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.gui;
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23 import java.awt.event.*;
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24 import jalview.datamodel.*;
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25 import javax.swing.*;
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27 import jalview.schemes.*;
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28 import jalview.analysis.Conservation;
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30 public class SeqPanel extends JPanel
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33 public SeqCanvas seqCanvas;
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34 public AlignmentPanel ap;
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36 protected int lastres;
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37 protected int startseq;
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41 protected AlignViewport av;
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43 // if character is inserted or deleted, we will need to recalculate the conservation
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44 int seqEditOccurred = -1;
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46 ScrollThread scrollThread = null;
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47 boolean mouseDragging = false;
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49 boolean editingSeqs = false;
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50 boolean groupEditing = false;
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53 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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56 seqCanvas = new SeqCanvas(avp);
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57 setLayout(new BorderLayout());
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58 add(seqCanvas, BorderLayout.CENTER);
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62 addMouseMotionListener( new MouseMotionAdapter()
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64 public void mouseMoved(MouseEvent evt)
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66 if(av.getWrapAlignment())
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68 doMouseMoved(evt); }
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70 public void mouseDragged(MouseEvent evt)
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72 if(av.getWrapAlignment())
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75 doMouseDragged(evt);
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77 doMouseDraggedDefineMode(evt);
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81 addMouseListener( new MouseAdapter()
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83 public void mouseReleased(MouseEvent evt)
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85 if(av.getWrapAlignment())
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88 doMouseReleased(evt);
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90 doMouseReleasedDefineMode(evt);
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93 public void mousePressed(MouseEvent evt)
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95 if(av.getWrapAlignment())
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97 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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99 if(evt.isAltDown() || evt.isControlDown())
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100 groupEditing = true;
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102 editingSeqs = true;
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103 doMousePressed(evt);
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106 doMousePressedDefineMode(evt);
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108 public void mouseExited(MouseEvent evt)
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110 if (av.getWrapAlignment() || editingSeqs)
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112 doMouseExitedDefineMode(evt);
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115 public void mouseEntered(MouseEvent evt)
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117 if (av.getWrapAlignment() || editingSeqs)
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119 doMouseEnteredDefineMode(evt);
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127 public void doMouseReleased(MouseEvent evt) {
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129 if(seqEditOccurred>-1)
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130 editOccurred(seqEditOccurred);
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134 seqEditOccurred = -1;
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135 editingSeqs = false;
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136 groupEditing = false;
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141 public void doMousePressed(MouseEvent evt) {
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143 ap.alignFrame.addHistoryItem( new HistoryItem(
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144 "Edit Sequence",av.alignment, HistoryItem.EDIT));
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149 int x = evt.getX();
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150 int y = evt.getY();
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152 res = x/av.getCharWidth() + av.getStartRes();
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153 seq = y/av.getCharHeight() + av.getStartSeq();
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155 if (seq < av.getAlignment().getHeight() &&
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156 res < av.getAlignment().getSequenceAt(seq).getLength())
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167 startEdit = lastres;
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173 public void doMouseMoved(MouseEvent evt)
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176 int x = evt.getX();
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177 int y = evt.getY();
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178 if(av.wrapAlignment)
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180 y -= 2*av.charHeight;
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181 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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184 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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187 seq = y / av.getCharHeight() + av.getStartSeq();
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192 res = x / av.getCharWidth() + av.getStartRes();
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193 seq = y / av.getCharHeight() + av.getStartSeq();
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197 if(seq>=av.getAlignment().getHeight())
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200 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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201 if(res>sequence.getLength())
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204 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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207 aa = obj.toString();
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209 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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211 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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213 ap.alignFrame.statusBar.setText(text.toString());
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215 // use aa to see if the mouse pointer is on a
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216 if( av.showSequenceFeatures)
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218 Vector features = sequence.getSequenceFeatures();
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219 Enumeration e = features.elements();
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220 StringBuffer sbuffer = new StringBuffer();
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223 while (e.hasMoreElements())
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225 SequenceFeature sf = (SequenceFeature) e.nextElement();
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226 if (sf.getStart() <= sequence.findPosition(res) &&
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227 sf.getEnd() >= sequence.findPosition(res))
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229 if(sbuffer.length()>0)
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230 sbuffer.append("; ");
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231 sbuffer.append(sf.getType() + " " + sf.getDescription());
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232 if(sf.getStatus().length()>0)
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233 sbuffer.append(" ("+sf.getStatus()+")");
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238 ToolTipManager.sharedInstance().registerComponent(this);
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239 this.setToolTipText(sbuffer.toString());
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245 public void doMouseDragged(MouseEvent evt) {
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247 // If we're dragging we're editing
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248 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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252 if (lastres == -1 || lastres == res)
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255 boolean dragRight = true;
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256 if (res < av.getAlignment().getWidth() && res < lastres)
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260 if (res != lastres)
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265 SequenceGroup sg = av.getSelectionGroup();
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274 sg.setEndRes(sg.getEndRes() + (res-lastres));
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279 /// Are we able to delete?
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280 // ie are all columns blank?
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281 boolean deleteAllowed = false;
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282 for (int s = 0; s < sg.getSize(); s++)
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284 SequenceI seq = sg.getSequenceAt(s);
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285 for (int j=res; j<lastres; j++)
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287 if(seq.getSequence().length()<=j)
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290 if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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292 // Not a gap, block edit not valid
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294 deleteAllowed = false;
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297 deleteAllowed = true;
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307 sg.setEndRes(sg.getEndRes() - (lastres-res));
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311 for (int i = 0; i < sg.getSize(); i++)
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313 SequenceI s = sg.getSequenceAt(i);
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314 int k = av.alignment.findIndex(s);
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318 for (int j = lastres; j < res; j++)
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324 for (int j = res; j < lastres; j++)
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326 if(s.getLength()>j)
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327 deleteChar(res, k);
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332 else /////Editing a single sequence///////////
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334 if (res < av.getAlignment().getWidth() && res > lastres)
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336 // dragging to the right
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337 for (int j = lastres; j < res; j++)
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338 insertChar(j, startseq);
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340 else if (res < av.getAlignment().getWidth() && res < lastres)
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342 // dragging to the left
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343 for (int j = lastres; j > res; j--)
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345 if( jalview.util.Comparison.isGap(
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346 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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348 deleteChar(res, startseq);
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365 public void drawChars(int seqstart, int seqend, int start) {
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366 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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370 public void insertChar(int j, int seq)
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372 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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373 seqEditOccurred=seq;
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376 public void deleteChar(int j, int seq)
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378 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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379 seqEditOccurred=seq;
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381 av.alignment.getWidth();
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386 void editOccurred(int i)
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388 if(endEdit==startEdit)
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390 ap.alignFrame.historyList.pop();
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391 ap.alignFrame.updateEditMenuBar();
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394 av.updateConservation();
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395 av.updateConsensus();
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398 ColourSchemeI cs = av.getGlobalColourScheme();
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399 if(cs instanceof ConservationColourScheme)
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401 ConservationColourScheme ccs = (ConservationColourScheme) cs;
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402 if(ccs.cs instanceof ClustalxColourScheme)
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404 Conservation c = new Conservation("All",
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405 ResidueProperties.propHash, 3,
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406 av.alignment.getSequences(), 0,
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407 av.alignment.getWidth() - 1);
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409 c.verdict(false, av.ConsPercGaps);
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411 ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
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412 cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());
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413 ccs = new ConservationColourScheme(c, cxs);
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414 av.setGlobalColourScheme(ccs);
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418 if(cs instanceof ClustalxColourScheme)
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420 ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
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421 av.alignment.getWidth());
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422 av.setGlobalColourScheme(cs);
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427 //////////////////////////////////////////
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428 /////Everything below this is for defining the boundary of the rubberband
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429 //////////////////////////////////////////
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431 public void doMousePressedDefineMode(MouseEvent evt)
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433 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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434 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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437 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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439 if(sequence==null || res>sequence.getLength())
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442 stretchGroup = av.getSelectionGroup();
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444 if(stretchGroup == null)
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446 stretchGroup = av.alignment.findGroup( sequence );
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447 if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
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448 av.setSelectionGroup(stretchGroup);
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450 stretchGroup = null;
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453 else if(!stretchGroup.sequences.contains(sequence)
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454 || stretchGroup.getStartRes()>res
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455 || stretchGroup.getEndRes()<res)
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457 stretchGroup = null;
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459 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
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461 if (allGroups != null)
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462 for (int i = 0; i < allGroups.length; i++)
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463 if (allGroups[i].getStartRes() <= res &&
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464 allGroups[i].getEndRes() >= res)
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466 stretchGroup = allGroups[i];
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467 av.setSelectionGroup(stretchGroup);
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472 if(stretchGroup==null)
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474 // define a new group here
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475 SequenceGroup sg = new SequenceGroup();
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476 sg.setStartRes(res);
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478 sg.addSequence( sequence );
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479 av.setSelectionGroup( sg );
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482 if(av.getConservationSelected())
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483 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
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484 if(av.getAbovePIDThreshold())
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485 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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488 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
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490 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
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491 pop.show(this, evt.getX(), evt.getY());
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493 // edit the properties of existing group
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496 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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497 // Edit end res position of selected group
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498 changeEndRes = true;
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500 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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501 // Edit end res position of selected group
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502 changeStartRes = true;
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504 stretchGroup.getWidth();
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510 boolean changeEndSeq = false;
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511 boolean changeStartSeq = false;
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512 boolean changeEndRes = false;
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513 boolean changeStartRes = false;
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514 SequenceGroup stretchGroup = null;
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516 public void doMouseReleasedDefineMode(MouseEvent evt)
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518 mouseDragging = false;
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520 if(stretchGroup==null)
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523 if(stretchGroup.cs instanceof ClustalxColourScheme)
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525 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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529 else if(stretchGroup.cs instanceof ConservationColourScheme)
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531 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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532 stretchGroup.cs = ccs;
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533 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
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538 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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541 changeEndRes = false;
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542 changeStartRes = false;
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543 stretchGroup = null;
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544 ap.idPanel.repaint();
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548 boolean remove = false;
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549 public void doMouseDraggedDefineMode(MouseEvent evt)
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551 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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552 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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554 if(stretchGroup==null)
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557 if(res>av.alignment.getWidth())
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558 res = av.alignment.getWidth()-1;
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561 if(stretchGroup.getEndRes()==res)
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562 // Edit end res position of selected group
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563 changeEndRes = true;
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565 else if(stretchGroup.getStartRes()==res)
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566 // Edit start res position of selected group
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567 changeStartRes = true;
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570 if(res<av.getStartRes())
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571 res = av.getStartRes();
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572 else if(res>av.getEndRes())
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573 res = av.getEndRes();
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577 if(res>stretchGroup.getStartRes()-1)
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578 stretchGroup.setEndRes( res );
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580 else if(changeStartRes)
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582 if(res<stretchGroup.getEndRes()+1)
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583 stretchGroup.setStartRes( res );
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586 int dragDirection = 0;
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589 else if (y < oldSeq)
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590 dragDirection = -1;
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592 while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
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594 // This routine ensures we don't skip any sequences, as the
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595 // selection is quite slow.
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596 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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598 oldSeq += dragDirection;
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599 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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601 if (stretchGroup.sequences.contains(nextSeq))
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603 stretchGroup.deleteSequence(seq);
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604 stretchGroup.deleteSequence(nextSeq);
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609 stretchGroup.addSequence(seq);
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610 stretchGroup.addSequence(nextSeq);
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614 mouseDragging = true;
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615 if(scrollThread!=null)
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616 scrollThread.setEvent(evt);
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621 public void doMouseEnteredDefineMode(MouseEvent e)
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623 if (scrollThread != null)
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624 scrollThread.running = false;
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627 public void doMouseExitedDefineMode(MouseEvent e)
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629 if (av.getWrapAlignment())
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633 scrollThread = new ScrollThread();
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636 // this class allows scrolling off the bottom of the visible alignment
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637 class ScrollThread extends Thread
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640 boolean running = false;
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641 public ScrollThread()
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646 public void setEvent(MouseEvent e)
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651 public void stopScrolling()
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664 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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665 running = ap.scrollUp(true);
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667 if (mouseDragging && evt.getY() >= getHeight() &&
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668 av.alignment.getHeight() > av.getEndSeq())
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669 running = ap.scrollUp(false);
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671 if (mouseDragging && evt.getX() < 0)
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672 running = ap.scrollRight(true);
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674 else if (mouseDragging && evt.getX() >= getWidth())
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675 running = ap.scrollRight(false);
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682 catch (Exception ex)
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