2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2005 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("defaultColour")!=null)
588 url.append("&colour=" +
589 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
593 if(viewport.applet.getParameter("userDefinedColour")!=null)
595 url.append( "&colour=" +
596 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
600 showURL(url.toString(), "FULL_APP");
604 String removeWhiteSpace(String colour)
606 StringBuffer sb = new StringBuffer();
607 for (int i = 0; i < colour.length(); i++)
609 if (Character.isWhitespace(colour.charAt(i)))
612 sb.append(colour.charAt(i));
615 return sb.toString();
619 String appendProtocol(String url)
623 }catch(java.net.MalformedURLException ex)
625 url = viewport.applet.getCodeBase()+url;
630 public void closeMenuItem_actionPerformed()
632 PaintRefresher.components.remove(viewport.alignment);
633 if(PaintRefresher.components.size()==0 && viewport.applet==null)
639 Stack historyList = new Stack();
640 Stack redoList = new Stack();
642 void updateEditMenuBar()
644 if (historyList.size() > 0)
646 undoMenuItem.setEnabled(true);
647 HistoryItem hi = (HistoryItem) historyList.peek();
648 undoMenuItem.setLabel("Undo " + hi.getDescription());
652 undoMenuItem.setEnabled(false);
653 undoMenuItem.setLabel("Undo");
656 if (redoList.size() > 0)
658 redoMenuItem.setEnabled(true);
659 HistoryItem hi = (HistoryItem) redoList.peek();
660 redoMenuItem.setLabel("Redo " + hi.getDescription());
664 redoMenuItem.setEnabled(false);
665 redoMenuItem.setLabel("Redo");
669 public void addHistoryItem(HistoryItem hi)
671 historyList.push(hi);
676 protected void undoMenuItem_actionPerformed()
678 HistoryItem nh,hi = (HistoryItem) historyList.pop();
679 redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
681 if (hi.alColumnChanges!=null)
682 nh.alColumnChanges=hi.alColumnChanges.getInverse();
683 restoreHistoryItem(hi);
684 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
687 protected void redoMenuItem_actionPerformed()
689 HistoryItem nh,hi = (HistoryItem) redoList.pop();
690 historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
692 if (hi.alColumnChanges!=null)
693 nh.alColumnChanges=hi.alColumnChanges.getInverse();
694 restoreHistoryItem(hi);
696 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
699 // used by undo and redo
700 void restoreHistoryItem(HistoryItem hi)
702 hi.restore(viewport.getColumnSelection());
705 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
708 public void moveSelectedSequences(boolean up)
710 SequenceGroup sg = viewport.getSelectionGroup();
718 for (int i = 1; i < viewport.alignment.getHeight(); i++)
720 SequenceI seq = viewport.alignment.getSequenceAt(i);
721 if (!sg.getSequences(false).contains(seq))
726 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
727 if (sg.getSequences(false).contains(temp))
732 viewport.alignment.getSequences().setElementAt(temp, i);
733 viewport.alignment.getSequences().setElementAt(seq, i - 1);
738 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
740 SequenceI seq = viewport.alignment.getSequenceAt(i);
741 if (!sg.getSequences(true).contains(seq))
746 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
747 if (sg.getSequences(true).contains(temp))
752 viewport.alignment.getSequences().setElementAt(temp, i);
753 viewport.alignment.getSequences().setElementAt(seq, i + 1);
757 alignPanel.repaint();
760 static StringBuffer copiedSequences;
761 static Vector copiedHiddenColumns;
762 protected void copy_actionPerformed()
764 if (viewport.getSelectionGroup() == null)
769 SequenceGroup sg = viewport.getSelectionGroup();
770 copiedSequences = new StringBuffer();
771 Hashtable orderedSeqs = new Hashtable();
772 for (int i = 0; i < sg.getSize(false); i++)
774 SequenceI seq = sg.getSequenceAt(i);
775 int index = viewport.alignment.findIndex(seq);
776 orderedSeqs.put(index + "", seq);
779 int index = 0, startRes, endRes;
782 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
784 copiedHiddenColumns = new Vector();
785 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
786 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
789 int[] region = (int[])
790 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
792 copiedHiddenColumns.addElement(new int[]
793 {region[0] - hiddenOffset,
794 region[1] - hiddenOffset});
798 copiedHiddenColumns = null;
801 for (int i = 0; i < sg.getSize(false); i++)
803 SequenceI seq = null;
807 if (orderedSeqs.containsKey(index + ""))
809 seq = (SequenceI) orderedSeqs.get(index + "");
821 //Returns residue following index if gap
822 startRes = seq.findPosition(sg.getStartRes());
825 //Need to find the residue preceeding index if gap
828 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
830 ch = seq.getCharAt(j);
831 if (!jalview.util.Comparison.isGap( (ch)))
839 endRes += seq.getStart() -1;
842 copiedSequences.append(seq.getName() + "\t" +
845 seq.getSequence(sg.getStartRes(),
846 sg.getEndRes() + 1) + "\n");
851 protected void pasteNew_actionPerformed()
856 protected void pasteThis_actionPerformed()
858 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
863 void paste(boolean newAlignment)
867 if (copiedSequences == null)
872 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
873 Vector seqs = new Vector();
874 while (st.hasMoreElements())
876 String name = st.nextToken();
877 int start = Integer.parseInt(st.nextToken());
878 int end = Integer.parseInt(st.nextToken());
879 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
883 viewport.alignment.addSequence(sequence);
887 seqs.addElement(sequence);
893 SequenceI[] newSeqs = new SequenceI[seqs.size()];
894 for (int i = 0; i < seqs.size(); i++)
896 newSeqs[i] = (SequenceI) seqs.elementAt(i);
899 String newtitle = new String("Copied sequences");
900 if (getTitle().startsWith("Copied sequences"))
902 newtitle = getTitle();
906 newtitle = newtitle.concat("- from " + getTitle());
908 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
912 if (copiedHiddenColumns != null)
914 for (int i = 0; i < copiedHiddenColumns.size(); i++)
916 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
917 af.viewport.hideColumns(region[0], region[1]);
922 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
927 viewport.setEndSeq(viewport.alignment.getHeight());
928 viewport.alignment.getWidth();
929 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
934 {} // could be anything being pasted in here
938 protected void cut_actionPerformed()
940 copy_actionPerformed();
941 delete_actionPerformed();
944 protected void delete_actionPerformed()
946 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
948 if (viewport.getSelectionGroup() == null)
954 SequenceGroup sg = viewport.getSelectionGroup();
955 boolean allSequences = false;
956 if(sg.getSize(false)==viewport.alignment.getHeight())
959 for (int i = 0; i < sg.getSize(false); i++)
961 SequenceI seq = sg.getSequenceAt(i);
962 int index = viewport.getAlignment().findIndex(seq);
963 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
965 // If the cut affects all sequences, remove highlighted columns
968 viewport.getColumnSelection().removeElements(sg.getStartRes(),
973 if (seq.getSequence().length() < 1)
975 viewport.getAlignment().deleteSequence(seq);
979 viewport.getAlignment().getSequences().setElementAt(seq, index);
983 viewport.setSelectionGroup(null);
984 viewport.alignment.deleteGroup(sg);
985 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
986 if (viewport.getAlignment().getHeight() < 1)
990 this.setVisible(false);
995 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
999 protected void deleteGroups_actionPerformed()
1001 viewport.alignment.deleteAllGroups();
1002 viewport.setSelectionGroup(null);
1004 alignPanel.repaint();
1007 public void selectAllSequenceMenuItem_actionPerformed()
1009 SequenceGroup sg = new SequenceGroup();
1010 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1012 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1014 sg.setEndRes(viewport.alignment.getWidth()-1);
1015 viewport.setSelectionGroup(sg);
1016 alignPanel.repaint();
1017 PaintRefresher.Refresh(null, viewport.alignment);
1020 public void deselectAllSequenceMenuItem_actionPerformed()
1022 if(viewport.cursorMode)
1024 alignPanel.seqPanel.keyboardNo1=null;
1025 alignPanel.seqPanel.keyboardNo2=null;
1027 viewport.setSelectionGroup(null);
1028 viewport.getColumnSelection().clear();
1029 viewport.setSelectionGroup(null);
1030 alignPanel.idPanel.idCanvas.searchResults = null;
1031 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1032 alignPanel.repaint();
1033 PaintRefresher.Refresh(null, viewport.alignment);
1036 public void invertSequenceMenuItem_actionPerformed()
1038 SequenceGroup sg = viewport.getSelectionGroup();
1039 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1041 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1044 PaintRefresher.Refresh(null, viewport.alignment);
1047 public void remove2LeftMenuItem_actionPerformed()
1049 ColumnSelection colSel = viewport.getColumnSelection();
1050 if (colSel.size() > 0)
1053 addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
1055 int min = colSel.getMin();
1056 viewport.getAlignment().trimLeft(min);
1057 colSel.compensateForEdit(0, min);
1058 edit.addShift(0, min);
1059 if (viewport.getSelectionGroup() != null)
1061 viewport.getSelectionGroup().adjustForRemoveLeft(min);
1064 Vector groups = viewport.alignment.getGroups();
1065 for (int i = 0; i < groups.size(); i++)
1067 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1068 if (!sg.adjustForRemoveLeft(min))
1070 viewport.alignment.deleteGroup(sg);
1073 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1077 public void remove2RightMenuItem_actionPerformed()
1079 ColumnSelection colSel = viewport.getColumnSelection();
1080 if (colSel.size() > 0)
1082 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
1084 int max = colSel.getMax();
1085 viewport.getAlignment().trimRight(max);
1087 if (viewport.getSelectionGroup() != null)
1089 viewport.getSelectionGroup().adjustForRemoveRight(max);
1092 Vector groups = viewport.alignment.getGroups();
1093 for (int i = 0; i < groups.size(); i++)
1095 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1096 if (!sg.adjustForRemoveRight(max))
1098 viewport.alignment.deleteGroup(sg);
1101 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1106 public void removeGappedColumnMenuItem_actionPerformed()
1109 addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
1113 //This is to maintain viewport position on first residue
1115 SequenceI seq = viewport.alignment.getSequenceAt(0);
1116 int startRes = seq.findPosition(viewport.startRes);
1118 viewport.getAlignment().removeGaps();
1120 viewport.setStartRes(seq.findIndex(startRes)-1);
1122 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1125 public void removeAllGapsMenuItem_actionPerformed()
1127 // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
1128 // TODO: columnSelection.compensateforedits should be called (and passed to history item)
1129 HistoryItem editgaps;
1130 addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment,
1133 //This is to maintain viewport position on first residue
1135 SequenceI seq = viewport.alignment.getSequenceAt(0);
1136 int startRes = seq.findPosition(viewport.startRes);
1141 int start=0, end = viewport.alignment.getWidth();
1143 if (viewport.getSelectionGroup() != null
1144 && viewport.getSelectionGroup().getSequences(false) != null
1145 && viewport.getSelectionGroup().getSize(false)>0)
1147 seqs = viewport.getSelectionGroup().getSequences(true);
1148 start = viewport.getSelectionGroup().getStartRes();
1149 end = viewport.getSelectionGroup().getEndRes()+1;
1152 seqs = viewport.alignment.getSequences();
1154 /* Commented out regions below are partial implementation of todo above.
1155 * divide start,end into visible chunks, and for each:
1156 int diff=end-start+1;
1158 int dr[] = new int[seqs.size()];
1160 for (int i = 0; i < seqs.size(); i++)
1162 current = (SequenceI) seqs.elementAt(i);
1164 current.removeGaps(start, end);
1165 /*if (d<diff) // can only shift
1171 /* // after the end of each chunk -
1173 // record shift for history.
1174 editgaps.addShift(start, diff);
1175 if (viewport.hasHiddenColumns && diffmax>diff) {
1177 StringBuffer gaps=new StringBuffer(diffmax);
1178 for (int i=0,j=diffmax-diff; i<j; i++)
1179 gaps.append(viewport.getGapCharacter());
1180 for (int i=0, j=seqs.size(); i<j; i++) {
1181 current = (SequenceI) seqs.elementAt(i);
1183 String sq = current.getSequence();
1184 current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
1190 viewport.setStartRes(seq.findIndex(startRes)-1);
1191 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1194 public void alignmentChanged()
1196 viewport.alignment.padGaps();
1197 if(viewport.autocalculateConsensus)
1199 viewport.updateConsensus();
1200 viewport.updateConservation();
1203 resetAllColourSchemes();
1204 if(alignPanel.overviewPanel!=null)
1205 alignPanel.overviewPanel.updateOverviewImage();
1207 viewport.alignment.adjustSequenceAnnotations();
1208 alignPanel.repaint();
1211 void resetAllColourSchemes()
1213 ColourSchemeI cs = viewport.globalColourScheme;
1216 if (cs instanceof ClustalxColourScheme)
1218 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
1219 resetClustalX(viewport.alignment.getSequences(),
1220 viewport.alignment.getWidth());
1223 cs.setConsensus(viewport.vconsensus);
1224 if (cs.conservationApplied())
1226 Alignment al = (Alignment) viewport.alignment;
1227 Conservation c = new Conservation("All",
1228 ResidueProperties.propHash, 3,
1229 al.getSequences(), 0,
1232 c.verdict(false, viewport.ConsPercGaps);
1234 cs.setConservation(c);
1238 int s, sSize = viewport.alignment.getGroups().size();
1239 for(s=0; s<sSize; s++)
1241 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
1242 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
1244 ((ClustalxColourScheme)sg.cs).resetClustalX(
1245 sg.getSequences(true), sg.getWidth());
1247 sg.recalcConservation();
1253 public void findMenuItem_actionPerformed()
1255 new Finder(alignPanel);
1258 public void font_actionPerformed()
1260 new FontChooser(alignPanel);
1264 public void seqLimits_itemStateChanged()
1266 viewport.setShowJVSuffix(seqLimits.getState());
1267 alignPanel.fontChanged();
1268 alignPanel.repaint();
1272 protected void colourTextMenuItem_actionPerformed()
1274 viewport.setColourText(colourTextMenuItem.getState());
1275 alignPanel.repaint();
1278 protected void wrapMenuItem_actionPerformed()
1280 viewport.setWrapAlignment(wrapMenuItem.getState());
1281 alignPanel.setWrapAlignment(wrapMenuItem.getState());
1282 scaleAbove.setEnabled(wrapMenuItem.getState());
1283 scaleLeft.setEnabled(wrapMenuItem.getState());
1284 scaleRight.setEnabled(wrapMenuItem.getState());
1285 alignPanel.repaint();
1289 protected void scaleAbove_actionPerformed()
1291 viewport.setScaleAboveWrapped(scaleAbove.getState());
1292 alignPanel.repaint();
1295 protected void scaleLeft_actionPerformed()
1297 viewport.setScaleLeftWrapped(scaleLeft.getState());
1298 alignPanel.repaint();
1301 protected void scaleRight_actionPerformed()
1303 viewport.setScaleRightWrapped(scaleRight.getState());
1304 alignPanel.repaint();
1307 public void viewBoxesMenuItem_actionPerformed()
1309 viewport.setShowBoxes(viewBoxesMenuItem.getState());
1310 alignPanel.repaint();
1313 public void viewTextMenuItem_actionPerformed()
1315 viewport.setShowText(viewTextMenuItem.getState());
1316 alignPanel.repaint();
1319 protected void renderGapsMenuItem_actionPerformed()
1321 viewport.setRenderGaps(renderGapsMenuItem.getState());
1322 alignPanel.repaint();
1325 public void annotationPanelMenuItem_actionPerformed()
1327 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
1328 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
1331 public void featureSettings_actionPerformed()
1333 new FeatureSettings(viewport, alignPanel);
1336 public void overviewMenuItem_actionPerformed()
1338 if (alignPanel.overviewPanel != null)
1343 Frame frame = new Frame();
1344 OverviewPanel overview = new OverviewPanel(alignPanel);
1345 frame.add(overview);
1346 // +50 must allow for applet frame window
1347 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
1348 overview.preferredSize().width,
1349 overview.preferredSize().height + 50);
1352 frame.addWindowListener(new WindowAdapter()
1354 public void windowClosing(WindowEvent e)
1356 alignPanel.setOverviewPanel(null);
1360 alignPanel.setOverviewPanel(overview);
1364 protected void noColourmenuItem_actionPerformed()
1369 public void clustalColour_actionPerformed()
1371 abovePIDThreshold.setState(false);
1372 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
1373 viewport.alignment.getWidth()));
1376 public void zappoColour_actionPerformed()
1378 changeColour(new ZappoColourScheme());
1381 public void taylorColour_actionPerformed()
1383 changeColour(new TaylorColourScheme());
1386 public void hydrophobicityColour_actionPerformed()
1388 changeColour(new HydrophobicColourScheme());
1391 public void helixColour_actionPerformed()
1393 changeColour(new HelixColourScheme());
1396 public void strandColour_actionPerformed()
1398 changeColour(new StrandColourScheme());
1401 public void turnColour_actionPerformed()
1403 changeColour(new TurnColourScheme());
1406 public void buriedColour_actionPerformed()
1408 changeColour(new BuriedColourScheme());
1411 public void nucleotideColour_actionPerformed()
1413 changeColour(new NucleotideColourScheme());
1416 protected void applyToAllGroups_actionPerformed()
1418 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
1421 void changeColour(ColourSchemeI cs)
1427 if (viewport.getAbovePIDThreshold())
1429 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
1431 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1433 viewport.setGlobalColourScheme(cs);
1437 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1440 if (viewport.getConservationSelected())
1443 Alignment al = (Alignment) viewport.alignment;
1444 Conservation c = new Conservation("All",
1445 ResidueProperties.propHash, 3,
1446 al.getSequences(), 0,
1450 c.verdict(false, viewport.ConsPercGaps);
1452 cs.setConservation(c);
1454 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
1460 cs.setConservation(null);
1463 cs.setConsensus(viewport.vconsensus);
1466 viewport.setGlobalColourScheme(cs);
1468 if (viewport.getColourAppliesToAllGroups())
1470 Vector groups = viewport.alignment.getGroups();
1471 for (int i = 0; i < groups.size(); i++)
1473 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1480 if (cs instanceof ClustalxColourScheme)
1482 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
1488 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
1490 catch (Exception ex)
1492 ex.printStackTrace();
1497 if (viewport.getAbovePIDThreshold()
1498 || cs instanceof PIDColourScheme
1499 || cs instanceof Blosum62ColourScheme)
1501 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1502 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
1505 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1507 if (viewport.getConservationSelected())
1509 Conservation c = new Conservation("Group",
1510 ResidueProperties.propHash, 3,
1511 sg.getSequences(true), 0,
1512 viewport.alignment.getWidth() - 1);
1514 c.verdict(false, viewport.ConsPercGaps);
1515 sg.cs.setConservation(c);
1519 sg.cs.setConservation(null);
1520 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1527 if (alignPanel.getOverviewPanel() != null)
1529 alignPanel.getOverviewPanel().updateOverviewImage();
1532 alignPanel.repaint();
1537 protected void modifyPID_actionPerformed()
1539 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
1541 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
1543 SliderPanel.showPIDSlider();
1547 protected void modifyConservation_actionPerformed()
1549 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
1551 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
1553 SliderPanel.showConservationSlider();
1557 protected void conservationMenuItem_actionPerformed()
1559 viewport.setConservationSelected(conservationMenuItem.getState());
1561 viewport.setAbovePIDThreshold(false);
1562 abovePIDThreshold.setState(false);
1564 changeColour(viewport.getGlobalColourScheme());
1566 modifyConservation_actionPerformed();
1569 public void abovePIDThreshold_actionPerformed()
1571 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
1573 conservationMenuItem.setState(false);
1574 viewport.setConservationSelected(false);
1576 changeColour(viewport.getGlobalColourScheme());
1578 modifyPID_actionPerformed();
1581 public void userDefinedColour_actionPerformed()
1583 new UserDefinedColours(alignPanel, null);
1586 public void PIDColour_actionPerformed()
1588 changeColour(new PIDColourScheme());
1591 public void BLOSUM62Colour_actionPerformed()
1593 changeColour(new Blosum62ColourScheme());
1596 public void sortPairwiseMenuItem_actionPerformed()
1598 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
1600 AlignmentSorter.sortByPID(viewport.getAlignment(),
1601 viewport.getAlignment().getSequenceAt(0));
1602 alignPanel.repaint();
1605 public void sortIDMenuItem_actionPerformed()
1607 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
1609 AlignmentSorter.sortByID(viewport.getAlignment());
1610 alignPanel.repaint();
1613 public void sortGroupMenuItem_actionPerformed()
1615 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
1617 AlignmentSorter.sortByGroup(viewport.getAlignment());
1618 alignPanel.repaint();
1622 public void removeRedundancyMenuItem_actionPerformed()
1624 new RedundancyPanel(alignPanel);
1627 public void pairwiseAlignmentMenuItem_actionPerformed()
1629 if (viewport.getSelectionGroup()!=null
1630 && viewport.getSelectionGroup().getSize(false) > 1)
1632 Frame frame = new Frame();
1633 frame.add(new PairwiseAlignPanel(alignPanel));
1634 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
1638 public void PCAMenuItem_actionPerformed()
1640 //are the sequences aligned?
1641 if (!viewport.alignment.isAligned())
1644 int Width = viewport.getAlignment().getWidth();
1646 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1649 current = viewport.getAlignment().getSequenceAt(i);
1651 if (current.getLength() < Width)
1653 current.insertCharAt(Width - 1, viewport.getGapCharacter());
1656 alignPanel.repaint();
1659 if ( (viewport.getSelectionGroup() != null &&
1660 viewport.getSelectionGroup().getSize(false) < 4 &&
1661 viewport.getSelectionGroup().getSize(false) > 0)
1662 || viewport.getAlignment().getHeight() < 4)
1669 new PCAPanel(viewport);
1671 catch (java.lang.OutOfMemoryError ex)
1677 public void averageDistanceTreeMenuItem_actionPerformed()
1679 NewTreePanel("AV", "PID", "Average distance tree using PID");
1682 public void neighbourTreeMenuItem_actionPerformed()
1684 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
1687 protected void njTreeBlosumMenuItem_actionPerformed()
1689 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
1692 protected void avTreeBlosumMenuItem_actionPerformed()
1694 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
1697 void NewTreePanel(String type, String pwType, String title)
1699 //are the sequences aligned?
1700 if (!viewport.alignment.isAligned())
1703 int Width = viewport.getAlignment().getWidth();
1705 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1708 current = viewport.getAlignment().getSequenceAt(i);
1710 if (current.getLength() < Width)
1712 current.insertCharAt(Width - 1, viewport.getGapCharacter());
1715 alignPanel.repaint();
1719 if ( (viewport.getSelectionGroup() != null &&
1720 viewport.getSelectionGroup().getSize(false) > 1)
1721 || (viewport.getSelectionGroup() == null
1722 && viewport.alignment.getHeight() > 1))
1724 final TreePanel tp = new TreePanel(viewport,
1728 addTreeMenuItem(tp, title);
1730 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
1734 void loadTree_actionPerformed()
1736 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1737 cap.setText("Paste your Newick tree file here.");
1738 cap.treeImport = true;
1739 Frame frame = new Frame();
1741 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
1744 public void loadTree(jalview.io.NewickFile tree, String treeFile)
1746 TreePanel tp = new TreePanel(viewport,
1750 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
1751 addTreeMenuItem(tp, treeFile);
1754 void addTreeMenuItem(final TreePanel treePanel, String title)
1756 final MenuItem item = new MenuItem(title);
1757 sortByTreeMenu.add(item);
1758 item.addActionListener(new java.awt.event.ActionListener()
1760 public void actionPerformed(ActionEvent evt)
1762 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
1764 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
1765 alignPanel.repaint();
1769 treePanel.addWindowListener(new WindowAdapter()
1771 public void windowClosing(WindowEvent e)
1773 sortByTreeMenu.remove(item);
1778 protected void documentation_actionPerformed()
1780 showURL("http://www.jalview.org/help.html", "HELP");
1783 protected void about_actionPerformed()
1786 class AboutPanel extends Canvas
1789 public AboutPanel(String version)
1790 { this.version = version; }
1792 public void paint(Graphics g)
1794 g.setColor(Color.white);
1795 g.fillRect(0, 0, getSize().width, getSize().height);
1796 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
1797 FontMetrics fm = g.getFontMetrics();
1798 int fh = fm.getHeight();
1800 g.setColor(Color.black);
1801 g.setFont(new Font("Helvetica", Font.BOLD, 14));
1802 g.drawString("Jalview - Release "+version, 200, y += fh);
1803 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
1804 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
1806 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
1809 "For any issues relating to Jalview, email help@jalview.org", x,
1811 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
1812 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
1814 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
1818 String version = "test";
1819 java.net.URL url = getClass().getResource("/.build_properties");
1824 BufferedReader reader = new BufferedReader(new InputStreamReader(
1827 while ( (line = reader.readLine()) != null)
1829 if (line.indexOf("VERSION") > -1)
1831 version = line.substring(line.indexOf("=") + 1);
1835 catch (Exception ex)
1837 ex.printStackTrace();
1842 Frame frame = new Frame();
1843 frame.add(new AboutPanel(version));
1844 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
1848 public void showURL(String url, String target)
1850 if (viewport.applet == null)
1852 System.out.println("Not running as applet - no browser available.");
1858 System.out.println("Show url: "+url);
1859 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
1862 catch (Exception ex)
1864 ex.printStackTrace();
1870 //////////////////////////////////////////////////////////////////////////////////
1871 //JBuilder Graphics here
1873 protected MenuBar alignFrameMenuBar = new MenuBar();
1874 protected Menu fileMenu = new Menu("File");
1875 protected MenuItem loadApplication = new MenuItem("View in Full Application");
1876 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
1877 protected MenuItem closeMenuItem = new MenuItem("Close");
1878 protected Menu editMenu = new Menu("Edit");
1879 protected Menu viewMenu = new Menu("View");
1880 protected Menu colourMenu = new Menu("Colour");
1881 protected Menu calculateMenu = new Menu("Calculate");
1882 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
1883 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
1884 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
1885 protected MenuItem remove2LeftMenuItem = new MenuItem();
1886 protected MenuItem remove2RightMenuItem = new MenuItem();
1887 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
1888 protected MenuItem removeAllGapsMenuItem = new MenuItem();
1889 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
1890 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
1891 protected MenuItem sortPairwiseMenuItem = new MenuItem();
1892 protected MenuItem sortIDMenuItem = new MenuItem();
1893 protected MenuItem sortGroupMenuItem = new MenuItem();
1894 protected MenuItem removeRedundancyMenuItem = new MenuItem();
1895 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
1896 protected MenuItem PCAMenuItem = new MenuItem();
1897 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
1898 protected MenuItem neighbourTreeMenuItem = new MenuItem();
1899 BorderLayout borderLayout1 = new BorderLayout();
1900 public Label statusBar = new Label();
1901 protected Menu outputTextboxMenu = new Menu();
1902 protected MenuItem clustalColour = new MenuItem();
1903 protected MenuItem zappoColour = new MenuItem();
1904 protected MenuItem taylorColour = new MenuItem();
1905 protected MenuItem hydrophobicityColour = new MenuItem();
1906 protected MenuItem helixColour = new MenuItem();
1907 protected MenuItem strandColour = new MenuItem();
1908 protected MenuItem turnColour = new MenuItem();
1909 protected MenuItem buriedColour = new MenuItem();
1910 protected MenuItem userDefinedColour = new MenuItem();
1911 protected MenuItem PIDColour = new MenuItem();
1912 protected MenuItem BLOSUM62Colour = new MenuItem();
1913 MenuItem njTreeBlosumMenuItem = new MenuItem();
1914 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
1915 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
1916 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
1917 MenuItem overviewMenuItem = new MenuItem();
1918 protected MenuItem undoMenuItem = new MenuItem();
1919 protected MenuItem redoMenuItem = new MenuItem();
1920 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
1921 MenuItem noColourmenuItem = new MenuItem();
1922 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
1923 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
1924 MenuItem findMenuItem = new MenuItem();
1925 Menu searchMenu = new Menu();
1926 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
1927 protected MenuItem nucleotideColour = new MenuItem();
1928 MenuItem deleteGroups = new MenuItem();
1929 MenuItem delete = new MenuItem();
1930 MenuItem copy = new MenuItem();
1931 MenuItem cut = new MenuItem();
1932 Menu pasteMenu = new Menu();
1933 MenuItem pasteNew = new MenuItem();
1934 MenuItem pasteThis = new MenuItem();
1935 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
1936 protected MenuItem font = new MenuItem();
1937 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
1938 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
1939 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
1940 MenuItem modifyPID = new MenuItem();
1941 MenuItem modifyConservation = new MenuItem();
1942 protected CheckboxMenuItem autoCalculate
1943 = new CheckboxMenuItem("Autocalculate Consensus", true);
1944 protected Menu sortByTreeMenu = new Menu();
1945 Menu sort = new Menu();
1946 Menu calculate = new Menu();
1947 MenuItem inputText = new MenuItem();
1948 Menu helpMenu = new Menu();
1949 MenuItem documentation = new MenuItem();
1950 MenuItem about = new MenuItem();
1951 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
1954 Label embeddedSearch;
1956 Label embeddedColour;
1959 Label embeddedCalculate;
1960 FlowLayout flowLayout1;
1962 private void jbInit() throws Exception {
1964 setMenuBar(alignFrameMenuBar);
1968 // dynamically fill save as menu with available formats
1969 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
1972 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
1974 item.addActionListener(new java.awt.event.ActionListener()
1976 public void actionPerformed(ActionEvent e)
1978 outputText_actionPerformed(e);
1982 outputTextboxMenu.add(item);
1984 closeMenuItem.addActionListener(this);
1985 loadApplication.addActionListener(this);
1987 loadTree.addActionListener(this);
1988 selectAllSequenceMenuItem.addActionListener(this);
1989 deselectAllSequenceMenuItem.addActionListener(this);
1990 invertSequenceMenuItem.addActionListener(this);
1991 remove2LeftMenuItem.setLabel("Remove Left");
1992 remove2LeftMenuItem.addActionListener(this);
1993 remove2RightMenuItem.setLabel("Remove Right");
1994 remove2RightMenuItem.addActionListener(this);
1995 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
1996 removeGappedColumnMenuItem.addActionListener(this);
1997 removeAllGapsMenuItem.setLabel("Remove All Gaps");
1998 removeAllGapsMenuItem.addActionListener(this);
1999 viewBoxesMenuItem.setLabel("Boxes");
2000 viewBoxesMenuItem.setState(true);
2001 viewBoxesMenuItem.addItemListener(this);
2002 viewTextMenuItem.setLabel("Text");
2003 viewTextMenuItem.setState(true);
2004 viewTextMenuItem.addItemListener(this);
2005 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2006 sortPairwiseMenuItem.addActionListener(this);
2007 sortIDMenuItem.setLabel("by ID");
2008 sortIDMenuItem.addActionListener(this);
2009 sortGroupMenuItem.setLabel("by Group");
2010 sortGroupMenuItem.addActionListener(this);
2011 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2012 removeRedundancyMenuItem.addActionListener(this);
2013 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2014 pairwiseAlignmentMenuItem.addActionListener(this);
2015 PCAMenuItem.setLabel("Principal Component Analysis");
2016 PCAMenuItem.addActionListener(this);
2017 averageDistanceTreeMenuItem.setLabel(
2018 "Average Distance Using % Identity");
2019 averageDistanceTreeMenuItem.addActionListener(this);
2020 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2021 neighbourTreeMenuItem.addActionListener(this);
2022 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
2023 statusBar.setBackground(Color.white);
2024 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2025 statusBar.setText("Status bar");
2026 outputTextboxMenu.setLabel("Output to Textbox");
2027 clustalColour.setLabel("Clustalx");
2029 clustalColour.addActionListener(this);
2030 zappoColour.setLabel("Zappo");
2031 zappoColour.addActionListener(this);
2032 taylorColour.setLabel("Taylor");
2033 taylorColour.addActionListener(this);
2034 hydrophobicityColour.setLabel("Hydrophobicity");
2035 hydrophobicityColour.addActionListener(this);
2036 helixColour.setLabel("Helix Propensity");
2037 helixColour.addActionListener(this);
2038 strandColour.setLabel("Strand Propensity");
2039 strandColour.addActionListener(this);
2040 turnColour.setLabel("Turn Propensity");
2041 turnColour.addActionListener(this);
2042 buriedColour.setLabel("Buried Index");
2043 buriedColour.addActionListener(this);
2044 userDefinedColour.setLabel("User Defined...");
2045 userDefinedColour.addActionListener(this);
2046 PIDColour.setLabel("Percentage Identity");
2047 PIDColour.addActionListener(this);
2048 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2049 BLOSUM62Colour.addActionListener(this);
2050 avDistanceTreeBlosumMenuItem.setLabel(
2051 "Average Distance Using BLOSUM62");
2052 avDistanceTreeBlosumMenuItem.addActionListener(this);
2053 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2054 njTreeBlosumMenuItem.addActionListener(this);
2055 annotationPanelMenuItem.setLabel("Show Annotations");
2056 annotationPanelMenuItem.addItemListener(this);
2057 colourTextMenuItem.setLabel("Colour Text");
2058 colourTextMenuItem.addItemListener(this);
2059 overviewMenuItem.setLabel("Overview Window");
2060 overviewMenuItem.addActionListener(this);
2061 undoMenuItem.setEnabled(false);
2062 undoMenuItem.setLabel("Undo");
2063 undoMenuItem.addActionListener(this);
2064 redoMenuItem.setEnabled(false);
2065 redoMenuItem.setLabel("Redo");
2066 redoMenuItem.addActionListener(this);
2067 conservationMenuItem.setLabel("by Conservation");
2068 conservationMenuItem.addItemListener(this);
2069 noColourmenuItem.setLabel("None");
2070 noColourmenuItem.addActionListener(this);
2071 wrapMenuItem.setLabel("Wrap");
2072 wrapMenuItem.addItemListener(this);
2073 renderGapsMenuItem.setLabel("Show Gaps");
2074 renderGapsMenuItem.setState(true);
2075 renderGapsMenuItem.addItemListener(this);
2076 findMenuItem.setLabel("Find...");
2077 findMenuItem.addActionListener(this);
2078 searchMenu.setLabel("Search");
2080 abovePIDThreshold.setLabel("Above Identity Threshold");
2081 abovePIDThreshold.addItemListener(this);
2082 nucleotideColour.setLabel("Nucleotide");
2083 nucleotideColour.addActionListener(this);
2084 deleteGroups.setLabel("Undefine Groups");
2085 deleteGroups.addActionListener(this);
2086 copy.setLabel("Copy");
2087 copy.addActionListener(this);
2088 cut.setLabel("Cut");
2089 cut.addActionListener(this);
2090 delete.setLabel("Delete");
2091 delete.addActionListener(this);
2092 pasteMenu.setLabel("Paste");
2093 pasteNew.setLabel("To New Alignment");
2094 pasteNew.addActionListener(this);
2095 pasteThis.setLabel("Add To This Alignment");
2096 pasteThis.addActionListener(this);
2097 applyToAllGroups.setLabel("Apply Colour To All Groups");
2098 applyToAllGroups.setState(true);
2099 applyToAllGroups.addItemListener(this);
2100 font.setLabel("Font...");
2101 font.addActionListener(this);
2102 scaleAbove.setLabel("Scale Above");
2103 scaleAbove.setState(true);
2104 scaleAbove.setEnabled(false);
2105 scaleAbove.addItemListener(this);
2106 scaleLeft.setEnabled(false);
2107 scaleLeft.setState(true);
2108 scaleLeft.setLabel("Scale Left");
2109 scaleLeft.addItemListener(this);
2110 scaleRight.setEnabled(false);
2111 scaleRight.setState(true);
2112 scaleRight.setLabel("Scale Right");
2113 scaleRight.addItemListener(this);
2114 modifyPID.setLabel("Modify Identity Threshold...");
2115 modifyPID.addActionListener(this);
2116 modifyConservation.setLabel("Modify Conservation Threshold...");
2117 modifyConservation.addActionListener(this);
2118 sortByTreeMenu.setLabel("By Tree Order");
2119 sort.setLabel("Sort");
2120 calculate.setLabel("Calculate Tree");
2121 autoCalculate.addItemListener(this);
2122 inputText.setLabel("Input from textbox");
2123 inputText.addActionListener(this);
2125 helpMenu.setLabel("Help");
2126 documentation.setLabel("Documentation");
2127 documentation.addActionListener(this);
2129 about.setLabel("About...");
2130 about.addActionListener(this);
2131 seqLimits.setState(true);
2132 seqLimits.setLabel("Show Sequence Limits");
2133 seqLimits.addItemListener(this);
2134 featureSettings.setLabel("Feature Settings...");
2135 featureSettings.addActionListener(this);
2136 sequenceFeatures.setLabel("Sequence Features");
2137 sequenceFeatures.addItemListener(this);
2138 sequenceFeatures.setState(false);
2139 annotationColour.setLabel("by Annotation...");
2140 annotationColour.addActionListener(this);
2141 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2142 invertColSel.setLabel("Invert Column Selection");
2143 menu1.setLabel("Show");
2144 showColumns.setLabel("All Columns ");
2145 showSeqs.setLabel("All Sequences");
2146 menu2.setLabel("Hide");
2147 hideColumns.setLabel("Selected Columns");
2148 hideSequences.setLabel("Selected Sequences");
2149 invertColSel.addActionListener(this);
2150 showColumns.addActionListener(this);
2151 showSeqs.addActionListener(this);
2152 hideColumns.addActionListener(this);
2153 hideSequences.addActionListener(this);
2156 alignFrameMenuBar.add(fileMenu);
2157 alignFrameMenuBar.add(editMenu);
2158 alignFrameMenuBar.add(searchMenu);
2159 alignFrameMenuBar.add(viewMenu);
2160 alignFrameMenuBar.add(colourMenu);
2161 alignFrameMenuBar.add(calculateMenu);
2162 alignFrameMenuBar.add(helpMenu);
2163 fileMenu.add(inputText);
2164 fileMenu.add(outputTextboxMenu);
2165 if(jalviewServletURL!=null)
2166 fileMenu.add(loadApplication);
2167 fileMenu.addSeparator();
2168 fileMenu.add(loadTree);
2169 fileMenu.add(closeMenuItem);
2170 editMenu.add(undoMenuItem);
2171 editMenu.add(redoMenuItem);
2174 editMenu.add(pasteMenu);
2175 editMenu.add(delete);
2176 editMenu.addSeparator();
2177 editMenu.add(selectAllSequenceMenuItem);
2178 editMenu.add(deselectAllSequenceMenuItem);
2179 editMenu.add(invertSequenceMenuItem);
2180 editMenu.add(invertColSel);
2181 editMenu.add(deleteGroups);
2182 editMenu.addSeparator();
2183 editMenu.add(remove2LeftMenuItem);
2184 editMenu.add(remove2RightMenuItem);
2185 editMenu.add(removeGappedColumnMenuItem);
2186 editMenu.add(removeAllGapsMenuItem);
2187 editMenu.add(removeRedundancyMenuItem);
2188 searchMenu.add(findMenuItem);
2190 viewMenu.addSeparator();
2191 viewMenu.add(menu1);
2192 viewMenu.add(menu2);
2193 viewMenu.addSeparator();
2194 viewMenu.add(wrapMenuItem);
2195 viewMenu.add(scaleAbove);
2196 viewMenu.add(scaleLeft);
2197 viewMenu.add(scaleRight);
2198 viewMenu.addSeparator();
2199 viewMenu.add(seqLimits);
2200 viewMenu.add(viewBoxesMenuItem);
2201 viewMenu.add(viewTextMenuItem);
2202 viewMenu.add(colourTextMenuItem);
2203 viewMenu.add(renderGapsMenuItem);
2204 viewMenu.add(annotationPanelMenuItem);
2205 viewMenu.addSeparator();
2206 viewMenu.add(sequenceFeatures);
2207 viewMenu.add(featureSettings);
2208 viewMenu.addSeparator();
2209 viewMenu.add(overviewMenuItem);
2210 colourMenu.add(applyToAllGroups);
2211 colourMenu.addSeparator();
2212 colourMenu.add(noColourmenuItem);
2213 colourMenu.add(clustalColour);
2214 colourMenu.add(BLOSUM62Colour);
2215 colourMenu.add(PIDColour);
2216 colourMenu.add(zappoColour);
2217 colourMenu.add(taylorColour);
2218 colourMenu.add(hydrophobicityColour);
2219 colourMenu.add(helixColour);
2220 colourMenu.add(strandColour);
2221 colourMenu.add(turnColour);
2222 colourMenu.add(buriedColour);
2223 colourMenu.add(nucleotideColour);
2224 colourMenu.add(userDefinedColour);
2225 colourMenu.addSeparator();
2226 colourMenu.add(conservationMenuItem);
2227 colourMenu.add(modifyConservation);
2228 colourMenu.add(abovePIDThreshold);
2229 colourMenu.add(modifyPID);
2230 colourMenu.add(annotationColour);
2231 calculateMenu.add(sort);
2232 calculateMenu.add(calculate);
2233 calculateMenu.addSeparator();
2234 calculateMenu.add(pairwiseAlignmentMenuItem);
2235 calculateMenu.add(PCAMenuItem);
2236 calculateMenu.add(autoCalculate);
2237 this.add(statusBar, BorderLayout.SOUTH);
2238 pasteMenu.add(pasteNew);
2239 pasteMenu.add(pasteThis);
2240 sort.add(sortIDMenuItem);
2241 sort.add(sortByTreeMenu);
2242 sort.add(sortGroupMenuItem);
2243 sort.add(sortPairwiseMenuItem);
2244 calculate.add(averageDistanceTreeMenuItem);
2245 calculate.add(neighbourTreeMenuItem);
2246 calculate.add(avDistanceTreeBlosumMenuItem);
2247 calculate.add(njTreeBlosumMenuItem);
2248 helpMenu.add(documentation);
2249 helpMenu.add(about);
2250 menu1.add(showColumns);
2251 menu1.add(showSeqs);
2252 menu2.add(hideColumns);
2253 menu2.add(hideSequences);
2256 public void setEmbedded()
2259 embeddedMenu = new Panel();
2260 embeddedEdit = new Label();
2261 embeddedSearch = new Label();
2262 embeddedView = new Label();
2263 embeddedColour = new Label();
2264 embeddedFile = new Label();
2265 embeddedHelp = new Label();
2266 embeddedCalculate = new Label();
2267 flowLayout1 = new FlowLayout();
2268 embeddedMenu.setBackground(Color.lightGray);
2269 embeddedMenu.setLayout(flowLayout1);
2270 embeddedEdit.setText("Edit");
2271 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2272 embeddedSearch.setText("Search");
2273 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2274 embeddedView.setText("View");
2275 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2276 embeddedColour.setText("Colour");
2277 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2278 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2279 embeddedFile.setText("File");
2280 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2281 embeddedHelp.setText("Help");
2282 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2283 embeddedCalculate.setText("Calculate");
2284 embeddedMenu.add(embeddedFile);
2285 embeddedMenu.add(embeddedEdit);
2286 embeddedMenu.add(embeddedSearch);
2287 embeddedMenu.add(embeddedView);
2288 embeddedMenu.add(embeddedColour);
2289 embeddedMenu.add(embeddedCalculate);
2290 embeddedMenu.add(embeddedHelp);
2291 flowLayout1.setAlignment(FlowLayout.LEFT);
2292 flowLayout1.setHgap(2);
2293 flowLayout1.setVgap(0);
2294 embeddedFile.addMouseListener(this);
2295 embeddedEdit.addMouseListener(this);
2296 embeddedSearch.addMouseListener(this);
2297 embeddedView.addMouseListener(this);
2298 embeddedColour.addMouseListener(this);
2299 embeddedCalculate.addMouseListener(this);
2300 embeddedHelp.addMouseListener(this);
2302 // setVisible(false);
2303 fileMenu.remove(closeMenuItem);
2304 fileMenu.remove(3); // Seperator
2306 viewport.applet.setLayout(new BorderLayout());
2307 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
2308 viewport.applet.add(statusBar, BorderLayout.SOUTH);
2309 // viewport.applet.validate();
2311 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
2312 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
2314 viewport.applet.add(alignPanel, BorderLayout.CENTER);
2315 viewport.applet.validate();
2321 PopupMenu filePopup, editPopup, searchPopup,
2322 viewPopup, colourPopup, calculatePopup, helpPopup;
2323 MenuItem featureSettings = new MenuItem();
2324 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
2325 MenuItem annotationColour = new MenuItem();
2326 MenuItem invertColSel = new MenuItem();
2327 Menu menu1 = new Menu();
2328 MenuItem showColumns = new MenuItem();
2329 MenuItem showSeqs = new MenuItem();
2330 Menu menu2 = new Menu();
2331 MenuItem hideColumns = new MenuItem();
2332 MenuItem hideSequences = new MenuItem();
2334 public void mousePressed(MouseEvent evt)
2336 PopupMenu popup = null;
2337 Label source = (Label)evt.getSource();
2338 if(source==embeddedFile)
2340 popup = filePopup = genPopupMenu(filePopup, fileMenu);
2342 else if(source==embeddedEdit)
2344 popup = editPopup = genPopupMenu(editPopup, editMenu);
2346 else if(source==embeddedSearch)
2348 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
2350 else if(source==embeddedView)
2352 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
2354 else if(source==embeddedColour)
2356 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
2358 else if(source==embeddedCalculate)
2360 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
2362 else if(source==embeddedHelp)
2364 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
2367 embeddedMenu.add(popup);
2368 popup.show(embeddedMenu,
2369 source.getBounds().x,
2370 source.getBounds().y + source.getBounds().getSize().height);
2373 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
2379 popup = new PopupMenu();
2380 int m, mSize = original.getItemCount();
2381 for(m=0; m<mSize; m++)
2383 popup.add(original.getItem(m));
2390 public void mouseClicked(MouseEvent evt)
2392 public void mouseReleased(MouseEvent evt)
2394 public void mouseEntered(MouseEvent evt)
2396 public void mouseExited(MouseEvent evt)