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 startWrapBlock=-1;
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156 int wrappedBlock=-1;
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157 int findRes(MouseEvent evt)
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160 int x = evt.getX();
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162 if (av.wrapAlignment)
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164 int y = evt.getY();
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165 y -= (2 * av.charHeight);
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166 x -= seqCanvas.LABEL_WEST;
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168 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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169 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);
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170 wrappedBlock = y/chunkHeight;
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171 wrappedBlock += av.getStartRes()/cwidth;
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173 res = wrappedBlock*cwidth + x / av.getCharWidth();
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177 res = (x / av.getCharWidth()) + av.getStartRes();
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184 int findSeq(MouseEvent evt)
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187 int y = evt.getY();
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189 if (av.wrapAlignment)
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191 y -= (2 * av.charHeight);
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192 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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193 seq = ( (y % chunkHeight) / av.getCharHeight());
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197 seq = (y / av.getCharHeight()) + av.getStartSeq();
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204 public void doMousePressed(MouseEvent evt)
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206 ap.alignFrame.addHistoryItem(new HistoryItem(
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207 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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209 int seq = findSeq(evt);
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210 int res = findRes(evt);
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212 if (seq < av.getAlignment().getHeight() &&
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213 res < av.getAlignment().getSequenceAt(seq).getLength())
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215 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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216 // Find the residue's position in the sequence (res is the position
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217 // in the alignment
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231 public void doMouseMoved(MouseEvent evt)
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233 int res = findRes(evt);
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234 int seq = findSeq(evt);
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236 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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241 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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242 if (res > sequence.getLength())
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247 Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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251 aa = obj.toString();
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254 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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255 sequence.getName());
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258 text.append(" Residue: " + aa + " (" +
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259 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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262 ap.alignFrame.statusBar.setText(text.toString());
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264 // use aa to see if the mouse pointer is on a
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265 if (av.showSequenceFeatures)
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267 Vector features = sequence.getSequenceFeatures();
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268 Enumeration e = features.elements();
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269 StringBuffer sbuffer = new StringBuffer();
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271 while (e.hasMoreElements())
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273 SequenceFeature sf = (SequenceFeature) e.nextElement();
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274 if (sf.getStart() <= sequence.findPosition(res) &&
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275 sf.getEnd() >= sequence.findPosition(res))
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277 if (sbuffer.length() > 0)
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279 sbuffer.append("; ");
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281 sbuffer.append(sf.getType() + " " + sf.getDescription());
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282 if (sf.getStatus().length() > 0)
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284 sbuffer.append(" (" + sf.getStatus() + ")");
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293 public void doMouseDragged(MouseEvent evt)
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296 // If we're dragging we're editing
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297 int res = findRes(evt);
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303 if (lastres == -1 || lastres == res)
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308 boolean dragRight = true;
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309 if (res < av.getAlignment().getWidth() && res < lastres)
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314 if (res != lastres)
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319 SequenceGroup sg = av.getSelectionGroup();
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329 sg.setEndRes(sg.getEndRes() + (res - lastres));
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335 /// Are we able to delete?
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336 // ie are all columns blank?
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337 boolean deleteAllowed = false;
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338 for (int s = 0; s < sg.getSize(); s++)
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340 SequenceI seq = sg.getSequenceAt(s);
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341 for (int j = res; j < lastres; j++)
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343 if (seq.getSequence().length() <= j)
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348 if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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350 // Not a gap, block edit not valid
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352 deleteAllowed = false;
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355 deleteAllowed = true;
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359 if (!deleteAllowed)
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365 sg.setEndRes(sg.getEndRes() - (lastres - res));
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368 for (int i = 0; i < sg.getSize(); i++)
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370 SequenceI s = sg.getSequenceAt(i);
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371 int k = av.alignment.findIndex(s);
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376 for (int j = lastres; j < res; j++)
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385 for (int j = res; j < lastres; j++)
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387 if (s.getLength() > j)
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389 deleteChar(res, k);
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395 else /////Editing a single sequence///////////
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397 if (res < av.getAlignment().getWidth() && res > lastres)
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399 // dragging to the right
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400 for (int j = lastres; j < res; j++)
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402 insertChar(j, startseq);
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405 else if (res < av.getAlignment().getWidth() && res < lastres)
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407 // dragging to the left
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408 for (int j = lastres; j > res; j--)
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410 if (jalview.util.Comparison.isGap(
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411 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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414 deleteChar(res, startseq);
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429 seqCanvas.repaint();
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432 public void drawChars(int seqstart, int seqend, int start)
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434 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
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435 av.getStartRes(), av.getStartSeq(), 0);
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436 seqCanvas.repaint();
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439 public void insertChar(int j, int seq)
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441 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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442 seqEditOccurred = seq;
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445 public void deleteChar(int j, int seq)
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448 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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449 seqEditOccurred = seq;
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450 av.alignment.getWidth();
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454 void editOccurred(int i)
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456 if (endEdit == startEdit)
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458 ap.alignFrame.historyList.pop();
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459 ap.alignFrame.updateEditMenuBar();
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462 av.updateConservation();
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463 av.updateConsensus();
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466 //Does the edit affect any groups?
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467 //////////////////////////////
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468 Vector groupsToUpdate = new Vector();
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469 SequenceGroup sg = av.getSelectionGroup();
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471 int s, g, gSize = av.alignment.getGroups().size();
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474 groupsToUpdate.addElement(av.getSelectionGroup());
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475 int sSize = sg.getSize();
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476 for (s = 0; s < sSize; s++)
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478 SequenceI seq = sg.getSequenceAt(s);
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480 for (g = 0; g < gSize; g++)
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482 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().
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485 if (sg2.sequences.contains(seq))
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487 if (!groupsToUpdate.contains(sg2))
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488 groupsToUpdate.addElement(sg2);
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496 SequenceI seq = av.alignment.getSequenceAt(startseq);
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497 for (g = 0; g < gSize; g++)
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499 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(
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501 if (sg2.sequences.contains(seq))
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503 if (!groupsToUpdate.contains(sg2))
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504 groupsToUpdate.addElement(sg2);
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510 gSize = groupsToUpdate.size();
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511 for (g = 0; g < gSize; g++)
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513 ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();
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515 ////End of updating groups
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516 //////////////////////////////////////////
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520 ColourSchemeI cs = av.getGlobalColourScheme();
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522 if (av.getSelectionGroup() != null)
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524 av.getSelectionGroup().recalcConservation();
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529 if (cs.conservationApplied())
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531 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
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532 ResidueProperties.propHash, 3,
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533 av.alignment.getSequences(),
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534 0, av.alignment.getWidth() - 1);
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536 c.verdict(false, av.ConsPercGaps);
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538 if (cs instanceof ClustalxColourScheme)
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540 ((ClustalxColourScheme)cs).
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541 resetClustalX(av.alignment.getSequences(),
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542 av.alignment.getWidth());
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543 cs.setConservation(c);
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544 av.setGlobalColourScheme(cs);
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548 cs.setConservation(c);
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549 av.setGlobalColourScheme(cs);
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554 if (cs instanceof ClustalxColourScheme)
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556 ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
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557 av.alignment.getWidth());
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558 av.setGlobalColourScheme(cs);
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563 //////////////////////////////////////////
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564 /////Everything below this is for defining the boundary of the rubberband
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565 //////////////////////////////////////////
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567 public void doMousePressedDefineMode(MouseEvent evt)
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569 int res = findRes(evt);
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570 int seq = findSeq(evt);
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572 startWrapBlock=wrappedBlock;
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574 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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576 if (sequence == null || res > sequence.getLength())
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581 stretchGroup = av.getSelectionGroup();
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583 if (stretchGroup == null)
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585 stretchGroup = av.alignment.findGroup(sequence);
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586 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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587 res < stretchGroup.getEndRes())
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589 av.setSelectionGroup(stretchGroup);
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593 stretchGroup = null;
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597 else if (!stretchGroup.sequences.contains(sequence)
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598 || stretchGroup.getStartRes() > res
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599 || stretchGroup.getEndRes() < res)
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601 stretchGroup = null;
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603 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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605 if (allGroups != null)
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607 for (int i = 0; i < allGroups.length; i++)
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609 if (allGroups[i].getStartRes() <= res &&
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610 allGroups[i].getEndRes() >= res)
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612 stretchGroup = allGroups[i];
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613 av.setSelectionGroup(stretchGroup);
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620 if (stretchGroup == null)
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622 // define a new group here
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623 SequenceGroup sg = new SequenceGroup();
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624 sg.setStartRes(res);
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626 sg.addSequence(sequence, false);
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627 av.setSelectionGroup(sg);
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630 if (av.getConservationSelected())
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632 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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635 if (av.getAbovePIDThreshold())
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637 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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643 // DETECT RIGHT MOUSE BUTTON IN AWT
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644 else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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645 InputEvent.BUTTON3_MASK)
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647 APopupMenu popup = new APopupMenu(ap, null, null);
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649 popup.show(this, evt.getX(), evt.getY());
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652 if (stretchGroup != null && stretchGroup.getEndRes() == res)
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654 // Edit end res position of selected group
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655 changeEndRes = true;
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658 else if (stretchGroup != null && stretchGroup.getStartRes() == res)
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660 // Edit end res position of selected group
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661 changeStartRes = true;
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666 boolean changeEndSeq = false;
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667 boolean changeStartSeq = false;
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668 boolean changeEndRes = false;
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669 boolean changeStartRes = false;
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670 SequenceGroup stretchGroup = null;
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672 public void doMouseReleasedDefineMode(MouseEvent evt)
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676 stretchGroup.recalcConservation();
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677 mouseDragging = false;
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680 if (stretchGroup == null)
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685 if(stretchGroup.cs!=null)
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687 if (stretchGroup.cs.conservationApplied())
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689 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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690 stretchGroup.getName());
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694 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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695 stretchGroup.getName());
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698 changeEndRes = false;
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699 changeStartRes = false;
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700 stretchGroup = null;
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701 seqCanvas.repaint();
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705 boolean remove = false;
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706 public void doMouseDraggedDefineMode(MouseEvent evt)
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708 int res = findRes(evt);
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709 int y = findSeq(evt);
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711 if(wrappedBlock!=startWrapBlock)
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714 if(y>=av.alignment.getHeight())
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715 y = av.alignment.getHeight()-1;
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717 if (stretchGroup == null)
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722 if (res > av.alignment.getWidth())
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724 res = av.alignment.getWidth() - 1;
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727 if (stretchGroup.getEndRes() == res)
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729 // Edit end res position of selected group
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730 changeEndRes = true;
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733 else if (stretchGroup.getStartRes() == res)
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735 // Edit start res position of selected group
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736 changeStartRes = true;
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739 if (res < av.getStartRes())
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741 res = av.getStartRes();
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743 else if (res > av.getEndRes() && !av.getWrapAlignment())
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745 res = av.getEndRes();
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750 if (res > stretchGroup.getStartRes() - 1)
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752 stretchGroup.setEndRes(res);
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755 else if (changeStartRes)
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757 if (res < stretchGroup.getEndRes() + 1)
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759 stretchGroup.setStartRes(res);
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763 int dragDirection = 0;
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768 else if (y < oldSeq)
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770 dragDirection = -1;
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773 while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
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775 // This routine ensures we don't skip any sequences, as the
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776 // selection is quite slow.
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777 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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779 oldSeq += dragDirection;
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780 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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782 if (stretchGroup.sequences.contains(nextSeq))
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784 stretchGroup.deleteSequence(seq, false);
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790 stretchGroup.addSequence(seq, false);
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792 stretchGroup.addSequence(nextSeq, false);
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796 mouseDragging = true;
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797 if (scrollThread != null)
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799 scrollThread.setEvent(evt);
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802 seqCanvas.repaint();
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805 public void doMouseEnteredDefineMode(MouseEvent e)
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807 if (scrollThread != null)
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809 scrollThread.running = false;
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813 public void doMouseExitedDefineMode(MouseEvent e)
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817 scrollThread = new ScrollThread();
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821 // this class allows scrolling off the bottom of the visible alignment
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826 boolean running = false;
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827 public ScrollThread()
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832 public void setEvent(MouseEvent e)
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837 public void stopScrolling()
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850 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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852 running = ap.scrollUp(true);
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855 if (mouseDragging && evt.getY() >= getSize().height &&
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856 av.alignment.getHeight() > av.getEndSeq())
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858 running = ap.scrollUp(false);
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861 if (mouseDragging && evt.getX() < 0)
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863 running = ap.scrollRight(true);
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866 else if (mouseDragging && evt.getX() >= getSize().width)
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868 running = ap.scrollRight(false);
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876 catch (Exception ex)
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