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 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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33 seqCanvas = new SeqCanvas(avp);
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34 setLayout(new BorderLayout());
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35 add(seqCanvas, BorderLayout.CENTER);
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39 addMouseMotionListener( new MouseMotionAdapter()
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41 public void mouseMoved(MouseEvent evt)
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43 if(av.getWrapAlignment())
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45 doMouseMoved(evt); }
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47 public void mouseDragged(MouseEvent evt)
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49 if(av.getWrapAlignment())
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51 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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52 doMouseDragged(evt);
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54 doMouseDraggedDefineMode(evt);
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58 addMouseListener( new MouseAdapter()
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60 public void mouseReleased(MouseEvent evt)
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62 if(av.getWrapAlignment())
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64 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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65 doMouseReleased(evt);
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67 doMouseReleasedDefineMode(evt);
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69 public void mousePressed(MouseEvent evt)
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71 if(av.getWrapAlignment())
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73 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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74 doMousePressed(evt);
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76 doMousePressedDefineMode(evt);
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84 public void doMouseReleased(MouseEvent evt) {
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87 int res = x/av.getCharWidth() + av.getStartRes();
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94 if(seqEditOccurred>-1)
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95 updateConservation(seqEditOccurred);
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97 seqEditOccurred = -1;
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104 public void doMousePressed(MouseEvent evt) {
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105 ap.alignFrame.addHistoryItem("sequence edit");
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109 int x = evt.getX();
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110 int y = evt.getY();
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112 res = x/av.getCharWidth() + av.getStartRes();
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113 seq = y/av.getCharHeight() + av.getStartSeq();
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115 if (seq < av.getAlignment().getHeight() &&
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116 res < av.getAlignment().getSequenceAt(seq).getLength())
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118 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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119 // Find the residue's position in the sequence (res is the position
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120 // in the alignment
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124 if (startseq == (av.getAlignment().getHeight() - 1))
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143 public void doMouseMoved(MouseEvent evt)
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146 int x = evt.getX();
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147 int y = evt.getY();
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148 if(av.wrapAlignment)
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150 y -= 2*av.charHeight;
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151 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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154 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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157 seq = y / av.getCharHeight() + av.getStartSeq();
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159 // chunkHeight = (da.getHeight() + 2)*charHeight;
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160 // startx += chunkWidth;
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164 res = x / av.getCharWidth() + av.getStartRes();
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165 seq = y / av.getCharHeight() + av.getStartSeq();
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169 if(seq>=av.getAlignment().getHeight())
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172 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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173 if(res>sequence.getLength())
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176 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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179 aa = obj.toString();
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181 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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183 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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185 ap.alignFrame.statusBar.setText(text.toString());
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187 // use aa to see if the mouse pointer is on a
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188 if( av.showSequenceFeatures)
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190 Vector features = sequence.getSequenceFeatures();
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191 Enumeration e = features.elements();
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192 StringBuffer sbuffer = new StringBuffer();
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195 while (e.hasMoreElements())
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197 SequenceFeature sf = (SequenceFeature) e.nextElement();
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198 if (sf.getStart() <= sequence.findPosition(res) &&
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199 sf.getEnd() >= sequence.findPosition(res))
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201 if(sbuffer.length()>0)
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202 sbuffer.append("; ");
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203 sbuffer.append(sf.getType() + " " + sf.getDescription());
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204 if(sf.getStatus().length()>0)
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205 sbuffer.append(" ("+sf.getStatus()+")");
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210 ToolTipManager.sharedInstance().registerComponent(this);
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211 this.setToolTipText(sbuffer.toString());
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217 public void doMouseDragged(MouseEvent evt) {
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218 // If we're dragging we're editing
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223 int x = evt.getX();
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225 int res = x/av.getCharWidth() + av.getStartRes();
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229 if (res != lastres)
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232 if (evt.isAltDown() || evt.isControlDown())
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234 SequenceGroup sg = av.getAlignment().findGroup(startseq);
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237 boolean deleteAllowed = false;
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238 if (res < av.getAlignment().getWidth() && res < lastres)
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240 /// Are we able to delete?
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241 boolean allGaps = true;
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242 for (int i = 0; i < sg.getSize(); i++)
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244 SequenceI s = sg.getSequenceAt(i);
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245 for (int j = lastres-1; j >= res && allGaps; j--)
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247 if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
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254 if(!deleteAllowed && allGaps)
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255 deleteAllowed = true;
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260 if (res < av.getAlignment().getWidth() && res > lastres)
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261 sg.setEndRes(sg.getEndRes() + 1);
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264 else if (deleteAllowed && res < av.getAlignment().getWidth() &&
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266 sg.setEndRes(sg.getEndRes() - 1);
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271 for (int i = 0; i < sg.getSize(); i++)
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273 SequenceI s = sg.getSequenceAt(i);
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274 int k = av.alignment.findIndex(s);
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277 if (res < av.getAlignment().getWidth() && res > lastres)
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278 for (int j = lastres; j < res; j++)
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282 else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
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284 for (int j = res; j < lastres; j++)
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293 else /////Editing a single sequence///////////
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295 if (res < av.getAlignment().getWidth() && res > lastres)
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297 // dragging to the right
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298 for (int j = lastres; j < res; j++)
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299 insertChar(j, startseq);
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301 else if (res < av.getAlignment().getWidth() && res < lastres)
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303 // dragging to the left
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304 for (int j = res; j < lastres; j++)
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306 deleteChar(j, startseq);
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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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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 /* Alignment al = (Alignment) av.getAlignment();
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345 SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
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346 if(sg==null || !(sg.cs instanceof ConservationColourScheme))
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349 Conservation c = sg.getConservation();
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351 c = new Conservation("All", al.cons,
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352 ResidueProperties.propHash, 3, sg.sequences, 0,
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355 c.verdict(false, 100);
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356 sg.setConservation(c);
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357 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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358 ccs.conserve = c;*/
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361 //////////////////////////////////////////
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362 /////Everything below this is for defining the boundary of the rubberband
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363 //////////////////////////////////////////
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365 public void doMousePressedDefineMode(MouseEvent evt)
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367 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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368 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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371 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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372 if(res>sequence.getLength())
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375 stretchGroup = av.getRubberbandGroup();
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377 if(stretchGroup == null)
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379 stretchGroup = av.alignment.findGroup( sequence );
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380 av.setRubberbandGroup( stretchGroup );
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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.setRubberbandGroup(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.setRubberbandGroup( sg );
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412 if(av.getConservationSelected())
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413 Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
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414 else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
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416 ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
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417 int threshold = rcs.getThreshold();
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419 Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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423 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
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425 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
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426 pop.show(this, evt.getX(), evt.getY());
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428 // edit the properties of existing group
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431 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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432 // Edit end res position of selected group
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433 changeEndRes = true;
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435 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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436 // Edit end res position of selected group
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437 changeStartRes = true;
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440 seqCanvas.paintFlag = true;
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445 boolean changeEndSeq = false;
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446 boolean changeStartSeq = false;
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447 boolean changeEndRes = false;
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448 boolean changeStartRes = false;
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449 SequenceGroup stretchGroup = null;
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451 public void doMouseReleasedDefineMode(MouseEvent evt)
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453 if(stretchGroup==null)
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456 if(stretchGroup.cs instanceof ClustalxColourScheme)
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458 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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459 seqCanvas.paintFlag = true;
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463 else if(stretchGroup.cs instanceof ConservationColourScheme)
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465 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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467 Conservation c = new Conservation("Group",
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468 ResidueProperties.propHash, 3, stretchGroup.sequences, 0,
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469 av.alignment.getWidth() );
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472 c.verdict(false, 100);
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473 ccs = new ConservationColourScheme(c, ccs.cs);
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475 stretchGroup.cs = ccs;
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478 Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
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480 seqCanvas.paintFlag = true;
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485 if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
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487 ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;
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488 int threshold = rcs.getThreshold();
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490 Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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496 changeEndRes = false;
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497 changeStartRes = false;
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498 stretchGroup = null;
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502 boolean remove = false;
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503 public void doMouseDraggedDefineMode(MouseEvent evt)
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505 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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506 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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508 if(stretchGroup==null)
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511 if(stretchGroup.getEndRes()==res)
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512 // Edit end res position of selected group
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513 changeEndRes = true;
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515 else if(stretchGroup.getStartRes()==res)
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516 // Edit start res position of selected group
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517 changeStartRes = true;
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520 if(res<av.getStartRes())
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521 res = av.getStartRes();
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522 else if(res>av.getEndRes())
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523 res = av.getEndRes();
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527 if(res>stretchGroup.getStartRes()-1)
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528 stretchGroup.setEndRes( res );
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530 else if(changeStartRes)
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532 if(res<stretchGroup.getEndRes()+1)
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533 stretchGroup.setStartRes( res );
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537 int dragDirection = 0;
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540 else if (y < oldSeq)
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541 dragDirection = -1;
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543 while (y != oldSeq)
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545 // This routine ensures we don't skip any sequences, as the
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546 // selection is quite slow.
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547 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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549 oldSeq += dragDirection;
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550 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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552 if (stretchGroup.sequences.contains(nextSeq))
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554 stretchGroup.deleteSequence(seq);
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555 stretchGroup.deleteSequence(nextSeq);
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559 stretchGroup.addSequence(seq);
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560 stretchGroup.addSequence(nextSeq);
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565 seqCanvas.paintFlag = true;
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