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.*;
26 import jalview.commands.*;
28 import java.awt.event.*;
30 import java.io.InputStreamReader;
31 import java.io.BufferedReader;
35 public class AlignFrame extends Frame implements ActionListener,
36 ItemListener, KeyListener, MouseListener
38 public AlignmentPanel alignPanel;
39 public AlignViewport viewport;
40 int DEFAULT_WIDTH = 700;
41 int DEFAULT_HEIGHT = 500;
43 String jalviewServletURL;
46 public AlignFrame(AlignmentI al,
47 jalview.bin.JalviewLite applet,
52 jalviewServletURL = applet.getParameter("APPLICATION_URL");
61 viewport = new AlignViewport(al, applet);
62 alignPanel = new AlignmentPanel(this, viewport);
64 viewport.updateConservation(alignPanel);
65 viewport.updateConsensus(alignPanel);
67 annotationPanelMenuItem.setState(viewport.showAnnotation);
69 seqLimits.setState(viewport.showJVSuffix);
73 String param = applet.getParameter("sortBy");
76 if (param.equalsIgnoreCase("Id"))
77 sortIDMenuItem_actionPerformed();
78 else if (param.equalsIgnoreCase("Pairwise Identity"))
79 sortPairwiseMenuItem_actionPerformed();
82 param = applet.getParameter("wrap");
85 if (param.equalsIgnoreCase("true"))
87 wrapMenuItem.setState(true);
88 wrapMenuItem_actionPerformed();
94 param = applet.getParameter("windowWidth");
97 int width = Integer.parseInt(param);
98 DEFAULT_WIDTH = width;
100 param = applet.getParameter("windowHeight");
103 int height = Integer.parseInt(param);
104 DEFAULT_HEIGHT = height;
112 //Some JVMS send keyevents to Top frame or lowest panel,
113 //Havent worked out why yet. So add to both this frame and seqCanvas for now
114 this.addKeyListener(this);
115 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
116 alignPanel.idPanel.idCanvas.addKeyListener(this);
117 alignPanel.scalePanel.addKeyListener(this);
118 alignPanel.annotationPanel.addKeyListener(this);
127 add(alignPanel, BorderLayout.CENTER);
128 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
131 alignPanel.validate();
132 alignPanel.repaint();
134 public AlignViewport getAlignViewport()
139 public SeqCanvas getSeqcanvas()
141 return alignPanel.seqPanel.seqCanvas;
148 * @param String DOCUMENT ME!
151 public void parseFeaturesFile(String file, String type)
153 Hashtable featureLinks = new Hashtable();
154 boolean featuresFile = false;
156 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
157 alignPanel.seqPanel.seqCanvas.
158 getFeatureRenderer().featureColours,
164 ex.printStackTrace();
169 if(featureLinks.size()>0)
170 alignPanel.seqPanel.seqCanvas
171 .getFeatureRenderer().featureLinks = featureLinks;
172 viewport.showSequenceFeatures = true;
173 sequenceFeatures.setState(true);
174 alignPanel.repaint();
180 public void keyPressed(KeyEvent evt)
182 if (viewport.cursorMode
183 && evt.getKeyCode() >= KeyEvent.VK_0
184 && evt.getKeyCode() <= KeyEvent.VK_9)
186 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
189 switch (evt.getKeyCode())
191 case 27: // escape key
192 deselectAllSequenceMenuItem_actionPerformed();
195 if (evt.isControlDown() || evt.isMetaDown())
197 cut_actionPerformed();
201 if (viewport.cursorMode && !evt.isControlDown())
203 alignPanel.seqPanel.setCursorColumn();
205 if (evt.isControlDown() || evt.isMetaDown())
207 copy_actionPerformed();
211 if (evt.isControlDown())
213 paste(evt.isShiftDown());
217 if (evt.isControlDown() || evt.isMetaDown())
219 selectAllSequenceMenuItem_actionPerformed();
222 case KeyEvent.VK_DOWN:
223 if(viewport.cursorMode)
225 alignPanel.seqPanel.moveCursor(0,1);
228 moveSelectedSequences(false);
232 if (viewport.cursorMode)
234 alignPanel.seqPanel.moveCursor(0,-1);
237 moveSelectedSequences(true);
240 case KeyEvent.VK_LEFT:
241 if(viewport.cursorMode)
243 alignPanel.seqPanel.moveCursor(-1,0);
247 case KeyEvent.VK_RIGHT:
248 if (viewport.cursorMode)
250 alignPanel.seqPanel.moveCursor(1,0);
253 case KeyEvent.VK_SPACE:
254 if(viewport.cursorMode)
256 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
263 case KeyEvent.VK_DELETE:
264 case KeyEvent.VK_BACK_SPACE:
265 if(viewport.cursorMode)
267 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
273 cut_actionPerformed();
274 alignPanel.seqPanel.seqCanvas.repaint();
279 if(viewport.cursorMode)
281 alignPanel.seqPanel.setCursorRow();
285 if(viewport.cursorMode)
287 alignPanel.seqPanel.setCursorPosition();
291 case KeyEvent.VK_ENTER:
292 case KeyEvent.VK_COMMA:
293 if(viewport.cursorMode)
295 alignPanel.seqPanel.setCursorRowAndColumn();
300 if(viewport.cursorMode)
302 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
306 if(viewport.cursorMode)
308 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
313 viewport.cursorMode = ! viewport.cursorMode;
314 statusBar.setText("Keyboard editing mode is "+
315 (viewport.cursorMode ? "on" : "off"));
316 if(viewport.cursorMode)
318 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
319 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
324 if (evt.isControlDown())
326 findMenuItem_actionPerformed();
332 boolean toggleSeqs = !evt.isControlDown();
333 boolean toggleCols = !evt.isShiftDown();
334 boolean hide = false;
335 SequenceGroup sg = viewport.getSelectionGroup();
339 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
342 viewport.hideAllSelectedSeqs();
344 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
345 viewport.showAllHiddenSeqs();
350 if (viewport.colSel.getSelected().size() > 0)
352 viewport.hideSelectedColumns();
354 viewport.selectionGroup = sg;
357 viewport.showAllHiddenColumns();
362 case KeyEvent.VK_PAGE_UP:
363 if (viewport.wrapAlignment)
364 alignPanel.scrollUp(true);
366 alignPanel.setScrollValues(viewport.startRes,
368 - viewport.endSeq + viewport.startSeq);
371 case KeyEvent.VK_PAGE_DOWN:
372 if (viewport.wrapAlignment)
373 alignPanel.scrollUp(false);
375 alignPanel.setScrollValues(viewport.startRes,
377 + viewport.endSeq - viewport.startSeq);
381 if (evt.isControlDown())
383 undoMenuItem_actionPerformed();
388 if (evt.isControlDown())
390 redoMenuItem_actionPerformed();
395 if (evt.isControlDown())
402 if (evt.isControlDown())
404 trimAlignment(false);
409 if (evt.isControlDown())
411 if (evt.isShiftDown())
412 this.removeAllGapsMenuItem_actionPerformed();
414 removeGappedColumnMenuItem_actionPerformed();
418 if (evt.isControlDown())
421 viewport.invertColumnSelection();
423 this.invertSequenceMenuItem_actionPerformed();
428 if (evt.isControlDown())
430 this.deleteGroups_actionPerformed();
435 if (evt.isControlDown())
443 alignPanel.repaint();
445 public void keyReleased(KeyEvent evt)
447 public void keyTyped(KeyEvent evt)
450 public void itemStateChanged(ItemEvent evt)
452 if(evt.getSource()==colourTextMenuItem)
453 colourTextMenuItem_actionPerformed();
454 else if(evt.getSource()==wrapMenuItem)
455 wrapMenuItem_actionPerformed();
456 else if(evt.getSource()==scaleAbove)
457 viewport.setScaleAboveWrapped(scaleAbove.getState());
458 else if(evt.getSource()==scaleLeft)
459 viewport.setScaleLeftWrapped(scaleLeft.getState());
460 else if(evt.getSource()==scaleRight)
461 viewport.setScaleRightWrapped(scaleRight.getState());
462 else if(evt.getSource()==seqLimits)
463 seqLimits_itemStateChanged();
464 else if(evt.getSource()==viewBoxesMenuItem)
465 viewport.setShowBoxes(viewBoxesMenuItem.getState());
466 else if(evt.getSource()==viewTextMenuItem)
467 viewport.setShowText(viewTextMenuItem.getState());
468 else if(evt.getSource()==renderGapsMenuItem)
469 viewport.setRenderGaps(renderGapsMenuItem.getState());
470 else if(evt.getSource()==annotationPanelMenuItem)
472 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
473 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
475 else if(evt.getSource()==sequenceFeatures)
477 viewport.showSequenceFeatures(sequenceFeatures.getState());
478 alignPanel.seqPanel.seqCanvas.repaint();
480 else if(evt.getSource()==conservationMenuItem)
481 conservationMenuItem_actionPerformed();
482 else if(evt.getSource()==abovePIDThreshold)
483 abovePIDThreshold_actionPerformed();
484 else if(evt.getSource()==applyToAllGroups)
485 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
486 else if(evt.getSource()==autoCalculate)
487 viewport.autocalculateConsensus = autoCalculate.getState();
489 alignPanel.repaint();
491 public void actionPerformed(ActionEvent evt)
493 Object source = evt.getSource();
495 if(source==inputText)
496 inputText_actionPerformed();
497 else if(source==loadTree)
498 loadTree_actionPerformed();
499 else if(source==loadApplication)
500 launchFullApplication();
501 else if(source==closeMenuItem)
502 closeMenuItem_actionPerformed();
503 else if(source==copy)
504 copy_actionPerformed();
505 else if(source==undoMenuItem)
506 undoMenuItem_actionPerformed();
507 else if(source==redoMenuItem)
508 redoMenuItem_actionPerformed();
509 else if(source==inputText)
510 inputText_actionPerformed();
511 else if(source==closeMenuItem)
512 closeMenuItem_actionPerformed();
513 else if(source==undoMenuItem)
514 undoMenuItem_actionPerformed();
515 else if(source==redoMenuItem)
516 redoMenuItem_actionPerformed();
517 else if(source==copy)
518 copy_actionPerformed();
519 else if(source==pasteNew)
520 pasteNew_actionPerformed();
521 else if(source==pasteThis)
522 pasteThis_actionPerformed();
524 cut_actionPerformed();
525 else if(source==delete)
526 delete_actionPerformed();
527 else if(source==deleteGroups)
528 deleteGroups_actionPerformed();
529 else if(source==selectAllSequenceMenuItem)
530 selectAllSequenceMenuItem_actionPerformed();
531 else if(source==deselectAllSequenceMenuItem)
532 deselectAllSequenceMenuItem_actionPerformed();
533 else if(source==invertSequenceMenuItem)
534 invertSequenceMenuItem_actionPerformed();
535 else if(source==invertColSel)
536 { viewport.invertColumnSelection(); alignPanel.repaint(); }
537 else if(source==remove2LeftMenuItem)
539 else if(source==remove2RightMenuItem)
540 trimAlignment(false);
541 else if(source==removeGappedColumnMenuItem)
542 removeGappedColumnMenuItem_actionPerformed();
543 else if(source==removeAllGapsMenuItem)
544 removeAllGapsMenuItem_actionPerformed();
545 else if(source==findMenuItem)
546 findMenuItem_actionPerformed();
547 else if(source==font)
548 new FontChooser(alignPanel);
549 else if (source == newView)
551 else if(source==showColumns)
553 viewport.showAllHiddenColumns(); alignPanel.repaint();
555 else if(source==showSeqs)
557 viewport.showAllHiddenSeqs();
559 else if(source == hideColumns)
561 viewport.hideSelectedColumns(); alignPanel.repaint();
563 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
565 viewport.hideAllSelectedSeqs();
567 else if(source==featureSettings)
568 new FeatureSettings(alignPanel);
569 else if(source==overviewMenuItem)
570 overviewMenuItem_actionPerformed();
571 else if(source==noColourmenuItem)
573 else if(source==clustalColour)
575 abovePIDThreshold.setState(false);
576 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
577 viewport.alignment.getWidth()));
579 else if(source==zappoColour)
580 changeColour(new ZappoColourScheme());
581 else if(source==taylorColour)
582 changeColour(new TaylorColourScheme());
583 else if(source==hydrophobicityColour)
584 changeColour(new HydrophobicColourScheme());
585 else if(source==helixColour)
586 changeColour(new HelixColourScheme());
587 else if(source==strandColour)
588 changeColour(new StrandColourScheme());
589 else if(source==turnColour)
590 changeColour(new TurnColourScheme());
591 else if(source==buriedColour)
592 changeColour(new BuriedColourScheme());
593 else if(source==nucleotideColour)
594 changeColour(new NucleotideColourScheme());
595 else if(source==modifyPID)
596 modifyPID_actionPerformed();
597 else if(source==modifyConservation)
598 modifyConservation_actionPerformed();
599 else if(source==userDefinedColour)
600 new UserDefinedColours(alignPanel, null);
601 else if(source==PIDColour)
602 changeColour(new PIDColourScheme());
603 else if(source==BLOSUM62Colour)
604 changeColour(new Blosum62ColourScheme());
605 else if(source==annotationColour)
606 new AnnotationColourChooser(viewport, alignPanel);
607 else if(source==sortPairwiseMenuItem)
608 sortPairwiseMenuItem_actionPerformed();
609 else if(source==sortIDMenuItem)
610 sortIDMenuItem_actionPerformed();
611 else if(source==sortGroupMenuItem)
612 sortGroupMenuItem_actionPerformed();
613 else if(source==removeRedundancyMenuItem)
614 removeRedundancyMenuItem_actionPerformed();
615 else if(source==pairwiseAlignmentMenuItem)
616 pairwiseAlignmentMenuItem_actionPerformed();
617 else if(source==PCAMenuItem)
618 PCAMenuItem_actionPerformed();
619 else if(source==averageDistanceTreeMenuItem)
620 averageDistanceTreeMenuItem_actionPerformed();
621 else if(source==neighbourTreeMenuItem)
622 neighbourTreeMenuItem_actionPerformed();
623 else if(source==njTreeBlosumMenuItem)
624 njTreeBlosumMenuItem_actionPerformed();
625 else if(source==avDistanceTreeBlosumMenuItem)
626 avTreeBlosumMenuItem_actionPerformed();
627 else if(source==documentation)
628 documentation_actionPerformed();
629 else if(source==about)
630 about_actionPerformed();
634 public void inputText_actionPerformed()
636 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
637 Frame frame = new Frame();
639 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
642 protected void outputText_actionPerformed(ActionEvent e)
644 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
645 Frame frame = new Frame();
647 jalview.bin.JalviewLite.addFrame(frame,
648 "Alignment output - " + e.getActionCommand(),
650 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
651 viewport.getAlignment().getSequences(),
652 viewport.showJVSuffix));
655 void launchFullApplication()
657 StringBuffer url = new StringBuffer(jalviewServletURL);
660 appendProtocol( viewport.applet.getParameter("file") ) );
662 if(viewport.applet.getParameter("features")!=null)
664 url.append( "&features=" );
665 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
668 if(viewport.applet.getParameter("annotations")!=null)
670 url.append( "&annotations=" );
671 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
674 if(viewport.applet.getParameter("jnetfile")!=null)
676 url.append( "&annotations=" );
677 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
680 if(viewport.applet.getParameter("defaultColour")!=null)
682 url.append("&colour=" +
683 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
687 if(viewport.applet.getParameter("userDefinedColour")!=null)
689 url.append( "&colour=" +
690 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
694 showURL(url.toString(), "FULL_APP");
698 String removeWhiteSpace(String colour)
700 StringBuffer sb = new StringBuffer();
701 for (int i = 0; i < colour.length(); i++)
703 if (Character.isWhitespace(colour.charAt(i)))
706 sb.append(colour.charAt(i));
709 return sb.toString();
713 String appendProtocol(String url)
717 }catch(java.net.MalformedURLException ex)
719 url = viewport.applet.getCodeBase()+url;
724 public void closeMenuItem_actionPerformed()
726 PaintRefresher.RemoveComponent(alignPanel);
727 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
728 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
730 if(PaintRefresher.components.size()==0 && viewport.applet==null)
740 void updateEditMenuBar()
743 if (viewport.historyList.size() > 0)
745 undoMenuItem.setEnabled(true);
746 CommandI command = (CommandI) viewport.historyList.peek();
747 undoMenuItem.setLabel("Undo " + command.getDescription());
751 undoMenuItem.setEnabled(false);
752 undoMenuItem.setLabel("Undo");
755 if (viewport.redoList.size() > 0)
757 redoMenuItem.setEnabled(true);
759 CommandI command = (CommandI) viewport.redoList.peek();
760 redoMenuItem.setLabel("Redo " + command.getDescription());
764 redoMenuItem.setEnabled(false);
765 redoMenuItem.setLabel("Redo");
769 public void addHistoryItem(CommandI command)
771 if(command.getSize()>0)
773 viewport.historyList.push(command);
774 viewport.redoList.removeAllElements();
776 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
783 * @param e DOCUMENT ME!
785 protected void undoMenuItem_actionPerformed()
787 if(viewport.historyList.size()<1)
790 CommandI command = (CommandI)viewport.historyList.pop();
791 viewport.redoList.push(command);
792 command.undoCommand();
794 AlignViewport originalSource = getOriginatingSource(command);
796 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
798 originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());
804 * @param e DOCUMENT ME!
806 protected void redoMenuItem_actionPerformed()
808 if(viewport.redoList.size()<1)
811 CommandI command = (CommandI) viewport.redoList.pop();
812 viewport.historyList.push(command);
815 AlignViewport originalSource = getOriginatingSource(command);
816 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
819 originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());
822 AlignViewport getOriginatingSource(CommandI command)
824 AlignViewport originalSource = null;
825 //For sequence removal and addition, we need to fire
826 //the property change event FROM the viewport where the
827 //original alignment was altered
828 AlignmentI al = null;
829 if (command instanceof EditCommand)
831 EditCommand editCommand = (EditCommand) command;
832 al = editCommand.getAlignment();
833 Vector comps = (Vector) PaintRefresher.components
834 .get(viewport.getSequenceSetId());
835 for (int i = 0; i < comps.size(); i++)
837 if (comps.elementAt(i) instanceof AlignmentPanel)
839 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
841 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
848 if (originalSource == null)
850 //The original view is closed, we must validate
851 //the current view against the closed view first
853 PaintRefresher.validateSequences(al, viewport.alignment);
855 originalSource = viewport;
859 return originalSource;
862 public void moveSelectedSequences(boolean up)
864 SequenceGroup sg = viewport.getSelectionGroup();
872 for (int i = 1; i < viewport.alignment.getHeight(); i++)
874 SequenceI seq = viewport.alignment.getSequenceAt(i);
875 if (!sg.getSequences(false).contains(seq))
880 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
881 if (sg.getSequences(false).contains(temp))
886 viewport.alignment.getSequences().setElementAt(temp, i);
887 viewport.alignment.getSequences().setElementAt(seq, i - 1);
892 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
894 SequenceI seq = viewport.alignment.getSequenceAt(i);
895 if (!sg.getSequences(true).contains(seq))
900 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
901 if (sg.getSequences(true).contains(temp))
906 viewport.alignment.getSequences().setElementAt(temp, i);
907 viewport.alignment.getSequences().setElementAt(seq, i + 1);
911 alignPanel.repaint();
914 static StringBuffer copiedSequences;
915 static Vector copiedHiddenColumns;
916 protected void copy_actionPerformed()
918 if (viewport.getSelectionGroup() == null)
923 SequenceGroup sg = viewport.getSelectionGroup();
924 copiedSequences = new StringBuffer();
925 Hashtable orderedSeqs = new Hashtable();
926 for (int i = 0; i < sg.getSize(false); i++)
928 SequenceI seq = sg.getSequenceAt(i);
929 int index = viewport.alignment.findIndex(seq);
930 orderedSeqs.put(index + "", seq);
933 int index = 0, startRes, endRes;
936 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
938 copiedHiddenColumns = new Vector();
939 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
940 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
943 int[] region = (int[])
944 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
946 copiedHiddenColumns.addElement(new int[]
947 {region[0] - hiddenOffset,
948 region[1] - hiddenOffset});
952 copiedHiddenColumns = null;
955 for (int i = 0; i < sg.getSize(false); i++)
957 SequenceI seq = null;
961 if (orderedSeqs.containsKey(index + ""))
963 seq = (SequenceI) orderedSeqs.get(index + "");
975 //Returns residue following index if gap
976 startRes = seq.findPosition(sg.getStartRes());
979 //Need to find the residue preceeding index if gap
982 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
984 ch = seq.getCharAt(j);
985 if (!jalview.util.Comparison.isGap( (ch)))
993 endRes += seq.getStart() -1;
996 copiedSequences.append(seq.getName() + "\t" +
999 seq.getSequenceAsString(sg.getStartRes(),
1000 sg.getEndRes() + 1) + "\n");
1005 protected void pasteNew_actionPerformed()
1010 protected void pasteThis_actionPerformed()
1015 void paste(boolean newAlignment)
1020 if (copiedSequences == null)
1025 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1026 Vector seqs = new Vector();
1027 while (st.hasMoreElements())
1029 String name = st.nextToken();
1030 int start = Integer.parseInt(st.nextToken());
1031 int end = Integer.parseInt(st.nextToken());
1032 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1034 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1035 for (int i = 0; i < seqs.size(); i++)
1037 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1042 String newtitle = new String("Copied sequences");
1043 if (getTitle().startsWith("Copied sequences"))
1045 newtitle = getTitle();
1049 newtitle = newtitle.concat("- from " + getTitle());
1051 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1055 if (copiedHiddenColumns != null)
1057 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1059 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1060 af.viewport.hideColumns(region[0], region[1]);
1065 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1070 for (int i = 0; i < newSeqs.length; i++)
1072 viewport.alignment.addSequence(newSeqs[i]);
1076 addHistoryItem(new EditCommand(
1081 viewport.alignment.getWidth(),
1085 viewport.setEndSeq(viewport.alignment.getHeight());
1086 viewport.alignment.getWidth();
1087 viewport.firePropertyChange("alignment", null, viewport.alignment.getSequences());
1091 catch (Exception ex)
1092 {} // could be anything being pasted in here
1096 protected void cut_actionPerformed()
1098 copy_actionPerformed();
1099 delete_actionPerformed();
1102 protected void delete_actionPerformed()
1105 SequenceGroup sg = viewport.getSelectionGroup();
1111 Vector seqs = new Vector();
1113 for (int i = 0; i < sg.getSize(false); i++)
1115 seq = sg.getSequenceAt(i);
1116 seqs.addElement(seq);
1120 // If the cut affects all sequences, remove highlighted columns
1121 if (sg.getSize(false) == viewport.alignment.getHeight())
1123 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1124 sg.getEndRes() + 1);
1128 SequenceI [] cut = new SequenceI[seqs.size()];
1129 for(int i=0; i<seqs.size(); i++)
1130 cut[i] = (SequenceI)seqs.elementAt(i);
1136 addHistoryItem(new EditCommand("Cut Sequences",
1140 sg.getEndRes()-sg.getStartRes()+1,
1141 viewport.alignment));
1144 viewport.setSelectionGroup(null);
1145 viewport.alignment.deleteGroup(sg);
1147 viewport.firePropertyChange("alignment", null,
1148 viewport.getAlignment().getSequences());
1150 if (viewport.getAlignment().getHeight() < 1)
1152 this.setVisible(false);
1156 protected void deleteGroups_actionPerformed()
1158 viewport.alignment.deleteAllGroups();
1159 viewport.sequenceColours=null;
1160 viewport.setSelectionGroup(null);
1162 alignPanel.repaint();
1165 public void selectAllSequenceMenuItem_actionPerformed()
1167 SequenceGroup sg = new SequenceGroup();
1168 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1170 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1172 sg.setEndRes(viewport.alignment.getWidth()-1);
1173 viewport.setSelectionGroup(sg);
1174 alignPanel.repaint();
1175 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1178 public void deselectAllSequenceMenuItem_actionPerformed()
1180 if(viewport.cursorMode)
1182 alignPanel.seqPanel.keyboardNo1=null;
1183 alignPanel.seqPanel.keyboardNo2=null;
1185 viewport.setSelectionGroup(null);
1186 viewport.getColumnSelection().clear();
1187 viewport.setSelectionGroup(null);
1188 alignPanel.idPanel.idCanvas.searchResults = null;
1189 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1190 alignPanel.repaint();
1191 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1194 public void invertSequenceMenuItem_actionPerformed()
1196 SequenceGroup sg = viewport.getSelectionGroup();
1197 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1199 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1202 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1205 void trimAlignment(boolean trimLeft)
1207 ColumnSelection colSel = viewport.getColumnSelection();
1210 if (colSel.size() > 0)
1213 column = colSel.getMin();
1215 column = colSel.getMax();
1218 if(viewport.getSelectionGroup()!=null)
1219 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1221 seqs = viewport.alignment.getSequencesArray();
1224 TrimRegionCommand trimRegion;
1227 trimRegion = new TrimRegionCommand("Remove Left",
1228 TrimRegionCommand.TRIM_LEFT,
1233 viewport.selectionGroup);
1234 viewport.setStartRes(0);
1238 trimRegion = new TrimRegionCommand("Remove Right",
1239 TrimRegionCommand.TRIM_RIGHT,
1244 viewport.selectionGroup);
1247 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1250 addHistoryItem(trimRegion);
1252 Vector groups = viewport.alignment.getGroups();
1254 for (int i = 0; i < groups.size(); i++)
1256 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1258 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1259 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1261 viewport.alignment.deleteGroup(sg);
1265 viewport.firePropertyChange("alignment", null,
1266 viewport.getAlignment().getSequences());
1271 public void removeGappedColumnMenuItem_actionPerformed()
1273 int start = 0, end = viewport.alignment.getWidth()-1;
1276 if (viewport.getSelectionGroup() != null)
1278 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1279 start = viewport.getSelectionGroup().getStartRes();
1280 end = viewport.getSelectionGroup().getEndRes();
1283 seqs = viewport.alignment.getSequencesArray();
1286 RemoveGapColCommand removeGapCols =
1287 new RemoveGapColCommand("Remove Gapped Columns",
1290 viewport.getGapCharacter());
1292 addHistoryItem(removeGapCols);
1294 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1296 //This is to maintain viewport position on first residue
1298 SequenceI seq = viewport.alignment.getSequenceAt(0);
1299 int startRes = seq.findPosition(viewport.startRes);
1300 // ShiftList shifts;
1301 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1302 // edit.alColumnChanges=shifts.getInverse();
1303 // if (viewport.hasHiddenColumns)
1304 // viewport.getColumnSelection().compensateForEdits(shifts);
1305 viewport.setStartRes(seq.findIndex(startRes)-1);
1306 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1310 public void removeAllGapsMenuItem_actionPerformed()
1312 int start = 0, end = viewport.alignment.getWidth()-1;
1315 if (viewport.getSelectionGroup() != null)
1317 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1318 start = viewport.getSelectionGroup().getStartRes();
1319 end = viewport.getSelectionGroup().getEndRes();
1322 seqs = viewport.alignment.getSequencesArray();
1324 //This is to maintain viewport position on first residue
1326 SequenceI seq = viewport.alignment.getSequenceAt(0);
1327 int startRes = seq.findPosition(viewport.startRes);
1329 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1332 viewport.getGapCharacter()));
1334 viewport.setStartRes(seq.findIndex(startRes)-1);
1336 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1340 public void findMenuItem_actionPerformed()
1342 new Finder(alignPanel);
1345 public void newView()
1348 if (viewport.hasHiddenRows)
1349 newal = new Alignment(viewport.getAlignment().
1350 getHiddenSequences()
1351 .getFullAlignment().
1352 getSequencesArray());
1354 newal = new Alignment(viewport.alignment.getSequencesArray());
1356 AlignFrame newaf = new AlignFrame(newal,
1361 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
1362 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
1363 PaintRefresher.Register(newaf.alignPanel,
1364 newaf.alignPanel.av.getSequenceSetId());
1366 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
1367 newaf.alignPanel.av.getSequenceSetId());
1368 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
1369 newaf.alignPanel.av.getSequenceSetId());
1371 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
1373 for (int i = 0; i < comps.size(); i++)
1375 if (comps.elementAt(i) instanceof AlignmentPanel)
1379 String title = new String(this.getTitle());
1380 if (title.indexOf("(View") > -1)
1381 title = title.substring(0, title.indexOf("(View"));
1383 title+= "(View "+viewSize+")";
1385 newaf.setTitle(title.toString());
1388 newaf.viewport.historyList = viewport.historyList;
1389 newaf.viewport.redoList = viewport.redoList;
1394 public void seqLimits_itemStateChanged()
1396 viewport.setShowJVSuffix(seqLimits.getState());
1397 alignPanel.fontChanged();
1398 alignPanel.repaint();
1402 protected void colourTextMenuItem_actionPerformed()
1404 viewport.setColourText(colourTextMenuItem.getState());
1405 alignPanel.repaint();
1408 protected void wrapMenuItem_actionPerformed()
1410 viewport.setWrapAlignment(wrapMenuItem.getState());
1411 alignPanel.setWrapAlignment(wrapMenuItem.getState());
1412 scaleAbove.setEnabled(wrapMenuItem.getState());
1413 scaleLeft.setEnabled(wrapMenuItem.getState());
1414 scaleRight.setEnabled(wrapMenuItem.getState());
1415 alignPanel.repaint();
1419 public void overviewMenuItem_actionPerformed()
1421 if (alignPanel.overviewPanel != null)
1426 Frame frame = new Frame();
1427 OverviewPanel overview = new OverviewPanel(alignPanel);
1428 frame.add(overview);
1429 // +50 must allow for applet frame window
1430 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
1431 overview.preferredSize().width,
1432 overview.preferredSize().height + 50);
1435 frame.addWindowListener(new WindowAdapter()
1437 public void windowClosing(WindowEvent e)
1439 alignPanel.setOverviewPanel(null);
1443 alignPanel.setOverviewPanel(overview);
1448 void changeColour(ColourSchemeI cs)
1454 if (viewport.getAbovePIDThreshold())
1456 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
1458 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1460 viewport.setGlobalColourScheme(cs);
1464 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1467 if (viewport.getConservationSelected())
1470 Alignment al = (Alignment) viewport.alignment;
1471 Conservation c = new Conservation("All",
1472 ResidueProperties.propHash, 3,
1473 al.getSequences(), 0,
1477 c.verdict(false, viewport.ConsPercGaps);
1479 cs.setConservation(c);
1481 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
1487 cs.setConservation(null);
1490 cs.setConsensus(viewport.hconsensus);
1493 viewport.setGlobalColourScheme(cs);
1495 if (viewport.getColourAppliesToAllGroups())
1497 Vector groups = viewport.alignment.getGroups();
1498 for (int i = 0; i < groups.size(); i++)
1500 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1507 if (cs instanceof ClustalxColourScheme)
1509 sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
1515 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
1517 catch (Exception ex)
1519 ex.printStackTrace();
1524 if (viewport.getAbovePIDThreshold()
1525 || cs instanceof PIDColourScheme
1526 || cs instanceof Blosum62ColourScheme)
1528 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1529 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
1532 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1534 if (viewport.getConservationSelected())
1536 Conservation c = new Conservation("Group",
1537 ResidueProperties.propHash, 3,
1538 sg.getSequences(true), 0,
1539 viewport.alignment.getWidth() - 1);
1541 c.verdict(false, viewport.ConsPercGaps);
1542 sg.cs.setConservation(c);
1546 sg.cs.setConservation(null);
1547 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1554 if (alignPanel.getOverviewPanel() != null)
1556 alignPanel.getOverviewPanel().updateOverviewImage();
1559 alignPanel.repaint();
1564 protected void modifyPID_actionPerformed()
1566 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
1568 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
1570 SliderPanel.showPIDSlider();
1574 protected void modifyConservation_actionPerformed()
1576 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
1578 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
1580 SliderPanel.showConservationSlider();
1584 protected void conservationMenuItem_actionPerformed()
1586 viewport.setConservationSelected(conservationMenuItem.getState());
1588 viewport.setAbovePIDThreshold(false);
1589 abovePIDThreshold.setState(false);
1591 changeColour(viewport.getGlobalColourScheme());
1593 modifyConservation_actionPerformed();
1596 public void abovePIDThreshold_actionPerformed()
1598 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
1600 conservationMenuItem.setState(false);
1601 viewport.setConservationSelected(false);
1603 changeColour(viewport.getGlobalColourScheme());
1605 modifyPID_actionPerformed();
1610 public void sortPairwiseMenuItem_actionPerformed()
1612 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
1613 AlignmentSorter.sortByPID(viewport.getAlignment(),
1614 viewport.getAlignment().getSequenceAt(0));
1615 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
1616 alignPanel.repaint();
1619 public void sortIDMenuItem_actionPerformed()
1621 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
1622 // HistoryItem.SORT));
1623 AlignmentSorter.sortByID(viewport.getAlignment());
1624 alignPanel.repaint();
1627 public void sortGroupMenuItem_actionPerformed()
1629 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
1630 // HistoryItem.SORT));
1631 AlignmentSorter.sortByGroup(viewport.getAlignment());
1632 alignPanel.repaint();
1636 public void removeRedundancyMenuItem_actionPerformed()
1638 new RedundancyPanel(alignPanel);
1641 public void pairwiseAlignmentMenuItem_actionPerformed()
1643 if (viewport.getSelectionGroup()!=null
1644 && viewport.getSelectionGroup().getSize(false) > 1)
1646 Frame frame = new Frame();
1647 frame.add(new PairwiseAlignPanel(alignPanel));
1648 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
1652 public void PCAMenuItem_actionPerformed()
1654 //are the sequences aligned?
1655 if (!viewport.alignment.isAligned())
1658 int Width = viewport.getAlignment().getWidth();
1660 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1663 current = viewport.getAlignment().getSequenceAt(i);
1665 if (current.getLength() < Width)
1667 current.insertCharAt(Width - 1, viewport.getGapCharacter());
1670 alignPanel.repaint();
1673 if ( (viewport.getSelectionGroup() != null &&
1674 viewport.getSelectionGroup().getSize(false) < 4 &&
1675 viewport.getSelectionGroup().getSize(false) > 0)
1676 || viewport.getAlignment().getHeight() < 4)
1683 new PCAPanel(viewport);
1685 catch (java.lang.OutOfMemoryError ex)
1691 public void averageDistanceTreeMenuItem_actionPerformed()
1693 NewTreePanel("AV", "PID", "Average distance tree using PID");
1696 public void neighbourTreeMenuItem_actionPerformed()
1698 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
1701 protected void njTreeBlosumMenuItem_actionPerformed()
1703 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
1706 protected void avTreeBlosumMenuItem_actionPerformed()
1708 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
1711 void NewTreePanel(String type, String pwType, String title)
1713 //are the sequences aligned?
1714 if (!viewport.alignment.isAligned())
1717 int Width = viewport.getAlignment().getWidth();
1719 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1722 current = viewport.getAlignment().getSequenceAt(i);
1724 if (current.getLength() < Width)
1726 current.insertCharAt(Width - 1, viewport.getGapCharacter());
1729 alignPanel.repaint();
1733 if ( (viewport.getSelectionGroup() != null &&
1734 viewport.getSelectionGroup().getSize(false) > 1)
1735 || (viewport.getSelectionGroup() == null
1736 && viewport.alignment.getHeight() > 1))
1738 final TreePanel tp = new TreePanel(viewport,
1742 addTreeMenuItem(tp, title);
1744 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
1748 void loadTree_actionPerformed()
1750 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1751 cap.setText("Paste your Newick tree file here.");
1752 cap.setTreeImport();
1753 Frame frame = new Frame();
1755 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
1758 public void loadTree(jalview.io.NewickFile tree, String treeFile)
1760 TreePanel tp = new TreePanel(viewport,
1764 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
1765 addTreeMenuItem(tp, treeFile);
1768 void addTreeMenuItem(final TreePanel treePanel, String title)
1770 final MenuItem item = new MenuItem(title);
1771 sortByTreeMenu.add(item);
1772 item.addActionListener(new java.awt.event.ActionListener()
1774 public void actionPerformed(ActionEvent evt)
1776 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
1777 // HistoryItem.SORT));
1778 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
1779 alignPanel.repaint();
1783 treePanel.addWindowListener(new WindowAdapter()
1785 public void windowClosing(WindowEvent e)
1787 sortByTreeMenu.remove(item);
1792 protected void documentation_actionPerformed()
1794 showURL("http://www.jalview.org/help.html", "HELP");
1797 protected void about_actionPerformed()
1800 class AboutPanel extends Canvas
1803 public AboutPanel(String version)
1804 { this.version = version; }
1806 public void paint(Graphics g)
1808 g.setColor(Color.white);
1809 g.fillRect(0, 0, getSize().width, getSize().height);
1810 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
1811 FontMetrics fm = g.getFontMetrics();
1812 int fh = fm.getHeight();
1814 g.setColor(Color.black);
1815 g.setFont(new Font("Helvetica", Font.BOLD, 14));
1816 g.drawString("Jalview - Release "+version, 200, y += fh);
1817 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
1818 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
1820 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
1823 "For any issues relating to Jalview, email help@jalview.org", x,
1825 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
1826 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
1828 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
1832 String version = "test";
1833 java.net.URL url = getClass().getResource("/.build_properties");
1838 BufferedReader reader = new BufferedReader(new InputStreamReader(
1841 while ( (line = reader.readLine()) != null)
1843 if (line.indexOf("VERSION") > -1)
1845 version = line.substring(line.indexOf("=") + 1);
1849 catch (Exception ex)
1851 ex.printStackTrace();
1856 Frame frame = new Frame();
1857 frame.add(new AboutPanel(version));
1858 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
1862 public void showURL(String url, String target)
1864 if (viewport.applet == null)
1866 System.out.println("Not running as applet - no browser available.");
1872 System.out.println("Show url: "+url);
1873 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
1876 catch (Exception ex)
1878 ex.printStackTrace();
1884 //////////////////////////////////////////////////////////////////////////////////
1885 //JBuilder Graphics here
1887 protected MenuBar alignFrameMenuBar = new MenuBar();
1888 protected Menu fileMenu = new Menu("File");
1889 protected MenuItem loadApplication = new MenuItem("View in Full Application");
1890 protected MenuItem loadTree = new MenuItem("Load Associated Tree");
1891 protected MenuItem closeMenuItem = new MenuItem("Close");
1892 protected Menu editMenu = new Menu("Edit");
1893 protected Menu viewMenu = new Menu("View");
1894 protected Menu colourMenu = new Menu("Colour");
1895 protected Menu calculateMenu = new Menu("Calculate");
1896 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
1897 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
1898 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
1899 protected MenuItem remove2LeftMenuItem = new MenuItem();
1900 protected MenuItem remove2RightMenuItem = new MenuItem();
1901 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
1902 protected MenuItem removeAllGapsMenuItem = new MenuItem();
1903 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
1904 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
1905 protected MenuItem sortPairwiseMenuItem = new MenuItem();
1906 protected MenuItem sortIDMenuItem = new MenuItem();
1907 protected MenuItem sortGroupMenuItem = new MenuItem();
1908 protected MenuItem removeRedundancyMenuItem = new MenuItem();
1909 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
1910 protected MenuItem PCAMenuItem = new MenuItem();
1911 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
1912 protected MenuItem neighbourTreeMenuItem = new MenuItem();
1913 BorderLayout borderLayout1 = new BorderLayout();
1914 public Label statusBar = new Label();
1915 protected Menu outputTextboxMenu = new Menu();
1916 protected MenuItem clustalColour = new MenuItem();
1917 protected MenuItem zappoColour = new MenuItem();
1918 protected MenuItem taylorColour = new MenuItem();
1919 protected MenuItem hydrophobicityColour = new MenuItem();
1920 protected MenuItem helixColour = new MenuItem();
1921 protected MenuItem strandColour = new MenuItem();
1922 protected MenuItem turnColour = new MenuItem();
1923 protected MenuItem buriedColour = new MenuItem();
1924 protected MenuItem userDefinedColour = new MenuItem();
1925 protected MenuItem PIDColour = new MenuItem();
1926 protected MenuItem BLOSUM62Colour = new MenuItem();
1927 MenuItem njTreeBlosumMenuItem = new MenuItem();
1928 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
1929 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
1930 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
1931 MenuItem overviewMenuItem = new MenuItem();
1932 protected MenuItem undoMenuItem = new MenuItem();
1933 protected MenuItem redoMenuItem = new MenuItem();
1934 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
1935 MenuItem noColourmenuItem = new MenuItem();
1936 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
1937 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
1938 MenuItem findMenuItem = new MenuItem();
1939 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
1940 protected MenuItem nucleotideColour = new MenuItem();
1941 MenuItem deleteGroups = new MenuItem();
1942 MenuItem delete = new MenuItem();
1943 MenuItem copy = new MenuItem();
1944 MenuItem cut = new MenuItem();
1945 Menu pasteMenu = new Menu();
1946 MenuItem pasteNew = new MenuItem();
1947 MenuItem pasteThis = new MenuItem();
1948 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
1949 protected MenuItem font = new MenuItem();
1950 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
1951 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
1952 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
1953 MenuItem modifyPID = new MenuItem();
1954 MenuItem modifyConservation = new MenuItem();
1955 protected CheckboxMenuItem autoCalculate
1956 = new CheckboxMenuItem("Autocalculate Consensus", true);
1957 protected Menu sortByTreeMenu = new Menu();
1958 Menu sort = new Menu();
1959 Menu calculate = new Menu();
1960 MenuItem inputText = new MenuItem();
1961 Menu helpMenu = new Menu();
1962 MenuItem documentation = new MenuItem();
1963 MenuItem about = new MenuItem();
1964 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
1967 Label embeddedSelect;
1969 Label embeddedFormat;
1970 Label embeddedColour;
1973 Label embeddedCalculate;
1974 FlowLayout flowLayout1;
1976 private void jbInit() throws Exception {
1978 setMenuBar(alignFrameMenuBar);
1982 // dynamically fill save as menu with available formats
1983 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
1986 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
1988 item.addActionListener(new java.awt.event.ActionListener()
1990 public void actionPerformed(ActionEvent e)
1992 outputText_actionPerformed(e);
1996 outputTextboxMenu.add(item);
1998 closeMenuItem.addActionListener(this);
1999 loadApplication.addActionListener(this);
2001 loadTree.addActionListener(this);
2002 selectAllSequenceMenuItem.addActionListener(this);
2003 deselectAllSequenceMenuItem.addActionListener(this);
2004 invertSequenceMenuItem.addActionListener(this);
2005 remove2LeftMenuItem.setLabel("Remove Left");
2006 remove2LeftMenuItem.addActionListener(this);
2007 remove2RightMenuItem.setLabel("Remove Right");
2008 remove2RightMenuItem.addActionListener(this);
2009 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2010 removeGappedColumnMenuItem.addActionListener(this);
2011 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2012 removeAllGapsMenuItem.addActionListener(this);
2013 viewBoxesMenuItem.setLabel("Boxes");
2014 viewBoxesMenuItem.setState(true);
2015 viewBoxesMenuItem.addItemListener(this);
2016 viewTextMenuItem.setLabel("Text");
2017 viewTextMenuItem.setState(true);
2018 viewTextMenuItem.addItemListener(this);
2019 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2020 sortPairwiseMenuItem.addActionListener(this);
2021 sortIDMenuItem.setLabel("by ID");
2022 sortIDMenuItem.addActionListener(this);
2023 sortGroupMenuItem.setLabel("by Group");
2024 sortGroupMenuItem.addActionListener(this);
2025 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2026 removeRedundancyMenuItem.addActionListener(this);
2027 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2028 pairwiseAlignmentMenuItem.addActionListener(this);
2029 PCAMenuItem.setLabel("Principal Component Analysis");
2030 PCAMenuItem.addActionListener(this);
2031 averageDistanceTreeMenuItem.setLabel(
2032 "Average Distance Using % Identity");
2033 averageDistanceTreeMenuItem.addActionListener(this);
2034 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2035 neighbourTreeMenuItem.addActionListener(this);
2036 statusBar.setBackground(Color.white);
2037 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2038 statusBar.setText("Status bar");
2039 outputTextboxMenu.setLabel("Output to Textbox");
2040 clustalColour.setLabel("Clustalx");
2042 clustalColour.addActionListener(this);
2043 zappoColour.setLabel("Zappo");
2044 zappoColour.addActionListener(this);
2045 taylorColour.setLabel("Taylor");
2046 taylorColour.addActionListener(this);
2047 hydrophobicityColour.setLabel("Hydrophobicity");
2048 hydrophobicityColour.addActionListener(this);
2049 helixColour.setLabel("Helix Propensity");
2050 helixColour.addActionListener(this);
2051 strandColour.setLabel("Strand Propensity");
2052 strandColour.addActionListener(this);
2053 turnColour.setLabel("Turn Propensity");
2054 turnColour.addActionListener(this);
2055 buriedColour.setLabel("Buried Index");
2056 buriedColour.addActionListener(this);
2057 userDefinedColour.setLabel("User Defined...");
2058 userDefinedColour.addActionListener(this);
2059 PIDColour.setLabel("Percentage Identity");
2060 PIDColour.addActionListener(this);
2061 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2062 BLOSUM62Colour.addActionListener(this);
2063 avDistanceTreeBlosumMenuItem.setLabel(
2064 "Average Distance Using BLOSUM62");
2065 avDistanceTreeBlosumMenuItem.addActionListener(this);
2066 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2067 njTreeBlosumMenuItem.addActionListener(this);
2068 annotationPanelMenuItem.setLabel("Show Annotations");
2069 annotationPanelMenuItem.addItemListener(this);
2070 colourTextMenuItem.setLabel("Colour Text");
2071 colourTextMenuItem.addItemListener(this);
2072 overviewMenuItem.setLabel("Overview Window");
2073 overviewMenuItem.addActionListener(this);
2074 undoMenuItem.setEnabled(false);
2075 undoMenuItem.setLabel("Undo");
2076 undoMenuItem.addActionListener(this);
2077 redoMenuItem.setEnabled(false);
2078 redoMenuItem.setLabel("Redo");
2079 redoMenuItem.addActionListener(this);
2080 conservationMenuItem.setLabel("by Conservation");
2081 conservationMenuItem.addItemListener(this);
2082 noColourmenuItem.setLabel("None");
2083 noColourmenuItem.addActionListener(this);
2084 wrapMenuItem.setLabel("Wrap");
2085 wrapMenuItem.addItemListener(this);
2086 renderGapsMenuItem.setLabel("Show Gaps");
2087 renderGapsMenuItem.setState(true);
2088 renderGapsMenuItem.addItemListener(this);
2089 findMenuItem.setLabel("Find...");
2090 findMenuItem.addActionListener(this);
2091 abovePIDThreshold.setLabel("Above Identity Threshold");
2092 abovePIDThreshold.addItemListener(this);
2093 nucleotideColour.setLabel("Nucleotide");
2094 nucleotideColour.addActionListener(this);
2095 deleteGroups.setLabel("Undefine Groups");
2096 deleteGroups.addActionListener(this);
2097 copy.setLabel("Copy");
2098 copy.addActionListener(this);
2099 cut.setLabel("Cut");
2100 cut.addActionListener(this);
2101 delete.setLabel("Delete");
2102 delete.addActionListener(this);
2103 pasteMenu.setLabel("Paste");
2104 pasteNew.setLabel("To New Alignment");
2105 pasteNew.addActionListener(this);
2106 pasteThis.setLabel("Add To This Alignment");
2107 pasteThis.addActionListener(this);
2108 applyToAllGroups.setLabel("Apply Colour To All Groups");
2109 applyToAllGroups.setState(true);
2110 applyToAllGroups.addItemListener(this);
2111 font.setLabel("Font...");
2112 font.addActionListener(this);
2113 scaleAbove.setLabel("Scale Above");
2114 scaleAbove.setState(true);
2115 scaleAbove.setEnabled(false);
2116 scaleAbove.addItemListener(this);
2117 scaleLeft.setEnabled(false);
2118 scaleLeft.setState(true);
2119 scaleLeft.setLabel("Scale Left");
2120 scaleLeft.addItemListener(this);
2121 scaleRight.setEnabled(false);
2122 scaleRight.setState(true);
2123 scaleRight.setLabel("Scale Right");
2124 scaleRight.addItemListener(this);
2125 modifyPID.setLabel("Modify Identity Threshold...");
2126 modifyPID.addActionListener(this);
2127 modifyConservation.setLabel("Modify Conservation Threshold...");
2128 modifyConservation.addActionListener(this);
2129 sortByTreeMenu.setLabel("By Tree Order");
2130 sort.setLabel("Sort");
2131 calculate.setLabel("Calculate Tree");
2132 autoCalculate.addItemListener(this);
2133 inputText.setLabel("Input from textbox");
2134 inputText.addActionListener(this);
2136 helpMenu.setLabel("Help");
2137 documentation.setLabel("Documentation");
2138 documentation.addActionListener(this);
2140 about.setLabel("About...");
2141 about.addActionListener(this);
2142 seqLimits.setState(true);
2143 seqLimits.setLabel("Show Sequence Limits");
2144 seqLimits.addItemListener(this);
2145 featureSettings.setLabel("Feature Settings...");
2146 featureSettings.addActionListener(this);
2147 sequenceFeatures.setLabel("Sequence Features");
2148 sequenceFeatures.addItemListener(this);
2149 sequenceFeatures.setState(false);
2150 annotationColour.setLabel("by Annotation...");
2151 annotationColour.addActionListener(this);
2152 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2153 invertColSel.setLabel("Invert Column Selection");
2154 menu1.setLabel("Show");
2155 showColumns.setLabel("All Columns ");
2156 showSeqs.setLabel("All Sequences");
2157 menu2.setLabel("Hide");
2158 hideColumns.setLabel("Selected Columns");
2159 hideSequences.setLabel("Selected Sequences");
2160 invertColSel.addActionListener(this);
2161 showColumns.addActionListener(this);
2162 showSeqs.addActionListener(this);
2163 hideColumns.addActionListener(this);
2164 hideSequences.addActionListener(this);
2165 formatMenu.setLabel("Format");
2166 selectMenu.setLabel("Select");
2167 newView.setLabel("New View");
2168 newView.addActionListener(this);
2169 alignFrameMenuBar.add(fileMenu);
2170 alignFrameMenuBar.add(editMenu);
2171 alignFrameMenuBar.add(selectMenu);
2172 alignFrameMenuBar.add(viewMenu);
2173 alignFrameMenuBar.add(formatMenu);
2174 alignFrameMenuBar.add(colourMenu);
2175 alignFrameMenuBar.add(calculateMenu);
2176 alignFrameMenuBar.add(helpMenu);
2177 fileMenu.add(inputText);
2178 fileMenu.add(outputTextboxMenu);
2179 if(jalviewServletURL!=null)
2180 fileMenu.add(loadApplication);
2181 fileMenu.addSeparator();
2182 fileMenu.add(loadTree);
2183 fileMenu.add(closeMenuItem);
2184 editMenu.add(undoMenuItem);
2185 editMenu.add(redoMenuItem);
2188 editMenu.add(pasteMenu);
2189 editMenu.add(delete);
2190 editMenu.addSeparator();
2191 editMenu.add(remove2LeftMenuItem);
2192 editMenu.add(remove2RightMenuItem);
2193 editMenu.add(removeGappedColumnMenuItem);
2194 editMenu.add(removeAllGapsMenuItem);
2195 editMenu.add(removeRedundancyMenuItem);
2196 viewMenu.add(newView);
2197 viewMenu.addSeparator();
2198 viewMenu.add(menu1);
2199 viewMenu.add(menu2);
2200 viewMenu.addSeparator();
2201 viewMenu.add(annotationPanelMenuItem);
2202 viewMenu.addSeparator();
2203 viewMenu.add(sequenceFeatures);
2204 viewMenu.add(featureSettings);
2205 viewMenu.addSeparator();
2206 viewMenu.add(overviewMenuItem);
2207 colourMenu.add(applyToAllGroups);
2208 colourMenu.addSeparator();
2209 colourMenu.add(noColourmenuItem);
2210 colourMenu.add(clustalColour);
2211 colourMenu.add(BLOSUM62Colour);
2212 colourMenu.add(PIDColour);
2213 colourMenu.add(zappoColour);
2214 colourMenu.add(taylorColour);
2215 colourMenu.add(hydrophobicityColour);
2216 colourMenu.add(helixColour);
2217 colourMenu.add(strandColour);
2218 colourMenu.add(turnColour);
2219 colourMenu.add(buriedColour);
2220 colourMenu.add(nucleotideColour);
2221 colourMenu.add(userDefinedColour);
2222 colourMenu.addSeparator();
2223 colourMenu.add(conservationMenuItem);
2224 colourMenu.add(modifyConservation);
2225 colourMenu.add(abovePIDThreshold);
2226 colourMenu.add(modifyPID);
2227 colourMenu.add(annotationColour);
2228 calculateMenu.add(sort);
2229 calculateMenu.add(calculate);
2230 calculateMenu.addSeparator();
2231 calculateMenu.add(pairwiseAlignmentMenuItem);
2232 calculateMenu.add(PCAMenuItem);
2233 calculateMenu.add(autoCalculate);
2234 this.add(statusBar, BorderLayout.SOUTH);
2235 pasteMenu.add(pasteNew);
2236 pasteMenu.add(pasteThis);
2237 sort.add(sortIDMenuItem);
2238 sort.add(sortByTreeMenu);
2239 sort.add(sortGroupMenuItem);
2240 sort.add(sortPairwiseMenuItem);
2241 calculate.add(averageDistanceTreeMenuItem);
2242 calculate.add(neighbourTreeMenuItem);
2243 calculate.add(avDistanceTreeBlosumMenuItem);
2244 calculate.add(njTreeBlosumMenuItem);
2245 helpMenu.add(documentation);
2246 helpMenu.add(about);
2247 menu1.add(showColumns);
2248 menu1.add(showSeqs);
2249 menu2.add(hideColumns);
2250 menu2.add(hideSequences);
2251 formatMenu.add(font);
2252 formatMenu.add(seqLimits);
2253 formatMenu.add(wrapMenuItem);
2254 formatMenu.add(scaleAbove);
2255 formatMenu.add(scaleLeft);
2256 formatMenu.add(scaleRight);
2257 formatMenu.add(viewBoxesMenuItem);
2258 formatMenu.add(viewTextMenuItem);
2259 formatMenu.add(colourTextMenuItem);
2260 formatMenu.add(renderGapsMenuItem);
2261 selectMenu.add(findMenuItem);
2262 selectMenu.addSeparator();
2263 selectMenu.add(selectAllSequenceMenuItem);
2264 selectMenu.add(deselectAllSequenceMenuItem);
2265 selectMenu.add(invertSequenceMenuItem);
2266 selectMenu.add(invertColSel);
2267 selectMenu.add(deleteGroups);
2270 public void setEmbedded()
2273 embeddedMenu = new Panel();
2274 embeddedEdit = new Label("Edit");
2275 embeddedSelect = new Label("Select");
2276 embeddedView = new Label("View");
2277 embeddedFormat = new Label("Format");
2278 embeddedColour = new Label("Colour");
2279 embeddedFile = new Label("File");
2280 embeddedHelp = new Label("Help");
2281 embeddedCalculate = new Label("Calculate");
2282 flowLayout1 = new FlowLayout();
2283 embeddedMenu.setBackground(Color.lightGray);
2284 embeddedMenu.setLayout(flowLayout1);
2285 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2286 embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2287 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2288 embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2289 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2290 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2291 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2292 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
2293 embeddedMenu.add(embeddedFile);
2294 embeddedMenu.add(embeddedEdit);
2295 embeddedMenu.add(embeddedSelect);
2296 embeddedMenu.add(embeddedView);
2297 embeddedMenu.add(embeddedFormat);
2298 embeddedMenu.add(embeddedColour);
2299 embeddedMenu.add(embeddedCalculate);
2300 embeddedMenu.add(embeddedHelp);
2301 flowLayout1.setAlignment(FlowLayout.LEFT);
2302 flowLayout1.setHgap(2);
2303 flowLayout1.setVgap(0);
2304 embeddedFile.addMouseListener(this);
2305 embeddedEdit.addMouseListener(this);
2306 embeddedSelect.addMouseListener(this);
2307 embeddedView.addMouseListener(this);
2308 embeddedFormat.addMouseListener(this);
2309 embeddedColour.addMouseListener(this);
2310 embeddedCalculate.addMouseListener(this);
2311 embeddedHelp.addMouseListener(this);
2313 // setVisible(false);
2314 fileMenu.remove(closeMenuItem);
2315 fileMenu.remove(3); // Seperator
2317 viewport.applet.setLayout(new BorderLayout());
2318 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
2319 viewport.applet.add(statusBar, BorderLayout.SOUTH);
2320 // viewport.applet.validate();
2322 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
2323 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
2325 viewport.applet.add(alignPanel, BorderLayout.CENTER);
2326 viewport.applet.validate();
2332 PopupMenu filePopup, editPopup, searchPopup,
2333 viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
2334 MenuItem featureSettings = new MenuItem();
2335 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
2336 MenuItem annotationColour = new MenuItem();
2337 MenuItem invertColSel = new MenuItem();
2338 Menu menu1 = new Menu();
2339 MenuItem showColumns = new MenuItem();
2340 MenuItem showSeqs = new MenuItem();
2341 Menu menu2 = new Menu();
2342 MenuItem hideColumns = new MenuItem();
2343 MenuItem hideSequences = new MenuItem();
2344 Menu formatMenu = new Menu();
2345 Menu selectMenu = new Menu();
2346 MenuItem newView = new MenuItem();
2348 public void mousePressed(MouseEvent evt)
2350 PopupMenu popup = null;
2351 Label source = (Label)evt.getSource();
2352 if(source==embeddedFile)
2354 popup = filePopup = genPopupMenu(filePopup, fileMenu);
2356 else if(source==embeddedEdit)
2358 popup = editPopup = genPopupMenu(editPopup, editMenu);
2360 else if(source==embeddedSelect)
2362 popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
2364 else if(source==embeddedView)
2366 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
2368 else if (source ==embeddedFormat)
2370 popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
2372 else if(source==embeddedColour)
2374 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
2376 else if(source==embeddedCalculate)
2378 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
2380 else if(source==embeddedHelp)
2382 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
2385 embeddedMenu.add(popup);
2386 popup.show(embeddedMenu,
2387 source.getBounds().x,
2388 source.getBounds().y + source.getBounds().getSize().height);
2391 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
2397 popup = new PopupMenu();
2398 int m, mSize = original.getItemCount();
2399 for(m=0; m<mSize; m++)
2401 popup.add(original.getItem(m));
2408 public void mouseClicked(MouseEvent evt)
2410 public void mouseReleased(MouseEvent evt)
2412 public void mouseEntered(MouseEvent evt)
2414 public void mouseExited(MouseEvent evt)