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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10 public class SeqPanel extends JPanel
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13 public SeqCanvas seqCanvas;
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14 public AlignmentPanel ap;
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16 protected int lastres;
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17 protected int startseq;
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21 protected AlignViewport av;
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23 // if character is inserted or deleted, we will need to recalculate the conservation
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24 int seqEditOccurred = -1;
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26 ScrollThread scrollThread = null;
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27 boolean mouseDragging = false;
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29 boolean editingSeqs = false;
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30 boolean groupEditing = false;
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33 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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36 seqCanvas = new SeqCanvas(avp);
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37 setLayout(new BorderLayout());
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38 add(seqCanvas, BorderLayout.CENTER);
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42 addMouseMotionListener( new MouseMotionAdapter()
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44 public void mouseMoved(MouseEvent evt)
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46 if(av.getWrapAlignment())
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48 doMouseMoved(evt); }
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50 public void mouseDragged(MouseEvent evt)
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52 if(av.getWrapAlignment())
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55 doMouseDragged(evt);
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57 doMouseDraggedDefineMode(evt);
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61 addMouseListener( new MouseAdapter()
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63 public void mouseReleased(MouseEvent evt)
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65 if(av.getWrapAlignment())
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68 doMouseReleased(evt);
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70 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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79 if(evt.isAltDown() || evt.isControlDown())
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80 groupEditing = true;
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83 doMousePressed(evt);
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86 doMousePressedDefineMode(evt);
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88 public void mouseExited(MouseEvent evt)
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90 if (av.getWrapAlignment() || editingSeqs)
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92 doMouseExitedDefineMode(evt);
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95 public void mouseEntered(MouseEvent evt)
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97 if (av.getWrapAlignment() || editingSeqs)
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99 doMouseEnteredDefineMode(evt);
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107 public void doMouseReleased(MouseEvent evt) {
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109 if(seqEditOccurred>-1)
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110 editOccurred(seqEditOccurred);
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114 seqEditOccurred = -1;
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115 editingSeqs = false;
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116 groupEditing = false;
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121 public void doMousePressed(MouseEvent evt) {
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123 ap.alignFrame.addHistoryItem( new HistoryItem(
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124 "Edit Sequence",av.alignment, HistoryItem.EDIT));
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129 int x = evt.getX();
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130 int y = evt.getY();
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132 res = x/av.getCharWidth() + av.getStartRes();
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133 seq = y/av.getCharHeight() + av.getStartSeq();
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135 if (seq < av.getAlignment().getHeight() &&
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136 res < av.getAlignment().getSequenceAt(seq).getLength())
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147 startEdit = lastres;
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153 public void doMouseMoved(MouseEvent evt)
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156 int x = evt.getX();
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157 int y = evt.getY();
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158 if(av.wrapAlignment)
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160 y -= 2*av.charHeight;
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161 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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164 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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167 seq = y / av.getCharHeight() + av.getStartSeq();
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172 res = x / av.getCharWidth() + av.getStartRes();
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173 seq = y / av.getCharHeight() + av.getStartSeq();
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177 if(seq>=av.getAlignment().getHeight())
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180 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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181 if(res>sequence.getLength())
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184 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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187 aa = obj.toString();
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189 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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191 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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193 ap.alignFrame.statusBar.setText(text.toString());
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195 // use aa to see if the mouse pointer is on a
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196 if( av.showSequenceFeatures)
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198 Vector features = sequence.getSequenceFeatures();
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199 Enumeration e = features.elements();
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200 StringBuffer sbuffer = new StringBuffer();
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203 while (e.hasMoreElements())
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205 SequenceFeature sf = (SequenceFeature) e.nextElement();
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206 if (sf.getStart() <= sequence.findPosition(res) &&
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207 sf.getEnd() >= sequence.findPosition(res))
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209 if(sbuffer.length()>0)
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210 sbuffer.append("; ");
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211 sbuffer.append(sf.getType() + " " + sf.getDescription());
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212 if(sf.getStatus().length()>0)
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213 sbuffer.append(" ("+sf.getStatus()+")");
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218 ToolTipManager.sharedInstance().registerComponent(this);
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219 this.setToolTipText(sbuffer.toString());
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225 public void doMouseDragged(MouseEvent evt) {
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227 // If we're dragging we're editing
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228 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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232 if (lastres == -1 || lastres == res)
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235 boolean dragRight = true;
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236 if (res < av.getAlignment().getWidth() && res < lastres)
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240 if (res != lastres)
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245 SequenceGroup sg = av.getSelectionGroup();
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254 sg.setEndRes(sg.getEndRes() + (res-lastres));
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259 /// Are we able to delete?
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260 // ie are all columns blank?
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261 boolean deleteAllowed = false;
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262 for (int s = 0; s < sg.getSize(); s++)
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264 SequenceI seq = sg.getSequenceAt(s);
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265 for (int j=res; j<lastres; j++)
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267 if(seq.getSequence().length()<=j)
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270 if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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272 // Not a gap, block edit not valid
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274 deleteAllowed = false;
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277 deleteAllowed = true;
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287 sg.setEndRes(sg.getEndRes() - (lastres-res));
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291 for (int i = 0; i < sg.getSize(); i++)
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293 SequenceI s = sg.getSequenceAt(i);
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294 int k = av.alignment.findIndex(s);
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298 for (int j = lastres; j < res; j++)
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304 for (int j = res; j < lastres; j++)
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306 if(s.getLength()>j)
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307 deleteChar(res, k);
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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 = lastres; j > res; j--)
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325 if( jalview.util.Comparison.isGap(
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326 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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328 deleteChar(res, startseq);
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345 public void drawChars(int seqstart, int seqend, int start) {
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346 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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350 public void insertChar(int j, int seq)
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352 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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353 seqEditOccurred=seq;
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356 public void deleteChar(int j, int seq)
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358 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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359 seqEditOccurred=seq;
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361 av.alignment.getWidth();
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366 void editOccurred(int i)
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368 if(endEdit==startEdit)
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370 ap.alignFrame.historyList.pop();
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371 ap.alignFrame.updateEditMenuBar();
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374 av.updateConservation();
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375 av.updateConsensus();
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377 ColourSchemeI cs = av.getGlobalColourScheme();
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378 if(cs instanceof ConservationColourScheme)
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379 cs = ( (ConservationColourScheme) cs).cs;
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381 if(cs instanceof ClustalxColourScheme)
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382 cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());
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384 ap.alignFrame.changeColour(cs);
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388 //////////////////////////////////////////
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389 /////Everything below this is for defining the boundary of the rubberband
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390 //////////////////////////////////////////
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392 public void doMousePressedDefineMode(MouseEvent evt)
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394 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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395 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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398 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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400 if(sequence==null || res>sequence.getLength())
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403 stretchGroup = av.getSelectionGroup();
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405 if(stretchGroup == null)
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407 stretchGroup = av.alignment.findGroup( sequence );
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408 if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
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409 av.setSelectionGroup(stretchGroup);
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411 stretchGroup = null;
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414 else if(!stretchGroup.sequences.contains(sequence)
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415 || stretchGroup.getStartRes()>res
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416 || stretchGroup.getEndRes()<res)
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418 stretchGroup = null;
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420 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
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422 if (allGroups != null)
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423 for (int i = 0; i < allGroups.length; i++)
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424 if (allGroups[i].getStartRes() <= res &&
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425 allGroups[i].getEndRes() >= res)
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427 stretchGroup = allGroups[i];
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428 av.setSelectionGroup(stretchGroup);
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433 if(stretchGroup==null)
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435 // define a new group here
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436 SequenceGroup sg = new SequenceGroup();
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437 sg.setStartRes(res);
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439 sg.addSequence( sequence );
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440 av.setSelectionGroup( sg );
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443 if(av.getConservationSelected())
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444 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
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445 if(av.getAbovePIDThreshold())
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446 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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449 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
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451 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
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452 pop.show(this, evt.getX(), evt.getY());
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454 // edit the properties of existing group
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457 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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458 // Edit end res position of selected group
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459 changeEndRes = true;
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461 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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462 // Edit end res position of selected group
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463 changeStartRes = true;
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465 stretchGroup.getWidth();
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471 boolean changeEndSeq = false;
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472 boolean changeStartSeq = false;
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473 boolean changeEndRes = false;
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474 boolean changeStartRes = false;
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475 SequenceGroup stretchGroup = null;
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477 public void doMouseReleasedDefineMode(MouseEvent evt)
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479 mouseDragging = false;
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481 if(stretchGroup==null)
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484 if(stretchGroup.cs instanceof ClustalxColourScheme)
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486 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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490 else if(stretchGroup.cs instanceof ConservationColourScheme)
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492 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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493 stretchGroup.cs = ccs;
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494 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
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500 if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
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502 ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;
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503 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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509 changeEndRes = false;
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510 changeStartRes = false;
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511 stretchGroup = null;
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512 ap.idPanel.repaint();
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516 boolean remove = false;
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517 public void doMouseDraggedDefineMode(MouseEvent evt)
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519 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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520 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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522 if(stretchGroup==null)
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525 if(res>av.alignment.getWidth())
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526 res = av.alignment.getWidth()-1;
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529 if(stretchGroup.getEndRes()==res)
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530 // Edit end res position of selected group
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531 changeEndRes = true;
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533 else if(stretchGroup.getStartRes()==res)
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534 // Edit start res position of selected group
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535 changeStartRes = true;
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538 if(res<av.getStartRes())
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539 res = av.getStartRes();
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540 else if(res>av.getEndRes())
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541 res = av.getEndRes();
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545 if(res>stretchGroup.getStartRes()-1)
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546 stretchGroup.setEndRes( res );
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548 else if(changeStartRes)
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550 if(res<stretchGroup.getEndRes()+1)
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551 stretchGroup.setStartRes( res );
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554 int dragDirection = 0;
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557 else if (y < oldSeq)
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558 dragDirection = -1;
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560 while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
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562 // This routine ensures we don't skip any sequences, as the
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563 // selection is quite slow.
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564 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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566 oldSeq += dragDirection;
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567 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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569 if (stretchGroup.sequences.contains(nextSeq))
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571 stretchGroup.deleteSequence(seq);
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572 stretchGroup.deleteSequence(nextSeq);
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577 stretchGroup.addSequence(seq);
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578 stretchGroup.addSequence(nextSeq);
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582 mouseDragging = true;
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583 if(scrollThread!=null)
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584 scrollThread.setEvent(evt);
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589 public void doMouseEnteredDefineMode(MouseEvent e)
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591 if (scrollThread != null)
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592 scrollThread.running = false;
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595 public void doMouseExitedDefineMode(MouseEvent e)
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597 if (av.getWrapAlignment())
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601 scrollThread = new ScrollThread();
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604 // this class allows scrolling off the bottom of the visible alignment
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605 class ScrollThread extends Thread
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608 boolean running = false;
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609 public ScrollThread()
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614 public void setEvent(MouseEvent e)
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619 public void stopScrolling()
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632 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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633 running = ap.scrollUp(true);
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635 if (mouseDragging && evt.getY() >= getHeight() &&
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636 av.alignment.getHeight() > av.getEndSeq())
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637 running = ap.scrollUp(false);
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639 if (mouseDragging && evt.getX() < 0)
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640 running = ap.scrollRight(true);
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642 else if (mouseDragging && evt.getX() >= getWidth())
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643 running = ap.scrollRight(false);
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650 catch (Exception ex)
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