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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257 int findSeq(MouseEvent evt)
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261 int y = evt.getY();
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263 if (av.wrapAlignment)
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265 int hgap = av.charHeight;
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266 if (av.scaleAboveWrapped)
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267 hgap += av.charHeight;
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269 int cHeight = av.getAlignment().getHeight() * av.charHeight
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270 + hgap + seqCanvas.getAnnotationHeight();
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274 seq = ( (y % cHeight) / av.getCharHeight());
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278 seq = (y / av.getCharHeight()) + av.getStartSeq();
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288 * @param evt DOCUMENT ME!
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290 public void doMouseReleased(MouseEvent evt)
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292 if (seqEditOccurred > -1)
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294 editOccurred(seqEditOccurred);
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299 seqEditOccurred = -1;
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300 editingSeqs = false;
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301 groupEditing = false;
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309 * @param evt DOCUMENT ME!
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311 public void doMousePressed(MouseEvent evt)
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313 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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314 av.alignment, HistoryItem.EDIT));
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316 int seq = findSeq(evt);
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317 int res = findRes(evt);
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322 if ((seq < av.getAlignment().getHeight()) &&
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323 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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334 startEdit = lastres;
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343 * @param evt DOCUMENT ME!
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345 public void doMouseMoved(MouseEvent evt)
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347 int res = findRes(evt);
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348 int seq = findSeq(evt);
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350 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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353 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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355 if (res > sequence.getLength())
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360 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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361 sequence.getName());
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364 if (av.alignment.isNucleotide())
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366 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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369 text.append(" Nucleotide: ");
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373 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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375 text.append(" Residue: ");
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383 text.append( obj + " (" +
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384 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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388 ap.alignFrame.statusBar.setText(text.toString());
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390 // use aa to see if the mouse pointer is on a
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391 if (av.showSequenceFeatures)
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393 Vector features = sequence.getDatasetSequence().getSequenceFeatures();
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396 StringBuffer sbuffer = new StringBuffer("<html>");
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398 for (int i = 0; i < features.size(); i++)
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400 SequenceFeature sf = (SequenceFeature) features.elementAt(i);
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402 if ( (sf.getBegin() <= sequence.findPosition(res)) &&
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403 (sf.getEnd() >= sequence.findPosition(res)))
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405 if (sf.getType().equals("disulfide bond"))
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407 if (sf.getBegin() == sequence.findPosition(res)
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408 || sf.getEnd() == sequence.findPosition(res))
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410 if (sbuffer.length() > 6)
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411 sbuffer.append("<br>");
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412 sbuffer.append("disulfide bond " + sf.getBegin() + ":" +
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418 if (sbuffer.length() > 6)
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419 sbuffer.append("<br>");
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420 sbuffer.append(sf.getType());
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421 if (sf.getDescription() != null)
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422 sbuffer.append(" " + sf.getDescription());
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424 if (sf.getStatus() != null)
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426 sbuffer.append(" (" + sf.getStatus() + ")");
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433 sbuffer.append("</html>");
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434 if(sbuffer.length()==13) // <html></html>
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435 setToolTipText("");
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437 setToolTipText(sbuffer.toString());
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440 setToolTipText("");
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447 * @param evt DOCUMENT ME!
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449 public void doMouseDragged(MouseEvent evt)
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451 // If we're dragging we're editing
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452 int res = findRes(evt);
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459 if ((lastres == -1) || (lastres == res))
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464 boolean dragRight = true;
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466 if ((res < av.getAlignment().getWidth()) && (res < lastres))
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471 if (res != lastres)
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476 SequenceGroup sg = av.getSelectionGroup();
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488 sg.setEndRes(sg.getEndRes() + (res - lastres));
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494 /// Are we able to delete?
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495 // ie are all columns blank?
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496 boolean deleteAllowed = false;
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498 for (int s = 0; s < sg.getSize(); s++)
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500 SequenceI seq = sg.getSequenceAt(s);
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502 for (int j = res; j < lastres; j++)
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504 if (seq.getSequence().length() <= j)
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509 if (!jalview.util.Comparison.isGap(
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510 seq.getSequence().charAt(j)))
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512 // Not a gap, block edit not valid
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514 deleteAllowed = false;
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519 deleteAllowed = true;
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523 if (!deleteAllowed)
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530 sg.setEndRes(sg.getEndRes() - (lastres - res));
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533 for (int i = 0; i < sg.getSize(); i++)
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535 SequenceI s = sg.getSequenceAt(i);
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536 int k = av.alignment.findIndex(s);
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541 for (int j = lastres; j < res; j++)
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550 for (int j = res; j < lastres; j++)
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552 if (s.getLength() > j)
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554 deleteChar(res, k);
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560 else /////Editing a single sequence///////////
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562 if ((res < av.getAlignment().getWidth()) && (res > lastres))
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564 // dragging to the right
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565 for (int j = lastres; j < res; j++)
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567 insertChar(j, startseq);
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570 else if ((res < av.getAlignment().getWidth()) &&
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573 // dragging to the left
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574 for (int j = lastres; j > res; j--)
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576 if (jalview.util.Comparison.isGap(
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577 av.alignment.getSequenceAt(startseq)
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578 .getSequence().charAt(res)))
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580 deleteChar(res, startseq);
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593 seqCanvas.repaint();
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599 * @param seqstart DOCUMENT ME!
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600 * @param seqend DOCUMENT ME!
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601 * @param start DOCUMENT ME!
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603 public void drawChars(int seqstart, int seqend, int start)
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605 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
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606 seqend, av.getStartRes(), av.getStartSeq(), 0);
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607 seqCanvas.repaint();
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613 * @param j DOCUMENT ME!
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614 * @param seq DOCUMENT ME!
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616 public void insertChar(int j, int seq)
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618 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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619 seqEditOccurred = seq;
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625 * @param j DOCUMENT ME!
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626 * @param seq DOCUMENT ME!
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628 public void deleteChar(int j, int seq)
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630 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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631 seqEditOccurred = seq;
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633 av.alignment.getWidth();
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634 seqCanvas.repaint();
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640 * @param i DOCUMENT ME!
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642 void editOccurred(int i)
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644 if (endEdit == startEdit)
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646 ap.alignFrame.historyList.pop();
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647 ap.alignFrame.updateEditMenuBar();
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650 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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657 * @param evt DOCUMENT ME!
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659 public void doMousePressedDefineMode(MouseEvent evt)
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661 int res = findRes(evt);
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662 int seq = findSeq(evt);
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665 startWrapBlock=wrappedBlock;
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667 if(av.wrapAlignment && seq>av.alignment.getHeight())
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669 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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670 "Cannot edit annotations in wrapped view.",
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671 "Wrapped view - no edit",
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672 JOptionPane.WARNING_MESSAGE);
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680 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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682 if ((sequence == null) || (res > sequence.getLength()))
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687 stretchGroup = av.getSelectionGroup();
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689 if (stretchGroup == null)
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691 stretchGroup = av.alignment.findGroup(sequence);
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693 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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694 (res < stretchGroup.getEndRes()))
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696 av.setSelectionGroup(stretchGroup);
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700 stretchGroup = null;
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703 else if (!stretchGroup.sequences.contains(sequence) ||
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704 (stretchGroup.getStartRes() > res) ||
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705 (stretchGroup.getEndRes() < res))
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707 stretchGroup = null;
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709 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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711 if (allGroups != null)
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713 for (int i = 0; i < allGroups.length; i++)
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715 if ((allGroups[i].getStartRes() <= res) &&
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716 (allGroups[i].getEndRes() >= res))
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718 stretchGroup = allGroups[i];
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719 av.setSelectionGroup(stretchGroup);
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727 if (stretchGroup == null)
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729 // define a new group here
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730 SequenceGroup sg = new SequenceGroup();
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731 sg.setStartRes(res);
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733 sg.addSequence(sequence, false);
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734 av.setSelectionGroup(sg);
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737 if (av.getConservationSelected())
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739 SliderPanel.setConservationSlider(ap,
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740 av.getGlobalColourScheme(), "Background");
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743 if (av.getAbovePIDThreshold())
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745 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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749 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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751 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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752 pop.show(this, evt.getX(), evt.getY());
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754 // edit the properties of existing group
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757 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
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759 // Edit end res position of selected group
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760 changeEndRes = true;
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762 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
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764 // Edit end res position of selected group
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765 changeStartRes = true;
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768 stretchGroup.getWidth();
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770 seqCanvas.repaint();
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776 * @param evt DOCUMENT ME!
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778 public void doMouseReleasedDefineMode(MouseEvent evt)
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782 stretchGroup.recalcConservation();
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783 mouseDragging = false;
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786 if (stretchGroup == null)
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791 if(stretchGroup.cs!=null)
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793 if (stretchGroup.cs instanceof ClustalxColourScheme)
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795 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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797 stretchGroup.getWidth());
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800 if (stretchGroup.cs.conservationApplied())
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802 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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803 stretchGroup.getName());
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807 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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808 stretchGroup.getName());
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811 changeEndRes = false;
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812 changeStartRes = false;
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813 stretchGroup = null;
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814 PaintRefresher.Refresh(av.alignment);
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820 * @param evt DOCUMENT ME!
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822 public void doMouseDraggedDefineMode(MouseEvent evt)
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824 int res = findRes(evt);
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825 int y = findSeq(evt);
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827 if(wrappedBlock!=startWrapBlock)
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830 if (stretchGroup == null)
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835 if (res > av.alignment.getWidth())
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837 res = av.alignment.getWidth() - 1;
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840 if (stretchGroup.getEndRes() == res)
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842 // Edit end res position of selected group
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843 changeEndRes = true;
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845 else if (stretchGroup.getStartRes() == res)
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847 // Edit start res position of selected group
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848 changeStartRes = true;
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851 if (res < av.getStartRes())
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853 res = av.getStartRes();
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855 else if (res > av.getEndRes() && !av.getWrapAlignment())
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857 res = av.getEndRes();
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862 if (res > (stretchGroup.getStartRes() - 1))
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864 stretchGroup.setEndRes(res);
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867 else if (changeStartRes)
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869 if (res < (stretchGroup.getEndRes() + 1))
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871 stretchGroup.setStartRes(res);
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875 int dragDirection = 0;
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881 else if (y < oldSeq)
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883 dragDirection = -1;
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886 while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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888 // This routine ensures we don't skip any sequences, as the
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889 // selection is quite slow.
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890 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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892 oldSeq += dragDirection;
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894 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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896 if (stretchGroup.sequences.contains(nextSeq))
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898 stretchGroup.deleteSequence(seq, false);
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904 stretchGroup.addSequence(seq, false);
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907 stretchGroup.addSequence(nextSeq, false);
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912 mouseDragging = true;
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914 if (scrollThread != null)
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916 scrollThread.setEvent(evt);
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919 seqCanvas.repaint();
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925 * @param e DOCUMENT ME!
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927 public void doMouseEnteredDefineMode(MouseEvent e)
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929 if (scrollThread != null)
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931 scrollThread.running = false;
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938 * @param e DOCUMENT ME!
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940 public void doMouseExitedDefineMode(MouseEvent e)
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942 if (av.getWrapAlignment())
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949 scrollThread = new ScrollThread();
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953 // this class allows scrolling off the bottom of the visible alignment
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954 class ScrollThread extends Thread
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957 boolean running = false;
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959 public ScrollThread()
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964 public void setEvent(MouseEvent e)
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969 public void stopScrolling()
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982 if (mouseDragging && (evt.getY() < 0) &&
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983 (av.getStartSeq() > 0))
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985 running = ap.scrollUp(true);
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988 if (mouseDragging && (evt.getY() >= getHeight()) &&
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989 (av.alignment.getHeight() > av.getEndSeq()))
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991 running = ap.scrollUp(false);
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994 if (mouseDragging && (evt.getX() < 0))
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996 running = ap.scrollRight(true);
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998 else if (mouseDragging && (evt.getX() >= getWidth()))
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1000 running = ap.scrollRight(false);
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1008 catch (Exception ex)
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