2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
20 package jalview.appletgui;
\r
22 import jalview.schemes.*;
\r
23 import jalview.datamodel.*;
\r
24 import jalview.analysis.*;
\r
25 import jalview.io.*;
\r
26 import jalview.commands.*;
\r
28 import java.awt.event.*;
\r
30 import java.io.InputStreamReader;
\r
31 import java.io.BufferedReader;
\r
32 import java.net.URL;
\r
35 public class AlignFrame extends Frame implements ActionListener,
\r
36 ItemListener, KeyListener, MouseListener
\r
38 public AlignmentPanel alignPanel;
\r
39 public AlignViewport viewport;
\r
40 int DEFAULT_WIDTH = 700;
\r
41 int DEFAULT_HEIGHT = 500;
\r
43 String jalviewServletURL;
\r
46 public AlignFrame(AlignmentI al,
\r
47 jalview.bin.JalviewLite applet,
\r
53 jalviewServletURL = applet.getParameter("APPLICATION_URL");
\r
57 }catch(Exception ex)
\r
59 ex.printStackTrace();
\r
62 viewport = new AlignViewport(al, applet);
\r
63 alignPanel = new AlignmentPanel(this, viewport);
\r
65 viewport.updateConservation(alignPanel);
\r
66 viewport.updateConsensus(alignPanel);
\r
68 annotationPanelMenuItem.setState(viewport.showAnnotation);
\r
70 seqLimits.setState(viewport.showJVSuffix);
\r
74 String param = applet.getParameter("sortBy");
\r
77 if (param.equalsIgnoreCase("Id"))
\r
78 sortIDMenuItem_actionPerformed();
\r
79 else if (param.equalsIgnoreCase("Pairwise Identity"))
\r
80 sortPairwiseMenuItem_actionPerformed();
\r
83 param = applet.getParameter("wrap");
\r
86 if (param.equalsIgnoreCase("true"))
\r
88 wrapMenuItem.setState(true);
\r
89 wrapMenuItem_actionPerformed();
\r
95 param = applet.getParameter("windowWidth");
\r
98 int width = Integer.parseInt(param);
\r
99 DEFAULT_WIDTH = width;
\r
101 param = applet.getParameter("windowHeight");
\r
104 int height = Integer.parseInt(param);
\r
105 DEFAULT_HEIGHT = height;
\r
108 catch (Exception ex)
\r
113 //Some JVMS send keyevents to Top frame or lowest panel,
\r
114 //Havent worked out why yet. So add to both this frame and seqCanvas for now
\r
115 this.addKeyListener(this);
\r
116 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
\r
117 alignPanel.idPanel.idCanvas.addKeyListener(this);
\r
118 alignPanel.scalePanel.addKeyListener(this);
\r
119 alignPanel.annotationPanel.addKeyListener(this);
\r
128 add(alignPanel, BorderLayout.CENTER);
\r
129 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
132 alignPanel.validate();
\r
133 alignPanel.repaint();
\r
135 public AlignViewport getAlignViewport()
\r
140 public SeqCanvas getSeqcanvas()
\r
142 return alignPanel.seqPanel.seqCanvas;
\r
149 * @param String DOCUMENT ME!
\r
152 public void parseFeaturesFile(String file, String type)
\r
154 Hashtable featureLinks = new Hashtable();
\r
155 boolean featuresFile = false;
\r
157 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
\r
158 alignPanel.seqPanel.seqCanvas.
\r
159 getFeatureRenderer().featureColours,
\r
163 catch(Exception ex)
\r
165 ex.printStackTrace();
\r
170 if(featureLinks.size()>0)
\r
171 alignPanel.seqPanel.seqCanvas
\r
172 .getFeatureRenderer().featureLinks = featureLinks;
\r
173 viewport.showSequenceFeatures = true;
\r
174 sequenceFeatures.setState(true);
\r
175 alignPanel.repaint();
\r
181 public void keyPressed(KeyEvent evt)
\r
183 if (viewport.cursorMode
\r
184 && evt.getKeyCode() >= KeyEvent.VK_0
\r
185 && evt.getKeyCode() <= KeyEvent.VK_9)
\r
187 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
\r
190 switch (evt.getKeyCode())
\r
192 case 27: // escape key
\r
193 deselectAllSequenceMenuItem_actionPerformed();
\r
195 case KeyEvent.VK_X:
\r
196 if (evt.isControlDown() || evt.isMetaDown())
\r
198 cut_actionPerformed();
\r
201 case KeyEvent.VK_C:
\r
202 if (viewport.cursorMode && !evt.isControlDown())
\r
204 alignPanel.seqPanel.setCursorColumn();
\r
206 if (evt.isControlDown() || evt.isMetaDown())
\r
208 copy_actionPerformed();
\r
211 case KeyEvent.VK_V:
\r
212 if (evt.isControlDown())
\r
214 paste(evt.isShiftDown());
\r
217 case KeyEvent.VK_A:
\r
218 if (evt.isControlDown() || evt.isMetaDown())
\r
220 selectAllSequenceMenuItem_actionPerformed();
\r
223 case KeyEvent.VK_DOWN:
\r
224 if(viewport.cursorMode)
\r
226 alignPanel.seqPanel.moveCursor(0,1);
\r
229 moveSelectedSequences(false);
\r
232 case KeyEvent.VK_UP:
\r
233 if (viewport.cursorMode)
\r
235 alignPanel.seqPanel.moveCursor(0,-1);
\r
238 moveSelectedSequences(true);
\r
241 case KeyEvent.VK_LEFT:
\r
242 if(viewport.cursorMode)
\r
244 alignPanel.seqPanel.moveCursor(-1,0);
\r
248 case KeyEvent.VK_RIGHT:
\r
249 if (viewport.cursorMode)
\r
251 alignPanel.seqPanel.moveCursor(1,0);
\r
254 case KeyEvent.VK_SPACE:
\r
255 if(viewport.cursorMode)
\r
257 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
\r
258 || evt.isShiftDown()
\r
264 case KeyEvent.VK_DELETE:
\r
265 case KeyEvent.VK_BACK_SPACE:
\r
266 if(viewport.cursorMode)
\r
268 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
\r
269 || evt.isShiftDown()
\r
270 || evt.isAltDown());
\r
274 cut_actionPerformed();
\r
275 alignPanel.seqPanel.seqCanvas.repaint();
\r
279 case KeyEvent.VK_S:
\r
280 if(viewport.cursorMode)
\r
282 alignPanel.seqPanel.setCursorRow();
\r
285 case KeyEvent.VK_P:
\r
286 if(viewport.cursorMode)
\r
288 alignPanel.seqPanel.setCursorPosition();
\r
292 case KeyEvent.VK_ENTER:
\r
293 case KeyEvent.VK_COMMA:
\r
294 if(viewport.cursorMode)
\r
296 alignPanel.seqPanel.setCursorRowAndColumn();
\r
300 case KeyEvent.VK_Q:
\r
301 if(viewport.cursorMode)
\r
303 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
\r
306 case KeyEvent.VK_M:
\r
307 if(viewport.cursorMode)
\r
309 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
\r
313 case KeyEvent.VK_F2:
\r
314 viewport.cursorMode = ! viewport.cursorMode;
\r
315 statusBar.setText("Keyboard editing mode is "+
\r
316 (viewport.cursorMode ? "on" : "off"));
\r
317 if(viewport.cursorMode)
\r
319 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
\r
320 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
\r
324 case KeyEvent.VK_F:
\r
325 if (evt.isControlDown())
\r
327 findMenuItem_actionPerformed();
\r
331 case KeyEvent.VK_H:
\r
333 boolean toggleSeqs = !evt.isControlDown();
\r
334 boolean toggleCols = !evt.isShiftDown();
\r
335 boolean hide = false;
\r
336 SequenceGroup sg = viewport.getSelectionGroup();
\r
340 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
\r
343 viewport.hideAllSelectedSeqs();
\r
345 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
\r
346 viewport.showAllHiddenSeqs();
\r
351 if (viewport.colSel.getSelected().size() > 0)
\r
353 viewport.hideSelectedColumns();
\r
355 viewport.selectionGroup = sg;
\r
358 viewport.showAllHiddenColumns();
\r
363 case KeyEvent.VK_PAGE_UP:
\r
364 if (viewport.wrapAlignment)
\r
365 alignPanel.scrollUp(true);
\r
367 alignPanel.setScrollValues(viewport.startRes,
\r
369 - viewport.endSeq + viewport.startSeq);
\r
372 case KeyEvent.VK_PAGE_DOWN:
\r
373 if (viewport.wrapAlignment)
\r
374 alignPanel.scrollUp(false);
\r
376 alignPanel.setScrollValues(viewport.startRes,
\r
378 + viewport.endSeq - viewport.startSeq);
\r
381 case KeyEvent.VK_Z:
\r
382 if (evt.isControlDown())
\r
384 undoMenuItem_actionPerformed();
\r
388 case KeyEvent.VK_Y:
\r
389 if (evt.isControlDown())
\r
391 redoMenuItem_actionPerformed();
\r
395 case KeyEvent.VK_L:
\r
396 if (evt.isControlDown())
\r
398 trimAlignment(true);
\r
402 case KeyEvent.VK_R:
\r
403 if (evt.isControlDown())
\r
405 trimAlignment(false);
\r
409 case KeyEvent.VK_E:
\r
410 if (evt.isControlDown())
\r
412 if (evt.isShiftDown())
\r
413 this.removeAllGapsMenuItem_actionPerformed();
\r
415 removeGappedColumnMenuItem_actionPerformed();
\r
418 case KeyEvent.VK_I:
\r
419 if (evt.isControlDown())
\r
421 if (evt.isAltDown())
\r
422 viewport.invertColumnSelection();
\r
424 this.invertSequenceMenuItem_actionPerformed();
\r
428 case KeyEvent.VK_U:
\r
429 if (evt.isControlDown())
\r
431 this.deleteGroups_actionPerformed();
\r
435 case KeyEvent.VK_T:
\r
436 if (evt.isControlDown())
\r
444 alignPanel.repaint();
\r
446 public void keyReleased(KeyEvent evt)
\r
448 public void keyTyped(KeyEvent evt)
\r
451 public void itemStateChanged(ItemEvent evt)
\r
453 if(evt.getSource()==colourTextMenuItem)
\r
454 colourTextMenuItem_actionPerformed();
\r
455 else if(evt.getSource()==wrapMenuItem)
\r
456 wrapMenuItem_actionPerformed();
\r
457 else if(evt.getSource()==scaleAbove)
\r
458 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
459 else if(evt.getSource()==scaleLeft)
\r
460 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
461 else if(evt.getSource()==scaleRight)
\r
462 viewport.setScaleRightWrapped(scaleRight.getState());
\r
463 else if(evt.getSource()==seqLimits)
\r
464 seqLimits_itemStateChanged();
\r
465 else if(evt.getSource()==viewBoxesMenuItem)
\r
466 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
467 else if(evt.getSource()==viewTextMenuItem)
\r
468 viewport.setShowText(viewTextMenuItem.getState());
\r
469 else if(evt.getSource()==renderGapsMenuItem)
\r
470 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
471 else if(evt.getSource()==annotationPanelMenuItem)
\r
473 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
474 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
476 else if(evt.getSource()==sequenceFeatures)
\r
478 viewport.showSequenceFeatures(sequenceFeatures.getState());
\r
479 alignPanel.seqPanel.seqCanvas.repaint();
\r
481 else if(evt.getSource()==conservationMenuItem)
\r
482 conservationMenuItem_actionPerformed();
\r
483 else if(evt.getSource()==abovePIDThreshold)
\r
484 abovePIDThreshold_actionPerformed();
\r
485 else if(evt.getSource()==applyToAllGroups)
\r
486 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
487 else if(evt.getSource()==autoCalculate)
\r
488 viewport.autocalculateConsensus = autoCalculate.getState();
\r
490 alignPanel.repaint();
\r
492 public void actionPerformed(ActionEvent evt)
\r
494 Object source = evt.getSource();
\r
496 if(source==inputText)
\r
497 inputText_actionPerformed();
\r
498 else if(source==loadTree)
\r
499 loadTree_actionPerformed();
\r
500 else if(source==loadApplication)
\r
501 launchFullApplication();
\r
502 else if (source == loadAnnotations)
\r
504 else if (source == outputAnnotations)
\r
505 outputAnnotations();
\r
506 else if(source == outputFeatures)
\r
507 outputFeatures(true, "Jalview");
\r
508 else if(source==closeMenuItem)
\r
509 closeMenuItem_actionPerformed();
\r
510 else if(source==copy)
\r
511 copy_actionPerformed();
\r
512 else if(source==undoMenuItem)
\r
513 undoMenuItem_actionPerformed();
\r
514 else if(source==redoMenuItem)
\r
515 redoMenuItem_actionPerformed();
\r
516 else if(source==inputText)
\r
517 inputText_actionPerformed();
\r
518 else if(source==closeMenuItem)
\r
519 closeMenuItem_actionPerformed();
\r
520 else if(source==undoMenuItem)
\r
521 undoMenuItem_actionPerformed();
\r
522 else if(source==redoMenuItem)
\r
523 redoMenuItem_actionPerformed();
\r
524 else if(source==copy)
\r
525 copy_actionPerformed();
\r
526 else if(source==pasteNew)
\r
527 pasteNew_actionPerformed();
\r
528 else if(source==pasteThis)
\r
529 pasteThis_actionPerformed();
\r
530 else if(source==cut)
\r
531 cut_actionPerformed();
\r
532 else if(source==delete)
\r
533 delete_actionPerformed();
\r
534 else if(source==deleteGroups)
\r
535 deleteGroups_actionPerformed();
\r
536 else if(source==selectAllSequenceMenuItem)
\r
537 selectAllSequenceMenuItem_actionPerformed();
\r
538 else if(source==deselectAllSequenceMenuItem)
\r
539 deselectAllSequenceMenuItem_actionPerformed();
\r
540 else if(source==invertSequenceMenuItem)
\r
541 invertSequenceMenuItem_actionPerformed();
\r
542 else if(source==invertColSel)
\r
543 { viewport.invertColumnSelection(); alignPanel.repaint(); }
\r
544 else if(source==remove2LeftMenuItem)
\r
545 trimAlignment(true);
\r
546 else if(source==remove2RightMenuItem)
\r
547 trimAlignment(false);
\r
548 else if(source==removeGappedColumnMenuItem)
\r
549 removeGappedColumnMenuItem_actionPerformed();
\r
550 else if(source==removeAllGapsMenuItem)
\r
551 removeAllGapsMenuItem_actionPerformed();
\r
552 else if(source==findMenuItem)
\r
553 findMenuItem_actionPerformed();
\r
554 else if(source==font)
\r
555 new FontChooser(alignPanel);
\r
556 else if (source == newView)
\r
558 else if(source==showColumns)
\r
560 viewport.showAllHiddenColumns(); alignPanel.repaint();
\r
562 else if(source==showSeqs)
\r
564 viewport.showAllHiddenSeqs();
\r
566 else if(source == hideColumns)
\r
568 viewport.hideSelectedColumns(); alignPanel.repaint();
\r
570 else if(source == hideSequences && viewport.getSelectionGroup()!=null)
\r
572 viewport.hideAllSelectedSeqs();
\r
574 else if(source==featureSettings)
\r
575 new FeatureSettings(alignPanel);
\r
576 else if(source==overviewMenuItem)
\r
577 overviewMenuItem_actionPerformed();
\r
578 else if(source==noColourmenuItem)
\r
579 changeColour(null);
\r
580 else if(source==clustalColour)
\r
582 abovePIDThreshold.setState(false);
\r
583 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
584 viewport.alignment.getWidth()));
\r
586 else if(source==zappoColour)
\r
587 changeColour(new ZappoColourScheme());
\r
588 else if(source==taylorColour)
\r
589 changeColour(new TaylorColourScheme());
\r
590 else if(source==hydrophobicityColour)
\r
591 changeColour(new HydrophobicColourScheme());
\r
592 else if(source==helixColour)
\r
593 changeColour(new HelixColourScheme());
\r
594 else if(source==strandColour)
\r
595 changeColour(new StrandColourScheme());
\r
596 else if(source==turnColour)
\r
597 changeColour(new TurnColourScheme());
\r
598 else if(source==buriedColour)
\r
599 changeColour(new BuriedColourScheme());
\r
600 else if(source==nucleotideColour)
\r
601 changeColour(new NucleotideColourScheme());
\r
602 else if(source==modifyPID)
\r
603 modifyPID_actionPerformed();
\r
604 else if(source==modifyConservation)
\r
605 modifyConservation_actionPerformed();
\r
606 else if(source==userDefinedColour)
\r
607 new UserDefinedColours(alignPanel, null);
\r
608 else if(source==PIDColour)
\r
609 changeColour(new PIDColourScheme());
\r
610 else if(source==BLOSUM62Colour)
\r
611 changeColour(new Blosum62ColourScheme());
\r
612 else if(source==annotationColour)
\r
613 new AnnotationColourChooser(viewport, alignPanel);
\r
614 else if(source==sortPairwiseMenuItem)
\r
615 sortPairwiseMenuItem_actionPerformed();
\r
616 else if(source==sortIDMenuItem)
\r
617 sortIDMenuItem_actionPerformed();
\r
618 else if(source==sortGroupMenuItem)
\r
619 sortGroupMenuItem_actionPerformed();
\r
620 else if(source==removeRedundancyMenuItem)
\r
621 removeRedundancyMenuItem_actionPerformed();
\r
622 else if(source==pairwiseAlignmentMenuItem)
\r
623 pairwiseAlignmentMenuItem_actionPerformed();
\r
624 else if(source==PCAMenuItem)
\r
625 PCAMenuItem_actionPerformed();
\r
626 else if(source==averageDistanceTreeMenuItem)
\r
627 averageDistanceTreeMenuItem_actionPerformed();
\r
628 else if(source==neighbourTreeMenuItem)
\r
629 neighbourTreeMenuItem_actionPerformed();
\r
630 else if(source==njTreeBlosumMenuItem)
\r
631 njTreeBlosumMenuItem_actionPerformed();
\r
632 else if(source==avDistanceTreeBlosumMenuItem)
\r
633 avTreeBlosumMenuItem_actionPerformed();
\r
634 else if(source==documentation)
\r
635 documentation_actionPerformed();
\r
636 else if(source==about)
\r
637 about_actionPerformed();
\r
641 public void inputText_actionPerformed()
\r
643 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
644 Frame frame = new Frame();
\r
646 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
649 protected void outputText_actionPerformed(ActionEvent e)
\r
651 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
652 Frame frame = new Frame();
\r
654 jalview.bin.JalviewLite.addFrame(frame,
\r
655 "Alignment output - " + e.getActionCommand(),
\r
657 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
\r
658 viewport.getAlignment(),
\r
659 viewport.showJVSuffix));
\r
662 public void loadAnnotations()
\r
664 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
665 cap.setText("Paste your features / annotations file here.");
\r
666 cap.setAnnotationImport();
\r
667 Frame frame = new Frame();
\r
669 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
673 public void outputAnnotations()
\r
675 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
676 Frame frame = new Frame();
\r
678 jalview.bin.JalviewLite.addFrame(frame,
\r
681 cap.setText( new AnnotationFile().printAnnotations(
\r
682 viewport.alignment.getAlignmentAnnotation() ) );
\r
685 public String outputFeatures(boolean displayTextbox, String format)
\r
688 if (format.equalsIgnoreCase("Jalview"))
\r
689 features = new FeaturesFile().printJalviewFormat(
\r
690 viewport.alignment.getSequencesArray(),
\r
691 viewport.featuresDisplayed);
\r
693 features = new FeaturesFile().printGFFFormat(
\r
694 viewport.alignment.getSequencesArray(),
\r
695 viewport.featuresDisplayed);
\r
700 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
701 Frame frame = new Frame();
\r
703 jalview.bin.JalviewLite.addFrame(frame,
\r
707 cap.setText(features);
\r
713 void launchFullApplication()
\r
715 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
717 url.append("?open="+
\r
718 appendProtocol( viewport.applet.getParameter("file") ) );
\r
720 if(viewport.applet.getParameter("features")!=null)
\r
722 url.append( "&features=" );
\r
723 url.append( appendProtocol( viewport.applet.getParameter("features") ) );
\r
726 if(viewport.applet.getParameter("annotations")!=null)
\r
728 url.append( "&annotations=" );
\r
729 url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
\r
732 if(viewport.applet.getParameter("jnetfile")!=null)
\r
734 url.append( "&annotations=" );
\r
735 url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
\r
738 if(viewport.applet.getParameter("defaultColour")!=null)
\r
740 url.append("&colour=" +
\r
741 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
\r
745 if(viewport.applet.getParameter("userDefinedColour")!=null)
\r
747 url.append( "&colour=" +
\r
748 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
\r
752 showURL(url.toString(), "FULL_APP");
\r
756 String removeWhiteSpace(String colour)
\r
758 StringBuffer sb = new StringBuffer();
\r
759 for (int i = 0; i < colour.length(); i++)
\r
761 if (Character.isWhitespace(colour.charAt(i)))
\r
764 sb.append(colour.charAt(i));
\r
767 return sb.toString();
\r
771 String appendProtocol(String url)
\r
775 }catch(java.net.MalformedURLException ex)
\r
777 url = viewport.applet.getCodeBase()+url;
\r
782 public void closeMenuItem_actionPerformed()
\r
784 PaintRefresher.RemoveComponent(alignPanel);
\r
785 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
786 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
788 if(PaintRefresher.components.size()==0 && viewport.applet==null)
\r
798 void updateEditMenuBar()
\r
801 if (viewport.historyList.size() > 0)
\r
803 undoMenuItem.setEnabled(true);
\r
804 CommandI command = (CommandI) viewport.historyList.peek();
\r
805 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
809 undoMenuItem.setEnabled(false);
\r
810 undoMenuItem.setLabel("Undo");
\r
813 if (viewport.redoList.size() > 0)
\r
815 redoMenuItem.setEnabled(true);
\r
817 CommandI command = (CommandI) viewport.redoList.peek();
\r
818 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
822 redoMenuItem.setEnabled(false);
\r
823 redoMenuItem.setLabel("Redo");
\r
827 public void addHistoryItem(CommandI command)
\r
829 if(command.getSize()>0)
\r
831 viewport.historyList.push(command);
\r
832 viewport.redoList.removeAllElements();
\r
833 updateEditMenuBar();
\r
834 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
841 * @param e DOCUMENT ME!
\r
843 protected void undoMenuItem_actionPerformed()
\r
845 if(viewport.historyList.size()<1)
\r
848 CommandI command = (CommandI)viewport.historyList.pop();
\r
849 viewport.redoList.push(command);
\r
850 command.undoCommand();
\r
852 AlignViewport originalSource = getOriginatingSource(command);
\r
854 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
855 updateEditMenuBar();
\r
856 originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());
\r
862 * @param e DOCUMENT ME!
\r
864 protected void redoMenuItem_actionPerformed()
\r
866 if(viewport.redoList.size()<1)
\r
869 CommandI command = (CommandI) viewport.redoList.pop();
\r
870 viewport.historyList.push(command);
\r
871 command.doCommand();
\r
873 AlignViewport originalSource = getOriginatingSource(command);
\r
874 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
\r
876 updateEditMenuBar();
\r
877 originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());
\r
880 AlignViewport getOriginatingSource(CommandI command)
\r
882 AlignViewport originalSource = null;
\r
883 //For sequence removal and addition, we need to fire
\r
884 //the property change event FROM the viewport where the
\r
885 //original alignment was altered
\r
886 AlignmentI al = null;
\r
887 if (command instanceof EditCommand)
\r
889 EditCommand editCommand = (EditCommand) command;
\r
890 al = editCommand.getAlignment();
\r
891 Vector comps = (Vector) PaintRefresher.components
\r
892 .get(viewport.getSequenceSetId());
\r
893 for (int i = 0; i < comps.size(); i++)
\r
895 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
897 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
899 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
\r
906 if (originalSource == null)
\r
908 //The original view is closed, we must validate
\r
909 //the current view against the closed view first
\r
911 PaintRefresher.validateSequences(al, viewport.alignment);
\r
913 originalSource = viewport;
\r
917 return originalSource;
\r
920 public void moveSelectedSequences(boolean up)
\r
922 SequenceGroup sg = viewport.getSelectionGroup();
\r
930 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
932 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
933 if (!sg.getSequences(null).contains(seq))
\r
938 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
939 if (sg.getSequences(null).contains(temp))
\r
944 viewport.alignment.getSequences().setElementAt(temp, i);
\r
945 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
950 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
952 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
953 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
958 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
959 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
964 viewport.alignment.getSequences().setElementAt(temp, i);
\r
965 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
969 alignPanel.repaint();
\r
972 static StringBuffer copiedSequences;
\r
973 static Vector copiedHiddenColumns;
\r
974 protected void copy_actionPerformed()
\r
976 if (viewport.getSelectionGroup() == null)
\r
981 SequenceGroup sg = viewport.getSelectionGroup();
\r
982 copiedSequences = new StringBuffer();
\r
983 Hashtable orderedSeqs = new Hashtable();
\r
984 for (int i = 0; i < sg.getSize(); i++)
\r
986 SequenceI seq = sg.getSequenceAt(i);
\r
987 int index = viewport.alignment.findIndex(seq);
\r
988 orderedSeqs.put(index + "", seq);
\r
991 int index = 0, startRes, endRes;
\r
994 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
996 copiedHiddenColumns = new Vector();
\r
997 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
998 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
\r
1001 int[] region = (int[])
\r
1002 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
\r
1004 copiedHiddenColumns.addElement(new int[]
\r
1005 {region[0] - hiddenOffset,
\r
1006 region[1] - hiddenOffset});
\r
1010 copiedHiddenColumns = null;
\r
1013 for (int i = 0; i < sg.getSize(); i++)
\r
1015 SequenceI seq = null;
\r
1017 while (seq == null)
\r
1019 if (orderedSeqs.containsKey(index + ""))
\r
1021 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1033 //Returns residue following index if gap
\r
1034 startRes = seq.findPosition(sg.getStartRes());
\r
1037 //Need to find the residue preceeding index if gap
\r
1040 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
1042 ch = seq.getCharAt(j);
\r
1043 if (!jalview.util.Comparison.isGap( (ch)))
\r
1051 endRes += seq.getStart() -1;
\r
1054 copiedSequences.append(seq.getName() + "\t" +
\r
1057 seq.getSequenceAsString(sg.getStartRes(),
\r
1058 sg.getEndRes() + 1) + "\n");
\r
1063 protected void pasteNew_actionPerformed()
\r
1068 protected void pasteThis_actionPerformed()
\r
1073 void paste(boolean newAlignment)
\r
1078 if (copiedSequences == null)
\r
1083 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1084 Vector seqs = new Vector();
\r
1085 while (st.hasMoreElements())
\r
1087 String name = st.nextToken();
\r
1088 int start = Integer.parseInt(st.nextToken());
\r
1089 int end = Integer.parseInt(st.nextToken());
\r
1090 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1092 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1093 for (int i = 0; i < seqs.size(); i++)
\r
1095 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1100 String newtitle = new String("Copied sequences");
\r
1101 if (getTitle().startsWith("Copied sequences"))
\r
1103 newtitle = getTitle();
\r
1107 newtitle = newtitle.concat("- from " + getTitle());
\r
1109 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1113 if (copiedHiddenColumns != null)
\r
1115 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1117 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1118 af.viewport.hideColumns(region[0], region[1]);
\r
1123 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1128 addSequences(newSeqs);
\r
1132 catch (Exception ex)
\r
1133 {} // could be anything being pasted in here
\r
1137 void addSequences(SequenceI[] seqs)
\r
1139 for (int i = 0; i < seqs.length; i++)
\r
1141 viewport.alignment.addSequence(seqs[i]);
\r
1145 addHistoryItem(new EditCommand(
\r
1147 EditCommand.PASTE,
\r
1150 viewport.alignment.getWidth(),
\r
1151 viewport.alignment)
\r
1154 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1155 viewport.alignment.getWidth();
\r
1156 viewport.firePropertyChange("alignment", null,
\r
1157 viewport.alignment.getSequences());
\r
1161 protected void cut_actionPerformed()
\r
1163 copy_actionPerformed();
\r
1164 delete_actionPerformed();
\r
1167 protected void delete_actionPerformed()
\r
1170 SequenceGroup sg = viewport.getSelectionGroup();
\r
1176 Vector seqs = new Vector();
\r
1178 for (int i = 0; i < sg.getSize(); i++)
\r
1180 seq = sg.getSequenceAt(i);
\r
1181 seqs.addElement(seq);
\r
1185 // If the cut affects all sequences, remove highlighted columns
\r
1186 if (sg.getSize() == viewport.alignment.getHeight())
\r
1188 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1189 sg.getEndRes() + 1);
\r
1193 SequenceI [] cut = new SequenceI[seqs.size()];
\r
1194 for(int i=0; i<seqs.size(); i++)
\r
1195 cut[i] = (SequenceI)seqs.elementAt(i);
\r
1199 //ADD HISTORY ITEM
\r
1201 addHistoryItem(new EditCommand("Cut Sequences",
\r
1205 sg.getEndRes()-sg.getStartRes()+1,
\r
1206 viewport.alignment));
\r
1209 viewport.setSelectionGroup(null);
\r
1210 viewport.alignment.deleteGroup(sg);
\r
1212 viewport.firePropertyChange("alignment", null,
\r
1213 viewport.getAlignment().getSequences());
\r
1215 if (viewport.getAlignment().getHeight() < 1)
\r
1217 this.setVisible(false);
\r
1221 protected void deleteGroups_actionPerformed()
\r
1223 viewport.alignment.deleteAllGroups();
\r
1224 viewport.sequenceColours=null;
\r
1225 viewport.setSelectionGroup(null);
\r
1227 alignPanel.repaint();
\r
1230 public void selectAllSequenceMenuItem_actionPerformed()
\r
1232 SequenceGroup sg = new SequenceGroup();
\r
1233 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1235 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1237 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
1238 viewport.setSelectionGroup(sg);
\r
1239 alignPanel.repaint();
\r
1240 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1243 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1245 if(viewport.cursorMode)
\r
1247 alignPanel.seqPanel.keyboardNo1=null;
\r
1248 alignPanel.seqPanel.keyboardNo2=null;
\r
1250 viewport.setSelectionGroup(null);
\r
1251 viewport.getColumnSelection().clear();
\r
1252 viewport.setSelectionGroup(null);
\r
1253 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1254 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1255 alignPanel.repaint();
\r
1256 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1259 public void invertSequenceMenuItem_actionPerformed()
\r
1261 SequenceGroup sg = viewport.getSelectionGroup();
\r
1262 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1264 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1267 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1270 void trimAlignment(boolean trimLeft)
\r
1272 ColumnSelection colSel = viewport.getColumnSelection();
\r
1275 if (colSel.size() > 0)
\r
1278 column = colSel.getMin();
\r
1280 column = colSel.getMax();
\r
1282 SequenceI [] seqs;
\r
1283 if(viewport.getSelectionGroup()!=null)
\r
1284 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
\r
1286 seqs = viewport.alignment.getSequencesArray();
\r
1289 TrimRegionCommand trimRegion;
\r
1292 trimRegion = new TrimRegionCommand("Remove Left",
\r
1293 TrimRegionCommand.TRIM_LEFT,
\r
1296 viewport.alignment,
\r
1298 viewport.selectionGroup);
\r
1299 viewport.setStartRes(0);
\r
1303 trimRegion = new TrimRegionCommand("Remove Right",
\r
1304 TrimRegionCommand.TRIM_RIGHT,
\r
1307 viewport.alignment,
\r
1309 viewport.selectionGroup);
\r
1312 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
\r
1315 addHistoryItem(trimRegion);
\r
1317 Vector groups = viewport.alignment.getGroups();
\r
1319 for (int i = 0; i < groups.size(); i++)
\r
1321 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1323 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
\r
1324 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1326 viewport.alignment.deleteGroup(sg);
\r
1330 viewport.firePropertyChange("alignment", null,
\r
1331 viewport.getAlignment().getSequences());
\r
1336 public void removeGappedColumnMenuItem_actionPerformed()
\r
1338 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1341 if (viewport.getSelectionGroup() != null)
\r
1343 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
\r
1344 start = viewport.getSelectionGroup().getStartRes();
\r
1345 end = viewport.getSelectionGroup().getEndRes();
\r
1348 seqs = viewport.alignment.getSequencesArray();
\r
1351 RemoveGapColCommand removeGapCols =
\r
1352 new RemoveGapColCommand("Remove Gapped Columns",
\r
1355 viewport.getGapCharacter());
\r
1357 addHistoryItem(removeGapCols);
\r
1359 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
\r
1361 //This is to maintain viewport position on first residue
\r
1362 //of first sequence
\r
1363 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1364 int startRes = seq.findPosition(viewport.startRes);
\r
1365 // ShiftList shifts;
\r
1366 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1367 // edit.alColumnChanges=shifts.getInverse();
\r
1368 // if (viewport.hasHiddenColumns)
\r
1369 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1370 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1371 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1375 public void removeAllGapsMenuItem_actionPerformed()
\r
1377 int start = 0, end = viewport.alignment.getWidth()-1;
\r
1380 if (viewport.getSelectionGroup() != null)
\r
1382 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
\r
1383 start = viewport.getSelectionGroup().getStartRes();
\r
1384 end = viewport.getSelectionGroup().getEndRes();
\r
1387 seqs = viewport.alignment.getSequencesArray();
\r
1389 //This is to maintain viewport position on first residue
\r
1390 //of first sequence
\r
1391 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1392 int startRes = seq.findPosition(viewport.startRes);
\r
1394 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
\r
1397 viewport.getGapCharacter()));
\r
1399 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1401 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1405 public void findMenuItem_actionPerformed()
\r
1407 new Finder(alignPanel);
\r
1410 public void newView()
\r
1413 if (viewport.hasHiddenRows)
\r
1414 newal = new Alignment(viewport.getAlignment().
\r
1415 getHiddenSequences()
\r
1416 .getFullAlignment().
\r
1417 getSequencesArray());
\r
1419 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
1421 AlignFrame newaf = new AlignFrame(newal,
\r
1426 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
1427 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
1428 PaintRefresher.Register(newaf.alignPanel,
\r
1429 newaf.alignPanel.av.getSequenceSetId());
\r
1431 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
1432 newaf.alignPanel.av.getSequenceSetId());
\r
1433 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
1434 newaf.alignPanel.av.getSequenceSetId());
\r
1436 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
\r
1437 int viewSize = -1;
\r
1438 for (int i = 0; i < comps.size(); i++)
\r
1440 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1444 String title = new String(this.getTitle());
\r
1445 if (title.indexOf("(View") > -1)
\r
1446 title = title.substring(0, title.indexOf("(View"));
\r
1448 title+= "(View "+viewSize+")";
\r
1450 newaf.setTitle(title.toString());
\r
1453 newaf.viewport.historyList = viewport.historyList;
\r
1454 newaf.viewport.redoList = viewport.redoList;
\r
1459 public void seqLimits_itemStateChanged()
\r
1461 viewport.setShowJVSuffix(seqLimits.getState());
\r
1462 alignPanel.fontChanged();
\r
1463 alignPanel.repaint();
\r
1467 protected void colourTextMenuItem_actionPerformed()
\r
1469 viewport.setColourText(colourTextMenuItem.getState());
\r
1470 alignPanel.repaint();
\r
1473 protected void wrapMenuItem_actionPerformed()
\r
1475 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1476 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1477 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1478 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1479 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1480 alignPanel.repaint();
\r
1484 public void overviewMenuItem_actionPerformed()
\r
1486 if (alignPanel.overviewPanel != null)
\r
1491 Frame frame = new Frame();
\r
1492 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1493 frame.add(overview);
\r
1494 // +50 must allow for applet frame window
\r
1495 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1496 overview.preferredSize().width,
\r
1497 overview.preferredSize().height + 50);
\r
1500 frame.addWindowListener(new WindowAdapter()
\r
1502 public void windowClosing(WindowEvent e)
\r
1504 alignPanel.setOverviewPanel(null);
\r
1508 alignPanel.setOverviewPanel(overview);
\r
1513 void changeColour(ColourSchemeI cs)
\r
1515 int threshold = 0;
\r
1519 if (viewport.getAbovePIDThreshold())
\r
1521 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1523 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1525 viewport.setGlobalColourScheme(cs);
\r
1529 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1532 if (viewport.getConservationSelected())
\r
1535 Alignment al = (Alignment) viewport.alignment;
\r
1536 Conservation c = new Conservation("All",
\r
1537 ResidueProperties.propHash, 3,
\r
1538 al.getSequences(), 0,
\r
1539 al.getWidth() - 1);
\r
1542 c.verdict(false, viewport.ConsPercGaps);
\r
1544 cs.setConservation(c);
\r
1546 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1552 cs.setConservation(null);
\r
1555 cs.setConsensus(viewport.hconsensus);
\r
1558 viewport.setGlobalColourScheme(cs);
\r
1560 if (viewport.getColourAppliesToAllGroups())
\r
1562 Vector groups = viewport.alignment.getGroups();
\r
1563 for (int i = 0; i < groups.size(); i++)
\r
1565 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1572 if (cs instanceof ClustalxColourScheme)
\r
1574 sg.cs = new ClustalxColourScheme(
\r
1575 sg.getSequences(viewport.hiddenRepSequences),
\r
1582 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1584 catch (Exception ex)
\r
1586 ex.printStackTrace();
\r
1591 if (viewport.getAbovePIDThreshold()
\r
1592 || cs instanceof PIDColourScheme
\r
1593 || cs instanceof Blosum62ColourScheme)
\r
1595 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1596 sg.cs.setConsensus(AAFrequency.calculate(
\r
1597 sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
\r
1600 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1602 if (viewport.getConservationSelected())
\r
1604 Conservation c = new Conservation("Group",
\r
1605 ResidueProperties.propHash, 3,
\r
1606 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
1607 viewport.alignment.getWidth() - 1);
\r
1609 c.verdict(false, viewport.ConsPercGaps);
\r
1610 sg.cs.setConservation(c);
\r
1614 sg.cs.setConservation(null);
\r
1615 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1622 if (alignPanel.getOverviewPanel() != null)
\r
1624 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1627 alignPanel.repaint();
\r
1632 protected void modifyPID_actionPerformed()
\r
1634 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1636 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1638 SliderPanel.showPIDSlider();
\r
1642 protected void modifyConservation_actionPerformed()
\r
1644 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1646 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1648 SliderPanel.showConservationSlider();
\r
1652 protected void conservationMenuItem_actionPerformed()
\r
1654 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1656 viewport.setAbovePIDThreshold(false);
\r
1657 abovePIDThreshold.setState(false);
\r
1659 changeColour(viewport.getGlobalColourScheme());
\r
1661 modifyConservation_actionPerformed();
\r
1664 public void abovePIDThreshold_actionPerformed()
\r
1666 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1668 conservationMenuItem.setState(false);
\r
1669 viewport.setConservationSelected(false);
\r
1671 changeColour(viewport.getGlobalColourScheme());
\r
1673 modifyPID_actionPerformed();
\r
1678 public void sortPairwiseMenuItem_actionPerformed()
\r
1680 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
\r
1681 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1682 viewport.getAlignment().getSequenceAt(0));
\r
1683 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
\r
1684 alignPanel.repaint();
\r
1687 public void sortIDMenuItem_actionPerformed()
\r
1689 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1690 // HistoryItem.SORT));
\r
1691 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1692 alignPanel.repaint();
\r
1695 public void sortGroupMenuItem_actionPerformed()
\r
1697 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1698 // HistoryItem.SORT));
\r
1699 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1700 alignPanel.repaint();
\r
1704 public void removeRedundancyMenuItem_actionPerformed()
\r
1706 new RedundancyPanel(alignPanel);
\r
1709 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1711 if (viewport.getSelectionGroup()!=null
\r
1712 && viewport.getSelectionGroup().getSize() > 1)
\r
1714 Frame frame = new Frame();
\r
1715 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1716 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1720 public void PCAMenuItem_actionPerformed()
\r
1722 //are the sequences aligned?
\r
1723 if (!viewport.alignment.isAligned())
\r
1725 SequenceI current;
\r
1726 int Width = viewport.getAlignment().getWidth();
\r
1728 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1731 current = viewport.getAlignment().getSequenceAt(i);
\r
1733 if (current.getLength() < Width)
\r
1735 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1738 alignPanel.repaint();
\r
1741 if ( (viewport.getSelectionGroup() != null &&
\r
1742 viewport.getSelectionGroup().getSize() < 4 &&
\r
1743 viewport.getSelectionGroup().getSize() > 0)
\r
1744 || viewport.getAlignment().getHeight() < 4)
\r
1751 new PCAPanel(viewport);
\r
1753 catch (java.lang.OutOfMemoryError ex)
\r
1759 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1761 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1764 public void neighbourTreeMenuItem_actionPerformed()
\r
1766 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1769 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1771 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1774 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1776 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1779 void NewTreePanel(String type, String pwType, String title)
\r
1781 //are the sequences aligned?
\r
1782 if (!viewport.alignment.isAligned())
\r
1784 SequenceI current;
\r
1785 int Width = viewport.getAlignment().getWidth();
\r
1787 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1790 current = viewport.getAlignment().getSequenceAt(i);
\r
1792 if (current.getLength() < Width)
\r
1794 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1797 alignPanel.repaint();
\r
1801 if ( (viewport.getSelectionGroup() != null &&
\r
1802 viewport.getSelectionGroup().getSize() > 1)
\r
1803 || (viewport.getSelectionGroup() == null
\r
1804 && viewport.alignment.getHeight() > 1))
\r
1806 final TreePanel tp = new TreePanel(viewport,
\r
1810 addTreeMenuItem(tp, title);
\r
1812 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1816 void loadTree_actionPerformed()
\r
1818 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1819 cap.setText("Paste your Newick tree file here.");
\r
1820 cap.setTreeImport();
\r
1821 Frame frame = new Frame();
\r
1823 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
1826 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
1828 TreePanel tp = new TreePanel(viewport,
\r
1832 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
1833 addTreeMenuItem(tp, treeFile);
\r
1836 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1838 final MenuItem item = new MenuItem(title);
\r
1839 sortByTreeMenu.add(item);
\r
1840 item.addActionListener(new java.awt.event.ActionListener()
\r
1842 public void actionPerformed(ActionEvent evt)
\r
1844 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1845 // HistoryItem.SORT));
\r
1846 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1847 alignPanel.repaint();
\r
1851 treePanel.addWindowListener(new WindowAdapter()
\r
1853 public void windowClosing(WindowEvent e)
\r
1855 sortByTreeMenu.remove(item);
\r
1860 protected void documentation_actionPerformed()
\r
1862 showURL("http://www.jalview.org/help.html", "HELP");
\r
1865 protected void about_actionPerformed()
\r
1868 class AboutPanel extends Canvas
\r
1871 public AboutPanel(String version)
\r
1872 { this.version = version; }
\r
1874 public void paint(Graphics g)
\r
1876 g.setColor(Color.white);
\r
1877 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1878 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1879 FontMetrics fm = g.getFontMetrics();
\r
1880 int fh = fm.getHeight();
\r
1882 g.setColor(Color.black);
\r
1883 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1884 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1885 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1886 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1888 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1891 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1893 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1894 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1896 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
\r
1900 String version = "test";
\r
1901 java.net.URL url = getClass().getResource("/.build_properties");
\r
1906 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1907 url.openStream()));
\r
1909 while ( (line = reader.readLine()) != null)
\r
1911 if (line.indexOf("VERSION") > -1)
\r
1913 version = line.substring(line.indexOf("=") + 1);
\r
1917 catch (Exception ex)
\r
1919 ex.printStackTrace();
\r
1924 Frame frame = new Frame();
\r
1925 frame.add(new AboutPanel(version));
\r
1926 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1930 public void showURL(String url, String target)
\r
1932 if (viewport.applet == null)
\r
1934 System.out.println("Not running as applet - no browser available.");
\r
1940 System.out.println("Show url: "+url);
\r
1941 viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1944 catch (Exception ex)
\r
1946 ex.printStackTrace();
\r
1952 //////////////////////////////////////////////////////////////////////////////////
\r
1953 //JBuilder Graphics here
\r
1955 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1956 protected Menu fileMenu = new Menu("File");
\r
1957 protected MenuItem loadApplication = new MenuItem("View in Full Application");
\r
1958 protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
1959 protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
1960 protected MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
1961 protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
1963 protected MenuItem closeMenuItem = new MenuItem("Close");
\r
1964 protected Menu editMenu = new Menu("Edit");
\r
1965 protected Menu viewMenu = new Menu("View");
\r
1966 protected Menu colourMenu = new Menu("Colour");
\r
1967 protected Menu calculateMenu = new Menu("Calculate");
\r
1968 protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
1969 protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
1970 protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
1971 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1972 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1973 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1974 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1975 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1976 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1977 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1978 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1979 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1980 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1981 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1982 protected MenuItem PCAMenuItem = new MenuItem();
\r
1983 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1984 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1985 BorderLayout borderLayout1 = new BorderLayout();
\r
1986 public Label statusBar = new Label();
\r
1987 protected Menu outputTextboxMenu = new Menu();
\r
1988 protected MenuItem clustalColour = new MenuItem();
\r
1989 protected MenuItem zappoColour = new MenuItem();
\r
1990 protected MenuItem taylorColour = new MenuItem();
\r
1991 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1992 protected MenuItem helixColour = new MenuItem();
\r
1993 protected MenuItem strandColour = new MenuItem();
\r
1994 protected MenuItem turnColour = new MenuItem();
\r
1995 protected MenuItem buriedColour = new MenuItem();
\r
1996 protected MenuItem userDefinedColour = new MenuItem();
\r
1997 protected MenuItem PIDColour = new MenuItem();
\r
1998 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1999 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2000 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2001 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2002 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2003 MenuItem overviewMenuItem = new MenuItem();
\r
2004 protected MenuItem undoMenuItem = new MenuItem();
\r
2005 protected MenuItem redoMenuItem = new MenuItem();
\r
2006 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2007 MenuItem noColourmenuItem = new MenuItem();
\r
2008 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2009 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2010 MenuItem findMenuItem = new MenuItem();
\r
2011 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2012 protected MenuItem nucleotideColour = new MenuItem();
\r
2013 MenuItem deleteGroups = new MenuItem();
\r
2014 MenuItem delete = new MenuItem();
\r
2015 MenuItem copy = new MenuItem();
\r
2016 MenuItem cut = new MenuItem();
\r
2017 Menu pasteMenu = new Menu();
\r
2018 MenuItem pasteNew = new MenuItem();
\r
2019 MenuItem pasteThis = new MenuItem();
\r
2020 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2021 protected MenuItem font = new MenuItem();
\r
2022 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2023 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2024 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2025 MenuItem modifyPID = new MenuItem();
\r
2026 MenuItem modifyConservation = new MenuItem();
\r
2027 protected CheckboxMenuItem autoCalculate
\r
2028 = new CheckboxMenuItem("Autocalculate Consensus", true);
\r
2029 protected Menu sortByTreeMenu = new Menu();
\r
2030 Menu sort = new Menu();
\r
2031 Menu calculate = new Menu();
\r
2032 MenuItem inputText = new MenuItem();
\r
2033 Menu helpMenu = new Menu();
\r
2034 MenuItem documentation = new MenuItem();
\r
2035 MenuItem about = new MenuItem();
\r
2036 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2037 Panel embeddedMenu;
\r
2038 Label embeddedEdit;
\r
2039 Label embeddedSelect;
\r
2040 Label embeddedView;
\r
2041 Label embeddedFormat;
\r
2042 Label embeddedColour;
\r
2043 Label embeddedFile;
\r
2044 Label embeddedHelp;
\r
2045 Label embeddedCalculate;
\r
2046 FlowLayout flowLayout1;
\r
2048 private void jbInit() throws Exception {
\r
2050 setMenuBar(alignFrameMenuBar);
\r
2054 // dynamically fill save as menu with available formats
\r
2055 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2058 item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2060 item.addActionListener(new java.awt.event.ActionListener()
\r
2062 public void actionPerformed(ActionEvent e)
\r
2064 outputText_actionPerformed(e);
\r
2068 outputTextboxMenu.add(item);
\r
2070 closeMenuItem.addActionListener(this);
\r
2071 loadApplication.addActionListener(this);
\r
2073 loadTree.addActionListener(this);
\r
2074 loadAnnotations.addActionListener(this);
\r
2075 outputFeatures.addActionListener(this);
\r
2076 outputAnnotations.addActionListener(this);
\r
2077 selectAllSequenceMenuItem.addActionListener(this);
\r
2078 deselectAllSequenceMenuItem.addActionListener(this);
\r
2079 invertSequenceMenuItem.addActionListener(this);
\r
2080 remove2LeftMenuItem.setLabel("Remove Left");
\r
2081 remove2LeftMenuItem.addActionListener(this);
\r
2082 remove2RightMenuItem.setLabel("Remove Right");
\r
2083 remove2RightMenuItem.addActionListener(this);
\r
2084 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2085 removeGappedColumnMenuItem.addActionListener(this);
\r
2086 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2087 removeAllGapsMenuItem.addActionListener(this);
\r
2088 viewBoxesMenuItem.setLabel("Boxes");
\r
2089 viewBoxesMenuItem.setState(true);
\r
2090 viewBoxesMenuItem.addItemListener(this);
\r
2091 viewTextMenuItem.setLabel("Text");
\r
2092 viewTextMenuItem.setState(true);
\r
2093 viewTextMenuItem.addItemListener(this);
\r
2094 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2095 sortPairwiseMenuItem.addActionListener(this);
\r
2096 sortIDMenuItem.setLabel("by ID");
\r
2097 sortIDMenuItem.addActionListener(this);
\r
2098 sortGroupMenuItem.setLabel("by Group");
\r
2099 sortGroupMenuItem.addActionListener(this);
\r
2100 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2101 removeRedundancyMenuItem.addActionListener(this);
\r
2102 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2103 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2104 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2105 PCAMenuItem.addActionListener(this);
\r
2106 averageDistanceTreeMenuItem.setLabel(
\r
2107 "Average Distance Using % Identity");
\r
2108 averageDistanceTreeMenuItem.addActionListener(this);
\r
2109 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2110 neighbourTreeMenuItem.addActionListener(this);
\r
2111 statusBar.setBackground(Color.white);
\r
2112 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2113 statusBar.setText("Status bar");
\r
2114 outputTextboxMenu.setLabel("Output to Textbox");
\r
2115 clustalColour.setLabel("Clustalx");
\r
2117 clustalColour.addActionListener(this);
\r
2118 zappoColour.setLabel("Zappo");
\r
2119 zappoColour.addActionListener(this);
\r
2120 taylorColour.setLabel("Taylor");
\r
2121 taylorColour.addActionListener(this);
\r
2122 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2123 hydrophobicityColour.addActionListener(this);
\r
2124 helixColour.setLabel("Helix Propensity");
\r
2125 helixColour.addActionListener(this);
\r
2126 strandColour.setLabel("Strand Propensity");
\r
2127 strandColour.addActionListener(this);
\r
2128 turnColour.setLabel("Turn Propensity");
\r
2129 turnColour.addActionListener(this);
\r
2130 buriedColour.setLabel("Buried Index");
\r
2131 buriedColour.addActionListener(this);
\r
2132 userDefinedColour.setLabel("User Defined...");
\r
2133 userDefinedColour.addActionListener(this);
\r
2134 PIDColour.setLabel("Percentage Identity");
\r
2135 PIDColour.addActionListener(this);
\r
2136 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2137 BLOSUM62Colour.addActionListener(this);
\r
2138 avDistanceTreeBlosumMenuItem.setLabel(
\r
2139 "Average Distance Using BLOSUM62");
\r
2140 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2141 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2142 njTreeBlosumMenuItem.addActionListener(this);
\r
2143 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2144 annotationPanelMenuItem.addItemListener(this);
\r
2145 colourTextMenuItem.setLabel("Colour Text");
\r
2146 colourTextMenuItem.addItemListener(this);
\r
2147 overviewMenuItem.setLabel("Overview Window");
\r
2148 overviewMenuItem.addActionListener(this);
\r
2149 undoMenuItem.setEnabled(false);
\r
2150 undoMenuItem.setLabel("Undo");
\r
2151 undoMenuItem.addActionListener(this);
\r
2152 redoMenuItem.setEnabled(false);
\r
2153 redoMenuItem.setLabel("Redo");
\r
2154 redoMenuItem.addActionListener(this);
\r
2155 conservationMenuItem.setLabel("by Conservation");
\r
2156 conservationMenuItem.addItemListener(this);
\r
2157 noColourmenuItem.setLabel("None");
\r
2158 noColourmenuItem.addActionListener(this);
\r
2159 wrapMenuItem.setLabel("Wrap");
\r
2160 wrapMenuItem.addItemListener(this);
\r
2161 renderGapsMenuItem.setLabel("Show Gaps");
\r
2162 renderGapsMenuItem.setState(true);
\r
2163 renderGapsMenuItem.addItemListener(this);
\r
2164 findMenuItem.setLabel("Find...");
\r
2165 findMenuItem.addActionListener(this);
\r
2166 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2167 abovePIDThreshold.addItemListener(this);
\r
2168 nucleotideColour.setLabel("Nucleotide");
\r
2169 nucleotideColour.addActionListener(this);
\r
2170 deleteGroups.setLabel("Undefine Groups");
\r
2171 deleteGroups.addActionListener(this);
\r
2172 copy.setLabel("Copy");
\r
2173 copy.addActionListener(this);
\r
2174 cut.setLabel("Cut");
\r
2175 cut.addActionListener(this);
\r
2176 delete.setLabel("Delete");
\r
2177 delete.addActionListener(this);
\r
2178 pasteMenu.setLabel("Paste");
\r
2179 pasteNew.setLabel("To New Alignment");
\r
2180 pasteNew.addActionListener(this);
\r
2181 pasteThis.setLabel("Add To This Alignment");
\r
2182 pasteThis.addActionListener(this);
\r
2183 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
2184 applyToAllGroups.setState(true);
\r
2185 applyToAllGroups.addItemListener(this);
\r
2186 font.setLabel("Font...");
\r
2187 font.addActionListener(this);
\r
2188 scaleAbove.setLabel("Scale Above");
\r
2189 scaleAbove.setState(true);
\r
2190 scaleAbove.setEnabled(false);
\r
2191 scaleAbove.addItemListener(this);
\r
2192 scaleLeft.setEnabled(false);
\r
2193 scaleLeft.setState(true);
\r
2194 scaleLeft.setLabel("Scale Left");
\r
2195 scaleLeft.addItemListener(this);
\r
2196 scaleRight.setEnabled(false);
\r
2197 scaleRight.setState(true);
\r
2198 scaleRight.setLabel("Scale Right");
\r
2199 scaleRight.addItemListener(this);
\r
2200 modifyPID.setLabel("Modify Identity Threshold...");
\r
2201 modifyPID.addActionListener(this);
\r
2202 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
2203 modifyConservation.addActionListener(this);
\r
2204 sortByTreeMenu.setLabel("By Tree Order");
\r
2205 sort.setLabel("Sort");
\r
2206 calculate.setLabel("Calculate Tree");
\r
2207 autoCalculate.addItemListener(this);
\r
2208 inputText.setLabel("Input from textbox");
\r
2209 inputText.addActionListener(this);
\r
2211 helpMenu.setLabel("Help");
\r
2212 documentation.setLabel("Documentation");
\r
2213 documentation.addActionListener(this);
\r
2215 about.setLabel("About...");
\r
2216 about.addActionListener(this);
\r
2217 seqLimits.setState(true);
\r
2218 seqLimits.setLabel("Show Sequence Limits");
\r
2219 seqLimits.addItemListener(this);
\r
2220 featureSettings.setLabel("Feature Settings...");
\r
2221 featureSettings.addActionListener(this);
\r
2222 sequenceFeatures.setLabel("Sequence Features");
\r
2223 sequenceFeatures.addItemListener(this);
\r
2224 sequenceFeatures.setState(false);
\r
2225 annotationColour.setLabel("by Annotation...");
\r
2226 annotationColour.addActionListener(this);
\r
2227 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
2228 invertColSel.setLabel("Invert Column Selection");
\r
2229 menu1.setLabel("Show");
\r
2230 showColumns.setLabel("All Columns ");
\r
2231 showSeqs.setLabel("All Sequences");
\r
2232 menu2.setLabel("Hide");
\r
2233 hideColumns.setLabel("Selected Columns");
\r
2234 hideSequences.setLabel("Selected Sequences");
\r
2235 invertColSel.addActionListener(this);
\r
2236 showColumns.addActionListener(this);
\r
2237 showSeqs.addActionListener(this);
\r
2238 hideColumns.addActionListener(this);
\r
2239 hideSequences.addActionListener(this);
\r
2240 formatMenu.setLabel("Format");
\r
2241 selectMenu.setLabel("Select");
\r
2242 newView.setLabel("New View");
\r
2243 newView.addActionListener(this);
\r
2244 alignFrameMenuBar.add(fileMenu);
\r
2245 alignFrameMenuBar.add(editMenu);
\r
2246 alignFrameMenuBar.add(selectMenu);
\r
2247 alignFrameMenuBar.add(viewMenu);
\r
2248 alignFrameMenuBar.add(formatMenu);
\r
2249 alignFrameMenuBar.add(colourMenu);
\r
2250 alignFrameMenuBar.add(calculateMenu);
\r
2251 alignFrameMenuBar.add(helpMenu);
\r
2253 fileMenu.add(inputText);
\r
2254 fileMenu.add(loadTree);
\r
2255 fileMenu.add(loadAnnotations);
\r
2257 fileMenu.addSeparator();
\r
2258 fileMenu.add(outputTextboxMenu);
\r
2259 fileMenu.add(outputFeatures);
\r
2260 fileMenu.add(outputAnnotations);
\r
2262 if(jalviewServletURL!=null)
\r
2263 fileMenu.add(loadApplication);
\r
2265 fileMenu.addSeparator();
\r
2266 fileMenu.add(closeMenuItem);
\r
2268 editMenu.add(undoMenuItem);
\r
2269 editMenu.add(redoMenuItem);
\r
2270 editMenu.add(cut);
\r
2271 editMenu.add(copy);
\r
2272 editMenu.add(pasteMenu);
\r
2273 editMenu.add(delete);
\r
2274 editMenu.addSeparator();
\r
2275 editMenu.add(remove2LeftMenuItem);
\r
2276 editMenu.add(remove2RightMenuItem);
\r
2277 editMenu.add(removeGappedColumnMenuItem);
\r
2278 editMenu.add(removeAllGapsMenuItem);
\r
2279 editMenu.add(removeRedundancyMenuItem);
\r
2280 viewMenu.add(newView);
\r
2281 viewMenu.addSeparator();
\r
2282 viewMenu.add(menu1);
\r
2283 viewMenu.add(menu2);
\r
2284 viewMenu.addSeparator();
\r
2285 viewMenu.add(annotationPanelMenuItem);
\r
2286 viewMenu.addSeparator();
\r
2287 viewMenu.add(sequenceFeatures);
\r
2288 viewMenu.add(featureSettings);
\r
2289 viewMenu.addSeparator();
\r
2290 viewMenu.add(overviewMenuItem);
\r
2291 colourMenu.add(applyToAllGroups);
\r
2292 colourMenu.addSeparator();
\r
2293 colourMenu.add(noColourmenuItem);
\r
2294 colourMenu.add(clustalColour);
\r
2295 colourMenu.add(BLOSUM62Colour);
\r
2296 colourMenu.add(PIDColour);
\r
2297 colourMenu.add(zappoColour);
\r
2298 colourMenu.add(taylorColour);
\r
2299 colourMenu.add(hydrophobicityColour);
\r
2300 colourMenu.add(helixColour);
\r
2301 colourMenu.add(strandColour);
\r
2302 colourMenu.add(turnColour);
\r
2303 colourMenu.add(buriedColour);
\r
2304 colourMenu.add(nucleotideColour);
\r
2305 colourMenu.add(userDefinedColour);
\r
2306 colourMenu.addSeparator();
\r
2307 colourMenu.add(conservationMenuItem);
\r
2308 colourMenu.add(modifyConservation);
\r
2309 colourMenu.add(abovePIDThreshold);
\r
2310 colourMenu.add(modifyPID);
\r
2311 colourMenu.add(annotationColour);
\r
2312 calculateMenu.add(sort);
\r
2313 calculateMenu.add(calculate);
\r
2314 calculateMenu.addSeparator();
\r
2315 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2316 calculateMenu.add(PCAMenuItem);
\r
2317 calculateMenu.add(autoCalculate);
\r
2318 this.add(statusBar, BorderLayout.SOUTH);
\r
2319 pasteMenu.add(pasteNew);
\r
2320 pasteMenu.add(pasteThis);
\r
2321 sort.add(sortIDMenuItem);
\r
2322 sort.add(sortByTreeMenu);
\r
2323 sort.add(sortGroupMenuItem);
\r
2324 sort.add(sortPairwiseMenuItem);
\r
2325 calculate.add(averageDistanceTreeMenuItem);
\r
2326 calculate.add(neighbourTreeMenuItem);
\r
2327 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2328 calculate.add(njTreeBlosumMenuItem);
\r
2329 helpMenu.add(documentation);
\r
2330 helpMenu.add(about);
\r
2331 menu1.add(showColumns);
\r
2332 menu1.add(showSeqs);
\r
2333 menu2.add(hideColumns);
\r
2334 menu2.add(hideSequences);
\r
2335 formatMenu.add(font);
\r
2336 formatMenu.add(seqLimits);
\r
2337 formatMenu.add(wrapMenuItem);
\r
2338 formatMenu.add(scaleAbove);
\r
2339 formatMenu.add(scaleLeft);
\r
2340 formatMenu.add(scaleRight);
\r
2341 formatMenu.add(viewBoxesMenuItem);
\r
2342 formatMenu.add(viewTextMenuItem);
\r
2343 formatMenu.add(colourTextMenuItem);
\r
2344 formatMenu.add(renderGapsMenuItem);
\r
2345 selectMenu.add(findMenuItem);
\r
2346 selectMenu.addSeparator();
\r
2347 selectMenu.add(selectAllSequenceMenuItem);
\r
2348 selectMenu.add(deselectAllSequenceMenuItem);
\r
2349 selectMenu.add(invertSequenceMenuItem);
\r
2350 selectMenu.add(invertColSel);
\r
2351 selectMenu.add(deleteGroups);
\r
2354 public void setEmbedded()
\r
2357 embeddedMenu = new Panel();
\r
2358 embeddedEdit = new Label("Edit");
\r
2359 embeddedSelect = new Label("Select");
\r
2360 embeddedView = new Label("View");
\r
2361 embeddedFormat = new Label("Format");
\r
2362 embeddedColour = new Label("Colour");
\r
2363 embeddedFile = new Label("File");
\r
2364 embeddedHelp = new Label("Help");
\r
2365 embeddedCalculate = new Label("Calculate");
\r
2366 flowLayout1 = new FlowLayout();
\r
2367 embeddedMenu.setBackground(Color.lightGray);
\r
2368 embeddedMenu.setLayout(flowLayout1);
\r
2369 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2370 embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2371 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2372 embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2373 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2374 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2375 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2376 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2377 embeddedMenu.add(embeddedFile);
\r
2378 embeddedMenu.add(embeddedEdit);
\r
2379 embeddedMenu.add(embeddedSelect);
\r
2380 embeddedMenu.add(embeddedView);
\r
2381 embeddedMenu.add(embeddedFormat);
\r
2382 embeddedMenu.add(embeddedColour);
\r
2383 embeddedMenu.add(embeddedCalculate);
\r
2384 embeddedMenu.add(embeddedHelp);
\r
2385 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2386 flowLayout1.setHgap(2);
\r
2387 flowLayout1.setVgap(0);
\r
2388 embeddedFile.addMouseListener(this);
\r
2389 embeddedEdit.addMouseListener(this);
\r
2390 embeddedSelect.addMouseListener(this);
\r
2391 embeddedView.addMouseListener(this);
\r
2392 embeddedFormat.addMouseListener(this);
\r
2393 embeddedColour.addMouseListener(this);
\r
2394 embeddedCalculate.addMouseListener(this);
\r
2395 embeddedHelp.addMouseListener(this);
\r
2397 fileMenu.remove(closeMenuItem);
\r
2398 fileMenu.remove(3); // Seperator
\r
2400 viewport.applet.setLayout(new BorderLayout());
\r
2401 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2402 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
2404 alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
\r
2405 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2407 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
2408 viewport.applet.validate();
\r
2414 PopupMenu filePopup, editPopup, searchPopup,
\r
2415 viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
\r
2416 MenuItem featureSettings = new MenuItem();
\r
2417 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2418 MenuItem annotationColour = new MenuItem();
\r
2419 MenuItem invertColSel = new MenuItem();
\r
2420 Menu menu1 = new Menu();
\r
2421 MenuItem showColumns = new MenuItem();
\r
2422 MenuItem showSeqs = new MenuItem();
\r
2423 Menu menu2 = new Menu();
\r
2424 MenuItem hideColumns = new MenuItem();
\r
2425 MenuItem hideSequences = new MenuItem();
\r
2426 Menu formatMenu = new Menu();
\r
2427 Menu selectMenu = new Menu();
\r
2428 MenuItem newView = new MenuItem();
\r
2430 public void mousePressed(MouseEvent evt)
\r
2432 PopupMenu popup = null;
\r
2433 Label source = (Label)evt.getSource();
\r
2434 if(source==embeddedFile)
\r
2436 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2438 else if(source==embeddedEdit)
\r
2440 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2442 else if(source==embeddedSelect)
\r
2444 popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
\r
2446 else if(source==embeddedView)
\r
2448 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2450 else if (source ==embeddedFormat)
\r
2452 popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
\r
2454 else if(source==embeddedColour)
\r
2456 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2458 else if(source==embeddedCalculate)
\r
2460 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2462 else if(source==embeddedHelp)
\r
2464 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2467 embeddedMenu.add(popup);
\r
2468 popup.show(embeddedMenu,
\r
2469 source.getBounds().x,
\r
2470 source.getBounds().y + source.getBounds().getSize().height);
\r
2473 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2479 popup = new PopupMenu();
\r
2480 int m, mSize = original.getItemCount();
\r
2481 for(m=0; m<mSize; m++)
\r
2483 popup.add(original.getItem(m));
\r
2490 public void mouseClicked(MouseEvent evt)
\r
2492 public void mouseReleased(MouseEvent evt)
\r
2494 public void mouseEntered(MouseEvent evt)
\r
2496 public void mouseExited(MouseEvent evt)
\r