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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28 import javax.swing.*;
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35 * @version $Revision$
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37 public class SeqPanel extends JPanel implements MouseListener,
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38 MouseMotionListener, MouseWheelListener
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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 boolean seqEditOccurred = false;
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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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94 addMouseMotionListener(this);
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95 addMouseListener(this);
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96 addMouseWheelListener(this);
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100 int startWrapBlock=-1;
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101 int wrappedBlock=-1;
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102 int findRes(MouseEvent evt)
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105 int x = evt.getX();
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107 if (av.wrapAlignment)
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110 int hgap = av.charHeight;
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111 if (av.scaleAboveWrapped)
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112 hgap += av.charHeight;
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114 int cHeight = av.getAlignment().getHeight() * av.charHeight
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115 + hgap + seqCanvas.getAnnotationHeight();
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117 int y = evt.getY();
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119 x -= seqCanvas.LABEL_WEST;
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122 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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124 wrappedBlock = y / cHeight;
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125 wrappedBlock += av.getStartRes() / cwidth;
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127 res = wrappedBlock * cwidth + x / av.getCharWidth();
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132 res = (x / av.getCharWidth()) + av.getStartRes();
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135 if(av.hasHiddenColumns)
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136 res = av.getColumnSelection().adjustForHiddenColumns(res);
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142 int findSeq(MouseEvent evt)
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146 int y = evt.getY();
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148 if (av.wrapAlignment)
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150 int hgap = av.charHeight;
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151 if (av.scaleAboveWrapped)
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152 hgap += av.charHeight;
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154 int cHeight = av.getAlignment().getHeight() * av.charHeight
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155 + hgap + seqCanvas.getAnnotationHeight();
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159 seq = ( (y % cHeight) / av.getCharHeight());
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163 seq = (y / av.getCharHeight()) + av.getStartSeq();
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173 seqEditOccurred = false;
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174 editingSeqs = false;
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175 groupEditing = false;
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181 * @param evt DOCUMENT ME!
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183 public void mouseReleased(MouseEvent evt)
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185 mouseDragging = false;
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189 doMouseReleasedDefineMode(evt);
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193 if (seqEditOccurred)
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207 * @param evt DOCUMENT ME!
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209 public void mousePressed(MouseEvent evt)
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211 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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213 mouseWheelPressed = true;
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217 if (evt.isShiftDown() || evt.isAltDown() ||
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218 evt.isControlDown())
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220 if (evt.isAltDown() || evt.isControlDown())
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222 groupEditing = true;
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224 editingSeqs = true;
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228 doMousePressedDefineMode(evt);
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233 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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234 av.alignment, HistoryItem.EDIT));
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236 int seq = findSeq(evt);
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237 int res = findRes(evt);
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242 if ((seq < av.getAlignment().getHeight()) &&
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243 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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254 startEdit = lastres;
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263 * @param evt DOCUMENT ME!
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265 public void mouseMoved(MouseEvent evt)
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269 // This is because MacOSX creates a mouseMoved
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270 // If control is down, other platforms will not.
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274 int res = findRes(evt);
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275 int seq = findSeq(evt);
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277 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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280 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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282 if (res > sequence.getLength())
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287 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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289 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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293 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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294 sequence.getName());
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297 if (av.alignment.isNucleotide())
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299 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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302 text.append(" Nucleotide: ");
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306 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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308 text.append(" Residue: ");
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316 text.append( obj + " (" +
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317 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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321 ap.alignFrame.statusBar.setText(text.toString());
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323 // use aa to see if the mouse pointer is on a
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324 if (av.showSequenceFeatures)
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326 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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329 StringBuffer sbuffer = new StringBuffer("<html>");
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331 for (int i = 0; i < features.length; i++)
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334 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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335 (features[i].getEnd() >= sequence.findPosition(res)))
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337 if(!av.featuresDisplayed.containsKey(features[i].getType()))
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341 if (features[i].getType().equals("disulfide bond"))
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343 if (features[i].getBegin() == sequence.findPosition(res)
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344 || features[i].getEnd() == sequence.findPosition(res))
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346 if (sbuffer.length() > 6)
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347 sbuffer.append("<br>");
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348 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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349 features[i].getEnd());
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354 if (sbuffer.length() > 6)
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355 sbuffer.append("<br>");
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356 if(features[i].featureGroup!=null)
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357 sbuffer.append(features[i].featureGroup+";");
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359 sbuffer.append(features[i].getType());
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361 if (features[i].getDescription() != null
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362 && !features[i].description.equals(features[i].getType()))
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363 sbuffer.append("; " + features[i].getDescription());
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365 if (features[i].getStatus() != null && features[i].getStatus().length()>0)
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367 sbuffer.append("; (" + features[i].getStatus() + ")");
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374 sbuffer.append("</html>");
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375 if(sbuffer.length()==13) // <html></html>
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376 setToolTipText("");
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378 setToolTipText(sbuffer.toString());
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381 setToolTipText("");
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388 * @param evt DOCUMENT ME!
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390 public void mouseDragged(MouseEvent evt)
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394 doMouseDraggedDefineMode(evt);
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398 int res = findRes(evt);
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405 if ((lastres == -1) || (lastres == res))
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410 boolean dragRight = true;
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412 if ((res < av.getAlignment().getWidth()) && (res < lastres))
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416 else if(av.hasHiddenColumns)
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418 //Stop editing if the user has dragged beyond hiddenBoundary
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419 int lastCol = av.getColumnSelection().getHiddenRegionBoundary(lastres);
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422 if(lastres!=lastCol)
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430 if(!groupEditing && av.hasHiddenRows)
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432 if(av.alignment.getSequenceAt(startseq).getHiddenSequences()!=null)
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434 groupEditing = true;
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439 if (res != lastres)
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445 SequenceGroup sg = av.getSelectionGroup();
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447 if (av.hasHiddenRows)
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449 //sg might be null as the user may only see 1 sequence
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452 sg = new SequenceGroup();
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453 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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456 SequenceGroup tmp = new SequenceGroup();
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458 //Do any of the sequences have hidden associates?
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459 for (int s = 0; s < sg.getSize(); s++)
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461 seq = sg.getSequenceAt(s);
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462 tmp.addSequence(seq, false);
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463 if (seq.getHiddenSequences()!=null)
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465 for(int h=0; h<seq.getHiddenSequences().getSize(); h++)
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466 tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
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481 int blankColumn = -1;
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488 // Find the next gap before the end
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489 // of the visible region boundary
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490 if (av.hasHiddenColumns)
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492 if(res-lastres > 1)
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498 int lastCol = av.getColumnSelection().
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499 getHiddenRegionBoundary(res);
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503 for (blankColumn = lastCol;
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504 blankColumn > lastres;
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507 boolean blank = true;
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508 for (int s = 0; s < sg.getSize(); s++)
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510 seq = sg.getSequenceAt(s);
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512 if (seq.getSequence().length() <= blankColumn)
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517 if (!jalview.util.Comparison.isGap(
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518 seq.getSequence().charAt(blankColumn)))
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529 if (blankColumn <= lastres)
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540 sg.setEndRes(sg.getEndRes() + (res - lastres));
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546 /// Are we able to delete?
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547 // ie are all columns blank?
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549 for (int s = 0; s < sg.getSize(); s++)
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551 seq = sg.getSequenceAt(s);
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553 for (int j = res; j < lastres; j++)
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555 if (seq.getSequence().length() <= j)
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560 if (!jalview.util.Comparison.isGap(
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561 seq.getSequence().charAt(j)))
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563 // Not a gap, block edit not valid
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570 if(res<sg.getStartRes())
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572 sg.setStartRes(sg.getStartRes() - 1);
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574 sg.setEndRes(sg.getEndRes() - (lastres - res));
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577 for (int i = 0; i < sg.getSize(); i++)
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579 seq = sg.getSequenceAt(i);
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584 for (int j = lastres; j < res; j++)
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586 insertChar(j, seq, blankColumn);
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593 for (int j = res; j < lastres; j++)
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595 if (seq.getLength()-1 > res)
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597 deleteChar(res, seq);
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603 else /////Editing a single sequence///////////
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605 seq = av.alignment.getSequenceAt(startseq);
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606 if ((res < av.getAlignment().getWidth()) && (res > lastres))
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608 // dragging to the right
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609 for (int j = lastres; j < res; j++)
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611 insertChar(j, seq, j);
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614 else if ((res < av.getAlignment().getWidth()) &&
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617 // dragging to the left
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618 for (int j = lastres; j > res; j--)
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620 if (jalview.util.Comparison.isGap(
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621 av.alignment.getSequenceAt(startseq)
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622 .getSequence().charAt(res)))
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624 deleteChar(res, seq);
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635 mouseDragging = true;
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636 if(scrollThread!=null)
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637 scrollThread.setEvent(evt);
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641 seqCanvas.repaint();
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647 * @param e DOCUMENT ME!
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649 public void mouseEntered(MouseEvent e)
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654 if (scrollThread != null)
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656 scrollThread.running = false;
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657 scrollThread = null;
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664 * @param e DOCUMENT ME!
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666 public void mouseExited(MouseEvent e)
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668 if (av.getWrapAlignment())
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675 scrollThread = new ScrollThread();
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679 public void mouseClicked(MouseEvent evt)
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682 public void mouseWheelMoved(MouseWheelEvent e)
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684 if (mouseWheelPressed)
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686 Font font = av.getFont();
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687 int fontSize = font.getSize();
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688 if (e.getWheelRotation() > 0 && fontSize < 51)
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690 else if (fontSize > 1)
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693 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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698 if (e.getWheelRotation() > 0)
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699 ap.scrollUp(false);
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710 * @param j DOCUMENT ME!
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711 * @param seq DOCUMENT ME!
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713 void insertChar(int j, SequenceI seq, int blankColumn)
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715 if(av.hasHiddenColumns)
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717 //Find the next gap before the end of the visible region boundary
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718 int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);
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721 if (!groupEditing || lastCol <= j)
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723 blankColumn = lastCol;
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724 //If lastCol > j, theres a boundary after the gap insertion
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727 for (blankColumn = lastCol; blankColumn > j; blankColumn--)
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729 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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731 //Theres a space, so break and insert the gap
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736 if (blankColumn <= j)
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745 // Editing with hidden regions only!!
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746 seq.deleteCharAt(blankColumn);
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750 seq.insertCharAt(j, av.getGapCharacter());
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751 seqEditOccurred = true;
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757 * @param j DOCUMENT ME!
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758 * @param seq DOCUMENT ME!
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760 public void deleteChar(int j, SequenceI seq)
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762 if (av.hasHiddenColumns)
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764 //Find the next gap before the end of the visible region boundary
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765 int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);
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767 //If lastCol > j, theres a boundary after the gap insertion
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770 seq.insertCharAt(lastCol, av.getGapCharacter());
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774 seq.deleteCharAt(j);
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775 seqEditOccurred = true;
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777 seqCanvas.repaint();
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783 * @param i DOCUMENT ME!
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785 void editOccurred()
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787 if (endEdit == startEdit)
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789 ap.alignFrame.historyList.pop();
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790 ap.alignFrame.updateEditMenuBar();
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793 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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800 * @param evt DOCUMENT ME!
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802 public void doMousePressedDefineMode(MouseEvent evt)
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804 int res = findRes(evt);
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805 int seq = findSeq(evt);
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808 startWrapBlock=wrappedBlock;
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810 if(av.wrapAlignment && seq>av.alignment.getHeight())
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812 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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813 "Cannot edit annotations in wrapped view.",
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814 "Wrapped view - no edit",
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815 JOptionPane.WARNING_MESSAGE);
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823 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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825 if ((sequence == null) || (res > sequence.getLength()))
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830 stretchGroup = av.getSelectionGroup();
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832 if (stretchGroup == null)
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834 stretchGroup = av.alignment.findGroup(sequence);
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836 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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837 (res < stretchGroup.getEndRes()))
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839 av.setSelectionGroup(stretchGroup);
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843 stretchGroup = null;
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846 else if (!stretchGroup.sequences.contains(sequence) ||
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847 (stretchGroup.getStartRes() > res) ||
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848 (stretchGroup.getEndRes() < res))
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850 stretchGroup = null;
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852 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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854 if (allGroups != null)
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856 for (int i = 0; i < allGroups.length; i++)
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858 if ((allGroups[i].getStartRes() <= res) &&
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859 (allGroups[i].getEndRes() >= res))
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861 stretchGroup = allGroups[i];
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862 av.setSelectionGroup(stretchGroup);
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870 if (stretchGroup == null)
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872 // define a new group here
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873 SequenceGroup sg = new SequenceGroup();
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874 sg.setStartRes(res);
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876 sg.addSequence(sequence, false);
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877 av.setSelectionGroup(sg);
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880 if (av.getConservationSelected())
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882 SliderPanel.setConservationSlider(ap,
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883 av.getGlobalColourScheme(), "Background");
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886 if (av.getAbovePIDThreshold())
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888 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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892 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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894 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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895 pop.show(this, evt.getX(), evt.getY());
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897 // edit the properties of existing group
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900 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
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902 // Edit end res position of selected group
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903 changeEndRes = true;
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905 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
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907 // Edit end res position of selected group
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908 changeStartRes = true;
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911 stretchGroup.getWidth();
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913 seqCanvas.repaint();
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919 * @param evt DOCUMENT ME!
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921 public void doMouseReleasedDefineMode(MouseEvent evt)
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923 if (stretchGroup == null)
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929 if(stretchGroup.cs!=null)
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931 if (stretchGroup.cs instanceof ClustalxColourScheme)
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933 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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935 stretchGroup.getWidth());
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938 if (stretchGroup.cs.conservationApplied())
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940 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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941 stretchGroup.getName());
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942 stretchGroup.recalcConservation();
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946 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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947 stretchGroup.getName());
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950 changeEndRes = false;
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951 changeStartRes = false;
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952 stretchGroup = null;
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953 PaintRefresher.Refresh(av.alignment);
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959 * @param evt DOCUMENT ME!
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961 public void doMouseDraggedDefineMode(MouseEvent evt)
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963 int res = findRes(evt);
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964 int y = findSeq(evt);
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966 if(wrappedBlock!=startWrapBlock)
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969 if (stretchGroup == null)
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975 if(y > av.alignment.getHeight())
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977 y = av.alignment.getHeight() -1;
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980 if (stretchGroup.getEndRes() == res)
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982 // Edit end res position of selected group
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983 changeEndRes = true;
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985 else if (stretchGroup.getStartRes() == res)
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987 // Edit start res position of selected group
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988 changeStartRes = true;
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991 if (res < av.getStartRes())
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993 res = av.getStartRes();
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998 if (res > (stretchGroup.getStartRes() - 1))
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1000 stretchGroup.setEndRes(res);
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1003 else if (changeStartRes)
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1005 if (res < (stretchGroup.getEndRes() + 1))
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1007 stretchGroup.setStartRes(res);
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1011 int dragDirection = 0;
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1015 dragDirection = 1;
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1017 else if (y < oldSeq)
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1019 dragDirection = -1;
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1023 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
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1025 // This routine ensures we don't skip any sequences, as the
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1026 // selection is quite slow.
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1027 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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1029 oldSeq += dragDirection;
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1034 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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1036 if (stretchGroup.sequences.contains(nextSeq))
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1038 stretchGroup.deleteSequence(seq, false);
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1044 stretchGroup.addSequence(seq, false);
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1047 stretchGroup.addSequence(nextSeq, false);
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1054 mouseDragging = true;
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1056 if (scrollThread != null)
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1058 scrollThread.setEvent(evt);
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1061 seqCanvas.repaint();
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1066 // this class allows scrolling off the bottom of the visible alignment
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1067 class ScrollThread extends Thread
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1070 boolean running = false;
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1072 public ScrollThread()
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1077 public void setEvent(MouseEvent e)
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1082 public void stopScrolling()
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1095 if (mouseDragging && (evt.getY() < 0) &&
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1096 (av.getStartSeq() > 0))
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1098 running = ap.scrollUp(true);
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1101 if (mouseDragging && (evt.getY() >= getHeight()) &&
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1102 (av.alignment.getHeight() > av.getEndSeq()))
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1104 running = ap.scrollUp(false);
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1107 if (mouseDragging && (evt.getX() < 0))
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1109 running = ap.scrollRight(true);
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1111 else if (mouseDragging && (evt.getX() >= getWidth()))
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1113 running = ap.scrollRight(false);
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1121 catch (Exception ex)
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