
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338 if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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340 // Not a gap, block edit not valid
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342 deleteAllowed = false;
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345 deleteAllowed = true;
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349 if (!deleteAllowed)
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355 sg.setEndRes(sg.getEndRes() - (lastres - res));
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358 for (int i = 0; i < sg.getSize(); i++)
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360 SequenceI s = sg.getSequenceAt(i);
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361 int k = av.alignment.findIndex(s);
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366 for (int j = lastres; j < res; j++)
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375 for (int j = res; j < lastres; j++)
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377 if (s.getLength() > j)
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379 deleteChar(res, k);
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385 else /////Editing a single sequence///////////
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387 if (res < av.getAlignment().getWidth() && res > lastres)
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389 // dragging to the right
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390 for (int j = lastres; j < res; j++)
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392 insertChar(j, startseq);
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395 else if (res < av.getAlignment().getWidth() && res < lastres)
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397 // dragging to the left
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398 for (int j = lastres; j > res; j--)
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400 if (jalview.util.Comparison.isGap(
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401 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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404 deleteChar(res, startseq);
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419 seqCanvas.repaint();
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422 public void drawChars(int seqstart, int seqend, int start)
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424 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
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425 av.getStartRes(), av.getStartSeq(), 0);
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426 seqCanvas.repaint();
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429 public void insertChar(int j, int seq)
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431 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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432 seqEditOccurred = seq;
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435 public void deleteChar(int j, int seq)
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438 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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439 seqEditOccurred = seq;
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440 av.alignment.getWidth();
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444 void editOccurred(int i)
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446 if (endEdit == startEdit)
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448 ap.alignFrame.historyList.pop();
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449 ap.alignFrame.updateEditMenuBar();
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452 av.updateConservation();
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453 av.updateConsensus();
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456 //Does the edit affect any groups?
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457 //////////////////////////////
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458 Vector groupsToUpdate = new Vector();
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459 SequenceGroup sg = av.getSelectionGroup();
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461 int s, g, gSize = av.alignment.getGroups().size();
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464 groupsToUpdate.addElement(av.getSelectionGroup());
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465 int sSize = sg.getSize();
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466 for (s = 0; s < sSize; s++)
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468 SequenceI seq = sg.getSequenceAt(s);
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470 for (g = 0; g < gSize; g++)
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472 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().
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475 if (sg2.sequences.contains(seq))
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477 if (!groupsToUpdate.contains(sg2))
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478 groupsToUpdate.addElement(sg2);
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486 SequenceI seq = av.alignment.getSequenceAt(startseq);
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487 for (g = 0; g < gSize; g++)
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489 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(
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491 if (sg2.sequences.contains(seq))
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493 if (!groupsToUpdate.contains(sg2))
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494 groupsToUpdate.addElement(sg2);
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500 gSize = groupsToUpdate.size();
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501 for (g = 0; g < gSize; g++)
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503 ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();
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505 ////End of updating groups
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506 //////////////////////////////////////////
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510 ColourSchemeI cs = av.getGlobalColourScheme();
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512 if (av.getSelectionGroup() != null)
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514 av.getSelectionGroup().recalcConservation();
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519 if (cs.conservationApplied())
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521 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
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522 ResidueProperties.propHash, 3,
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523 av.alignment.getSequences(),
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524 0, av.alignment.getWidth() - 1);
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526 c.verdict(false, av.ConsPercGaps);
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528 if (cs instanceof ClustalxColourScheme)
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530 ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
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531 cxs.resetClustalX(av.alignment.getSequences(),
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532 av.alignment.getWidth());
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533 cs.setConservation(c);
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534 av.setGlobalColourScheme(cs);
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538 cs.setConservation(c);
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539 av.setGlobalColourScheme(cs);
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544 if (cs instanceof ClustalxColourScheme)
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546 ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
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547 av.alignment.getWidth());
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548 av.setGlobalColourScheme(cs);
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553 //////////////////////////////////////////
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554 /////Everything below this is for defining the boundary of the rubberband
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555 //////////////////////////////////////////
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557 public void doMousePressedDefineMode(MouseEvent evt)
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559 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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560 int seq = evt.getY() / av.getCharHeight() + av.getStartSeq();
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563 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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565 if (sequence == null || res > sequence.getLength())
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570 stretchGroup = av.getSelectionGroup();
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572 if (stretchGroup == null)
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574 stretchGroup = av.alignment.findGroup(sequence);
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575 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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576 res < stretchGroup.getEndRes())
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578 av.setSelectionGroup(stretchGroup);
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582 stretchGroup = null;
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586 else if (!stretchGroup.sequences.contains(sequence)
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587 || stretchGroup.getStartRes() > res
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588 || stretchGroup.getEndRes() < res)
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590 stretchGroup = null;
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592 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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594 if (allGroups != null)
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596 for (int i = 0; i < allGroups.length; i++)
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598 if (allGroups[i].getStartRes() <= res &&
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599 allGroups[i].getEndRes() >= res)
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601 stretchGroup = allGroups[i];
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602 av.setSelectionGroup(stretchGroup);
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609 if (stretchGroup == null)
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611 // define a new group here
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612 SequenceGroup sg = new SequenceGroup();
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613 sg.setStartRes(res);
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615 sg.addSequence(sequence, false);
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616 av.setSelectionGroup(sg);
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619 if (av.getConservationSelected())
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621 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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624 if (av.getAbovePIDThreshold())
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626 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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632 // DETECT RIGHT MOUSE BUTTON IN AWT
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633 else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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634 InputEvent.BUTTON3_MASK)
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636 APopupMenu popup = new APopupMenu(ap, null, null);
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638 popup.show(this, evt.getX(), evt.getY());
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641 if (stretchGroup != null && stretchGroup.getEndRes() == res)
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643 // Edit end res position of selected group
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644 changeEndRes = true;
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647 else if (stretchGroup != null && stretchGroup.getStartRes() == res)
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649 // Edit end res position of selected group
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650 changeStartRes = true;
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655 boolean changeEndSeq = false;
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656 boolean changeStartSeq = false;
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657 boolean changeEndRes = false;
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658 boolean changeStartRes = false;
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659 SequenceGroup stretchGroup = null;
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661 public void doMouseReleasedDefineMode(MouseEvent evt)
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665 stretchGroup.recalcConservation();
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666 mouseDragging = false;
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669 if (stretchGroup == null)
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674 if(stretchGroup.cs!=null)
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676 if (stretchGroup.cs.conservationApplied())
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678 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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679 stretchGroup.getName());
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683 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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684 stretchGroup.getName());
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687 changeEndRes = false;
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688 changeStartRes = false;
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689 stretchGroup = null;
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690 seqCanvas.repaint();
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694 boolean remove = false;
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695 public void doMouseDraggedDefineMode(MouseEvent evt)
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697 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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698 int y = evt.getY() / av.getCharHeight() + av.getStartSeq();
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700 if (stretchGroup == null)
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705 if (res > av.alignment.getWidth())
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707 res = av.alignment.getWidth() - 1;
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710 if (stretchGroup.getEndRes() == res)
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712 // Edit end res position of selected group
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713 changeEndRes = true;
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716 else if (stretchGroup.getStartRes() == res)
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718 // Edit start res position of selected group
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719 changeStartRes = true;
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722 if (res < av.getStartRes())
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724 res = av.getStartRes();
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726 else if (res > av.getEndRes())
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728 res = av.getEndRes();
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733 if (res > stretchGroup.getStartRes() - 1)
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735 stretchGroup.setEndRes(res);
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738 else if (changeStartRes)
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740 if (res < stretchGroup.getEndRes() + 1)
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742 stretchGroup.setStartRes(res);
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746 int dragDirection = 0;
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751 else if (y < oldSeq)
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753 dragDirection = -1;
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756 while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
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758 // This routine ensures we don't skip any sequences, as the
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759 // selection is quite slow.
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760 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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762 oldSeq += dragDirection;
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763 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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765 if (stretchGroup.sequences.contains(nextSeq))
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767 stretchGroup.deleteSequence(seq, false);
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773 stretchGroup.addSequence(seq, false);
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775 stretchGroup.addSequence(nextSeq, false);
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779 mouseDragging = true;
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780 if (scrollThread != null)
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782 scrollThread.setEvent(evt);
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785 seqCanvas.repaint();
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788 public void doMouseEnteredDefineMode(MouseEvent e)
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790 if (scrollThread != null)
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792 scrollThread.running = false;
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796 public void doMouseExitedDefineMode(MouseEvent e)
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798 if (av.getWrapAlignment())
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805 scrollThread = new ScrollThread();
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810 // this class allows scrolling off the bottom of the visible alignment
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815 boolean running = false;
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816 public ScrollThread()
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821 public void setEvent(MouseEvent e)
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826 public void stopScrolling()
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839 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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841 running = ap.scrollUp(true);
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844 if (mouseDragging && evt.getY() >= getSize().height &&
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845 av.alignment.getHeight() > av.getEndSeq())
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847 running = ap.scrollUp(false);
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850 if (mouseDragging && evt.getX() < 0)
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852 running = ap.scrollRight(true);
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855 else if (mouseDragging && evt.getX() >= getSize().width)
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857 running = ap.scrollRight(false);
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865 catch (Exception ex)
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