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.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.schemes.*;
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28 import java.awt.event.*;
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32 import javax.swing.*;
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39 * @version $Revision$
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41 public class SeqPanel extends JPanel
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43 /** DOCUMENT ME!! */
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44 public SeqCanvas seqCanvas;
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46 /** DOCUMENT ME!! */
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47 public AlignmentPanel ap;
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48 protected int lastres;
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49 protected int startseq;
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52 protected AlignViewport av;
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54 // if character is inserted or deleted, we will need to recalculate the conservation
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55 int seqEditOccurred = -1;
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56 ScrollThread scrollThread = null;
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57 boolean mouseDragging = false;
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58 boolean editingSeqs = false;
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59 boolean groupEditing = false;
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61 //////////////////////////////////////////
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62 /////Everything below this is for defining the boundary of the rubberband
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63 //////////////////////////////////////////
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65 boolean changeEndSeq = false;
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66 boolean changeStartSeq = false;
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67 boolean changeEndRes = false;
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68 boolean changeStartRes = false;
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69 SequenceGroup stretchGroup = null;
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70 boolean remove = false;
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72 boolean mouseWheelPressed = false;
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75 * Creates a new SeqPanel object.
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77 * @param avp DOCUMENT ME!
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78 * @param p DOCUMENT ME!
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80 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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82 ToolTipManager.sharedInstance().registerComponent(this);
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83 ToolTipManager.sharedInstance().setInitialDelay(0);
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84 ToolTipManager.sharedInstance().setDismissDelay(10000);
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86 setBackground(Color.white);
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88 seqCanvas = new SeqCanvas(avp);
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89 setLayout(new BorderLayout());
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90 add(seqCanvas, BorderLayout.CENTER);
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94 addMouseMotionListener(new MouseMotionAdapter()
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96 public void mouseMoved(MouseEvent evt)
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101 public void mouseDragged(MouseEvent evt)
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105 doMouseDragged(evt);
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109 doMouseDraggedDefineMode(evt);
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114 addMouseWheelListener(new MouseWheelListener()
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116 public void mouseWheelMoved(MouseWheelEvent e)
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119 if (mouseWheelPressed)
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121 Font font = av.getFont();
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122 int fontSize = font.getSize();
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123 if (e.getWheelRotation() > 0 && fontSize < 30)
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125 else if (fontSize > 1)
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128 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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133 if (e.getWheelRotation() > 0)
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134 ap.scrollUp(false);
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143 addMouseListener(new MouseAdapter()
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145 public void mouseReleased(MouseEvent evt)
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147 mouseWheelPressed = false;
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151 doMouseReleased(evt);
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155 doMouseReleasedDefineMode(evt);
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159 public void mousePressed(MouseEvent evt)
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161 if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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163 mouseWheelPressed = true;
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167 if (evt.isShiftDown() || evt.isAltDown() ||
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168 evt.isControlDown())
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170 if (evt.isAltDown() || evt.isControlDown())
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172 groupEditing = true;
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175 editingSeqs = true;
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176 doMousePressed(evt);
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180 doMousePressedDefineMode(evt);
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184 public void mouseExited(MouseEvent evt)
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191 doMouseExitedDefineMode(evt);
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194 public void mouseEntered(MouseEvent evt)
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201 doMouseEnteredDefineMode(evt);
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206 int startWrapBlock=-1;
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207 int wrappedBlock=-1;
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208 int findRes(MouseEvent evt)
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211 int x = evt.getX();
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213 if (av.wrapAlignment)
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216 int hgap = av.charHeight;
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217 if (av.scaleAboveWrapped)
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218 hgap += av.charHeight;
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220 int cHeight = av.getAlignment().getHeight() * av.charHeight
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221 + hgap + seqCanvas.getAnnotationHeight();
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223 int y = evt.getY();
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225 x -= seqCanvas.LABEL_WEST;
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228 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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230 wrappedBlock = y / cHeight;
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231 wrappedBlock += av.getStartRes() / cwidth;
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233 res = wrappedBlock * cwidth + x / av.getCharWidth();
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238 res = (x / av.getCharWidth()) + av.getStartRes();
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245 int findSeq(MouseEvent evt)
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249 int y = evt.getY();
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251 if (av.wrapAlignment)
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253 int hgap = av.charHeight;
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254 if (av.scaleAboveWrapped)
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255 hgap += av.charHeight;
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257 int cHeight = av.getAlignment().getHeight() * av.charHeight
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258 + hgap + seqCanvas.getAnnotationHeight();
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262 seq = ( (y % cHeight) / av.getCharHeight());
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266 seq = (y / av.getCharHeight()) + av.getStartSeq();
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276 * @param evt DOCUMENT ME!
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278 public void doMouseReleased(MouseEvent evt)
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280 if (seqEditOccurred > -1)
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282 editOccurred(seqEditOccurred);
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287 seqEditOccurred = -1;
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288 editingSeqs = false;
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289 groupEditing = false;
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297 * @param evt DOCUMENT ME!
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299 public void doMousePressed(MouseEvent evt)
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301 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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302 av.alignment, HistoryItem.EDIT));
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304 int seq = findSeq(evt);
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305 int res = findRes(evt);
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310 if ((seq < av.getAlignment().getHeight()) &&
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311 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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322 startEdit = lastres;
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331 * @param evt DOCUMENT ME!
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333 public void doMouseMoved(MouseEvent evt)
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335 int res = findRes(evt);
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336 int seq = findSeq(evt);
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338 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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341 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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343 if (res > sequence.getLength())
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348 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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349 sequence.getName());
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352 if (av.alignment.isNucleotide())
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354 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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357 text.append(" Nucleotide: ");
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361 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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363 text.append(" Residue: ");
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371 text.append( obj + " (" +
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372 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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376 ap.alignFrame.statusBar.setText(text.toString());
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378 // use aa to see if the mouse pointer is on a
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379 if (av.showSequenceFeatures)
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381 Vector features = sequence.getSequenceFeatures();
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382 Enumeration e = features.elements();
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383 StringBuffer sbuffer = new StringBuffer();
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385 while (e.hasMoreElements())
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387 SequenceFeature sf = (SequenceFeature) e.nextElement();
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389 if ((sf.getStart() <= sequence.findPosition(res)) &&
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390 (sf.getEnd() >= sequence.findPosition(res)))
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392 if (sbuffer.length() > 0)
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394 sbuffer.append("; ");
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397 sbuffer.append(sf.getType() + " " + sf.getDescription());
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399 if (sf.getStatus().length() > 0)
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401 sbuffer.append(" (" + sf.getStatus() + ")");
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406 this.setToolTipText(sbuffer.toString());
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413 * @param evt DOCUMENT ME!
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415 public void doMouseDragged(MouseEvent evt)
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417 // If we're dragging we're editing
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418 int res = findRes(evt);
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425 if ((lastres == -1) || (lastres == res))
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430 boolean dragRight = true;
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432 if ((res < av.getAlignment().getWidth()) && (res < lastres))
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437 if (res != lastres)
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442 SequenceGroup sg = av.getSelectionGroup();
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454 sg.setEndRes(sg.getEndRes() + (res - lastres));
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460 /// Are we able to delete?
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461 // ie are all columns blank?
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462 boolean deleteAllowed = false;
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464 for (int s = 0; s < sg.getSize(); s++)
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466 SequenceI seq = sg.getSequenceAt(s);
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468 for (int j = res; j < lastres; j++)
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470 if (seq.getSequence().length() <= j)
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475 if (!jalview.util.Comparison.isGap(
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476 seq.getSequence().charAt(j)))
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478 // Not a gap, block edit not valid
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480 deleteAllowed = false;
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485 deleteAllowed = true;
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489 if (!deleteAllowed)
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496 sg.setEndRes(sg.getEndRes() - (lastres - res));
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499 for (int i = 0; i < sg.getSize(); i++)
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501 SequenceI s = sg.getSequenceAt(i);
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502 int k = av.alignment.findIndex(s);
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507 for (int j = lastres; j < res; j++)
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516 for (int j = res; j < lastres; j++)
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518 if (s.getLength() > j)
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520 deleteChar(res, k);
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526 else /////Editing a single sequence///////////
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528 if ((res < av.getAlignment().getWidth()) && (res > lastres))
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530 // dragging to the right
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531 for (int j = lastres; j < res; j++)
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533 insertChar(j, startseq);
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536 else if ((res < av.getAlignment().getWidth()) &&
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539 // dragging to the left
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540 for (int j = lastres; j > res; j--)
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542 if (jalview.util.Comparison.isGap(
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543 av.alignment.getSequenceAt(startseq)
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544 .getSequence().charAt(res)))
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546 deleteChar(res, startseq);
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559 seqCanvas.repaint();
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565 * @param seqstart DOCUMENT ME!
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566 * @param seqend DOCUMENT ME!
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567 * @param start DOCUMENT ME!
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569 public void drawChars(int seqstart, int seqend, int start)
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571 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
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572 seqend, av.getStartRes(), av.getStartSeq(), 0);
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573 seqCanvas.repaint();
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579 * @param j DOCUMENT ME!
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580 * @param seq DOCUMENT ME!
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582 public void insertChar(int j, int seq)
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584 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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585 seqEditOccurred = seq;
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591 * @param j DOCUMENT ME!
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592 * @param seq DOCUMENT ME!
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594 public void deleteChar(int j, int seq)
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596 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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597 seqEditOccurred = seq;
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599 av.alignment.getWidth();
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600 seqCanvas.repaint();
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606 * @param i DOCUMENT ME!
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608 void editOccurred(int i)
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610 if (endEdit == startEdit)
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612 ap.alignFrame.historyList.pop();
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613 ap.alignFrame.updateEditMenuBar();
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616 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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623 * @param evt DOCUMENT ME!
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625 public void doMousePressedDefineMode(MouseEvent evt)
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627 int res = findRes(evt);
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628 int seq = findSeq(evt);
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631 startWrapBlock=wrappedBlock;
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633 if(av.wrapAlignment && seq>av.alignment.getHeight())
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635 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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636 "Cannot edit annotations in wrapped view.",
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637 "Wrapped view - no edit",
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638 JOptionPane.WARNING_MESSAGE);
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646 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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648 if ((sequence == null) || (res > sequence.getLength()))
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653 stretchGroup = av.getSelectionGroup();
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655 if (stretchGroup == null)
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657 stretchGroup = av.alignment.findGroup(sequence);
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659 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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660 (res < stretchGroup.getEndRes()))
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662 av.setSelectionGroup(stretchGroup);
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666 stretchGroup = null;
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669 else if (!stretchGroup.sequences.contains(sequence) ||
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670 (stretchGroup.getStartRes() > res) ||
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671 (stretchGroup.getEndRes() < res))
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673 stretchGroup = null;
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675 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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677 if (allGroups != null)
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679 for (int i = 0; i < allGroups.length; i++)
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681 if ((allGroups[i].getStartRes() <= res) &&
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682 (allGroups[i].getEndRes() >= res))
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684 stretchGroup = allGroups[i];
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685 av.setSelectionGroup(stretchGroup);
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693 if (stretchGroup == null)
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695 // define a new group here
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696 SequenceGroup sg = new SequenceGroup();
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697 sg.setStartRes(res);
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699 sg.addSequence(sequence, false);
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700 av.setSelectionGroup(sg);
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703 if (av.getConservationSelected())
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705 SliderPanel.setConservationSlider(ap,
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706 av.getGlobalColourScheme(), "Background");
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709 if (av.getAbovePIDThreshold())
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711 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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715 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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717 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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718 pop.show(this, evt.getX(), evt.getY());
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720 // edit the properties of existing group
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723 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
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725 // Edit end res position of selected group
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726 changeEndRes = true;
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728 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
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730 // Edit end res position of selected group
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731 changeStartRes = true;
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734 stretchGroup.getWidth();
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736 seqCanvas.repaint();
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742 * @param evt DOCUMENT ME!
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744 public void doMouseReleasedDefineMode(MouseEvent evt)
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748 stretchGroup.recalcConservation();
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749 mouseDragging = false;
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752 if (stretchGroup == null)
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757 if(stretchGroup.cs!=null)
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759 if (stretchGroup.cs instanceof ClustalxColourScheme)
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761 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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763 stretchGroup.getWidth());
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766 if (stretchGroup.cs.conservationApplied())
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768 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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769 stretchGroup.getName());
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773 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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774 stretchGroup.getName());
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777 changeEndRes = false;
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778 changeStartRes = false;
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779 stretchGroup = null;
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780 PaintRefresher.Refresh(av.alignment);
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786 * @param evt DOCUMENT ME!
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788 public void doMouseDraggedDefineMode(MouseEvent evt)
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790 int res = findRes(evt);
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791 int y = findSeq(evt);
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793 if(wrappedBlock!=startWrapBlock)
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796 if (stretchGroup == null)
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801 if (res > av.alignment.getWidth())
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803 res = av.alignment.getWidth() - 1;
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806 if (stretchGroup.getEndRes() == res)
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808 // Edit end res position of selected group
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809 changeEndRes = true;
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811 else if (stretchGroup.getStartRes() == res)
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813 // Edit start res position of selected group
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814 changeStartRes = true;
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817 if (res < av.getStartRes())
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819 res = av.getStartRes();
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821 else if (res > av.getEndRes() && !av.getWrapAlignment())
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823 res = av.getEndRes();
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828 if (res > (stretchGroup.getStartRes() - 1))
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830 stretchGroup.setEndRes(res);
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833 else if (changeStartRes)
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835 if (res < (stretchGroup.getEndRes() + 1))
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837 stretchGroup.setStartRes(res);
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841 int dragDirection = 0;
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847 else if (y < oldSeq)
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849 dragDirection = -1;
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852 while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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854 // This routine ensures we don't skip any sequences, as the
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855 // selection is quite slow.
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856 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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858 oldSeq += dragDirection;
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860 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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862 if (stretchGroup.sequences.contains(nextSeq))
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864 stretchGroup.deleteSequence(seq, false);
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870 stretchGroup.addSequence(seq, false);
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873 stretchGroup.addSequence(nextSeq, false);
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878 mouseDragging = true;
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880 if (scrollThread != null)
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882 scrollThread.setEvent(evt);
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885 seqCanvas.repaint();
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891 * @param e DOCUMENT ME!
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893 public void doMouseEnteredDefineMode(MouseEvent e)
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895 if (scrollThread != null)
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897 scrollThread.running = false;
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904 * @param e DOCUMENT ME!
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906 public void doMouseExitedDefineMode(MouseEvent e)
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908 if (av.getWrapAlignment())
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915 scrollThread = new ScrollThread();
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919 // this class allows scrolling off the bottom of the visible alignment
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920 class ScrollThread extends Thread
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923 boolean running = false;
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925 public ScrollThread()
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930 public void setEvent(MouseEvent e)
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935 public void stopScrolling()
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948 if (mouseDragging && (evt.getY() < 0) &&
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949 (av.getStartSeq() > 0))
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951 running = ap.scrollUp(true);
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954 if (mouseDragging && (evt.getY() >= getHeight()) &&
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955 (av.alignment.getHeight() > av.getEndSeq()))
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957 running = ap.scrollUp(false);
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960 if (mouseDragging && (evt.getX() < 0))
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962 running = ap.scrollRight(true);
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964 else if (mouseDragging && (evt.getX() >= getWidth()))
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966 running = ap.scrollRight(false);
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974 catch (Exception ex)
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