4 import java.awt.event.*;
\r
5 import jalview.datamodel.*;
\r
6 import javax.swing.*;
\r
8 import jalview.schemes.*;
\r
10 public class SeqPanel extends JPanel
\r
13 public SeqCanvas seqCanvas;
\r
14 public AlignmentPanel ap;
\r
16 protected int startres;
\r
17 protected int lastres;
\r
18 protected int endres;
\r
20 protected int startseq;
\r
21 protected int padseq;
\r
23 protected AlignViewport av;
\r
25 // if character is inserted or deleted, we will need to recalculate the conservation
\r
26 int seqEditOccurred = -1;
\r
28 ScrollThread scrollThread = null;
\r
29 boolean mouseDragging = false;
\r
32 public SeqPanel(AlignViewport avp, AlignmentPanel p) {
\r
35 seqCanvas = new SeqCanvas(avp);
\r
36 setLayout(new BorderLayout());
\r
37 add(seqCanvas, BorderLayout.CENTER);
\r
41 addMouseMotionListener( new MouseMotionAdapter()
\r
43 public void mouseMoved(MouseEvent evt)
\r
45 if(av.getWrapAlignment())
\r
47 doMouseMoved(evt); }
\r
49 public void mouseDragged(MouseEvent evt)
\r
51 if(av.getWrapAlignment())
\r
53 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
\r
54 doMouseDragged(evt);
\r
56 doMouseDraggedDefineMode(evt);
\r
60 addMouseListener( new MouseAdapter()
\r
62 public void mouseReleased(MouseEvent evt)
\r
64 if(av.getWrapAlignment())
\r
66 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
\r
67 doMouseReleased(evt);
\r
69 doMouseReleasedDefineMode(evt);
\r
71 public void mousePressed(MouseEvent evt)
\r
73 if(av.getWrapAlignment())
\r
75 if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
\r
76 doMousePressed(evt);
\r
78 doMousePressedDefineMode(evt);
\r
80 public void mouseExited(MouseEvent evt)
\r
82 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
\r
83 evt.isControlDown())
\r
85 doMouseExitedDefineMode(evt);
\r
88 public void mouseEntered(MouseEvent evt)
\r
90 if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
\r
91 evt.isControlDown())
\r
93 doMouseEnteredDefineMode(evt);
\r
101 public void doMouseReleased(MouseEvent evt) {
\r
103 int x = evt.getX();
\r
104 int res = x/av.getCharWidth() + av.getStartRes();
\r
111 if(seqEditOccurred>-1)
\r
112 updateConservation(seqEditOccurred);
\r
114 seqEditOccurred = -1;
\r
120 public void doMousePressed(MouseEvent evt) {
\r
121 ap.alignFrame.addHistoryItem("sequence edit");
\r
125 int x = evt.getX();
\r
126 int y = evt.getY();
\r
128 res = x/av.getCharWidth() + av.getStartRes();
\r
129 seq = y/av.getCharHeight() + av.getStartSeq();
\r
131 if (seq < av.getAlignment().getHeight() &&
\r
132 res < av.getAlignment().getSequenceAt(seq).getLength())
\r
134 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
\r
135 // Find the residue's position in the sequence (res is the position
\r
136 // in the alignment
\r
140 if (startseq == (av.getAlignment().getHeight() - 1))
\r
159 public void doMouseMoved(MouseEvent evt)
\r
162 int x = evt.getX();
\r
163 int y = evt.getY();
\r
164 if(av.wrapAlignment)
\r
166 y -= 2*av.charHeight;
\r
167 int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
\r
170 res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();
\r
173 seq = y / av.getCharHeight() + av.getStartSeq();
\r
178 res = x / av.getCharWidth() + av.getStartRes();
\r
179 seq = y / av.getCharHeight() + av.getStartSeq();
\r
183 if(seq>=av.getAlignment().getHeight())
\r
186 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
\r
187 if(res>sequence.getLength())
\r
190 Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
\r
193 aa = obj.toString();
\r
195 StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
\r
197 text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
\r
199 ap.alignFrame.statusBar.setText(text.toString());
\r
201 // use aa to see if the mouse pointer is on a
\r
202 if( av.showSequenceFeatures)
\r
204 Vector features = sequence.getSequenceFeatures();
\r
205 Enumeration e = features.elements();
\r
206 StringBuffer sbuffer = new StringBuffer();
\r
209 while (e.hasMoreElements())
\r
211 SequenceFeature sf = (SequenceFeature) e.nextElement();
\r
212 if (sf.getStart() <= sequence.findPosition(res) &&
\r
213 sf.getEnd() >= sequence.findPosition(res))
\r
215 if(sbuffer.length()>0)
\r
216 sbuffer.append("; ");
\r
217 sbuffer.append(sf.getType() + " " + sf.getDescription());
\r
218 if(sf.getStatus().length()>0)
\r
219 sbuffer.append(" ("+sf.getStatus()+")");
\r
224 ToolTipManager.sharedInstance().registerComponent(this);
\r
225 this.setToolTipText(sbuffer.toString());
\r
231 public void doMouseDragged(MouseEvent evt) {
\r
232 // If we're dragging we're editing
\r
237 int x = evt.getX();
\r
239 int res = x/av.getCharWidth() + av.getStartRes();
\r
243 if (res != lastres)
\r
246 if (evt.isAltDown() || evt.isControlDown())
\r
248 SequenceGroup sg = av.getSelectionGroup();
\r
250 av.getAlignment().findGroup(startseq);
\r
253 boolean deleteAllowed = false;
\r
254 if (res < av.getAlignment().getWidth() && res < lastres)
\r
256 /// Are we able to delete?
\r
257 boolean allGaps = true;
\r
258 for (int i = 0; i < sg.getSize(); i++)
\r
260 SequenceI s = sg.getSequenceAt(i);
\r
261 for (int j = lastres-1; j >= res && allGaps; j--)
\r
263 if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
\r
270 if(!deleteAllowed && allGaps)
\r
271 deleteAllowed = true;
\r
276 if (res < av.getAlignment().getWidth() && res > lastres)
\r
277 sg.setEndRes(sg.getEndRes() + 1);
\r
280 else if (deleteAllowed && res < av.getAlignment().getWidth() &&
\r
282 sg.setEndRes(sg.getEndRes() - 1);
\r
287 for (int i = 0; i < sg.getSize(); i++)
\r
289 SequenceI s = sg.getSequenceAt(i);
\r
290 int k = av.alignment.findIndex(s);
\r
293 if (res < av.getAlignment().getWidth() && res > lastres)
\r
294 for (int j = lastres; j < res; j++)
\r
298 else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
\r
300 for (int j = res; j < lastres; j++)
\r
309 else /////Editing a single sequence///////////
\r
311 if (res < av.getAlignment().getWidth() && res > lastres)
\r
313 // dragging to the right
\r
314 for (int j = lastres; j < res; j++)
\r
315 insertChar(j, startseq);
\r
317 else if (res < av.getAlignment().getWidth() && res < lastres)
\r
319 // dragging to the left
\r
320 for (int j = res; j < lastres; j++)
\r
322 deleteChar(j, startseq);
\r
335 public void drawChars(int seqstart, int seqend, int start) {
\r
336 seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
\r
340 public void insertChar(int j, int seq)
\r
342 av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
\r
343 seqEditOccurred=seq;
\r
346 public void deleteChar(int j, int seq)
\r
349 if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
\r
350 av.alignment.getSequenceAt(seq).deleteCharAt(j);
\r
352 av.alignment.getWidth();
\r
354 seqEditOccurred=seq;
\r
358 void updateConservation(int i)
\r
360 if(av.getGlobalColourScheme() instanceof jalview.schemes.ClustalxColourScheme)
\r
362 av.setGlobalColourScheme(
\r
363 new jalview.schemes.ClustalxColourScheme(av.alignment.getSequences(),av.alignment.getWidth() ));
\r
365 av.updateConservation();
\r
366 av.updateConsensus();
\r
369 //////////////////////////////////////////
\r
370 /////Everything below this is for defining the boundary of the rubberband
\r
371 //////////////////////////////////////////
\r
373 public void doMousePressedDefineMode(MouseEvent evt)
\r
375 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
\r
376 int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
\r
379 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
381 if(sequence==null || res>sequence.getLength())
\r
384 stretchGroup = av.getSelectionGroup();
\r
386 if(stretchGroup == null)
\r
388 stretchGroup = av.alignment.findGroup( sequence );
\r
389 if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
\r
390 av.setSelectionGroup(stretchGroup);
\r
392 stretchGroup = null;
\r
395 else if(!stretchGroup.sequences.contains(sequence)
\r
396 || stretchGroup.getStartRes()>res
\r
397 || stretchGroup.getEndRes()<res)
\r
399 stretchGroup = null;
\r
401 SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
\r
403 if (allGroups != null)
\r
404 for (int i = 0; i < allGroups.length; i++)
\r
405 if (allGroups[i].getStartRes() <= res &&
\r
406 allGroups[i].getEndRes() >= res)
\r
408 stretchGroup = allGroups[i];
\r
409 av.setSelectionGroup(stretchGroup);
\r
414 if(stretchGroup==null)
\r
416 // define a new group here
\r
417 SequenceGroup sg = new SequenceGroup();
\r
418 sg.setStartRes(res);
\r
420 sg.addSequence( sequence );
\r
421 av.setSelectionGroup( sg );
\r
424 if(av.getConservationSelected())
\r
425 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
\r
426 if(av.getAbovePIDThreshold())
\r
427 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
\r
430 else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
432 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
\r
433 pop.show(this, evt.getX(), evt.getY());
\r
435 // edit the properties of existing group
\r
438 if(stretchGroup!=null && stretchGroup.getEndRes()==res)
\r
439 // Edit end res position of selected group
\r
440 changeEndRes = true;
\r
442 else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
\r
443 // Edit end res position of selected group
\r
444 changeStartRes = true;
\r
451 boolean changeEndSeq = false;
\r
452 boolean changeStartSeq = false;
\r
453 boolean changeEndRes = false;
\r
454 boolean changeStartRes = false;
\r
455 SequenceGroup stretchGroup = null;
\r
457 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
459 mouseDragging = false;
\r
461 if(stretchGroup==null)
\r
464 if(stretchGroup.cs instanceof ClustalxColourScheme)
\r
466 stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
\r
470 else if(stretchGroup.cs instanceof ConservationColourScheme)
\r
472 ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
\r
473 stretchGroup.cs = ccs;
\r
474 SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
\r
480 if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
\r
482 ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;
\r
483 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
\r
489 changeEndRes = false;
\r
490 changeStartRes = false;
\r
491 stretchGroup = null;
\r
492 ap.idPanel.repaint();
\r
496 boolean remove = false;
\r
497 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
499 int res = evt.getX()/av.getCharWidth() + av.getStartRes();
\r
500 int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
\r
502 if(stretchGroup==null)
\r
505 if(res>av.alignment.getWidth())
\r
506 res = av.alignment.getWidth()-1;
\r
509 if(stretchGroup.getEndRes()==res)
\r
510 // Edit end res position of selected group
\r
511 changeEndRes = true;
\r
513 else if(stretchGroup.getStartRes()==res)
\r
514 // Edit start res position of selected group
\r
515 changeStartRes = true;
\r
518 if(res<av.getStartRes())
\r
519 res = av.getStartRes();
\r
520 else if(res>av.getEndRes())
\r
521 res = av.getEndRes();
\r
525 if(res>stretchGroup.getStartRes()-1)
\r
526 stretchGroup.setEndRes( res );
\r
528 else if(changeStartRes)
\r
530 if(res<stretchGroup.getEndRes()+1)
\r
531 stretchGroup.setStartRes( res );
\r
534 int dragDirection = 0;
\r
537 else if (y < oldSeq)
\r
538 dragDirection = -1;
\r
540 while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
\r
542 // This routine ensures we don't skip any sequences, as the
\r
543 // selection is quite slow.
\r
544 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
546 oldSeq += dragDirection;
\r
547 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
549 if (stretchGroup.sequences.contains(nextSeq))
\r
551 stretchGroup.deleteSequence(seq);
\r
552 stretchGroup.deleteSequence(nextSeq);
\r
557 stretchGroup.addSequence(seq);
\r
558 stretchGroup.addSequence(nextSeq);
\r
562 mouseDragging = true;
\r
563 if(scrollThread!=null)
\r
564 scrollThread.setEvent(evt);
\r
569 public void doMouseEnteredDefineMode(MouseEvent e)
\r
571 if (scrollThread != null)
\r
572 scrollThread.running = false;
\r
575 public void doMouseExitedDefineMode(MouseEvent e)
\r
577 if (av.getWrapAlignment())
\r
581 scrollThread = new ScrollThread();
\r
584 // this class allows scrolling off the bottom of the visible alignment
\r
585 class ScrollThread extends Thread
\r
588 boolean running = false;
\r
589 public ScrollThread()
\r
594 public void setEvent(MouseEvent e)
\r
599 public void stopScrolling()
\r
612 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
613 running = ap.scrollUp(true);
\r
615 if (mouseDragging && evt.getY() >= getHeight() &&
\r
616 av.alignment.getHeight() > av.getEndSeq())
\r
617 running = ap.scrollUp(false);
\r
619 if (mouseDragging && evt.getX() < 0)
\r
620 running = ap.scrollRight(true);
\r
622 else if (mouseDragging && evt.getX() >= getWidth())
\r
623 running = ap.scrollRight(false);
\r
630 catch (Exception ex)
\r