4 import java.awt.event.*;
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5 import jalview.datamodel.*;
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6 import javax.swing.*;
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8 import jalview.schemes.*;
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9 import jalview.analysis.Conservation;
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11 public class SeqPanel extends JPanel
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14 public SeqCanvas seqCanvas;
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15 public AlignmentPanel ap;
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17 protected int lastres;
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18 protected int startseq;
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22 protected AlignViewport av;
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24 // if character is inserted or deleted, we will need to recalculate the conservation
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25 int seqEditOccurred = -1;
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27 ScrollThread scrollThread = null;
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28 boolean mouseDragging = false;
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30 boolean editingSeqs = false;
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31 boolean groupEditing = false;
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34 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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37 seqCanvas = new SeqCanvas(avp);
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38 setLayout(new BorderLayout());
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39 add(seqCanvas, BorderLayout.CENTER);
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43 addMouseMotionListener( new MouseMotionAdapter()
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45 public void mouseMoved(MouseEvent evt)
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47 if(av.getWrapAlignment())
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49 doMouseMoved(evt); }
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51 public void mouseDragged(MouseEvent evt)
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53 if(av.getWrapAlignment())
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56 doMouseDragged(evt);
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58 doMouseDraggedDefineMode(evt);
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62 addMouseListener( new MouseAdapter()
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64 public void mouseReleased(MouseEvent evt)
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66 if(av.getWrapAlignment())
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69 doMouseReleased(evt);
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71 doMouseReleasedDefineMode(evt);
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74 public void mousePressed(MouseEvent evt)
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76 if(av.getWrapAlignment())
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78 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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80 if(evt.isAltDown() || evt.isControlDown())
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81 groupEditing = true;
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84 doMousePressed(evt);
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87 doMousePressedDefineMode(evt);
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89 public void mouseExited(MouseEvent evt)
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91 if (av.getWrapAlignment() || editingSeqs)
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93 doMouseExitedDefineMode(evt);
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96 public void mouseEntered(MouseEvent evt)
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98 if (av.getWrapAlignment() || editingSeqs)
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100 doMouseEnteredDefineMode(evt);
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108 public void doMouseReleased(MouseEvent evt) {
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110 if(seqEditOccurred>-1)
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111 editOccurred(seqEditOccurred);
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115 seqEditOccurred = -1;
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116 editingSeqs = false;
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117 groupEditing = false;
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122 public void doMousePressed(MouseEvent evt) {
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124 ap.alignFrame.addHistoryItem( new HistoryItem(
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125 "Edit Sequence",av.alignment, HistoryItem.EDIT));
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130 int x = evt.getX();
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131 int y = evt.getY();
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133 res = x/av.getCharWidth() + av.getStartRes();
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134 seq = y/av.getCharHeight() + av.getStartSeq();
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136 if (seq < av.getAlignment().getHeight() &&
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137 res < av.getAlignment().getSequenceAt(seq).getLength())
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148 startEdit = lastres;
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154 public void doMouseMoved(MouseEvent evt)
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157 int x = evt.getX();
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158 int y = evt.getY();
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159 if(av.wrapAlignment)
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161 y -= 2*av.charHeight;
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162 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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165 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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168 seq = y / av.getCharHeight() + av.getStartSeq();
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173 res = x / av.getCharWidth() + av.getStartRes();
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174 seq = y / av.getCharHeight() + av.getStartSeq();
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178 if(seq>=av.getAlignment().getHeight())
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181 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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182 if(res>sequence.getLength())
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185 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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188 aa = obj.toString();
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190 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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192 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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194 ap.alignFrame.statusBar.setText(text.toString());
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196 // use aa to see if the mouse pointer is on a
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197 if( av.showSequenceFeatures)
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199 Vector features = sequence.getSequenceFeatures();
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200 Enumeration e = features.elements();
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201 StringBuffer sbuffer = new StringBuffer();
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204 while (e.hasMoreElements())
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206 SequenceFeature sf = (SequenceFeature) e.nextElement();
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207 if (sf.getStart() <= sequence.findPosition(res) &&
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208 sf.getEnd() >= sequence.findPosition(res))
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210 if(sbuffer.length()>0)
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211 sbuffer.append("; ");
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212 sbuffer.append(sf.getType() + " " + sf.getDescription());
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213 if(sf.getStatus().length()>0)
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214 sbuffer.append(" ("+sf.getStatus()+")");
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219 ToolTipManager.sharedInstance().registerComponent(this);
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220 this.setToolTipText(sbuffer.toString());
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226 public void doMouseDragged(MouseEvent evt) {
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228 // If we're dragging we're editing
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229 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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233 if (lastres == -1 || lastres == res)
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236 boolean dragRight = true;
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237 if (res < av.getAlignment().getWidth() && res < lastres)
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241 if (res != lastres)
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246 SequenceGroup sg = av.getSelectionGroup();
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255 sg.setEndRes(sg.getEndRes() + (res-lastres));
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260 /// Are we able to delete?
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261 // ie are all columns blank?
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262 boolean deleteAllowed = false;
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263 for (int s = 0; s < sg.getSize(); s++)
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265 SequenceI seq = sg.getSequenceAt(s);
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266 for (int j=res; j<lastres; j++)
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268 if(seq.getSequence().length()<=j)
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271 if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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273 // Not a gap, block edit not valid
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275 deleteAllowed = false;
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278 deleteAllowed = true;
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288 sg.setEndRes(sg.getEndRes() - (lastres-res));
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292 for (int i = 0; i < sg.getSize(); i++)
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294 SequenceI s = sg.getSequenceAt(i);
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295 int k = av.alignment.findIndex(s);
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299 for (int j = lastres; j < res; j++)
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305 for (int j = res; j < lastres; j++)
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307 if(s.getLength()>j)
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308 deleteChar(res, k);
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313 else /////Editing a single sequence///////////
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315 if (res < av.getAlignment().getWidth() && res > lastres)
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317 // dragging to the right
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318 for (int j = lastres; j < res; j++)
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319 insertChar(j, startseq);
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321 else if (res < av.getAlignment().getWidth() && res < lastres)
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323 // dragging to the left
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324 for (int j = lastres; j > res; j--)
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326 if( jalview.util.Comparison.isGap(
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327 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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329 deleteChar(res, startseq);
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346 public void drawChars(int seqstart, int seqend, int start) {
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347 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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351 public void insertChar(int j, int seq)
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353 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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354 seqEditOccurred=seq;
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357 public void deleteChar(int j, int seq)
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359 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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360 seqEditOccurred=seq;
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362 av.alignment.getWidth();
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367 void editOccurred(int i)
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369 if(endEdit==startEdit)
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371 ap.alignFrame.historyList.pop();
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372 ap.alignFrame.updateEditMenuBar();
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375 av.updateConservation();
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376 av.updateConsensus();
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379 ColourSchemeI cs = av.getGlobalColourScheme();
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380 if(cs instanceof ConservationColourScheme)
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382 ConservationColourScheme ccs = (ConservationColourScheme) cs;
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383 if(ccs.cs instanceof ClustalxColourScheme)
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385 Conservation c = new Conservation("All",
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386 ResidueProperties.propHash, 3,
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387 av.alignment.getSequences(), 0,
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388 av.alignment.getWidth() - 1);
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390 c.verdict(false, av.ConsPercGaps);
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392 ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
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393 cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());
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394 ccs = new ConservationColourScheme(c, cxs);
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395 av.setGlobalColourScheme(ccs);
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399 if(cs instanceof ClustalxColourScheme)
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401 ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
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402 av.alignment.getWidth());
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403 av.setGlobalColourScheme(cs);
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408 //////////////////////////////////////////
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409 /////Everything below this is for defining the boundary of the rubberband
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410 //////////////////////////////////////////
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412 public void doMousePressedDefineMode(MouseEvent evt)
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414 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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415 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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418 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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420 if(sequence==null || res>sequence.getLength())
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423 stretchGroup = av.getSelectionGroup();
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425 if(stretchGroup == null)
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427 stretchGroup = av.alignment.findGroup( sequence );
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428 if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
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429 av.setSelectionGroup(stretchGroup);
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431 stretchGroup = null;
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434 else if(!stretchGroup.sequences.contains(sequence)
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435 || stretchGroup.getStartRes()>res
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436 || stretchGroup.getEndRes()<res)
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438 stretchGroup = null;
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440 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
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442 if (allGroups != null)
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443 for (int i = 0; i < allGroups.length; i++)
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444 if (allGroups[i].getStartRes() <= res &&
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445 allGroups[i].getEndRes() >= res)
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447 stretchGroup = allGroups[i];
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448 av.setSelectionGroup(stretchGroup);
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453 if(stretchGroup==null)
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455 // define a new group here
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456 SequenceGroup sg = new SequenceGroup();
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457 sg.setStartRes(res);
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459 sg.addSequence( sequence );
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460 av.setSelectionGroup( sg );
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463 if(av.getConservationSelected())
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464 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
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465 if(av.getAbovePIDThreshold())
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466 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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469 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
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471 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
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472 pop.show(this, evt.getX(), evt.getY());
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474 // edit the properties of existing group
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477 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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478 // Edit end res position of selected group
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479 changeEndRes = true;
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481 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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482 // Edit end res position of selected group
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483 changeStartRes = true;
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485 stretchGroup.getWidth();
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491 boolean changeEndSeq = false;
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492 boolean changeStartSeq = false;
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493 boolean changeEndRes = false;
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494 boolean changeStartRes = false;
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495 SequenceGroup stretchGroup = null;
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497 public void doMouseReleasedDefineMode(MouseEvent evt)
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499 mouseDragging = false;
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501 if(stretchGroup==null)
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504 if(stretchGroup.cs instanceof ClustalxColourScheme)
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506 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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510 else if(stretchGroup.cs instanceof ConservationColourScheme)
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512 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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513 stretchGroup.cs = ccs;
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514 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
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519 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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522 changeEndRes = false;
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523 changeStartRes = false;
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524 stretchGroup = null;
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525 ap.idPanel.repaint();
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529 boolean remove = false;
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530 public void doMouseDraggedDefineMode(MouseEvent evt)
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532 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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533 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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535 if(stretchGroup==null)
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538 if(res>av.alignment.getWidth())
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539 res = av.alignment.getWidth()-1;
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542 if(stretchGroup.getEndRes()==res)
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543 // Edit end res position of selected group
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544 changeEndRes = true;
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546 else if(stretchGroup.getStartRes()==res)
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547 // Edit start res position of selected group
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548 changeStartRes = true;
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551 if(res<av.getStartRes())
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552 res = av.getStartRes();
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553 else if(res>av.getEndRes())
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554 res = av.getEndRes();
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558 if(res>stretchGroup.getStartRes()-1)
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559 stretchGroup.setEndRes( res );
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561 else if(changeStartRes)
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563 if(res<stretchGroup.getEndRes()+1)
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564 stretchGroup.setStartRes( res );
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567 int dragDirection = 0;
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570 else if (y < oldSeq)
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571 dragDirection = -1;
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573 while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
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575 // This routine ensures we don't skip any sequences, as the
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576 // selection is quite slow.
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577 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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579 oldSeq += dragDirection;
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580 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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582 if (stretchGroup.sequences.contains(nextSeq))
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584 stretchGroup.deleteSequence(seq);
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585 stretchGroup.deleteSequence(nextSeq);
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590 stretchGroup.addSequence(seq);
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591 stretchGroup.addSequence(nextSeq);
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595 mouseDragging = true;
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596 if(scrollThread!=null)
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597 scrollThread.setEvent(evt);
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602 public void doMouseEnteredDefineMode(MouseEvent e)
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604 if (scrollThread != null)
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605 scrollThread.running = false;
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608 public void doMouseExitedDefineMode(MouseEvent e)
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610 if (av.getWrapAlignment())
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614 scrollThread = new ScrollThread();
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617 // this class allows scrolling off the bottom of the visible alignment
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618 class ScrollThread extends Thread
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621 boolean running = false;
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622 public ScrollThread()
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627 public void setEvent(MouseEvent e)
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632 public void stopScrolling()
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645 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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646 running = ap.scrollUp(true);
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648 if (mouseDragging && evt.getY() >= getHeight() &&
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649 av.alignment.getHeight() > av.getEndSeq())
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650 running = ap.scrollUp(false);
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652 if (mouseDragging && evt.getX() < 0)
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653 running = ap.scrollRight(true);
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655 else if (mouseDragging && evt.getX() >= getWidth())
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656 running = ap.scrollRight(false);
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663 catch (Exception ex)
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