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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20 package jalview.appletgui;
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25 import java.awt.event.*;
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27 import jalview.datamodel.*;
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28 import jalview.schemes.*;
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30 public class SeqPanel
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34 public SeqCanvas seqCanvas;
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35 public AlignmentPanel ap;
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37 protected int lastres;
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38 protected int startseq;
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42 protected AlignViewport av;
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44 // if character is inserted or deleted, we will need to recalculate the conservation
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45 int seqEditOccurred = -1;
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47 ScrollThread scrollThread = null;
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48 boolean mouseDragging = false;
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50 boolean editingSeqs = false;
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51 boolean groupEditing = false;
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53 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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57 seqCanvas = new SeqCanvas(avp);
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58 setLayout(new BorderLayout());
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63 seqCanvas.addMouseMotionListener(new MouseMotionAdapter()
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65 public void mouseMoved(MouseEvent evt)
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70 public void mouseDragged(MouseEvent evt)
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74 doMouseDragged(evt);
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78 doMouseDraggedDefineMode(evt);
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83 seqCanvas.addMouseListener(new MouseAdapter()
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85 public void mouseReleased(MouseEvent evt)
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89 doMouseReleased(evt);
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93 doMouseReleasedDefineMode(evt);
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98 public void mousePressed(MouseEvent evt)
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100 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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102 if (evt.isAltDown() || evt.isControlDown())
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104 groupEditing = true;
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107 editingSeqs = true;
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108 doMousePressed(evt);
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112 doMousePressedDefineMode(evt);
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116 public void mouseExited(MouseEvent evt)
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122 doMouseExitedDefineMode(evt);
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126 public void mouseEntered(MouseEvent evt)
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132 doMouseEnteredDefineMode(evt);
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136 seqCanvas.repaint();
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139 public void doMouseReleased(MouseEvent evt)
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142 if (seqEditOccurred > -1)
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144 editOccurred(seqEditOccurred);
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149 seqEditOccurred = -1;
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150 editingSeqs = false;
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151 groupEditing = false;
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155 int startWrapBlock=-1;
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156 int wrappedBlock=-1;
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157 int findRes(MouseEvent evt)
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160 int x = evt.getX();
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162 if (av.wrapAlignment)
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165 int hgap = av.charHeight;
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166 if (av.scaleAboveWrapped)
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167 hgap += av.charHeight;
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169 int cHeight = av.getAlignment().getHeight() * av.charHeight
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170 + hgap + seqCanvas.getAnnotationHeight();
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172 int y = evt.getY();
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174 x -= seqCanvas.LABEL_WEST;
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177 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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179 wrappedBlock = y / cHeight;
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180 wrappedBlock += av.getStartRes() / cwidth;
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182 res = wrappedBlock * cwidth + x / av.getCharWidth();
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187 res = (x / av.getCharWidth()) + av.getStartRes();
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194 int findSeq(MouseEvent evt)
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198 int y = evt.getY();
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200 if (av.wrapAlignment)
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202 int hgap = av.charHeight;
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203 if (av.scaleAboveWrapped)
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204 hgap += av.charHeight;
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206 int cHeight = av.getAlignment().getHeight() * av.charHeight
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207 + hgap + seqCanvas.getAnnotationHeight();
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211 seq = ( (y % cHeight) / av.getCharHeight());
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215 seq = (y / av.getCharHeight()) + av.getStartSeq();
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222 public void doMousePressed(MouseEvent evt)
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224 ap.alignFrame.addHistoryItem(new HistoryItem(
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225 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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227 int seq = findSeq(evt);
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228 int res = findRes(evt);
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230 if (seq < av.getAlignment().getHeight() &&
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231 res < av.getAlignment().getSequenceAt(seq).getLength())
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233 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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234 // Find the residue's position in the sequence (res is the position
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235 // in the alignment
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249 public void doMouseMoved(MouseEvent evt)
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251 int res = findRes(evt);
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252 int seq = findSeq(evt);
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254 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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259 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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260 if (res > sequence.getLength())
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265 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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266 sequence.getName());
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269 if (av.alignment.isNucleotide())
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271 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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274 text.append(" Nucleotide: ");
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278 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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280 text.append(" Residue: ");
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288 text.append(obj + " (" +
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289 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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293 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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295 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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299 // use aa to see if the mouse pointer is on a
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300 if (av.showSequenceFeatures && sequence.getSequenceFeatures()!=null)
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302 Vector features = sequence.getSequenceFeatures();
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303 Enumeration e = features.elements();
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304 text.append(" Sequence Feature: ");
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306 while (e.hasMoreElements())
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308 SequenceFeature sf = (SequenceFeature) e.nextElement();
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309 if (sf.getBegin() <= sequence.findPosition(res) &&
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310 sf.getEnd() >= sequence.findPosition(res))
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312 text.append(sf.getDescription());
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313 if (sf.getStatus().length() > 0)
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315 text.append(" (" + sf.getStatus() + ")");
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323 ap.alignFrame.statusBar.setText(text.toString());
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327 public void doMouseDragged(MouseEvent evt)
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330 // If we're dragging we're editing
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331 int res = findRes(evt);
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337 if (lastres == -1 || lastres == res)
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342 boolean dragRight = true;
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343 if (res < av.getAlignment().getWidth() && res < lastres)
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348 if (res != lastres)
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353 SequenceGroup sg = av.getSelectionGroup();
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363 sg.setEndRes(sg.getEndRes() + (res - lastres));
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369 /// Are we able to delete?
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370 // ie are all columns blank?
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371 boolean deleteAllowed = false;
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372 for (int s = 0; s < sg.getSize(); s++)
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374 SequenceI seq = sg.getSequenceAt(s);
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375 for (int j = res; j < lastres; j++)
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377 if (seq.getSequence().length() <= j)
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382 if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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384 // Not a gap, block edit not valid
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386 deleteAllowed = false;
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389 deleteAllowed = true;
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393 if (!deleteAllowed)
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399 sg.setEndRes(sg.getEndRes() - (lastres - res));
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402 for (int i = 0; i < sg.getSize(); i++)
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404 SequenceI s = sg.getSequenceAt(i);
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405 int k = av.alignment.findIndex(s);
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410 for (int j = lastres; j < res; j++)
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419 for (int j = res; j < lastres; j++)
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421 if (s.getLength() > j)
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423 deleteChar(res, k);
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429 else /////Editing a single sequence///////////
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431 if (res < av.getAlignment().getWidth() && res > lastres)
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433 // dragging to the right
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434 for (int j = lastres; j < res; j++)
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436 insertChar(j, startseq);
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439 else if (res < av.getAlignment().getWidth() && res < lastres)
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441 // dragging to the left
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442 for (int j = lastres; j > res; j--)
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444 if (jalview.util.Comparison.isGap(
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445 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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448 deleteChar(res, startseq);
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463 seqCanvas.repaint();
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466 public void drawChars(int seqstart, int seqend, int start)
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468 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
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469 av.getStartRes(), av.getStartSeq(), 0);
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470 seqCanvas.repaint();
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473 public void insertChar(int j, int seq)
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475 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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476 seqEditOccurred = seq;
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479 public void deleteChar(int j, int seq)
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482 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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483 seqEditOccurred = seq;
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484 av.alignment.getWidth();
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488 void editOccurred(int i)
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490 if (endEdit == startEdit)
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492 ap.alignFrame.historyList.pop();
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493 ap.alignFrame.updateEditMenuBar();
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496 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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499 //////////////////////////////////////////
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500 /////Everything below this is for defining the boundary of the rubberband
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501 //////////////////////////////////////////
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503 public void doMousePressedDefineMode(MouseEvent evt)
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505 int res = findRes(evt);
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506 int seq = findSeq(evt);
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508 startWrapBlock=wrappedBlock;
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513 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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515 if (sequence == null || res > sequence.getLength())
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520 stretchGroup = av.getSelectionGroup();
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522 if (stretchGroup == null)
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524 stretchGroup = av.alignment.findGroup(sequence);
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525 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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526 res < stretchGroup.getEndRes())
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528 av.setSelectionGroup(stretchGroup);
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532 stretchGroup = null;
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536 else if (!stretchGroup.sequences.contains(sequence)
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537 || stretchGroup.getStartRes() > res
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538 || stretchGroup.getEndRes() < res)
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540 stretchGroup = null;
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542 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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544 if (allGroups != null)
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546 for (int i = 0; i < allGroups.length; i++)
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548 if (allGroups[i].getStartRes() <= res &&
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549 allGroups[i].getEndRes() >= res)
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551 stretchGroup = allGroups[i];
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552 av.setSelectionGroup(stretchGroup);
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559 if (stretchGroup == null)
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561 // define a new group here
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562 SequenceGroup sg = new SequenceGroup();
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563 sg.setStartRes(res);
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565 sg.addSequence(sequence, false);
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566 av.setSelectionGroup(sg);
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569 if (av.getConservationSelected())
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571 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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574 if (av.getAbovePIDThreshold())
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576 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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582 // DETECT RIGHT MOUSE BUTTON IN AWT
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583 else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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584 InputEvent.BUTTON3_MASK)
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586 APopupMenu popup = new APopupMenu(ap, null, null);
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588 popup.show(this, evt.getX(), evt.getY());
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591 if (stretchGroup != null && stretchGroup.getEndRes() == res)
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593 // Edit end res position of selected group
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594 changeEndRes = true;
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597 else if (stretchGroup != null && stretchGroup.getStartRes() == res)
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599 // Edit end res position of selected group
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600 changeStartRes = true;
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605 boolean changeEndSeq = false;
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606 boolean changeStartSeq = false;
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607 boolean changeEndRes = false;
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608 boolean changeStartRes = false;
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609 SequenceGroup stretchGroup = null;
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611 public void doMouseReleasedDefineMode(MouseEvent evt)
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615 stretchGroup.recalcConservation();
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616 mouseDragging = false;
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619 if (stretchGroup == null)
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624 if(stretchGroup.cs!=null)
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626 if (stretchGroup.cs.conservationApplied())
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628 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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629 stretchGroup.getName());
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633 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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634 stretchGroup.getName());
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637 changeEndRes = false;
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638 changeStartRes = false;
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639 stretchGroup = null;
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640 seqCanvas.repaint();
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644 boolean remove = false;
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645 public void doMouseDraggedDefineMode(MouseEvent evt)
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647 int res = findRes(evt);
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648 int y = findSeq(evt);
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650 if(wrappedBlock!=startWrapBlock)
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653 if(y>=av.alignment.getHeight())
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654 y = av.alignment.getHeight()-1;
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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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672 else if (stretchGroup.getStartRes() == res)
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674 // Edit start res position of selected group
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675 changeStartRes = true;
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678 if (res < av.getStartRes())
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680 res = av.getStartRes();
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682 else if (res > av.getEndRes() && !av.getWrapAlignment())
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684 res = av.getEndRes();
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689 if (res > stretchGroup.getStartRes() - 1)
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691 stretchGroup.setEndRes(res);
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694 else if (changeStartRes)
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696 if (res < stretchGroup.getEndRes() + 1)
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698 stretchGroup.setStartRes(res);
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702 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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719 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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721 if (stretchGroup.sequences.contains(nextSeq))
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723 stretchGroup.deleteSequence(seq, false);
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729 stretchGroup.addSequence(seq, false);
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731 stretchGroup.addSequence(nextSeq, false);
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735 mouseDragging = true;
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736 if (scrollThread != null)
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738 scrollThread.setEvent(evt);
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741 seqCanvas.repaint();
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744 public void doMouseEnteredDefineMode(MouseEvent e)
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746 if (scrollThread != null)
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748 scrollThread.running = false;
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752 public void doMouseExitedDefineMode(MouseEvent e)
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756 scrollThread = new ScrollThread();
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760 // this class allows scrolling off the bottom of the visible alignment
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765 boolean running = false;
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766 public ScrollThread()
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771 public void setEvent(MouseEvent e)
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776 public void stopScrolling()
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789 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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791 running = ap.scrollUp(true);
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794 if (mouseDragging && evt.getY() >= getSize().height &&
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795 av.alignment.getHeight() > av.getEndSeq())
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797 running = ap.scrollUp(false);
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800 if (mouseDragging && evt.getX() < 0)
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802 running = ap.scrollRight(true);
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805 else if (mouseDragging && evt.getX() >= getSize().width)
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807 running = ap.scrollRight(false);
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815 catch (Exception ex)
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