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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62 ToolTipManager.sharedInstance().registerComponent(this);
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63 ToolTipManager.sharedInstance().setInitialDelay(0);
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64 ToolTipManager.sharedInstance().setDismissDelay(10000);
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66 setBackground(Color.white);
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68 seqCanvas = new SeqCanvas(avp);
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69 setLayout(new BorderLayout());
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70 add(seqCanvas, BorderLayout.CENTER);
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74 addMouseMotionListener(new MouseMotionAdapter()
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76 public void mouseMoved(MouseEvent evt)
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78 if (av.getWrapAlignment())
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86 public void mouseDragged(MouseEvent evt)
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88 if (av.getWrapAlignment())
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95 doMouseDragged(evt);
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99 doMouseDraggedDefineMode(evt);
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104 addMouseListener(new MouseAdapter()
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106 public void mouseReleased(MouseEvent evt)
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108 if (av.getWrapAlignment())
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115 doMouseReleased(evt);
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119 doMouseReleasedDefineMode(evt);
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123 public void mousePressed(MouseEvent evt)
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125 if (av.getWrapAlignment())
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130 if (evt.isShiftDown() || evt.isAltDown() ||
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131 evt.isControlDown())
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133 if (evt.isAltDown() || evt.isControlDown())
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135 groupEditing = true;
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138 editingSeqs = true;
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139 doMousePressed(evt);
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143 doMousePressedDefineMode(evt);
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147 public void mouseExited(MouseEvent evt)
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149 if (av.getWrapAlignment() || editingSeqs)
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154 doMouseExitedDefineMode(evt);
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157 public void mouseEntered(MouseEvent evt)
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159 if (av.getWrapAlignment() || editingSeqs)
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164 doMouseEnteredDefineMode(evt);
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170 public void doMouseReleased(MouseEvent evt)
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172 if (seqEditOccurred > -1)
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174 editOccurred(seqEditOccurred);
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179 seqEditOccurred = -1;
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180 editingSeqs = false;
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181 groupEditing = false;
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186 public void doMousePressed(MouseEvent evt)
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188 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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189 av.alignment, HistoryItem.EDIT));
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194 int x = evt.getX();
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195 int y = evt.getY();
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197 res = (x / av.getCharWidth()) + av.getStartRes();
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198 seq = (y / av.getCharHeight()) + av.getStartSeq();
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200 if ( (seq < av.getAlignment().getHeight()) &&
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201 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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212 startEdit = lastres;
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218 public void doMouseMoved(MouseEvent evt)
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222 int x = evt.getX();
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223 int y = evt.getY();
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225 if (av.wrapAlignment)
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227 y -= (2 * av.charHeight);
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229 int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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231 res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +
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232 (x / av.getCharWidth()) + av.getStartRes();
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235 seq = (y / av.getCharHeight()) + av.getStartSeq();
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239 res = (x / av.getCharWidth()) + av.getStartRes();
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240 seq = (y / av.getCharHeight()) + av.getStartSeq();
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243 if (seq >= av.getAlignment().getHeight())
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248 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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250 if (res > sequence.getLength())
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255 Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
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261 aa = obj.toString();
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264 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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265 sequence.getName());
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269 text.append(" Residue: " + aa + " (" +
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270 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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273 ap.alignFrame.statusBar.setText(text.toString());
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275 // use aa to see if the mouse pointer is on a
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276 if (av.showSequenceFeatures)
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278 Vector features = sequence.getSequenceFeatures();
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279 Enumeration e = features.elements();
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280 StringBuffer sbuffer = new StringBuffer();
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282 while (e.hasMoreElements())
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284 SequenceFeature sf = (SequenceFeature) e.nextElement();
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286 if ( (sf.getStart() <= sequence.findPosition(res)) &&
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287 (sf.getEnd() >= sequence.findPosition(res)))
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289 if (sbuffer.length() > 0)
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291 sbuffer.append("; ");
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294 sbuffer.append(sf.getType() + " " + sf.getDescription());
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296 if (sf.getStatus().length() > 0)
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298 sbuffer.append(" (" + sf.getStatus() + ")");
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303 this.setToolTipText(sbuffer.toString());
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307 public void doMouseDragged(MouseEvent evt)
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309 // If we're dragging we're editing
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310 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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317 if ( (lastres == -1) || (lastres == res))
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322 boolean dragRight = true;
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324 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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329 if (res != lastres)
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334 SequenceGroup sg = av.getSelectionGroup();
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346 sg.setEndRes(sg.getEndRes() + (res - lastres));
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351 /// Are we able to delete?
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352 // ie are all columns blank?
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353 boolean deleteAllowed = false;
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355 for (int s = 0; s < sg.getSize(); s++)
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357 SequenceI seq = sg.getSequenceAt(s);
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359 for (int j = res; j < lastres; j++)
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361 if (seq.getSequence().length() <= j)
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366 if (!jalview.util.Comparison.isGap(
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367 seq.getSequence().charAt(j)))
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369 // Not a gap, block edit not valid
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371 deleteAllowed = false;
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376 deleteAllowed = true;
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380 if (!deleteAllowed)
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387 sg.setEndRes(sg.getEndRes() - (lastres - res));
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390 for (int i = 0; i < sg.getSize(); i++)
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392 SequenceI s = sg.getSequenceAt(i);
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393 int k = av.alignment.findIndex(s);
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398 for (int j = lastres; j < res; j++)
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406 for (int j = res; j < lastres; j++)
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408 if (s.getLength() > j)
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410 deleteChar(res, k);
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416 else /////Editing a single sequence///////////
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418 if ( (res < av.getAlignment().getWidth()) && (res > lastres))
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420 // dragging to the right
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421 for (int j = lastres; j < res; j++)
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423 insertChar(j, startseq);
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426 else if ( (res < av.getAlignment().getWidth()) &&
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429 // dragging to the left
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430 for (int j = lastres; j > res; j--)
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432 if (jalview.util.Comparison.isGap(
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433 av.alignment.getSequenceAt(startseq)
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434 .getSequence().charAt(res)))
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436 deleteChar(res, startseq);
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449 seqCanvas.repaint();
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452 public void drawChars(int seqstart, int seqend, int start)
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454 seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
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455 seqend, av.getStartRes(), av.getStartSeq(), 0);
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456 seqCanvas.repaint();
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459 public void insertChar(int j, int seq)
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461 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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462 seqEditOccurred = seq;
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465 public void deleteChar(int j, int seq)
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467 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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468 seqEditOccurred = seq;
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470 av.alignment.getWidth();
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471 seqCanvas.repaint();
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474 void editOccurred(int i)
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476 if (endEdit == startEdit)
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478 ap.alignFrame.historyList.pop();
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479 ap.alignFrame.updateEditMenuBar();
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482 av.updateConservation();
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483 av.updateConsensus();
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486 ColourSchemeI cs = av.getGlobalColourScheme();
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488 if(av.getSelectionGroup()!=null)
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489 av.getSelectionGroup().recalcConservation();
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492 if (cs instanceof ConservationColourScheme)
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494 ConservationColourScheme ccs = (ConservationColourScheme) cs;
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495 Conservation c = new Conservation("All",
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496 ResidueProperties.propHash, 3,
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497 av.alignment.getSequences(), 0,
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498 av.alignment.getWidth() - 1);
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500 c.verdict(false, av.ConsPercGaps);
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502 if (ccs.cs instanceof ClustalxColourScheme)
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505 ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
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506 cxs.resetClustalX(av.alignment.getSequences(),
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507 av.alignment.getWidth());
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508 ccs = new ConservationColourScheme(c, cxs);
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509 av.setGlobalColourScheme(ccs);
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513 ccs = new ConservationColourScheme(c, ccs.cs);
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514 av.setGlobalColourScheme(ccs);
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518 if (cs instanceof ClustalxColourScheme)
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520 ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
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521 av.alignment.getWidth());
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522 av.setGlobalColourScheme(cs);
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526 public void doMousePressedDefineMode(MouseEvent evt)
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528 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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529 int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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532 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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534 if ( (sequence == null) || (res > sequence.getLength()))
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539 stretchGroup = av.getSelectionGroup();
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541 if (stretchGroup == null)
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543 stretchGroup = av.alignment.findGroup(sequence);
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545 if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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546 (res < stretchGroup.getEndRes()))
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548 av.setSelectionGroup(stretchGroup);
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552 stretchGroup = null;
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555 else if (!stretchGroup.sequences.contains(sequence) ||
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556 (stretchGroup.getStartRes() > res) ||
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557 (stretchGroup.getEndRes() < res))
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559 stretchGroup = null;
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561 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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563 if (allGroups != null)
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565 for (int i = 0; i < allGroups.length; i++)
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567 if ( (allGroups[i].getStartRes() <= res) &&
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568 (allGroups[i].getEndRes() >= res))
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570 stretchGroup = allGroups[i];
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571 av.setSelectionGroup(stretchGroup);
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579 if (stretchGroup == null)
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581 // define a new group here
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582 SequenceGroup sg = new SequenceGroup();
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583 sg.setStartRes(res);
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585 sg.addSequence(sequence, false);
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586 av.setSelectionGroup(sg);
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589 if (av.getConservationSelected())
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591 SliderPanel.setConservationSlider(ap,
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592 av.getGlobalColourScheme(),
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596 if (av.getAbovePIDThreshold())
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598 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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602 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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604 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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605 pop.show(this, evt.getX(), evt.getY());
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607 // edit the properties of existing group
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610 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
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612 // Edit end res position of selected group
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613 changeEndRes = true;
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615 else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))
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617 // Edit end res position of selected group
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618 changeStartRes = true;
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621 stretchGroup.getWidth();
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623 seqCanvas.repaint();
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626 public void doMouseReleasedDefineMode(MouseEvent evt)
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630 stretchGroup.recalcConservation();
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631 mouseDragging = false;
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634 if (stretchGroup == null)
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639 if (stretchGroup.cs instanceof ClustalxColourScheme)
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641 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,
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642 stretchGroup.getWidth());
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645 if (stretchGroup.cs instanceof ConservationColourScheme)
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647 ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
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648 stretchGroup.cs = ccs;
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649 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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650 stretchGroup.getName());
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655 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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656 stretchGroup.getName());
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659 changeEndRes = false;
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660 changeStartRes = false;
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661 stretchGroup = null;
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662 seqCanvas.repaint();
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663 ap.idPanel.repaint();
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666 public void doMouseDraggedDefineMode(MouseEvent evt)
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668 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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669 int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
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671 if (stretchGroup == null)
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676 if (res > av.alignment.getWidth())
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678 res = av.alignment.getWidth() - 1;
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681 if (stretchGroup.getEndRes() == res)
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683 // Edit end res position of selected group
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684 changeEndRes = true;
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686 else if (stretchGroup.getStartRes() == res)
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688 // Edit start res position of selected group
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689 changeStartRes = true;
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692 if (res < av.getStartRes())
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694 res = av.getStartRes();
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696 else if (res > av.getEndRes())
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698 res = av.getEndRes();
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703 if (res > (stretchGroup.getStartRes() - 1))
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705 stretchGroup.setEndRes(res);
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708 else if (changeStartRes)
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710 if (res < (stretchGroup.getEndRes() + 1))
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712 stretchGroup.setStartRes(res);
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716 int dragDirection = 0;
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722 else if (y < oldSeq)
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724 dragDirection = -1;
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727 while ( (y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
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729 // This routine ensures we don't skip any sequences, as the
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730 // selection is quite slow.
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731 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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733 oldSeq += dragDirection;
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735 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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737 if (stretchGroup.sequences.contains(nextSeq))
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739 stretchGroup.deleteSequence(seq, false);
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745 stretchGroup.addSequence(seq, false);
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747 stretchGroup.addSequence(nextSeq, false);
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752 mouseDragging = true;
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754 if (scrollThread != null)
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756 scrollThread.setEvent(evt);
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759 seqCanvas.repaint();
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762 public void doMouseEnteredDefineMode(MouseEvent e)
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764 if (scrollThread != null)
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766 scrollThread.running = false;
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770 public void doMouseExitedDefineMode(MouseEvent e)
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772 if (av.getWrapAlignment())
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779 scrollThread = new ScrollThread();
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783 // this class allows scrolling off the bottom of the visible alignment
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788 boolean running = false;
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790 public ScrollThread()
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795 public void setEvent(MouseEvent e)
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800 public void stopScrolling()
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813 if (mouseDragging && (evt.getY() < 0) &&
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814 (av.getStartSeq() > 0))
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816 running = ap.scrollUp(true);
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819 if (mouseDragging && (evt.getY() >= getHeight()) &&
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820 (av.alignment.getHeight() > av.getEndSeq()))
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822 running = ap.scrollUp(false);
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825 if (mouseDragging && (evt.getX() < 0))
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827 running = ap.scrollRight(true);
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829 else if (mouseDragging && (evt.getX() >= getWidth()))
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831 running = ap.scrollRight(false);
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839 catch (Exception ex)
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