2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.datamodel.*;
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23 import jalview.schemes.*;
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26 import java.awt.event.*;
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30 import javax.swing.*;
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37 * @version $Revision$
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39 public class SeqPanel extends JPanel
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41 /** DOCUMENT ME!! */
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42 public SeqCanvas seqCanvas;
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44 /** DOCUMENT ME!! */
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45 public AlignmentPanel ap;
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46 protected int lastres;
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47 protected int startseq;
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50 protected AlignViewport av;
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52 // if character is inserted or deleted, we will need to recalculate the conservation
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53 int seqEditOccurred = -1;
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54 ScrollThread scrollThread = null;
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55 boolean mouseDragging = false;
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56 boolean editingSeqs = false;
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57 boolean groupEditing = false;
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59 //////////////////////////////////////////
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60 /////Everything below this is for defining the boundary of the rubberband
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61 //////////////////////////////////////////
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63 boolean changeEndSeq = false;
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64 boolean changeStartSeq = false;
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65 boolean changeEndRes = false;
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66 boolean changeStartRes = false;
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67 SequenceGroup stretchGroup = null;
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68 boolean remove = false;
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70 boolean mouseWheelPressed = false;
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73 * Creates a new SeqPanel object.
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75 * @param avp DOCUMENT ME!
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76 * @param p DOCUMENT ME!
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78 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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80 ToolTipManager.sharedInstance().registerComponent(this);
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81 ToolTipManager.sharedInstance().setInitialDelay(0);
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82 ToolTipManager.sharedInstance().setDismissDelay(10000);
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84 setBackground(Color.white);
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86 seqCanvas = new SeqCanvas(avp);
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87 setLayout(new BorderLayout());
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88 add(seqCanvas, BorderLayout.CENTER);
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93 addMouseMotionListener(new MouseMotionAdapter()
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95 public void mouseMoved(MouseEvent evt)
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100 public void mouseDragged(MouseEvent evt)
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104 if(!av.isDataset())
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105 doMouseDragged(evt);
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109 if(!av.isDataset())
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110 doMouseDraggedDefineMode(evt);
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115 addMouseWheelListener(new MouseWheelListener()
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117 public void mouseWheelMoved(MouseWheelEvent e)
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120 if (mouseWheelPressed)
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122 Font font = av.getFont();
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123 int fontSize = font.getSize();
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124 if (e.getWheelRotation() > 0 && fontSize < 51)
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126 else if (fontSize > 1)
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129 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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134 if (e.getWheelRotation() > 0)
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135 ap.scrollUp(false);
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144 if(!av.isDataset())
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146 addMouseListener(new MouseAdapter()
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148 public void mouseReleased(MouseEvent evt)
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150 mouseWheelPressed = false;
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154 doMouseReleased(evt);
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158 doMouseReleasedDefineMode(evt);
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162 public void mousePressed(MouseEvent evt)
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164 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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166 mouseWheelPressed = true;
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170 if (evt.isShiftDown() || evt.isAltDown() ||
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171 evt.isControlDown())
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173 if (evt.isAltDown() || evt.isControlDown())
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175 groupEditing = true;
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178 editingSeqs = true;
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179 doMousePressed(evt);
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183 doMousePressedDefineMode(evt);
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187 public void mouseExited(MouseEvent evt)
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194 doMouseExitedDefineMode(evt);
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197 public void mouseEntered(MouseEvent evt)
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204 doMouseEnteredDefineMode(evt);
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210 int startWrapBlock=-1;
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211 int wrappedBlock=-1;
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212 int findRes(MouseEvent evt)
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215 int x = evt.getX();
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217 if (av.wrapAlignment)
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220 int hgap = av.charHeight;
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221 if (av.scaleAboveWrapped)
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222 hgap += av.charHeight;
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224 int cHeight = av.getAlignment().getHeight() * av.charHeight
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225 + hgap + seqCanvas.getAnnotationHeight();
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227 int y = evt.getY();
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229 x -= seqCanvas.LABEL_WEST;
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232 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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234 wrappedBlock = y / cHeight;
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235 wrappedBlock += av.getStartRes() / cwidth;
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237 res = wrappedBlock * cwidth + x / av.getCharWidth();
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242 res = (x / av.getCharWidth()) + av.getStartRes();
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249 int findSeq(MouseEvent evt)
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253 int y = evt.getY();
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255 if (av.wrapAlignment)
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257 int hgap = av.charHeight;
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258 if (av.scaleAboveWrapped)
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259 hgap += av.charHeight;
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261 int cHeight = av.getAlignment().getHeight() * av.charHeight
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262 + hgap + seqCanvas.getAnnotationHeight();
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266 seq = ( (y % cHeight) / av.getCharHeight());
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270 seq = (y / av.getCharHeight()) + av.getStartSeq();
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280 * @param evt DOCUMENT ME!
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282 public void doMouseReleased(MouseEvent evt)
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284 if (seqEditOccurred > -1)
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286 editOccurred(seqEditOccurred);
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291 seqEditOccurred = -1;
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292 editingSeqs = false;
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293 groupEditing = false;
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301 * @param evt DOCUMENT ME!
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303 public void doMousePressed(MouseEvent evt)
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305 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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306 av.alignment, HistoryItem.EDIT));
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308 int seq = findSeq(evt);
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309 int res = findRes(evt);
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314 if ((seq < av.getAlignment().getHeight()) &&
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315 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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326 startEdit = lastres;
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335 * @param evt DOCUMENT ME!
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337 public void doMouseMoved(MouseEvent evt)
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339 int res = findRes(evt);
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340 int seq = findSeq(evt);
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342 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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345 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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347 if (res > sequence.getLength())
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352 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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353 sequence.getName());
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356 if (av.alignment.isNucleotide())
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358 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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361 text.append(" Nucleotide: ");
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365 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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367 text.append(" Residue: ");
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375 text.append( obj + " (" +
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376 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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380 ap.alignFrame.statusBar.setText(text.toString());
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382 // use aa to see if the mouse pointer is on a
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383 if (av.showSequenceFeatures)
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385 Vector features = sequence.getSequenceFeatures();
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388 StringBuffer sbuffer = new StringBuffer("<html>");
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390 for (int i = 0; i < features.size(); i++)
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392 SequenceFeature sf = (SequenceFeature) features.elementAt(i);
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394 if ( (sf.getBegin() <= sequence.findPosition(res)) &&
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395 (sf.getEnd() >= sequence.findPosition(res)))
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397 if (sbuffer.length() > 6)
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398 sbuffer.append("<br>");
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400 sbuffer.append(sf.getType());
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401 if (sf.getDescription() != null)
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402 sbuffer.append(" " + sf.getDescription());
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404 if (sf.getStatus() != null)
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406 sbuffer.append(" (" + sf.getStatus() + ")");
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412 sbuffer.append("</html>");
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413 if(sbuffer.equals("<html></html>"))
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414 setToolTipText("");
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416 setToolTipText(sbuffer.toString());
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424 * @param evt DOCUMENT ME!
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426 public void doMouseDragged(MouseEvent evt)
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428 // If we're dragging we're editing
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429 int res = findRes(evt);
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436 if ((lastres == -1) || (lastres == res))
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441 boolean dragRight = true;
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443 if ((res < av.getAlignment().getWidth()) && (res < lastres))
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448 if (res != lastres)
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453 SequenceGroup sg = av.getSelectionGroup();
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465 sg.setEndRes(sg.getEndRes() + (res - lastres));
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471 /// Are we able to delete?
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472 // ie are all columns blank?
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473 boolean deleteAllowed = false;
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475 for (int s = 0; s < sg.getSize(); s++)
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477 SequenceI seq = sg.getSequenceAt(s);
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479 for (int j = res; j < lastres; j++)
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481 if (seq.getSequence().length() <= j)
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486 if (!jalview.util.Comparison.isGap(
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487 seq.getSequence().charAt(j)))
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489 // Not a gap, block edit not valid
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491 deleteAllowed = false;
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496 deleteAllowed = true;
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500 if (!deleteAllowed)
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507 sg.setEndRes(sg.getEndRes() - (lastres - res));
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510 for (int i = 0; i < sg.getSize(); i++)
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512 SequenceI s = sg.getSequenceAt(i);
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513 int k = av.alignment.findIndex(s);
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518 for (int j = lastres; j < res; j++)
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527 for (int j = res; j < lastres; j++)
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529 if (s.getLength() > j)
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531 deleteChar(res, k);
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537 else /////Editing a single sequence///////////
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539 if ((res < av.getAlignment().getWidth()) && (res > lastres))
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541 // dragging to the right
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542 for (int j = lastres; j < res; j++)
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544 insertChar(j, startseq);
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547 else if ((res < av.getAlignment().getWidth()) &&
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550 // dragging to the left
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551 for (int j = lastres; j > res; j--)
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553 if (jalview.util.Comparison.isGap(
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554 av.alignment.getSequenceAt(startseq)
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555 .getSequence().charAt(res)))
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557 deleteChar(res, startseq);
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570 seqCanvas.repaint();
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576 * @param seqstart DOCUMENT ME!
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577 * @param seqend DOCUMENT ME!
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578 * @param start DOCUMENT ME!
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580 public void drawChars(int seqstart, int seqend, int start)
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582 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
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583 seqend, av.getStartRes(), av.getStartSeq(), 0);
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584 seqCanvas.repaint();
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590 * @param j DOCUMENT ME!
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591 * @param seq DOCUMENT ME!
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593 public void insertChar(int j, int seq)
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595 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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596 seqEditOccurred = seq;
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602 * @param j DOCUMENT ME!
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603 * @param seq DOCUMENT ME!
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605 public void deleteChar(int j, int seq)
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607 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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608 seqEditOccurred = seq;
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610 av.alignment.getWidth();
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611 seqCanvas.repaint();
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617 * @param i DOCUMENT ME!
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619 void editOccurred(int i)
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621 if (endEdit == startEdit)
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623 ap.alignFrame.historyList.pop();
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624 ap.alignFrame.updateEditMenuBar();
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627 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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634 * @param evt DOCUMENT ME!
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636 public void doMousePressedDefineMode(MouseEvent evt)
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638 int res = findRes(evt);
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639 int seq = findSeq(evt);
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642 startWrapBlock=wrappedBlock;
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644 if(av.wrapAlignment && seq>av.alignment.getHeight())
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646 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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647 "Cannot edit annotations in wrapped view.",
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648 "Wrapped view - no edit",
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649 JOptionPane.WARNING_MESSAGE);
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657 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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659 if ((sequence == null) || (res > sequence.getLength()))
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664 stretchGroup = av.getSelectionGroup();
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666 if (stretchGroup == null)
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668 stretchGroup = av.alignment.findGroup(sequence);
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670 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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671 (res < stretchGroup.getEndRes()))
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673 av.setSelectionGroup(stretchGroup);
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677 stretchGroup = null;
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680 else if (!stretchGroup.sequences.contains(sequence) ||
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681 (stretchGroup.getStartRes() > res) ||
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682 (stretchGroup.getEndRes() < res))
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684 stretchGroup = null;
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686 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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688 if (allGroups != null)
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690 for (int i = 0; i < allGroups.length; i++)
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692 if ((allGroups[i].getStartRes() <= res) &&
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693 (allGroups[i].getEndRes() >= res))
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695 stretchGroup = allGroups[i];
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696 av.setSelectionGroup(stretchGroup);
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704 if (stretchGroup == null)
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706 // define a new group here
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707 SequenceGroup sg = new SequenceGroup();
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708 sg.setStartRes(res);
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710 sg.addSequence(sequence, false);
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711 av.setSelectionGroup(sg);
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714 if (av.getConservationSelected())
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716 SliderPanel.setConservationSlider(ap,
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717 av.getGlobalColourScheme(), "Background");
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720 if (av.getAbovePIDThreshold())
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722 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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726 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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728 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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729 pop.show(this, evt.getX(), evt.getY());
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731 // edit the properties of existing group
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734 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
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736 // Edit end res position of selected group
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737 changeEndRes = true;
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739 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
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741 // Edit end res position of selected group
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742 changeStartRes = true;
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745 stretchGroup.getWidth();
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747 seqCanvas.repaint();
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753 * @param evt DOCUMENT ME!
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755 public void doMouseReleasedDefineMode(MouseEvent evt)
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759 stretchGroup.recalcConservation();
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760 mouseDragging = false;
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763 if (stretchGroup == null)
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768 if(stretchGroup.cs!=null)
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770 if (stretchGroup.cs instanceof ClustalxColourScheme)
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772 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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774 stretchGroup.getWidth());
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777 if (stretchGroup.cs.conservationApplied())
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779 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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780 stretchGroup.getName());
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784 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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785 stretchGroup.getName());
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788 changeEndRes = false;
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789 changeStartRes = false;
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790 stretchGroup = null;
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791 PaintRefresher.Refresh(av.alignment);
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797 * @param evt DOCUMENT ME!
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799 public void doMouseDraggedDefineMode(MouseEvent evt)
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801 int res = findRes(evt);
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802 int y = findSeq(evt);
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804 if(wrappedBlock!=startWrapBlock)
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807 if (stretchGroup == null)
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812 if (res > av.alignment.getWidth())
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814 res = av.alignment.getWidth() - 1;
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817 if (stretchGroup.getEndRes() == res)
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819 // Edit end res position of selected group
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820 changeEndRes = true;
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822 else if (stretchGroup.getStartRes() == res)
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824 // Edit start res position of selected group
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825 changeStartRes = true;
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828 if (res < av.getStartRes())
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830 res = av.getStartRes();
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832 else if (res > av.getEndRes() && !av.getWrapAlignment())
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834 res = av.getEndRes();
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839 if (res > (stretchGroup.getStartRes() - 1))
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841 stretchGroup.setEndRes(res);
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844 else if (changeStartRes)
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846 if (res < (stretchGroup.getEndRes() + 1))
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848 stretchGroup.setStartRes(res);
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852 int dragDirection = 0;
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858 else if (y < oldSeq)
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860 dragDirection = -1;
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863 while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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865 // This routine ensures we don't skip any sequences, as the
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866 // selection is quite slow.
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867 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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869 oldSeq += dragDirection;
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871 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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873 if (stretchGroup.sequences.contains(nextSeq))
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875 stretchGroup.deleteSequence(seq, false);
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881 stretchGroup.addSequence(seq, false);
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884 stretchGroup.addSequence(nextSeq, false);
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889 mouseDragging = true;
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891 if (scrollThread != null)
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893 scrollThread.setEvent(evt);
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896 seqCanvas.repaint();
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902 * @param e DOCUMENT ME!
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904 public void doMouseEnteredDefineMode(MouseEvent e)
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906 if (scrollThread != null)
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908 scrollThread.running = false;
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915 * @param e DOCUMENT ME!
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917 public void doMouseExitedDefineMode(MouseEvent e)
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919 if (av.getWrapAlignment())
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926 scrollThread = new ScrollThread();
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930 // this class allows scrolling off the bottom of the visible alignment
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931 class ScrollThread extends Thread
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934 boolean running = false;
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936 public ScrollThread()
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941 public void setEvent(MouseEvent e)
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946 public void stopScrolling()
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959 if (mouseDragging && (evt.getY() < 0) &&
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960 (av.getStartSeq() > 0))
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962 running = ap.scrollUp(true);
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965 if (mouseDragging && (evt.getY() >= getHeight()) &&
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966 (av.alignment.getHeight() > av.getEndSeq()))
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968 running = ap.scrollUp(false);
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971 if (mouseDragging && (evt.getX() < 0))
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973 running = ap.scrollRight(true);
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975 else if (mouseDragging && (evt.getX() >= getWidth()))
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977 running = ap.scrollRight(false);
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985 catch (Exception ex)
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