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 // This is because MacOSX creates a mouseMoved
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101 // If control is down
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102 if(!av.isDataset())
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103 doMouseDragged(evt);
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107 public void mouseDragged(MouseEvent evt)
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111 if(!av.isDataset())
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112 doMouseDragged(evt);
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116 if(!av.isDataset())
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117 doMouseDraggedDefineMode(evt);
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122 addMouseWheelListener(new MouseWheelListener()
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124 public void mouseWheelMoved(MouseWheelEvent e)
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127 if (mouseWheelPressed)
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129 Font font = av.getFont();
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130 int fontSize = font.getSize();
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131 if (e.getWheelRotation() > 0 && fontSize < 51)
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133 else if (fontSize > 1)
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136 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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141 if (e.getWheelRotation() > 0)
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142 ap.scrollUp(false);
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151 if(!av.isDataset())
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153 addMouseListener(new MouseAdapter()
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155 public void mouseReleased(MouseEvent evt)
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157 mouseWheelPressed = false;
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161 doMouseReleased(evt);
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165 doMouseReleasedDefineMode(evt);
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169 public void mousePressed(MouseEvent evt)
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171 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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173 mouseWheelPressed = true;
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177 if (evt.isShiftDown() || evt.isAltDown() ||
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178 evt.isControlDown())
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180 if (evt.isAltDown() || evt.isControlDown())
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182 groupEditing = true;
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186 editingSeqs = true;
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187 doMousePressed(evt);
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191 doMousePressedDefineMode(evt);
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195 public void mouseExited(MouseEvent evt)
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202 doMouseExitedDefineMode(evt);
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205 public void mouseEntered(MouseEvent evt)
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212 doMouseEnteredDefineMode(evt);
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218 int startWrapBlock=-1;
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219 int wrappedBlock=-1;
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220 int findRes(MouseEvent evt)
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223 int x = evt.getX();
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225 if (av.wrapAlignment)
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228 int hgap = av.charHeight;
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229 if (av.scaleAboveWrapped)
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230 hgap += av.charHeight;
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232 int cHeight = av.getAlignment().getHeight() * av.charHeight
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233 + hgap + seqCanvas.getAnnotationHeight();
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235 int y = evt.getY();
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237 x -= seqCanvas.LABEL_WEST;
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240 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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242 wrappedBlock = y / cHeight;
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243 wrappedBlock += av.getStartRes() / cwidth;
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245 res = wrappedBlock * cwidth + x / av.getCharWidth();
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250 res = (x / av.getCharWidth()) + av.getStartRes();
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253 if(av.hasHiddenColumns)
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254 res = av.getColumnSelection().adjustForHiddenColumns(res);
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260 int findSeq(MouseEvent evt)
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264 int y = evt.getY();
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266 if (av.wrapAlignment)
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268 int hgap = av.charHeight;
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269 if (av.scaleAboveWrapped)
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270 hgap += av.charHeight;
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272 int cHeight = av.getAlignment().getHeight() * av.charHeight
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273 + hgap + seqCanvas.getAnnotationHeight();
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277 seq = ( (y % cHeight) / av.getCharHeight());
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281 seq = (y / av.getCharHeight()) + av.getStartSeq();
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291 * @param evt DOCUMENT ME!
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293 public void doMouseReleased(MouseEvent evt)
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295 if (seqEditOccurred > -1)
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297 editOccurred(seqEditOccurred);
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302 seqEditOccurred = -1;
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303 editingSeqs = false;
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304 groupEditing = false;
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312 * @param evt DOCUMENT ME!
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314 public void doMousePressed(MouseEvent evt)
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316 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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317 av.alignment, HistoryItem.EDIT));
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319 int seq = findSeq(evt);
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320 int res = findRes(evt);
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325 if ((seq < av.getAlignment().getHeight()) &&
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326 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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337 startEdit = lastres;
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346 * @param evt DOCUMENT ME!
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348 public void doMouseMoved(MouseEvent evt)
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350 int res = findRes(evt);
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351 int seq = findSeq(evt);
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353 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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356 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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358 if (res > sequence.getLength())
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363 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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365 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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369 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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370 sequence.getName());
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373 if (av.alignment.isNucleotide())
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375 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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378 text.append(" Nucleotide: ");
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382 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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384 text.append(" Residue: ");
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392 text.append( obj + " (" +
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393 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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397 ap.alignFrame.statusBar.setText(text.toString());
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399 // use aa to see if the mouse pointer is on a
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400 if (av.showSequenceFeatures)
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402 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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405 StringBuffer sbuffer = new StringBuffer("<html>");
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407 for (int i = 0; i < features.length; i++)
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410 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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411 (features[i].getEnd() >= sequence.findPosition(res)))
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413 if(!av.featuresDisplayed.containsKey(features[i].getType()))
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417 if (features[i].getType().equals("disulfide bond"))
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419 if (features[i].getBegin() == sequence.findPosition(res)
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420 || features[i].getEnd() == sequence.findPosition(res))
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422 if (sbuffer.length() > 6)
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423 sbuffer.append("<br>");
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424 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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425 features[i].getEnd());
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430 if (sbuffer.length() > 6)
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431 sbuffer.append("<br>");
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432 if(features[i].featureGroup!=null)
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433 sbuffer.append(features[i].featureGroup+";");
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435 sbuffer.append(features[i].getType());
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437 if (features[i].getDescription() != null
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438 && !features[i].description.equals(features[i].getType()))
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439 sbuffer.append("; " + features[i].getDescription());
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441 if (features[i].getStatus() != null && features[i].getStatus().length()>0)
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443 sbuffer.append("; (" + features[i].getStatus() + ")");
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450 sbuffer.append("</html>");
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451 if(sbuffer.length()==13) // <html></html>
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452 setToolTipText("");
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454 setToolTipText(sbuffer.toString());
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457 setToolTipText("");
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464 * @param evt DOCUMENT ME!
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466 public void doMouseDragged(MouseEvent evt)
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468 // If we're dragging we're editing
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469 int res = findRes(evt);
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476 if ((lastres == -1) || (lastres == res))
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481 boolean dragRight = true;
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483 if ((res < av.getAlignment().getWidth()) && (res < lastres))
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488 if (res != lastres)
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493 SequenceGroup sg = av.getSelectionGroup();
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505 sg.setEndRes(sg.getEndRes() + (res - lastres));
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511 /// Are we able to delete?
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512 // ie are all columns blank?
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513 boolean deleteAllowed = false;
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515 for (int s = 0; s < sg.getSize(); s++)
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517 SequenceI seq = sg.getSequenceAt(s);
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519 for (int j = res; j < lastres; j++)
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521 if (seq.getSequence().length() <= j)
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526 if (!jalview.util.Comparison.isGap(
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527 seq.getSequence().charAt(j)))
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529 // Not a gap, block edit not valid
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531 deleteAllowed = false;
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536 deleteAllowed = true;
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540 if (!deleteAllowed)
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547 sg.setEndRes(sg.getEndRes() - (lastres - res));
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550 for (int i = 0; i < sg.getSize(); i++)
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552 SequenceI s = sg.getSequenceAt(i);
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553 int k = av.alignment.findIndex(s);
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558 for (int j = lastres; j < res; j++)
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567 for (int j = res; j < lastres; j++)
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569 if (s.getLength() > j)
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571 deleteChar(res, k);
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577 else /////Editing a single sequence///////////
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579 if ((res < av.getAlignment().getWidth()) && (res > lastres))
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581 // dragging to the right
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582 for (int j = lastres; j < res; j++)
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584 insertChar(j, startseq);
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587 else if ((res < av.getAlignment().getWidth()) &&
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590 // dragging to the left
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591 for (int j = lastres; j > res; j--)
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593 if (jalview.util.Comparison.isGap(
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594 av.alignment.getSequenceAt(startseq)
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595 .getSequence().charAt(res)))
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597 deleteChar(res, startseq);
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610 seqCanvas.repaint();
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617 * @param j DOCUMENT ME!
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618 * @param seq DOCUMENT ME!
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620 public void insertChar(int j, int seq)
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622 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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623 seqEditOccurred = seq;
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629 * @param j DOCUMENT ME!
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630 * @param seq DOCUMENT ME!
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632 public void deleteChar(int j, int seq)
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634 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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635 seqEditOccurred = seq;
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637 av.alignment.getWidth();
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638 seqCanvas.repaint();
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644 * @param i DOCUMENT ME!
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646 void editOccurred(int i)
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648 if (endEdit == startEdit)
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650 ap.alignFrame.historyList.pop();
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651 ap.alignFrame.updateEditMenuBar();
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654 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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661 * @param evt DOCUMENT ME!
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663 public void doMousePressedDefineMode(MouseEvent evt)
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665 int res = findRes(evt);
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666 int seq = findSeq(evt);
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669 startWrapBlock=wrappedBlock;
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671 if(av.wrapAlignment && seq>av.alignment.getHeight())
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673 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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674 "Cannot edit annotations in wrapped view.",
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675 "Wrapped view - no edit",
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676 JOptionPane.WARNING_MESSAGE);
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684 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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686 if ((sequence == null) || (res > sequence.getLength()))
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691 stretchGroup = av.getSelectionGroup();
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693 if (stretchGroup == null)
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695 stretchGroup = av.alignment.findGroup(sequence);
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697 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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698 (res < stretchGroup.getEndRes()))
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700 av.setSelectionGroup(stretchGroup);
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704 stretchGroup = null;
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707 else if (!stretchGroup.sequences.contains(sequence) ||
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708 (stretchGroup.getStartRes() > res) ||
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709 (stretchGroup.getEndRes() < res))
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711 stretchGroup = null;
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713 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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715 if (allGroups != null)
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717 for (int i = 0; i < allGroups.length; i++)
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719 if ((allGroups[i].getStartRes() <= res) &&
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720 (allGroups[i].getEndRes() >= res))
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722 stretchGroup = allGroups[i];
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723 av.setSelectionGroup(stretchGroup);
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731 if (stretchGroup == null)
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733 // define a new group here
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734 SequenceGroup sg = new SequenceGroup();
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735 sg.setStartRes(res);
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737 sg.addSequence(sequence, false);
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738 av.setSelectionGroup(sg);
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741 if (av.getConservationSelected())
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743 SliderPanel.setConservationSlider(ap,
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744 av.getGlobalColourScheme(), "Background");
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747 if (av.getAbovePIDThreshold())
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749 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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753 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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755 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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756 pop.show(this, evt.getX(), evt.getY());
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758 // edit the properties of existing group
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761 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
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763 // Edit end res position of selected group
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764 changeEndRes = true;
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766 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
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768 // Edit end res position of selected group
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769 changeStartRes = true;
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772 stretchGroup.getWidth();
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774 seqCanvas.repaint();
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780 * @param evt DOCUMENT ME!
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782 public void doMouseReleasedDefineMode(MouseEvent evt)
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786 stretchGroup.recalcConservation();
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787 mouseDragging = false;
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790 if (stretchGroup == null)
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795 if(stretchGroup.cs!=null)
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797 if (stretchGroup.cs instanceof ClustalxColourScheme)
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799 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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801 stretchGroup.getWidth());
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804 if (stretchGroup.cs.conservationApplied())
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806 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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807 stretchGroup.getName());
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811 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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812 stretchGroup.getName());
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815 changeEndRes = false;
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816 changeStartRes = false;
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817 stretchGroup = null;
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818 PaintRefresher.Refresh(av.alignment);
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824 * @param evt DOCUMENT ME!
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826 public void doMouseDraggedDefineMode(MouseEvent evt)
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828 int res = findRes(evt);
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829 int y = findSeq(evt);
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831 if(wrappedBlock!=startWrapBlock)
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834 if (stretchGroup == null)
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839 if (res > av.alignment.getWidth())
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841 res = av.alignment.getWidth() - 1;
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844 if (stretchGroup.getEndRes() == res)
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846 // Edit end res position of selected group
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847 changeEndRes = true;
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849 else if (stretchGroup.getStartRes() == res)
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851 // Edit start res position of selected group
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852 changeStartRes = true;
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855 if (res < av.getStartRes())
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857 res = av.getStartRes();
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859 else if (res > av.getEndRes() && !av.getWrapAlignment())
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861 res = av.getEndRes();
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866 if (res > (stretchGroup.getStartRes() - 1))
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868 stretchGroup.setEndRes(res);
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871 else if (changeStartRes)
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873 if (res < (stretchGroup.getEndRes() + 1))
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875 stretchGroup.setStartRes(res);
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879 int dragDirection = 0;
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885 else if (y < oldSeq)
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887 dragDirection = -1;
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890 while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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892 // This routine ensures we don't skip any sequences, as the
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893 // selection is quite slow.
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894 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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896 oldSeq += dragDirection;
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898 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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900 if (stretchGroup.sequences.contains(nextSeq))
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902 stretchGroup.deleteSequence(seq, false);
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908 stretchGroup.addSequence(seq, false);
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911 stretchGroup.addSequence(nextSeq, false);
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916 mouseDragging = true;
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918 if (scrollThread != null)
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920 scrollThread.setEvent(evt);
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923 seqCanvas.repaint();
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929 * @param e DOCUMENT ME!
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931 public void doMouseEnteredDefineMode(MouseEvent e)
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933 if (scrollThread != null)
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935 scrollThread.running = false;
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942 * @param e DOCUMENT ME!
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944 public void doMouseExitedDefineMode(MouseEvent e)
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946 if (av.getWrapAlignment())
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953 scrollThread = new ScrollThread();
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957 // this class allows scrolling off the bottom of the visible alignment
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958 class ScrollThread extends Thread
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961 boolean running = false;
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963 public ScrollThread()
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968 public void setEvent(MouseEvent e)
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973 public void stopScrolling()
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986 if (mouseDragging && (evt.getY() < 0) &&
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987 (av.getStartSeq() > 0))
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989 running = ap.scrollUp(true);
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992 if (mouseDragging && (evt.getY() >= getHeight()) &&
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993 (av.alignment.getHeight() > av.getEndSeq()))
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995 running = ap.scrollUp(false);
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998 if (mouseDragging && (evt.getX() < 0))
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1000 running = ap.scrollRight(true);
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1002 else if (mouseDragging && (evt.getX() >= getWidth()))
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1004 running = ap.scrollRight(false);
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1012 catch (Exception ex)
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