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 parent;
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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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41 { doMouseMoved(evt); }
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43 public void mouseDragged(MouseEvent evt)
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45 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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46 doMouseDragged(evt);
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48 doMouseDraggedDefineMode(evt);
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52 addMouseListener( new MouseAdapter()
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54 public void mouseReleased(MouseEvent evt)
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56 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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57 doMouseReleased(evt);
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59 doMouseReleasedDefineMode(evt);
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61 public void mousePressed(MouseEvent evt)
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63 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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64 doMousePressed(evt);
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66 doMousePressedDefineMode(evt);
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74 public void doMouseReleased(MouseEvent evt) {
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77 int res = x/av.getCharWidth() + av.getStartRes();
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84 if(seqEditOccurred>-1)
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85 updateConservation(seqEditOccurred);
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87 seqEditOccurred = -1;
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89 parent.RefreshPanels();
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94 public void doMousePressed(MouseEvent evt) {
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95 parent.alignFrame.addHistoryItem("sequence edit");
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100 int y = evt.getY();
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102 res = x/av.getCharWidth() + av.getStartRes();
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103 seq = y/av.getCharHeight() + av.getStartSeq();
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105 if (seq < av.getAlignment().getHeight() &&
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106 res < av.getAlignment().getSequenceAt(seq).getLength())
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108 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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109 // Find the residue's position in the sequence (res is the position
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110 // in the alignment
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114 if (startseq == (av.getAlignment().getHeight() - 1))
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133 public void doMouseMoved(MouseEvent evt)
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136 int x = evt.getX();
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137 int y = evt.getY();
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138 if(av.wrapAlignment)
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140 y -= 2*av.charHeight;
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141 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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144 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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147 seq = y / av.getCharHeight() + av.getStartSeq();
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149 // chunkHeight = (da.getHeight() + 2)*charHeight;
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150 // startx += chunkWidth;
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154 res = x / av.getCharWidth() + av.getStartRes();
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155 seq = y / av.getCharHeight() + av.getStartSeq();
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159 if(seq>=av.getAlignment().getHeight())
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162 Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;
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165 aa = obj.toString();
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167 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
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169 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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171 parent.alignFrame.statusBar.setText(text.toString());
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175 public void doMouseDragged(MouseEvent evt) {
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176 // If we're dragging we're editing
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178 int x = evt.getX();
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180 int res = x/av.getCharWidth() + av.getStartRes();
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184 if (res != lastres)
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187 if (evt.isAltDown() || evt.isControlDown())
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189 SequenceGroup sg = av.getAlignment().findGroup(startseq);
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192 boolean deleteAllowed = false;
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193 if (res < av.getAlignment().getWidth() && res < lastres)
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195 /// Are we able to delete?
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196 boolean allGaps = true;
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197 for (int i = 0; i < sg.getSize(); i++)
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199 SequenceI s = sg.getSequenceAt(i);
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200 for (int j = lastres-1; j >= res && allGaps; j--)
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202 if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
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209 if(!deleteAllowed && allGaps)
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210 deleteAllowed = true;
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215 if (res < av.getAlignment().getWidth() && res > lastres)
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216 sg.setEndRes(sg.getEndRes() + 1);
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219 else if (deleteAllowed && res < av.getAlignment().getWidth() &&
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221 sg.setEndRes(sg.getEndRes() - 1);
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226 for (int i = 0; i < sg.getSize(); i++)
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228 SequenceI s = sg.getSequenceAt(i);
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229 int k = av.alignment.findIndex(s);
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232 if (res < av.getAlignment().getWidth() && res > lastres)
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233 for (int j = lastres; j < res; j++)
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237 else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
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239 for (int j = res; j < lastres; j++)
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248 else /////Editing a single sequence///////////
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250 if (res < av.getAlignment().getWidth() && res > lastres)
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252 // dragging to the right
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253 for (int j = lastres; j < res; j++)
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254 insertChar(j, startseq);
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256 else if (res < av.getAlignment().getWidth() && res < lastres)
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258 // dragging to the left
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259 for (int j = res; j < lastres; j++)
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261 deleteChar(j, startseq);
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274 public void drawChars(int seqstart, int seqend, int start) {
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275 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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279 public void insertChar(int j, int seq)
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281 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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282 seqEditOccurred=seq;
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285 public void deleteChar(int j, int seq)
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288 if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
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289 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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291 av.alignment.getWidth();
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293 seqEditOccurred=seq;
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297 void updateConservation(int i)
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299 /* Alignment al = (Alignment) av.getAlignment();
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300 SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
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301 if(sg==null || !(sg.cs instanceof ConservationColourScheme))
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304 Conservation c = sg.getConservation();
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306 c = new Conservation("All", al.cons,
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307 ResidueProperties.propHash, 3, sg.sequences, 0,
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310 c.verdict(false, 100);
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311 sg.setConservation(c);
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312 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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313 ccs.conserve = c;*/
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316 //////////////////////////////////////////
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317 /////Everything below this is for defining the boundary of the rubberband
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318 //////////////////////////////////////////
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320 public void doMousePressedDefineMode(MouseEvent evt)
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322 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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323 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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326 stretchGroup = av.getRubberbandGroup();
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328 if(stretchGroup == null)
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329 stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
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331 else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
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332 || stretchGroup.getStartRes()>res
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333 || stretchGroup.getEndRes()<res)
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335 stretchGroup = null;
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337 SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.
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339 getSequenceAt(seq));
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341 if (allGroups != null)
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342 for (int i = 0; i < allGroups.length; i++)
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343 if (allGroups[i].getStartRes() <= res &&
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344 allGroups[i].getEndRes() >= res)
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346 stretchGroup = allGroups[i];
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347 av.setRubberbandGroup(stretchGroup);
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352 if(stretchGroup==null)
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354 // define a new group here
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355 SequenceGroup sg = new SequenceGroup();
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356 sg.setStartRes(res);
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358 sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
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359 av.setRubberbandGroup( sg );
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362 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
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364 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);
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365 pop.show(this, evt.getX(), evt.getY());
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367 // edit the properties of existing group
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370 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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371 // Edit end res position of selected group
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372 changeEndRes = true;
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374 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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375 // Edit end res position of selected group
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376 changeStartRes = true;
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379 seqCanvas.paintFlag = true;
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385 boolean changeEndSeq = false;
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386 boolean changeStartSeq = false;
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387 boolean changeEndRes = false;
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388 boolean changeStartRes = false;
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389 SequenceGroup stretchGroup = null;
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391 public void doMouseReleasedDefineMode(MouseEvent evt)
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393 changeEndRes = false;
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394 changeStartRes = false;
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395 stretchGroup = null;
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399 boolean remove = false;
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400 public void doMouseDraggedDefineMode(MouseEvent evt)
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402 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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403 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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406 if(stretchGroup.getEndRes()==res)
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407 // Edit end res position of selected group
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408 changeEndRes = true;
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410 else if(stretchGroup.getStartRes()==res)
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411 // Edit end res position of selected group
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412 changeStartRes = true;
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415 if(res<av.getStartRes())
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416 res = av.getStartRes();
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417 else if(res>av.getEndRes())
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418 res = av.getEndRes();
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422 if(res>stretchGroup.getStartRes()-1)
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423 stretchGroup.setEndRes( res );
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425 else if(changeStartRes)
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427 if(res<stretchGroup.getEndRes()+1)
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428 stretchGroup.setStartRes( res );
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432 int dragDirection = 0;
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435 else if (y < oldSeq)
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436 dragDirection = -1;
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438 while (y != oldSeq)
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440 // This routine ensures we don't skip any sequences, as the
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441 // selection is quite slow.
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442 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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444 oldSeq += dragDirection;
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445 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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447 if (stretchGroup.sequences.contains(nextSeq))
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449 stretchGroup.deleteSequence(seq);
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450 stretchGroup.deleteSequence(nextSeq);
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454 stretchGroup.addSequence(seq);
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455 stretchGroup.addSequence(nextSeq);
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460 seqCanvas.paintFlag = true;
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