2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
20 package jalview.appletgui;
22 import jalview.schemes.*;
23 import jalview.datamodel.*;
24 import jalview.analysis.*;
27 import java.awt.event.*;
29 import java.io.InputStreamReader;
30 import java.io.BufferedReader;
34 public class AlignFrame extends Frame implements ActionListener,
35 ItemListener, KeyListener, MouseListener
37 public AlignmentPanel alignPanel;
38 public AlignViewport viewport;
39 int NEW_WINDOW_WIDTH = 700;
40 int NEW_WINDOW_HEIGHT = 500;
42 String jalviewServletURL;
45 public AlignFrame(AlignmentI al,
46 jalview.bin.JalviewLite applet,
51 jalviewServletURL = applet.getParameter("APPLICATION_URL");
60 viewport = new AlignViewport(al, applet);
61 alignPanel = new AlignmentPanel(this, viewport);
63 annotationPanelMenuItem.setState(viewport.showAnnotation);
65 seqLimits.setState(viewport.showJVSuffix);
69 String param = applet.getParameter("sortBy");
72 if (param.equalsIgnoreCase("Id"))
73 sortIDMenuItem_actionPerformed();
74 else if (param.equalsIgnoreCase("Pairwise Identity"))
75 sortPairwiseMenuItem_actionPerformed();
78 param = applet.getParameter("wrap");
81 if (param.equalsIgnoreCase("true"))
83 wrapMenuItem.setState(true);
84 wrapMenuItem_actionPerformed();
90 param = applet.getParameter("windowWidth");
93 int width = Integer.parseInt(param);
94 NEW_WINDOW_WIDTH = width;
96 param = applet.getParameter("windowHeight");
99 int height = Integer.parseInt(param);
100 NEW_WINDOW_HEIGHT = height;
108 //Some JVMS send keyevents to Top frame or lowest panel,
109 //Havent worked out why yet. So add to both this frame and seqCanvas for now
110 this.addKeyListener(this);
111 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
112 alignPanel.idPanel.idCanvas.addKeyListener(this);
113 alignPanel.scalePanel.addKeyListener(this);
114 alignPanel.annotationPanel.addKeyListener(this);
116 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
118 public void propertyChange(java.beans.PropertyChangeEvent evt)
120 if (evt.getPropertyName().equals("alignment"))
134 add(alignPanel, BorderLayout.CENTER);
135 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
138 alignPanel.validate();
139 alignPanel.repaint();
141 public AlignViewport getAlignViewport()
146 public SeqCanvas getSeqcanvas()
148 return alignPanel.seqPanel.seqCanvas;
155 * @param String DOCUMENT ME!
158 public void parseFeaturesFile(String file, String type)
160 Hashtable featureLinks = new Hashtable();
161 boolean featuresFile = false;
163 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
164 alignPanel.seqPanel.seqCanvas.
165 getFeatureRenderer().featureColours,
171 ex.printStackTrace();
176 if(featureLinks.size()>0)
177 alignPanel.seqPanel.seqCanvas
178 .getFeatureRenderer().featureLinks = featureLinks;
179 viewport.showSequenceFeatures = true;
180 sequenceFeatures.setState(true);
181 alignPanel.repaint();
187 public void keyPressed(KeyEvent evt)
189 if (viewport.cursorMode
190 && evt.getKeyCode() >= KeyEvent.VK_0
191 && evt.getKeyCode() <= KeyEvent.VK_9)
193 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
196 switch (evt.getKeyCode())
198 case 27: // escape key
199 deselectAllSequenceMenuItem_actionPerformed();
202 if (evt.isControlDown() || evt.isMetaDown())
204 cut_actionPerformed();
208 if (viewport.cursorMode && !evt.isControlDown())
210 alignPanel.seqPanel.setCursorColumn();
212 if (evt.isControlDown() || evt.isMetaDown())
214 copy_actionPerformed();
218 if (evt.isControlDown() || evt.isMetaDown())
224 if (evt.isControlDown() || evt.isMetaDown())
226 selectAllSequenceMenuItem_actionPerformed();
229 case KeyEvent.VK_DOWN:
230 if(viewport.cursorMode)
232 alignPanel.seqPanel.moveCursor(0,1);
235 moveSelectedSequences(false);
239 if (viewport.cursorMode)
241 alignPanel.seqPanel.moveCursor(0,-1);
244 moveSelectedSequences(true);
247 case KeyEvent.VK_LEFT:
248 if(viewport.cursorMode)
250 alignPanel.seqPanel.moveCursor(-1,0);
254 case KeyEvent.VK_RIGHT:
255 if (viewport.cursorMode)
257 alignPanel.seqPanel.moveCursor(1,0);
260 case KeyEvent.VK_SPACE:
261 if(viewport.cursorMode)
263 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
267 case KeyEvent.VK_DELETE:
268 case KeyEvent.VK_BACK_SPACE:
269 if(viewport.cursorMode)
271 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
275 cut_actionPerformed();
276 alignPanel.seqPanel.seqCanvas.repaint();
281 if(viewport.cursorMode)
283 alignPanel.seqPanel.setCursorRow();
287 if(viewport.cursorMode)
289 alignPanel.seqPanel.setCursorPosition();
293 case KeyEvent.VK_ENTER:
294 case KeyEvent.VK_COMMA:
295 if(viewport.cursorMode)
297 alignPanel.seqPanel.setCursorRowAndColumn();
302 if(viewport.cursorMode)
304 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
308 if(viewport.cursorMode)
310 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
315 viewport.cursorMode = ! viewport.cursorMode;
316 statusBar.setText("Keyboard editing mode is "+
317 (viewport.cursorMode ? "on" : "off"));
318 if(viewport.cursorMode)
320 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
321 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
323 alignPanel.seqPanel.seqCanvas.repaint();
327 if (evt.isControlDown())
329 findMenuItem_actionPerformed();
334 boolean toggleSeqs = !evt.isControlDown();
335 boolean toggleCols = !evt.isShiftDown();
336 boolean hide = false;
337 SequenceGroup sg = viewport.getSelectionGroup();
341 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
344 viewport.hideAllSelectedSeqs();
346 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
347 viewport.showAllHiddenSeqs();
352 if (viewport.colSel.getSelected().size() > 0)
354 viewport.hideSelectedColumns();
356 viewport.selectionGroup = sg;
359 viewport.showAllHiddenColumns();
362 alignPanel.repaint();
368 public void keyReleased(KeyEvent evt)
370 public void keyTyped(KeyEvent evt)
373 public void itemStateChanged(ItemEvent evt)
375 if(evt.getSource()==colourTextMenuItem)
376 colourTextMenuItem_actionPerformed();
377 else if(evt.getSource()==wrapMenuItem)
378 wrapMenuItem_actionPerformed();
379 else if(evt.getSource()==scaleAbove)
380 scaleAbove_actionPerformed();
381 else if(evt.getSource()==scaleLeft)
382 scaleLeft_actionPerformed();
383 else if(evt.getSource()==scaleRight)
384 scaleRight_actionPerformed();
385 else if(evt.getSource()==seqLimits)
386 seqLimits_itemStateChanged();
387 else if(evt.getSource()==viewBoxesMenuItem)
388 viewBoxesMenuItem_actionPerformed();
389 else if(evt.getSource()==viewTextMenuItem)
390 viewTextMenuItem_actionPerformed();
391 else if(evt.getSource()==renderGapsMenuItem)
392 renderGapsMenuItem_actionPerformed();
393 else if(evt.getSource()==annotationPanelMenuItem)
394 annotationPanelMenuItem_actionPerformed();
395 else if(evt.getSource()==sequenceFeatures)
397 viewport.showSequenceFeatures(sequenceFeatures.getState());
398 alignPanel.seqPanel.seqCanvas.repaint();
400 else if(evt.getSource()==conservationMenuItem)
401 conservationMenuItem_actionPerformed();
402 else if(evt.getSource()==abovePIDThreshold)
403 abovePIDThreshold_actionPerformed();
404 else if(evt.getSource()==applyToAllGroups)
405 applyToAllGroups_actionPerformed();
406 else if(evt.getSource()==autoCalculate)
407 viewport.autocalculateConsensus = autoCalculate.getState();
409 public void actionPerformed(ActionEvent evt)
411 Object source = evt.getSource();
413 if(source==inputText)
414 inputText_actionPerformed();
415 else if(source==loadTree)
416 loadTree_actionPerformed();
417 else if(source==loadApplication)
418 launchFullApplication();
419 else if(source==closeMenuItem)
420 closeMenuItem_actionPerformed();
421 else if(source==copy)
422 copy_actionPerformed();
423 else if(source==undoMenuItem)
424 undoMenuItem_actionPerformed();
425 else if(source==redoMenuItem)
426 redoMenuItem_actionPerformed();
427 else if(source==inputText)
428 inputText_actionPerformed();
429 else if(source==closeMenuItem)
430 closeMenuItem_actionPerformed();
431 else if(source==undoMenuItem)
432 undoMenuItem_actionPerformed();
433 else if(source==redoMenuItem)
434 redoMenuItem_actionPerformed();
435 else if(source==copy)
436 copy_actionPerformed();
437 else if(source==pasteNew)
438 pasteNew_actionPerformed();
439 else if(source==pasteThis)
440 pasteThis_actionPerformed();
442 cut_actionPerformed();
443 else if(source==delete)
444 delete_actionPerformed();
445 else if(source==deleteGroups)
446 deleteGroups_actionPerformed();
447 else if(source==selectAllSequenceMenuItem)
448 selectAllSequenceMenuItem_actionPerformed();
449 else if(source==deselectAllSequenceMenuItem)
450 deselectAllSequenceMenuItem_actionPerformed();
451 else if(source==invertSequenceMenuItem)
452 invertSequenceMenuItem_actionPerformed();
453 else if(source==invertColSel)
454 { viewport.invertColumnSelection(); alignPanel.repaint(); }
455 else if(source==remove2LeftMenuItem)
456 remove2LeftMenuItem_actionPerformed();
457 else if(source==remove2RightMenuItem)
458 remove2RightMenuItem_actionPerformed();
459 else if(source==removeGappedColumnMenuItem)
460 removeGappedColumnMenuItem_actionPerformed();
461 else if(source==removeAllGapsMenuItem)
462 removeAllGapsMenuItem_actionPerformed();
463 else if(source==findMenuItem)
464 findMenuItem_actionPerformed();
465 else if(source==font)
466 font_actionPerformed();
467 else if(source==showColumns)
469 viewport.showAllHiddenColumns(); alignPanel.repaint();
471 else if(source==showSeqs)
473 viewport.showAllHiddenSeqs();
475 else if(source == hideColumns)
477 viewport.hideSelectedColumns(); alignPanel.repaint();
479 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
481 viewport.hideAllSelectedSeqs();
483 else if(source==featureSettings)
484 featureSettings_actionPerformed();
485 else if(source==overviewMenuItem)
486 overviewMenuItem_actionPerformed();
487 else if(source==noColourmenuItem)
488 noColourmenuItem_actionPerformed();
489 else if(source==clustalColour)
490 clustalColour_actionPerformed();
491 else if(source==zappoColour)
492 zappoColour_actionPerformed();
493 else if(source==taylorColour)
494 taylorColour_actionPerformed();
495 else if(source==hydrophobicityColour)
496 hydrophobicityColour_actionPerformed();
497 else if(source==helixColour)
498 helixColour_actionPerformed();
499 else if(source==strandColour)
500 strandColour_actionPerformed();
501 else if(source==turnColour)
502 turnColour_actionPerformed();
503 else if(source==buriedColour)
504 buriedColour_actionPerformed();
505 else if(source==nucleotideColour)
506 nucleotideColour_actionPerformed();
507 else if(source==modifyPID)
508 modifyPID_actionPerformed();
509 else if(source==modifyConservation)
510 modifyConservation_actionPerformed();
511 else if(source==userDefinedColour)
512 userDefinedColour_actionPerformed();
513 else if(source==PIDColour)
514 PIDColour_actionPerformed();
515 else if(source==BLOSUM62Colour)
516 BLOSUM62Colour_actionPerformed();
517 else if(source==annotationColour)
518 new AnnotationColourChooser(viewport, alignPanel);
519 else if(source==sortPairwiseMenuItem)
520 sortPairwiseMenuItem_actionPerformed();
521 else if(source==sortIDMenuItem)
522 sortIDMenuItem_actionPerformed();
523 else if(source==sortGroupMenuItem)
524 sortGroupMenuItem_actionPerformed();
525 else if(source==removeRedundancyMenuItem)
526 removeRedundancyMenuItem_actionPerformed();
527 else if(source==pairwiseAlignmentMenuItem)
528 pairwiseAlignmentMenuItem_actionPerformed();
529 else if(source==PCAMenuItem)
530 PCAMenuItem_actionPerformed();
531 else if(source==averageDistanceTreeMenuItem)
532 averageDistanceTreeMenuItem_actionPerformed();
533 else if(source==neighbourTreeMenuItem)
534 neighbourTreeMenuItem_actionPerformed();
535 else if(source==njTreeBlosumMenuItem)
536 njTreeBlosumMenuItem_actionPerformed();
537 else if(source==avDistanceTreeBlosumMenuItem)
538 avTreeBlosumMenuItem_actionPerformed();
539 else if(source==documentation)
540 documentation_actionPerformed();
541 else if(source==about)
542 about_actionPerformed();
546 public void inputText_actionPerformed()
548 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
549 Frame frame = new Frame();
551 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
554 protected void outputText_actionPerformed(ActionEvent e)
556 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
557 Frame frame = new Frame();
559 jalview.bin.JalviewLite.addFrame(frame,
560 "Alignment output - " + e.getActionCommand(),
562 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
563 viewport.getAlignment().getSequences(),
564 viewport.showJVSuffix));
567 void launchFullApplication()
569 StringBuffer url = new StringBuffer(jalviewServletURL);
572 appendProtocol( viewport.applet.getParameter("file") ) );
574 if(viewport.applet.getParameter("features")!=null)
576 url.append( "&features=" );
577 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
580 if(viewport.applet.getParameter("annotations")!=null)
582 url.append( "&annotations=" );
583 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
586 if(viewport.applet.getParameter("jnetfile")!=null)
588 url.append( "&annotations=" );
589 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
592 if(viewport.applet.getParameter("defaultColour")!=null)
594 url.append("&colour=" +
595 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
599 if(viewport.applet.getParameter("userDefinedColour")!=null)
601 url.append( "&colour=" +
602 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
606 showURL(url.toString(), "FULL_APP");
610 String removeWhiteSpace(String colour)
612 StringBuffer sb = new StringBuffer();
613 for (int i = 0; i < colour.length(); i++)
615 if (Character.isWhitespace(colour.charAt(i)))
618 sb.append(colour.charAt(i));
621 return sb.toString();
625 String appendProtocol(String url)
629 }catch(java.net.MalformedURLException ex)
631 url = viewport.applet.getCodeBase()+url;
636 public void closeMenuItem_actionPerformed()
638 PaintRefresher.components.remove(viewport.alignment);
639 if(PaintRefresher.components.size()==0 && viewport.applet==null)
645 Stack historyList = new Stack();
646 Stack redoList = new Stack();
648 void updateEditMenuBar()
650 if (historyList.size() > 0)
652 undoMenuItem.setEnabled(true);
653 HistoryItem hi = (HistoryItem) historyList.peek();
654 undoMenuItem.setLabel("Undo " + hi.getDescription());
658 undoMenuItem.setEnabled(false);
659 undoMenuItem.setLabel("Undo");
662 if (redoList.size() > 0)
664 redoMenuItem.setEnabled(true);
665 HistoryItem hi = (HistoryItem) redoList.peek();
666 redoMenuItem.setLabel("Redo " + hi.getDescription());
670 redoMenuItem.setEnabled(false);
671 redoMenuItem.setLabel("Redo");
675 public void addHistoryItem(HistoryItem hi)
677 historyList.push(hi);
678 redoList.removeAllElements();
682 protected void undoMenuItem_actionPerformed()
684 HistoryItem nh,hi = (HistoryItem) historyList.pop();
685 redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
687 if (hi.alColumnChanges!=null)
688 nh.alColumnChanges=hi.alColumnChanges.getInverse();
689 restoreHistoryItem(hi);
690 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
693 protected void redoMenuItem_actionPerformed()
695 HistoryItem nh,hi = (HistoryItem) redoList.pop();
696 historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
698 if (hi.alColumnChanges!=null)
699 nh.alColumnChanges=hi.alColumnChanges.getInverse();
700 restoreHistoryItem(hi);
702 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
705 // used by undo and redo
706 void restoreHistoryItem(HistoryItem hi)
708 hi.restore(viewport.getColumnSelection());
711 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
714 public void moveSelectedSequences(boolean up)
716 SequenceGroup sg = viewport.getSelectionGroup();
724 for (int i = 1; i < viewport.alignment.getHeight(); i++)
726 SequenceI seq = viewport.alignment.getSequenceAt(i);
727 if (!sg.getSequences(false).contains(seq))
732 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
733 if (sg.getSequences(false).contains(temp))
738 viewport.alignment.getSequences().setElementAt(temp, i);
739 viewport.alignment.getSequences().setElementAt(seq, i - 1);
744 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
746 SequenceI seq = viewport.alignment.getSequenceAt(i);
747 if (!sg.getSequences(true).contains(seq))
752 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
753 if (sg.getSequences(true).contains(temp))
758 viewport.alignment.getSequences().setElementAt(temp, i);
759 viewport.alignment.getSequences().setElementAt(seq, i + 1);
763 alignPanel.repaint();
766 static StringBuffer copiedSequences;
767 static Vector copiedHiddenColumns;
768 protected void copy_actionPerformed()
770 if (viewport.getSelectionGroup() == null)
775 SequenceGroup sg = viewport.getSelectionGroup();
776 copiedSequences = new StringBuffer();
777 Hashtable orderedSeqs = new Hashtable();
778 for (int i = 0; i < sg.getSize(false); i++)
780 SequenceI seq = sg.getSequenceAt(i);
781 int index = viewport.alignment.findIndex(seq);
782 orderedSeqs.put(index + "", seq);
785 int index = 0, startRes, endRes;
788 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
790 copiedHiddenColumns = new Vector();
791 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
792 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
795 int[] region = (int[])
796 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
798 copiedHiddenColumns.addElement(new int[]
799 {region[0] - hiddenOffset,
800 region[1] - hiddenOffset});
804 copiedHiddenColumns = null;
807 for (int i = 0; i < sg.getSize(false); i++)
809 SequenceI seq = null;
813 if (orderedSeqs.containsKey(index + ""))
815 seq = (SequenceI) orderedSeqs.get(index + "");
827 //Returns residue following index if gap
828 startRes = seq.findPosition(sg.getStartRes());
831 //Need to find the residue preceeding index if gap
834 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
836 ch = seq.getCharAt(j);
837 if (!jalview.util.Comparison.isGap( (ch)))
845 endRes += seq.getStart() -1;
848 copiedSequences.append(seq.getName() + "\t" +
851 seq.getSequence(sg.getStartRes(),
852 sg.getEndRes() + 1) + "\n");
857 protected void pasteNew_actionPerformed()
862 protected void pasteThis_actionPerformed()
864 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
869 void paste(boolean newAlignment)
873 if (copiedSequences == null)
878 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
879 Vector seqs = new Vector();
880 while (st.hasMoreElements())
882 String name = st.nextToken();
883 int start = Integer.parseInt(st.nextToken());
884 int end = Integer.parseInt(st.nextToken());
885 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
889 viewport.alignment.addSequence(sequence);
893 seqs.addElement(sequence);
899 SequenceI[] newSeqs = new SequenceI[seqs.size()];
900 for (int i = 0; i < seqs.size(); i++)
902 newSeqs[i] = (SequenceI) seqs.elementAt(i);
905 String newtitle = new String("Copied sequences");
906 if (getTitle().startsWith("Copied sequences"))
908 newtitle = getTitle();
912 newtitle = newtitle.concat("- from " + getTitle());
914 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
918 if (copiedHiddenColumns != null)
920 for (int i = 0; i < copiedHiddenColumns.size(); i++)
922 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
923 af.viewport.hideColumns(region[0], region[1]);
928 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
933 viewport.setEndSeq(viewport.alignment.getHeight());
934 viewport.alignment.getWidth();
935 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
940 {} // could be anything being pasted in here
944 protected void cut_actionPerformed()
946 copy_actionPerformed();
947 delete_actionPerformed();
950 protected void delete_actionPerformed()
952 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
954 if (viewport.getSelectionGroup() == null)
960 SequenceGroup sg = viewport.getSelectionGroup();
961 boolean allSequences = false;
962 if(sg.getSize(false)==viewport.alignment.getHeight())
965 for (int i = 0; i < sg.getSize(false); i++)
967 SequenceI seq = sg.getSequenceAt(i);
968 int index = viewport.getAlignment().findIndex(seq);
969 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
971 // If the cut affects all sequences, remove highlighted columns
974 viewport.getColumnSelection().removeElements(sg.getStartRes(),
979 if (seq.getSequence().length() < 1)
981 viewport.getAlignment().deleteSequence(seq);
985 viewport.getAlignment().getSequences().setElementAt(seq, index);
989 viewport.setSelectionGroup(null);
990 viewport.alignment.deleteGroup(sg);
991 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
992 if (viewport.getAlignment().getHeight() < 1)
996 this.setVisible(false);
1001 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1005 protected void deleteGroups_actionPerformed()
1007 viewport.alignment.deleteAllGroups();
1008 viewport.setSelectionGroup(null);
1010 alignPanel.repaint();
1013 public void selectAllSequenceMenuItem_actionPerformed()
1015 SequenceGroup sg = new SequenceGroup();
1016 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1018 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1020 sg.setEndRes(viewport.alignment.getWidth()-1);
1021 viewport.setSelectionGroup(sg);
1022 alignPanel.repaint();
1023 PaintRefresher.Refresh(null, viewport.alignment);
1026 public void deselectAllSequenceMenuItem_actionPerformed()
1028 if(viewport.cursorMode)
1030 alignPanel.seqPanel.keyboardNo1=null;
1031 alignPanel.seqPanel.keyboardNo2=null;
1033 viewport.setSelectionGroup(null);
1034 viewport.getColumnSelection().clear();
1035 viewport.setSelectionGroup(null);
1036 alignPanel.idPanel.idCanvas.searchResults = null;
1037 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1038 alignPanel.repaint();
1039 PaintRefresher.Refresh(null, viewport.alignment);
1042 public void invertSequenceMenuItem_actionPerformed()
1044 SequenceGroup sg = viewport.getSelectionGroup();
1045 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1047 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1050 PaintRefresher.Refresh(null, viewport.alignment);
1053 public void remove2LeftMenuItem_actionPerformed()
1055 ColumnSelection colSel = viewport.getColumnSelection();
1056 if (colSel.size() > 0)
1059 addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
1061 int min = colSel.getMin();
1062 viewport.getAlignment().trimLeft(min);
1063 colSel.compensateForEdit(0, min);
1064 edit.addShift(0, min);
1065 if (viewport.getSelectionGroup() != null)
1067 viewport.getSelectionGroup().adjustForRemoveLeft(min);
1070 Vector groups = viewport.alignment.getGroups();
1071 for (int i = 0; i < groups.size(); i++)
1073 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1074 if (!sg.adjustForRemoveLeft(min))
1076 viewport.alignment.deleteGroup(sg);
1079 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1083 public void remove2RightMenuItem_actionPerformed()
1085 ColumnSelection colSel = viewport.getColumnSelection();
1086 if (colSel.size() > 0)
1088 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
1090 int max = colSel.getMax();
1091 viewport.getAlignment().trimRight(max);
1093 if (viewport.getSelectionGroup() != null)
1095 viewport.getSelectionGroup().adjustForRemoveRight(max);
1098 Vector groups = viewport.alignment.getGroups();
1099 for (int i = 0; i < groups.size(); i++)
1101 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1102 if (!sg.adjustForRemoveRight(max))
1104 viewport.alignment.deleteGroup(sg);
1107 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1112 public void removeGappedColumnMenuItem_actionPerformed()
1115 addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
1119 //This is to maintain viewport position on first residue
1121 SequenceI seq = viewport.alignment.getSequenceAt(0);
1122 int startRes = seq.findPosition(viewport.startRes);
1124 viewport.getAlignment().removeGaps();
1126 viewport.setStartRes(seq.findIndex(startRes)-1);
1128 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1131 public void removeAllGapsMenuItem_actionPerformed()
1133 // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
1134 // TODO: columnSelection.compensateforedits should be called (and passed to history item)
1135 HistoryItem editgaps;
1136 addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment,
1139 //This is to maintain viewport position on first residue
1141 SequenceI seq = viewport.alignment.getSequenceAt(0);
1142 int startRes = seq.findPosition(viewport.startRes);
1147 int start=0, end = viewport.alignment.getWidth();
1149 if (viewport.getSelectionGroup() != null
1150 && viewport.getSelectionGroup().getSequences(false) != null
1151 && viewport.getSelectionGroup().getSize(false)>0)
1153 seqs = viewport.getSelectionGroup().getSequences(true);
1154 start = viewport.getSelectionGroup().getStartRes();
1155 end = viewport.getSelectionGroup().getEndRes()+1;
1158 seqs = viewport.alignment.getSequences();
1160 /* Commented out regions below are partial implementation of todo above.
1161 * divide start,end into visible chunks, and for each:
1162 int diff=end-start+1;
1164 int dr[] = new int[seqs.size()];
1166 for (int i = 0; i < seqs.size(); i++)
1168 current = (SequenceI) seqs.elementAt(i);
1170 current.removeGaps(start, end);
1171 /*if (d<diff) // can only shift
1177 /* // after the end of each chunk -
1179 // record shift for history.
1180 editgaps.addShift(start, diff);
1181 if (viewport.hasHiddenColumns && diffmax>diff) {
1183 StringBuffer gaps=new StringBuffer(diffmax);
1184 for (int i=0,j=diffmax-diff; i<j; i++)
1185 gaps.append(viewport.getGapCharacter());
1186 for (int i=0, j=seqs.size(); i<j; i++) {
1187 current = (SequenceI) seqs.elementAt(i);
1189 String sq = current.getSequence();
1190 current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
1196 viewport.setStartRes(seq.findIndex(startRes)-1);
1197 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1200 public void alignmentChanged()
1202 viewport.alignment.padGaps();
1203 if(viewport.autocalculateConsensus)
1205 viewport.updateConsensus();
1206 viewport.updateConservation();
1209 resetAllColourSchemes();
1210 if(alignPanel.overviewPanel!=null)
1211 alignPanel.overviewPanel.updateOverviewImage();
1213 viewport.alignment.adjustSequenceAnnotations();
1214 alignPanel.repaint();
1217 void resetAllColourSchemes()
1219 ColourSchemeI cs = viewport.globalColourScheme;
1222 if (cs instanceof ClustalxColourScheme)
1224 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
1225 resetClustalX(viewport.alignment.getSequences(),
1226 viewport.alignment.getWidth());
1229 cs.setConsensus(viewport.vconsensus);
1230 if (cs.conservationApplied())
1232 Alignment al = (Alignment) viewport.alignment;
1233 Conservation c = new Conservation("All",
1234 ResidueProperties.propHash, 3,
1235 al.getSequences(), 0,
1238 c.verdict(false, viewport.ConsPercGaps);
1240 cs.setConservation(c);
1244 int s, sSize = viewport.alignment.getGroups().size();
1245 for(s=0; s<sSize; s++)
1247 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
1248 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
1250 ((ClustalxColourScheme)sg.cs).resetClustalX(
1251 sg.getSequences(true), sg.getWidth());
1253 sg.recalcConservation();
1259 public void findMenuItem_actionPerformed()
1261 new Finder(alignPanel);
1264 public void font_actionPerformed()
1266 new FontChooser(alignPanel);
1270 public void seqLimits_itemStateChanged()
1272 viewport.setShowJVSuffix(seqLimits.getState());
1273 alignPanel.fontChanged();
1274 alignPanel.repaint();
1278 protected void colourTextMenuItem_actionPerformed()
1280 viewport.setColourText(colourTextMenuItem.getState());
1281 alignPanel.repaint();
1284 protected void wrapMenuItem_actionPerformed()
1286 viewport.setWrapAlignment(wrapMenuItem.getState());
1287 alignPanel.setWrapAlignment(wrapMenuItem.getState());
1288 scaleAbove.setEnabled(wrapMenuItem.getState());
1289 scaleLeft.setEnabled(wrapMenuItem.getState());
1290 scaleRight.setEnabled(wrapMenuItem.getState());
1291 alignPanel.repaint();
1295 protected void scaleAbove_actionPerformed()
1297 viewport.setScaleAboveWrapped(scaleAbove.getState());
1298 alignPanel.repaint();
1301 protected void scaleLeft_actionPerformed()
1303 viewport.setScaleLeftWrapped(scaleLeft.getState());
1304 alignPanel.repaint();
1307 protected void scaleRight_actionPerformed()
1309 viewport.setScaleRightWrapped(scaleRight.getState());
1310 alignPanel.repaint();
1313 public void viewBoxesMenuItem_actionPerformed()
1315 viewport.setShowBoxes(viewBoxesMenuItem.getState());
1316 alignPanel.repaint();
1319 public void viewTextMenuItem_actionPerformed()
1321 viewport.setShowText(viewTextMenuItem.getState());
1322 alignPanel.repaint();
1325 protected void renderGapsMenuItem_actionPerformed()
1327 viewport.setRenderGaps(renderGapsMenuItem.getState());
1328 alignPanel.repaint();
1331 public void annotationPanelMenuItem_actionPerformed()
1333 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
1334 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
1337 public void featureSettings_actionPerformed()
1339 new FeatureSettings(viewport, alignPanel);
1342 public void overviewMenuItem_actionPerformed()
1344 if (alignPanel.overviewPanel != null)
1349 Frame frame = new Frame();
1350 OverviewPanel overview = new OverviewPanel(alignPanel);
1351 frame.add(overview);
1352 // +50 must allow for applet frame window
1353 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
1354 overview.preferredSize().width,
1355 overview.preferredSize().height + 50);
1358 frame.addWindowListener(new WindowAdapter()
1360 public void windowClosing(WindowEvent e)
1362 alignPanel.setOverviewPanel(null);
1366 alignPanel.setOverviewPanel(overview);
1370 protected void noColourmenuItem_actionPerformed()
1375 public void clustalColour_actionPerformed()
1377 abovePIDThreshold.setState(false);
1378 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
1379 viewport.alignment.getWidth()));
1382 public void zappoColour_actionPerformed()
1384 changeColour(new ZappoColourScheme());
1387 public void taylorColour_actionPerformed()
1389 changeColour(new TaylorColourScheme());
1392 public void hydrophobicityColour_actionPerformed()
1394 changeColour(new HydrophobicColourScheme());
1397 public void helixColour_actionPerformed()
1399 changeColour(new HelixColourScheme());
1402 public void strandColour_actionPerformed()
1404 changeColour(new StrandColourScheme());
1407 public void turnColour_actionPerformed()
1409 changeColour(new TurnColourScheme());
1412 public void buriedColour_actionPerformed()
1414 changeColour(new BuriedColourScheme());
1417 public void nucleotideColour_actionPerformed()
1419 changeColour(new NucleotideColourScheme());
1422 protected void applyToAllGroups_actionPerformed()
1424 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
1427 void changeColour(ColourSchemeI cs)
1433 if (viewport.getAbovePIDThreshold())
1435 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
1437 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1439 viewport.setGlobalColourScheme(cs);
1443 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1446 if (viewport.getConservationSelected())
1449 Alignment al = (Alignment) viewport.alignment;
1450 Conservation c = new Conservation("All",
1451 ResidueProperties.propHash, 3,
1452 al.getSequences(), 0,
1456 c.verdict(false, viewport.ConsPercGaps);
1458 cs.setConservation(c);
1460 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
1466 cs.setConservation(null);
1469 cs.setConsensus(viewport.vconsensus);
1472 viewport.setGlobalColourScheme(cs);
1474 if (viewport.getColourAppliesToAllGroups())
1476 Vector groups = viewport.alignment.getGroups();
1477 for (int i = 0; i < groups.size(); i++)
1479 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1486 if (cs instanceof ClustalxColourScheme)
1488 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
1494 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
1496 catch (Exception ex)
1498 ex.printStackTrace();
1503 if (viewport.getAbovePIDThreshold()
1504 || cs instanceof PIDColourScheme
1505 || cs instanceof Blosum62ColourScheme)
1507 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1508 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
1511 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1513 if (viewport.getConservationSelected())
1515 Conservation c = new Conservation("Group",
1516 ResidueProperties.propHash, 3,
1517 sg.getSequences(true), 0,
1518 viewport.alignment.getWidth() - 1);
1520 c.verdict(false, viewport.ConsPercGaps);
1521 sg.cs.setConservation(c);
1525 sg.cs.setConservation(null);
1526 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1533 if (alignPanel.getOverviewPanel() != null)
1535 alignPanel.getOverviewPanel().updateOverviewImage();
1538 alignPanel.repaint();
1543 protected void modifyPID_actionPerformed()
1545 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
1547 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
1549 SliderPanel.showPIDSlider();
1553 protected void modifyConservation_actionPerformed()
1555 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
1557 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
1559 SliderPanel.showConservationSlider();
1563 protected void conservationMenuItem_actionPerformed()
1565 viewport.setConservationSelected(conservationMenuItem.getState());
1567 viewport.setAbovePIDThreshold(false);
1568 abovePIDThreshold.setState(false);
1570 changeColour(viewport.getGlobalColourScheme());
1572 modifyConservation_actionPerformed();
1575 public void abovePIDThreshold_actionPerformed()
1577 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
1579 conservationMenuItem.setState(false);
1580 viewport.setConservationSelected(false);
1582 changeColour(viewport.getGlobalColourScheme());
1584 modifyPID_actionPerformed();
1587 public void userDefinedColour_actionPerformed()
1589 new UserDefinedColours(alignPanel, null);
1592 public void PIDColour_actionPerformed()
1594 changeColour(new PIDColourScheme());
1597 public void BLOSUM62Colour_actionPerformed()
1599 changeColour(new Blosum62ColourScheme());
1602 public void sortPairwiseMenuItem_actionPerformed()
1604 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
1606 AlignmentSorter.sortByPID(viewport.getAlignment(),
1607 viewport.getAlignment().getSequenceAt(0));
1608 alignPanel.repaint();
1611 public void sortIDMenuItem_actionPerformed()
1613 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
1615 AlignmentSorter.sortByID(viewport.getAlignment());
1616 alignPanel.repaint();
1619 public void sortGroupMenuItem_actionPerformed()
1621 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
1623 AlignmentSorter.sortByGroup(viewport.getAlignment());
1624 alignPanel.repaint();
1628 public void removeRedundancyMenuItem_actionPerformed()
1630 new RedundancyPanel(alignPanel);
1633 public void pairwiseAlignmentMenuItem_actionPerformed()
1635 if (viewport.getSelectionGroup()!=null
1636 && viewport.getSelectionGroup().getSize(false) > 1)
1638 Frame frame = new Frame();
1639 frame.add(new PairwiseAlignPanel(alignPanel));
1640 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
1644 public void PCAMenuItem_actionPerformed()
1646 //are the sequences aligned?
1647 if (!viewport.alignment.isAligned())
1650 int Width = viewport.getAlignment().getWidth();
1652 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1655 current = viewport.getAlignment().getSequenceAt(i);
1657 if (current.getLength() < Width)
1659 current.insertCharAt(Width - 1, viewport.getGapCharacter());
1662 alignPanel.repaint();
1665 if ( (viewport.getSelectionGroup() != null &&
1666 viewport.getSelectionGroup().getSize(false) < 4 &&
1667 viewport.getSelectionGroup().getSize(false) > 0)
1668 || viewport.getAlignment().getHeight() < 4)
1675 new PCAPanel(viewport);
1677 catch (java.lang.OutOfMemoryError ex)
1683 public void averageDistanceTreeMenuItem_actionPerformed()
1685 NewTreePanel("AV", "PID", "Average distance tree using PID");
1688 public void neighbourTreeMenuItem_actionPerformed()
1690 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
1693 protected void njTreeBlosumMenuItem_actionPerformed()
1695 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
1698 protected void avTreeBlosumMenuItem_actionPerformed()
1700 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
1703 void NewTreePanel(String type, String pwType, String title)
1705 //are the sequences aligned?
1706 if (!viewport.alignment.isAligned())
1709 int Width = viewport.getAlignment().getWidth();
1711 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1714 current = viewport.getAlignment().getSequenceAt(i);
1716 if (current.getLength() < Width)
1718 current.insertCharAt(Width - 1, viewport.getGapCharacter());
1721 alignPanel.repaint();
1725 if ( (viewport.getSelectionGroup() != null &&
1726 viewport.getSelectionGroup().getSize(false) > 1)
1727 || (viewport.getSelectionGroup() == null
1728 && viewport.alignment.getHeight() > 1))
1730 final TreePanel tp = new TreePanel(viewport,
1734 addTreeMenuItem(tp, title);
1736 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
1740 void loadTree_actionPerformed()
1742 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1743 cap.setText("Paste your Newick tree file here.");
1744 cap.treeImport = true;
1745 Frame frame = new Frame();
1747 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
1750 public void loadTree(jalview.io.NewickFile tree, String treeFile)
1752 TreePanel tp = new TreePanel(viewport,
1756 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
1757 addTreeMenuItem(tp, treeFile);
1760 void addTreeMenuItem(final TreePanel treePanel, String title)
1762 final MenuItem item = new MenuItem(title);
1763 sortByTreeMenu.add(item);
1764 item.addActionListener(new java.awt.event.ActionListener()
1766 public void actionPerformed(ActionEvent evt)
1768 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
1770 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
1771 alignPanel.repaint();
1775 treePanel.addWindowListener(new WindowAdapter()
1777 public void windowClosing(WindowEvent e)
1779 sortByTreeMenu.remove(item);
1784 protected void documentation_actionPerformed()
1786 showURL("http://www.jalview.org/help.html", "HELP");
1789 protected void about_actionPerformed()
1792 class AboutPanel extends Canvas
1795 public AboutPanel(String version)
1796 { this.version = version; }
1798 public void paint(Graphics g)
1800 g.setColor(Color.white);
1801 g.fillRect(0, 0, getSize().width, getSize().height);
1802 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
1803 FontMetrics fm = g.getFontMetrics();
1804 int fh = fm.getHeight();
1806 g.setColor(Color.black);
1807 g.setFont(new Font("Helvetica", Font.BOLD, 14));
1808 g.drawString("Jalview - Release "+version, 200, y += fh);
1809 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
1810 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
1812 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
1815 "For any issues relating to Jalview, email help@jalview.org", x,
1817 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
1818 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
1820 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
1824 String version = "test";
1825 java.net.URL url = getClass().getResource("/.build_properties");
1830 BufferedReader reader = new BufferedReader(new InputStreamReader(
1833 while ( (line = reader.readLine()) != null)
1835 if (line.indexOf("VERSION") > -1)
1837 version = line.substring(line.indexOf("=") + 1);
1841 catch (Exception ex)
1843 ex.printStackTrace();
1848 Frame frame = new Frame();
1849 frame.add(new AboutPanel(version));
1850 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
1854 public void showURL(String url, String target)
1856 if (viewport.applet == null)
1858 System.out.println("Not running as applet - no browser available.");
1864 System.out.println("Show url: "+url);
1865 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
1868 catch (Exception ex)
1870 ex.printStackTrace();
1876 //////////////////////////////////////////////////////////////////////////////////
1877 //JBuilder Graphics here
1879 protected MenuBar alignFrameMenuBar = new MenuBar();
1880 protected Menu fileMenu = new Menu("File");
1881 protected MenuItem loadApplication = new MenuItem("View in Full Application");
1882 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
1883 protected MenuItem closeMenuItem = new MenuItem("Close");
1884 protected Menu editMenu = new Menu("Edit");
1885 protected Menu viewMenu = new Menu("View");
1886 protected Menu colourMenu = new Menu("Colour");
1887 protected Menu calculateMenu = new Menu("Calculate");
1888 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
1889 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
1890 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
1891 protected MenuItem remove2LeftMenuItem = new MenuItem();
1892 protected MenuItem remove2RightMenuItem = new MenuItem();
1893 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
1894 protected MenuItem removeAllGapsMenuItem = new MenuItem();
1895 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
1896 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
1897 protected MenuItem sortPairwiseMenuItem = new MenuItem();
1898 protected MenuItem sortIDMenuItem = new MenuItem();
1899 protected MenuItem sortGroupMenuItem = new MenuItem();
1900 protected MenuItem removeRedundancyMenuItem = new MenuItem();
1901 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
1902 protected MenuItem PCAMenuItem = new MenuItem();
1903 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
1904 protected MenuItem neighbourTreeMenuItem = new MenuItem();
1905 BorderLayout borderLayout1 = new BorderLayout();
1906 public Label statusBar = new Label();
1907 protected Menu outputTextboxMenu = new Menu();
1908 protected MenuItem clustalColour = new MenuItem();
1909 protected MenuItem zappoColour = new MenuItem();
1910 protected MenuItem taylorColour = new MenuItem();
1911 protected MenuItem hydrophobicityColour = new MenuItem();
1912 protected MenuItem helixColour = new MenuItem();
1913 protected MenuItem strandColour = new MenuItem();
1914 protected MenuItem turnColour = new MenuItem();
1915 protected MenuItem buriedColour = new MenuItem();
1916 protected MenuItem userDefinedColour = new MenuItem();
1917 protected MenuItem PIDColour = new MenuItem();
1918 protected MenuItem BLOSUM62Colour = new MenuItem();
1919 MenuItem njTreeBlosumMenuItem = new MenuItem();
1920 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
1921 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
1922 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
1923 MenuItem overviewMenuItem = new MenuItem();
1924 protected MenuItem undoMenuItem = new MenuItem();
1925 protected MenuItem redoMenuItem = new MenuItem();
1926 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
1927 MenuItem noColourmenuItem = new MenuItem();
1928 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
1929 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
1930 MenuItem findMenuItem = new MenuItem();
1931 Menu searchMenu = new Menu();
1932 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
1933 protected MenuItem nucleotideColour = new MenuItem();
1934 MenuItem deleteGroups = new MenuItem();
1935 MenuItem delete = new MenuItem();
1936 MenuItem copy = new MenuItem();
1937 MenuItem cut = new MenuItem();
1938 Menu pasteMenu = new Menu();
1939 MenuItem pasteNew = new MenuItem();
1940 MenuItem pasteThis = new MenuItem();
1941 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
1942 protected MenuItem font = new MenuItem();
1943 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
1944 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
1945 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
1946 MenuItem modifyPID = new MenuItem();
1947 MenuItem modifyConservation = new MenuItem();
1948 protected CheckboxMenuItem autoCalculate
1949 = new CheckboxMenuItem("Autocalculate Consensus", true);
1950 protected Menu sortByTreeMenu = new Menu();
1951 Menu sort = new Menu();
1952 Menu calculate = new Menu();
1953 MenuItem inputText = new MenuItem();
1954 Menu helpMenu = new Menu();
1955 MenuItem documentation = new MenuItem();
1956 MenuItem about = new MenuItem();
1957 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
1960 Label embeddedSearch;
1962 Label embeddedColour;
1965 Label embeddedCalculate;
1966 FlowLayout flowLayout1;
1968 private void jbInit() throws Exception {
1970 setMenuBar(alignFrameMenuBar);
1974 // dynamically fill save as menu with available formats
1975 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
1978 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
1980 item.addActionListener(new java.awt.event.ActionListener()
1982 public void actionPerformed(ActionEvent e)
1984 outputText_actionPerformed(e);
1988 outputTextboxMenu.add(item);
1990 closeMenuItem.addActionListener(this);
1991 loadApplication.addActionListener(this);
1993 loadTree.addActionListener(this);
1994 selectAllSequenceMenuItem.addActionListener(this);
1995 deselectAllSequenceMenuItem.addActionListener(this);
1996 invertSequenceMenuItem.addActionListener(this);
1997 remove2LeftMenuItem.setLabel("Remove Left");
1998 remove2LeftMenuItem.addActionListener(this);
1999 remove2RightMenuItem.setLabel("Remove Right");
2000 remove2RightMenuItem.addActionListener(this);
2001 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2002 removeGappedColumnMenuItem.addActionListener(this);
2003 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2004 removeAllGapsMenuItem.addActionListener(this);
2005 viewBoxesMenuItem.setLabel("Boxes");
2006 viewBoxesMenuItem.setState(true);
2007 viewBoxesMenuItem.addItemListener(this);
2008 viewTextMenuItem.setLabel("Text");
2009 viewTextMenuItem.setState(true);
2010 viewTextMenuItem.addItemListener(this);
2011 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2012 sortPairwiseMenuItem.addActionListener(this);
2013 sortIDMenuItem.setLabel("by ID");
2014 sortIDMenuItem.addActionListener(this);
2015 sortGroupMenuItem.setLabel("by Group");
2016 sortGroupMenuItem.addActionListener(this);
2017 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2018 removeRedundancyMenuItem.addActionListener(this);
2019 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2020 pairwiseAlignmentMenuItem.addActionListener(this);
2021 PCAMenuItem.setLabel("Principal Component Analysis");
2022 PCAMenuItem.addActionListener(this);
2023 averageDistanceTreeMenuItem.setLabel(
2024 "Average Distance Using % Identity");
2025 averageDistanceTreeMenuItem.addActionListener(this);
2026 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2027 neighbourTreeMenuItem.addActionListener(this);
2028 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
2029 statusBar.setBackground(Color.white);
2030 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2031 statusBar.setText("Status bar");
2032 outputTextboxMenu.setLabel("Output to Textbox");
2033 clustalColour.setLabel("Clustalx");
2035 clustalColour.addActionListener(this);
2036 zappoColour.setLabel("Zappo");
2037 zappoColour.addActionListener(this);
2038 taylorColour.setLabel("Taylor");
2039 taylorColour.addActionListener(this);
2040 hydrophobicityColour.setLabel("Hydrophobicity");
2041 hydrophobicityColour.addActionListener(this);
2042 helixColour.setLabel("Helix Propensity");
2043 helixColour.addActionListener(this);
2044 strandColour.setLabel("Strand Propensity");
2045 strandColour.addActionListener(this);
2046 turnColour.setLabel("Turn Propensity");
2047 turnColour.addActionListener(this);
2048 buriedColour.setLabel("Buried Index");
2049 buriedColour.addActionListener(this);
2050 userDefinedColour.setLabel("User Defined...");
2051 userDefinedColour.addActionListener(this);
2052 PIDColour.setLabel("Percentage Identity");
2053 PIDColour.addActionListener(this);
2054 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2055 BLOSUM62Colour.addActionListener(this);
2056 avDistanceTreeBlosumMenuItem.setLabel(
2057 "Average Distance Using BLOSUM62");
2058 avDistanceTreeBlosumMenuItem.addActionListener(this);
2059 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2060 njTreeBlosumMenuItem.addActionListener(this);
2061 annotationPanelMenuItem.setLabel("Show Annotations");
2062 annotationPanelMenuItem.addItemListener(this);
2063 colourTextMenuItem.setLabel("Colour Text");
2064 colourTextMenuItem.addItemListener(this);
2065 overviewMenuItem.setLabel("Overview Window");
2066 overviewMenuItem.addActionListener(this);
2067 undoMenuItem.setEnabled(false);
2068 undoMenuItem.setLabel("Undo");
2069 undoMenuItem.addActionListener(this);
2070 redoMenuItem.setEnabled(false);
2071 redoMenuItem.setLabel("Redo");
2072 redoMenuItem.addActionListener(this);
2073 conservationMenuItem.setLabel("by Conservation");
2074 conservationMenuItem.addItemListener(this);
2075 noColourmenuItem.setLabel("None");
2076 noColourmenuItem.addActionListener(this);
2077 wrapMenuItem.setLabel("Wrap");
2078 wrapMenuItem.addItemListener(this);
2079 renderGapsMenuItem.setLabel("Show Gaps");
2080 renderGapsMenuItem.setState(true);
2081 renderGapsMenuItem.addItemListener(this);
2082 findMenuItem.setLabel("Find...");
2083 findMenuItem.addActionListener(this);
2084 searchMenu.setLabel("Search");
2086 abovePIDThreshold.setLabel("Above Identity Threshold");
2087 abovePIDThreshold.addItemListener(this);
2088 nucleotideColour.setLabel("Nucleotide");
2089 nucleotideColour.addActionListener(this);
2090 deleteGroups.setLabel("Undefine Groups");
2091 deleteGroups.addActionListener(this);
2092 copy.setLabel("Copy");
2093 copy.addActionListener(this);
2094 cut.setLabel("Cut");
2095 cut.addActionListener(this);
2096 delete.setLabel("Delete");
2097 delete.addActionListener(this);
2098 pasteMenu.setLabel("Paste");
2099 pasteNew.setLabel("To New Alignment");
2100 pasteNew.addActionListener(this);
2101 pasteThis.setLabel("Add To This Alignment");
2102 pasteThis.addActionListener(this);
2103 applyToAllGroups.setLabel("Apply Colour To All Groups");
2104 applyToAllGroups.setState(true);
2105 applyToAllGroups.addItemListener(this);
2106 font.setLabel("Font...");
2107 font.addActionListener(this);
2108 scaleAbove.setLabel("Scale Above");
2109 scaleAbove.setState(true);
2110 scaleAbove.setEnabled(false);
2111 scaleAbove.addItemListener(this);
2112 scaleLeft.setEnabled(false);
2113 scaleLeft.setState(true);
2114 scaleLeft.setLabel("Scale Left");
2115 scaleLeft.addItemListener(this);
2116 scaleRight.setEnabled(false);
2117 scaleRight.setState(true);
2118 scaleRight.setLabel("Scale Right");
2119 scaleRight.addItemListener(this);
2120 modifyPID.setLabel("Modify Identity Threshold...");
2121 modifyPID.addActionListener(this);
2122 modifyConservation.setLabel("Modify Conservation Threshold...");
2123 modifyConservation.addActionListener(this);
2124 sortByTreeMenu.setLabel("By Tree Order");
2125 sort.setLabel("Sort");
2126 calculate.setLabel("Calculate Tree");
2127 autoCalculate.addItemListener(this);
2128 inputText.setLabel("Input from textbox");
2129 inputText.addActionListener(this);
2131 helpMenu.setLabel("Help");
2132 documentation.setLabel("Documentation");
2133 documentation.addActionListener(this);
2135 about.setLabel("About...");
2136 about.addActionListener(this);
2137 seqLimits.setState(true);
2138 seqLimits.setLabel("Show Sequence Limits");
2139 seqLimits.addItemListener(this);
2140 featureSettings.setLabel("Feature Settings...");
2141 featureSettings.addActionListener(this);
2142 sequenceFeatures.setLabel("Sequence Features");
2143 sequenceFeatures.addItemListener(this);
2144 sequenceFeatures.setState(false);
2145 annotationColour.setLabel("by Annotation...");
2146 annotationColour.addActionListener(this);
2147 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2148 invertColSel.setLabel("Invert Column Selection");
2149 menu1.setLabel("Show");
2150 showColumns.setLabel("All Columns ");
2151 showSeqs.setLabel("All Sequences");
2152 menu2.setLabel("Hide");
2153 hideColumns.setLabel("Selected Columns");
2154 hideSequences.setLabel("Selected Sequences");
2155 invertColSel.addActionListener(this);
2156 showColumns.addActionListener(this);
2157 showSeqs.addActionListener(this);
2158 hideColumns.addActionListener(this);
2159 hideSequences.addActionListener(this);
2162 alignFrameMenuBar.add(fileMenu);
2163 alignFrameMenuBar.add(editMenu);
2164 alignFrameMenuBar.add(searchMenu);
2165 alignFrameMenuBar.add(viewMenu);
2166 alignFrameMenuBar.add(colourMenu);
2167 alignFrameMenuBar.add(calculateMenu);
2168 alignFrameMenuBar.add(helpMenu);
2169 fileMenu.add(inputText);
2170 fileMenu.add(outputTextboxMenu);
2171 if(jalviewServletURL!=null)
2172 fileMenu.add(loadApplication);
2173 fileMenu.addSeparator();
2174 fileMenu.add(loadTree);
2175 fileMenu.add(closeMenuItem);
2176 editMenu.add(undoMenuItem);
2177 editMenu.add(redoMenuItem);
2180 editMenu.add(pasteMenu);
2181 editMenu.add(delete);
2182 editMenu.addSeparator();
2183 editMenu.add(selectAllSequenceMenuItem);
2184 editMenu.add(deselectAllSequenceMenuItem);
2185 editMenu.add(invertSequenceMenuItem);
2186 editMenu.add(invertColSel);
2187 editMenu.add(deleteGroups);
2188 editMenu.addSeparator();
2189 editMenu.add(remove2LeftMenuItem);
2190 editMenu.add(remove2RightMenuItem);
2191 editMenu.add(removeGappedColumnMenuItem);
2192 editMenu.add(removeAllGapsMenuItem);
2193 editMenu.add(removeRedundancyMenuItem);
2194 searchMenu.add(findMenuItem);
2196 viewMenu.addSeparator();
2197 viewMenu.add(menu1);
2198 viewMenu.add(menu2);
2199 viewMenu.addSeparator();
2200 viewMenu.add(wrapMenuItem);
2201 viewMenu.add(scaleAbove);
2202 viewMenu.add(scaleLeft);
2203 viewMenu.add(scaleRight);
2204 viewMenu.addSeparator();
2205 viewMenu.add(seqLimits);
2206 viewMenu.add(viewBoxesMenuItem);
2207 viewMenu.add(viewTextMenuItem);
2208 viewMenu.add(colourTextMenuItem);
2209 viewMenu.add(renderGapsMenuItem);
2210 viewMenu.add(annotationPanelMenuItem);
2211 viewMenu.addSeparator();
2212 viewMenu.add(sequenceFeatures);
2213 viewMenu.add(featureSettings);
2214 viewMenu.addSeparator();
2215 viewMenu.add(overviewMenuItem);
2216 colourMenu.add(applyToAllGroups);
2217 colourMenu.addSeparator();
2218 colourMenu.add(noColourmenuItem);
2219 colourMenu.add(clustalColour);
2220 colourMenu.add(BLOSUM62Colour);
2221 colourMenu.add(PIDColour);
2222 colourMenu.add(zappoColour);
2223 colourMenu.add(taylorColour);
2224 colourMenu.add(hydrophobicityColour);
2225 colourMenu.add(helixColour);
2226 colourMenu.add(strandColour);
2227 colourMenu.add(turnColour);
2228 colourMenu.add(buriedColour);
2229 colourMenu.add(nucleotideColour);
2230 colourMenu.add(userDefinedColour);
2231 colourMenu.addSeparator();
2232 colourMenu.add(conservationMenuItem);
2233 colourMenu.add(modifyConservation);
2234 colourMenu.add(abovePIDThreshold);
2235 colourMenu.add(modifyPID);
2236 colourMenu.add(annotationColour);
2237 calculateMenu.add(sort);
2238 calculateMenu.add(calculate);
2239 calculateMenu.addSeparator();
2240 calculateMenu.add(pairwiseAlignmentMenuItem);
2241 calculateMenu.add(PCAMenuItem);
2242 calculateMenu.add(autoCalculate);
2243 this.add(statusBar, BorderLayout.SOUTH);
2244 pasteMenu.add(pasteNew);
2245 pasteMenu.add(pasteThis);
2246 sort.add(sortIDMenuItem);
2247 sort.add(sortByTreeMenu);
2248 sort.add(sortGroupMenuItem);
2249 sort.add(sortPairwiseMenuItem);
2250 calculate.add(averageDistanceTreeMenuItem);
2251 calculate.add(neighbourTreeMenuItem);
2252 calculate.add(avDistanceTreeBlosumMenuItem);
2253 calculate.add(njTreeBlosumMenuItem);
2254 helpMenu.add(documentation);
2255 helpMenu.add(about);
2256 menu1.add(showColumns);
2257 menu1.add(showSeqs);
2258 menu2.add(hideColumns);
2259 menu2.add(hideSequences);
2262 public void setEmbedded()
2265 embeddedMenu = new Panel();
2266 embeddedEdit = new Label();
2267 embeddedSearch = new Label();
2268 embeddedView = new Label();
2269 embeddedColour = new Label();
2270 embeddedFile = new Label();
2271 embeddedHelp = new Label();
2272 embeddedCalculate = new Label();
2273 flowLayout1 = new FlowLayout();
2274 embeddedMenu.setBackground(Color.lightGray);
2275 embeddedMenu.setLayout(flowLayout1);
2276 embeddedEdit.setText("Edit");
2277 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2278 embeddedSearch.setText("Search");
2279 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2280 embeddedView.setText("View");
2281 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2282 embeddedColour.setText("Colour");
2283 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2284 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2285 embeddedFile.setText("File");
2286 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2287 embeddedHelp.setText("Help");
2288 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2289 embeddedCalculate.setText("Calculate");
2290 embeddedMenu.add(embeddedFile);
2291 embeddedMenu.add(embeddedEdit);
2292 embeddedMenu.add(embeddedSearch);
2293 embeddedMenu.add(embeddedView);
2294 embeddedMenu.add(embeddedColour);
2295 embeddedMenu.add(embeddedCalculate);
2296 embeddedMenu.add(embeddedHelp);
2297 flowLayout1.setAlignment(FlowLayout.LEFT);
2298 flowLayout1.setHgap(2);
2299 flowLayout1.setVgap(0);
2300 embeddedFile.addMouseListener(this);
2301 embeddedEdit.addMouseListener(this);
2302 embeddedSearch.addMouseListener(this);
2303 embeddedView.addMouseListener(this);
2304 embeddedColour.addMouseListener(this);
2305 embeddedCalculate.addMouseListener(this);
2306 embeddedHelp.addMouseListener(this);
2308 // setVisible(false);
2309 fileMenu.remove(closeMenuItem);
2310 fileMenu.remove(3); // Seperator
2312 viewport.applet.setLayout(new BorderLayout());
2313 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
2314 viewport.applet.add(statusBar, BorderLayout.SOUTH);
2315 // viewport.applet.validate();
2317 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
2318 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
2320 viewport.applet.add(alignPanel, BorderLayout.CENTER);
2321 viewport.applet.validate();
2327 PopupMenu filePopup, editPopup, searchPopup,
2328 viewPopup, colourPopup, calculatePopup, helpPopup;
2329 MenuItem featureSettings = new MenuItem();
2330 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
2331 MenuItem annotationColour = new MenuItem();
2332 MenuItem invertColSel = new MenuItem();
2333 Menu menu1 = new Menu();
2334 MenuItem showColumns = new MenuItem();
2335 MenuItem showSeqs = new MenuItem();
2336 Menu menu2 = new Menu();
2337 MenuItem hideColumns = new MenuItem();
2338 MenuItem hideSequences = new MenuItem();
2340 public void mousePressed(MouseEvent evt)
2342 PopupMenu popup = null;
2343 Label source = (Label)evt.getSource();
2344 if(source==embeddedFile)
2346 popup = filePopup = genPopupMenu(filePopup, fileMenu);
2348 else if(source==embeddedEdit)
2350 popup = editPopup = genPopupMenu(editPopup, editMenu);
2352 else if(source==embeddedSearch)
2354 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
2356 else if(source==embeddedView)
2358 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
2360 else if(source==embeddedColour)
2362 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
2364 else if(source==embeddedCalculate)
2366 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
2368 else if(source==embeddedHelp)
2370 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
2373 embeddedMenu.add(popup);
2374 popup.show(embeddedMenu,
2375 source.getBounds().x,
2376 source.getBounds().y + source.getBounds().getSize().height);
2379 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
2385 popup = new PopupMenu();
2386 int m, mSize = original.getItemCount();
2387 for(m=0; m<mSize; m++)
2389 popup.add(original.getItem(m));
2396 public void mouseClicked(MouseEvent evt)
2398 public void mouseReleased(MouseEvent evt)
2400 public void mouseEntered(MouseEvent evt)
2402 public void mouseExited(MouseEvent evt)