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.*;
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12 public class SeqPanel extends JPanel
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15 public SeqCanvas seqCanvas;
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16 public AlignmentPanel ap;
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18 protected int startres;
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19 protected int lastres;
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20 protected int endres;
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22 protected int startseq;
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23 protected int padseq;
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25 protected AlignViewport av;
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27 // if character is inserted or deleted, we will need to recalculate the conservation
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28 int seqEditOccurred = -1;
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30 ScrollThread scrollThread = null;
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31 boolean mouseDragging = 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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55 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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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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68 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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69 doMouseReleased(evt);
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71 doMouseReleasedDefineMode(evt);
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73 public void mousePressed(MouseEvent evt)
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75 if(av.getWrapAlignment())
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77 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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78 doMousePressed(evt);
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80 doMousePressedDefineMode(evt);
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82 public void mouseExited(MouseEvent evt)
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84 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
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85 evt.isControlDown())
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87 doMouseExitedDefineMode(evt);
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90 public void mouseEntered(MouseEvent evt)
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92 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
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93 evt.isControlDown())
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95 doMouseEnteredDefineMode(evt);
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103 public void doMouseReleased(MouseEvent evt) {
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105 int x = evt.getX();
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106 int res = x/av.getCharWidth() + av.getStartRes();
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113 if(seqEditOccurred>-1)
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114 updateConservation(seqEditOccurred);
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116 seqEditOccurred = -1;
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118 ap.RefreshPanels();
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123 public void doMousePressed(MouseEvent evt) {
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124 ap.alignFrame.addHistoryItem("sequence edit");
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128 int x = evt.getX();
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129 int y = evt.getY();
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131 res = x/av.getCharWidth() + av.getStartRes();
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132 seq = y/av.getCharHeight() + av.getStartSeq();
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134 if (seq < av.getAlignment().getHeight() &&
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135 res < av.getAlignment().getSequenceAt(seq).getLength())
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137 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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138 // Find the residue's position in the sequence (res is the position
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139 // in the alignment
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143 if (startseq == (av.getAlignment().getHeight() - 1))
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162 public void doMouseMoved(MouseEvent evt)
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165 int x = evt.getX();
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166 int y = evt.getY();
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167 if(av.wrapAlignment)
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169 y -= 2*av.charHeight;
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170 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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173 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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176 seq = y / av.getCharHeight() + av.getStartSeq();
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178 // chunkHeight = (da.getHeight() + 2)*charHeight;
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179 // startx += chunkWidth;
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183 res = x / av.getCharWidth() + av.getStartRes();
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184 seq = y / av.getCharHeight() + av.getStartSeq();
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188 if(seq>=av.getAlignment().getHeight())
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191 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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192 if(res>sequence.getLength())
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195 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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198 aa = obj.toString();
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200 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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202 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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204 ap.alignFrame.statusBar.setText(text.toString());
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206 // use aa to see if the mouse pointer is on a
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207 if( av.showSequenceFeatures)
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209 Vector features = sequence.getSequenceFeatures();
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210 Enumeration e = features.elements();
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211 StringBuffer sbuffer = new StringBuffer();
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214 while (e.hasMoreElements())
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216 SequenceFeature sf = (SequenceFeature) e.nextElement();
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217 if (sf.getStart() <= sequence.findPosition(res) &&
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218 sf.getEnd() >= sequence.findPosition(res))
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220 if(sbuffer.length()>0)
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221 sbuffer.append("; ");
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222 sbuffer.append(sf.getType() + " " + sf.getDescription());
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223 if(sf.getStatus().length()>0)
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224 sbuffer.append(" ("+sf.getStatus()+")");
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229 ToolTipManager.sharedInstance().registerComponent(this);
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230 this.setToolTipText(sbuffer.toString());
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236 public void doMouseDragged(MouseEvent evt) {
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237 // If we're dragging we're editing
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242 int x = evt.getX();
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244 int res = x/av.getCharWidth() + av.getStartRes();
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248 if (res != lastres)
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251 if (evt.isAltDown() || evt.isControlDown())
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253 SequenceGroup sg = av.getAlignment().findGroup(startseq);
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256 boolean deleteAllowed = false;
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257 if (res < av.getAlignment().getWidth() && res < lastres)
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259 /// Are we able to delete?
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260 boolean allGaps = true;
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261 for (int i = 0; i < sg.getSize(); i++)
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263 SequenceI s = sg.getSequenceAt(i);
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264 for (int j = lastres-1; j >= res && allGaps; j--)
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266 if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
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273 if(!deleteAllowed && allGaps)
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274 deleteAllowed = true;
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279 if (res < av.getAlignment().getWidth() && res > lastres)
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280 sg.setEndRes(sg.getEndRes() + 1);
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283 else if (deleteAllowed && res < av.getAlignment().getWidth() &&
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285 sg.setEndRes(sg.getEndRes() - 1);
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290 for (int i = 0; i < sg.getSize(); i++)
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292 SequenceI s = sg.getSequenceAt(i);
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293 int k = av.alignment.findIndex(s);
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296 if (res < av.getAlignment().getWidth() && res > lastres)
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297 for (int j = lastres; j < res; j++)
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301 else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
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303 for (int j = res; j < lastres; j++)
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312 else /////Editing a single sequence///////////
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314 if (res < av.getAlignment().getWidth() && res > lastres)
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316 // dragging to the right
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317 for (int j = lastres; j < res; j++)
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318 insertChar(j, startseq);
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320 else if (res < av.getAlignment().getWidth() && res < lastres)
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322 // dragging to the left
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323 for (int j = res; j < lastres; j++)
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325 deleteChar(j, startseq);
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338 public void drawChars(int seqstart, int seqend, int start) {
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339 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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343 public void insertChar(int j, int seq)
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345 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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346 seqEditOccurred=seq;
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349 public void deleteChar(int j, int seq)
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352 if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
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353 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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355 av.alignment.getWidth();
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357 seqEditOccurred=seq;
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361 void updateConservation(int i)
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363 /* Alignment al = (Alignment) av.getAlignment();
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364 SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
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365 if(sg==null || !(sg.cs instanceof ConservationColourScheme))
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368 Conservation c = sg.getConservation();
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370 c = new Conservation("All", al.cons,
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371 ResidueProperties.propHash, 3, sg.sequences, 0,
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374 c.verdict(false, 100);
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375 sg.setConservation(c);
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376 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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377 ccs.conserve = c;*/
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380 //////////////////////////////////////////
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381 /////Everything below this is for defining the boundary of the rubberband
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382 //////////////////////////////////////////
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384 public void doMousePressedDefineMode(MouseEvent evt)
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386 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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387 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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390 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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391 if(res>sequence.getLength())
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394 stretchGroup = av.getSelectionGroup();
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396 if(stretchGroup == null)
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398 stretchGroup = av.alignment.findGroup( sequence );
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399 av.setSelectionGroup( stretchGroup );
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402 else if(!stretchGroup.sequences.contains(sequence)
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403 || stretchGroup.getStartRes()>res
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404 || stretchGroup.getEndRes()<res)
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406 stretchGroup = null;
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408 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
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410 if (allGroups != null)
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411 for (int i = 0; i < allGroups.length; i++)
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412 if (allGroups[i].getStartRes() <= res &&
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413 allGroups[i].getEndRes() >= res)
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415 stretchGroup = allGroups[i];
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416 av.setSelectionGroup(stretchGroup);
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421 if(stretchGroup==null)
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423 // define a new group here
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424 SequenceGroup sg = new SequenceGroup();
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425 sg.setStartRes(res);
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427 sg.addSequence( sequence );
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428 av.setSelectionGroup( sg );
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431 if(av.getConservationSelected())
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432 Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
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433 else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
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435 ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
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436 int threshold = rcs.getThreshold();
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438 Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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442 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
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444 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
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445 pop.show(this, evt.getX(), evt.getY());
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447 // edit the properties of existing group
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450 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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451 // Edit end res position of selected group
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452 changeEndRes = true;
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454 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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455 // Edit end res position of selected group
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456 changeStartRes = true;
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459 seqCanvas.paintFlag = true;
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464 boolean changeEndSeq = false;
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465 boolean changeStartSeq = false;
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466 boolean changeEndRes = false;
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467 boolean changeStartRes = false;
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468 SequenceGroup stretchGroup = null;
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470 public void doMouseReleasedDefineMode(MouseEvent evt)
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472 mouseDragging = false;
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474 if(stretchGroup==null)
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477 if(stretchGroup.cs instanceof ClustalxColourScheme)
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479 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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480 seqCanvas.paintFlag = true;
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484 else if(stretchGroup.cs instanceof ConservationColourScheme)
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486 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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488 Conservation c = new Conservation("Group",
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489 ResidueProperties.propHash, 3, stretchGroup.sequences, 0,
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490 av.alignment.getWidth() );
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493 c.verdict(false, 100);
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494 ccs = new ConservationColourScheme(c, ccs.cs);
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496 stretchGroup.cs = ccs;
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499 Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
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501 seqCanvas.paintFlag = true;
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506 if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
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508 ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;
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509 int threshold = rcs.getThreshold();
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511 Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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517 changeEndRes = false;
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518 changeStartRes = false;
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519 stretchGroup = null;
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520 ap.idPanel.repaint();
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524 boolean remove = false;
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525 public void doMouseDraggedDefineMode(MouseEvent evt)
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527 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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528 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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530 if(stretchGroup==null)
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533 if(stretchGroup.getEndRes()==res)
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534 // Edit end res position of selected group
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535 changeEndRes = true;
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537 else if(stretchGroup.getStartRes()==res)
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538 // Edit start res position of selected group
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539 changeStartRes = true;
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542 if(res<av.getStartRes())
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543 res = av.getStartRes();
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544 else if(res>av.getEndRes())
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545 res = av.getEndRes();
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549 if(res>stretchGroup.getStartRes()-1)
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550 stretchGroup.setEndRes( res );
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552 else if(changeStartRes)
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554 if(res<stretchGroup.getEndRes()+1)
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555 stretchGroup.setStartRes( res );
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558 int dragDirection = 0;
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561 else if (y < oldSeq)
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562 dragDirection = -1;
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564 while (y != oldSeq && oldSeq>0)
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566 // This routine ensures we don't skip any sequences, as the
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567 // selection is quite slow.
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568 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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570 oldSeq += dragDirection;
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571 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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573 if (stretchGroup.sequences.contains(nextSeq))
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575 stretchGroup.deleteSequence(seq);
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576 stretchGroup.deleteSequence(nextSeq);
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580 stretchGroup.addSequence(seq);
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581 stretchGroup.addSequence(nextSeq);
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585 mouseDragging = true;
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586 if(scrollThread!=null)
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587 scrollThread.setEvent(evt);
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589 seqCanvas.paintFlag = true;
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593 public void doMouseEnteredDefineMode(MouseEvent e)
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595 if (scrollThread != null)
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596 scrollThread.running = false;
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599 public void doMouseExitedDefineMode(MouseEvent e)
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601 if (av.getWrapAlignment())
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605 scrollThread = new ScrollThread();
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608 // this class allows scrolling off the bottom of the visible alignment
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609 class ScrollThread extends Thread
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612 boolean running = false;
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613 public ScrollThread()
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618 public void setEvent(MouseEvent e)
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623 public void stopScrolling()
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636 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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637 running = ap.scrollUp(true);
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639 if (mouseDragging && evt.getY() >= getHeight() &&
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640 av.alignment.getHeight() > av.getEndSeq())
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641 running = ap.scrollUp(false);
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643 if (mouseDragging && evt.getX() < 0)
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644 running = ap.scrollRight(true);
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646 else if (mouseDragging && evt.getX() >= getWidth())
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647 running = ap.scrollRight(false);
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655 catch (Exception ex)
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