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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24 import java.awt.event.*;
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25 import javax.swing.*;
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27 import jalview.analysis.*;
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28 import jalview.datamodel.*;
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29 import jalview.schemes.*;
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31 public class SeqPanel
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34 public SeqCanvas seqCanvas;
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35 public AlignmentPanel ap;
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36 protected int lastres;
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37 protected int startseq;
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40 protected AlignViewport av;
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42 // if character is inserted or deleted, we will need to recalculate the conservation
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43 int seqEditOccurred = -1;
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44 ScrollThread scrollThread = null;
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45 boolean mouseDragging = false;
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46 boolean editingSeqs = false;
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47 boolean groupEditing = false;
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49 //////////////////////////////////////////
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50 /////Everything below this is for defining the boundary of the rubberband
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51 //////////////////////////////////////////
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53 boolean changeEndSeq = false;
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54 boolean changeStartSeq = false;
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55 boolean changeEndRes = false;
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56 boolean changeStartRes = false;
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57 SequenceGroup stretchGroup = null;
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58 boolean remove = false;
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60 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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63 setBackground(Color.white);
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65 seqCanvas = new SeqCanvas(avp);
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66 setLayout(new BorderLayout());
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67 add(seqCanvas, BorderLayout.CENTER);
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71 addMouseMotionListener(new MouseMotionAdapter()
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73 public void mouseMoved(MouseEvent evt)
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75 if (av.getWrapAlignment())
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83 public void mouseDragged(MouseEvent evt)
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85 if (av.getWrapAlignment())
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92 doMouseDragged(evt);
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96 doMouseDraggedDefineMode(evt);
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101 addMouseListener(new MouseAdapter()
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103 public void mouseReleased(MouseEvent evt)
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105 if (av.getWrapAlignment())
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112 doMouseReleased(evt);
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116 doMouseReleasedDefineMode(evt);
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120 public void mousePressed(MouseEvent evt)
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122 if (av.getWrapAlignment())
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127 if (evt.isShiftDown() || evt.isAltDown() ||
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128 evt.isControlDown())
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130 if (evt.isAltDown() || evt.isControlDown())
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132 groupEditing = true;
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135 editingSeqs = true;
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136 doMousePressed(evt);
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140 doMousePressedDefineMode(evt);
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144 public void mouseExited(MouseEvent evt)
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146 if (av.getWrapAlignment() || editingSeqs)
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151 doMouseExitedDefineMode(evt);
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154 public void mouseEntered(MouseEvent evt)
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156 if (av.getWrapAlignment() || editingSeqs)
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161 doMouseEnteredDefineMode(evt);
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167 public void doMouseReleased(MouseEvent evt)
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169 if (seqEditOccurred > -1)
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171 editOccurred(seqEditOccurred);
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176 seqEditOccurred = -1;
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177 editingSeqs = false;
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178 groupEditing = false;
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180 seqCanvas.repaint();
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183 public void doMousePressed(MouseEvent evt)
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185 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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186 av.alignment, HistoryItem.EDIT));
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191 int x = evt.getX();
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192 int y = evt.getY();
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194 res = (x / av.getCharWidth()) + av.getStartRes();
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195 seq = (y / av.getCharHeight()) + av.getStartSeq();
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197 if ( (seq < av.getAlignment().getHeight()) &&
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198 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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209 startEdit = lastres;
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215 public void doMouseMoved(MouseEvent evt)
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219 int x = evt.getX();
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220 int y = evt.getY();
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222 if (av.wrapAlignment)
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224 y -= (2 * av.charHeight);
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226 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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228 res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +
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229 (x / av.getCharWidth()) + av.getStartRes();
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232 seq = (y / av.getCharHeight()) + av.getStartSeq();
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236 res = (x / av.getCharWidth()) + av.getStartRes();
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237 seq = (y / av.getCharHeight()) + av.getStartSeq();
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240 if (seq >= av.getAlignment().getHeight())
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245 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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247 if (res > sequence.getLength())
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252 Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
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258 aa = obj.toString();
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261 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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262 sequence.getName());
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266 text.append(" Residue: " + aa + " (" +
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267 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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270 ap.alignFrame.statusBar.setText(text.toString());
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272 // use aa to see if the mouse pointer is on a
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273 if (av.showSequenceFeatures)
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275 Vector features = sequence.getSequenceFeatures();
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276 Enumeration e = features.elements();
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277 StringBuffer sbuffer = new StringBuffer();
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279 while (e.hasMoreElements())
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281 SequenceFeature sf = (SequenceFeature) e.nextElement();
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283 if ( (sf.getStart() <= sequence.findPosition(res)) &&
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284 (sf.getEnd() >= sequence.findPosition(res)))
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286 if (sbuffer.length() > 0)
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288 sbuffer.append("; ");
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291 sbuffer.append(sf.getType() + " " + sf.getDescription());
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293 if (sf.getStatus().length() > 0)
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295 sbuffer.append(" (" + sf.getStatus() + ")");
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300 ToolTipManager.sharedInstance().registerComponent(this);
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301 this.setToolTipText(sbuffer.toString());
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305 public void doMouseDragged(MouseEvent evt)
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307 // If we're dragging we're editing
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308 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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315 if ( (lastres == -1) || (lastres == res))
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320 boolean dragRight = true;
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322 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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327 if (res != lastres)
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332 SequenceGroup sg = av.getSelectionGroup();
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344 sg.setEndRes(sg.getEndRes() + (res - lastres));
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349 /// Are we able to delete?
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350 // ie are all columns blank?
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351 boolean deleteAllowed = false;
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353 for (int s = 0; s < sg.getSize(); s++)
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355 SequenceI seq = sg.getSequenceAt(s);
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357 for (int j = res; j < lastres; j++)
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359 if (seq.getSequence().length() <= j)
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364 if (!jalview.util.Comparison.isGap(
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365 seq.getSequence().charAt(j)))
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367 // Not a gap, block edit not valid
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369 deleteAllowed = false;
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374 deleteAllowed = true;
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378 if (!deleteAllowed)
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385 sg.setEndRes(sg.getEndRes() - (lastres - res));
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388 for (int i = 0; i < sg.getSize(); i++)
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390 SequenceI s = sg.getSequenceAt(i);
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391 int k = av.alignment.findIndex(s);
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396 for (int j = lastres; j < res; j++)
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404 for (int j = res; j < lastres; j++)
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406 if (s.getLength() > j)
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408 deleteChar(res, k);
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414 else /////Editing a single sequence///////////
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416 if ( (res < av.getAlignment().getWidth()) && (res > lastres))
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418 // dragging to the right
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419 for (int j = lastres; j < res; j++)
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421 insertChar(j, startseq);
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424 else if ( (res < av.getAlignment().getWidth()) &&
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427 // dragging to the left
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428 for (int j = lastres; j > res; j--)
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430 if (jalview.util.Comparison.isGap(
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431 av.alignment.getSequenceAt(startseq)
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432 .getSequence().charAt(res)))
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434 deleteChar(res, startseq);
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447 seqCanvas.repaint();
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450 public void drawChars(int seqstart, int seqend, int start)
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452 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
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453 seqend, av.getStartRes(), av.getStartSeq(), 0);
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454 seqCanvas.repaint();
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457 public void insertChar(int j, int seq)
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459 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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460 seqEditOccurred = seq;
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463 public void deleteChar(int j, int seq)
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465 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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466 seqEditOccurred = seq;
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468 av.alignment.getWidth();
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469 seqCanvas.repaint();
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472 void editOccurred(int i)
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474 if (endEdit == startEdit)
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476 ap.alignFrame.historyList.pop();
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477 ap.alignFrame.updateEditMenuBar();
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480 av.updateConservation();
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481 av.updateConsensus();
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484 ColourSchemeI cs = av.getGlobalColourScheme();
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486 if (cs instanceof ConservationColourScheme)
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488 ConservationColourScheme ccs = (ConservationColourScheme) cs;
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490 if (ccs.cs instanceof ClustalxColourScheme)
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492 Conservation c = new Conservation("All",
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493 ResidueProperties.propHash, 3,
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494 av.alignment.getSequences(), 0,
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495 av.alignment.getWidth() - 1);
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497 c.verdict(false, av.ConsPercGaps);
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499 ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
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500 cxs.resetClustalX(av.alignment.getSequences(),
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501 av.alignment.getWidth());
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502 ccs = new ConservationColourScheme(c, cxs);
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503 av.setGlobalColourScheme(ccs);
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507 if (cs instanceof ClustalxColourScheme)
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509 ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
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510 av.alignment.getWidth());
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511 av.setGlobalColourScheme(cs);
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515 public void doMousePressedDefineMode(MouseEvent evt)
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517 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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518 int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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521 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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523 if ( (sequence == null) || (res > sequence.getLength()))
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528 stretchGroup = av.getSelectionGroup();
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530 if (stretchGroup == null)
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532 stretchGroup = av.alignment.findGroup(sequence);
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534 if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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535 (res < stretchGroup.getEndRes()))
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537 av.setSelectionGroup(stretchGroup);
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541 stretchGroup = null;
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544 else if (!stretchGroup.sequences.contains(sequence) ||
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545 (stretchGroup.getStartRes() > res) ||
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546 (stretchGroup.getEndRes() < res))
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548 stretchGroup = null;
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550 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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552 if (allGroups != null)
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554 for (int i = 0; i < allGroups.length; i++)
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556 if ( (allGroups[i].getStartRes() <= res) &&
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557 (allGroups[i].getEndRes() >= res))
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559 stretchGroup = allGroups[i];
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560 av.setSelectionGroup(stretchGroup);
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568 if (stretchGroup == null)
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570 // define a new group here
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571 SequenceGroup sg = new SequenceGroup();
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572 sg.setStartRes(res);
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574 sg.addSequence(sequence, false);
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575 av.setSelectionGroup(sg);
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578 if (av.getConservationSelected())
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580 SliderPanel.setConservationSlider(ap,
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581 av.getGlobalColourScheme(),
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585 if (av.getAbovePIDThreshold())
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587 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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591 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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593 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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594 pop.show(this, evt.getX(), evt.getY());
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596 // edit the properties of existing group
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599 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
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601 // Edit end res position of selected group
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602 changeEndRes = true;
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604 else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))
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606 // Edit end res position of selected group
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607 changeStartRes = true;
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610 stretchGroup.getWidth();
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612 seqCanvas.repaint();
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615 public void doMouseReleasedDefineMode(MouseEvent evt)
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619 stretchGroup.recalcConservation();
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620 mouseDragging = false;
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623 if (stretchGroup == null)
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628 if (stretchGroup.cs instanceof ClustalxColourScheme)
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630 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,
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631 stretchGroup.getWidth());
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634 if (stretchGroup.cs instanceof ConservationColourScheme)
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636 ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
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637 stretchGroup.cs = ccs;
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638 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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639 stretchGroup.getName());
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644 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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645 stretchGroup.getName());
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648 changeEndRes = false;
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649 changeStartRes = false;
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650 stretchGroup = null;
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651 seqCanvas.repaint();
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652 ap.idPanel.repaint();
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655 public void doMouseDraggedDefineMode(MouseEvent evt)
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657 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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658 int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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660 if (stretchGroup == null)
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665 if (res > av.alignment.getWidth())
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667 res = av.alignment.getWidth() - 1;
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670 if (stretchGroup.getEndRes() == res)
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672 // Edit end res position of selected group
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673 changeEndRes = true;
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675 else if (stretchGroup.getStartRes() == res)
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677 // Edit start res position of selected group
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678 changeStartRes = true;
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681 if (res < av.getStartRes())
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683 res = av.getStartRes();
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685 else if (res > av.getEndRes())
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687 res = av.getEndRes();
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692 if (res > (stretchGroup.getStartRes() - 1))
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694 stretchGroup.setEndRes(res);
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697 else if (changeStartRes)
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699 if (res < (stretchGroup.getEndRes() + 1))
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701 stretchGroup.setStartRes(res);
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705 int dragDirection = 0;
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711 else if (y < oldSeq)
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713 dragDirection = -1;
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716 while ( (y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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718 // This routine ensures we don't skip any sequences, as the
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719 // selection is quite slow.
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720 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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722 oldSeq += dragDirection;
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724 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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726 if (stretchGroup.sequences.contains(nextSeq))
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728 stretchGroup.deleteSequence(seq, false);
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729 stretchGroup.deleteSequence(nextSeq, false);
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735 stretchGroup.addSequence(seq, false);
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738 stretchGroup.addSequence(nextSeq, false);
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743 mouseDragging = true;
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745 if (scrollThread != null)
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747 scrollThread.setEvent(evt);
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750 seqCanvas.repaint();
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753 public void doMouseEnteredDefineMode(MouseEvent e)
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755 if (scrollThread != null)
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757 scrollThread.running = false;
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761 public void doMouseExitedDefineMode(MouseEvent e)
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763 if (av.getWrapAlignment())
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770 scrollThread = new ScrollThread();
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774 // this class allows scrolling off the bottom of the visible alignment
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779 boolean running = false;
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781 public ScrollThread()
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786 public void setEvent(MouseEvent e)
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791 public void stopScrolling()
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804 if (mouseDragging && (evt.getY() < 0) &&
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805 (av.getStartSeq() > 0))
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807 running = ap.scrollUp(true);
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810 if (mouseDragging && (evt.getY() >= getHeight()) &&
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811 (av.alignment.getHeight() > av.getEndSeq()))
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813 running = ap.scrollUp(false);
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816 if (mouseDragging && (evt.getX() < 0))
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818 running = ap.scrollRight(true);
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820 else if (mouseDragging && (evt.getX() >= getWidth()))
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822 running = ap.scrollRight(false);
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830 catch (Exception ex)
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