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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64 seqCanvas = new SeqCanvas(avp);
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65 setLayout(new BorderLayout());
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66 add(seqCanvas, BorderLayout.CENTER);
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70 addMouseMotionListener(new MouseMotionAdapter()
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72 public void mouseMoved(MouseEvent evt)
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74 if (av.getWrapAlignment())
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82 public void mouseDragged(MouseEvent evt)
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84 if (av.getWrapAlignment())
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91 doMouseDragged(evt);
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95 doMouseDraggedDefineMode(evt);
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100 addMouseListener(new MouseAdapter()
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102 public void mouseReleased(MouseEvent evt)
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104 if (av.getWrapAlignment())
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111 doMouseReleased(evt);
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115 doMouseReleasedDefineMode(evt);
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119 public void mousePressed(MouseEvent evt)
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121 if (av.getWrapAlignment())
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126 if (evt.isShiftDown() || evt.isAltDown() ||
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127 evt.isControlDown())
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129 if (evt.isAltDown() || evt.isControlDown())
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131 groupEditing = true;
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134 editingSeqs = true;
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135 doMousePressed(evt);
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139 doMousePressedDefineMode(evt);
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143 public void mouseExited(MouseEvent evt)
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145 if (av.getWrapAlignment() || editingSeqs)
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150 doMouseExitedDefineMode(evt);
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153 public void mouseEntered(MouseEvent evt)
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155 if (av.getWrapAlignment() || editingSeqs)
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160 doMouseEnteredDefineMode(evt);
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166 public void doMouseReleased(MouseEvent evt)
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168 if (seqEditOccurred > -1)
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170 editOccurred(seqEditOccurred);
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175 seqEditOccurred = -1;
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176 editingSeqs = false;
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177 groupEditing = false;
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182 public void doMousePressed(MouseEvent evt)
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184 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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185 av.alignment, HistoryItem.EDIT));
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190 int x = evt.getX();
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191 int y = evt.getY();
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193 res = (x / av.getCharWidth()) + av.getStartRes();
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194 seq = (y / av.getCharHeight()) + av.getStartSeq();
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196 if ( (seq < av.getAlignment().getHeight()) &&
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197 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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208 startEdit = lastres;
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214 public void doMouseMoved(MouseEvent evt)
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218 int x = evt.getX();
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219 int y = evt.getY();
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221 if (av.wrapAlignment)
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223 y -= (2 * av.charHeight);
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225 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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227 res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +
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228 (x / av.getCharWidth()) + av.getStartRes();
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231 seq = (y / av.getCharHeight()) + av.getStartSeq();
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235 res = (x / av.getCharWidth()) + av.getStartRes();
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236 seq = (y / av.getCharHeight()) + av.getStartSeq();
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239 if (seq >= av.getAlignment().getHeight())
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244 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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246 if (res > sequence.getLength())
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251 Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
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257 aa = obj.toString();
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260 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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261 sequence.getName());
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265 text.append(" Residue: " + aa + " (" +
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266 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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269 ap.alignFrame.statusBar.setText(text.toString());
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271 // use aa to see if the mouse pointer is on a
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272 if (av.showSequenceFeatures)
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274 Vector features = sequence.getSequenceFeatures();
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275 Enumeration e = features.elements();
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276 StringBuffer sbuffer = new StringBuffer();
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278 while (e.hasMoreElements())
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280 SequenceFeature sf = (SequenceFeature) e.nextElement();
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282 if ( (sf.getStart() <= sequence.findPosition(res)) &&
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283 (sf.getEnd() >= sequence.findPosition(res)))
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285 if (sbuffer.length() > 0)
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287 sbuffer.append("; ");
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290 sbuffer.append(sf.getType() + " " + sf.getDescription());
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292 if (sf.getStatus().length() > 0)
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294 sbuffer.append(" (" + sf.getStatus() + ")");
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299 ToolTipManager.sharedInstance().registerComponent(this);
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300 this.setToolTipText(sbuffer.toString());
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304 public void doMouseDragged(MouseEvent evt)
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306 // If we're dragging we're editing
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307 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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314 if ( (lastres == -1) || (lastres == res))
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319 boolean dragRight = true;
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321 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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326 if (res != lastres)
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331 SequenceGroup sg = av.getSelectionGroup();
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343 sg.setEndRes(sg.getEndRes() + (res - lastres));
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348 /// Are we able to delete?
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349 // ie are all columns blank?
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350 boolean deleteAllowed = false;
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352 for (int s = 0; s < sg.getSize(); s++)
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354 SequenceI seq = sg.getSequenceAt(s);
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356 for (int j = res; j < lastres; j++)
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358 if (seq.getSequence().length() <= j)
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363 if (!jalview.util.Comparison.isGap(
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364 seq.getSequence().charAt(j)))
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366 // Not a gap, block edit not valid
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368 deleteAllowed = false;
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373 deleteAllowed = true;
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377 if (!deleteAllowed)
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384 sg.setEndRes(sg.getEndRes() - (lastres - res));
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387 for (int i = 0; i < sg.getSize(); i++)
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389 SequenceI s = sg.getSequenceAt(i);
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390 int k = av.alignment.findIndex(s);
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395 for (int j = lastres; j < res; j++)
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403 for (int j = res; j < lastres; j++)
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405 if (s.getLength() > j)
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407 deleteChar(res, k);
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413 else /////Editing a single sequence///////////
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415 if ( (res < av.getAlignment().getWidth()) && (res > lastres))
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417 // dragging to the right
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418 for (int j = lastres; j < res; j++)
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420 insertChar(j, startseq);
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423 else if ( (res < av.getAlignment().getWidth()) &&
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426 // dragging to the left
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427 for (int j = lastres; j > res; j--)
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429 if (jalview.util.Comparison.isGap(
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430 av.alignment.getSequenceAt(startseq)
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431 .getSequence().charAt(res)))
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433 deleteChar(res, startseq);
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449 public void drawChars(int seqstart, int seqend, int start)
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451 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
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452 seqend, av.getStartRes(), av.getStartSeq(), 0);
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456 public void insertChar(int j, int seq)
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458 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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459 seqEditOccurred = seq;
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462 public void deleteChar(int j, int seq)
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464 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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465 seqEditOccurred = seq;
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467 av.alignment.getWidth();
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471 void editOccurred(int i)
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473 if (endEdit == startEdit)
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475 ap.alignFrame.historyList.pop();
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476 ap.alignFrame.updateEditMenuBar();
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479 av.updateConservation();
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480 av.updateConsensus();
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483 ColourSchemeI cs = av.getGlobalColourScheme();
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485 if (cs instanceof ConservationColourScheme)
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487 ConservationColourScheme ccs = (ConservationColourScheme) cs;
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489 if (ccs.cs instanceof ClustalxColourScheme)
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491 Conservation c = new Conservation("All",
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492 ResidueProperties.propHash, 3,
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493 av.alignment.getSequences(), 0,
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494 av.alignment.getWidth() - 1);
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496 c.verdict(false, av.ConsPercGaps);
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498 ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
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499 cxs.resetClustalX(av.alignment.getSequences(),
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500 av.alignment.getWidth());
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501 ccs = new ConservationColourScheme(c, cxs);
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502 av.setGlobalColourScheme(ccs);
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506 if (cs instanceof ClustalxColourScheme)
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508 ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
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509 av.alignment.getWidth());
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510 av.setGlobalColourScheme(cs);
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514 public void doMousePressedDefineMode(MouseEvent evt)
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516 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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517 int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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520 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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522 if ( (sequence == null) || (res > sequence.getLength()))
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527 stretchGroup = av.getSelectionGroup();
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529 if (stretchGroup == null)
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531 stretchGroup = av.alignment.findGroup(sequence);
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533 if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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534 (res < stretchGroup.getEndRes()))
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536 av.setSelectionGroup(stretchGroup);
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540 stretchGroup = null;
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543 else if (!stretchGroup.sequences.contains(sequence) ||
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544 (stretchGroup.getStartRes() > res) ||
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545 (stretchGroup.getEndRes() < res))
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547 stretchGroup = null;
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549 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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551 if (allGroups != null)
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553 for (int i = 0; i < allGroups.length; i++)
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555 if ( (allGroups[i].getStartRes() <= res) &&
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556 (allGroups[i].getEndRes() >= res))
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558 stretchGroup = allGroups[i];
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559 av.setSelectionGroup(stretchGroup);
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567 if (stretchGroup == null)
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569 // define a new group here
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570 SequenceGroup sg = new SequenceGroup();
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571 sg.setStartRes(res);
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573 sg.addSequence(sequence, false);
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574 av.setSelectionGroup(sg);
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577 if (av.getConservationSelected())
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579 SliderPanel.setConservationSlider(ap,
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580 av.getGlobalColourScheme(),
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584 if (av.getAbovePIDThreshold())
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586 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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590 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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592 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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593 pop.show(this, evt.getX(), evt.getY());
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595 // edit the properties of existing group
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598 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
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600 // Edit end res position of selected group
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601 changeEndRes = true;
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603 else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))
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605 // Edit end res position of selected group
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606 changeStartRes = true;
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609 stretchGroup.getWidth();
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614 public void doMouseReleasedDefineMode(MouseEvent evt)
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616 mouseDragging = false;
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618 if (stretchGroup == null)
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623 stretchGroup.recalcConservation();
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625 if (stretchGroup.cs instanceof ClustalxColourScheme)
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627 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,
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628 av.alignment.getWidth());
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630 else if (stretchGroup.cs instanceof ConservationColourScheme)
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632 ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
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633 stretchGroup.cs = ccs;
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634 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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635 stretchGroup.getName());
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640 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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641 stretchGroup.getName());
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644 changeEndRes = false;
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645 changeStartRes = false;
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646 stretchGroup = null;
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648 ap.idPanel.repaint();
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651 public void doMouseDraggedDefineMode(MouseEvent evt)
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653 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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654 int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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656 if (stretchGroup == null)
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661 if (res > av.alignment.getWidth())
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663 res = av.alignment.getWidth() - 1;
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666 if (stretchGroup.getEndRes() == res)
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668 // Edit end res position of selected group
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669 changeEndRes = true;
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671 else if (stretchGroup.getStartRes() == res)
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673 // Edit start res position of selected group
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674 changeStartRes = true;
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677 if (res < av.getStartRes())
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679 res = av.getStartRes();
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681 else if (res > av.getEndRes())
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683 res = av.getEndRes();
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688 if (res > (stretchGroup.getStartRes() - 1))
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690 stretchGroup.setEndRes(res);
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693 else if (changeStartRes)
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695 if (res < (stretchGroup.getEndRes() + 1))
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697 stretchGroup.setStartRes(res);
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701 int dragDirection = 0;
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707 else if (y < oldSeq)
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709 dragDirection = -1;
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712 while ( (y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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714 // This routine ensures we don't skip any sequences, as the
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715 // selection is quite slow.
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716 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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718 oldSeq += dragDirection;
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720 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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722 if (stretchGroup.sequences.contains(nextSeq))
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724 stretchGroup.deleteSequence(seq, false);
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725 stretchGroup.deleteSequence(nextSeq, false);
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731 stretchGroup.addSequence(seq, false);
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734 stretchGroup.addSequence(nextSeq, false);
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739 mouseDragging = true;
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741 if (scrollThread != null)
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743 scrollThread.setEvent(evt);
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749 public void doMouseEnteredDefineMode(MouseEvent e)
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751 if (scrollThread != null)
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753 scrollThread.running = false;
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757 public void doMouseExitedDefineMode(MouseEvent e)
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759 if (av.getWrapAlignment())
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766 scrollThread = new ScrollThread();
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770 // this class allows scrolling off the bottom of the visible alignment
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775 boolean running = false;
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777 public ScrollThread()
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782 public void setEvent(MouseEvent e)
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787 public void stopScrolling()
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800 if (mouseDragging && (evt.getY() < 0) &&
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801 (av.getStartSeq() > 0))
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803 running = ap.scrollUp(true);
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806 if (mouseDragging && (evt.getY() >= getHeight()) &&
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807 (av.alignment.getHeight() > av.getEndSeq()))
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809 running = ap.scrollUp(false);
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812 if (mouseDragging && (evt.getX() < 0))
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814 running = ap.scrollRight(true);
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816 else if (mouseDragging && (evt.getX() >= getWidth()))
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818 running = ap.scrollRight(false);
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826 catch (Exception ex)
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