2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
20 package jalview.appletgui;
\r
22 import jalview.schemes.*;
\r
23 import jalview.datamodel.*;
\r
24 import jalview.analysis.*;
\r
25 import jalview.io.*;
\r
27 import java.awt.event.*;
\r
29 import java.io.InputStreamReader;
\r
30 import java.io.BufferedReader;
\r
31 import java.net.URL;
\r
34 public class AlignFrame extends Frame implements ActionListener,
\r
35 ItemListener, KeyListener, MouseListener
\r
37 public AlignmentPanel alignPanel;
\r
38 public AlignViewport viewport;
\r
39 int NEW_WINDOW_WIDTH = 700;
\r
40 int NEW_WINDOW_HEIGHT = 500;
\r
41 jalview.bin.JalviewLite applet;
\r
44 public AlignFrame(AlignmentI al,
\r
45 jalview.bin.JalviewLite applet,
\r
51 }catch(Exception ex)
\r
53 ex.printStackTrace();
\r
56 this.applet = applet;
\r
57 viewport = new AlignViewport(al, applet);
\r
58 alignPanel = new AlignmentPanel(this, viewport);
\r
60 annotationPanelMenuItem.setState(viewport.showAnnotation);
\r
62 seqLimits.setState(viewport.showJVSuffix);
\r
66 String param = applet.getParameter("sortBy");
\r
69 if (param.equalsIgnoreCase("Id"))
\r
70 sortIDMenuItem_actionPerformed();
\r
71 else if (param.equalsIgnoreCase("Pairwise Identity"))
\r
72 sortPairwiseMenuItem_actionPerformed();
\r
75 param = applet.getParameter("wrap");
\r
78 if (param.equalsIgnoreCase("true"))
\r
80 wrapMenuItem.setState(true);
\r
81 wrapMenuItem_actionPerformed();
\r
87 param = applet.getParameter("windowWidth");
\r
90 int width = Integer.parseInt(param);
\r
91 NEW_WINDOW_WIDTH = width;
\r
93 param = applet.getParameter("windowHeight");
\r
96 int height = Integer.parseInt(param);
\r
97 NEW_WINDOW_HEIGHT = height;
\r
100 catch (Exception ex)
\r
105 //Some JVMS send keyevents to Top frame or lowest panel,
\r
106 //Havent worked out why yet. So add to both this frame and seqCanvas for now
\r
107 this.addKeyListener(this);
\r
108 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
\r
109 alignPanel.idPanel.idCanvas.addKeyListener(this);
\r
111 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
113 public void propertyChange(java.beans.PropertyChangeEvent evt)
\r
115 if (evt.getPropertyName().equals("alignment"))
\r
117 alignmentChanged();
\r
129 add(alignPanel, BorderLayout.CENTER);
\r
130 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
\r
131 NEW_WINDOW_HEIGHT);
\r
133 alignPanel.validate();
\r
134 alignPanel.repaint();
\r
136 public AlignViewport getAlignViewport()
\r
141 public SeqCanvas getSeqcanvas()
\r
143 return alignPanel.seqPanel.seqCanvas;
\r
150 * @param String DOCUMENT ME!
\r
153 public void parseFeaturesFile(String file, String type)
\r
155 Hashtable featureLinks = new Hashtable();
\r
156 boolean featuresFile = false;
\r
158 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
\r
159 alignPanel.seqPanel.seqCanvas.
\r
160 getFeatureRenderer().featureColours,
\r
164 catch(Exception ex)
\r
166 ex.printStackTrace();
\r
171 if(featureLinks.size()>0)
\r
172 alignPanel.seqPanel.seqCanvas
\r
173 .getFeatureRenderer().featureLinks = featureLinks;
\r
174 viewport.showSequenceFeatures = true;
\r
175 sequenceFeatures.setState(true);
\r
176 alignPanel.repaint();
\r
182 public void keyPressed(KeyEvent evt)
\r
184 if (viewport.cursorMode
\r
185 && evt.getKeyCode() >= KeyEvent.VK_0
\r
186 && evt.getKeyCode() <= KeyEvent.VK_9)
\r
188 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
\r
191 switch (evt.getKeyCode())
\r
193 case 27: // escape key
\r
194 deselectAllSequenceMenuItem_actionPerformed();
\r
196 case KeyEvent.VK_X:
\r
197 if (evt.isControlDown() || evt.isMetaDown())
\r
199 cut_actionPerformed();
\r
202 case KeyEvent.VK_C:
\r
203 if (viewport.cursorMode && !evt.isControlDown())
\r
205 alignPanel.seqPanel.setCursorColumn();
\r
207 if (evt.isControlDown() || evt.isMetaDown())
\r
209 copy_actionPerformed();
\r
212 case KeyEvent.VK_V:
\r
213 if (evt.isControlDown() || evt.isMetaDown())
\r
218 case KeyEvent.VK_A:
\r
219 if (evt.isControlDown() || evt.isMetaDown())
\r
221 selectAllSequenceMenuItem_actionPerformed();
\r
224 case KeyEvent.VK_DOWN:
\r
225 if(viewport.cursorMode)
\r
227 alignPanel.seqPanel.moveCursor(0,1);
\r
230 moveSelectedSequences(false);
\r
233 case KeyEvent.VK_UP:
\r
234 if (viewport.cursorMode)
\r
236 alignPanel.seqPanel.moveCursor(0,-1);
\r
239 moveSelectedSequences(true);
\r
242 case KeyEvent.VK_LEFT:
\r
243 if(viewport.cursorMode)
\r
245 alignPanel.seqPanel.moveCursor(-1,0);
\r
249 case KeyEvent.VK_RIGHT:
\r
250 if (viewport.cursorMode)
\r
252 alignPanel.seqPanel.moveCursor(1,0);
\r
255 case KeyEvent.VK_SPACE:
\r
256 if(viewport.cursorMode)
\r
258 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
\r
262 case KeyEvent.VK_DELETE:
\r
263 case KeyEvent.VK_BACK_SPACE:
\r
264 if(viewport.cursorMode)
\r
266 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
\r
270 cut_actionPerformed();
\r
271 alignPanel.seqPanel.seqCanvas.repaint();
\r
275 case KeyEvent.VK_S:
\r
276 if(viewport.cursorMode)
\r
278 alignPanel.seqPanel.setCursorRow();
\r
281 case KeyEvent.VK_P:
\r
282 if(viewport.cursorMode)
\r
284 alignPanel.seqPanel.setCursorPosition();
\r
288 case KeyEvent.VK_ENTER:
\r
289 case KeyEvent.VK_COMMA:
\r
290 if(viewport.cursorMode)
\r
292 alignPanel.seqPanel.setCursorRowAndColumn();
\r
296 case KeyEvent.VK_Q:
\r
297 if(viewport.cursorMode)
\r
299 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
\r
302 case KeyEvent.VK_M:
\r
303 if(viewport.cursorMode)
\r
305 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
\r
309 case KeyEvent.VK_F2:
\r
310 viewport.cursorMode = ! viewport.cursorMode;
\r
311 statusBar.setText("Keyboard editing mode is "+
\r
312 (viewport.cursorMode ? "on" : "off"));
\r
313 if(viewport.cursorMode)
\r
315 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
\r
316 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
\r
318 alignPanel.seqPanel.seqCanvas.repaint();
\r
321 case KeyEvent.VK_F:
\r
322 if (evt.isControlDown())
\r
324 findMenuItem_actionPerformed();
\r
329 public void keyReleased(KeyEvent evt)
\r
331 public void keyTyped(KeyEvent evt)
\r
334 public void itemStateChanged(ItemEvent evt)
\r
336 if(evt.getSource()==colourTextMenuItem)
\r
337 colourTextMenuItem_actionPerformed();
\r
338 else if(evt.getSource()==wrapMenuItem)
\r
339 wrapMenuItem_actionPerformed();
\r
340 else if(evt.getSource()==scaleAbove)
\r
341 scaleAbove_actionPerformed();
\r
342 else if(evt.getSource()==scaleLeft)
\r
343 scaleLeft_actionPerformed();
\r
344 else if(evt.getSource()==scaleRight)
\r
345 scaleRight_actionPerformed();
\r
346 else if(evt.getSource()==seqLimits)
\r
347 seqLimits_itemStateChanged();
\r
348 else if(evt.getSource()==viewBoxesMenuItem)
\r
349 viewBoxesMenuItem_actionPerformed();
\r
350 else if(evt.getSource()==viewTextMenuItem)
\r
351 viewTextMenuItem_actionPerformed();
\r
352 else if(evt.getSource()==renderGapsMenuItem)
\r
353 renderGapsMenuItem_actionPerformed();
\r
354 else if(evt.getSource()==annotationPanelMenuItem)
\r
355 annotationPanelMenuItem_actionPerformed();
\r
356 else if(evt.getSource()==sequenceFeatures)
\r
358 viewport.showSequenceFeatures(sequenceFeatures.getState());
\r
359 alignPanel.seqPanel.seqCanvas.repaint();
\r
361 else if(evt.getSource()==conservationMenuItem)
\r
362 conservationMenuItem_actionPerformed();
\r
363 else if(evt.getSource()==abovePIDThreshold)
\r
364 abovePIDThreshold_actionPerformed();
\r
365 else if(evt.getSource()==applyToAllGroups)
\r
366 applyToAllGroups_actionPerformed();
\r
367 else if(evt.getSource()==autoCalculate)
\r
368 viewport.autocalculateConsensus = autoCalculate.getState();
\r
370 public void actionPerformed(ActionEvent evt)
\r
372 if(evt.getSource()==inputText)
\r
373 inputText_actionPerformed();
\r
374 else if(evt.getSource()==loadTree)
\r
375 loadTree_actionPerformed();
\r
376 else if(evt.getSource()==loadApplication)
\r
377 launchFullApplication();
\r
378 else if(evt.getSource()==closeMenuItem)
\r
379 closeMenuItem_actionPerformed();
\r
380 else if(evt.getSource()==copy)
\r
381 copy_actionPerformed();
\r
382 else if(evt.getSource()==undoMenuItem)
\r
383 undoMenuItem_actionPerformed();
\r
384 else if(evt.getSource()==redoMenuItem)
\r
385 redoMenuItem_actionPerformed();
\r
386 else if(evt.getSource()==inputText)
\r
387 inputText_actionPerformed();
\r
388 else if(evt.getSource()==closeMenuItem)
\r
389 closeMenuItem_actionPerformed();
\r
390 else if(evt.getSource()==undoMenuItem)
\r
391 undoMenuItem_actionPerformed();
\r
392 else if(evt.getSource()==redoMenuItem)
\r
393 redoMenuItem_actionPerformed();
\r
394 else if(evt.getSource()==copy)
\r
395 copy_actionPerformed();
\r
396 else if(evt.getSource()==pasteNew)
\r
397 pasteNew_actionPerformed();
\r
398 else if(evt.getSource()==pasteThis)
\r
399 pasteThis_actionPerformed();
\r
400 else if(evt.getSource()==cut)
\r
401 cut_actionPerformed();
\r
402 else if(evt.getSource()==delete)
\r
403 delete_actionPerformed();
\r
404 else if(evt.getSource()==deleteGroups)
\r
405 deleteGroups_actionPerformed();
\r
406 else if(evt.getSource()==selectAllSequenceMenuItem)
\r
407 selectAllSequenceMenuItem_actionPerformed();
\r
408 else if(evt.getSource()==deselectAllSequenceMenuItem)
\r
409 deselectAllSequenceMenuItem_actionPerformed();
\r
410 else if(evt.getSource()==invertSequenceMenuItem)
\r
411 invertSequenceMenuItem_actionPerformed();
\r
412 else if(evt.getSource()==remove2LeftMenuItem)
\r
413 remove2LeftMenuItem_actionPerformed();
\r
414 else if(evt.getSource()==remove2RightMenuItem)
\r
415 remove2RightMenuItem_actionPerformed();
\r
416 else if(evt.getSource()==removeGappedColumnMenuItem)
\r
417 removeGappedColumnMenuItem_actionPerformed();
\r
418 else if(evt.getSource()==removeAllGapsMenuItem)
\r
419 removeAllGapsMenuItem_actionPerformed();
\r
420 else if(evt.getSource()==findMenuItem)
\r
421 findMenuItem_actionPerformed();
\r
422 else if(evt.getSource()==font)
\r
423 font_actionPerformed();
\r
424 else if(evt.getSource()==featureSettings)
\r
425 featureSettings_actionPerformed();
\r
426 else if(evt.getSource()==overviewMenuItem)
\r
427 overviewMenuItem_actionPerformed();
\r
428 else if(evt.getSource()==noColourmenuItem)
\r
429 noColourmenuItem_actionPerformed();
\r
430 else if(evt.getSource()==clustalColour)
\r
431 clustalColour_actionPerformed();
\r
432 else if(evt.getSource()==zappoColour)
\r
433 zappoColour_actionPerformed();
\r
434 else if(evt.getSource()==taylorColour)
\r
435 taylorColour_actionPerformed();
\r
436 else if(evt.getSource()==hydrophobicityColour)
\r
437 hydrophobicityColour_actionPerformed();
\r
438 else if(evt.getSource()==helixColour)
\r
439 helixColour_actionPerformed();
\r
440 else if(evt.getSource()==strandColour)
\r
441 strandColour_actionPerformed();
\r
442 else if(evt.getSource()==turnColour)
\r
443 turnColour_actionPerformed();
\r
444 else if(evt.getSource()==buriedColour)
\r
445 buriedColour_actionPerformed();
\r
446 else if(evt.getSource()==nucleotideColour)
\r
447 nucleotideColour_actionPerformed();
\r
448 else if(evt.getSource()==modifyPID)
\r
449 modifyPID_actionPerformed();
\r
450 else if(evt.getSource()==modifyConservation)
\r
451 modifyConservation_actionPerformed();
\r
452 else if(evt.getSource()==userDefinedColour)
\r
453 userDefinedColour_actionPerformed();
\r
454 else if(evt.getSource()==PIDColour)
\r
455 PIDColour_actionPerformed();
\r
456 else if(evt.getSource()==BLOSUM62Colour)
\r
457 BLOSUM62Colour_actionPerformed();
\r
458 else if(evt.getSource()==annotationColour)
\r
459 new AnnotationColourChooser(viewport, alignPanel);
\r
460 else if(evt.getSource()==sortPairwiseMenuItem)
\r
461 sortPairwiseMenuItem_actionPerformed();
\r
462 else if(evt.getSource()==sortIDMenuItem)
\r
463 sortIDMenuItem_actionPerformed();
\r
464 else if(evt.getSource()==sortGroupMenuItem)
\r
465 sortGroupMenuItem_actionPerformed();
\r
466 else if(evt.getSource()==removeRedundancyMenuItem)
\r
467 removeRedundancyMenuItem_actionPerformed();
\r
468 else if(evt.getSource()==pairwiseAlignmentMenuItem)
\r
469 pairwiseAlignmentMenuItem_actionPerformed();
\r
470 else if(evt.getSource()==PCAMenuItem)
\r
471 PCAMenuItem_actionPerformed();
\r
472 else if(evt.getSource()==averageDistanceTreeMenuItem)
\r
473 averageDistanceTreeMenuItem_actionPerformed();
\r
474 else if(evt.getSource()==neighbourTreeMenuItem)
\r
475 neighbourTreeMenuItem_actionPerformed();
\r
476 else if(evt.getSource()==njTreeBlosumMenuItem)
\r
477 njTreeBlosumMenuItem_actionPerformed();
\r
478 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
\r
479 avTreeBlosumMenuItem_actionPerformed();
\r
480 else if(evt.getSource()==documentation)
\r
481 documentation_actionPerformed();
\r
482 else if(evt.getSource()==about)
\r
483 about_actionPerformed();
\r
487 public void inputText_actionPerformed()
\r
489 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
490 Frame frame = new Frame();
\r
492 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
495 protected void outputText_actionPerformed(ActionEvent e)
\r
497 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
498 Frame frame = new Frame();
\r
500 jalview.bin.JalviewLite.addFrame(frame,
\r
501 "Alignment output - " + e.getActionCommand(),
\r
503 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
\r
504 viewport.getAlignment().getSequences(),
\r
505 viewport.showJVSuffix));
\r
508 void launchFullApplication()
\r
510 StringBuffer url = new StringBuffer("http://bug.compbio.dundee.ac.uk:8080/Jalview/jalview?");
\r
512 url.append("open="+
\r
513 appendProtocol( applet.getParameter("file") ) );
\r
515 if(applet.getParameter("features")!=null)
\r
517 url.append( "&features=" );
\r
518 url.append( appendProtocol( applet.getParameter("features") ) );
\r
521 if(applet.getParameter("defaultColour")!=null)
\r
523 url.append("&colour=" +
\r
524 removeWhiteSpace(applet.getParameter("defaultColour"))
\r
528 if(applet.getParameter("userDefinedColour")!=null)
\r
530 url.append( "&colour=" +
\r
531 removeWhiteSpace( applet.getParameter("userDefinedColour") )
\r
535 showURL(url.toString(), "FULL_APP");
\r
539 String removeWhiteSpace(String colour)
\r
541 StringBuffer sb = new StringBuffer();
\r
542 for (int i = 0; i < colour.length(); i++)
\r
544 if (Character.isWhitespace(colour.charAt(i)))
\r
547 sb.append(colour.charAt(i));
\r
550 return sb.toString();
\r
554 String appendProtocol(String url)
\r
558 }catch(java.net.MalformedURLException ex)
\r
560 url = applet.getCodeBase()+url;
\r
565 public void closeMenuItem_actionPerformed()
\r
567 PaintRefresher.components.remove(viewport.alignment);
\r
568 if(PaintRefresher.components.size()==0 && applet==null)
\r
574 Stack historyList = new Stack();
\r
575 Stack redoList = new Stack();
\r
577 void updateEditMenuBar()
\r
579 if (historyList.size() > 0)
\r
581 undoMenuItem.setEnabled(true);
\r
582 HistoryItem hi = (HistoryItem) historyList.peek();
\r
583 undoMenuItem.setLabel("Undo " + hi.getDescription());
\r
587 undoMenuItem.setEnabled(false);
\r
588 undoMenuItem.setLabel("Undo");
\r
591 if (redoList.size() > 0)
\r
593 redoMenuItem.setEnabled(true);
\r
594 HistoryItem hi = (HistoryItem) redoList.peek();
\r
595 redoMenuItem.setLabel("Redo " + hi.getDescription());
\r
599 redoMenuItem.setEnabled(false);
\r
600 redoMenuItem.setLabel("Redo");
\r
604 public void addHistoryItem(HistoryItem hi)
\r
606 historyList.push(hi);
\r
607 updateEditMenuBar();
\r
610 protected void undoMenuItem_actionPerformed()
\r
612 HistoryItem hi = (HistoryItem) historyList.pop();
\r
613 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
\r
614 HistoryItem.HIDE));
\r
615 restoreHistoryItem(hi);
\r
616 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
619 protected void redoMenuItem_actionPerformed()
\r
621 HistoryItem hi = (HistoryItem) redoList.pop();
\r
622 restoreHistoryItem(hi);
\r
623 updateEditMenuBar();
\r
624 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
627 // used by undo and redo
\r
628 void restoreHistoryItem(HistoryItem hi)
\r
632 updateEditMenuBar();
\r
634 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
637 public void moveSelectedSequences(boolean up)
\r
639 SequenceGroup sg = viewport.getSelectionGroup();
\r
647 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
649 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
650 if (!sg.getSequences(false).contains(seq))
\r
655 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
656 if (sg.getSequences(false).contains(temp))
\r
661 viewport.alignment.getSequences().setElementAt(temp, i);
\r
662 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
667 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
669 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
670 if (!sg.getSequences(true).contains(seq))
\r
675 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
676 if (sg.getSequences(true).contains(temp))
\r
681 viewport.alignment.getSequences().setElementAt(temp, i);
\r
682 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
686 alignPanel.repaint();
\r
689 StringBuffer copiedSequences;
\r
690 protected void copy_actionPerformed()
\r
692 if (viewport.getSelectionGroup() == null)
\r
697 SequenceGroup sg = viewport.getSelectionGroup();
\r
698 copiedSequences = new StringBuffer();
\r
699 Hashtable orderedSeqs = new Hashtable();
\r
700 for (int i = 0; i < sg.getSize(false); i++)
\r
702 SequenceI seq = sg.getSequenceAt(i);
\r
703 int index = viewport.alignment.findIndex(seq);
\r
704 orderedSeqs.put(index + "", seq);
\r
707 int index = 0, startRes, endRes;
\r
710 for (int i = 0; i < sg.getSize(false); i++)
\r
712 SequenceI seq = null;
\r
714 while (seq == null)
\r
716 if (orderedSeqs.containsKey(index + ""))
\r
718 seq = (SequenceI) orderedSeqs.get(index + "");
\r
730 //Returns residue following index if gap
\r
731 startRes = seq.findPosition(sg.getStartRes());
\r
734 //Need to find the residue preceeding index if gap
\r
737 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
739 ch = seq.getCharAt(j);
\r
740 if (!jalview.util.Comparison.isGap( (ch)))
\r
748 endRes += seq.getStart() -1;
\r
751 copiedSequences.append(seq.getName() + "\t" +
\r
754 seq.getSequence(sg.getStartRes(),
\r
755 sg.getEndRes() + 1) + "\n");
\r
760 protected void pasteNew_actionPerformed()
\r
765 protected void pasteThis_actionPerformed()
\r
767 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
768 HistoryItem.PASTE));
\r
772 void paste(boolean newAlignment)
\r
776 if (copiedSequences == null)
\r
781 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
782 Vector seqs = new Vector();
\r
783 while (st.hasMoreElements())
\r
785 String name = st.nextToken();
\r
786 int start = Integer.parseInt(st.nextToken());
\r
787 int end = Integer.parseInt(st.nextToken());
\r
788 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
\r
792 viewport.alignment.addSequence(sequence);
\r
796 seqs.addElement(sequence);
\r
802 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
803 for (int i = 0; i < seqs.size(); i++)
\r
805 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
808 String newtitle = new String("Copied sequences");
\r
809 if (getTitle().startsWith("Copied sequences"))
\r
811 newtitle = getTitle();
\r
815 newtitle = newtitle.concat("- from " + getTitle());
\r
817 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
822 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
823 NEW_WINDOW_HEIGHT);
\r
827 viewport.setEndSeq(viewport.alignment.getHeight());
\r
828 viewport.alignment.getWidth();
\r
829 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
833 catch (Exception ex)
\r
834 {} // could be anything being pasted in here
\r
838 protected void cut_actionPerformed()
\r
840 copy_actionPerformed();
\r
841 delete_actionPerformed();
\r
844 protected void delete_actionPerformed()
\r
846 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
847 HistoryItem.HIDE));
\r
848 if (viewport.getSelectionGroup() == null)
\r
854 SequenceGroup sg = viewport.getSelectionGroup();
\r
855 boolean allSequences = false;
\r
856 if(sg.getSize(false)==viewport.alignment.getHeight())
\r
857 allSequences = true;
\r
859 for (int i = 0; i < sg.getSize(false); i++)
\r
861 SequenceI seq = sg.getSequenceAt(i);
\r
862 int index = viewport.getAlignment().findIndex(seq);
\r
863 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
865 // If the cut affects all sequences, remove highlighted columns
\r
868 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
869 sg.getEndRes() + 1);
\r
873 if (seq.getSequence().length() < 1)
\r
875 viewport.getAlignment().deleteSequence(seq);
\r
879 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
883 viewport.setSelectionGroup(null);
\r
884 viewport.alignment.deleteGroup(sg);
\r
885 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
886 if (viewport.getAlignment().getHeight() < 1)
\r
890 this.setVisible(false);
\r
892 catch (Exception ex)
\r
895 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
899 protected void deleteGroups_actionPerformed()
\r
901 viewport.alignment.deleteAllGroups();
\r
902 viewport.setSelectionGroup(null);
\r
904 alignPanel.repaint();
\r
907 public void selectAllSequenceMenuItem_actionPerformed()
\r
909 SequenceGroup sg = new SequenceGroup();
\r
910 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
912 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
914 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
915 viewport.setSelectionGroup(sg);
\r
916 alignPanel.repaint();
\r
917 PaintRefresher.Refresh(null, viewport.alignment);
\r
920 public void deselectAllSequenceMenuItem_actionPerformed()
\r
922 if(viewport.cursorMode)
\r
924 alignPanel.seqPanel.keyboardNo1=null;
\r
925 alignPanel.seqPanel.keyboardNo2=null;
\r
927 viewport.setSelectionGroup(null);
\r
928 viewport.getColumnSelection().clear();
\r
929 viewport.setSelectionGroup(null);
\r
930 alignPanel.idPanel.idCanvas.searchResults = null;
\r
931 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
932 alignPanel.repaint();
\r
933 PaintRefresher.Refresh(null, viewport.alignment);
\r
936 public void invertSequenceMenuItem_actionPerformed()
\r
938 SequenceGroup sg = viewport.getSelectionGroup();
\r
939 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
941 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
944 PaintRefresher.Refresh(null, viewport.alignment);
\r
947 public void remove2LeftMenuItem_actionPerformed()
\r
949 ColumnSelection colSel = viewport.getColumnSelection();
\r
950 if (colSel.size() > 0)
\r
952 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
953 HistoryItem.HIDE));
\r
954 int min = colSel.getMin();
\r
955 viewport.getAlignment().trimLeft(min);
\r
956 colSel.compensateForEdit(0, min);
\r
958 if (viewport.getSelectionGroup() != null)
\r
960 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
963 Vector groups = viewport.alignment.getGroups();
\r
964 for (int i = 0; i < groups.size(); i++)
\r
966 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
967 if (!sg.adjustForRemoveLeft(min))
\r
969 viewport.alignment.deleteGroup(sg);
\r
972 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
976 public void remove2RightMenuItem_actionPerformed()
\r
978 ColumnSelection colSel = viewport.getColumnSelection();
\r
979 if (colSel.size() > 0)
\r
981 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
982 HistoryItem.HIDE));
\r
983 int max = colSel.getMax();
\r
984 viewport.getAlignment().trimRight(max);
\r
985 if (viewport.getSelectionGroup() != null)
\r
987 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
990 Vector groups = viewport.alignment.getGroups();
\r
991 for (int i = 0; i < groups.size(); i++)
\r
993 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
994 if (!sg.adjustForRemoveRight(max))
\r
996 viewport.alignment.deleteGroup(sg);
\r
999 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1004 public void removeGappedColumnMenuItem_actionPerformed()
\r
1006 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1007 viewport.alignment,
\r
1008 HistoryItem.HIDE));
\r
1010 //This is to maintain viewport position on first residue
\r
1011 //of first sequence
\r
1012 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1013 int startRes = seq.findPosition(viewport.startRes);
\r
1015 viewport.getAlignment().removeGaps();
\r
1017 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1019 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1022 public void removeAllGapsMenuItem_actionPerformed()
\r
1024 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1025 HistoryItem.HIDE));
\r
1027 //This is to maintain viewport position on first residue
\r
1028 //of first sequence
\r
1029 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1030 int startRes = seq.findPosition(viewport.startRes);
\r
1032 SequenceI current;
\r
1037 int start=0, end = viewport.alignment.getWidth();
\r
1039 if (viewport.getSelectionGroup() != null
\r
1040 && viewport.getSelectionGroup().getSequences(false) != null
\r
1041 && viewport.getSelectionGroup().getSize(false)>0)
\r
1043 seqs = viewport.getSelectionGroup().getSequences(true);
\r
1044 start = viewport.getSelectionGroup().getStartRes();
\r
1045 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1048 seqs = viewport.alignment.getSequences();
\r
1050 for (int i = 0; i < seqs.size(); i++)
\r
1052 current = (SequenceI) seqs.elementAt(i);
\r
1053 jSize = current.getLength();
\r
1055 // Removing a range is much quicker than removing gaps
\r
1056 // one by one for long sequences
\r
1058 int rangeStart=-1, rangeEnd=-1;
\r
1062 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1064 if(rangeStart==-1)
\r
1079 current.deleteChars(rangeStart, rangeEnd);
\r
1080 j-=rangeEnd-rangeStart;
\r
1081 jSize-=rangeEnd-rangeStart;
\r
1089 while (j < end && j < jSize);
\r
1092 current.deleteChars(rangeStart, rangeEnd);
\r
1095 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1096 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1099 public void alignmentChanged()
\r
1101 viewport.alignment.padGaps();
\r
1102 if(viewport.autocalculateConsensus)
\r
1104 viewport.updateConsensus();
\r
1105 viewport.updateConservation();
\r
1108 resetAllColourSchemes();
\r
1109 if(alignPanel.overviewPanel!=null)
\r
1110 alignPanel.overviewPanel.updateOverviewImage();
\r
1112 viewport.alignment.adjustSequenceAnnotations();
\r
1113 alignPanel.repaint();
\r
1116 void resetAllColourSchemes()
\r
1118 ColourSchemeI cs = viewport.globalColourScheme;
\r
1121 if (cs instanceof ClustalxColourScheme)
\r
1123 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1124 resetClustalX(viewport.alignment.getSequences(),
\r
1125 viewport.alignment.getWidth());
\r
1128 cs.setConsensus(viewport.vconsensus);
\r
1129 if (cs.conservationApplied())
\r
1131 Alignment al = (Alignment) viewport.alignment;
\r
1132 Conservation c = new Conservation("All",
\r
1133 ResidueProperties.propHash, 3,
\r
1134 al.getSequences(), 0,
\r
1135 al.getWidth() - 1);
\r
1137 c.verdict(false, viewport.ConsPercGaps);
\r
1139 cs.setConservation(c);
\r
1143 int s, sSize = viewport.alignment.getGroups().size();
\r
1144 for(s=0; s<sSize; s++)
\r
1146 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1147 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1149 ((ClustalxColourScheme)sg.cs).resetClustalX(
\r
1150 sg.getSequences(true), sg.getWidth());
\r
1152 sg.recalcConservation();
\r
1158 public void findMenuItem_actionPerformed()
\r
1160 new Finder(alignPanel);
\r
1163 public void font_actionPerformed()
\r
1165 new FontChooser(alignPanel);
\r
1169 public void seqLimits_itemStateChanged()
\r
1171 viewport.setShowJVSuffix(seqLimits.getState());
\r
1172 alignPanel.fontChanged();
\r
1173 alignPanel.repaint();
\r
1177 protected void colourTextMenuItem_actionPerformed()
\r
1179 viewport.setColourText(colourTextMenuItem.getState());
\r
1180 alignPanel.repaint();
\r
1183 protected void wrapMenuItem_actionPerformed()
\r
1185 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1186 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1187 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1188 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1189 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1190 alignPanel.repaint();
\r
1193 protected void scaleAbove_actionPerformed()
\r
1195 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1196 alignPanel.repaint();
\r
1199 protected void scaleLeft_actionPerformed()
\r
1201 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1202 alignPanel.repaint();
\r
1205 protected void scaleRight_actionPerformed()
\r
1207 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1208 alignPanel.repaint();
\r
1211 public void viewBoxesMenuItem_actionPerformed()
\r
1213 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1214 alignPanel.repaint();
\r
1217 public void viewTextMenuItem_actionPerformed()
\r
1219 viewport.setShowText(viewTextMenuItem.getState());
\r
1220 alignPanel.repaint();
\r
1223 protected void renderGapsMenuItem_actionPerformed()
\r
1225 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1226 alignPanel.repaint();
\r
1229 public void annotationPanelMenuItem_actionPerformed()
\r
1231 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1232 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1235 public void featureSettings_actionPerformed()
\r
1237 new FeatureSettings(viewport, alignPanel);
\r
1240 public void overviewMenuItem_actionPerformed()
\r
1242 if (alignPanel.overviewPanel != null)
\r
1247 Frame frame = new Frame();
\r
1248 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1249 frame.add(overview);
\r
1250 // +50 must allow for applet frame window
\r
1251 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1252 overview.preferredSize().width,
\r
1253 overview.preferredSize().height + 50);
\r
1256 frame.addWindowListener(new WindowAdapter()
\r
1258 public void windowClosing(WindowEvent e)
\r
1260 alignPanel.setOverviewPanel(null);
\r
1264 alignPanel.setOverviewPanel(overview);
\r
1268 protected void noColourmenuItem_actionPerformed()
\r
1270 changeColour(null);
\r
1273 public void clustalColour_actionPerformed()
\r
1275 abovePIDThreshold.setState(false);
\r
1276 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1277 viewport.alignment.getWidth()));
\r
1280 public void zappoColour_actionPerformed()
\r
1282 changeColour(new ZappoColourScheme());
\r
1285 public void taylorColour_actionPerformed()
\r
1287 changeColour(new TaylorColourScheme());
\r
1290 public void hydrophobicityColour_actionPerformed()
\r
1292 changeColour(new HydrophobicColourScheme());
\r
1295 public void helixColour_actionPerformed()
\r
1297 changeColour(new HelixColourScheme());
\r
1300 public void strandColour_actionPerformed()
\r
1302 changeColour(new StrandColourScheme());
\r
1305 public void turnColour_actionPerformed()
\r
1307 changeColour(new TurnColourScheme());
\r
1310 public void buriedColour_actionPerformed()
\r
1312 changeColour(new BuriedColourScheme());
\r
1315 public void nucleotideColour_actionPerformed()
\r
1317 changeColour(new NucleotideColourScheme());
\r
1320 protected void applyToAllGroups_actionPerformed()
\r
1322 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1325 void changeColour(ColourSchemeI cs)
\r
1327 int threshold = 0;
\r
1331 if (viewport.getAbovePIDThreshold())
\r
1333 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1335 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1337 viewport.setGlobalColourScheme(cs);
\r
1341 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1344 if (viewport.getConservationSelected())
\r
1347 Alignment al = (Alignment) viewport.alignment;
\r
1348 Conservation c = new Conservation("All",
\r
1349 ResidueProperties.propHash, 3,
\r
1350 al.getSequences(), 0,
\r
1351 al.getWidth() - 1);
\r
1354 c.verdict(false, viewport.ConsPercGaps);
\r
1356 cs.setConservation(c);
\r
1358 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1364 cs.setConservation(null);
\r
1367 cs.setConsensus(viewport.vconsensus);
\r
1370 viewport.setGlobalColourScheme(cs);
\r
1372 if (viewport.getColourAppliesToAllGroups())
\r
1374 Vector groups = viewport.alignment.getGroups();
\r
1375 for (int i = 0; i < groups.size(); i++)
\r
1377 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1384 if (cs instanceof ClustalxColourScheme)
\r
1386 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
\r
1392 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1394 catch (Exception ex)
\r
1396 ex.printStackTrace();
\r
1401 if (viewport.getAbovePIDThreshold()
\r
1402 || cs instanceof PIDColourScheme
\r
1403 || cs instanceof Blosum62ColourScheme)
\r
1405 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1406 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
\r
1409 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1411 if (viewport.getConservationSelected())
\r
1413 Conservation c = new Conservation("Group",
\r
1414 ResidueProperties.propHash, 3,
\r
1415 sg.getSequences(true), 0,
\r
1416 viewport.alignment.getWidth() - 1);
\r
1418 c.verdict(false, viewport.ConsPercGaps);
\r
1419 sg.cs.setConservation(c);
\r
1423 sg.cs.setConservation(null);
\r
1424 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1431 if (alignPanel.getOverviewPanel() != null)
\r
1433 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1436 alignPanel.repaint();
\r
1441 protected void modifyPID_actionPerformed()
\r
1443 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1445 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1447 SliderPanel.showPIDSlider();
\r
1451 protected void modifyConservation_actionPerformed()
\r
1453 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1455 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1457 SliderPanel.showConservationSlider();
\r
1461 protected void conservationMenuItem_actionPerformed()
\r
1463 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1465 viewport.setAbovePIDThreshold(false);
\r
1466 abovePIDThreshold.setState(false);
\r
1468 changeColour(viewport.getGlobalColourScheme());
\r
1470 modifyConservation_actionPerformed();
\r
1473 public void abovePIDThreshold_actionPerformed()
\r
1475 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1477 conservationMenuItem.setState(false);
\r
1478 viewport.setConservationSelected(false);
\r
1480 changeColour(viewport.getGlobalColourScheme());
\r
1482 modifyPID_actionPerformed();
\r
1485 public void userDefinedColour_actionPerformed()
\r
1487 new UserDefinedColours(alignPanel, null);
\r
1490 public void PIDColour_actionPerformed()
\r
1492 changeColour(new PIDColourScheme());
\r
1495 public void BLOSUM62Colour_actionPerformed()
\r
1497 changeColour(new Blosum62ColourScheme());
\r
1500 public void sortPairwiseMenuItem_actionPerformed()
\r
1502 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1503 HistoryItem.SORT));
\r
1504 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1505 viewport.getAlignment().getSequenceAt(0));
\r
1506 alignPanel.repaint();
\r
1509 public void sortIDMenuItem_actionPerformed()
\r
1511 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1512 HistoryItem.SORT));
\r
1513 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1514 alignPanel.repaint();
\r
1517 public void sortGroupMenuItem_actionPerformed()
\r
1519 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1520 HistoryItem.SORT));
\r
1521 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1522 alignPanel.repaint();
\r
1526 public void removeRedundancyMenuItem_actionPerformed()
\r
1528 new RedundancyPanel(alignPanel);
\r
1531 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1533 if (viewport.getSelectionGroup().getSize(false) > 1)
\r
1535 Frame frame = new Frame();
\r
1536 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1537 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1541 public void PCAMenuItem_actionPerformed()
\r
1543 //are the sequences aligned?
\r
1544 if (!viewport.alignment.isAligned())
\r
1546 SequenceI current;
\r
1547 int Width = viewport.getAlignment().getWidth();
\r
1549 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1552 current = viewport.getAlignment().getSequenceAt(i);
\r
1554 if (current.getLength() < Width)
\r
1556 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1559 alignPanel.repaint();
\r
1562 if ( (viewport.getSelectionGroup() != null &&
\r
1563 viewport.getSelectionGroup().getSize(false) < 4 &&
\r
1564 viewport.getSelectionGroup().getSize(false) > 0)
\r
1565 || viewport.getAlignment().getHeight() < 4)
\r
1572 new PCAPanel(viewport);
\r
1574 catch (java.lang.OutOfMemoryError ex)
\r
1580 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1582 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1585 public void neighbourTreeMenuItem_actionPerformed()
\r
1587 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1590 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1592 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1595 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1597 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1600 void NewTreePanel(String type, String pwType, String title)
\r
1602 //are the sequences aligned?
\r
1603 if (!viewport.alignment.isAligned())
\r
1605 SequenceI current;
\r
1606 int Width = viewport.getAlignment().getWidth();
\r
1608 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1611 current = viewport.getAlignment().getSequenceAt(i);
\r
1613 if (current.getLength() < Width)
\r
1615 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1618 alignPanel.repaint();
\r
1622 final TreePanel tp;
\r
1623 if (viewport.getSelectionGroup() != null &&
\r
1624 viewport.getSelectionGroup().getSize(false) > 3)
\r
1626 tp = new TreePanel(viewport,
\r
1627 viewport.getSelectionGroup().getSequences(false),
\r
1630 0, viewport.alignment.getWidth());
\r
1634 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1635 type, pwType, 0, viewport.alignment.getWidth());
\r
1638 addTreeMenuItem(tp, title);
\r
1640 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1643 void loadTree_actionPerformed()
\r
1645 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1646 cap.setText("Paste your Newick tree file here.");
\r
1647 cap.treeImport = true;
\r
1648 Frame frame = new Frame();
\r
1650 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1653 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1655 TreePanel tp = new TreePanel(viewport,
\r
1656 viewport.getAlignment().getSequences(),
\r
1657 tree, "From File - ", treeFile);
\r
1658 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1659 addTreeMenuItem(tp, treeFile);
\r
1662 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1664 final MenuItem item = new MenuItem(title);
\r
1665 sortByTreeMenu.add(item);
\r
1666 item.addActionListener(new java.awt.event.ActionListener()
\r
1668 public void actionPerformed(ActionEvent evt)
\r
1670 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1671 HistoryItem.SORT));
\r
1672 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1673 alignPanel.repaint();
\r
1677 treePanel.addWindowListener(new WindowAdapter()
\r
1679 public void windowClosing(WindowEvent e)
\r
1681 sortByTreeMenu.remove(item);
\r
1686 protected void documentation_actionPerformed()
\r
1688 showURL("http://www.jalview.org/help.html", "HELP");
\r
1691 protected void about_actionPerformed()
\r
1694 class AboutPanel extends Canvas
\r
1697 public AboutPanel(String version)
\r
1698 { this.version = version; }
\r
1700 public void paint(Graphics g)
\r
1702 g.setColor(Color.white);
\r
1703 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1704 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1705 FontMetrics fm = g.getFontMetrics();
\r
1706 int fh = fm.getHeight();
\r
1708 g.setColor(Color.black);
\r
1709 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1710 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1711 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1712 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1714 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1717 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1719 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1720 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1722 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1726 String version = "test";
\r
1727 java.net.URL url = getClass().getResource("/.build_properties");
\r
1732 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1733 url.openStream()));
\r
1735 while ( (line = reader.readLine()) != null)
\r
1737 if (line.indexOf("VERSION") > -1)
\r
1739 version = line.substring(line.indexOf("=") + 1);
\r
1743 catch (Exception ex)
\r
1745 ex.printStackTrace();
\r
1750 Frame frame = new Frame();
\r
1751 frame.add(new AboutPanel(version));
\r
1752 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1756 public void showURL(String url, String target)
\r
1758 if (applet == null)
\r
1760 System.out.println("Not running as applet - no browser available.");
\r
1766 System.out.println("Show url: "+url);
\r
1767 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1770 catch (Exception ex)
\r
1772 ex.printStackTrace();
\r
1778 //////////////////////////////////////////////////////////////////////////////////
\r
1779 //JBuilder Graphics here
\r
1781 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1782 protected Menu fileMenu = new Menu("File");
\r
1783 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1784 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
\r
1785 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1786 protected Menu editMenu = new Menu("Edit");
\r
1787 protected Menu viewMenu = new Menu("View");
\r
1788 protected Menu colourMenu = new Menu("Colour");
\r
1789 protected Menu calculateMenu = new Menu("Calculate");
\r
1790 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1791 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1792 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1793 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1794 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1795 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1796 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1797 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1798 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1799 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1800 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1801 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1802 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1803 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1804 protected MenuItem PCAMenuItem = new MenuItem();
\r
1805 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1806 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1807 BorderLayout borderLayout1 = new BorderLayout();
\r
1808 public Label statusBar = new Label();
\r
1809 protected Menu outputTextboxMenu = new Menu();
\r
1810 protected MenuItem clustalColour = new MenuItem();
\r
1811 protected MenuItem zappoColour = new MenuItem();
\r
1812 protected MenuItem taylorColour = new MenuItem();
\r
1813 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1814 protected MenuItem helixColour = new MenuItem();
\r
1815 protected MenuItem strandColour = new MenuItem();
\r
1816 protected MenuItem turnColour = new MenuItem();
\r
1817 protected MenuItem buriedColour = new MenuItem();
\r
1818 protected MenuItem userDefinedColour = new MenuItem();
\r
1819 protected MenuItem PIDColour = new MenuItem();
\r
1820 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1821 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1822 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1823 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1824 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1825 MenuItem overviewMenuItem = new MenuItem();
\r
1826 protected MenuItem undoMenuItem = new MenuItem();
\r
1827 protected MenuItem redoMenuItem = new MenuItem();
\r
1828 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1829 MenuItem noColourmenuItem = new MenuItem();
\r
1830 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1831 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1832 MenuItem findMenuItem = new MenuItem();
\r
1833 Menu searchMenu = new Menu();
\r
1834 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1835 protected MenuItem nucleotideColour = new MenuItem();
\r
1836 MenuItem deleteGroups = new MenuItem();
\r
1837 MenuItem delete = new MenuItem();
\r
1838 MenuItem copy = new MenuItem();
\r
1839 MenuItem cut = new MenuItem();
\r
1840 Menu pasteMenu = new Menu();
\r
1841 MenuItem pasteNew = new MenuItem();
\r
1842 MenuItem pasteThis = new MenuItem();
\r
1843 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1844 protected MenuItem font = new MenuItem();
\r
1845 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1846 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1847 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1848 MenuItem modifyPID = new MenuItem();
\r
1849 MenuItem modifyConservation = new MenuItem();
\r
1850 protected CheckboxMenuItem autoCalculate
\r
1851 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
1852 protected Menu sortByTreeMenu = new Menu();
\r
1853 Menu sort = new Menu();
\r
1854 Menu calculate = new Menu();
\r
1855 MenuItem inputText = new MenuItem();
\r
1856 Menu helpMenu = new Menu();
\r
1857 MenuItem documentation = new MenuItem();
\r
1858 MenuItem about = new MenuItem();
\r
1859 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1860 Panel embeddedMenu;
\r
1861 Label embeddedEdit;
\r
1862 Label embeddedSearch;
\r
1863 Label embeddedView;
\r
1864 Label embeddedColour;
\r
1865 Label embeddedFile;
\r
1866 Label embeddedHelp;
\r
1867 Label embeddedCalculate;
\r
1868 FlowLayout flowLayout1;
\r
1870 private void jbInit() throws Exception {
\r
1872 setMenuBar(alignFrameMenuBar);
\r
1876 // dynamically fill save as menu with available formats
\r
1877 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1880 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1883 item.addActionListener(new java.awt.event.ActionListener()
\r
1885 public void actionPerformed(ActionEvent e)
\r
1887 outputText_actionPerformed(e);
\r
1891 outputTextboxMenu.add(item);
\r
1893 closeMenuItem.addActionListener(this);
\r
1894 loadApplication.addActionListener(this);
\r
1896 loadTree.addActionListener(this);
\r
1897 selectAllSequenceMenuItem.addActionListener(this);
\r
1898 deselectAllSequenceMenuItem.addActionListener(this);
\r
1899 invertSequenceMenuItem.addActionListener(this);
\r
1900 remove2LeftMenuItem.setLabel("Remove Left");
\r
1901 remove2LeftMenuItem.addActionListener(this);
\r
1902 remove2RightMenuItem.setLabel("Remove Right");
\r
1903 remove2RightMenuItem.addActionListener(this);
\r
1904 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1905 removeGappedColumnMenuItem.addActionListener(this);
\r
1906 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1907 removeAllGapsMenuItem.addActionListener(this);
\r
1908 viewBoxesMenuItem.setLabel("Boxes");
\r
1909 viewBoxesMenuItem.setState(true);
\r
1910 viewBoxesMenuItem.addItemListener(this);
\r
1911 viewTextMenuItem.setLabel("Text");
\r
1912 viewTextMenuItem.setState(true);
\r
1913 viewTextMenuItem.addItemListener(this);
\r
1914 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1915 sortPairwiseMenuItem.addActionListener(this);
\r
1916 sortIDMenuItem.setLabel("by ID");
\r
1917 sortIDMenuItem.addActionListener(this);
\r
1918 sortGroupMenuItem.setLabel("by Group");
\r
1919 sortGroupMenuItem.addActionListener(this);
\r
1920 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1921 removeRedundancyMenuItem.addActionListener(this);
\r
1922 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1923 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1924 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1925 PCAMenuItem.addActionListener(this);
\r
1926 averageDistanceTreeMenuItem.setLabel(
\r
1927 "Average Distance Using % Identity");
\r
1928 averageDistanceTreeMenuItem.addActionListener(this);
\r
1929 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1930 neighbourTreeMenuItem.addActionListener(this);
\r
1931 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1932 statusBar.setBackground(Color.white);
\r
1933 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1934 statusBar.setText("Status bar");
\r
1935 outputTextboxMenu.setLabel("Output to Textbox");
\r
1936 clustalColour.setLabel("Clustalx");
\r
1938 clustalColour.addActionListener(this);
\r
1939 zappoColour.setLabel("Zappo");
\r
1940 zappoColour.addActionListener(this);
\r
1941 taylorColour.setLabel("Taylor");
\r
1942 taylorColour.addActionListener(this);
\r
1943 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1944 hydrophobicityColour.addActionListener(this);
\r
1945 helixColour.setLabel("Helix Propensity");
\r
1946 helixColour.addActionListener(this);
\r
1947 strandColour.setLabel("Strand Propensity");
\r
1948 strandColour.addActionListener(this);
\r
1949 turnColour.setLabel("Turn Propensity");
\r
1950 turnColour.addActionListener(this);
\r
1951 buriedColour.setLabel("Buried Index");
\r
1952 buriedColour.addActionListener(this);
\r
1953 userDefinedColour.setLabel("User Defined...");
\r
1954 userDefinedColour.addActionListener(this);
\r
1955 PIDColour.setLabel("Percentage Identity");
\r
1956 PIDColour.addActionListener(this);
\r
1957 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1958 BLOSUM62Colour.addActionListener(this);
\r
1959 avDistanceTreeBlosumMenuItem.setLabel(
\r
1960 "Average Distance Using BLOSUM62");
\r
1961 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1962 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1963 njTreeBlosumMenuItem.addActionListener(this);
\r
1964 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1965 annotationPanelMenuItem.addItemListener(this);
\r
1966 colourTextMenuItem.setLabel("Colour Text");
\r
1967 colourTextMenuItem.addItemListener(this);
\r
1968 overviewMenuItem.setLabel("Overview Window");
\r
1969 overviewMenuItem.addActionListener(this);
\r
1970 undoMenuItem.setEnabled(false);
\r
1971 undoMenuItem.setLabel("Undo");
\r
1972 undoMenuItem.addActionListener(this);
\r
1973 redoMenuItem.setEnabled(false);
\r
1974 redoMenuItem.setLabel("Redo");
\r
1975 redoMenuItem.addActionListener(this);
\r
1976 conservationMenuItem.setLabel("by Conservation");
\r
1977 conservationMenuItem.addItemListener(this);
\r
1978 noColourmenuItem.setLabel("None");
\r
1979 noColourmenuItem.addActionListener(this);
\r
1980 wrapMenuItem.setLabel("Wrap");
\r
1981 wrapMenuItem.addItemListener(this);
\r
1982 renderGapsMenuItem.setLabel("Show Gaps");
\r
1983 renderGapsMenuItem.setState(true);
\r
1984 renderGapsMenuItem.addItemListener(this);
\r
1985 findMenuItem.setLabel("Find...");
\r
1986 findMenuItem.addActionListener(this);
\r
1987 searchMenu.setLabel("Search");
\r
1989 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1990 abovePIDThreshold.addItemListener(this);
\r
1991 nucleotideColour.setLabel("Nucleotide");
\r
1992 nucleotideColour.addActionListener(this);
\r
1993 deleteGroups.setLabel("Undefine Groups");
\r
1994 deleteGroups.addActionListener(this);
\r
1995 copy.setLabel("Copy");
\r
1996 copy.addActionListener(this);
\r
1997 cut.setLabel("Cut");
\r
1998 cut.addActionListener(this);
\r
1999 delete.setLabel("Delete");
\r
2000 delete.addActionListener(this);
\r
2001 pasteMenu.setLabel("Paste");
\r
2002 pasteNew.setLabel("To New Alignment");
\r
2003 pasteNew.addActionListener(this);
\r
2004 pasteThis.setLabel("Add To This Alignment");
\r
2005 pasteThis.addActionListener(this);
\r
2006 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2007 applyToAllGroups.setState(true);
\r
2008 applyToAllGroups.addItemListener(this);
\r
2009 font.setLabel("Font...");
\r
2010 font.addActionListener(this);
\r
2011 scaleAbove.setLabel("Scale Above");
\r
2012 scaleAbove.setState(true);
\r
2013 scaleAbove.setEnabled(false);
\r
2014 scaleAbove.addItemListener(this);
\r
2015 scaleLeft.setEnabled(false);
\r
2016 scaleLeft.setState(true);
\r
2017 scaleLeft.setLabel("Scale Left");
\r
2018 scaleLeft.addItemListener(this);
\r
2019 scaleRight.setEnabled(false);
\r
2020 scaleRight.setState(true);
\r
2021 scaleRight.setLabel("Scale Right");
\r
2022 scaleRight.addItemListener(this);
\r
2023 modifyPID.setLabel("Modify Identity Threshold...");
\r
2024 modifyPID.addActionListener(this);
\r
2025 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2026 modifyConservation.addActionListener(this);
\r
2027 sortByTreeMenu.setLabel("By Tree Order");
\r
2028 sort.setLabel("Sort");
\r
2029 calculate.setLabel("Calculate Tree");
\r
2030 autoCalculate.addItemListener(this);
\r
2031 inputText.setLabel("Input from textbox");
\r
2032 inputText.addActionListener(this);
\r
2034 helpMenu.setLabel("Help");
\r
2035 documentation.setLabel("Documentation");
\r
2036 documentation.addActionListener(this);
\r
2038 about.setLabel("About...");
\r
2039 about.addActionListener(this);
\r
2040 seqLimits.setState(true);
\r
2041 seqLimits.setLabel("Show Sequence Limits");
\r
2042 seqLimits.addItemListener(this);
\r
2043 featureSettings.setLabel("Feature Settings...");
\r
2044 featureSettings.addActionListener(this);
\r
2045 sequenceFeatures.setLabel("Sequence Features");
\r
2046 sequenceFeatures.addItemListener(this);
\r
2047 sequenceFeatures.setState(false);
\r
2048 annotationColour.setLabel("by Annotation...");
\r
2049 annotationColour.addActionListener(this);
\r
2051 alignFrameMenuBar.add(fileMenu);
\r
2052 alignFrameMenuBar.add(editMenu);
\r
2053 alignFrameMenuBar.add(searchMenu);
\r
2054 alignFrameMenuBar.add(viewMenu);
\r
2055 alignFrameMenuBar.add(colourMenu);
\r
2056 alignFrameMenuBar.add(calculateMenu);
\r
2057 alignFrameMenuBar.add(helpMenu);
\r
2058 fileMenu.add(inputText);
\r
2059 fileMenu.add(outputTextboxMenu);
\r
2060 // fileMenu.add(loadApplication);
\r
2061 fileMenu.addSeparator();
\r
2062 fileMenu.add(loadTree);
\r
2063 fileMenu.add(closeMenuItem);
\r
2064 editMenu.add(undoMenuItem);
\r
2065 editMenu.add(redoMenuItem);
\r
2066 editMenu.add(cut);
\r
2067 editMenu.add(copy);
\r
2068 editMenu.add(pasteMenu);
\r
2069 editMenu.add(delete);
\r
2070 editMenu.addSeparator();
\r
2071 editMenu.add(selectAllSequenceMenuItem);
\r
2072 editMenu.add(deselectAllSequenceMenuItem);
\r
2073 editMenu.add(invertSequenceMenuItem);
\r
2074 editMenu.add(deleteGroups);
\r
2075 editMenu.addSeparator();
\r
2076 editMenu.add(remove2LeftMenuItem);
\r
2077 editMenu.add(remove2RightMenuItem);
\r
2078 editMenu.add(removeGappedColumnMenuItem);
\r
2079 editMenu.add(removeAllGapsMenuItem);
\r
2080 editMenu.add(removeRedundancyMenuItem);
\r
2081 searchMenu.add(findMenuItem);
\r
2082 viewMenu.add(font);
\r
2083 viewMenu.addSeparator();
\r
2084 viewMenu.add(seqLimits);
\r
2085 viewMenu.addSeparator();
\r
2086 viewMenu.add(wrapMenuItem);
\r
2087 viewMenu.add(scaleAbove);
\r
2088 viewMenu.add(scaleLeft);
\r
2089 viewMenu.add(scaleRight);
\r
2090 viewMenu.addSeparator();
\r
2091 viewMenu.add(viewBoxesMenuItem);
\r
2092 viewMenu.add(viewTextMenuItem);
\r
2093 viewMenu.add(colourTextMenuItem);
\r
2094 viewMenu.add(renderGapsMenuItem);
\r
2095 viewMenu.add(annotationPanelMenuItem);
\r
2096 viewMenu.addSeparator();
\r
2097 viewMenu.add(sequenceFeatures);
\r
2098 viewMenu.add(featureSettings);
\r
2099 viewMenu.addSeparator();
\r
2100 viewMenu.add(overviewMenuItem);
\r
2101 colourMenu.add(applyToAllGroups);
\r
2102 colourMenu.addSeparator();
\r
2103 colourMenu.add(noColourmenuItem);
\r
2104 colourMenu.add(clustalColour);
\r
2105 colourMenu.add(BLOSUM62Colour);
\r
2106 colourMenu.add(PIDColour);
\r
2107 colourMenu.add(zappoColour);
\r
2108 colourMenu.add(taylorColour);
\r
2109 colourMenu.add(hydrophobicityColour);
\r
2110 colourMenu.add(helixColour);
\r
2111 colourMenu.add(strandColour);
\r
2112 colourMenu.add(turnColour);
\r
2113 colourMenu.add(buriedColour);
\r
2114 colourMenu.add(nucleotideColour);
\r
2115 colourMenu.add(userDefinedColour);
\r
2116 colourMenu.addSeparator();
\r
2117 colourMenu.add(conservationMenuItem);
\r
2118 colourMenu.add(modifyConservation);
\r
2119 colourMenu.add(abovePIDThreshold);
\r
2120 colourMenu.add(modifyPID);
\r
2121 colourMenu.add(annotationColour);
\r
2122 calculateMenu.add(sort);
\r
2123 calculateMenu.add(calculate);
\r
2124 calculateMenu.addSeparator();
\r
2125 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2126 calculateMenu.add(PCAMenuItem);
\r
2127 calculateMenu.add(autoCalculate);
\r
2128 this.add(statusBar, BorderLayout.SOUTH);
\r
2129 pasteMenu.add(pasteNew);
\r
2130 pasteMenu.add(pasteThis);
\r
2131 sort.add(sortIDMenuItem);
\r
2132 sort.add(sortByTreeMenu);
\r
2133 sort.add(sortGroupMenuItem);
\r
2134 sort.add(sortPairwiseMenuItem);
\r
2135 calculate.add(averageDistanceTreeMenuItem);
\r
2136 calculate.add(neighbourTreeMenuItem);
\r
2137 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2138 calculate.add(njTreeBlosumMenuItem);
\r
2139 helpMenu.add(documentation);
\r
2140 helpMenu.add(about);
\r
2143 public void setEmbedded()
\r
2146 embeddedMenu = new Panel();
\r
2147 embeddedEdit = new Label();
\r
2148 embeddedSearch = new Label();
\r
2149 embeddedView = new Label();
\r
2150 embeddedColour = new Label();
\r
2151 embeddedFile = new Label();
\r
2152 embeddedHelp = new Label();
\r
2153 embeddedCalculate = new Label();
\r
2154 flowLayout1 = new FlowLayout();
\r
2155 embeddedMenu.setBackground(Color.lightGray);
\r
2156 embeddedMenu.setLayout(flowLayout1);
\r
2157 embeddedEdit.setText("Edit");
\r
2158 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2159 embeddedSearch.setText("Search");
\r
2160 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2161 embeddedView.setText("View");
\r
2162 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2163 embeddedColour.setText("Colour");
\r
2164 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2165 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2166 embeddedFile.setText("File");
\r
2167 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2168 embeddedHelp.setText("Help");
\r
2169 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2170 embeddedCalculate.setText("Calculate");
\r
2171 embeddedMenu.add(embeddedFile);
\r
2172 embeddedMenu.add(embeddedEdit);
\r
2173 embeddedMenu.add(embeddedSearch);
\r
2174 embeddedMenu.add(embeddedView);
\r
2175 embeddedMenu.add(embeddedColour);
\r
2176 embeddedMenu.add(embeddedCalculate);
\r
2177 embeddedMenu.add(embeddedHelp);
\r
2178 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2179 flowLayout1.setHgap(2);
\r
2180 flowLayout1.setVgap(0);
\r
2181 embeddedFile.addMouseListener(this);
\r
2182 embeddedEdit.addMouseListener(this);
\r
2183 embeddedSearch.addMouseListener(this);
\r
2184 embeddedView.addMouseListener(this);
\r
2185 embeddedColour.addMouseListener(this);
\r
2186 embeddedCalculate.addMouseListener(this);
\r
2187 embeddedHelp.addMouseListener(this);
\r
2189 // setVisible(false);
\r
2190 fileMenu.remove(closeMenuItem);
\r
2191 fileMenu.remove(3); // Seperator
\r
2193 applet.setLayout(new BorderLayout());
\r
2194 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2195 applet.add(statusBar, BorderLayout.SOUTH);
\r
2196 // applet.validate();
\r
2198 alignPanel.setSize(applet.size().width, applet.size().height
\r
2199 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2201 applet.add(alignPanel, BorderLayout.CENTER);
\r
2202 applet.validate();
\r
2208 PopupMenu filePopup, editPopup, searchPopup,
\r
2209 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2210 MenuItem featureSettings = new MenuItem();
\r
2211 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2212 MenuItem annotationColour = new MenuItem();
\r
2214 public void mousePressed(MouseEvent evt)
\r
2216 PopupMenu popup = null;
\r
2217 Label source = (Label)evt.getSource();
\r
2218 if(source==embeddedFile)
\r
2220 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2222 else if(source==embeddedEdit)
\r
2224 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2226 else if(source==embeddedSearch)
\r
2228 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2230 else if(source==embeddedView)
\r
2232 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2234 else if(source==embeddedColour)
\r
2236 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2238 else if(source==embeddedCalculate)
\r
2240 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2242 else if(source==embeddedHelp)
\r
2244 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2247 embeddedMenu.add(popup);
\r
2248 popup.show(embeddedMenu,
\r
2249 source.getBounds().x,
\r
2250 source.getBounds().y + source.getBounds().getSize().height);
\r
2253 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2259 popup = new PopupMenu();
\r
2260 int m, mSize = original.getItemCount();
\r
2261 for(m=0; m<mSize; m++)
\r
2263 popup.add(original.getItem(m));
\r
2270 public void mouseClicked(MouseEvent evt)
\r
2272 public void mouseReleased(MouseEvent evt)
\r
2274 public void mouseEntered(MouseEvent evt)
\r
2276 public void mouseExited(MouseEvent evt)
\r