1 package jalview.appletgui;
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4 import java.awt.event.*;
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5 import jalview.datamodel.*;
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7 import jalview.schemes.*;
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10 public class SeqPanel extends Panel
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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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34 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
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37 seqCanvas = new SeqCanvas(avp);
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38 setLayout(new BorderLayout());
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43 seqCanvas.addMouseMotionListener( new MouseMotionAdapter()
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45 public void mouseMoved(MouseEvent evt)
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47 if(av.getWrapAlignment())
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49 doMouseMoved(evt); }
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51 public void mouseDragged(MouseEvent evt)
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53 if(av.getWrapAlignment())
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56 doMouseDragged(evt);
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58 doMouseDraggedDefineMode(evt);
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62 seqCanvas.addMouseListener( new MouseAdapter()
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64 public void mouseReleased(MouseEvent evt)
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66 if(av.getWrapAlignment())
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69 doMouseReleased(evt);
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71 doMouseReleasedDefineMode(evt);
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74 public void mousePressed(MouseEvent evt)
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76 if(av.getWrapAlignment())
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78 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
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80 if(evt.isAltDown() || evt.isControlDown())
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81 groupEditing = true;
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84 doMousePressed(evt);
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87 doMousePressedDefineMode(evt);
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89 public void mouseExited(MouseEvent evt)
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91 if (av.getWrapAlignment() || editingSeqs)
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93 doMouseExitedDefineMode(evt);
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96 public void mouseEntered(MouseEvent evt)
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98 if (av.getWrapAlignment() || editingSeqs)
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100 doMouseEnteredDefineMode(evt);
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104 seqCanvas.repaint();
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108 public void doMouseReleased(MouseEvent evt) {
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110 if(seqEditOccurred>-1)
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111 editOccurred(seqEditOccurred);
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115 seqEditOccurred = -1;
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116 editingSeqs = false;
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117 groupEditing = false;
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121 public void doMousePressed(MouseEvent evt) {
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122 ap.alignFrame.addHistoryItem( new HistoryItem(
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123 "Edit Sequence",av.alignment, HistoryItem.EDIT));
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127 int x = evt.getX();
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128 int y = evt.getY();
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130 res = x/av.getCharWidth() + av.getStartRes();
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131 seq = y/av.getCharHeight() + av.getStartSeq();
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133 if (seq < av.getAlignment().getHeight() &&
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134 res < av.getAlignment().getSequenceAt(seq).getLength())
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136 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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137 // Find the residue's position in the sequence (res is the position
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138 // in the alignment
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152 public void doMouseMoved(MouseEvent evt)
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155 int x = evt.getX();
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156 int y = evt.getY();
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157 if(av.wrapAlignment)
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159 y -= 2*av.charHeight;
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160 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
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163 res = (int)((y/chunkHeight)*(getSize().width/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
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166 seq = y / av.getCharHeight() + av.getStartSeq();
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171 res = x / av.getCharWidth() + av.getStartRes();
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172 seq = y / av.getCharHeight() + av.getStartSeq();
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176 if(seq>=av.getAlignment().getHeight())
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179 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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180 if(res>sequence.getLength())
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183 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
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186 aa = obj.toString();
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188 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
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190 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
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192 ap.alignFrame.statusBar.setText(text.toString());
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194 // use aa to see if the mouse pointer is on a
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195 if( av.showSequenceFeatures)
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197 Vector features = sequence.getSequenceFeatures();
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198 Enumeration e = features.elements();
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199 StringBuffer sbuffer = new StringBuffer();
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202 while (e.hasMoreElements())
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204 SequenceFeature sf = (SequenceFeature) e.nextElement();
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205 if (sf.getStart() <= sequence.findPosition(res) &&
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206 sf.getEnd() >= sequence.findPosition(res))
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208 if(sbuffer.length()>0)
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209 sbuffer.append("; ");
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210 sbuffer.append(sf.getType() + " " + sf.getDescription());
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211 if(sf.getStatus().length()>0)
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212 sbuffer.append(" ("+sf.getStatus()+")");
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221 public void doMouseDragged(MouseEvent evt) {
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223 // If we're dragging we're editing
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224 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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228 if (lastres == -1 || lastres == res)
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231 boolean dragRight = true;
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232 if (res < av.getAlignment().getWidth() && res < lastres)
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236 if (res != lastres)
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241 SequenceGroup sg = av.getSelectionGroup();
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250 sg.setEndRes(sg.getEndRes() + (res-lastres));
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255 /// Are we able to delete?
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256 // ie are all columns blank?
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257 boolean deleteAllowed = false;
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258 for (int s = 0; s < sg.getSize(); s++)
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260 SequenceI seq = sg.getSequenceAt(s);
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261 for (int j=res; j<lastres; j++)
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263 if(seq.getSequence().length()<=j)
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266 if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
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268 // Not a gap, block edit not valid
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270 deleteAllowed = false;
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273 deleteAllowed = true;
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283 sg.setEndRes(sg.getEndRes() - (lastres-res));
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287 for (int i = 0; i < sg.getSize(); i++)
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289 SequenceI s = sg.getSequenceAt(i);
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290 int k = av.alignment.findIndex(s);
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294 for (int j = lastres; j < res; j++)
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300 for (int j = res; j < lastres; j++)
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302 if(s.getLength()>j)
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303 deleteChar(res, k);
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308 else /////Editing a single sequence///////////
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310 if (res < av.getAlignment().getWidth() && res > lastres)
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312 // dragging to the right
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313 for (int j = lastres; j < res; j++)
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314 insertChar(j, startseq);
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316 else if (res < av.getAlignment().getWidth() && res < lastres)
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318 // dragging to the left
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319 for (int j = lastres; j > res; j--)
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321 if( jalview.util.Comparison.isGap(
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322 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
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324 deleteChar(res, startseq);
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338 seqCanvas.repaint();
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341 public void drawChars(int seqstart, int seqend, int start) {
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342 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
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343 seqCanvas.repaint();
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346 public void insertChar(int j, int seq)
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348 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
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349 seqEditOccurred=seq;
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352 public void deleteChar(int j, int seq)
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355 av.alignment.getSequenceAt(seq).deleteCharAt(j);
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356 seqEditOccurred=seq;
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357 av.alignment.getWidth();
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362 void editOccurred(int i)
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364 if(endEdit==startEdit)
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366 ap.alignFrame.historyList.pop();
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367 ap.alignFrame.updateEditMenuBar();
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370 av.updateConservation();
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371 av.updateConsensus();
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374 ColourSchemeI cs = av.getGlobalColourScheme();
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375 if(cs instanceof ConservationColourScheme)
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377 ConservationColourScheme ccs = (ConservationColourScheme) cs;
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378 if(ccs.cs instanceof ClustalxColourScheme)
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380 jalview.analysis.Conservation c = new jalview.analysis.Conservation
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382 ResidueProperties.propHash, 3,
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383 av.alignment.getSequences(), 0,
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384 av.alignment.getWidth() - 1);
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386 c.verdict(false, av.ConsPercGaps);
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388 ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
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389 cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());
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390 ccs = new ConservationColourScheme(c, cxs);
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391 av.setGlobalColourScheme(ccs);
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395 if(cs instanceof ClustalxColourScheme)
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397 ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
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398 av.alignment.getWidth());
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399 av.setGlobalColourScheme(cs);
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405 //////////////////////////////////////////
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406 /////Everything below this is for defining the boundary of the rubberband
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407 //////////////////////////////////////////
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409 public void doMousePressedDefineMode(MouseEvent evt)
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411 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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412 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
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415 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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417 if(sequence==null || res>sequence.getLength())
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420 stretchGroup = av.getSelectionGroup();
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422 if(stretchGroup == null)
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424 stretchGroup = av.alignment.findGroup( sequence );
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425 if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
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426 av.setSelectionGroup(stretchGroup);
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428 stretchGroup = null;
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431 else if(!stretchGroup.sequences.contains(sequence)
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432 || stretchGroup.getStartRes()>res
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433 || stretchGroup.getEndRes()<res)
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435 stretchGroup = null;
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437 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
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439 if (allGroups != null)
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440 for (int i = 0; i < allGroups.length; i++)
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441 if (allGroups[i].getStartRes() <= res &&
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442 allGroups[i].getEndRes() >= res)
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444 stretchGroup = allGroups[i];
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445 av.setSelectionGroup(stretchGroup);
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450 if(stretchGroup==null)
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452 // define a new group here
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453 SequenceGroup sg = new SequenceGroup();
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454 sg.setStartRes(res);
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456 sg.addSequence( sequence );
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457 av.setSelectionGroup( sg );
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460 if(av.getConservationSelected())
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461 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
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462 if(av.getAbovePIDThreshold())
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463 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
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467 // DETECT RIGHT MOUSE BUTTON IN AWT
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468 else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )
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470 APopupMenu popup = new APopupMenu(ap, null);
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472 popup.show(this, evt.getX(), evt.getY());
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476 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
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477 // Edit end res position of selected group
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478 changeEndRes = true;
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480 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
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481 // Edit end res position of selected group
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482 changeStartRes = true;
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486 boolean changeEndSeq = false;
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487 boolean changeStartSeq = false;
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488 boolean changeEndRes = false;
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489 boolean changeStartRes = false;
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490 SequenceGroup stretchGroup = null;
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492 public void doMouseReleasedDefineMode(MouseEvent evt)
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494 mouseDragging = false;
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496 if(stretchGroup==null)
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499 if(stretchGroup.cs instanceof ClustalxColourScheme)
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501 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
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502 seqCanvas.repaint();
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505 else if(stretchGroup.cs instanceof ConservationColourScheme)
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507 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
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508 stretchGroup.cs = ccs;
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509 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
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511 seqCanvas.repaint();
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515 if(stretchGroup.cs !=null)
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517 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
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523 changeEndRes = false;
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524 changeStartRes = false;
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525 stretchGroup = null;
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530 boolean remove = false;
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531 public void doMouseDraggedDefineMode(MouseEvent evt)
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533 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
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534 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
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536 if(stretchGroup==null)
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539 if(res>av.alignment.getWidth())
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540 res = av.alignment.getWidth()-1;
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543 if(stretchGroup.getEndRes()==res)
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544 // Edit end res position of selected group
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545 changeEndRes = true;
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547 else if(stretchGroup.getStartRes()==res)
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548 // Edit start res position of selected group
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549 changeStartRes = true;
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552 if(res<av.getStartRes())
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553 res = av.getStartRes();
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554 else if(res>av.getEndRes())
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555 res = av.getEndRes();
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559 if(res>stretchGroup.getStartRes()-1)
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560 stretchGroup.setEndRes( res );
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562 else if(changeStartRes)
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564 if(res<stretchGroup.getEndRes()+1)
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565 stretchGroup.setStartRes( res );
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568 int dragDirection = 0;
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571 else if (y < oldSeq)
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572 dragDirection = -1;
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574 while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
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576 // This routine ensures we don't skip any sequences, as the
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577 // selection is quite slow.
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578 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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580 oldSeq += dragDirection;
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581 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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583 if (stretchGroup.sequences.contains(nextSeq))
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585 stretchGroup.deleteSequence(seq);
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586 stretchGroup.deleteSequence(nextSeq);
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591 stretchGroup.addSequence(seq);
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592 stretchGroup.addSequence(nextSeq);
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596 mouseDragging = true;
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597 if(scrollThread!=null)
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598 scrollThread.setEvent(evt);
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600 seqCanvas.repaint();
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603 public void doMouseEnteredDefineMode(MouseEvent e)
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605 if (scrollThread != null)
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606 scrollThread.running = false;
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609 public void doMouseExitedDefineMode(MouseEvent e)
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611 if (av.getWrapAlignment())
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615 scrollThread = new ScrollThread();
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618 // this class allows scrolling off the bottom of the visible alignment
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619 class ScrollThread extends Thread
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622 boolean running = false;
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623 public ScrollThread()
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628 public void setEvent(MouseEvent e)
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633 public void stopScrolling()
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646 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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647 running = ap.scrollUp(true);
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649 if (mouseDragging && evt.getY() >= getSize().height &&
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650 av.alignment.getHeight() > av.getEndSeq())
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651 running = ap.scrollUp(false);
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653 if (mouseDragging && evt.getX() < 0)
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654 running = ap.scrollRight(true);
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656 else if (mouseDragging && evt.getX() >= getSize().width)
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657 running = ap.scrollRight(false);
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664 catch (Exception ex)
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