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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70 public void mouseDragged(MouseEvent evt)
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74 doMouseDragged(evt);
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78 doMouseDraggedDefineMode(evt);
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83 seqCanvas.addMouseListener(new MouseAdapter()
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85 public void mouseReleased(MouseEvent evt)
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89 doMouseReleased(evt);
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93 doMouseReleasedDefineMode(evt);
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98 public void mousePressed(MouseEvent evt)
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100 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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102 if (evt.isAltDown() || evt.isControlDown())
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104 groupEditing = true;
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107 editingSeqs = true;
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108 doMousePressed(evt);
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112 doMousePressedDefineMode(evt);
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116 public void mouseExited(MouseEvent evt)
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122 doMouseExitedDefineMode(evt);
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126 public void mouseEntered(MouseEvent evt)
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132 doMouseEnteredDefineMode(evt);
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136 seqCanvas.repaint();
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139 public void doMouseReleased(MouseEvent evt)
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142 if (seqEditOccurred > -1)
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144 editOccurred(seqEditOccurred);
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149 seqEditOccurred = -1;
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150 editingSeqs = false;
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151 groupEditing = false;
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155 int findRes(MouseEvent evt)
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158 int x = evt.getX();
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160 if (av.wrapAlignment)
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162 int y = evt.getY();
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163 y -= (2 * av.charHeight);
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164 x -= seqCanvas.LABEL_WEST;
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166 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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167 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);
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168 int block = y/chunkHeight;
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169 block += av.getStartRes()/cwidth;
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171 res = block*cwidth + x / av.getCharWidth();
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175 res = (x / av.getCharWidth()) + av.getStartRes();
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182 int findSeq(MouseEvent evt)
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185 int y = evt.getY();
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187 if (av.wrapAlignment)
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189 y -= (2 * av.charHeight);
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190 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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191 seq = ( (y % chunkHeight) / av.getCharHeight());
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195 seq = (y / av.getCharHeight()) + av.getStartSeq();
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202 public void doMousePressed(MouseEvent evt)
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204 ap.alignFrame.addHistoryItem(new HistoryItem(
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205 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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207 int seq = findSeq(evt);
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208 int res = findRes(evt);
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210 if (seq < av.getAlignment().getHeight() &&
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211 res < av.getAlignment().getSequenceAt(seq).getLength())
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213 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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214 // Find the residue's position in the sequence (res is the position
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215 // in the alignment
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229 public void doMouseMoved(MouseEvent evt)
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231 int res = findRes(evt);
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232 int seq = findSeq(evt);
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234 if (seq >= av.getAlignment().getHeight() || seq<0)
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239 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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240 if (res > sequence.getLength())
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245 Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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249 aa = obj.toString();
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252 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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253 sequence.getName());
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256 text.append(" Residue: " + aa + " (" +
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257 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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260 ap.alignFrame.statusBar.setText(text.toString());
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262 // use aa to see if the mouse pointer is on a
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263 if (av.showSequenceFeatures)
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265 Vector features = sequence.getSequenceFeatures();
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266 Enumeration e = features.elements();
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267 StringBuffer sbuffer = new StringBuffer();
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269 while (e.hasMoreElements())
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271 SequenceFeature sf = (SequenceFeature) e.nextElement();
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272 if (sf.getStart() <= sequence.findPosition(res) &&
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273 sf.getEnd() >= sequence.findPosition(res))
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275 if (sbuffer.length() > 0)
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277 sbuffer.append("; ");
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279 sbuffer.append(sf.getType() + " " + sf.getDescription());
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280 if (sf.getStatus().length() > 0)
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282 sbuffer.append(" (" + sf.getStatus() + ")");
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291 public void doMouseDragged(MouseEvent evt)
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294 // If we're dragging we're editing
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295 int res = findRes(evt);
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301 if (lastres == -1 || lastres == res)
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306 boolean dragRight = true;
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307 if (res < av.getAlignment().getWidth() && res < lastres)
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312 if (res != lastres)
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317 SequenceGroup sg = av.getSelectionGroup();
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327 sg.setEndRes(sg.getEndRes() + (res - lastres));
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333 /// Are we able to delete?
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334 // ie are all columns blank?
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335 boolean deleteAllowed = false;
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336 for (int s = 0; s < sg.getSize(); s++)
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338 SequenceI seq = sg.getSequenceAt(s);
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339 for (int j = res; j < lastres; j++)
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341 if (seq.getSequence().length() <= j)
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346 if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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348 // Not a gap, block edit not valid
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350 deleteAllowed = false;
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353 deleteAllowed = true;
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357 if (!deleteAllowed)
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363 sg.setEndRes(sg.getEndRes() - (lastres - res));
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366 for (int i = 0; i < sg.getSize(); i++)
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368 SequenceI s = sg.getSequenceAt(i);
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369 int k = av.alignment.findIndex(s);
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374 for (int j = lastres; j < res; j++)
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383 for (int j = res; j < lastres; j++)
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385 if (s.getLength() > j)
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387 deleteChar(res, k);
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393 else /////Editing a single sequence///////////
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395 if (res < av.getAlignment().getWidth() && res > lastres)
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397 // dragging to the right
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398 for (int j = lastres; j < res; j++)
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400 insertChar(j, startseq);
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403 else if (res < av.getAlignment().getWidth() && res < lastres)
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405 // dragging to the left
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406 for (int j = lastres; j > res; j--)
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408 if (jalview.util.Comparison.isGap(
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409 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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412 deleteChar(res, startseq);
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427 seqCanvas.repaint();
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430 public void drawChars(int seqstart, int seqend, int start)
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432 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
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433 av.getStartRes(), av.getStartSeq(), 0);
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434 seqCanvas.repaint();
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437 public void insertChar(int j, int seq)
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439 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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440 seqEditOccurred = seq;
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443 public void deleteChar(int j, int seq)
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446 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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447 seqEditOccurred = seq;
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448 av.alignment.getWidth();
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452 void editOccurred(int i)
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454 if (endEdit == startEdit)
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456 ap.alignFrame.historyList.pop();
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457 ap.alignFrame.updateEditMenuBar();
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460 av.updateConservation();
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461 av.updateConsensus();
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464 //Does the edit affect any groups?
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465 //////////////////////////////
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466 Vector groupsToUpdate = new Vector();
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467 SequenceGroup sg = av.getSelectionGroup();
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469 int s, g, gSize = av.alignment.getGroups().size();
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472 groupsToUpdate.addElement(av.getSelectionGroup());
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473 int sSize = sg.getSize();
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474 for (s = 0; s < sSize; s++)
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476 SequenceI seq = sg.getSequenceAt(s);
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478 for (g = 0; g < gSize; g++)
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480 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().
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483 if (sg2.sequences.contains(seq))
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485 if (!groupsToUpdate.contains(sg2))
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486 groupsToUpdate.addElement(sg2);
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494 SequenceI seq = av.alignment.getSequenceAt(startseq);
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495 for (g = 0; g < gSize; g++)
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497 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(
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499 if (sg2.sequences.contains(seq))
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501 if (!groupsToUpdate.contains(sg2))
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502 groupsToUpdate.addElement(sg2);
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508 gSize = groupsToUpdate.size();
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509 for (g = 0; g < gSize; g++)
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511 ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();
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513 ////End of updating groups
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514 //////////////////////////////////////////
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518 ColourSchemeI cs = av.getGlobalColourScheme();
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520 if (av.getSelectionGroup() != null)
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522 av.getSelectionGroup().recalcConservation();
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527 if (cs.conservationApplied())
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529 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
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530 ResidueProperties.propHash, 3,
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531 av.alignment.getSequences(),
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532 0, av.alignment.getWidth() - 1);
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534 c.verdict(false, av.ConsPercGaps);
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536 if (cs instanceof ClustalxColourScheme)
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538 ((ClustalxColourScheme)cs).
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539 resetClustalX(av.alignment.getSequences(),
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540 av.alignment.getWidth());
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541 cs.setConservation(c);
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542 av.setGlobalColourScheme(cs);
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546 cs.setConservation(c);
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547 av.setGlobalColourScheme(cs);
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552 if (cs instanceof ClustalxColourScheme)
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554 ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
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555 av.alignment.getWidth());
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556 av.setGlobalColourScheme(cs);
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561 //////////////////////////////////////////
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562 /////Everything below this is for defining the boundary of the rubberband
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563 //////////////////////////////////////////
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565 public void doMousePressedDefineMode(MouseEvent evt)
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567 int res = findRes(evt);
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568 int seq = findSeq(evt);
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571 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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573 if (sequence == null || res > sequence.getLength())
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578 stretchGroup = av.getSelectionGroup();
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580 if (stretchGroup == null)
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582 stretchGroup = av.alignment.findGroup(sequence);
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583 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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584 res < stretchGroup.getEndRes())
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586 av.setSelectionGroup(stretchGroup);
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590 stretchGroup = null;
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594 else if (!stretchGroup.sequences.contains(sequence)
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595 || stretchGroup.getStartRes() > res
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596 || stretchGroup.getEndRes() < res)
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598 stretchGroup = null;
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600 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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602 if (allGroups != null)
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604 for (int i = 0; i < allGroups.length; i++)
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606 if (allGroups[i].getStartRes() <= res &&
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607 allGroups[i].getEndRes() >= res)
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609 stretchGroup = allGroups[i];
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610 av.setSelectionGroup(stretchGroup);
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617 if (stretchGroup == null)
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619 // define a new group here
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620 SequenceGroup sg = new SequenceGroup();
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621 sg.setStartRes(res);
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623 sg.addSequence(sequence, false);
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624 av.setSelectionGroup(sg);
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627 if (av.getConservationSelected())
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629 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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632 if (av.getAbovePIDThreshold())
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634 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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640 // DETECT RIGHT MOUSE BUTTON IN AWT
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641 else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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642 InputEvent.BUTTON3_MASK)
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644 APopupMenu popup = new APopupMenu(ap, null, null);
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646 popup.show(this, evt.getX(), evt.getY());
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649 if (stretchGroup != null && stretchGroup.getEndRes() == res)
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651 // Edit end res position of selected group
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652 changeEndRes = true;
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655 else if (stretchGroup != null && stretchGroup.getStartRes() == res)
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657 // Edit end res position of selected group
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658 changeStartRes = true;
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663 boolean changeEndSeq = false;
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664 boolean changeStartSeq = false;
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665 boolean changeEndRes = false;
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666 boolean changeStartRes = false;
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667 SequenceGroup stretchGroup = null;
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669 public void doMouseReleasedDefineMode(MouseEvent evt)
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673 stretchGroup.recalcConservation();
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674 mouseDragging = false;
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677 if (stretchGroup == null)
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682 if(stretchGroup.cs!=null)
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684 if (stretchGroup.cs.conservationApplied())
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686 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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687 stretchGroup.getName());
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691 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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692 stretchGroup.getName());
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695 changeEndRes = false;
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696 changeStartRes = false;
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697 stretchGroup = null;
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698 seqCanvas.repaint();
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702 boolean remove = false;
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703 public void doMouseDraggedDefineMode(MouseEvent evt)
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705 int res = findRes(evt);
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706 int y = findSeq(evt);
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708 if(y>=av.alignment.getHeight())
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709 y = av.alignment.getHeight()-1;
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711 if (stretchGroup == null)
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716 if (res > av.alignment.getWidth() && !av.getWrapAlignment())
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718 res = av.alignment.getWidth() - 1;
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721 if (stretchGroup.getEndRes() == res)
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723 // Edit end res position of selected group
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724 changeEndRes = true;
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727 else if (stretchGroup.getStartRes() == res)
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729 // Edit start res position of selected group
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730 changeStartRes = true;
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733 if (res < av.getStartRes())
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735 res = av.getStartRes();
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737 else if (res > av.getEndRes() && !av.getWrapAlignment())
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739 res = av.getEndRes();
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744 if (res > stretchGroup.getStartRes() - 1)
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746 stretchGroup.setEndRes(res);
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749 else if (changeStartRes)
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751 if (res < stretchGroup.getEndRes() + 1)
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753 stretchGroup.setStartRes(res);
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757 int dragDirection = 0;
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762 else if (y < oldSeq)
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764 dragDirection = -1;
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767 while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
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769 // This routine ensures we don't skip any sequences, as the
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770 // selection is quite slow.
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771 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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773 oldSeq += dragDirection;
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774 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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776 if (stretchGroup.sequences.contains(nextSeq))
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778 stretchGroup.deleteSequence(seq, false);
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784 stretchGroup.addSequence(seq, false);
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786 stretchGroup.addSequence(nextSeq, false);
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790 mouseDragging = true;
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791 if (scrollThread != null)
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793 scrollThread.setEvent(evt);
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796 seqCanvas.repaint();
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799 public void doMouseEnteredDefineMode(MouseEvent e)
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801 if (scrollThread != null)
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803 scrollThread.running = false;
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807 public void doMouseExitedDefineMode(MouseEvent e)
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811 scrollThread = new ScrollThread();
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815 // this class allows scrolling off the bottom of the visible alignment
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820 boolean running = false;
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821 public ScrollThread()
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826 public void setEvent(MouseEvent e)
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831 public void stopScrolling()
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844 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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846 running = ap.scrollUp(true);
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849 if (mouseDragging && evt.getY() >= getSize().height &&
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850 av.alignment.getHeight() > av.getEndSeq())
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852 running = ap.scrollUp(false);
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855 if (mouseDragging && evt.getX() < 0)
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857 running = ap.scrollRight(true);
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860 else if (mouseDragging && evt.getX() >= getSize().width)
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862 running = ap.scrollRight(false);
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870 catch (Exception ex)
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