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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31 extends Panel implements MouseMotionListener, MouseListener
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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(this);
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64 seqCanvas.addMouseListener(this);
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66 seqCanvas.repaint();
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70 public void mousePressed(MouseEvent evt)
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72 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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74 if (evt.isAltDown() || evt.isControlDown())
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76 groupEditing = true;
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80 doMousePressed(evt);
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84 doMousePressedDefineMode(evt);
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88 public void mouseClicked(MouseEvent evt){}
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91 public void mouseReleased(MouseEvent evt)
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95 doMouseReleasedDefineMode(evt);
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100 if (seqEditOccurred > -1)
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102 editOccurred(seqEditOccurred);
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107 seqEditOccurred = -1;
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108 editingSeqs = false;
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109 groupEditing = false;
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113 int startWrapBlock=-1;
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114 int wrappedBlock=-1;
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115 int findRes(MouseEvent evt)
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118 int x = evt.getX();
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120 if (av.wrapAlignment)
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123 int hgap = av.charHeight;
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124 if (av.scaleAboveWrapped)
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125 hgap += av.charHeight;
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127 int cHeight = av.getAlignment().getHeight() * av.charHeight
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128 + hgap + seqCanvas.getAnnotationHeight();
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130 int y = evt.getY();
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132 x -= seqCanvas.LABEL_WEST;
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135 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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137 wrappedBlock = y / cHeight;
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138 wrappedBlock += av.getStartRes() / cwidth;
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140 res = wrappedBlock * cwidth + x / av.getCharWidth();
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145 res = (x / av.getCharWidth()) + av.getStartRes();
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152 int findSeq(MouseEvent evt)
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156 int y = evt.getY();
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158 if (av.wrapAlignment)
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160 int hgap = av.charHeight;
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161 if (av.scaleAboveWrapped)
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162 hgap += av.charHeight;
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164 int cHeight = av.getAlignment().getHeight() * av.charHeight
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165 + hgap + seqCanvas.getAnnotationHeight();
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169 seq = ( (y % cHeight) / av.getCharHeight());
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173 seq = (y / av.getCharHeight()) + av.getStartSeq();
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180 public void doMousePressed(MouseEvent evt)
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182 ap.alignFrame.addHistoryItem(new HistoryItem(
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183 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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185 int seq = findSeq(evt);
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186 int res = findRes(evt);
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188 if (seq < av.getAlignment().getHeight() &&
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189 res < av.getAlignment().getSequenceAt(seq).getLength())
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191 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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192 // Find the residue's position in the sequence (res is the position
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193 // in the alignment
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207 public void mouseMoved(MouseEvent evt)
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209 int res = findRes(evt);
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210 int seq = findSeq(evt);
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212 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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217 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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218 if (res > sequence.getLength())
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223 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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224 sequence.getName());
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227 if (av.alignment.isNucleotide())
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229 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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232 text.append(" Nucleotide: ");
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236 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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238 text.append(" Residue: ");
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246 text.append(obj + " (" +
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247 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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251 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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253 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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257 // use aa to see if the mouse pointer is on a
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258 if (av.showSequenceFeatures && sequence.getSequenceFeatures()!=null)
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261 sequence.getSequenceFeatures();
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262 boolean first = true;
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263 while (index < sequence.getSequenceFeatures().length)
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265 SequenceFeature sf = sequence.getSequenceFeatures()[index];
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266 if (sf.getBegin() <= sequence.findPosition(res) &&
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267 sf.getEnd() >= sequence.findPosition(res))
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269 if(!av.featuresDisplayed.containsKey(sf.getType()))
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277 text.append(" Sequence Feature:");
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281 text.append(" "+sf.getType());
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283 if(sf.getDescription()!=null)
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284 text.append(" "+sf.getDescription());
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286 if (sf.getStatus()!=null && sf.getStatus().length() > 0)
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288 text.append(" (" + sf.getStatus() + ")");
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298 ap.alignFrame.statusBar.setText(text.toString());
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302 public void mouseDragged(MouseEvent evt)
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306 doMouseDraggedDefineMode(evt);
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310 // If we're dragging we're editing
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311 int res = findRes(evt);
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317 if (lastres == -1 || lastres == res)
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322 boolean dragRight = true;
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323 if (res < av.getAlignment().getWidth() && res < lastres)
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328 if (res != lastres)
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333 SequenceGroup sg = av.getSelectionGroup();
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343 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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352 for (int s = 0; s < sg.getSize(); s++)
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354 SequenceI seq = sg.getSequenceAt(s);
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355 for (int j = res; j < lastres; j++)
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357 if (seq.getSequence().length() <= j)
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362 if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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364 // Not a gap, block edit not valid
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366 deleteAllowed = false;
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369 deleteAllowed = true;
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373 if (!deleteAllowed)
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379 sg.setEndRes(sg.getEndRes() - (lastres - res));
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382 for (int i = 0; i < sg.getSize(); i++)
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384 SequenceI s = sg.getSequenceAt(i);
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385 int k = av.alignment.findIndex(s);
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390 for (int j = lastres; j < res; j++)
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399 for (int j = res; j < lastres; j++)
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401 if (s.getLength() > j)
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403 deleteChar(res, k);
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409 else /////Editing a single sequence///////////
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411 if (res < av.getAlignment().getWidth() && res > lastres)
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413 // dragging to the right
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414 for (int j = lastres; j < res; j++)
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416 insertChar(j, startseq);
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419 else if (res < av.getAlignment().getWidth() && res < lastres)
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421 // dragging to the left
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422 for (int j = lastres; j > res; j--)
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424 if (jalview.util.Comparison.isGap(
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425 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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428 deleteChar(res, startseq);
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443 seqCanvas.repaint();
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446 public void drawChars(int seqstart, int seqend, int start)
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448 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend, 0);
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449 seqCanvas.repaint();
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452 public void insertChar(int j, int seq)
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454 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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455 seqEditOccurred = seq;
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458 public void deleteChar(int j, int seq)
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461 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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462 seqEditOccurred = seq;
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463 av.alignment.getWidth();
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467 void editOccurred(int i)
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469 if (endEdit == startEdit)
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471 ap.alignFrame.historyList.pop();
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472 ap.alignFrame.updateEditMenuBar();
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475 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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478 //////////////////////////////////////////
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479 /////Everything below this is for defining the boundary of the rubberband
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480 //////////////////////////////////////////
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482 public void doMousePressedDefineMode(MouseEvent evt)
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484 int res = findRes(evt);
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485 int seq = findSeq(evt);
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487 startWrapBlock=wrappedBlock;
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492 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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494 if (sequence == null || res > sequence.getLength())
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499 stretchGroup = av.getSelectionGroup();
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501 if (stretchGroup == null)
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503 stretchGroup = av.alignment.findGroup(sequence);
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504 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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505 res < stretchGroup.getEndRes())
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507 av.setSelectionGroup(stretchGroup);
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511 stretchGroup = null;
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515 else if (!stretchGroup.sequences.contains(sequence)
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516 || stretchGroup.getStartRes() > res
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517 || stretchGroup.getEndRes() < res)
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519 stretchGroup = null;
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521 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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523 if (allGroups != null)
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525 for (int i = 0; i < allGroups.length; i++)
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527 if (allGroups[i].getStartRes() <= res &&
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528 allGroups[i].getEndRes() >= res)
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530 stretchGroup = allGroups[i];
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531 av.setSelectionGroup(stretchGroup);
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538 if (stretchGroup == null)
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540 // define a new group here
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541 SequenceGroup sg = new SequenceGroup();
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542 sg.setStartRes(res);
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544 sg.addSequence(sequence, false);
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545 av.setSelectionGroup(sg);
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548 if (av.getConservationSelected())
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550 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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553 if (av.getAbovePIDThreshold())
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555 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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561 // DETECT RIGHT MOUSE BUTTON IN AWT
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562 else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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563 InputEvent.BUTTON3_MASK)
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565 APopupMenu popup = new APopupMenu(ap, null, null);
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567 popup.show(this, evt.getX(), evt.getY());
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570 if (stretchGroup != null && stretchGroup.getEndRes() == res)
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572 // Edit end res position of selected group
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573 changeEndRes = true;
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576 else if (stretchGroup != null && stretchGroup.getStartRes() == res)
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578 // Edit end res position of selected group
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579 changeStartRes = true;
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584 boolean changeEndSeq = false;
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585 boolean changeStartSeq = false;
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586 boolean changeEndRes = false;
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587 boolean changeStartRes = false;
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588 SequenceGroup stretchGroup = null;
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590 public void doMouseReleasedDefineMode(MouseEvent evt)
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594 stretchGroup.recalcConservation();
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595 mouseDragging = false;
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598 if (stretchGroup == null)
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603 if(stretchGroup.cs!=null)
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605 if (stretchGroup.cs.conservationApplied())
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607 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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608 stretchGroup.getName());
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612 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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613 stretchGroup.getName());
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616 changeEndRes = false;
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617 changeStartRes = false;
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618 stretchGroup = null;
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619 seqCanvas.repaint();
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623 boolean remove = false;
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624 public void doMouseDraggedDefineMode(MouseEvent evt)
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626 int res = findRes(evt);
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627 int y = findSeq(evt);
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629 if(wrappedBlock!=startWrapBlock)
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632 if(y>=av.alignment.getHeight())
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633 y = av.alignment.getHeight()-1;
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635 if (stretchGroup == null)
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640 if (res > av.alignment.getWidth())
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642 res = av.alignment.getWidth() - 1;
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645 if (stretchGroup.getEndRes() == res)
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647 // Edit end res position of selected group
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648 changeEndRes = true;
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651 else if (stretchGroup.getStartRes() == res)
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653 // Edit start res position of selected group
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654 changeStartRes = true;
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657 if (res < av.getStartRes())
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659 res = av.getStartRes();
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661 else if (res > av.getEndRes() && !av.getWrapAlignment())
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663 res = av.getEndRes();
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668 if (res > stretchGroup.getStartRes() - 1)
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670 stretchGroup.setEndRes(res);
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673 else if (changeStartRes)
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675 if (res < stretchGroup.getEndRes() + 1)
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677 stretchGroup.setStartRes(res);
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681 int dragDirection = 0;
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686 else if (y < oldSeq)
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688 dragDirection = -1;
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691 while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
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693 // This routine ensures we don't skip any sequences, as the
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694 // selection is quite slow.
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695 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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697 oldSeq += dragDirection;
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698 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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700 if (stretchGroup.sequences.contains(nextSeq))
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702 stretchGroup.deleteSequence(seq, false);
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708 stretchGroup.addSequence(seq, false);
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710 stretchGroup.addSequence(nextSeq, false);
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714 mouseDragging = true;
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715 if (scrollThread != null)
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717 scrollThread.setEvent(evt);
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720 seqCanvas.repaint();
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723 public void mouseEntered(MouseEvent e)
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725 if (editingSeqs && scrollThread != null)
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727 scrollThread.running = false;
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731 public void mouseExited(MouseEvent e)
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735 scrollThread = new ScrollThread();
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739 // this class allows scrolling off the bottom of the visible alignment
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744 boolean running = false;
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745 public ScrollThread()
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750 public void setEvent(MouseEvent e)
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755 public void stopScrolling()
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768 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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770 running = ap.scrollUp(true);
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773 if (mouseDragging && evt.getY() >= getSize().height &&
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774 av.alignment.getHeight() > av.getEndSeq())
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776 running = ap.scrollUp(false);
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779 if (mouseDragging && evt.getX() < 0)
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781 running = ap.scrollRight(true);
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784 else if (mouseDragging && evt.getX() >= getSize().width)
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786 running = ap.scrollRight(false);
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794 catch (Exception ex)
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