2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.schemes.*;
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28 import java.awt.event.*;
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32 import javax.swing.*;
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39 * @version $Revision$
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41 public class SeqPanel extends JPanel
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43 /** DOCUMENT ME!! */
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44 public SeqCanvas seqCanvas;
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46 /** DOCUMENT ME!! */
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47 public AlignmentPanel ap;
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48 protected int lastres;
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49 protected int startseq;
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52 protected AlignViewport av;
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54 // if character is inserted or deleted, we will need to recalculate the conservation
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55 int seqEditOccurred = -1;
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56 ScrollThread scrollThread = null;
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57 boolean mouseDragging = false;
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58 boolean editingSeqs = false;
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59 boolean groupEditing = false;
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61 //////////////////////////////////////////
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62 /////Everything below this is for defining the boundary of the rubberband
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63 //////////////////////////////////////////
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65 boolean changeEndSeq = false;
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66 boolean changeStartSeq = false;
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67 boolean changeEndRes = false;
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68 boolean changeStartRes = false;
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69 SequenceGroup stretchGroup = null;
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70 boolean remove = false;
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72 boolean mouseWheelPressed = false;
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75 * Creates a new SeqPanel object.
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77 * @param avp DOCUMENT ME!
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78 * @param p DOCUMENT ME!
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80 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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82 ToolTipManager.sharedInstance().registerComponent(this);
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83 ToolTipManager.sharedInstance().setInitialDelay(0);
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84 ToolTipManager.sharedInstance().setDismissDelay(10000);
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86 setBackground(Color.white);
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88 seqCanvas = new SeqCanvas(avp);
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89 setLayout(new BorderLayout());
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90 add(seqCanvas, BorderLayout.CENTER);
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94 addMouseMotionListener(new MouseMotionAdapter()
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96 public void mouseMoved(MouseEvent evt)
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98 if (av.getWrapAlignment())
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106 public void mouseDragged(MouseEvent evt)
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108 if (av.getWrapAlignment())
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115 doMouseDragged(evt);
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119 doMouseDraggedDefineMode(evt);
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124 addMouseWheelListener(new MouseWheelListener()
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126 public void mouseWheelMoved(MouseWheelEvent e)
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129 if (mouseWheelPressed)
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131 Font font = av.getFont();
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132 int fontSize = font.getSize();
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133 if (e.getWheelRotation() > 0 && fontSize < 30)
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135 else if (fontSize > 1)
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138 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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145 if (e.getWheelRotation() > 0)
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146 ap.scrollUp(false);
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155 addMouseListener(new MouseAdapter()
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157 public void mouseReleased(MouseEvent evt)
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159 mouseWheelPressed = false;
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160 if (av.getWrapAlignment())
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167 doMouseReleased(evt);
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171 doMouseReleasedDefineMode(evt);
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175 public void mousePressed(MouseEvent evt)
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177 if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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179 mouseWheelPressed = true;
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182 if (av.getWrapAlignment())
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187 if (evt.isShiftDown() || evt.isAltDown() ||
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188 evt.isControlDown())
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190 if (evt.isAltDown() || evt.isControlDown())
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192 groupEditing = true;
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195 editingSeqs = true;
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196 doMousePressed(evt);
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200 doMousePressedDefineMode(evt);
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204 public void mouseExited(MouseEvent evt)
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206 if (av.getWrapAlignment() || editingSeqs)
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211 doMouseExitedDefineMode(evt);
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214 public void mouseEntered(MouseEvent evt)
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216 if (av.getWrapAlignment() || editingSeqs)
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221 doMouseEnteredDefineMode(evt);
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229 * @param evt DOCUMENT ME!
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231 public void doMouseReleased(MouseEvent evt)
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233 if (seqEditOccurred > -1)
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235 editOccurred(seqEditOccurred);
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240 seqEditOccurred = -1;
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241 editingSeqs = false;
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242 groupEditing = false;
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250 * @param evt DOCUMENT ME!
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252 public void doMousePressed(MouseEvent evt)
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254 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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255 av.alignment, HistoryItem.EDIT));
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260 int x = evt.getX();
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261 int y = evt.getY();
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263 res = (x / av.getCharWidth()) + av.getStartRes();
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264 seq = (y / av.getCharHeight()) + av.getStartSeq();
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266 if ((seq < av.getAlignment().getHeight()) &&
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267 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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278 startEdit = lastres;
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287 * @param evt DOCUMENT ME!
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289 public void doMouseMoved(MouseEvent evt)
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293 int x = evt.getX();
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294 int y = evt.getY();
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296 if (av.wrapAlignment)
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298 y -= (2 * av.charHeight);
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300 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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302 res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) +
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303 (x / av.getCharWidth()) + av.getStartRes();
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306 seq = (y / av.getCharHeight()) + av.getStartSeq();
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310 res = (x / av.getCharWidth()) + av.getStartRes();
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311 seq = (y / av.getCharHeight()) + av.getStartSeq();
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314 if (seq >= av.getAlignment().getHeight())
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319 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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321 if (res > sequence.getLength())
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326 Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
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332 aa = obj.toString();
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335 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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336 sequence.getName());
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340 text.append(" Residue: " + aa + " (" +
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341 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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344 ap.alignFrame.statusBar.setText(text.toString());
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346 // use aa to see if the mouse pointer is on a
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347 if (av.showSequenceFeatures)
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349 Vector features = sequence.getSequenceFeatures();
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350 Enumeration e = features.elements();
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351 StringBuffer sbuffer = new StringBuffer();
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353 while (e.hasMoreElements())
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355 SequenceFeature sf = (SequenceFeature) e.nextElement();
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357 if ((sf.getStart() <= sequence.findPosition(res)) &&
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358 (sf.getEnd() >= sequence.findPosition(res)))
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360 if (sbuffer.length() > 0)
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362 sbuffer.append("; ");
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365 sbuffer.append(sf.getType() + " " + sf.getDescription());
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367 if (sf.getStatus().length() > 0)
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369 sbuffer.append(" (" + sf.getStatus() + ")");
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374 this.setToolTipText(sbuffer.toString());
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381 * @param evt DOCUMENT ME!
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383 public void doMouseDragged(MouseEvent evt)
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385 // If we're dragging we're editing
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386 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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393 if ((lastres == -1) || (lastres == res))
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398 boolean dragRight = true;
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400 if ((res < av.getAlignment().getWidth()) && (res < lastres))
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405 if (res != lastres)
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410 SequenceGroup sg = av.getSelectionGroup();
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422 sg.setEndRes(sg.getEndRes() + (res - lastres));
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428 /// Are we able to delete?
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429 // ie are all columns blank?
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430 boolean deleteAllowed = false;
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432 for (int s = 0; s < sg.getSize(); s++)
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434 SequenceI seq = sg.getSequenceAt(s);
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436 for (int j = res; j < lastres; j++)
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438 if (seq.getSequence().length() <= j)
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443 if (!jalview.util.Comparison.isGap(
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444 seq.getSequence().charAt(j)))
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446 // Not a gap, block edit not valid
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448 deleteAllowed = false;
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453 deleteAllowed = true;
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457 if (!deleteAllowed)
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464 sg.setEndRes(sg.getEndRes() - (lastres - res));
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467 for (int i = 0; i < sg.getSize(); i++)
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469 SequenceI s = sg.getSequenceAt(i);
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470 int k = av.alignment.findIndex(s);
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475 for (int j = lastres; j < res; j++)
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484 for (int j = res; j < lastres; j++)
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486 if (s.getLength() > j)
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488 deleteChar(res, k);
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494 else /////Editing a single sequence///////////
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496 if ((res < av.getAlignment().getWidth()) && (res > lastres))
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498 // dragging to the right
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499 for (int j = lastres; j < res; j++)
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501 insertChar(j, startseq);
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504 else if ((res < av.getAlignment().getWidth()) &&
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507 // dragging to the left
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508 for (int j = lastres; j > res; j--)
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510 if (jalview.util.Comparison.isGap(
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511 av.alignment.getSequenceAt(startseq)
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512 .getSequence().charAt(res)))
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514 deleteChar(res, startseq);
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527 seqCanvas.repaint();
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533 * @param seqstart DOCUMENT ME!
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534 * @param seqend DOCUMENT ME!
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535 * @param start DOCUMENT ME!
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537 public void drawChars(int seqstart, int seqend, int start)
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539 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
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540 seqend, av.getStartRes(), av.getStartSeq(), 0);
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541 seqCanvas.repaint();
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547 * @param j DOCUMENT ME!
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548 * @param seq DOCUMENT ME!
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550 public void insertChar(int j, int seq)
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552 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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553 seqEditOccurred = seq;
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559 * @param j DOCUMENT ME!
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560 * @param seq DOCUMENT ME!
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562 public void deleteChar(int j, int seq)
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564 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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565 seqEditOccurred = seq;
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567 av.alignment.getWidth();
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568 seqCanvas.repaint();
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574 * @param i DOCUMENT ME!
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576 void editOccurred(int i)
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578 if (endEdit == startEdit)
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580 ap.alignFrame.historyList.pop();
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581 ap.alignFrame.updateEditMenuBar();
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584 av.updateConservation();
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585 av.updateConsensus();
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587 //Does the edit affect any groups?
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588 //////////////////////////////
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589 Vector groupsToUpdate = new Vector();
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590 SequenceGroup sg = av.getSelectionGroup();
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592 int s, g, gSize = av.alignment.getGroups().size();
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595 groupsToUpdate.addElement(av.getSelectionGroup());
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596 int sSize = sg.getSize();
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597 for (s = 0; s < sSize; s++)
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599 SequenceI seq = sg.getSequenceAt(s);
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601 for (g = 0; g < gSize; g++)
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603 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().
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606 if (sg2.sequences.contains(seq))
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608 if (!groupsToUpdate.contains(sg2))
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609 groupsToUpdate.addElement(sg2);
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617 SequenceI seq = av.alignment.getSequenceAt(startseq);
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618 for (g = 0; g < gSize; g++)
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620 SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(
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622 if (sg2.sequences.contains(seq))
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624 if (!groupsToUpdate.contains(sg2))
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625 groupsToUpdate.addElement(sg2);
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631 gSize = groupsToUpdate.size();
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632 for (g = 0; g < gSize; g++)
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634 ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();
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636 ////End of updating groups
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637 //////////////////////////////////////////
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640 ColourSchemeI cs = av.getGlobalColourScheme();
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643 if (cs.conservationApplied())
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645 Conservation c = new Conservation("All",
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646 ResidueProperties.propHash, 3,
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647 av.alignment.getSequences(),
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648 0, av.alignment.getWidth() - 1);
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650 c.verdict(false, av.ConsPercGaps);
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652 if (cs instanceof ClustalxColourScheme)
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654 ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
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655 cxs.resetClustalX(av.alignment.getSequences(),
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656 av.alignment.getWidth());
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657 cs.setConservation(c);
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658 av.setGlobalColourScheme(cs);
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662 cs.setConservation(c);
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663 av.setGlobalColourScheme(cs);
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668 if (cs instanceof ClustalxColourScheme)
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670 ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
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671 av.alignment.getWidth());
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672 av.setGlobalColourScheme(cs);
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680 * @param evt DOCUMENT ME!
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682 public void doMousePressedDefineMode(MouseEvent evt)
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684 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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685 int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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688 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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690 if ((sequence == null) || (res > sequence.getLength()))
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695 stretchGroup = av.getSelectionGroup();
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697 if (stretchGroup == null)
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699 stretchGroup = av.alignment.findGroup(sequence);
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701 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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702 (res < stretchGroup.getEndRes()))
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704 av.setSelectionGroup(stretchGroup);
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708 stretchGroup = null;
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711 else if (!stretchGroup.sequences.contains(sequence) ||
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712 (stretchGroup.getStartRes() > res) ||
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713 (stretchGroup.getEndRes() < res))
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715 stretchGroup = null;
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717 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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719 if (allGroups != null)
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721 for (int i = 0; i < allGroups.length; i++)
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723 if ((allGroups[i].getStartRes() <= res) &&
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724 (allGroups[i].getEndRes() >= res))
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726 stretchGroup = allGroups[i];
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727 av.setSelectionGroup(stretchGroup);
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735 if (stretchGroup == null)
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737 // define a new group here
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738 SequenceGroup sg = new SequenceGroup();
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739 sg.setStartRes(res);
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741 sg.addSequence(sequence, false);
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742 av.setSelectionGroup(sg);
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745 if (av.getConservationSelected())
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747 SliderPanel.setConservationSlider(ap,
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748 av.getGlobalColourScheme(), "Background");
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751 if (av.getAbovePIDThreshold())
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753 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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757 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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759 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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760 pop.show(this, evt.getX(), evt.getY());
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762 // edit the properties of existing group
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765 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
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767 // Edit end res position of selected group
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768 changeEndRes = true;
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770 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
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772 // Edit end res position of selected group
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773 changeStartRes = true;
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776 stretchGroup.getWidth();
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778 seqCanvas.repaint();
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784 * @param evt DOCUMENT ME!
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786 public void doMouseReleasedDefineMode(MouseEvent evt)
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790 stretchGroup.recalcConservation();
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791 mouseDragging = false;
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794 if (stretchGroup == null)
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799 if(stretchGroup.cs!=null)
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801 if (stretchGroup.cs instanceof ClustalxColourScheme)
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803 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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805 stretchGroup.getWidth());
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808 if (stretchGroup.cs.conservationApplied())
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810 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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811 stretchGroup.getName());
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815 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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816 stretchGroup.getName());
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819 changeEndRes = false;
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820 changeStartRes = false;
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821 stretchGroup = null;
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822 PaintRefresher.Refresh(av.alignment);
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828 * @param evt DOCUMENT ME!
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830 public void doMouseDraggedDefineMode(MouseEvent evt)
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832 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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833 int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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835 if (stretchGroup == null)
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840 if (res > av.alignment.getWidth())
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842 res = av.alignment.getWidth() - 1;
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845 if (stretchGroup.getEndRes() == res)
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847 // Edit end res position of selected group
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848 changeEndRes = true;
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850 else if (stretchGroup.getStartRes() == res)
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852 // Edit start res position of selected group
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853 changeStartRes = true;
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856 if (res < av.getStartRes())
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858 res = av.getStartRes();
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860 else if (res > av.getEndRes())
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862 res = av.getEndRes();
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867 if (res > (stretchGroup.getStartRes() - 1))
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869 stretchGroup.setEndRes(res);
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872 else if (changeStartRes)
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874 if (res < (stretchGroup.getEndRes() + 1))
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876 stretchGroup.setStartRes(res);
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880 int dragDirection = 0;
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886 else if (y < oldSeq)
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888 dragDirection = -1;
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891 while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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893 // This routine ensures we don't skip any sequences, as the
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894 // selection is quite slow.
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895 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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897 oldSeq += dragDirection;
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899 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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901 if (stretchGroup.sequences.contains(nextSeq))
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903 stretchGroup.deleteSequence(seq, false);
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909 stretchGroup.addSequence(seq, false);
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912 stretchGroup.addSequence(nextSeq, false);
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917 mouseDragging = true;
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919 if (scrollThread != null)
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921 scrollThread.setEvent(evt);
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924 seqCanvas.repaint();
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930 * @param e DOCUMENT ME!
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932 public void doMouseEnteredDefineMode(MouseEvent e)
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934 if (scrollThread != null)
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936 scrollThread.running = false;
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943 * @param e DOCUMENT ME!
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945 public void doMouseExitedDefineMode(MouseEvent e)
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947 if (av.getWrapAlignment())
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954 scrollThread = new ScrollThread();
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958 // this class allows scrolling off the bottom of the visible alignment
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959 class ScrollThread extends Thread
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962 boolean running = false;
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964 public ScrollThread()
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969 public void setEvent(MouseEvent e)
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974 public void stopScrolling()
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987 if (mouseDragging && (evt.getY() < 0) &&
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988 (av.getStartSeq() > 0))
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990 running = ap.scrollUp(true);
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993 if (mouseDragging && (evt.getY() >= getHeight()) &&
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994 (av.alignment.getHeight() > av.getEndSeq()))
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996 running = ap.scrollUp(false);
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999 if (mouseDragging && (evt.getX() < 0))
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1001 running = ap.scrollRight(true);
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1003 else if (mouseDragging && (evt.getX() >= getWidth()))
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1005 running = ap.scrollRight(false);
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1013 catch (Exception ex)
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