2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
\r
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
5 * This file is part of Jalview.
\r
7 * Jalview is free software: you can redistribute it and/or
\r
8 * modify it under the terms of the GNU General Public License
\r
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
\r
11 * Jalview is distributed in the hope that it will be useful, but
\r
12 * WITHOUT ANY WARRANTY; without even the implied warranty
\r
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
\r
14 * PURPOSE. See the GNU General Public License for more details.
\r
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
\r
18 package jalview.appletgui;
\r
24 import java.awt.event.*;
\r
26 import jalview.analysis.*;
\r
27 import jalview.api.SequenceStructureBinding;
\r
28 import jalview.bin.JalviewLite;
\r
29 import jalview.commands.*;
\r
30 import jalview.datamodel.*;
\r
31 import jalview.io.*;
\r
32 import jalview.schemes.*;
\r
33 import jalview.structure.StructureSelectionManager;
\r
35 public class AlignFrame extends EmbmenuFrame implements ActionListener,
\r
36 ItemListener, KeyListener
\r
38 public AlignmentPanel alignPanel;
\r
40 public AlignViewport viewport;
\r
42 int DEFAULT_WIDTH = 700;
\r
44 int DEFAULT_HEIGHT = 500;
\r
46 String jalviewServletURL;
\r
48 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
\r
49 String title, boolean embedded)
\r
54 jalviewServletURL = applet.getParameter("APPLICATION_URL");
\r
60 } catch (Exception ex)
\r
62 ex.printStackTrace();
\r
65 viewport = new AlignViewport(al, applet);
\r
66 alignPanel = new AlignmentPanel(this, viewport);
\r
68 viewport.updateConservation(alignPanel);
\r
69 viewport.updateConsensus(alignPanel);
\r
71 annotationPanelMenuItem.setState(viewport.showAnnotation);
\r
72 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
\r
73 followMouseOverFlag.setState(viewport.getFollowHighlight());
\r
74 showGroupConsensus.setState(viewport.showGroupConsensus);
\r
75 showGroupConservation.setState(viewport.showGroupConservation);
\r
76 showConsensusHistogram.setState(viewport.showConsensusHistogram);
\r
77 showSequenceLogo.setState(viewport.showSequenceLogo);
\r
79 seqLimits.setState(viewport.showJVSuffix);
\r
83 String param = applet.getParameter("sortBy");
\r
86 if (param.equalsIgnoreCase("Id"))
\r
88 sortIDMenuItem_actionPerformed();
\r
90 else if (param.equalsIgnoreCase("Pairwise Identity"))
\r
92 sortPairwiseMenuItem_actionPerformed();
\r
94 else if (param.equalsIgnoreCase("Length"))
\r
96 sortLengthMenuItem_actionPerformed();
\r
100 param = applet.getParameter("wrap");
\r
103 if (param.equalsIgnoreCase("true"))
\r
105 wrapMenuItem.setState(true);
\r
106 wrapMenuItem_actionPerformed();
\r
109 param = applet.getParameter("centrecolumnlabels");
\r
112 centreColumnLabelFlag.setState(true);
\r
113 centreColumnLabelFlag_stateChanged();
\r
117 param = applet.getParameter("windowWidth");
\r
120 int width = Integer.parseInt(param);
\r
121 DEFAULT_WIDTH = width;
\r
123 param = applet.getParameter("windowHeight");
\r
126 int height = Integer.parseInt(param);
\r
127 DEFAULT_HEIGHT = height;
\r
129 } catch (Exception ex)
\r
135 // Some JVMS send keyevents to Top frame or lowest panel,
\r
136 // Havent worked out why yet. So add to both this frame and seqCanvas for
\r
138 this.addKeyListener(this);
\r
139 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
\r
140 alignPanel.idPanel.idCanvas.addKeyListener(this);
\r
141 alignPanel.scalePanel.addKeyListener(this);
\r
142 alignPanel.annotationPanel.addKeyListener(this);
\r
143 alignPanel.annotationPanelHolder.addKeyListener(this);
\r
144 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
\r
145 alignPanel.alabels.addKeyListener(this);
\r
146 createAlignFrameWindow(embedded, title);
\r
149 alignPanel.adjustAnnotationHeight();
\r
150 alignPanel.paintAlignment(true);
\r
153 public AlignViewport getAlignViewport()
\r
158 public SeqCanvas getSeqcanvas()
\r
160 return alignPanel.seqPanel.seqCanvas;
\r
170 public void parseFeaturesFile(String file, String type)
\r
172 Hashtable featureLinks = new Hashtable();
\r
173 boolean featuresFile = false;
\r
176 featuresFile = new jalview.io.FeaturesFile(file, type)
\r
177 .parse(viewport.alignment,
\r
178 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
\r
179 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
\r
180 } catch (Exception ex)
\r
182 ex.printStackTrace();
\r
187 if (featureLinks.size() > 0)
\r
189 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
\r
191 viewport.showSequenceFeatures = true;
\r
192 sequenceFeatures.setState(true);
\r
193 if (viewport.featureSettings != null)
\r
195 viewport.featureSettings.refreshTable();
\r
197 alignPanel.paintAlignment(true);
\r
202 public void keyPressed(KeyEvent evt)
\r
204 if (viewport.cursorMode
\r
205 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
\r
206 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
\r
207 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
\r
208 && Character.isDigit(evt.getKeyChar()))
\r
209 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
\r
211 switch (evt.getKeyCode())
\r
213 case 27: // escape key
\r
214 deselectAllSequenceMenuItem_actionPerformed();
\r
216 alignPanel.alabels.cancelDrag();
\r
218 case KeyEvent.VK_X:
\r
219 if (evt.isControlDown() || evt.isMetaDown())
\r
221 cut_actionPerformed();
\r
224 case KeyEvent.VK_C:
\r
225 if (viewport.cursorMode && !evt.isControlDown())
\r
227 alignPanel.seqPanel.setCursorColumn();
\r
229 if (evt.isControlDown() || evt.isMetaDown())
\r
231 copy_actionPerformed();
\r
234 case KeyEvent.VK_V:
\r
235 if (evt.isControlDown())
\r
237 paste(evt.isShiftDown());
\r
240 case KeyEvent.VK_A:
\r
241 if (evt.isControlDown() || evt.isMetaDown())
\r
243 selectAllSequenceMenuItem_actionPerformed();
\r
246 case KeyEvent.VK_DOWN:
\r
247 if (viewport.cursorMode)
\r
249 alignPanel.seqPanel.moveCursor(0, 1);
\r
253 moveSelectedSequences(false);
\r
257 case KeyEvent.VK_UP:
\r
258 if (viewport.cursorMode)
\r
260 alignPanel.seqPanel.moveCursor(0, -1);
\r
264 moveSelectedSequences(true);
\r
268 case KeyEvent.VK_LEFT:
\r
269 if (evt.isAltDown() || !viewport.cursorMode)
\r
270 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
\r
272 alignPanel.seqPanel.moveCursor(-1, 0);
\r
275 case KeyEvent.VK_RIGHT:
\r
276 if (evt.isAltDown() || !viewport.cursorMode)
\r
277 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
\r
279 alignPanel.seqPanel.moveCursor(1, 0);
\r
282 case KeyEvent.VK_SPACE:
\r
283 if (viewport.cursorMode)
\r
285 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
\r
286 || evt.isShiftDown() || evt.isAltDown());
\r
290 case KeyEvent.VK_DELETE:
\r
291 case KeyEvent.VK_BACK_SPACE:
\r
292 if (viewport.cursorMode)
\r
294 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
\r
295 || evt.isShiftDown() || evt.isAltDown());
\r
299 cut_actionPerformed();
\r
300 alignPanel.seqPanel.seqCanvas.repaint();
\r
304 case KeyEvent.VK_S:
\r
305 if (viewport.cursorMode)
\r
307 alignPanel.seqPanel.setCursorRow();
\r
310 case KeyEvent.VK_P:
\r
311 if (viewport.cursorMode)
\r
313 alignPanel.seqPanel.setCursorPosition();
\r
317 case KeyEvent.VK_ENTER:
\r
318 case KeyEvent.VK_COMMA:
\r
319 if (viewport.cursorMode)
\r
321 alignPanel.seqPanel.setCursorRowAndColumn();
\r
325 case KeyEvent.VK_Q:
\r
326 if (viewport.cursorMode)
\r
328 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
\r
331 case KeyEvent.VK_M:
\r
332 if (viewport.cursorMode)
\r
334 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
\r
338 case KeyEvent.VK_F2:
\r
339 viewport.cursorMode = !viewport.cursorMode;
\r
340 statusBar.setText("Keyboard editing mode is "
\r
341 + (viewport.cursorMode ? "on" : "off"));
\r
342 if (viewport.cursorMode)
\r
344 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
\r
345 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
\r
349 case KeyEvent.VK_F:
\r
350 if (evt.isControlDown())
\r
352 findMenuItem_actionPerformed();
\r
356 case KeyEvent.VK_H:
\r
358 boolean toggleSeqs = !evt.isControlDown();
\r
359 boolean toggleCols = !evt.isShiftDown();
\r
360 toggleHiddenRegions(toggleSeqs, toggleCols);
\r
364 case KeyEvent.VK_PAGE_UP:
\r
365 if (viewport.wrapAlignment)
\r
367 alignPanel.scrollUp(true);
\r
371 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
\r
372 - viewport.endSeq + viewport.startSeq);
\r
376 case KeyEvent.VK_PAGE_DOWN:
\r
377 if (viewport.wrapAlignment)
\r
379 alignPanel.scrollUp(false);
\r
383 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
\r
384 + viewport.endSeq - viewport.startSeq);
\r
388 case KeyEvent.VK_Z:
\r
389 if (evt.isControlDown())
\r
391 undoMenuItem_actionPerformed();
\r
395 case KeyEvent.VK_Y:
\r
396 if (evt.isControlDown())
\r
398 redoMenuItem_actionPerformed();
\r
402 case KeyEvent.VK_L:
\r
403 if (evt.isControlDown())
\r
405 trimAlignment(true);
\r
409 case KeyEvent.VK_R:
\r
410 if (evt.isControlDown())
\r
412 trimAlignment(false);
\r
416 case KeyEvent.VK_E:
\r
417 if (evt.isControlDown())
\r
419 if (evt.isShiftDown())
\r
421 this.removeAllGapsMenuItem_actionPerformed();
\r
425 removeGappedColumnMenuItem_actionPerformed();
\r
429 case KeyEvent.VK_I:
\r
430 if (evt.isControlDown())
\r
432 if (evt.isAltDown())
\r
434 invertColSel_actionPerformed();
\r
438 invertSequenceMenuItem_actionPerformed();
\r
443 case KeyEvent.VK_U:
\r
444 if (evt.isControlDown())
\r
446 this.deleteGroups_actionPerformed();
\r
450 case KeyEvent.VK_T:
\r
451 if (evt.isControlDown())
\r
458 alignPanel.paintAlignment(true);
\r
462 * called by key handler and the hide all/show all menu items
\r
464 * @param toggleSeqs
\r
465 * @param toggleCols
\r
467 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
\r
469 boolean hide = false;
\r
470 SequenceGroup sg = viewport.getSelectionGroup();
\r
471 if (!toggleSeqs && !toggleCols)
\r
473 // Hide everything by the current selection - this is a hack - we do the
\r
474 // invert and then hide
\r
475 // first check that there will be visible columns after the invert.
\r
476 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
\r
477 .getSelected().size() > 0)
\r
478 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
\r
481 // now invert the sequence set, if required - empty selection implies
\r
482 // that no hiding is required.
\r
485 invertSequenceMenuItem_actionPerformed();
\r
486 sg = viewport.getSelectionGroup();
\r
490 viewport.expandColSelection(sg, true);
\r
491 // finally invert the column selection and get the new sequence
\r
492 // selection and indicate it should be hidden.
\r
493 invertColSel_actionPerformed();
\r
500 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
\r
503 viewport.hideAllSelectedSeqs();
\r
505 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
\r
507 viewport.showAllHiddenSeqs();
\r
513 if (viewport.colSel.getSelected().size() > 0)
\r
515 viewport.hideSelectedColumns();
\r
518 viewport.selectionGroup = sg;
\r
523 viewport.showAllHiddenColumns();
\r
528 public void keyReleased(KeyEvent evt)
\r
532 public void keyTyped(KeyEvent evt)
\r
536 public void itemStateChanged(ItemEvent evt)
\r
538 if (evt.getSource() == displayNonconservedMenuItem)
\r
540 displayNonconservedMenuItem_actionPerformed();
\r
542 else if (evt.getSource() == colourTextMenuItem)
\r
544 colourTextMenuItem_actionPerformed();
\r
546 else if (evt.getSource() == wrapMenuItem)
\r
548 wrapMenuItem_actionPerformed();
\r
550 else if (evt.getSource() == scaleAbove)
\r
552 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
554 else if (evt.getSource() == scaleLeft)
\r
556 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
558 else if (evt.getSource() == scaleRight)
\r
560 viewport.setScaleRightWrapped(scaleRight.getState());
\r
562 else if (evt.getSource() == seqLimits)
\r
564 seqLimits_itemStateChanged();
\r
566 else if (evt.getSource() == viewBoxesMenuItem)
\r
568 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
570 else if (evt.getSource() == viewTextMenuItem)
\r
572 viewport.setShowText(viewTextMenuItem.getState());
\r
574 else if (evt.getSource() == renderGapsMenuItem)
\r
576 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
578 else if (evt.getSource() == annotationPanelMenuItem)
\r
580 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
581 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
583 else if (evt.getSource() == sequenceFeatures)
\r
585 viewport.showSequenceFeatures(sequenceFeatures.getState());
\r
586 alignPanel.seqPanel.seqCanvas.repaint();
\r
588 else if (evt.getSource() == conservationMenuItem)
\r
590 conservationMenuItem_actionPerformed();
\r
592 else if (evt.getSource() == abovePIDThreshold)
\r
594 abovePIDThreshold_actionPerformed();
\r
596 else if (evt.getSource() == applyToAllGroups)
\r
598 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
600 else if (evt.getSource() == autoCalculate)
\r
602 viewport.autocalculateConsensus = autoCalculate.getState();
\r
604 else if (evt.getSource() == this.centreColumnLabelFlag)
\r
606 centreColumnLabelFlag_stateChanged();
\r
608 else if (evt.getSource() == this.followMouseOverFlag)
\r
610 mouseOverFlag_stateChanged();
\r
612 else if (evt.getSource() == showGroupConsensus)
\r
614 showGroupConsensus_actionPerformed();
\r
616 else if (evt.getSource() == showGroupConservation)
\r
618 showGroupConservation_actionPerformed();
\r
620 else if (evt.getSource() == showSequenceLogo)
\r
622 showSequenceLogo_actionPerformed();
\r
624 else if (evt.getSource() == showConsensusHistogram)
\r
626 showConsensusHistogram_actionPerformed();
\r
628 else if (evt.getSource() == applyAutoAnnotationSettings)
\r
630 applyAutoAnnotationSettings_actionPerformed();
\r
632 alignPanel.paintAlignment(true);
\r
635 private void mouseOverFlag_stateChanged()
\r
637 viewport.followHighlight = followMouseOverFlag.getState();
\r
638 // TODO: could kick the scrollTo mechanism to reset view for current
\r
642 private void centreColumnLabelFlag_stateChanged()
\r
644 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
\r
645 this.alignPanel.annotationPanel.repaint();
\r
648 public void actionPerformed(ActionEvent evt)
\r
650 Object source = evt.getSource();
\r
652 if (source == inputText)
\r
654 inputText_actionPerformed();
\r
656 else if (source == loadTree)
\r
658 loadTree_actionPerformed();
\r
660 else if (source == loadApplication)
\r
662 launchFullApplication();
\r
664 else if (source == loadAnnotations)
\r
668 else if (source == outputAnnotations)
\r
670 outputAnnotations(true);
\r
672 else if (source == outputFeatures)
\r
674 outputFeatures(true, "Jalview");
\r
676 else if (source == closeMenuItem)
\r
678 closeMenuItem_actionPerformed();
\r
680 else if (source == copy)
\r
682 copy_actionPerformed();
\r
684 else if (source == undoMenuItem)
\r
686 undoMenuItem_actionPerformed();
\r
688 else if (source == redoMenuItem)
\r
690 redoMenuItem_actionPerformed();
\r
692 else if (source == inputText)
\r
694 inputText_actionPerformed();
\r
696 else if (source == closeMenuItem)
\r
698 closeMenuItem_actionPerformed();
\r
700 else if (source == undoMenuItem)
\r
702 undoMenuItem_actionPerformed();
\r
704 else if (source == redoMenuItem)
\r
706 redoMenuItem_actionPerformed();
\r
708 else if (source == copy)
\r
710 copy_actionPerformed();
\r
712 else if (source == pasteNew)
\r
714 pasteNew_actionPerformed();
\r
716 else if (source == pasteThis)
\r
718 pasteThis_actionPerformed();
\r
720 else if (source == cut)
\r
722 cut_actionPerformed();
\r
724 else if (source == delete)
\r
726 delete_actionPerformed();
\r
728 else if (source == grpsFromSelection)
\r
730 makeGrpsFromSelection_actionPerformed();
\r
732 else if (source == deleteGroups)
\r
734 deleteGroups_actionPerformed();
\r
736 else if (source == selectAllSequenceMenuItem)
\r
738 selectAllSequenceMenuItem_actionPerformed();
\r
740 else if (source == deselectAllSequenceMenuItem)
\r
742 deselectAllSequenceMenuItem_actionPerformed();
\r
744 else if (source == invertSequenceMenuItem)
\r
746 invertSequenceMenuItem_actionPerformed();
\r
748 else if (source == invertColSel)
\r
750 viewport.invertColumnSelection();
\r
751 alignPanel.paintAlignment(true);
\r
753 else if (source == remove2LeftMenuItem)
\r
755 trimAlignment(true);
\r
757 else if (source == remove2RightMenuItem)
\r
759 trimAlignment(false);
\r
761 else if (source == removeGappedColumnMenuItem)
\r
763 removeGappedColumnMenuItem_actionPerformed();
\r
765 else if (source == removeAllGapsMenuItem)
\r
767 removeAllGapsMenuItem_actionPerformed();
\r
769 else if (source == findMenuItem)
\r
771 findMenuItem_actionPerformed();
\r
773 else if (source == font)
\r
775 new FontChooser(alignPanel);
\r
777 else if (source == newView)
\r
781 else if (source == showColumns)
\r
783 viewport.showAllHiddenColumns();
\r
784 alignPanel.paintAlignment(true);
\r
786 else if (source == showSeqs)
\r
788 viewport.showAllHiddenSeqs();
\r
789 alignPanel.paintAlignment(true);
\r
791 else if (source == hideColumns)
\r
793 viewport.hideSelectedColumns();
\r
794 alignPanel.paintAlignment(true);
\r
796 else if (source == hideSequences
\r
797 && viewport.getSelectionGroup() != null)
\r
799 viewport.hideAllSelectedSeqs();
\r
800 alignPanel.paintAlignment(true);
\r
802 else if (source == hideAllButSelection)
\r
804 toggleHiddenRegions(false, false);
\r
805 alignPanel.paintAlignment(true);
\r
807 else if (source == hideAllSelection)
\r
809 SequenceGroup sg = viewport.getSelectionGroup();
\r
810 viewport.expandColSelection(sg, false);
\r
811 viewport.hideAllSelectedSeqs();
\r
812 viewport.hideSelectedColumns();
\r
813 alignPanel.paintAlignment(true);
\r
815 else if (source == showAllHidden)
\r
817 viewport.showAllHiddenColumns();
\r
818 viewport.showAllHiddenSeqs();
\r
819 alignPanel.paintAlignment(true);
\r
821 else if (source == showGroupConsensus)
\r
823 showGroupConsensus_actionPerformed();
\r
825 else if (source == showGroupConservation)
\r
827 showGroupConservation_actionPerformed();
\r
829 else if (source == showSequenceLogo)
\r
831 showSequenceLogo_actionPerformed();
\r
833 else if (source == showConsensusHistogram)
\r
835 showConsensusHistogram_actionPerformed();
\r
837 else if (source == applyAutoAnnotationSettings)
\r
839 applyAutoAnnotationSettings_actionPerformed();
\r
841 else if (source == featureSettings)
\r
843 new FeatureSettings(alignPanel);
\r
845 else if (source == alProperties)
\r
847 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
848 viewport.alignment).formatAsString();
\r
849 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
850 cap.setText(contents.toString());
\r
851 Frame frame = new Frame();
\r
853 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
854 + getTitle(), 400, 250);
\r
856 else if (source == overviewMenuItem)
\r
858 overviewMenuItem_actionPerformed();
\r
860 else if (source == noColourmenuItem)
\r
862 changeColour(null);
\r
864 else if (source == clustalColour)
\r
866 abovePIDThreshold.setState(false);
\r
867 changeColour(new ClustalxColourScheme(
\r
868 viewport.alignment.getSequences(),
\r
869 viewport.alignment.getWidth()));
\r
871 else if (source == zappoColour)
\r
873 changeColour(new ZappoColourScheme());
\r
875 else if (source == taylorColour)
\r
877 changeColour(new TaylorColourScheme());
\r
879 else if (source == hydrophobicityColour)
\r
881 changeColour(new HydrophobicColourScheme());
\r
883 else if (source == helixColour)
\r
885 changeColour(new HelixColourScheme());
\r
887 else if (source == strandColour)
\r
889 changeColour(new StrandColourScheme());
\r
891 else if (source == turnColour)
\r
893 changeColour(new TurnColourScheme());
\r
895 else if (source == buriedColour)
\r
897 changeColour(new BuriedColourScheme());
\r
899 else if (source == nucleotideColour)
\r
901 changeColour(new NucleotideColourScheme());
\r
903 else if (source == modifyPID)
\r
905 modifyPID_actionPerformed();
\r
907 else if (source == modifyConservation)
\r
909 modifyConservation_actionPerformed();
\r
911 else if (source == userDefinedColour)
\r
913 new UserDefinedColours(alignPanel, null);
\r
915 else if (source == PIDColour)
\r
917 changeColour(new PIDColourScheme());
\r
919 else if (source == BLOSUM62Colour)
\r
921 changeColour(new Blosum62ColourScheme());
\r
923 else if (source == annotationColour)
\r
925 new AnnotationColourChooser(viewport, alignPanel);
\r
927 else if (source == sortPairwiseMenuItem)
\r
929 sortPairwiseMenuItem_actionPerformed();
\r
931 else if (source == sortIDMenuItem)
\r
933 sortIDMenuItem_actionPerformed();
\r
935 else if (source == sortLengthMenuItem)
\r
937 sortLengthMenuItem_actionPerformed();
\r
939 else if (source == sortGroupMenuItem)
\r
941 sortGroupMenuItem_actionPerformed();
\r
943 else if (source == removeRedundancyMenuItem)
\r
945 removeRedundancyMenuItem_actionPerformed();
\r
947 else if (source == pairwiseAlignmentMenuItem)
\r
949 pairwiseAlignmentMenuItem_actionPerformed();
\r
951 else if (source == PCAMenuItem)
\r
953 PCAMenuItem_actionPerformed();
\r
955 else if (source == averageDistanceTreeMenuItem)
\r
957 averageDistanceTreeMenuItem_actionPerformed();
\r
959 else if (source == neighbourTreeMenuItem)
\r
961 neighbourTreeMenuItem_actionPerformed();
\r
963 else if (source == njTreeBlosumMenuItem)
\r
965 njTreeBlosumMenuItem_actionPerformed();
\r
967 else if (source == avDistanceTreeBlosumMenuItem)
\r
969 avTreeBlosumMenuItem_actionPerformed();
\r
971 else if (source == documentation)
\r
973 documentation_actionPerformed();
\r
975 else if (source == about)
\r
977 about_actionPerformed();
\r
982 public void inputText_actionPerformed()
\r
984 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
985 Frame frame = new Frame();
\r
987 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
990 protected void outputText_actionPerformed(ActionEvent e)
\r
992 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
993 Frame frame = new Frame();
\r
995 jalview.bin.JalviewLite.addFrame(frame,
\r
996 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
997 cap.setText(new AppletFormatAdapter().formatSequences(
\r
998 e.getActionCommand(), viewport.getAlignment(),
\r
999 viewport.showJVSuffix));
\r
1002 public void loadAnnotations()
\r
1004 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1005 cap.setText("Paste your features / annotations file here.");
\r
1006 cap.setAnnotationImport();
\r
1007 Frame frame = new Frame();
\r
1009 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1013 public String outputAnnotations(boolean displayTextbox)
\r
1015 String annotation = new AnnotationFile().printAnnotations(
\r
1016 viewport.showAnnotation ? viewport.alignment
\r
1017 .getAlignmentAnnotation() : null, viewport.alignment
\r
1019 ((Alignment) viewport.alignment).alignmentProperties);
\r
1021 if (displayTextbox)
\r
1023 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1024 Frame frame = new Frame();
\r
1026 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1027 cap.setText(annotation);
\r
1030 return annotation;
\r
1033 private Hashtable getDisplayedFeatureCols()
\r
1035 if (alignPanel.getFeatureRenderer() != null)
\r
1037 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1038 Hashtable fcols = new Hashtable();
\r
1039 Enumeration en = viewport.featuresDisplayed.keys();
\r
1040 while (en.hasMoreElements())
\r
1042 Object col = en.nextElement();
\r
1043 fcols.put(col, fr.featureColours.get(col));
\r
1050 public String outputFeatures(boolean displayTextbox, String format)
\r
1053 if (format.equalsIgnoreCase("Jalview"))
\r
1055 features = new FeaturesFile().printJalviewFormat(
\r
1056 viewport.alignment.getSequencesArray(),
\r
1057 getDisplayedFeatureCols());
\r
1061 features = new FeaturesFile().printGFFFormat(
\r
1062 viewport.alignment.getSequencesArray(),
\r
1063 getDisplayedFeatureCols());
\r
1066 if (displayTextbox)
\r
1068 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1069 Frame frame = new Frame();
\r
1071 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1073 cap.setText(features);
\r
1079 void launchFullApplication()
\r
1081 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1083 url.append("?open="
\r
1084 + appendProtocol(viewport.applet.getParameter("file")));
\r
1086 if (viewport.applet.getParameter("features") != null)
\r
1088 url.append("&features=");
\r
1089 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1092 if (viewport.applet.getParameter("annotations") != null)
\r
1094 url.append("&annotations=");
\r
1095 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1098 if (viewport.applet.getParameter("jnetfile") != null)
\r
1100 url.append("&annotations=");
\r
1101 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1104 if (viewport.applet.getParameter("defaultColour") != null)
\r
1106 url.append("&colour="
\r
1107 + removeWhiteSpace(viewport.applet
\r
1108 .getParameter("defaultColour")));
\r
1111 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1113 url.append("&colour="
\r
1114 + removeWhiteSpace(viewport.applet
\r
1115 .getParameter("userDefinedColour")));
\r
1117 if (viewport.applet.getParameter("tree") != null)
\r
1119 url.append("&tree="
\r
1120 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1122 if (viewport.applet.getParameter("treeFile") != null)
\r
1124 url.append("&tree="
\r
1125 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1128 showURL(url.toString(), "FULL_APP");
\r
1131 String removeWhiteSpace(String colour)
\r
1133 StringBuffer sb = new StringBuffer();
\r
1134 for (int i = 0; i < colour.length(); i++)
\r
1136 if (Character.isWhitespace(colour.charAt(i)))
\r
1142 sb.append(colour.charAt(i));
\r
1146 return sb.toString();
\r
1149 String appendProtocol(String url)
\r
1154 url = URLEncoder.encode(url);
\r
1157 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1158 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1159 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1160 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1161 * ex.printStackTrace(); }
\r
1163 catch (java.net.MalformedURLException ex)
\r
1165 url = viewport.applet.getCodeBase() + url;
\r
1170 public void closeMenuItem_actionPerformed()
\r
1172 PaintRefresher.RemoveComponent(alignPanel);
\r
1173 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1174 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1176 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1182 alignPanel = null;
\r
1189 void updateEditMenuBar()
\r
1192 if (viewport.historyList.size() > 0)
\r
1194 undoMenuItem.setEnabled(true);
\r
1195 CommandI command = (CommandI) viewport.historyList.peek();
\r
1196 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1200 undoMenuItem.setEnabled(false);
\r
1201 undoMenuItem.setLabel("Undo");
\r
1204 if (viewport.redoList.size() > 0)
\r
1206 redoMenuItem.setEnabled(true);
\r
1208 CommandI command = (CommandI) viewport.redoList.peek();
\r
1209 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1213 redoMenuItem.setEnabled(false);
\r
1214 redoMenuItem.setLabel("Redo");
\r
1218 public void addHistoryItem(CommandI command)
\r
1220 if (command.getSize() > 0)
\r
1222 viewport.historyList.push(command);
\r
1223 viewport.redoList.removeAllElements();
\r
1224 updateEditMenuBar();
\r
1225 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1235 protected void undoMenuItem_actionPerformed()
\r
1237 if (viewport.historyList.size() < 1)
\r
1242 CommandI command = (CommandI) viewport.historyList.pop();
\r
1243 viewport.redoList.push(command);
\r
1244 command.undoCommand(null);
\r
1246 AlignViewport originalSource = getOriginatingSource(command);
\r
1248 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1249 updateEditMenuBar();
\r
1250 originalSource.firePropertyChange("alignment", null,
\r
1251 originalSource.alignment.getSequences());
\r
1260 protected void redoMenuItem_actionPerformed()
\r
1262 if (viewport.redoList.size() < 1)
\r
1267 CommandI command = (CommandI) viewport.redoList.pop();
\r
1268 viewport.historyList.push(command);
\r
1269 command.doCommand(null);
\r
1271 AlignViewport originalSource = getOriginatingSource(command);
\r
1272 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
\r
1274 updateEditMenuBar();
\r
1275 originalSource.firePropertyChange("alignment", null,
\r
1276 originalSource.alignment.getSequences());
\r
1279 AlignViewport getOriginatingSource(CommandI command)
\r
1281 AlignViewport originalSource = null;
\r
1282 // For sequence removal and addition, we need to fire
\r
1283 // the property change event FROM the viewport where the
\r
1284 // original alignment was altered
\r
1285 AlignmentI al = null;
\r
1286 if (command instanceof EditCommand)
\r
1288 EditCommand editCommand = (EditCommand) command;
\r
1289 al = editCommand.getAlignment();
\r
1290 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1291 .getSequenceSetId());
\r
1292 for (int i = 0; i < comps.size(); i++)
\r
1294 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1296 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
\r
1298 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1305 if (originalSource == null)
\r
1307 // The original view is closed, we must validate
\r
1308 // the current view against the closed view first
\r
1311 PaintRefresher.validateSequences(al, viewport.alignment);
\r
1314 originalSource = viewport;
\r
1317 return originalSource;
\r
1320 public void moveSelectedSequences(boolean up)
\r
1322 SequenceGroup sg = viewport.getSelectionGroup();
\r
1330 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
1332 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1333 if (!sg.getSequences(null).contains(seq))
\r
1338 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
1339 if (sg.getSequences(null).contains(temp))
\r
1344 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1345 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
1350 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
1352 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
1353 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
\r
1358 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
1359 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
\r
1364 viewport.alignment.getSequences().setElementAt(temp, i);
\r
1365 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
1369 alignPanel.paintAlignment(true);
\r
1372 synchronized void slideSequences(boolean right, int size)
\r
1374 Vector sg = new Vector();
\r
1375 if (viewport.cursorMode)
\r
1377 sg.addElement(viewport.alignment
\r
1378 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1380 else if (viewport.getSelectionGroup() != null
\r
1381 && viewport.getSelectionGroup().getSize() != viewport.alignment
\r
1384 sg = viewport.getSelectionGroup().getSequences(
\r
1385 viewport.hiddenRepSequences);
\r
1388 if (sg.size() < 1)
\r
1393 Vector invertGroup = new Vector();
\r
1395 for (int i = 0; i < viewport.alignment.getHeight(); i++)
\r
1397 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
\r
1398 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
\r
1401 SequenceI[] seqs1 = new SequenceI[sg.size()];
\r
1402 for (int i = 0; i < sg.size(); i++)
\r
1403 seqs1[i] = (SequenceI) sg.elementAt(i);
\r
1405 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
\r
1406 for (int i = 0; i < invertGroup.size(); i++)
\r
1407 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
\r
1409 SlideSequencesCommand ssc;
\r
1411 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1412 size, viewport.getGapCharacter());
\r
1414 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1415 size, viewport.getGapCharacter());
\r
1417 int groupAdjustment = 0;
\r
1418 if (ssc.getGapsInsertedBegin() && right)
\r
1420 if (viewport.cursorMode)
\r
1421 alignPanel.seqPanel.moveCursor(size, 0);
\r
1423 groupAdjustment = size;
\r
1425 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1427 if (viewport.cursorMode)
\r
1428 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1430 groupAdjustment = -size;
\r
1433 if (groupAdjustment != 0)
\r
1435 viewport.getSelectionGroup().setStartRes(
\r
1436 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1437 viewport.getSelectionGroup().setEndRes(
\r
1438 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1441 boolean appendHistoryItem = false;
\r
1442 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1443 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1445 appendHistoryItem = ssc
\r
1446 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1450 if (!appendHistoryItem)
\r
1451 addHistoryItem(ssc);
\r
1456 static StringBuffer copiedSequences;
\r
1458 static Vector copiedHiddenColumns;
\r
1460 protected void copy_actionPerformed()
\r
1462 if (viewport.getSelectionGroup() == null)
\r
1467 SequenceGroup sg = viewport.getSelectionGroup();
\r
1468 copiedSequences = new StringBuffer();
\r
1469 Hashtable orderedSeqs = new Hashtable();
\r
1470 for (int i = 0; i < sg.getSize(); i++)
\r
1472 SequenceI seq = sg.getSequenceAt(i);
\r
1473 int index = viewport.alignment.findIndex(seq);
\r
1474 orderedSeqs.put(index + "", seq);
\r
1477 int index = 0, startRes, endRes;
\r
1480 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
\r
1482 copiedHiddenColumns = new Vector();
\r
1483 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1484 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1487 int[] region = (int[]) viewport.getColumnSelection()
\r
1488 .getHiddenColumns().elementAt(i);
\r
1490 copiedHiddenColumns.addElement(new int[]
\r
1491 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1496 copiedHiddenColumns = null;
\r
1499 for (int i = 0; i < sg.getSize(); i++)
\r
1501 SequenceI seq = null;
\r
1503 while (seq == null)
\r
1505 if (orderedSeqs.containsKey(index + ""))
\r
1507 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1519 // Returns residue following index if gap
\r
1520 startRes = seq.findPosition(sg.getStartRes());
\r
1523 // Need to find the residue preceeding index if gap
\r
1526 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1528 ch = seq.getCharAt(j);
\r
1529 if (!jalview.util.Comparison.isGap((ch)))
\r
1537 endRes += seq.getStart() - 1;
\r
1540 copiedSequences.append(seq.getName()
\r
1546 + seq.getSequenceAsString(sg.getStartRes(),
\r
1547 sg.getEndRes() + 1) + "\n");
\r
1552 protected void pasteNew_actionPerformed()
\r
1557 protected void pasteThis_actionPerformed()
\r
1562 void paste(boolean newAlignment)
\r
1567 if (copiedSequences == null)
\r
1572 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1573 Vector seqs = new Vector();
\r
1574 while (st.hasMoreElements())
\r
1576 String name = st.nextToken();
\r
1577 int start = Integer.parseInt(st.nextToken());
\r
1578 int end = Integer.parseInt(st.nextToken());
\r
1579 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1581 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1582 for (int i = 0; i < seqs.size(); i++)
\r
1584 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1589 String newtitle = new String("Copied sequences");
\r
1590 if (getTitle().startsWith("Copied sequences"))
\r
1592 newtitle = getTitle();
\r
1596 newtitle = newtitle.concat("- from " + getTitle());
\r
1598 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1599 viewport.applet, newtitle, false);
\r
1600 if (copiedHiddenColumns != null)
\r
1602 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1604 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1605 af.viewport.hideColumns(region[0], region[1]);
\r
1609 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1614 addSequences(newSeqs);
\r
1617 } catch (Exception ex)
\r
1619 } // could be anything being pasted in here
\r
1623 void addSequences(SequenceI[] seqs)
\r
1625 for (int i = 0; i < seqs.length; i++)
\r
1627 viewport.alignment.addSequence(seqs[i]);
\r
1631 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1632 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
\r
1634 viewport.setEndSeq(viewport.alignment.getHeight());
\r
1635 viewport.alignment.getWidth();
\r
1636 viewport.firePropertyChange("alignment", null,
\r
1637 viewport.alignment.getSequences());
\r
1641 protected void cut_actionPerformed()
\r
1643 copy_actionPerformed();
\r
1644 delete_actionPerformed();
\r
1647 protected void delete_actionPerformed()
\r
1650 SequenceGroup sg = viewport.getSelectionGroup();
\r
1656 Vector seqs = new Vector();
\r
1658 for (int i = 0; i < sg.getSize(); i++)
\r
1660 seq = sg.getSequenceAt(i);
\r
1661 seqs.addElement(seq);
\r
1664 // If the cut affects all sequences, remove highlighted columns
\r
1665 if (sg.getSize() == viewport.alignment.getHeight())
\r
1667 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1668 sg.getEndRes() + 1);
\r
1671 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1672 for (int i = 0; i < seqs.size(); i++)
\r
1674 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1678 * //ADD HISTORY ITEM
\r
1680 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1681 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1682 viewport.alignment));
\r
1684 viewport.setSelectionGroup(null);
\r
1685 viewport.alignment.deleteGroup(sg);
\r
1687 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1690 if (viewport.getAlignment().getHeight() < 1)
\r
1692 this.setVisible(false);
\r
1694 viewport.sendSelection();
\r
1698 * group consensus toggled
\r
1701 protected void showGroupConsensus_actionPerformed()
\r
1703 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1704 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1709 * group conservation toggled.
\r
1711 protected void showGroupConservation_actionPerformed()
\r
1713 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1714 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1721 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1722 * .event.ActionEvent)
\r
1724 protected void showConsensusHistogram_actionPerformed()
\r
1726 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1727 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1733 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1734 * .event.ActionEvent)
\r
1736 protected void showSequenceLogo_actionPerformed()
\r
1738 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1739 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1742 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1744 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1747 protected void makeGrpsFromSelection_actionPerformed()
\r
1749 if (viewport.getSelectionGroup() != null)
\r
1751 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1752 viewport.getSequenceSelection(),
\r
1753 viewport.getAlignmentView(true).getSequenceStrings(
\r
1754 viewport.getGapCharacter()),
\r
1755 viewport.alignment.getGroups());
\r
1756 viewport.alignment.deleteAllGroups();
\r
1757 viewport.sequenceColours = null;
\r
1758 viewport.setSelectionGroup(null);
\r
1759 // set view properties for each group
\r
1760 for (int g = 0; g < gps.length; g++)
\r
1762 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1763 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1764 viewport.alignment.addGroup(gps[g]);
\r
1765 Color col = new Color((int) (Math.random() * 255),
\r
1766 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1767 col = col.brighter();
\r
1768 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
\r
1769 .hasMoreElements(); viewport.setSequenceColour(
\r
1770 (SequenceI) sq.nextElement(), col))
\r
1773 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1774 alignPanel.updateAnnotation();
\r
1775 alignPanel.paintAlignment(true);
\r
1779 protected void deleteGroups_actionPerformed()
\r
1781 viewport.alignment.deleteAllGroups();
\r
1782 viewport.sequenceColours = null;
\r
1783 viewport.setSelectionGroup(null);
\r
1785 alignPanel.paintAlignment(true);
\r
1788 public void selectAllSequenceMenuItem_actionPerformed()
\r
1790 SequenceGroup sg = new SequenceGroup();
\r
1791 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1793 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1795 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
1796 viewport.setSelectionGroup(sg);
\r
1797 alignPanel.paintAlignment(true);
\r
1798 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1799 viewport.sendSelection();
\r
1802 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1804 if (viewport.cursorMode)
\r
1806 alignPanel.seqPanel.keyboardNo1 = null;
\r
1807 alignPanel.seqPanel.keyboardNo2 = null;
\r
1809 viewport.setSelectionGroup(null);
\r
1810 viewport.getColumnSelection().clear();
\r
1811 viewport.setSelectionGroup(null);
\r
1812 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1813 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1814 alignPanel.paintAlignment(true);
\r
1815 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1816 viewport.sendSelection();
\r
1819 public void invertSequenceMenuItem_actionPerformed()
\r
1821 SequenceGroup sg = viewport.getSelectionGroup();
\r
1822 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1824 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1827 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1828 viewport.sendSelection();
\r
1831 public void invertColSel_actionPerformed()
\r
1833 viewport.invertColumnSelection();
\r
1834 alignPanel.paintAlignment(true);
\r
1835 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1836 viewport.sendSelection();
\r
1839 void trimAlignment(boolean trimLeft)
\r
1841 ColumnSelection colSel = viewport.getColumnSelection();
\r
1844 if (colSel.size() > 0)
\r
1848 column = colSel.getMin();
\r
1852 column = colSel.getMax();
\r
1856 if (viewport.getSelectionGroup() != null)
\r
1858 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1859 viewport.hiddenRepSequences);
\r
1863 seqs = viewport.alignment.getSequencesArray();
\r
1866 TrimRegionCommand trimRegion;
\r
1869 trimRegion = new TrimRegionCommand("Remove Left",
\r
1870 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1871 viewport.alignment, viewport.colSel,
\r
1872 viewport.selectionGroup);
\r
1873 viewport.setStartRes(0);
\r
1877 trimRegion = new TrimRegionCommand("Remove Right",
\r
1878 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1879 viewport.alignment, viewport.colSel,
\r
1880 viewport.selectionGroup);
\r
1883 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1885 addHistoryItem(trimRegion);
\r
1887 Vector groups = viewport.alignment.getGroups();
\r
1889 for (int i = 0; i < groups.size(); i++)
\r
1891 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1893 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
1894 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
1896 viewport.alignment.deleteGroup(sg);
\r
1900 viewport.firePropertyChange("alignment", null, viewport
\r
1901 .getAlignment().getSequences());
\r
1905 public void removeGappedColumnMenuItem_actionPerformed()
\r
1907 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1910 if (viewport.getSelectionGroup() != null)
\r
1912 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1913 viewport.hiddenRepSequences);
\r
1914 start = viewport.getSelectionGroup().getStartRes();
\r
1915 end = viewport.getSelectionGroup().getEndRes();
\r
1919 seqs = viewport.alignment.getSequencesArray();
\r
1922 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
1923 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
\r
1925 addHistoryItem(removeGapCols);
\r
1927 statusBar.setText("Removed " + removeGapCols.getSize()
\r
1928 + " empty columns.");
\r
1930 // This is to maintain viewport position on first residue
\r
1931 // of first sequence
\r
1932 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1933 int startRes = seq.findPosition(viewport.startRes);
\r
1934 // ShiftList shifts;
\r
1935 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
1936 // edit.alColumnChanges=shifts.getInverse();
\r
1937 // if (viewport.hasHiddenColumns)
\r
1938 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
1939 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1940 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1945 public void removeAllGapsMenuItem_actionPerformed()
\r
1947 int start = 0, end = viewport.alignment.getWidth() - 1;
\r
1950 if (viewport.getSelectionGroup() != null)
\r
1952 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1953 viewport.hiddenRepSequences);
\r
1954 start = viewport.getSelectionGroup().getStartRes();
\r
1955 end = viewport.getSelectionGroup().getEndRes();
\r
1959 seqs = viewport.alignment.getSequencesArray();
\r
1962 // This is to maintain viewport position on first residue
\r
1963 // of first sequence
\r
1964 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1965 int startRes = seq.findPosition(viewport.startRes);
\r
1967 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
1968 viewport.alignment));
\r
1970 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
1972 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1977 public void findMenuItem_actionPerformed()
\r
1979 new Finder(alignPanel);
\r
1983 * create a new view derived from the current view
\r
1985 * @param viewtitle
\r
1986 * @return frame for the new view
\r
1988 public AlignFrame newView(String viewtitle)
\r
1991 if (viewport.hasHiddenRows)
\r
1993 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
1994 .getFullAlignment().getSequencesArray());
\r
1998 newal = new Alignment(viewport.alignment.getSequencesArray());
\r
2001 if (viewport.alignment.getAlignmentAnnotation() != null)
\r
2003 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
\r
2005 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
\r
2007 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
\r
2012 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2014 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
\r
2015 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2016 PaintRefresher.Register(newaf.alignPanel,
\r
2017 newaf.alignPanel.av.getSequenceSetId());
\r
2019 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2020 newaf.alignPanel.av.getSequenceSetId());
\r
2021 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2022 newaf.alignPanel.av.getSequenceSetId());
\r
2024 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2025 .getSequenceSetId());
\r
2026 int viewSize = -1;
\r
2027 for (int i = 0; i < comps.size(); i++)
\r
2029 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2035 String title = new String(this.getTitle());
\r
2036 if (viewtitle != null)
\r
2038 title = viewtitle + " ( " + title + ")";
\r
2042 if (title.indexOf("(View") > -1)
\r
2044 title = title.substring(0, title.indexOf("(View"));
\r
2046 title += "(View " + viewSize + ")";
\r
2049 newaf.setTitle(title.toString());
\r
2051 newaf.viewport.historyList = viewport.historyList;
\r
2052 newaf.viewport.redoList = viewport.redoList;
\r
2058 * @return list of feature groups on the view
\r
2060 public String[] getFeatureGroups()
\r
2062 FeatureRenderer fr = null;
\r
2063 if (alignPanel != null
\r
2064 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2066 return fr.getGroups();
\r
2072 * get sequence feature groups that are hidden or shown
\r
2078 public String[] getFeatureGroupsOfState(boolean visible)
\r
2080 FeatureRenderer fr = null;
\r
2081 if (alignPanel != null
\r
2082 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2084 return fr.getGroups(visible);
\r
2090 * Change the display state for the given feature groups
\r
2093 * list of group strings
\r
2095 * visible or invisible
\r
2097 public void setFeatureGroupState(String[] groups, boolean state)
\r
2099 FeatureRenderer fr = null;
\r
2100 this.sequenceFeatures.setState(true);
\r
2101 viewport.showSequenceFeatures(true);
\r
2102 if (alignPanel != null
\r
2103 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2105 fr.setGroupState(groups, state);
\r
2106 alignPanel.seqPanel.seqCanvas.repaint();
\r
2107 if (alignPanel.overviewPanel != null)
\r
2109 alignPanel.overviewPanel.updateOverviewImage();
\r
2114 public void seqLimits_itemStateChanged()
\r
2116 viewport.setShowJVSuffix(seqLimits.getState());
\r
2117 alignPanel.fontChanged();
\r
2118 alignPanel.paintAlignment(true);
\r
2121 protected void colourTextMenuItem_actionPerformed()
\r
2123 viewport.setColourText(colourTextMenuItem.getState());
\r
2124 alignPanel.paintAlignment(true);
\r
2127 protected void displayNonconservedMenuItem_actionPerformed()
\r
2129 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2130 alignPanel.paintAlignment(true);
\r
2133 protected void wrapMenuItem_actionPerformed()
\r
2135 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2136 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2137 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2138 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2139 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2140 alignPanel.paintAlignment(true);
\r
2143 public void overviewMenuItem_actionPerformed()
\r
2145 if (alignPanel.overviewPanel != null)
\r
2150 Frame frame = new Frame();
\r
2151 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2152 frame.add(overview);
\r
2153 // +50 must allow for applet frame window
\r
2154 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2155 overview.getPreferredSize().width,
\r
2156 overview.getPreferredSize().height + 50);
\r
2159 frame.addWindowListener(new WindowAdapter()
\r
2161 public void windowClosing(WindowEvent e)
\r
2163 alignPanel.setOverviewPanel(null);
\r
2167 alignPanel.setOverviewPanel(overview);
\r
2171 void changeColour(ColourSchemeI cs)
\r
2173 int threshold = 0;
\r
2177 if (viewport.getAbovePIDThreshold())
\r
2179 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2182 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2184 viewport.setGlobalColourScheme(cs);
\r
2188 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2191 if (viewport.getConservationSelected())
\r
2194 Alignment al = (Alignment) viewport.alignment;
\r
2195 Conservation c = new Conservation("All",
\r
2196 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2197 al.getWidth() - 1);
\r
2200 c.verdict(false, viewport.ConsPercGaps);
\r
2202 cs.setConservation(c);
\r
2204 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2205 cs, "Background"));
\r
2210 cs.setConservation(null);
\r
2213 cs.setConsensus(viewport.hconsensus);
\r
2216 viewport.setGlobalColourScheme(cs);
\r
2218 if (viewport.getColourAppliesToAllGroups())
\r
2220 Vector groups = viewport.alignment.getGroups();
\r
2221 for (int i = 0; i < groups.size(); i++)
\r
2223 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
2230 if (cs instanceof ClustalxColourScheme)
\r
2232 sg.cs = new ClustalxColourScheme(
\r
2233 sg.getSequences(viewport.hiddenRepSequences),
\r
2240 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
2241 } catch (Exception ex)
\r
2243 ex.printStackTrace();
\r
2248 if (viewport.getAbovePIDThreshold()
\r
2249 || cs instanceof PIDColourScheme
\r
2250 || cs instanceof Blosum62ColourScheme)
\r
2252 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2253 sg.cs.setConsensus(AAFrequency.calculate(
\r
2254 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2259 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2262 if (viewport.getConservationSelected())
\r
2264 Conservation c = new Conservation("Group",
\r
2265 ResidueProperties.propHash, 3,
\r
2266 sg.getSequences(viewport.hiddenRepSequences), 0,
\r
2267 viewport.alignment.getWidth() - 1);
\r
2269 c.verdict(false, viewport.ConsPercGaps);
\r
2270 sg.cs.setConservation(c);
\r
2274 sg.cs.setConservation(null);
\r
2275 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2281 if (alignPanel.getOverviewPanel() != null)
\r
2283 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2286 jalview.structure.StructureSelectionManager
\r
2287 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2290 alignPanel.paintAlignment(true);
\r
2293 protected void modifyPID_actionPerformed()
\r
2295 if (viewport.getAbovePIDThreshold()
\r
2296 && viewport.globalColourScheme != null)
\r
2298 SliderPanel.setPIDSliderSource(alignPanel,
\r
2299 viewport.getGlobalColourScheme(), "Background");
\r
2300 SliderPanel.showPIDSlider();
\r
2304 protected void modifyConservation_actionPerformed()
\r
2306 if (viewport.getConservationSelected()
\r
2307 && viewport.globalColourScheme != null)
\r
2309 SliderPanel.setConservationSlider(alignPanel,
\r
2310 viewport.globalColourScheme, "Background");
\r
2311 SliderPanel.showConservationSlider();
\r
2315 protected void conservationMenuItem_actionPerformed()
\r
2317 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2319 viewport.setAbovePIDThreshold(false);
\r
2320 abovePIDThreshold.setState(false);
\r
2322 changeColour(viewport.getGlobalColourScheme());
\r
2324 modifyConservation_actionPerformed();
\r
2327 public void abovePIDThreshold_actionPerformed()
\r
2329 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2331 conservationMenuItem.setState(false);
\r
2332 viewport.setConservationSelected(false);
\r
2334 changeColour(viewport.getGlobalColourScheme());
\r
2336 modifyPID_actionPerformed();
\r
2339 public void sortPairwiseMenuItem_actionPerformed()
\r
2341 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2342 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2343 .getAlignment().getSequenceAt(0), null);
\r
2345 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2346 viewport.alignment));
\r
2347 alignPanel.paintAlignment(true);
\r
2350 public void sortIDMenuItem_actionPerformed()
\r
2352 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2353 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2354 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
\r
2355 alignPanel.paintAlignment(true);
\r
2358 public void sortLengthMenuItem_actionPerformed()
\r
2360 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2361 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2362 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2363 viewport.alignment));
\r
2364 alignPanel.paintAlignment(true);
\r
2367 public void sortGroupMenuItem_actionPerformed()
\r
2369 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2370 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2371 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2372 viewport.alignment));
\r
2373 alignPanel.paintAlignment(true);
\r
2377 public void removeRedundancyMenuItem_actionPerformed()
\r
2379 new RedundancyPanel(alignPanel);
\r
2382 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2384 if (viewport.getSelectionGroup() != null
\r
2385 && viewport.getSelectionGroup().getSize() > 1)
\r
2387 Frame frame = new Frame();
\r
2388 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2389 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2394 public void PCAMenuItem_actionPerformed()
\r
2396 // are the sequences aligned?
\r
2397 if (!viewport.alignment.isAligned(false))
\r
2399 SequenceI current;
\r
2400 int Width = viewport.getAlignment().getWidth();
\r
2402 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2404 current = viewport.getAlignment().getSequenceAt(i);
\r
2406 if (current.getLength() < Width)
\r
2408 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2411 alignPanel.paintAlignment(true);
\r
2414 if ((viewport.getSelectionGroup() != null
\r
2415 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2416 .getSelectionGroup().getSize() > 0)
\r
2417 || viewport.getAlignment().getHeight() < 4)
\r
2424 new PCAPanel(viewport);
\r
2425 } catch (java.lang.OutOfMemoryError ex)
\r
2431 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2433 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2436 public void neighbourTreeMenuItem_actionPerformed()
\r
2438 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2441 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2443 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2446 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2448 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2451 void NewTreePanel(String type, String pwType, String title)
\r
2453 // are the sequences aligned?
\r
2454 if (!viewport.alignment.isAligned(false))
\r
2456 SequenceI current;
\r
2457 int Width = viewport.getAlignment().getWidth();
\r
2459 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2461 current = viewport.getAlignment().getSequenceAt(i);
\r
2463 if (current.getLength() < Width)
\r
2465 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2468 alignPanel.paintAlignment(true);
\r
2472 if ((viewport.getSelectionGroup() != null && viewport
\r
2473 .getSelectionGroup().getSize() > 1)
\r
2474 || (viewport.getSelectionGroup() == null && viewport.alignment
\r
2475 .getHeight() > 1))
\r
2477 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2479 addTreeMenuItem(tp, title);
\r
2481 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2485 void loadTree_actionPerformed()
\r
2487 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2488 cap.setText("Paste your Newick tree file here.");
\r
2489 cap.setTreeImport();
\r
2490 Frame frame = new Frame();
\r
2492 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2495 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2497 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2498 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2499 addTreeMenuItem(tp, treeFile);
\r
2503 * sort the alignment using the given treePanel
\r
2505 * @param treePanel
\r
2506 * tree used to sort view
\r
2508 * string used for undo event name
\r
2510 public void sortByTree(TreePanel treePanel, String title)
\r
2512 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2514 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2515 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2516 // HistoryItem.SORT));
\r
2517 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2518 viewport.alignment));
\r
2519 alignPanel.paintAlignment(true);
\r
2523 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2524 * the menu structure for the new tree
\r
2526 * @param treePanel
\r
2529 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2530 final String title)
\r
2532 final MenuItem item = new MenuItem(title);
\r
2533 sortByTreeMenu.add(item);
\r
2534 item.addActionListener(new java.awt.event.ActionListener()
\r
2536 public void actionPerformed(ActionEvent evt)
\r
2538 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2542 treePanel.addWindowListener(new WindowAdapter()
\r
2544 public void windowOpened(WindowEvent e)
\r
2546 if (viewport.sortByTree)
\r
2548 sortByTree(treePanel, title);
\r
2550 super.windowOpened(e);
\r
2553 public void windowClosing(WindowEvent e)
\r
2555 sortByTreeMenu.remove(item);
\r
2559 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2561 SequenceI[] oldOrder = viewport.getAlignment()
\r
2562 .getSequencesArray();
\r
2563 if (viewport.applet.debug)
\r
2565 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2567 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2568 if (undoname!=null)
\r
2570 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
\r
2572 alignPanel.paintAlignment(true);
\r
2575 protected void documentation_actionPerformed()
\r
2577 showURL("http://www.jalview.org/help.html", "HELP");
\r
2580 protected void about_actionPerformed()
\r
2583 class AboutPanel extends Canvas
\r
2589 public AboutPanel(String version, String builddate)
\r
2591 this.version = version;
\r
2592 this.builddate = builddate;
\r
2595 public void paint(Graphics g)
\r
2597 g.setColor(Color.white);
\r
2598 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2599 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2600 FontMetrics fm = g.getFontMetrics();
\r
2601 int fh = fm.getHeight();
\r
2603 g.setColor(Color.black);
\r
2604 // TODO: update this text for each release or centrally store it for
\r
2605 // lite and application
\r
2606 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2607 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2608 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2609 g.drawString("Build date: " + builddate, x, y += fh);
\r
2610 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2612 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2613 x, y += fh * 1.5);
\r
2614 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2616 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2619 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2621 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2623 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2626 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2628 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2633 Frame frame = new Frame();
\r
2634 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2635 .getBuildDate()));
\r
2636 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2640 public void showURL(String url, String target)
\r
2642 if (viewport.applet == null)
\r
2644 System.out.println("Not running as applet - no browser available.");
\r
2650 if (url.indexOf(":") == -1)
\r
2652 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
\r
2654 // Should really use docbase, not codebase.
\r
2655 if (url.indexOf("/") == 0)
\r
2657 String codebase = viewport.applet.getCodeBase().toString();
\r
2658 url = codebase.substring(0, codebase.length()
\r
2659 - viewport.applet.getCodeBase().getFile().length())
\r
2664 url = viewport.applet.getCodeBase() + url;
\r
2666 System.out.println("Show url (prepended codebase): " + url);
\r
2670 System.out.println("Show url: " + url);
\r
2672 if (url.indexOf("javascript:") == 0)
\r
2674 // no target for the javascript context
\r
2675 viewport.applet.getAppletContext().showDocument(
\r
2676 new java.net.URL(url));
\r
2680 viewport.applet.getAppletContext().showDocument(
\r
2681 new java.net.URL(url), target);
\r
2683 } catch (Exception ex)
\r
2685 ex.printStackTrace();
\r
2690 // ////////////////////////////////////////////////////////////////////////////////
\r
2691 // JBuilder Graphics here
\r
2693 MenuBar alignFrameMenuBar = new MenuBar();
\r
2695 Menu fileMenu = new Menu("File");
\r
2697 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2699 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2701 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2703 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2705 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2707 MenuItem closeMenuItem = new MenuItem("Close");
\r
2709 Menu editMenu = new Menu("Edit");
\r
2711 Menu viewMenu = new Menu("View");
\r
2713 Menu colourMenu = new Menu("Colour");
\r
2715 Menu calculateMenu = new Menu("Calculate");
\r
2717 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2719 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2721 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2723 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2725 MenuItem remove2RightMenuItem = new MenuItem();
\r
2727 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2729 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2731 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2733 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2735 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2737 MenuItem sortIDMenuItem = new MenuItem();
\r
2739 MenuItem sortLengthMenuItem = new MenuItem();
\r
2741 MenuItem sortGroupMenuItem = new MenuItem();
\r
2743 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2745 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2747 MenuItem PCAMenuItem = new MenuItem();
\r
2749 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2751 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2753 BorderLayout borderLayout1 = new BorderLayout();
\r
2755 public Label statusBar = new Label();
\r
2757 Menu outputTextboxMenu = new Menu();
\r
2759 MenuItem clustalColour = new MenuItem();
\r
2761 MenuItem zappoColour = new MenuItem();
\r
2763 MenuItem taylorColour = new MenuItem();
\r
2765 MenuItem hydrophobicityColour = new MenuItem();
\r
2767 MenuItem helixColour = new MenuItem();
\r
2769 MenuItem strandColour = new MenuItem();
\r
2771 MenuItem turnColour = new MenuItem();
\r
2773 MenuItem buriedColour = new MenuItem();
\r
2775 MenuItem userDefinedColour = new MenuItem();
\r
2777 MenuItem PIDColour = new MenuItem();
\r
2779 MenuItem BLOSUM62Colour = new MenuItem();
\r
2781 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2783 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2785 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2787 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2789 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2791 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2793 MenuItem overviewMenuItem = new MenuItem();
\r
2795 MenuItem undoMenuItem = new MenuItem();
\r
2797 MenuItem redoMenuItem = new MenuItem();
\r
2799 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2801 MenuItem noColourmenuItem = new MenuItem();
\r
2803 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2805 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2807 MenuItem findMenuItem = new MenuItem();
\r
2809 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2811 MenuItem nucleotideColour = new MenuItem();
\r
2813 MenuItem deleteGroups = new MenuItem();
\r
2815 MenuItem grpsFromSelection = new MenuItem();
\r
2817 MenuItem delete = new MenuItem();
\r
2819 MenuItem copy = new MenuItem();
\r
2821 MenuItem cut = new MenuItem();
\r
2823 Menu pasteMenu = new Menu();
\r
2825 MenuItem pasteNew = new MenuItem();
\r
2827 MenuItem pasteThis = new MenuItem();
\r
2829 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2831 MenuItem font = new MenuItem();
\r
2833 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2835 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2837 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2839 MenuItem modifyPID = new MenuItem();
\r
2841 MenuItem modifyConservation = new MenuItem();
\r
2843 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2844 "Autocalculate Consensus", true);
\r
2846 Menu sortByTreeMenu = new Menu();
\r
2848 Menu sort = new Menu();
\r
2850 Menu calculate = new Menu();
\r
2852 MenuItem inputText = new MenuItem();
\r
2854 Menu helpMenu = new Menu();
\r
2856 MenuItem documentation = new MenuItem();
\r
2858 MenuItem about = new MenuItem();
\r
2860 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2862 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2864 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2865 Menu autoAnnMenu=new Menu();
\r
2866 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2867 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2868 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2869 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2870 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2872 private void jbInit() throws Exception
\r
2875 setMenuBar(alignFrameMenuBar);
\r
2879 // dynamically fill save as menu with available formats
\r
2880 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2883 item = new MenuItem(
\r
2884 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2886 item.addActionListener(new java.awt.event.ActionListener()
\r
2888 public void actionPerformed(ActionEvent e)
\r
2890 outputText_actionPerformed(e);
\r
2894 outputTextboxMenu.add(item);
\r
2896 closeMenuItem.addActionListener(this);
\r
2897 loadApplication.addActionListener(this);
\r
2899 loadTree.addActionListener(this);
\r
2900 loadAnnotations.addActionListener(this);
\r
2901 outputFeatures.addActionListener(this);
\r
2902 outputAnnotations.addActionListener(this);
\r
2903 selectAllSequenceMenuItem.addActionListener(this);
\r
2904 deselectAllSequenceMenuItem.addActionListener(this);
\r
2905 invertSequenceMenuItem.addActionListener(this);
\r
2906 remove2LeftMenuItem.setLabel("Remove Left");
\r
2907 remove2LeftMenuItem.addActionListener(this);
\r
2908 remove2RightMenuItem.setLabel("Remove Right");
\r
2909 remove2RightMenuItem.addActionListener(this);
\r
2910 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2911 removeGappedColumnMenuItem.addActionListener(this);
\r
2912 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2913 removeAllGapsMenuItem.addActionListener(this);
\r
2914 viewBoxesMenuItem.setLabel("Boxes");
\r
2915 viewBoxesMenuItem.setState(true);
\r
2916 viewBoxesMenuItem.addItemListener(this);
\r
2917 viewTextMenuItem.setLabel("Text");
\r
2918 viewTextMenuItem.setState(true);
\r
2919 viewTextMenuItem.addItemListener(this);
\r
2920 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2921 sortPairwiseMenuItem.addActionListener(this);
\r
2922 sortIDMenuItem.setLabel("by ID");
\r
2923 sortIDMenuItem.addActionListener(this);
\r
2924 sortLengthMenuItem.setLabel("by Length");
\r
2925 sortLengthMenuItem.addActionListener(this);
\r
2926 sortGroupMenuItem.setLabel("by Group");
\r
2927 sortGroupMenuItem.addActionListener(this);
\r
2928 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2929 removeRedundancyMenuItem.addActionListener(this);
\r
2930 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2931 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2932 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2933 PCAMenuItem.addActionListener(this);
\r
2934 averageDistanceTreeMenuItem
\r
2935 .setLabel("Average Distance Using % Identity");
\r
2936 averageDistanceTreeMenuItem.addActionListener(this);
\r
2937 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2938 neighbourTreeMenuItem.addActionListener(this);
\r
2939 statusBar.setBackground(Color.white);
\r
2940 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2941 statusBar.setText("Status bar");
\r
2942 outputTextboxMenu.setLabel("Output to Textbox");
\r
2943 clustalColour.setLabel("Clustalx");
\r
2945 clustalColour.addActionListener(this);
\r
2946 zappoColour.setLabel("Zappo");
\r
2947 zappoColour.addActionListener(this);
\r
2948 taylorColour.setLabel("Taylor");
\r
2949 taylorColour.addActionListener(this);
\r
2950 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2951 hydrophobicityColour.addActionListener(this);
\r
2952 helixColour.setLabel("Helix Propensity");
\r
2953 helixColour.addActionListener(this);
\r
2954 strandColour.setLabel("Strand Propensity");
\r
2955 strandColour.addActionListener(this);
\r
2956 turnColour.setLabel("Turn Propensity");
\r
2957 turnColour.addActionListener(this);
\r
2958 buriedColour.setLabel("Buried Index");
\r
2959 buriedColour.addActionListener(this);
\r
2960 userDefinedColour.setLabel("User Defined...");
\r
2961 userDefinedColour.addActionListener(this);
\r
2962 PIDColour.setLabel("Percentage Identity");
\r
2963 PIDColour.addActionListener(this);
\r
2964 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2965 BLOSUM62Colour.addActionListener(this);
\r
2966 avDistanceTreeBlosumMenuItem
\r
2967 .setLabel("Average Distance Using BLOSUM62");
\r
2968 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
2969 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
2970 njTreeBlosumMenuItem.addActionListener(this);
\r
2971 annotationPanelMenuItem.setLabel("Show Annotations");
\r
2972 annotationPanelMenuItem.addItemListener(this);
\r
2973 colourTextMenuItem.setLabel("Colour Text");
\r
2974 colourTextMenuItem.addItemListener(this);
\r
2975 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
2976 displayNonconservedMenuItem.addItemListener(this);
\r
2977 alProperties.addActionListener(this);
\r
2978 overviewMenuItem.setLabel("Overview Window");
\r
2979 overviewMenuItem.addActionListener(this);
\r
2980 undoMenuItem.setEnabled(false);
\r
2981 undoMenuItem.setLabel("Undo");
\r
2982 undoMenuItem.addActionListener(this);
\r
2983 redoMenuItem.setEnabled(false);
\r
2984 redoMenuItem.setLabel("Redo");
\r
2985 redoMenuItem.addActionListener(this);
\r
2986 conservationMenuItem.setLabel("by Conservation");
\r
2987 conservationMenuItem.addItemListener(this);
\r
2988 noColourmenuItem.setLabel("None");
\r
2989 noColourmenuItem.addActionListener(this);
\r
2990 wrapMenuItem.setLabel("Wrap");
\r
2991 wrapMenuItem.addItemListener(this);
\r
2992 renderGapsMenuItem.setLabel("Show Gaps");
\r
2993 renderGapsMenuItem.setState(true);
\r
2994 renderGapsMenuItem.addItemListener(this);
\r
2995 findMenuItem.setLabel("Find...");
\r
2996 findMenuItem.addActionListener(this);
\r
2997 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
2998 abovePIDThreshold.addItemListener(this);
\r
2999 nucleotideColour.setLabel("Nucleotide");
\r
3000 nucleotideColour.addActionListener(this);
\r
3001 deleteGroups.setLabel("Undefine Groups");
\r
3002 deleteGroups.addActionListener(this);
\r
3003 grpsFromSelection.setLabel("Make Groups for selection");
\r
3004 grpsFromSelection.addActionListener(this);
\r
3005 copy.setLabel("Copy");
\r
3006 copy.addActionListener(this);
\r
3007 cut.setLabel("Cut");
\r
3008 cut.addActionListener(this);
\r
3009 delete.setLabel("Delete");
\r
3010 delete.addActionListener(this);
\r
3011 pasteMenu.setLabel("Paste");
\r
3012 pasteNew.setLabel("To New Alignment");
\r
3013 pasteNew.addActionListener(this);
\r
3014 pasteThis.setLabel("Add To This Alignment");
\r
3015 pasteThis.addActionListener(this);
\r
3016 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3017 applyToAllGroups.setState(true);
\r
3018 applyToAllGroups.addItemListener(this);
\r
3019 font.setLabel("Font...");
\r
3020 font.addActionListener(this);
\r
3021 scaleAbove.setLabel("Scale Above");
\r
3022 scaleAbove.setState(true);
\r
3023 scaleAbove.setEnabled(false);
\r
3024 scaleAbove.addItemListener(this);
\r
3025 scaleLeft.setEnabled(false);
\r
3026 scaleLeft.setState(true);
\r
3027 scaleLeft.setLabel("Scale Left");
\r
3028 scaleLeft.addItemListener(this);
\r
3029 scaleRight.setEnabled(false);
\r
3030 scaleRight.setState(true);
\r
3031 scaleRight.setLabel("Scale Right");
\r
3032 scaleRight.addItemListener(this);
\r
3033 modifyPID.setLabel("Modify Identity Threshold...");
\r
3034 modifyPID.addActionListener(this);
\r
3035 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3036 modifyConservation.addActionListener(this);
\r
3037 sortByTreeMenu.setLabel("By Tree Order");
\r
3038 sort.setLabel("Sort");
\r
3039 calculate.setLabel("Calculate Tree");
\r
3040 autoCalculate.addItemListener(this);
\r
3041 inputText.setLabel("Input from textbox");
\r
3042 inputText.addActionListener(this);
\r
3043 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3044 centreColumnLabelFlag.addItemListener(this);
\r
3045 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3046 followMouseOverFlag.addItemListener(this);
\r
3047 helpMenu.setLabel("Help");
\r
3048 documentation.setLabel("Documentation");
\r
3049 documentation.addActionListener(this);
\r
3051 about.setLabel("About...");
\r
3052 about.addActionListener(this);
\r
3053 seqLimits.setState(true);
\r
3054 seqLimits.setLabel("Show Sequence Limits");
\r
3055 seqLimits.addItemListener(this);
\r
3056 featureSettings.setLabel("Feature Settings...");
\r
3057 featureSettings.addActionListener(this);
\r
3058 sequenceFeatures.setLabel("Sequence Features");
\r
3059 sequenceFeatures.addItemListener(this);
\r
3060 sequenceFeatures.setState(false);
\r
3061 annotationColour.setLabel("by Annotation...");
\r
3062 annotationColour.addActionListener(this);
\r
3063 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3064 invertColSel.setLabel("Invert Column Selection");
\r
3065 menu1.setLabel("Show");
\r
3066 showColumns.setLabel("All Columns ");
\r
3067 showSeqs.setLabel("All Sequences");
\r
3068 menu2.setLabel("Hide");
\r
3069 hideColumns.setLabel("Selected Columns");
\r
3070 hideSequences.setLabel("Selected Sequences");
\r
3071 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3072 hideAllSelection.setLabel("Selected Region");
\r
3073 showAllHidden.setLabel("All Sequences and Columns");
\r
3074 showGroupConsensus.setLabel("Group Consensus");
\r
3075 showGroupConservation.setLabel("Group Conservation");
\r
3076 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3077 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3078 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3079 applyAutoAnnotationSettings.setState(true);
\r
3080 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3082 invertColSel.addActionListener(this);
\r
3083 showColumns.addActionListener(this);
\r
3084 showSeqs.addActionListener(this);
\r
3085 hideColumns.addActionListener(this);
\r
3086 hideSequences.addActionListener(this);
\r
3087 hideAllButSelection.addActionListener(this);
\r
3088 hideAllSelection.addActionListener(this);
\r
3089 showAllHidden.addActionListener(this);
\r
3090 showGroupConsensus.addItemListener(this);
\r
3091 showGroupConservation.addItemListener(this);
\r
3092 showConsensusHistogram.addItemListener(this);
\r
3093 showSequenceLogo.addItemListener(this);
\r
3094 applyAutoAnnotationSettings.addItemListener(this);
\r
3095 formatMenu.setLabel("Format");
\r
3096 selectMenu.setLabel("Select");
\r
3097 newView.setLabel("New View");
\r
3098 newView.addActionListener(this);
\r
3099 alignFrameMenuBar.add(fileMenu);
\r
3100 alignFrameMenuBar.add(editMenu);
\r
3101 alignFrameMenuBar.add(selectMenu);
\r
3102 alignFrameMenuBar.add(viewMenu);
\r
3103 alignFrameMenuBar.add(formatMenu);
\r
3104 alignFrameMenuBar.add(colourMenu);
\r
3105 alignFrameMenuBar.add(calculateMenu);
\r
3106 alignFrameMenuBar.add(helpMenu);
\r
3108 fileMenu.add(inputText);
\r
3109 fileMenu.add(loadTree);
\r
3110 fileMenu.add(loadAnnotations);
\r
3112 fileMenu.addSeparator();
\r
3113 fileMenu.add(outputTextboxMenu);
\r
3114 fileMenu.add(outputFeatures);
\r
3115 fileMenu.add(outputAnnotations);
\r
3117 if (jalviewServletURL != null)
\r
3119 fileMenu.add(loadApplication);
\r
3122 fileMenu.addSeparator();
\r
3123 fileMenu.add(closeMenuItem);
\r
3125 editMenu.add(undoMenuItem);
\r
3126 editMenu.add(redoMenuItem);
\r
3127 editMenu.add(cut);
\r
3128 editMenu.add(copy);
\r
3129 editMenu.add(pasteMenu);
\r
3130 editMenu.add(delete);
\r
3131 editMenu.addSeparator();
\r
3132 editMenu.add(remove2LeftMenuItem);
\r
3133 editMenu.add(remove2RightMenuItem);
\r
3134 editMenu.add(removeGappedColumnMenuItem);
\r
3135 editMenu.add(removeAllGapsMenuItem);
\r
3136 editMenu.add(removeRedundancyMenuItem);
\r
3137 viewMenu.add(newView);
\r
3138 viewMenu.addSeparator();
\r
3139 viewMenu.add(menu1);
\r
3140 viewMenu.add(menu2);
\r
3141 viewMenu.addSeparator();
\r
3142 viewMenu.add(followMouseOverFlag);
\r
3143 viewMenu.add(annotationPanelMenuItem);
\r
3144 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3145 autoAnnMenu.add(showConsensusHistogram);
\r
3146 autoAnnMenu.add(showSequenceLogo);
\r
3147 autoAnnMenu.addSeparator();
\r
3148 autoAnnMenu.add(showGroupConservation);
\r
3149 autoAnnMenu.add(showGroupConsensus);
\r
3150 viewMenu.add(autoAnnMenu);
\r
3151 viewMenu.addSeparator();
\r
3152 viewMenu.add(sequenceFeatures);
\r
3153 viewMenu.add(featureSettings);
\r
3154 viewMenu.addSeparator();
\r
3155 viewMenu.add(alProperties);
\r
3156 viewMenu.addSeparator();
\r
3157 viewMenu.add(overviewMenuItem);
\r
3158 colourMenu.add(applyToAllGroups);
\r
3159 colourMenu.addSeparator();
\r
3160 colourMenu.add(noColourmenuItem);
\r
3161 colourMenu.add(clustalColour);
\r
3162 colourMenu.add(BLOSUM62Colour);
\r
3163 colourMenu.add(PIDColour);
\r
3164 colourMenu.add(zappoColour);
\r
3165 colourMenu.add(taylorColour);
\r
3166 colourMenu.add(hydrophobicityColour);
\r
3167 colourMenu.add(helixColour);
\r
3168 colourMenu.add(strandColour);
\r
3169 colourMenu.add(turnColour);
\r
3170 colourMenu.add(buriedColour);
\r
3171 colourMenu.add(nucleotideColour);
\r
3172 colourMenu.add(userDefinedColour);
\r
3173 colourMenu.addSeparator();
\r
3174 colourMenu.add(conservationMenuItem);
\r
3175 colourMenu.add(modifyConservation);
\r
3176 colourMenu.add(abovePIDThreshold);
\r
3177 colourMenu.add(modifyPID);
\r
3178 colourMenu.add(annotationColour);
\r
3179 calculateMenu.add(sort);
\r
3180 calculateMenu.add(calculate);
\r
3181 calculateMenu.addSeparator();
\r
3182 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3183 calculateMenu.add(PCAMenuItem);
\r
3184 calculateMenu.add(autoCalculate);
\r
3185 this.add(statusBar, BorderLayout.SOUTH);
\r
3186 pasteMenu.add(pasteNew);
\r
3187 pasteMenu.add(pasteThis);
\r
3188 sort.add(sortIDMenuItem);
\r
3189 sort.add(sortLengthMenuItem);
\r
3190 sort.add(sortByTreeMenu);
\r
3191 sort.add(sortGroupMenuItem);
\r
3192 sort.add(sortPairwiseMenuItem);
\r
3193 calculate.add(averageDistanceTreeMenuItem);
\r
3194 calculate.add(neighbourTreeMenuItem);
\r
3195 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3196 calculate.add(njTreeBlosumMenuItem);
\r
3197 helpMenu.add(documentation);
\r
3198 helpMenu.add(about);
\r
3199 menu1.add(showColumns);
\r
3200 menu1.add(showSeqs);
\r
3201 menu1.add(showAllHidden);
\r
3202 menu2.add(hideColumns);
\r
3203 menu2.add(hideSequences);
\r
3204 menu2.add(hideAllSelection);
\r
3205 menu2.add(hideAllButSelection);
\r
3206 formatMenu.add(font);
\r
3207 formatMenu.add(seqLimits);
\r
3208 formatMenu.add(wrapMenuItem);
\r
3209 formatMenu.add(scaleAbove);
\r
3210 formatMenu.add(scaleLeft);
\r
3211 formatMenu.add(scaleRight);
\r
3212 formatMenu.add(viewBoxesMenuItem);
\r
3213 formatMenu.add(viewTextMenuItem);
\r
3214 formatMenu.add(colourTextMenuItem);
\r
3215 formatMenu.add(displayNonconservedMenuItem);
\r
3216 formatMenu.add(renderGapsMenuItem);
\r
3217 formatMenu.add(centreColumnLabelFlag);
\r
3218 selectMenu.add(findMenuItem);
\r
3219 selectMenu.addSeparator();
\r
3220 selectMenu.add(selectAllSequenceMenuItem);
\r
3221 selectMenu.add(deselectAllSequenceMenuItem);
\r
3222 selectMenu.add(invertSequenceMenuItem);
\r
3223 selectMenu.add(invertColSel);
\r
3224 selectMenu.add(grpsFromSelection);
\r
3225 selectMenu.add(deleteGroups);
\r
3229 MenuItem featureSettings = new MenuItem();
\r
3231 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3233 MenuItem annotationColour = new MenuItem();
\r
3235 MenuItem invertColSel = new MenuItem();
\r
3237 Menu menu1 = new Menu();
\r
3239 MenuItem showColumns = new MenuItem();
\r
3241 MenuItem showSeqs = new MenuItem();
\r
3243 Menu menu2 = new Menu();
\r
3245 MenuItem hideColumns = new MenuItem();
\r
3247 MenuItem hideSequences = new MenuItem();
\r
3249 MenuItem hideAllButSelection = new MenuItem();
\r
3251 MenuItem hideAllSelection = new MenuItem();
\r
3253 MenuItem showAllHidden = new MenuItem();
\r
3255 Menu formatMenu = new Menu();
\r
3257 Menu selectMenu = new Menu();
\r
3259 MenuItem newView = new MenuItem();
\r
3262 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3263 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3264 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3266 * @param reallyEmbedded
\r
3267 * true to attach the view to the applet area on the page rather than
\r
3270 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3272 if (reallyEmbedded)
\r
3275 // Explicly build the embedded menu panel for the on-page applet
\r
3277 // view cannot be closed if its actually on the page
\r
3278 fileMenu.remove(closeMenuItem);
\r
3279 fileMenu.remove(3); // Remove Seperator
\r
3280 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3281 Font.PLAIN, 10, false); // use our own fonts.
\r
3282 // and actually add the components to the applet area
\r
3283 viewport.applet.setLayout(new BorderLayout());
\r
3284 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3285 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3286 alignPanel.setSize(viewport.applet.getSize().width,
\r
3287 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3288 - statusBar.HEIGHT);
\r
3289 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3290 final AlignFrame me = this;
\r
3291 viewport.applet.addFocusListener(new FocusListener()
\r
3295 public void focusLost(FocusEvent e)
\r
3297 if (me.viewport.applet.currentAlignFrame==me) {
\r
3298 me.viewport.applet.currentAlignFrame = null;
\r
3302 public void focusGained(FocusEvent e)
\r
3304 me.viewport.applet.currentAlignFrame = me;
\r
3307 viewport.applet.validate();
\r
3312 // test and embed menu bar if necessary.
\r
3314 if (embedMenuIfNeeded(alignPanel))
\r
3316 // adjust for status bar height too
\r
3317 alignPanel.setSize(getSize().width, getSize().height
\r
3318 - statusBar.HEIGHT);
\r
3320 add(statusBar, BorderLayout.SOUTH);
\r
3321 add(alignPanel, BorderLayout.CENTER);
\r
3322 // and register with the applet so it can pass external API calls to us
\r
3323 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3329 * create a new binding between structures in an existing jmol viewer instance
\r
3330 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3331 * this does not open a new Jmol window, or modify the display of the
\r
3332 * structures in the original jmol window. Note This method doesn't work
\r
3333 * without an additional javascript library to exchange messages between the
\r
3334 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3337 * JmolViewer instance
\r
3338 * @param sequenceIds
\r
3339 * - sequence Ids to search for associations
\r
3341 public SequenceStructureBinding addStructureViewInstance(
\r
3342 Object jmolviewer, String[] sequenceIds)
\r
3344 org.jmol.api.JmolViewer viewer = null;
\r
3347 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3348 } catch (ClassCastException ex)
\r
3350 System.err.println("Unsupported viewer object :"
\r
3351 + jmolviewer.getClass());
\r
3353 if (viewer == null)
\r
3355 System.err.println("Can't use this object as a structure viewer:"
\r
3356 + jmolviewer.getClass());
\r
3359 SequenceI[] seqs = null;
\r
3360 if (sequenceIds == null || sequenceIds.length == 0)
\r
3362 seqs = viewport.getAlignment().getSequencesArray();
\r
3366 Vector sqi = new Vector();
\r
3367 AlignmentI al = viewport.getAlignment();
\r
3368 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3370 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3373 sqi.addElement(sq);
\r
3376 if (sqi.size() > 0)
\r
3378 seqs = new SequenceI[sqi.size()];
\r
3379 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3381 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3389 ExtJmol jmv = null;
\r
3390 // TODO: search for a jmv that involves viewer
\r
3392 { // create a new viewer/jalview binding.
\r
3393 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3399 * bind a pdb file to a sequence in the current view
\r
3401 * @param sequenceId
\r
3402 * - sequenceId within the dataset.
\r
3403 * @param pdbEntryString
\r
3404 * - the short name for the PDB file
\r
3406 * - pdb file - either a URL or a valid PDB file.
\r
3407 * @return true if binding was as success TODO: consider making an exception
\r
3408 * structure for indicating when PDB parsing or sequenceId location
\r
3411 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3414 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3415 boolean needtoadd = false;
\r
3416 if (toaddpdb != null)
\r
3418 Vector pdbe = toaddpdb.getPDBId();
\r
3419 PDBEntry pdbentry = null;
\r
3420 if (pdbe != null && pdbe.size() > 0)
\r
3422 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3424 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3425 if (!pdbentry.getId().equals(pdbEntryString)
\r
3426 && !pdbentry.getFile().equals(pdbFile))
\r
3436 if (pdbentry == null)
\r
3438 pdbentry = new PDBEntry();
\r
3439 pdbentry.setId(pdbEntryString);
\r
3440 pdbentry.setFile(pdbFile);
\r
3441 needtoadd = true; // add this new entry to sequence.
\r
3443 // resolve data source
\r
3444 // TODO: this code should be a refactored to an io package
\r
3445 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3446 if (protocol == null)
\r
3452 // make a note of the access mode and add
\r
3453 if (pdbentry.getProperty() == null)
\r
3455 pdbentry.setProperty(new Hashtable());
\r
3457 pdbentry.getProperty().put("protocol", protocol);
\r
3458 toaddpdb.addPDBId(pdbentry);
\r
3464 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3468 Vector sequences = new Vector();
\r
3469 for (int i = 0; i < seqs.length; i++)
\r
3471 if (seqs[i] != null)
\r
3473 sequences.addElement(new Object[]
\r
3474 { seqs[i], (chains != null) ? chains[i] : null });
\r
3477 seqs = new SequenceI[sequences.size()];
\r
3478 chains = new String[sequences.size()];
\r
3479 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3481 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3483 seqs[i] = (SequenceI) oj[0];
\r
3484 chains[i] = (String) oj[1];
\r
3487 return new Object[]
\r
3492 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3493 SequenceI[] seqs, String[] chains, String protocol)
\r
3495 // Scrub any null sequences from the array
\r
3496 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3497 seqs = (SequenceI[]) sqch[0];
\r
3498 chains = (String[]) sqch[1];
\r
3499 if (seqs == null || seqs.length == 0)
\r
3502 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3504 if (protocol == null || protocol.trim().length() == 0
\r
3505 || protocol.equals("null"))
\r
3507 protocol = (String) pdb.getProperty().get("protocol");
\r
3508 if (protocol == null)
\r
3510 System.err.println("Couldn't work out protocol to open structure: "
\r
3515 if (applet.useXtrnalSviewer)
\r
3517 // register the association(s) and quit, don't create any windows.
\r
3518 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3519 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3523 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3525 // can only do alignments with Jmol
\r
3526 // find the last jmol window assigned to this alignment
\r
3527 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3528 Vector jmols = applet
\r
3529 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3530 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3532 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3533 if (tajm.ap.alignFrame == this)
\r
3542 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3543 // try and add the pdb structure
\r
3548 // otherwise, create a new window
\r
3549 if (applet.jmolAvailable)
\r
3551 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3553 applet.lastFrameX += 40;
\r
3554 applet.lastFrameY += 40;
\r
3558 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3563 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3564 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3566 // TODO Auto-generated method stub
\r
3567 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3571 * modify the current selection, providing the user has not made a selection already.
\r
3572 * @param sel - sequences from this alignment
\r
3573 * @param csel - columns to be selected on the alignment
\r
3575 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3577 alignPanel.seqPanel.selection(sel, csel, null);
\r
3580 public void scrollTo(int row, int column)
\r
3582 alignPanel.seqPanel.scrollTo(row, column);
\r