1 package jalview.appletgui;
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4 import java.awt.event.*;
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5 import jalview.datamodel.*;
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7 import jalview.schemes.*;
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10 public class SeqPanel extends Panel
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13 public SeqCanvas seqCanvas;
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14 public AlignmentPanel ap;
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16 protected int startres;
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17 protected int lastres;
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18 protected int endres;
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20 protected int startseq;
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21 protected int padseq;
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23 protected AlignViewport av;
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25 // if character is inserted or deleted, we will need to recalculate the conservation
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26 int seqEditOccurred = -1;
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28 ScrollThread scrollThread = null;
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29 boolean mouseDragging = false;
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32 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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35 seqCanvas = new SeqCanvas(avp);
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36 setLayout(new BorderLayout());
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41 seqCanvas.addMouseMotionListener( new MouseMotionAdapter()
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43 public void mouseMoved(MouseEvent evt)
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45 if(av.getWrapAlignment())
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47 doMouseMoved(evt); }
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49 public void mouseDragged(MouseEvent evt)
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51 if(av.getWrapAlignment())
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53 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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54 doMouseDragged(evt);
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56 doMouseDraggedDefineMode(evt);
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60 seqCanvas.addMouseListener( new MouseAdapter()
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62 public void mouseReleased(MouseEvent evt)
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64 if(av.getWrapAlignment())
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66 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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67 doMouseReleased(evt);
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69 doMouseReleasedDefineMode(evt);
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71 public void mousePressed(MouseEvent evt)
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73 if(av.getWrapAlignment())
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75 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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76 doMousePressed(evt);
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78 doMousePressedDefineMode(evt);
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80 public void mouseExited(MouseEvent evt)
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82 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
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83 evt.isControlDown())
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85 doMouseExitedDefineMode(evt);
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88 public void mouseEntered(MouseEvent evt)
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90 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
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91 evt.isControlDown())
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93 doMouseEnteredDefineMode(evt);
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97 seqCanvas.repaint();
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101 public void doMouseReleased(MouseEvent evt) {
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103 int x = evt.getX();
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104 int res = x/av.getCharWidth() + av.getStartRes();
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111 if(seqEditOccurred>-1)
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112 updateConservation(seqEditOccurred);
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114 seqEditOccurred = -1;
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120 public void doMousePressed(MouseEvent evt) {
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121 ap.alignFrame.addHistoryItem("sequence edit");
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125 int x = evt.getX();
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126 int y = evt.getY();
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128 res = x/av.getCharWidth() + av.getStartRes();
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129 seq = y/av.getCharHeight() + av.getStartSeq();
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131 if (seq < av.getAlignment().getHeight() &&
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132 res < av.getAlignment().getSequenceAt(seq).getLength())
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134 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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135 // Find the residue's position in the sequence (res is the position
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136 // in the alignment
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140 if (startseq == (av.getAlignment().getHeight() - 1))
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159 public void doMouseMoved(MouseEvent evt)
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162 int x = evt.getX();
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163 int y = evt.getY();
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164 if(av.wrapAlignment)
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166 y -= 2*av.charHeight;
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167 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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170 res = (int)((y/chunkHeight)*(getSize().width/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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173 seq = y / av.getCharHeight() + av.getStartSeq();
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178 res = x / av.getCharWidth() + av.getStartRes();
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179 seq = y / av.getCharHeight() + av.getStartSeq();
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183 if(seq>=av.getAlignment().getHeight())
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186 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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187 if(res>sequence.getLength())
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190 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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193 aa = obj.toString();
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195 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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197 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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199 ap.alignFrame.statusBar.setText(text.toString());
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201 // use aa to see if the mouse pointer is on a
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202 if( av.showSequenceFeatures)
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204 Vector features = sequence.getSequenceFeatures();
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205 Enumeration e = features.elements();
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206 StringBuffer sbuffer = new StringBuffer();
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209 while (e.hasMoreElements())
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211 SequenceFeature sf = (SequenceFeature) e.nextElement();
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212 if (sf.getStart() <= sequence.findPosition(res) &&
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213 sf.getEnd() >= sequence.findPosition(res))
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215 if(sbuffer.length()>0)
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216 sbuffer.append("; ");
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217 sbuffer.append(sf.getType() + " " + sf.getDescription());
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218 if(sf.getStatus().length()>0)
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219 sbuffer.append(" ("+sf.getStatus()+")");
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228 public void doMouseDragged(MouseEvent evt) {
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229 // If we're dragging we're editing
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234 int x = evt.getX();
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236 int res = x/av.getCharWidth() + av.getStartRes();
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240 if (res != lastres)
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243 if (evt.isAltDown() || evt.isControlDown())
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245 SequenceGroup sg = av.getSelectionGroup();
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247 av.getAlignment().findGroup(startseq);
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250 boolean deleteAllowed = false;
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251 if (res < av.getAlignment().getWidth() && res < lastres)
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253 /// Are we able to delete?
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254 boolean allGaps = true;
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255 for (int i = 0; i < sg.getSize(); i++)
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257 SequenceI s = sg.getSequenceAt(i);
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258 for (int j = lastres-1; j >= res && allGaps; j--)
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260 if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
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267 if(!deleteAllowed && allGaps)
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268 deleteAllowed = true;
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273 if (res < av.getAlignment().getWidth() && res > lastres)
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274 sg.setEndRes(sg.getEndRes() + 1);
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277 else if (deleteAllowed && res < av.getAlignment().getWidth() &&
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279 sg.setEndRes(sg.getEndRes() - 1);
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284 for (int i = 0; i < sg.getSize(); i++)
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286 SequenceI s = sg.getSequenceAt(i);
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287 int k = av.alignment.findIndex(s);
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290 if (res < av.getAlignment().getWidth() && res > lastres)
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291 for (int j = lastres; j < res; j++)
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295 else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
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297 for (int j = res; j < lastres; j++)
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306 else /////Editing a single sequence///////////
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308 if (res < av.getAlignment().getWidth() && res > lastres)
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310 // dragging to the right
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311 for (int j = lastres; j < res; j++)
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312 insertChar(j, startseq);
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314 else if (res < av.getAlignment().getWidth() && res < lastres)
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316 // dragging to the left
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317 for (int j = res; j < lastres; j++)
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319 deleteChar(j, startseq);
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329 seqCanvas.repaint();
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332 public void drawChars(int seqstart, int seqend, int start) {
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333 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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334 seqCanvas.repaint();
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337 public void insertChar(int j, int seq)
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339 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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340 seqEditOccurred=seq;
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343 public void deleteChar(int j, int seq)
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346 if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
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347 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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349 av.alignment.getWidth();
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350 seqCanvas.repaint();
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351 seqEditOccurred=seq;
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355 void updateConservation(int i)
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357 av.updateConservation();
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358 av.updateConsensus();
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360 ColourSchemeI cs = av.getGlobalColourScheme();
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361 if(cs instanceof ConservationColourScheme)
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362 cs = ( (ConservationColourScheme) cs).cs;
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364 if(cs instanceof ClustalxColourScheme)
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365 cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());
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367 ap.alignFrame.changeColour(cs);
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370 //////////////////////////////////////////
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371 /////Everything below this is for defining the boundary of the rubberband
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372 //////////////////////////////////////////
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374 public void doMousePressedDefineMode(MouseEvent evt)
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376 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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377 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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380 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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382 if(sequence==null || res>sequence.getLength())
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385 stretchGroup = av.getSelectionGroup();
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387 if(stretchGroup == null)
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389 stretchGroup = av.alignment.findGroup( sequence );
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390 if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
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391 av.setSelectionGroup(stretchGroup);
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393 stretchGroup = null;
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396 else if(!stretchGroup.sequences.contains(sequence)
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397 || stretchGroup.getStartRes()>res
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398 || stretchGroup.getEndRes()<res)
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400 stretchGroup = null;
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402 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
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404 if (allGroups != null)
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405 for (int i = 0; i < allGroups.length; i++)
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406 if (allGroups[i].getStartRes() <= res &&
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407 allGroups[i].getEndRes() >= res)
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409 stretchGroup = allGroups[i];
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410 av.setSelectionGroup(stretchGroup);
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415 if(stretchGroup==null)
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417 // define a new group here
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418 SequenceGroup sg = new SequenceGroup();
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419 sg.setStartRes(res);
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421 sg.addSequence( sequence );
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422 av.setSelectionGroup( sg );
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425 if(av.getConservationSelected())
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426 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
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427 if(av.getAbovePIDThreshold())
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428 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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432 // DETECT RIGHT MOUSE BUTTON IN AWT
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433 else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )
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435 APopupMenu popup = new APopupMenu(ap, null);
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437 popup.show(this, evt.getX(), evt.getY());
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441 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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442 // Edit end res position of selected group
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443 changeEndRes = true;
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445 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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446 // Edit end res position of selected group
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447 changeStartRes = true;
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451 boolean changeEndSeq = false;
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452 boolean changeStartSeq = false;
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453 boolean changeEndRes = false;
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454 boolean changeStartRes = false;
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455 SequenceGroup stretchGroup = null;
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457 public void doMouseReleasedDefineMode(MouseEvent evt)
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459 mouseDragging = false;
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461 if(stretchGroup==null)
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464 if(stretchGroup.cs instanceof ClustalxColourScheme)
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466 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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467 seqCanvas.repaint();
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470 else if(stretchGroup.cs instanceof ConservationColourScheme)
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472 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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473 stretchGroup.cs = ccs;
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474 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
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476 seqCanvas.repaint();
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480 if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
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482 ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;
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483 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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489 changeEndRes = false;
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490 changeStartRes = false;
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491 stretchGroup = null;
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496 boolean remove = false;
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497 public void doMouseDraggedDefineMode(MouseEvent evt)
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499 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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500 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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502 if(stretchGroup==null)
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505 if(res>av.alignment.getWidth())
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506 res = av.alignment.getWidth()-1;
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509 if(stretchGroup.getEndRes()==res)
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510 // Edit end res position of selected group
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511 changeEndRes = true;
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513 else if(stretchGroup.getStartRes()==res)
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514 // Edit start res position of selected group
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515 changeStartRes = true;
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518 if(res<av.getStartRes())
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519 res = av.getStartRes();
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520 else if(res>av.getEndRes())
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521 res = av.getEndRes();
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525 if(res>stretchGroup.getStartRes()-1)
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526 stretchGroup.setEndRes( res );
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528 else if(changeStartRes)
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530 if(res<stretchGroup.getEndRes()+1)
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531 stretchGroup.setStartRes( res );
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534 int dragDirection = 0;
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537 else if (y < oldSeq)
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538 dragDirection = -1;
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540 while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
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542 // This routine ensures we don't skip any sequences, as the
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543 // selection is quite slow.
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544 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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546 oldSeq += dragDirection;
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547 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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549 if (stretchGroup.sequences.contains(nextSeq))
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551 stretchGroup.deleteSequence(seq);
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552 stretchGroup.deleteSequence(nextSeq);
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557 stretchGroup.addSequence(seq);
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558 stretchGroup.addSequence(nextSeq);
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562 mouseDragging = true;
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563 if(scrollThread!=null)
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564 scrollThread.setEvent(evt);
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566 seqCanvas.repaint();
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569 public void doMouseEnteredDefineMode(MouseEvent e)
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571 if (scrollThread != null)
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572 scrollThread.running = false;
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575 public void doMouseExitedDefineMode(MouseEvent e)
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577 if (av.getWrapAlignment())
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581 scrollThread = new ScrollThread();
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584 // this class allows scrolling off the bottom of the visible alignment
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585 class ScrollThread extends Thread
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588 boolean running = false;
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589 public ScrollThread()
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594 public void setEvent(MouseEvent e)
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599 public void stopScrolling()
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612 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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613 running = ap.scrollUp(true);
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615 if (mouseDragging && evt.getY() >= getSize().height &&
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616 av.alignment.getHeight() > av.getEndSeq())
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617 running = ap.scrollUp(false);
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619 if (mouseDragging && evt.getX() < 0)
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620 running = ap.scrollRight(true);
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622 else if (mouseDragging && evt.getX() >= getSize().width)
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623 running = ap.scrollRight(false);
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630 catch (Exception ex)
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