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 lastres;
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17 protected int startseq;
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19 protected AlignViewport av;
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21 // if character is inserted or deleted, we will need to recalculate the conservation
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22 int seqEditOccurred = -1;
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24 ScrollThread scrollThread = null;
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25 boolean mouseDragging = false;
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28 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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31 seqCanvas = new SeqCanvas(avp);
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32 setLayout(new BorderLayout());
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37 seqCanvas.addMouseMotionListener( new MouseMotionAdapter()
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39 public void mouseMoved(MouseEvent evt)
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41 if(av.getWrapAlignment())
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43 doMouseMoved(evt); }
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45 public void mouseDragged(MouseEvent evt)
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47 if(av.getWrapAlignment())
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49 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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50 doMouseDragged(evt);
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52 doMouseDraggedDefineMode(evt);
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56 seqCanvas.addMouseListener( new MouseAdapter()
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58 public void mouseReleased(MouseEvent evt)
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60 if(av.getWrapAlignment())
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62 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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63 doMouseReleased(evt);
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65 doMouseReleasedDefineMode(evt);
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67 public void mousePressed(MouseEvent evt)
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69 if(av.getWrapAlignment())
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71 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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72 doMousePressed(evt);
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74 doMousePressedDefineMode(evt);
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76 public void mouseExited(MouseEvent evt)
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78 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
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79 evt.isControlDown())
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81 doMouseExitedDefineMode(evt);
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84 public void mouseEntered(MouseEvent evt)
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86 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
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87 evt.isControlDown())
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89 doMouseEnteredDefineMode(evt);
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93 seqCanvas.repaint();
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97 public void doMouseReleased(MouseEvent evt) {
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101 if(seqEditOccurred>-1)
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102 updateConservation(seqEditOccurred);
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104 seqEditOccurred = -1;
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109 public void doMousePressed(MouseEvent evt) {
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110 ap.alignFrame.addHistoryItem("sequence edit");
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114 int x = evt.getX();
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115 int y = evt.getY();
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117 res = x/av.getCharWidth() + av.getStartRes();
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118 seq = y/av.getCharHeight() + av.getStartSeq();
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120 if (seq < av.getAlignment().getHeight() &&
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121 res < av.getAlignment().getSequenceAt(seq).getLength())
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123 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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124 // Find the residue's position in the sequence (res is the position
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125 // in the alignment
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139 public void doMouseMoved(MouseEvent evt)
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142 int x = evt.getX();
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143 int y = evt.getY();
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144 if(av.wrapAlignment)
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146 y -= 2*av.charHeight;
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147 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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150 res = (int)((y/chunkHeight)*(getSize().width/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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153 seq = y / av.getCharHeight() + av.getStartSeq();
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158 res = x / av.getCharWidth() + av.getStartRes();
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159 seq = y / av.getCharHeight() + av.getStartSeq();
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163 if(seq>=av.getAlignment().getHeight())
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166 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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167 if(res>sequence.getLength())
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170 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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173 aa = obj.toString();
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175 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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177 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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179 ap.alignFrame.statusBar.setText(text.toString());
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181 // use aa to see if the mouse pointer is on a
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182 if( av.showSequenceFeatures)
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184 Vector features = sequence.getSequenceFeatures();
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185 Enumeration e = features.elements();
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186 StringBuffer sbuffer = new StringBuffer();
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189 while (e.hasMoreElements())
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191 SequenceFeature sf = (SequenceFeature) e.nextElement();
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192 if (sf.getStart() <= sequence.findPosition(res) &&
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193 sf.getEnd() >= sequence.findPosition(res))
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195 if(sbuffer.length()>0)
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196 sbuffer.append("; ");
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197 sbuffer.append(sf.getType() + " " + sf.getDescription());
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198 if(sf.getStatus().length()>0)
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199 sbuffer.append(" ("+sf.getStatus()+")");
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208 public void doMouseDragged(MouseEvent evt) {
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210 // If we're dragging we're editing
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211 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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215 if (lastres == -1 || lastres == res)
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218 boolean dragRight = true;
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219 if (res < av.getAlignment().getWidth() && res < lastres)
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223 if (res != lastres)
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226 if (evt.isAltDown() || evt.isControlDown())
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228 SequenceGroup sg = av.getSelectionGroup();
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237 sg.setEndRes(sg.getEndRes() + (res-lastres));
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242 /// Are we able to delete?
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243 // ie are all columns blank?
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244 boolean deleteAllowed = false;
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245 for (int s = 0; s < sg.getSize(); s++)
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247 SequenceI seq = sg.getSequenceAt(s);
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248 for (int j=res; j<lastres; j++)
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250 if(seq.getSequence().length()<=j)
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253 if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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255 // Not a gap, block edit not valid
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257 deleteAllowed = false;
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260 deleteAllowed = true;
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270 sg.setEndRes(sg.getEndRes() - (lastres-res));
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274 for (int i = 0; i < sg.getSize(); i++)
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276 SequenceI s = sg.getSequenceAt(i);
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277 int k = av.alignment.findIndex(s);
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281 for (int j = lastres; j < res; j++)
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287 for (int j = res; j < lastres; j++)
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289 if(s.getLength()>j)
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290 deleteChar(res, k);
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295 else /////Editing a single sequence///////////
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297 if (res < av.getAlignment().getWidth() && res > lastres)
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299 // dragging to the right
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300 for (int j = lastres; j < res; j++)
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301 insertChar(j, startseq);
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303 else if (res < av.getAlignment().getWidth() && res < lastres)
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305 // dragging to the left
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306 for (int j = lastres; j > res; j--)
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308 deleteChar(res, startseq);
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316 seqCanvas.repaint();
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319 public void drawChars(int seqstart, int seqend, int start) {
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320 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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321 seqCanvas.repaint();
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324 public void insertChar(int j, int seq)
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326 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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327 seqEditOccurred=seq;
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330 public void deleteChar(int j, int seq)
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333 if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
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334 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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336 av.alignment.getWidth();
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338 seqEditOccurred=seq;
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342 void updateConservation(int i)
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344 av.updateConservation();
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345 av.updateConsensus();
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347 ColourSchemeI cs = av.getGlobalColourScheme();
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348 if(cs instanceof ConservationColourScheme)
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349 cs = ( (ConservationColourScheme) cs).cs;
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351 if(cs instanceof ClustalxColourScheme)
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352 cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());
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354 ap.alignFrame.changeColour(cs);
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357 //////////////////////////////////////////
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358 /////Everything below this is for defining the boundary of the rubberband
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359 //////////////////////////////////////////
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361 public void doMousePressedDefineMode(MouseEvent evt)
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363 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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364 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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367 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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369 if(sequence==null || res>sequence.getLength())
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372 stretchGroup = av.getSelectionGroup();
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374 if(stretchGroup == null)
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376 stretchGroup = av.alignment.findGroup( sequence );
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377 if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
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378 av.setSelectionGroup(stretchGroup);
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380 stretchGroup = null;
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383 else if(!stretchGroup.sequences.contains(sequence)
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384 || stretchGroup.getStartRes()>res
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385 || stretchGroup.getEndRes()<res)
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387 stretchGroup = null;
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389 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
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391 if (allGroups != null)
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392 for (int i = 0; i < allGroups.length; i++)
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393 if (allGroups[i].getStartRes() <= res &&
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394 allGroups[i].getEndRes() >= res)
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396 stretchGroup = allGroups[i];
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397 av.setSelectionGroup(stretchGroup);
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402 if(stretchGroup==null)
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404 // define a new group here
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405 SequenceGroup sg = new SequenceGroup();
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406 sg.setStartRes(res);
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408 sg.addSequence( sequence );
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409 av.setSelectionGroup( sg );
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412 if(av.getConservationSelected())
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413 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
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414 if(av.getAbovePIDThreshold())
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415 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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419 // DETECT RIGHT MOUSE BUTTON IN AWT
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420 else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )
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422 APopupMenu popup = new APopupMenu(ap, null);
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424 popup.show(this, evt.getX(), evt.getY());
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428 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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429 // Edit end res position of selected group
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430 changeEndRes = true;
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432 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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433 // Edit end res position of selected group
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434 changeStartRes = true;
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438 boolean changeEndSeq = false;
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439 boolean changeStartSeq = false;
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440 boolean changeEndRes = false;
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441 boolean changeStartRes = false;
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442 SequenceGroup stretchGroup = null;
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444 public void doMouseReleasedDefineMode(MouseEvent evt)
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446 mouseDragging = false;
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448 if(stretchGroup==null)
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451 if(stretchGroup.cs instanceof ClustalxColourScheme)
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453 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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454 seqCanvas.repaint();
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457 else if(stretchGroup.cs instanceof ConservationColourScheme)
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459 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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460 stretchGroup.cs = ccs;
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461 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
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463 seqCanvas.repaint();
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467 if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
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469 ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;
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470 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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476 changeEndRes = false;
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477 changeStartRes = false;
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478 stretchGroup = null;
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483 boolean remove = false;
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484 public void doMouseDraggedDefineMode(MouseEvent evt)
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486 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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487 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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489 if(stretchGroup==null)
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492 if(res>av.alignment.getWidth())
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493 res = av.alignment.getWidth()-1;
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496 if(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.getStartRes()==res)
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501 // Edit start res position of selected group
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502 changeStartRes = true;
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505 if(res<av.getStartRes())
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506 res = av.getStartRes();
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507 else if(res>av.getEndRes())
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508 res = av.getEndRes();
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512 if(res>stretchGroup.getStartRes()-1)
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513 stretchGroup.setEndRes( res );
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515 else if(changeStartRes)
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517 if(res<stretchGroup.getEndRes()+1)
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518 stretchGroup.setStartRes( res );
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521 int dragDirection = 0;
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524 else if (y < oldSeq)
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525 dragDirection = -1;
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527 while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
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529 // This routine ensures we don't skip any sequences, as the
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530 // selection is quite slow.
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531 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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533 oldSeq += dragDirection;
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534 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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536 if (stretchGroup.sequences.contains(nextSeq))
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538 stretchGroup.deleteSequence(seq);
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539 stretchGroup.deleteSequence(nextSeq);
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544 stretchGroup.addSequence(seq);
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545 stretchGroup.addSequence(nextSeq);
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549 mouseDragging = true;
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550 if(scrollThread!=null)
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551 scrollThread.setEvent(evt);
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553 seqCanvas.repaint();
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556 public void doMouseEnteredDefineMode(MouseEvent e)
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558 if (scrollThread != null)
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559 scrollThread.running = false;
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562 public void doMouseExitedDefineMode(MouseEvent e)
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564 if (av.getWrapAlignment())
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568 scrollThread = new ScrollThread();
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571 // this class allows scrolling off the bottom of the visible alignment
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572 class ScrollThread extends Thread
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575 boolean running = false;
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576 public ScrollThread()
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581 public void setEvent(MouseEvent e)
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586 public void stopScrolling()
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599 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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600 running = ap.scrollUp(true);
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602 if (mouseDragging && evt.getY() >= getSize().height &&
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603 av.alignment.getHeight() > av.getEndSeq())
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604 running = ap.scrollUp(false);
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606 if (mouseDragging && evt.getX() < 0)
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607 running = ap.scrollRight(true);
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609 else if (mouseDragging && evt.getX() >= getSize().width)
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610 running = ap.scrollRight(false);
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617 catch (Exception ex)
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