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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7 import jalview.schemes.*;
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8 import jalview.analysis.*;
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11 public class SeqPanel extends JPanel
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14 public SeqCanvas seqCanvas;
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15 public AlignmentPanel ap;
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17 protected int startres;
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18 protected int lastres;
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19 protected int endres;
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21 protected int startseq;
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22 protected int padseq;
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24 protected AlignViewport av;
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26 // if character is inserted or deleted, we will need to recalculate the conservation
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27 int seqEditOccurred = -1;
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29 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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32 seqCanvas = new SeqCanvas(avp);
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33 setLayout(new BorderLayout());
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34 add(seqCanvas, BorderLayout.CENTER);
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38 addMouseMotionListener( new MouseMotionAdapter()
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40 public void mouseMoved(MouseEvent evt)
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42 if(av.getWrapAlignment())
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44 doMouseMoved(evt); }
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46 public void mouseDragged(MouseEvent evt)
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48 if(av.getWrapAlignment())
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50 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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51 doMouseDragged(evt);
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53 doMouseDraggedDefineMode(evt);
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57 addMouseListener( new MouseAdapter()
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59 public void mouseReleased(MouseEvent evt)
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61 if(av.getWrapAlignment())
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63 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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64 doMouseReleased(evt);
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66 doMouseReleasedDefineMode(evt);
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68 public void mousePressed(MouseEvent evt)
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70 if(av.getWrapAlignment())
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72 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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73 doMousePressed(evt);
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75 doMousePressedDefineMode(evt);
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83 public void doMouseReleased(MouseEvent evt) {
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86 int res = x/av.getCharWidth() + av.getStartRes();
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93 if(seqEditOccurred>-1)
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94 updateConservation(seqEditOccurred);
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96 seqEditOccurred = -1;
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103 public void doMousePressed(MouseEvent evt) {
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104 ap.alignFrame.addHistoryItem("sequence edit");
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108 int x = evt.getX();
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109 int y = evt.getY();
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111 res = x/av.getCharWidth() + av.getStartRes();
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112 seq = y/av.getCharHeight() + av.getStartSeq();
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114 if (seq < av.getAlignment().getHeight() &&
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115 res < av.getAlignment().getSequenceAt(seq).getLength())
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117 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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118 // Find the residue's position in the sequence (res is the position
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119 // in the alignment
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123 if (startseq == (av.getAlignment().getHeight() - 1))
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142 public void doMouseMoved(MouseEvent evt)
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145 int x = evt.getX();
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146 int y = evt.getY();
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147 if(av.wrapAlignment)
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149 y -= 2*av.charHeight;
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150 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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153 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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156 seq = y / av.getCharHeight() + av.getStartSeq();
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158 // chunkHeight = (da.getHeight() + 2)*charHeight;
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159 // startx += chunkWidth;
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163 res = x / av.getCharWidth() + av.getStartRes();
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164 seq = y / av.getCharHeight() + av.getStartSeq();
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168 if(seq>=av.getAlignment().getHeight())
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171 Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;
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174 aa = obj.toString();
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176 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
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178 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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180 ap.alignFrame.statusBar.setText(text.toString());
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184 public void doMouseDragged(MouseEvent evt) {
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185 // If we're dragging we're editing
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187 int x = evt.getX();
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189 int res = x/av.getCharWidth() + av.getStartRes();
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193 if (res != lastres)
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196 if (evt.isAltDown() || evt.isControlDown())
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198 SequenceGroup sg = av.getAlignment().findGroup(startseq);
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201 boolean deleteAllowed = false;
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202 if (res < av.getAlignment().getWidth() && res < lastres)
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204 /// Are we able to delete?
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205 boolean allGaps = true;
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206 for (int i = 0; i < sg.getSize(); i++)
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208 SequenceI s = sg.getSequenceAt(i);
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209 for (int j = lastres-1; j >= res && allGaps; j--)
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211 if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
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218 if(!deleteAllowed && allGaps)
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219 deleteAllowed = true;
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224 if (res < av.getAlignment().getWidth() && res > lastres)
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225 sg.setEndRes(sg.getEndRes() + 1);
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228 else if (deleteAllowed && res < av.getAlignment().getWidth() &&
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230 sg.setEndRes(sg.getEndRes() - 1);
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235 for (int i = 0; i < sg.getSize(); i++)
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237 SequenceI s = sg.getSequenceAt(i);
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238 int k = av.alignment.findIndex(s);
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241 if (res < av.getAlignment().getWidth() && res > lastres)
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242 for (int j = lastres; j < res; j++)
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246 else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
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248 for (int j = res; j < lastres; j++)
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257 else /////Editing a single sequence///////////
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259 if (res < av.getAlignment().getWidth() && res > lastres)
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261 // dragging to the right
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262 for (int j = lastres; j < res; j++)
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263 insertChar(j, startseq);
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265 else if (res < av.getAlignment().getWidth() && res < lastres)
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267 // dragging to the left
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268 for (int j = res; j < lastres; j++)
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270 deleteChar(j, startseq);
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283 public void drawChars(int seqstart, int seqend, int start) {
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284 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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288 public void insertChar(int j, int seq)
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290 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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291 seqEditOccurred=seq;
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294 public void deleteChar(int j, int seq)
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297 if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
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298 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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300 av.alignment.getWidth();
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302 seqEditOccurred=seq;
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306 void updateConservation(int i)
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308 /* Alignment al = (Alignment) av.getAlignment();
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309 SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
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310 if(sg==null || !(sg.cs instanceof ConservationColourScheme))
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313 Conservation c = sg.getConservation();
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315 c = new Conservation("All", al.cons,
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316 ResidueProperties.propHash, 3, sg.sequences, 0,
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319 c.verdict(false, 100);
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320 sg.setConservation(c);
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321 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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322 ccs.conserve = c;*/
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325 //////////////////////////////////////////
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326 /////Everything below this is for defining the boundary of the rubberband
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327 //////////////////////////////////////////
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329 public void doMousePressedDefineMode(MouseEvent evt)
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331 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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332 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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335 stretchGroup = av.getRubberbandGroup();
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337 if(stretchGroup == null)
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339 stretchGroup = av.alignment.findGroup( (Sequence) av.getAlignment().
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340 getSequenceAt(seq));
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341 av.setRubberbandGroup( stretchGroup );
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344 else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
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345 || stretchGroup.getStartRes()>res
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346 || stretchGroup.getEndRes()<res)
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348 stretchGroup = null;
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350 SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.
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352 getSequenceAt(seq));
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354 if (allGroups != null)
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355 for (int i = 0; i < allGroups.length; i++)
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356 if (allGroups[i].getStartRes() <= res &&
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357 allGroups[i].getEndRes() >= res)
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359 stretchGroup = allGroups[i];
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360 av.setRubberbandGroup(stretchGroup);
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365 if(stretchGroup==null)
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367 // define a new group here
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368 SequenceGroup sg = new SequenceGroup();
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369 sg.setStartRes(res);
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371 sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
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372 av.setRubberbandGroup( sg );
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375 if(av.getConservationSelected())
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376 Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
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377 else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
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379 ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
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380 int threshold = rcs.getThreshold();
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382 Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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386 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
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388 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
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389 pop.show(this, evt.getX(), evt.getY());
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391 // edit the properties of existing group
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394 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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395 // Edit end res position of selected group
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396 changeEndRes = true;
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398 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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399 // Edit end res position of selected group
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400 changeStartRes = true;
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403 seqCanvas.paintFlag = true;
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408 boolean changeEndSeq = false;
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409 boolean changeStartSeq = false;
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410 boolean changeEndRes = false;
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411 boolean changeStartRes = false;
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412 SequenceGroup stretchGroup = null;
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414 public void doMouseReleasedDefineMode(MouseEvent evt)
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417 if(stretchGroup.cs instanceof ClustalxColourScheme)
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419 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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420 seqCanvas.paintFlag = true;
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424 else if(stretchGroup.cs instanceof ConservationColourScheme)
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426 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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428 Conservation c = new Conservation("Group",
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429 ResidueProperties.propHash, 3, stretchGroup.sequences, 0,
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430 av.alignment.getWidth() );
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433 c.verdict(false, 100);
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434 ccs = new ConservationColourScheme(c, ccs.cs);
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436 stretchGroup.cs = ccs;
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439 Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
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441 seqCanvas.paintFlag = true;
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446 if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
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448 ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;
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449 int threshold = rcs.getThreshold();
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451 Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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457 changeEndRes = false;
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458 changeStartRes = false;
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459 stretchGroup = null;
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463 boolean remove = false;
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464 public void doMouseDraggedDefineMode(MouseEvent evt)
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466 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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467 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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470 if(stretchGroup.getEndRes()==res)
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471 // Edit end res position of selected group
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472 changeEndRes = true;
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474 else if(stretchGroup.getStartRes()==res)
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475 // Edit start res position of selected group
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476 changeStartRes = true;
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479 if(res<av.getStartRes())
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480 res = av.getStartRes();
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481 else if(res>av.getEndRes())
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482 res = av.getEndRes();
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486 if(res>stretchGroup.getStartRes()-1)
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487 stretchGroup.setEndRes( res );
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489 else if(changeStartRes)
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491 if(res<stretchGroup.getEndRes()+1)
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492 stretchGroup.setStartRes( res );
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496 int dragDirection = 0;
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499 else if (y < oldSeq)
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500 dragDirection = -1;
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502 while (y != oldSeq)
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504 // This routine ensures we don't skip any sequences, as the
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505 // selection is quite slow.
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506 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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508 oldSeq += dragDirection;
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509 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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511 if (stretchGroup.sequences.contains(nextSeq))
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513 stretchGroup.deleteSequence(seq);
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514 stretchGroup.deleteSequence(nextSeq);
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518 stretchGroup.addSequence(seq);
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519 stretchGroup.addSequence(nextSeq);
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524 seqCanvas.paintFlag = true;
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