2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
20 import jalview.analysis.AAFrequency;
\r
21 import jalview.analysis.AlignmentSorter;
\r
22 import jalview.analysis.Conservation;
\r
23 import jalview.api.SequenceStructureBinding;
\r
24 import jalview.bin.JalviewLite;
\r
25 import jalview.commands.CommandI;
\r
26 import jalview.commands.EditCommand;
\r
27 import jalview.commands.OrderCommand;
\r
28 import jalview.commands.RemoveGapColCommand;
\r
29 import jalview.commands.RemoveGapsCommand;
\r
30 import jalview.commands.SlideSequencesCommand;
\r
31 import jalview.commands.TrimRegionCommand;
\r
32 import jalview.datamodel.Alignment;
\r
33 import jalview.datamodel.AlignmentI;
\r
34 import jalview.datamodel.AlignmentOrder;
\r
35 import jalview.datamodel.ColumnSelection;
\r
36 import jalview.datamodel.PDBEntry;
\r
37 import jalview.datamodel.Sequence;
\r
38 import jalview.datamodel.SequenceCollectionI;
\r
39 import jalview.datamodel.SequenceGroup;
\r
40 import jalview.datamodel.SequenceI;
\r
41 import jalview.io.AnnotationFile;
\r
42 import jalview.io.AppletFormatAdapter;
\r
43 import jalview.io.FeaturesFile;
\r
44 import jalview.io.TCoffeeScoreFile;
\r
45 import jalview.schemes.Blosum62ColourScheme;
\r
46 import jalview.schemes.BuriedColourScheme;
\r
47 import jalview.schemes.ClustalxColourScheme;
\r
48 import jalview.schemes.ColourSchemeI;
\r
49 import jalview.schemes.HelixColourScheme;
\r
50 import jalview.schemes.HydrophobicColourScheme;
\r
51 import jalview.schemes.NucleotideColourScheme;
\r
52 import jalview.schemes.PIDColourScheme;
\r
53 import jalview.schemes.PurinePyrimidineColourScheme;
\r
54 import jalview.schemes.RNAHelicesColourChooser;
\r
55 import jalview.schemes.ResidueProperties;
\r
56 import jalview.schemes.StrandColourScheme;
\r
57 import jalview.schemes.TCoffeeColourScheme;
\r
58 import jalview.schemes.TaylorColourScheme;
\r
59 import jalview.schemes.TurnColourScheme;
\r
60 import jalview.schemes.ZappoColourScheme;
\r
61 import jalview.structure.StructureSelectionManager;
\r
63 import java.awt.BorderLayout;
\r
64 import java.awt.Canvas;
\r
65 import java.awt.CheckboxMenuItem;
\r
66 import java.awt.Color;
\r
67 import java.awt.Font;
\r
68 import java.awt.FontMetrics;
\r
69 import java.awt.Frame;
\r
70 import java.awt.Graphics;
\r
71 import java.awt.Label;
\r
72 import java.awt.Menu;
\r
73 import java.awt.MenuBar;
\r
74 import java.awt.MenuItem;
\r
75 import java.awt.event.ActionEvent;
\r
76 import java.awt.event.ActionListener;
\r
77 import java.awt.event.FocusEvent;
\r
78 import java.awt.event.FocusListener;
\r
79 import java.awt.event.ItemEvent;
\r
80 import java.awt.event.ItemListener;
\r
81 import java.awt.event.KeyEvent;
\r
82 import java.awt.event.KeyListener;
\r
83 import java.awt.event.WindowAdapter;
\r
84 import java.awt.event.WindowEvent;
\r
85 import java.io.IOException;
\r
86 import java.io.InputStreamReader;
\r
87 import java.net.URL;
\r
88 import java.net.URLEncoder;
\r
89 import java.util.Enumeration;
\r
90 import java.util.Hashtable;
\r
91 import java.util.List;
\r
92 import java.util.StringTokenizer;
\r
93 import java.util.Vector;
\r
95 public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener
\r
97 public AlignmentPanel alignPanel;
\r
99 public AlignViewport viewport;
\r
101 int DEFAULT_WIDTH = 700;
\r
103 int DEFAULT_HEIGHT = 500;
\r
105 String jalviewServletURL;
\r
108 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
\r
110 if (applet != null)
\r
112 jalviewServletURL = applet.getParameter("APPLICATION_URL");
\r
118 } catch (Exception ex)
\r
120 ex.printStackTrace();
\r
123 viewport = new AlignViewport(al, applet);
\r
124 alignPanel = new AlignmentPanel(this, viewport);
\r
126 viewport.updateConservation(alignPanel);
\r
127 viewport.updateConsensus(alignPanel);
\r
129 annotationPanelMenuItem.setState(viewport.showAnnotation);
\r
130 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
\r
131 followMouseOverFlag.setState(viewport.getFollowHighlight());
\r
132 showGroupConsensus.setState(viewport.isShowGroupConsensus());
\r
133 showGroupConservation.setState(viewport.isShowGroupConservation());
\r
134 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
\r
135 showSequenceLogo.setState(viewport.isShowSequenceLogo());
\r
136 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
\r
138 seqLimits.setState(viewport.showJVSuffix);
\r
140 if (applet != null)
\r
142 String param = applet.getParameter("sortBy");
\r
145 if (param.equalsIgnoreCase("Id"))
\r
147 sortIDMenuItem_actionPerformed();
\r
149 else if (param.equalsIgnoreCase("Pairwise Identity"))
\r
151 sortPairwiseMenuItem_actionPerformed();
\r
153 else if (param.equalsIgnoreCase("Length"))
\r
155 sortLengthMenuItem_actionPerformed();
\r
159 param = applet.getParameter("wrap");
\r
162 if (param.equalsIgnoreCase("true"))
\r
164 wrapMenuItem.setState(true);
\r
165 wrapMenuItem_actionPerformed();
\r
168 param = applet.getParameter("centrecolumnlabels");
\r
171 centreColumnLabelFlag.setState(true);
\r
172 centreColumnLabelFlag_stateChanged();
\r
176 param = applet.getParameter("windowWidth");
\r
179 int width = Integer.parseInt(param);
\r
180 DEFAULT_WIDTH = width;
\r
182 param = applet.getParameter("windowHeight");
\r
185 int height = Integer.parseInt(param);
\r
186 DEFAULT_HEIGHT = height;
\r
188 } catch (Exception ex)
\r
193 if (viewport.getAlignment().isNucleotide())
\r
195 viewport.updateStrucConsensus(alignPanel);
\r
196 if (viewport.getAlignment().hasRNAStructure())
\r
198 RNAHelixColour.setEnabled(true);
\r
201 RNAHelixColour.setEnabled(false);
\r
204 RNAHelixColour.setEnabled(false);
\r
205 purinePyrimidineColour.setEnabled(false);
\r
207 // Some JVMS send keyevents to Top frame or lowest panel,
\r
208 // Havent worked out why yet. So add to both this frame and seqCanvas for
\r
210 this.addKeyListener(this);
\r
211 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
\r
212 alignPanel.idPanel.idCanvas.addKeyListener(this);
\r
213 alignPanel.scalePanel.addKeyListener(this);
\r
214 alignPanel.annotationPanel.addKeyListener(this);
\r
215 alignPanel.annotationPanelHolder.addKeyListener(this);
\r
216 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
\r
217 alignPanel.alabels.addKeyListener(this);
\r
218 createAlignFrameWindow(embedded, title);
\r
221 alignPanel.adjustAnnotationHeight();
\r
222 alignPanel.paintAlignment(true);
\r
225 public AlignViewport getAlignViewport()
\r
230 public SeqCanvas getSeqcanvas()
\r
232 return alignPanel.seqPanel.seqCanvas;
\r
236 * Load a features file onto the alignment
\r
238 * @param file file URL, content, or other resolvable path
\r
239 * @param type is protocol for accessing data referred to by file
\r
242 public boolean parseFeaturesFile(String file, String type)
\r
244 return parseFeaturesFile(file, type, true);
\r
248 * Load a features file onto the alignment
\r
250 * @param file file URL, content, or other resolvable path
\r
251 * @param type is protocol for accessing data referred to by file
\r
252 * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
\r
253 * @return true if data parsed as a features file
\r
255 public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)
\r
257 // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.
\r
259 Hashtable featureLinks = new Hashtable();
\r
260 boolean featuresFile = false;
\r
263 featuresFile = new jalview.io.FeaturesFile(file, type)
\r
264 .parse(viewport.getAlignment(),
\r
265 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
\r
266 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
\r
267 } catch (Exception ex)
\r
269 ex.printStackTrace();
\r
274 if (featureLinks.size() > 0)
\r
276 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
\r
278 if (autoenabledisplay)
\r
280 viewport.showSequenceFeatures = true;
\r
281 sequenceFeatures.setState(true);
\r
283 if (viewport.featureSettings != null)
\r
285 viewport.featureSettings.refreshTable();
\r
287 alignPanel.paintAlignment(true);
\r
288 statusBar.setText("Successfully added features to alignment.");
\r
290 return featuresFile;
\r
294 public void keyPressed(KeyEvent evt)
\r
296 if (viewport.cursorMode
\r
297 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
\r
298 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
\r
299 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
\r
300 && Character.isDigit(evt.getKeyChar()))
\r
301 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
\r
303 switch (evt.getKeyCode())
\r
305 case 27: // escape key
\r
306 deselectAllSequenceMenuItem_actionPerformed();
\r
308 alignPanel.alabels.cancelDrag();
\r
310 case KeyEvent.VK_X:
\r
311 if (evt.isControlDown() || evt.isMetaDown())
\r
313 cut_actionPerformed();
\r
316 case KeyEvent.VK_C:
\r
317 if (viewport.cursorMode && !evt.isControlDown())
\r
319 alignPanel.seqPanel.setCursorColumn();
\r
321 if (evt.isControlDown() || evt.isMetaDown())
\r
323 copy_actionPerformed();
\r
326 case KeyEvent.VK_V:
\r
327 if (evt.isControlDown())
\r
329 paste(evt.isShiftDown());
\r
332 case KeyEvent.VK_A:
\r
333 if (evt.isControlDown() || evt.isMetaDown())
\r
335 selectAllSequenceMenuItem_actionPerformed();
\r
338 case KeyEvent.VK_DOWN:
\r
339 if (viewport.cursorMode)
\r
341 alignPanel.seqPanel.moveCursor(0, 1);
\r
345 moveSelectedSequences(false);
\r
349 case KeyEvent.VK_UP:
\r
350 if (viewport.cursorMode)
\r
352 alignPanel.seqPanel.moveCursor(0, -1);
\r
356 moveSelectedSequences(true);
\r
360 case KeyEvent.VK_LEFT:
\r
361 if (evt.isAltDown() || !viewport.cursorMode)
\r
362 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
\r
364 alignPanel.seqPanel.moveCursor(-1, 0);
\r
367 case KeyEvent.VK_RIGHT:
\r
368 if (evt.isAltDown() || !viewport.cursorMode)
\r
369 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
\r
371 alignPanel.seqPanel.moveCursor(1, 0);
\r
374 case KeyEvent.VK_SPACE:
\r
375 if (viewport.cursorMode)
\r
377 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
\r
378 || evt.isShiftDown() || evt.isAltDown());
\r
382 case KeyEvent.VK_DELETE:
\r
383 case KeyEvent.VK_BACK_SPACE:
\r
384 if (viewport.cursorMode)
\r
386 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
\r
387 || evt.isShiftDown() || evt.isAltDown());
\r
391 cut_actionPerformed();
\r
392 alignPanel.seqPanel.seqCanvas.repaint();
\r
396 case KeyEvent.VK_S:
\r
397 if (viewport.cursorMode)
\r
399 alignPanel.seqPanel.setCursorRow();
\r
402 case KeyEvent.VK_P:
\r
403 if (viewport.cursorMode)
\r
405 alignPanel.seqPanel.setCursorPosition();
\r
409 case KeyEvent.VK_ENTER:
\r
410 case KeyEvent.VK_COMMA:
\r
411 if (viewport.cursorMode)
\r
413 alignPanel.seqPanel.setCursorRowAndColumn();
\r
417 case KeyEvent.VK_Q:
\r
418 if (viewport.cursorMode)
\r
420 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
\r
423 case KeyEvent.VK_M:
\r
424 if (viewport.cursorMode)
\r
426 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
\r
430 case KeyEvent.VK_F2:
\r
431 viewport.cursorMode = !viewport.cursorMode;
\r
432 statusBar.setText("Keyboard editing mode is "
\r
433 + (viewport.cursorMode ? "on" : "off"));
\r
434 if (viewport.cursorMode)
\r
436 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
\r
437 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
\r
441 case KeyEvent.VK_F:
\r
442 if (evt.isControlDown())
\r
444 findMenuItem_actionPerformed();
\r
448 case KeyEvent.VK_H:
\r
450 boolean toggleSeqs = !evt.isControlDown();
\r
451 boolean toggleCols = !evt.isShiftDown();
\r
452 toggleHiddenRegions(toggleSeqs, toggleCols);
\r
456 case KeyEvent.VK_PAGE_UP:
\r
457 if (viewport.wrapAlignment)
\r
459 alignPanel.scrollUp(true);
\r
463 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
\r
464 - viewport.endSeq + viewport.startSeq);
\r
468 case KeyEvent.VK_PAGE_DOWN:
\r
469 if (viewport.wrapAlignment)
\r
471 alignPanel.scrollUp(false);
\r
475 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
\r
476 + viewport.endSeq - viewport.startSeq);
\r
480 case KeyEvent.VK_Z:
\r
481 if (evt.isControlDown())
\r
483 undoMenuItem_actionPerformed();
\r
487 case KeyEvent.VK_Y:
\r
488 if (evt.isControlDown())
\r
490 redoMenuItem_actionPerformed();
\r
494 case KeyEvent.VK_L:
\r
495 if (evt.isControlDown())
\r
497 trimAlignment(true);
\r
501 case KeyEvent.VK_R:
\r
502 if (evt.isControlDown())
\r
504 trimAlignment(false);
\r
508 case KeyEvent.VK_E:
\r
509 if (evt.isControlDown())
\r
511 if (evt.isShiftDown())
\r
513 this.removeAllGapsMenuItem_actionPerformed();
\r
517 removeGappedColumnMenuItem_actionPerformed();
\r
521 case KeyEvent.VK_I:
\r
522 if (evt.isControlDown())
\r
524 if (evt.isAltDown())
\r
526 invertColSel_actionPerformed();
\r
530 invertSequenceMenuItem_actionPerformed();
\r
535 case KeyEvent.VK_U:
\r
536 if (evt.isControlDown())
\r
538 this.deleteGroups_actionPerformed();
\r
542 case KeyEvent.VK_T:
\r
543 if (evt.isControlDown())
\r
550 alignPanel.paintAlignment(true);
\r
554 * called by key handler and the hide all/show all menu items
\r
556 * @param toggleSeqs
\r
557 * @param toggleCols
\r
559 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
\r
561 boolean hide = false;
\r
562 SequenceGroup sg = viewport.getSelectionGroup();
\r
563 if (!toggleSeqs && !toggleCols)
\r
565 // Hide everything by the current selection - this is a hack - we do the
\r
566 // invert and then hide
\r
567 // first check that there will be visible columns after the invert.
\r
568 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
\r
569 .getSelected().size() > 0)
\r
570 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
\r
573 // now invert the sequence set, if required - empty selection implies
\r
574 // that no hiding is required.
\r
577 invertSequenceMenuItem_actionPerformed();
\r
578 sg = viewport.getSelectionGroup();
\r
582 viewport.expandColSelection(sg, true);
\r
583 // finally invert the column selection and get the new sequence
\r
584 // selection and indicate it should be hidden.
\r
585 invertColSel_actionPerformed();
\r
592 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
\r
595 viewport.hideAllSelectedSeqs();
\r
597 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
\r
599 viewport.showAllHiddenSeqs();
\r
605 if (viewport.getColumnSelection().getSelected().size() > 0)
\r
607 viewport.hideSelectedColumns();
\r
610 viewport.setSelectionGroup(sg);
\r
615 viewport.showAllHiddenColumns();
\r
621 public void keyReleased(KeyEvent evt)
\r
626 public void keyTyped(KeyEvent evt)
\r
631 public void itemStateChanged(ItemEvent evt)
\r
633 if (evt.getSource() == displayNonconservedMenuItem)
\r
635 displayNonconservedMenuItem_actionPerformed();
\r
637 else if (evt.getSource() == colourTextMenuItem)
\r
639 colourTextMenuItem_actionPerformed();
\r
641 else if (evt.getSource() == wrapMenuItem)
\r
643 wrapMenuItem_actionPerformed();
\r
645 else if (evt.getSource() == scaleAbove)
\r
647 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
649 else if (evt.getSource() == scaleLeft)
\r
651 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
653 else if (evt.getSource() == scaleRight)
\r
655 viewport.setScaleRightWrapped(scaleRight.getState());
\r
657 else if (evt.getSource() == seqLimits)
\r
659 seqLimits_itemStateChanged();
\r
661 else if (evt.getSource() == viewBoxesMenuItem)
\r
663 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
665 else if (evt.getSource() == viewTextMenuItem)
\r
667 viewport.setShowText(viewTextMenuItem.getState());
\r
669 else if (evt.getSource() == renderGapsMenuItem)
\r
671 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
673 else if (evt.getSource() == annotationPanelMenuItem)
\r
675 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
676 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
678 else if (evt.getSource() == sequenceFeatures)
\r
680 viewport.showSequenceFeatures(sequenceFeatures.getState());
\r
681 alignPanel.seqPanel.seqCanvas.repaint();
\r
683 else if (evt.getSource() == conservationMenuItem)
\r
685 conservationMenuItem_actionPerformed();
\r
687 else if (evt.getSource() == abovePIDThreshold)
\r
689 abovePIDThreshold_actionPerformed();
\r
691 else if (evt.getSource() == applyToAllGroups)
\r
693 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
695 else if (evt.getSource() == autoCalculate)
\r
697 viewport.autoCalculateConsensus = autoCalculate.getState();
\r
699 else if (evt.getSource() == sortByTree)
\r
701 viewport.sortByTree = sortByTree.getState();
\r
703 else if (evt.getSource() == this.centreColumnLabelFlag)
\r
705 centreColumnLabelFlag_stateChanged();
\r
707 else if (evt.getSource() == this.followMouseOverFlag)
\r
709 mouseOverFlag_stateChanged();
\r
711 else if (evt.getSource() == showGroupConsensus)
\r
713 showGroupConsensus_actionPerformed();
\r
715 else if (evt.getSource() == showGroupConservation)
\r
717 showGroupConservation_actionPerformed();
\r
719 else if (evt.getSource() == showSequenceLogo)
\r
721 showSequenceLogo_actionPerformed();
\r
723 else if (evt.getSource() == normSequenceLogo)
\r
725 normSequenceLogo_actionPerformed();
\r
727 else if (evt.getSource() == showConsensusHistogram)
\r
729 showConsensusHistogram_actionPerformed();
\r
731 else if (evt.getSource() == applyAutoAnnotationSettings)
\r
733 applyAutoAnnotationSettings_actionPerformed();
\r
735 alignPanel.paintAlignment(true);
\r
738 private void mouseOverFlag_stateChanged()
\r
740 viewport.followHighlight = followMouseOverFlag.getState();
\r
741 // TODO: could kick the scrollTo mechanism to reset view for current
\r
745 private void centreColumnLabelFlag_stateChanged()
\r
747 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
\r
748 this.alignPanel.annotationPanel.repaint();
\r
752 public void actionPerformed(ActionEvent evt)
\r
754 Object source = evt.getSource();
\r
756 if (source == inputText)
\r
758 inputText_actionPerformed();
\r
760 else if (source == loadTree)
\r
762 loadTree_actionPerformed();
\r
764 else if (source == loadApplication)
\r
766 launchFullApplication();
\r
768 else if (source == loadAnnotations)
\r
772 else if (source == outputAnnotations)
\r
774 outputAnnotations(true);
\r
776 else if (source == outputFeatures)
\r
778 outputFeatures(true, "Jalview");
\r
780 else if (source == closeMenuItem)
\r
782 closeMenuItem_actionPerformed();
\r
784 else if (source == copy)
\r
786 copy_actionPerformed();
\r
788 else if (source == undoMenuItem)
\r
790 undoMenuItem_actionPerformed();
\r
792 else if (source == redoMenuItem)
\r
794 redoMenuItem_actionPerformed();
\r
796 else if (source == inputText)
\r
798 inputText_actionPerformed();
\r
800 else if (source == closeMenuItem)
\r
802 closeMenuItem_actionPerformed();
\r
804 else if (source == undoMenuItem)
\r
806 undoMenuItem_actionPerformed();
\r
808 else if (source == redoMenuItem)
\r
810 redoMenuItem_actionPerformed();
\r
812 else if (source == copy)
\r
814 copy_actionPerformed();
\r
816 else if (source == pasteNew)
\r
818 pasteNew_actionPerformed();
\r
820 else if (source == pasteThis)
\r
822 pasteThis_actionPerformed();
\r
824 else if (source == cut)
\r
826 cut_actionPerformed();
\r
828 else if (source == delete)
\r
830 delete_actionPerformed();
\r
832 else if (source == grpsFromSelection)
\r
834 makeGrpsFromSelection_actionPerformed();
\r
836 else if (source == deleteGroups)
\r
838 deleteGroups_actionPerformed();
\r
840 else if (source == selectAllSequenceMenuItem)
\r
842 selectAllSequenceMenuItem_actionPerformed();
\r
844 else if (source == deselectAllSequenceMenuItem)
\r
846 deselectAllSequenceMenuItem_actionPerformed();
\r
848 else if (source == invertSequenceMenuItem)
\r
850 invertSequenceMenuItem_actionPerformed();
\r
852 else if (source == invertColSel)
\r
854 viewport.invertColumnSelection();
\r
855 alignPanel.paintAlignment(true);
\r
857 else if (source == remove2LeftMenuItem)
\r
859 trimAlignment(true);
\r
861 else if (source == remove2RightMenuItem)
\r
863 trimAlignment(false);
\r
865 else if (source == removeGappedColumnMenuItem)
\r
867 removeGappedColumnMenuItem_actionPerformed();
\r
869 else if (source == removeAllGapsMenuItem)
\r
871 removeAllGapsMenuItem_actionPerformed();
\r
873 else if (source == findMenuItem)
\r
875 findMenuItem_actionPerformed();
\r
877 else if (source == font)
\r
879 new FontChooser(alignPanel);
\r
881 else if (source == newView)
\r
885 else if (source == showColumns)
\r
887 viewport.showAllHiddenColumns();
\r
888 alignPanel.paintAlignment(true);
\r
890 else if (source == showSeqs)
\r
892 viewport.showAllHiddenSeqs();
\r
893 alignPanel.paintAlignment(true);
\r
895 else if (source == hideColumns)
\r
897 viewport.hideSelectedColumns();
\r
898 alignPanel.paintAlignment(true);
\r
900 else if (source == hideSequences
\r
901 && viewport.getSelectionGroup() != null)
\r
903 viewport.hideAllSelectedSeqs();
\r
904 alignPanel.paintAlignment(true);
\r
906 else if (source == hideAllButSelection)
\r
908 toggleHiddenRegions(false, false);
\r
909 alignPanel.paintAlignment(true);
\r
911 else if (source == hideAllSelection)
\r
913 SequenceGroup sg = viewport.getSelectionGroup();
\r
914 viewport.expandColSelection(sg, false);
\r
915 viewport.hideAllSelectedSeqs();
\r
916 viewport.hideSelectedColumns();
\r
917 alignPanel.paintAlignment(true);
\r
919 else if (source == showAllHidden)
\r
921 viewport.showAllHiddenColumns();
\r
922 viewport.showAllHiddenSeqs();
\r
923 alignPanel.paintAlignment(true);
\r
925 else if (source == showGroupConsensus)
\r
927 showGroupConsensus_actionPerformed();
\r
929 else if (source == showGroupConservation)
\r
931 showGroupConservation_actionPerformed();
\r
933 else if (source == showSequenceLogo)
\r
935 showSequenceLogo_actionPerformed();
\r
937 else if (source == normSequenceLogo)
\r
939 normSequenceLogo_actionPerformed();
\r
941 else if (source == showConsensusHistogram)
\r
943 showConsensusHistogram_actionPerformed();
\r
945 else if (source == applyAutoAnnotationSettings)
\r
947 applyAutoAnnotationSettings_actionPerformed();
\r
949 else if (source == featureSettings)
\r
951 new FeatureSettings(alignPanel);
\r
953 else if (source == alProperties)
\r
955 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
956 viewport.getAlignment()).formatAsString();
\r
957 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
958 cap.setText(contents.toString());
\r
959 Frame frame = new Frame();
\r
961 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
962 + getTitle(), 400, 250);
\r
964 else if (source == overviewMenuItem)
\r
966 overviewMenuItem_actionPerformed();
\r
968 else if (source == noColourmenuItem)
\r
970 changeColour(null);
\r
972 else if (source == clustalColour)
\r
974 abovePIDThreshold.setState(false);
\r
975 changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
\r
977 else if (source == zappoColour)
\r
979 changeColour(new ZappoColourScheme());
\r
981 else if (source == taylorColour)
\r
983 changeColour(new TaylorColourScheme());
\r
985 else if (source == hydrophobicityColour)
\r
987 changeColour(new HydrophobicColourScheme());
\r
989 else if (source == helixColour)
\r
991 changeColour(new HelixColourScheme());
\r
993 else if (source == strandColour)
\r
995 changeColour(new StrandColourScheme());
\r
997 else if (source == turnColour)
\r
999 changeColour(new TurnColourScheme());
\r
1001 else if (source == buriedColour)
\r
1003 changeColour(new BuriedColourScheme());
\r
1005 else if (source == nucleotideColour)
\r
1007 changeColour(new NucleotideColourScheme());
\r
1009 else if (source == purinePyrimidineColour)
\r
1011 changeColour(new PurinePyrimidineColourScheme());
\r
1013 else if (source == RNAHelixColour)
\r
1015 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1017 else if (source == modifyPID)
\r
1019 modifyPID_actionPerformed();
\r
1021 else if (source == modifyConservation)
\r
1023 modifyConservation_actionPerformed();
\r
1025 else if (source == userDefinedColour)
\r
1027 new UserDefinedColours(alignPanel, null);
\r
1029 else if (source == PIDColour)
\r
1031 changeColour(new PIDColourScheme());
\r
1033 else if (source == BLOSUM62Colour)
\r
1035 changeColour(new Blosum62ColourScheme());
\r
1037 else if (source == tcoffeeColour) {
\r
1038 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1040 else if (source == annotationColour)
\r
1042 new AnnotationColourChooser(viewport, alignPanel);
\r
1044 else if (source == sortPairwiseMenuItem)
\r
1046 sortPairwiseMenuItem_actionPerformed();
\r
1048 else if (source == sortIDMenuItem)
\r
1050 sortIDMenuItem_actionPerformed();
\r
1052 else if (source == sortLengthMenuItem)
\r
1054 sortLengthMenuItem_actionPerformed();
\r
1056 else if (source == sortGroupMenuItem)
\r
1058 sortGroupMenuItem_actionPerformed();
\r
1060 else if (source == removeRedundancyMenuItem)
\r
1062 removeRedundancyMenuItem_actionPerformed();
\r
1064 else if (source == pairwiseAlignmentMenuItem)
\r
1066 pairwiseAlignmentMenuItem_actionPerformed();
\r
1068 else if (source == PCAMenuItem)
\r
1070 PCAMenuItem_actionPerformed();
\r
1072 else if (source == averageDistanceTreeMenuItem)
\r
1074 averageDistanceTreeMenuItem_actionPerformed();
\r
1076 else if (source == neighbourTreeMenuItem)
\r
1078 neighbourTreeMenuItem_actionPerformed();
\r
1080 else if (source == njTreeBlosumMenuItem)
\r
1082 njTreeBlosumMenuItem_actionPerformed();
\r
1084 else if (source == avDistanceTreeBlosumMenuItem)
\r
1086 avTreeBlosumMenuItem_actionPerformed();
\r
1088 else if (source == documentation)
\r
1090 documentation_actionPerformed();
\r
1092 else if (source == about)
\r
1094 about_actionPerformed();
\r
1099 public void inputText_actionPerformed()
\r
1101 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1102 Frame frame = new Frame();
\r
1104 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1107 protected void outputText_actionPerformed(ActionEvent e)
\r
1109 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1110 Frame frame = new Frame();
\r
1112 jalview.bin.JalviewLite.addFrame(frame,
\r
1113 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1114 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1115 e.getActionCommand(), viewport.getAlignment(),
\r
1116 viewport.showJVSuffix));
\r
1119 public void loadAnnotations()
\r
1121 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1122 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1123 cap.setAnnotationImport();
\r
1124 Frame frame = new Frame();
\r
1126 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1130 public String outputAnnotations(boolean displayTextbox)
\r
1132 String annotation = new AnnotationFile().printAnnotations(
\r
1133 viewport.showAnnotation ? viewport.getAlignment()
\r
1134 .getAlignmentAnnotation() : null, viewport.getAlignment()
\r
1136 ((Alignment) viewport.getAlignment()).alignmentProperties);
\r
1138 if (displayTextbox)
\r
1140 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1141 Frame frame = new Frame();
\r
1143 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1144 cap.setText(annotation);
\r
1147 return annotation;
\r
1150 private Hashtable getDisplayedFeatureCols()
\r
1152 if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
\r
1154 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1155 Hashtable fcols = new Hashtable();
\r
1156 Enumeration en = viewport.featuresDisplayed.keys();
\r
1157 while (en.hasMoreElements())
\r
1159 Object col = en.nextElement();
\r
1160 fcols.put(col, fr.featureColours.get(col));
\r
1167 public String outputFeatures(boolean displayTextbox, String format)
\r
1170 if (format.equalsIgnoreCase("Jalview"))
\r
1172 features = new FeaturesFile().printJalviewFormat(
\r
1173 viewport.getAlignment().getSequencesArray(),
\r
1174 getDisplayedFeatureCols());
\r
1178 features = new FeaturesFile().printGFFFormat(
\r
1179 viewport.getAlignment().getSequencesArray(),
\r
1180 getDisplayedFeatureCols());
\r
1183 if (displayTextbox)
\r
1185 boolean frimport=false;
\r
1186 if (features==null || features.equals("No Features Visible"))
\r
1188 features = "# No features visible - paste some and import them here.";
\r
1192 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1195 cap.setAnnotationImport();
\r
1197 Frame frame = new Frame();
\r
1199 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1200 cap.setText(features);
\r
1202 if (features==null)
\r
1209 void launchFullApplication()
\r
1211 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1213 url.append("?open="
\r
1214 + appendProtocol(viewport.applet.getParameter("file")));
\r
1216 if (viewport.applet.getParameter("features") != null)
\r
1218 url.append("&features=");
\r
1219 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1222 if (viewport.applet.getParameter("annotations") != null)
\r
1224 url.append("&annotations=");
\r
1225 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1228 if (viewport.applet.getParameter("jnetfile") != null)
\r
1230 url.append("&annotations=");
\r
1231 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1234 if (viewport.applet.getParameter("defaultColour") != null)
\r
1236 url.append("&colour="
\r
1237 + removeWhiteSpace(viewport.applet
\r
1238 .getParameter("defaultColour")));
\r
1241 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1243 url.append("&colour="
\r
1244 + removeWhiteSpace(viewport.applet
\r
1245 .getParameter("userDefinedColour")));
\r
1247 if (viewport.applet.getParameter("tree") != null)
\r
1249 url.append("&tree="
\r
1250 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1252 if (viewport.applet.getParameter("treeFile") != null)
\r
1254 url.append("&tree="
\r
1255 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1258 showURL(url.toString(), "FULL_APP");
\r
1261 String removeWhiteSpace(String colour)
\r
1263 StringBuffer sb = new StringBuffer();
\r
1264 for (int i = 0; i < colour.length(); i++)
\r
1266 if (Character.isWhitespace(colour.charAt(i)))
\r
1272 sb.append(colour.charAt(i));
\r
1276 return sb.toString();
\r
1279 String appendProtocol(String url)
\r
1284 url = URLEncoder.encode(url);
\r
1287 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1288 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1289 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1290 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1291 * ex.printStackTrace(); }
\r
1293 catch (java.net.MalformedURLException ex)
\r
1295 url = viewport.applet.getCodeBase() + url;
\r
1300 public void closeMenuItem_actionPerformed()
\r
1302 PaintRefresher.RemoveComponent(alignPanel);
\r
1303 if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
\r
1305 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1307 if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
\r
1308 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1311 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1317 alignPanel = null;
\r
1324 void updateEditMenuBar()
\r
1327 if (viewport.historyList.size() > 0)
\r
1329 undoMenuItem.setEnabled(true);
\r
1330 CommandI command = (CommandI) viewport.historyList.peek();
\r
1331 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1335 undoMenuItem.setEnabled(false);
\r
1336 undoMenuItem.setLabel("Undo");
\r
1339 if (viewport.redoList.size() > 0)
\r
1341 redoMenuItem.setEnabled(true);
\r
1343 CommandI command = (CommandI) viewport.redoList.peek();
\r
1344 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1348 redoMenuItem.setEnabled(false);
\r
1349 redoMenuItem.setLabel("Redo");
\r
1356 public void addHistoryItem(CommandI command)
\r
1358 if (command.getSize() > 0)
\r
1360 viewport.historyList.push(command);
\r
1361 viewport.redoList.removeAllElements();
\r
1362 updateEditMenuBar();
\r
1363 viewport.updateHiddenColumns();
\r
1374 protected void undoMenuItem_actionPerformed()
\r
1376 if (viewport.historyList.size() < 1)
\r
1381 CommandI command = (CommandI) viewport.historyList.pop();
\r
1382 viewport.redoList.push(command);
\r
1383 command.undoCommand(null);
\r
1385 AlignViewport originalSource = getOriginatingSource(command);
\r
1387 if (originalSource!=viewport) {
\r
1388 System.err.println("Warning: Viewport object mismatch whilst undoing");
\r
1390 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1391 updateEditMenuBar();
\r
1392 originalSource.firePropertyChange("alignment", null,
\r
1393 originalSource.getAlignment().getSequences());
\r
1403 protected void redoMenuItem_actionPerformed()
\r
1405 if (viewport.redoList.size() < 1)
\r
1410 CommandI command = (CommandI) viewport.redoList.pop();
\r
1411 viewport.historyList.push(command);
\r
1412 command.doCommand(null);
\r
1414 AlignViewport originalSource = getOriginatingSource(command);
\r
1416 if (originalSource!=viewport) {
\r
1417 System.err.println("Warning: Viewport object mismatch whilst re-doing");
\r
1419 originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
\r
1421 updateEditMenuBar();
\r
1422 originalSource.firePropertyChange("alignment", null,
\r
1423 originalSource.getAlignment().getSequences());
\r
1426 AlignViewport getOriginatingSource(CommandI command)
\r
1428 AlignViewport originalSource = null;
\r
1429 // For sequence removal and addition, we need to fire
\r
1430 // the property change event FROM the viewport where the
\r
1431 // original alignment was altered
\r
1432 AlignmentI al = null;
\r
1433 if (command instanceof EditCommand)
\r
1435 EditCommand editCommand = (EditCommand) command;
\r
1436 al = editCommand.getAlignment();
\r
1437 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1438 .getSequenceSetId());
\r
1439 for (int i = 0; i < comps.size(); i++)
\r
1441 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1443 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1445 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1452 if (originalSource == null)
\r
1454 // The original view is closed, we must validate
\r
1455 // the current view against the closed view first
\r
1458 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1461 originalSource = viewport;
\r
1464 return originalSource;
\r
1467 public void moveSelectedSequences(boolean up)
\r
1469 SequenceGroup sg = viewport.getSelectionGroup();
\r
1474 viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);
\r
1475 alignPanel.paintAlignment(true);
\r
1478 synchronized void slideSequences(boolean right, int size)
\r
1480 List<SequenceI>sg = new Vector<SequenceI>();
\r
1481 if (viewport.cursorMode)
\r
1483 sg.add(viewport.getAlignment()
\r
1484 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
\r
1486 else if (viewport.getSelectionGroup() != null
\r
1487 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
\r
1490 sg = viewport.getSelectionGroup().getSequences(
\r
1491 viewport.getHiddenRepSequences());
\r
1494 if (sg.size() < 1)
\r
1499 Vector<SequenceI> invertGroup = new Vector();
\r
1501 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1503 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1504 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1507 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1509 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
\r
1510 for (int i = 0; i < invertGroup.size(); i++)
\r
1511 seqs2[i] = invertGroup.elementAt(i);
\r
1513 SlideSequencesCommand ssc;
\r
1515 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1516 size, viewport.getGapCharacter());
\r
1518 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1519 size, viewport.getGapCharacter());
\r
1521 int groupAdjustment = 0;
\r
1522 if (ssc.getGapsInsertedBegin() && right)
\r
1524 if (viewport.cursorMode)
\r
1525 alignPanel.seqPanel.moveCursor(size, 0);
\r
1527 groupAdjustment = size;
\r
1529 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1531 if (viewport.cursorMode)
\r
1532 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1534 groupAdjustment = -size;
\r
1537 if (groupAdjustment != 0)
\r
1539 viewport.getSelectionGroup().setStartRes(
\r
1540 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1541 viewport.getSelectionGroup().setEndRes(
\r
1542 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1545 boolean appendHistoryItem = false;
\r
1546 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1547 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1549 appendHistoryItem = ssc
\r
1550 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1554 if (!appendHistoryItem)
\r
1555 addHistoryItem(ssc);
\r
1560 static StringBuffer copiedSequences;
\r
1562 static Vector copiedHiddenColumns;
\r
1564 protected void copy_actionPerformed()
\r
1566 if (viewport.getSelectionGroup() == null)
\r
1571 SequenceGroup sg = viewport.getSelectionGroup();
\r
1572 copiedSequences = new StringBuffer();
\r
1573 Hashtable orderedSeqs = new Hashtable();
\r
1574 for (int i = 0; i < sg.getSize(); i++)
\r
1576 SequenceI seq = sg.getSequenceAt(i);
\r
1577 int index = viewport.getAlignment().findIndex(seq);
\r
1578 orderedSeqs.put(index + "", seq);
\r
1581 int index = 0, startRes, endRes;
\r
1584 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1586 copiedHiddenColumns = new Vector();
\r
1587 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1588 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1591 int[] region = (int[]) viewport.getColumnSelection()
\r
1592 .getHiddenColumns().elementAt(i);
\r
1594 copiedHiddenColumns.addElement(new int[]
\r
1595 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1600 copiedHiddenColumns = null;
\r
1603 for (int i = 0; i < sg.getSize(); i++)
\r
1605 SequenceI seq = null;
\r
1607 while (seq == null)
\r
1609 if (orderedSeqs.containsKey(index + ""))
\r
1611 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1623 // Returns residue following index if gap
\r
1624 startRes = seq.findPosition(sg.getStartRes());
\r
1627 // Need to find the residue preceeding index if gap
\r
1630 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1632 ch = seq.getCharAt(j);
\r
1633 if (!jalview.util.Comparison.isGap((ch)))
\r
1641 endRes += seq.getStart() - 1;
\r
1644 copiedSequences.append(seq.getName()
\r
1650 + seq.getSequenceAsString(sg.getStartRes(),
\r
1651 sg.getEndRes() + 1) + "\n");
\r
1656 protected void pasteNew_actionPerformed()
\r
1661 protected void pasteThis_actionPerformed()
\r
1666 void paste(boolean newAlignment)
\r
1671 if (copiedSequences == null)
\r
1676 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1677 Vector seqs = new Vector();
\r
1678 while (st.hasMoreElements())
\r
1680 String name = st.nextToken();
\r
1681 int start = Integer.parseInt(st.nextToken());
\r
1682 int end = Integer.parseInt(st.nextToken());
\r
1683 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1685 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1686 for (int i = 0; i < seqs.size(); i++)
\r
1688 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1693 String newtitle = new String("Copied sequences");
\r
1694 if (getTitle().startsWith("Copied sequences"))
\r
1696 newtitle = getTitle();
\r
1700 newtitle = newtitle.concat("- from " + getTitle());
\r
1702 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1703 viewport.applet, newtitle, false);
\r
1704 if (copiedHiddenColumns != null)
\r
1706 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1708 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1709 af.viewport.hideColumns(region[0], region[1]);
\r
1713 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1718 addSequences(newSeqs);
\r
1721 } catch (Exception ex)
\r
1723 } // could be anything being pasted in here
\r
1727 void addSequences(SequenceI[] seqs)
\r
1729 for (int i = 0; i < seqs.length; i++)
\r
1731 viewport.getAlignment().addSequence(seqs[i]);
\r
1735 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1736 seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
\r
1738 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1739 viewport.getAlignment().getWidth();
\r
1740 viewport.firePropertyChange("alignment", null,
\r
1741 viewport.getAlignment().getSequences());
\r
1745 protected void cut_actionPerformed()
\r
1747 copy_actionPerformed();
\r
1748 delete_actionPerformed();
\r
1751 protected void delete_actionPerformed()
\r
1754 SequenceGroup sg = viewport.getSelectionGroup();
\r
1760 Vector seqs = new Vector();
\r
1762 for (int i = 0; i < sg.getSize(); i++)
\r
1764 seq = sg.getSequenceAt(i);
\r
1765 seqs.addElement(seq);
\r
1768 // If the cut affects all sequences, remove highlighted columns
\r
1769 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1771 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1772 sg.getEndRes() + 1);
\r
1775 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1776 for (int i = 0; i < seqs.size(); i++)
\r
1778 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1782 * //ADD HISTORY ITEM
\r
1784 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1785 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1786 viewport.getAlignment()));
\r
1788 viewport.setSelectionGroup(null);
\r
1789 viewport.getAlignment().deleteGroup(sg);
\r
1791 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1794 if (viewport.getAlignment().getHeight() < 1)
\r
1796 this.setVisible(false);
\r
1798 viewport.sendSelection();
\r
1802 * group consensus toggled
\r
1805 protected void showGroupConsensus_actionPerformed()
\r
1807 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1808 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1813 * group conservation toggled.
\r
1815 protected void showGroupConservation_actionPerformed()
\r
1817 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1818 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1825 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1826 * .event.ActionEvent)
\r
1828 protected void showConsensusHistogram_actionPerformed()
\r
1830 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1831 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1837 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1838 * .event.ActionEvent)
\r
1840 protected void showSequenceLogo_actionPerformed()
\r
1842 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1843 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1845 protected void normSequenceLogo_actionPerformed()
\r
1847 showSequenceLogo.setState(true);
\r
1848 viewport.setShowSequenceLogo(true);
\r
1849 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
\r
1850 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1853 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1855 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1858 protected void makeGrpsFromSelection_actionPerformed()
\r
1860 if (viewport.getSelectionGroup() != null)
\r
1862 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1863 viewport.getSequenceSelection(),
\r
1864 viewport.getAlignmentView(true).getSequenceStrings(
\r
1865 viewport.getGapCharacter()),
\r
1866 viewport.getAlignment().getGroups());
\r
1867 viewport.getAlignment().deleteAllGroups();
\r
1868 viewport.sequenceColours = null;
\r
1869 viewport.setSelectionGroup(null);
\r
1870 // set view properties for each group
\r
1871 for (int g = 0; g < gps.length; g++)
\r
1873 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1874 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1875 viewport.getAlignment().addGroup(gps[g]);
\r
1876 Color col = new Color((int) (Math.random() * 255),
\r
1877 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1878 col = col.brighter();
\r
1879 for (SequenceI sq : gps[g].getSequences(null))
\r
1880 viewport.setSequenceColour(
\r
1884 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1885 alignPanel.updateAnnotation();
\r
1886 alignPanel.paintAlignment(true);
\r
1890 protected void deleteGroups_actionPerformed()
\r
1892 viewport.getAlignment().deleteAllGroups();
\r
1893 viewport.sequenceColours = null;
\r
1894 viewport.setSelectionGroup(null);
\r
1896 alignPanel.paintAlignment(true);
\r
1899 public void selectAllSequenceMenuItem_actionPerformed()
\r
1901 SequenceGroup sg = new SequenceGroup();
\r
1902 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1904 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1906 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1907 viewport.setSelectionGroup(sg);
\r
1908 alignPanel.paintAlignment(true);
\r
1909 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1910 viewport.sendSelection();
\r
1913 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1915 if (viewport.cursorMode)
\r
1917 alignPanel.seqPanel.keyboardNo1 = null;
\r
1918 alignPanel.seqPanel.keyboardNo2 = null;
\r
1920 viewport.setSelectionGroup(null);
\r
1921 viewport.getColumnSelection().clear();
\r
1922 viewport.setSelectionGroup(null);
\r
1923 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1924 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1925 alignPanel.paintAlignment(true);
\r
1926 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1927 viewport.sendSelection();
\r
1930 public void invertSequenceMenuItem_actionPerformed()
\r
1932 SequenceGroup sg = viewport.getSelectionGroup();
\r
1933 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1935 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1938 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1939 viewport.sendSelection();
\r
1942 public void invertColSel_actionPerformed()
\r
1944 viewport.invertColumnSelection();
\r
1945 alignPanel.paintAlignment(true);
\r
1946 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1947 viewport.sendSelection();
\r
1950 void trimAlignment(boolean trimLeft)
\r
1952 ColumnSelection colSel = viewport.getColumnSelection();
\r
1955 if (colSel.size() > 0)
\r
1959 column = colSel.getMin();
\r
1963 column = colSel.getMax();
\r
1967 if (viewport.getSelectionGroup() != null)
\r
1969 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
1970 viewport.getHiddenRepSequences());
\r
1974 seqs = viewport.getAlignment().getSequencesArray();
\r
1977 TrimRegionCommand trimRegion;
\r
1980 trimRegion = new TrimRegionCommand("Remove Left",
\r
1981 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
1982 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1983 viewport.getSelectionGroup());
\r
1984 viewport.setStartRes(0);
\r
1988 trimRegion = new TrimRegionCommand("Remove Right",
\r
1989 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
1990 viewport.getAlignment(), viewport.getColumnSelection(),
\r
1991 viewport.getSelectionGroup());
\r
1994 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
1996 addHistoryItem(trimRegion);
\r
2000 for (SequenceGroup sg:viewport.getAlignment().getGroups())
\r
2002 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2003 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2005 viewport.getAlignment().deleteGroup(sg);
\r
2009 viewport.firePropertyChange("alignment", null, viewport
\r
2010 .getAlignment().getSequences());
\r
2014 public void removeGappedColumnMenuItem_actionPerformed()
\r
2016 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2019 if (viewport.getSelectionGroup() != null)
\r
2021 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2022 viewport.getHiddenRepSequences());
\r
2023 start = viewport.getSelectionGroup().getStartRes();
\r
2024 end = viewport.getSelectionGroup().getEndRes();
\r
2028 seqs = viewport.getAlignment().getSequencesArray();
\r
2031 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2032 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
\r
2034 addHistoryItem(removeGapCols);
\r
2036 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2037 + " empty columns.");
\r
2039 // This is to maintain viewport position on first residue
\r
2040 // of first sequence
\r
2041 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2042 int startRes = seq.findPosition(viewport.startRes);
\r
2043 // ShiftList shifts;
\r
2044 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2045 // edit.alColumnChanges=shifts.getInverse();
\r
2046 // if (viewport.hasHiddenColumns)
\r
2047 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2048 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2049 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2054 public void removeAllGapsMenuItem_actionPerformed()
\r
2056 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2059 if (viewport.getSelectionGroup() != null)
\r
2061 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2062 viewport.getHiddenRepSequences());
\r
2063 start = viewport.getSelectionGroup().getStartRes();
\r
2064 end = viewport.getSelectionGroup().getEndRes();
\r
2068 seqs = viewport.getAlignment().getSequencesArray();
\r
2071 // This is to maintain viewport position on first residue
\r
2072 // of first sequence
\r
2073 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2074 int startRes = seq.findPosition(viewport.startRes);
\r
2076 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2077 viewport.getAlignment()));
\r
2079 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2081 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2086 public void findMenuItem_actionPerformed()
\r
2088 new Finder(alignPanel);
\r
2092 * create a new view derived from the current view
\r
2094 * @param viewtitle
\r
2095 * @return frame for the new view
\r
2097 public AlignFrame newView(String viewtitle)
\r
2100 if (viewport.hasHiddenRows())
\r
2102 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2103 .getFullAlignment().getSequencesArray());
\r
2107 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2110 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2112 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2114 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2116 newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
\r
2121 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2123 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2124 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2125 PaintRefresher.Register(newaf.alignPanel,
\r
2126 newaf.alignPanel.av.getSequenceSetId());
\r
2128 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2129 newaf.alignPanel.av.getSequenceSetId());
\r
2130 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2131 newaf.alignPanel.av.getSequenceSetId());
\r
2133 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2134 .getSequenceSetId());
\r
2135 int viewSize = -1;
\r
2136 for (int i = 0; i < comps.size(); i++)
\r
2138 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2144 String title = new String(this.getTitle());
\r
2145 if (viewtitle != null)
\r
2147 title = viewtitle + " ( " + title + ")";
\r
2151 if (title.indexOf("(View") > -1)
\r
2153 title = title.substring(0, title.indexOf("(View"));
\r
2155 title += "(View " + viewSize + ")";
\r
2158 newaf.setTitle(title.toString());
\r
2160 newaf.viewport.historyList = viewport.historyList;
\r
2161 newaf.viewport.redoList = viewport.redoList;
\r
2167 * @return list of feature groups on the view
\r
2169 public String[] getFeatureGroups()
\r
2171 FeatureRenderer fr = null;
\r
2172 if (alignPanel != null
\r
2173 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2175 return fr.getGroups();
\r
2181 * get sequence feature groups that are hidden or shown
\r
2187 public String[] getFeatureGroupsOfState(boolean visible)
\r
2189 FeatureRenderer fr = null;
\r
2190 if (alignPanel != null
\r
2191 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2193 return fr.getGroups(visible);
\r
2199 * Change the display state for the given feature groups
\r
2202 * list of group strings
\r
2204 * visible or invisible
\r
2206 public void setFeatureGroupState(String[] groups, boolean state)
\r
2208 FeatureRenderer fr = null;
\r
2209 this.sequenceFeatures.setState(true);
\r
2210 viewport.showSequenceFeatures(true);
\r
2211 if (alignPanel != null
\r
2212 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2214 fr.setGroupState(groups, state);
\r
2215 alignPanel.seqPanel.seqCanvas.repaint();
\r
2216 if (alignPanel.overviewPanel != null)
\r
2218 alignPanel.overviewPanel.updateOverviewImage();
\r
2223 public void seqLimits_itemStateChanged()
\r
2225 viewport.setShowJVSuffix(seqLimits.getState());
\r
2226 alignPanel.fontChanged();
\r
2227 alignPanel.paintAlignment(true);
\r
2230 protected void colourTextMenuItem_actionPerformed()
\r
2232 viewport.setColourText(colourTextMenuItem.getState());
\r
2233 alignPanel.paintAlignment(true);
\r
2236 protected void displayNonconservedMenuItem_actionPerformed()
\r
2238 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2239 alignPanel.paintAlignment(true);
\r
2242 protected void wrapMenuItem_actionPerformed()
\r
2244 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2245 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2246 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2247 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2248 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2249 alignPanel.paintAlignment(true);
\r
2252 public void overviewMenuItem_actionPerformed()
\r
2254 if (alignPanel.overviewPanel != null)
\r
2259 Frame frame = new Frame();
\r
2260 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2261 frame.add(overview);
\r
2262 // +50 must allow for applet frame window
\r
2263 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2264 overview.getPreferredSize().width,
\r
2265 overview.getPreferredSize().height + 50);
\r
2268 final AlignmentPanel ap=alignPanel;
\r
2269 frame.addWindowListener(new WindowAdapter()
\r
2272 public void windowClosing(WindowEvent e)
\r
2275 ap.setOverviewPanel(null);
\r
2280 alignPanel.setOverviewPanel(overview);
\r
2284 void changeColour(ColourSchemeI cs)
\r
2286 int threshold = 0;
\r
2290 if (viewport.getAbovePIDThreshold())
\r
2292 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2295 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2297 viewport.setGlobalColourScheme(cs);
\r
2301 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2304 if (viewport.getConservationSelected())
\r
2307 Alignment al = (Alignment) viewport.getAlignment();
\r
2308 Conservation c = new Conservation("All",
\r
2309 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2310 al.getWidth() - 1);
\r
2313 c.verdict(false, viewport.getConsPercGaps());
\r
2315 cs.setConservation(c);
\r
2317 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2318 cs, "Background"));
\r
2323 cs.setConservation(null);
\r
2326 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2329 viewport.setGlobalColourScheme(cs);
\r
2332 if (alignPanel.getOverviewPanel() != null)
\r
2334 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2337 jalview.structure.StructureSelectionManager
\r
2338 .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
\r
2341 alignPanel.paintAlignment(true);
\r
2344 protected void modifyPID_actionPerformed()
\r
2346 if (viewport.getAbovePIDThreshold()
\r
2347 && viewport.getGlobalColourScheme() != null)
\r
2349 SliderPanel.setPIDSliderSource(alignPanel,
\r
2350 viewport.getGlobalColourScheme(), "Background");
\r
2351 SliderPanel.showPIDSlider();
\r
2355 protected void modifyConservation_actionPerformed()
\r
2357 if (viewport.getConservationSelected()
\r
2358 && viewport.getGlobalColourScheme() != null)
\r
2360 SliderPanel.setConservationSlider(alignPanel,
\r
2361 viewport.getGlobalColourScheme(), "Background");
\r
2362 SliderPanel.showConservationSlider();
\r
2366 protected void conservationMenuItem_actionPerformed()
\r
2368 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2370 viewport.setAbovePIDThreshold(false);
\r
2371 abovePIDThreshold.setState(false);
\r
2373 changeColour(viewport.getGlobalColourScheme());
\r
2375 modifyConservation_actionPerformed();
\r
2378 public void abovePIDThreshold_actionPerformed()
\r
2380 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2382 conservationMenuItem.setState(false);
\r
2383 viewport.setConservationSelected(false);
\r
2385 changeColour(viewport.getGlobalColourScheme());
\r
2387 modifyPID_actionPerformed();
\r
2390 public void sortPairwiseMenuItem_actionPerformed()
\r
2392 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2393 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2394 .getAlignment().getSequenceAt(0), null);
\r
2396 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2397 viewport.getAlignment()));
\r
2398 alignPanel.paintAlignment(true);
\r
2401 public void sortIDMenuItem_actionPerformed()
\r
2403 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2404 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2405 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
\r
2406 alignPanel.paintAlignment(true);
\r
2409 public void sortLengthMenuItem_actionPerformed()
\r
2411 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2412 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2413 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2414 viewport.getAlignment()));
\r
2415 alignPanel.paintAlignment(true);
\r
2418 public void sortGroupMenuItem_actionPerformed()
\r
2420 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2421 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2422 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2423 viewport.getAlignment()));
\r
2424 alignPanel.paintAlignment(true);
\r
2428 public void removeRedundancyMenuItem_actionPerformed()
\r
2430 new RedundancyPanel(alignPanel);
\r
2433 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2435 if (viewport.getSelectionGroup() != null
\r
2436 && viewport.getSelectionGroup().getSize() > 1)
\r
2438 Frame frame = new Frame();
\r
2439 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2440 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2445 public void PCAMenuItem_actionPerformed()
\r
2447 // are the sequences aligned?
\r
2448 if (!viewport.getAlignment().isAligned(false))
\r
2450 SequenceI current;
\r
2451 int Width = viewport.getAlignment().getWidth();
\r
2453 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2455 current = viewport.getAlignment().getSequenceAt(i);
\r
2457 if (current.getLength() < Width)
\r
2459 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2462 alignPanel.paintAlignment(true);
\r
2465 if ((viewport.getSelectionGroup() != null
\r
2466 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2467 .getSelectionGroup().getSize() > 0)
\r
2468 || viewport.getAlignment().getHeight() < 4)
\r
2475 new PCAPanel(viewport);
\r
2476 } catch (java.lang.OutOfMemoryError ex)
\r
2482 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2484 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2487 public void neighbourTreeMenuItem_actionPerformed()
\r
2489 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2492 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2494 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2497 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2499 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2502 void NewTreePanel(String type, String pwType, String title)
\r
2504 // are the sequences aligned?
\r
2505 if (!viewport.getAlignment().isAligned(false))
\r
2507 SequenceI current;
\r
2508 int Width = viewport.getAlignment().getWidth();
\r
2510 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2512 current = viewport.getAlignment().getSequenceAt(i);
\r
2514 if (current.getLength() < Width)
\r
2516 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2519 alignPanel.paintAlignment(true);
\r
2523 if ((viewport.getSelectionGroup() != null && viewport
\r
2524 .getSelectionGroup().getSize() > 1)
\r
2525 || (viewport.getSelectionGroup() == null && viewport.getAlignment()
\r
2526 .getHeight() > 1))
\r
2528 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2530 addTreeMenuItem(tp, title);
\r
2532 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2536 void loadTree_actionPerformed()
\r
2538 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2539 cap.setText("Paste your Newick tree file here.");
\r
2540 cap.setTreeImport();
\r
2541 Frame frame = new Frame();
\r
2543 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2546 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2548 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2549 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2550 addTreeMenuItem(tp, treeFile);
\r
2554 * sort the alignment using the given treePanel
\r
2556 * @param treePanel
\r
2557 * tree used to sort view
\r
2559 * string used for undo event name
\r
2561 public void sortByTree(TreePanel treePanel, String title)
\r
2563 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2565 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2566 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2567 // HistoryItem.SORT));
\r
2568 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2569 viewport.getAlignment()));
\r
2570 alignPanel.paintAlignment(true);
\r
2574 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2575 * the menu structure for the new tree
\r
2577 * @param treePanel
\r
2580 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2581 final String title)
\r
2583 final MenuItem item = new MenuItem(title);
\r
2584 sortByTreeMenu.add(item);
\r
2585 item.addActionListener(new java.awt.event.ActionListener()
\r
2588 public void actionPerformed(ActionEvent evt)
\r
2590 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2594 treePanel.addWindowListener(new WindowAdapter()
\r
2597 public void windowOpened(WindowEvent e)
\r
2599 if (viewport.sortByTree)
\r
2601 sortByTree(treePanel, title);
\r
2603 super.windowOpened(e);
\r
2607 public void windowClosing(WindowEvent e)
\r
2609 sortByTreeMenu.remove(item);
\r
2613 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2615 SequenceI[] oldOrder = viewport.getAlignment()
\r
2616 .getSequencesArray();
\r
2617 if (viewport.applet.debug)
\r
2619 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
\r
2621 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2622 if (undoname!=null)
\r
2624 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
\r
2626 alignPanel.paintAlignment(true);
\r
2630 protected void documentation_actionPerformed()
\r
2632 alignPanel.av.applet.openJalviewHelpUrl();
\r
2635 protected void about_actionPerformed()
\r
2638 class AboutPanel extends Canvas
\r
2644 public AboutPanel(String version, String builddate)
\r
2646 this.version = version;
\r
2647 this.builddate = builddate;
\r
2651 public void paint(Graphics g)
\r
2653 g.setColor(Color.white);
\r
2654 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2655 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2656 FontMetrics fm = g.getFontMetrics();
\r
2657 int fh = fm.getHeight();
\r
2659 g.setColor(Color.black);
\r
2660 // TODO: update this text for each release or centrally store it for
\r
2661 // lite and application
\r
2662 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2663 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2664 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2665 g.drawString("Build date: " + builddate, x, y += fh);
\r
2666 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2668 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
\r
2669 x, y += fh * 1.5);
\r
2670 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
\r
2672 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2675 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2677 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2679 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2682 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2684 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2689 Frame frame = new Frame();
\r
2690 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2691 .getBuildDate()));
\r
2692 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2696 public void showURL(String url, String target)
\r
2698 if (viewport.applet == null)
\r
2700 System.out.println("Not running as applet - no browser available.");
\r
2704 viewport.applet.showURL(url, target);
\r
2708 // ////////////////////////////////////////////////////////////////////////////////
\r
2709 // JBuilder Graphics here
\r
2711 MenuBar alignFrameMenuBar = new MenuBar();
\r
2713 Menu fileMenu = new Menu("File");
\r
2715 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2717 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2719 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2721 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2723 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2725 MenuItem closeMenuItem = new MenuItem("Close");
\r
2727 Menu editMenu = new Menu("Edit");
\r
2729 Menu viewMenu = new Menu("View");
\r
2731 Menu colourMenu = new Menu("Colour");
\r
2733 Menu calculateMenu = new Menu("Calculate");
\r
2735 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2737 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2739 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2741 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2743 MenuItem remove2RightMenuItem = new MenuItem();
\r
2745 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2747 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2749 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2751 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2753 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2755 MenuItem sortIDMenuItem = new MenuItem();
\r
2757 MenuItem sortLengthMenuItem = new MenuItem();
\r
2759 MenuItem sortGroupMenuItem = new MenuItem();
\r
2761 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2763 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2765 MenuItem PCAMenuItem = new MenuItem();
\r
2767 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2769 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2771 BorderLayout borderLayout1 = new BorderLayout();
\r
2773 public Label statusBar = new Label();
\r
2775 Menu outputTextboxMenu = new Menu();
\r
2777 MenuItem clustalColour = new MenuItem();
\r
2779 MenuItem zappoColour = new MenuItem();
\r
2781 MenuItem taylorColour = new MenuItem();
\r
2783 MenuItem hydrophobicityColour = new MenuItem();
\r
2785 MenuItem helixColour = new MenuItem();
\r
2787 MenuItem strandColour = new MenuItem();
\r
2789 MenuItem turnColour = new MenuItem();
\r
2791 MenuItem buriedColour = new MenuItem();
\r
2793 MenuItem purinePyrimidineColour = new MenuItem();
\r
2794 MenuItem RNAHelixColour = new MenuItem();
\r
2796 MenuItem userDefinedColour = new MenuItem();
\r
2798 MenuItem PIDColour = new MenuItem();
\r
2800 MenuItem BLOSUM62Colour = new MenuItem();
\r
2802 MenuItem tcoffeeColour = new MenuItem();
\r
2804 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2806 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2808 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2810 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2812 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2814 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2816 MenuItem overviewMenuItem = new MenuItem();
\r
2818 MenuItem undoMenuItem = new MenuItem();
\r
2820 MenuItem redoMenuItem = new MenuItem();
\r
2822 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2824 MenuItem noColourmenuItem = new MenuItem();
\r
2826 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2828 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2830 MenuItem findMenuItem = new MenuItem();
\r
2832 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2834 MenuItem nucleotideColour = new MenuItem();
\r
2836 MenuItem deleteGroups = new MenuItem();
\r
2838 MenuItem grpsFromSelection = new MenuItem();
\r
2840 MenuItem delete = new MenuItem();
\r
2842 MenuItem copy = new MenuItem();
\r
2844 MenuItem cut = new MenuItem();
\r
2846 Menu pasteMenu = new Menu();
\r
2848 MenuItem pasteNew = new MenuItem();
\r
2850 MenuItem pasteThis = new MenuItem();
\r
2852 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2854 MenuItem font = new MenuItem();
\r
2856 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2858 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2860 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2862 MenuItem modifyPID = new MenuItem();
\r
2864 MenuItem modifyConservation = new MenuItem();
\r
2866 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2867 "Autocalculate Consensus", true);
\r
2869 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2870 "Sort Alignment With New Tree", true);
\r
2872 Menu sortByTreeMenu = new Menu();
\r
2874 Menu sort = new Menu();
\r
2876 Menu calculate = new Menu();
\r
2878 MenuItem inputText = new MenuItem();
\r
2880 Menu helpMenu = new Menu();
\r
2882 MenuItem documentation = new MenuItem();
\r
2884 MenuItem about = new MenuItem();
\r
2886 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2888 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2890 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2891 Menu autoAnnMenu=new Menu();
\r
2892 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
\r
2893 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2894 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2895 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2896 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2897 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
\r
2899 private void jbInit() throws Exception
\r
2902 setMenuBar(alignFrameMenuBar);
\r
2906 // dynamically fill save as menu with available formats
\r
2907 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2910 item = new MenuItem(
\r
2911 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2913 item.addActionListener(new java.awt.event.ActionListener()
\r
2916 public void actionPerformed(ActionEvent e)
\r
2918 outputText_actionPerformed(e);
\r
2922 outputTextboxMenu.add(item);
\r
2924 closeMenuItem.addActionListener(this);
\r
2925 loadApplication.addActionListener(this);
\r
2927 loadTree.addActionListener(this);
\r
2928 loadAnnotations.addActionListener(this);
\r
2929 outputFeatures.addActionListener(this);
\r
2930 outputAnnotations.addActionListener(this);
\r
2931 selectAllSequenceMenuItem.addActionListener(this);
\r
2932 deselectAllSequenceMenuItem.addActionListener(this);
\r
2933 invertSequenceMenuItem.addActionListener(this);
\r
2934 remove2LeftMenuItem.setLabel("Remove Left");
\r
2935 remove2LeftMenuItem.addActionListener(this);
\r
2936 remove2RightMenuItem.setLabel("Remove Right");
\r
2937 remove2RightMenuItem.addActionListener(this);
\r
2938 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2939 removeGappedColumnMenuItem.addActionListener(this);
\r
2940 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2941 removeAllGapsMenuItem.addActionListener(this);
\r
2942 viewBoxesMenuItem.setLabel("Boxes");
\r
2943 viewBoxesMenuItem.setState(true);
\r
2944 viewBoxesMenuItem.addItemListener(this);
\r
2945 viewTextMenuItem.setLabel("Text");
\r
2946 viewTextMenuItem.setState(true);
\r
2947 viewTextMenuItem.addItemListener(this);
\r
2948 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
2949 sortPairwiseMenuItem.addActionListener(this);
\r
2950 sortIDMenuItem.setLabel("by ID");
\r
2951 sortIDMenuItem.addActionListener(this);
\r
2952 sortLengthMenuItem.setLabel("by Length");
\r
2953 sortLengthMenuItem.addActionListener(this);
\r
2954 sortGroupMenuItem.setLabel("by Group");
\r
2955 sortGroupMenuItem.addActionListener(this);
\r
2956 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
2957 removeRedundancyMenuItem.addActionListener(this);
\r
2958 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
2959 pairwiseAlignmentMenuItem.addActionListener(this);
\r
2960 PCAMenuItem.setLabel("Principal Component Analysis");
\r
2961 PCAMenuItem.addActionListener(this);
\r
2962 averageDistanceTreeMenuItem
\r
2963 .setLabel("Average Distance Using % Identity");
\r
2964 averageDistanceTreeMenuItem.addActionListener(this);
\r
2965 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
2966 neighbourTreeMenuItem.addActionListener(this);
\r
2967 statusBar.setBackground(Color.white);
\r
2968 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
2969 statusBar.setText("Status bar");
\r
2970 outputTextboxMenu.setLabel("Output to Textbox");
\r
2971 clustalColour.setLabel("Clustalx");
\r
2973 clustalColour.addActionListener(this);
\r
2974 zappoColour.setLabel("Zappo");
\r
2975 zappoColour.addActionListener(this);
\r
2976 taylorColour.setLabel("Taylor");
\r
2977 taylorColour.addActionListener(this);
\r
2978 hydrophobicityColour.setLabel("Hydrophobicity");
\r
2979 hydrophobicityColour.addActionListener(this);
\r
2980 helixColour.setLabel("Helix Propensity");
\r
2981 helixColour.addActionListener(this);
\r
2982 strandColour.setLabel("Strand Propensity");
\r
2983 strandColour.addActionListener(this);
\r
2984 turnColour.setLabel("Turn Propensity");
\r
2985 turnColour.addActionListener(this);
\r
2986 buriedColour.setLabel("Buried Index");
\r
2987 buriedColour.addActionListener(this);
\r
2988 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
2989 purinePyrimidineColour.addActionListener(this);
\r
2990 RNAHelixColour.setLabel("by RNA Helices");
\r
2991 RNAHelixColour.addActionListener(this);
\r
2992 userDefinedColour.setLabel("User Defined...");
\r
2993 userDefinedColour.addActionListener(this);
\r
2994 PIDColour.setLabel("Percentage Identity");
\r
2995 PIDColour.addActionListener(this);
\r
2996 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
2997 BLOSUM62Colour.addActionListener(this);
\r
2998 tcoffeeColour.setLabel("T-Coffee Scores");
\r
2999 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided
\r
3000 tcoffeeColour.addActionListener(this);
\r
3001 avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
\r
3002 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3003 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3004 njTreeBlosumMenuItem.addActionListener(this);
\r
3005 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3006 annotationPanelMenuItem.addItemListener(this);
\r
3007 colourTextMenuItem.setLabel("Colour Text");
\r
3008 colourTextMenuItem.addItemListener(this);
\r
3009 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3010 displayNonconservedMenuItem.addItemListener(this);
\r
3011 alProperties.addActionListener(this);
\r
3012 overviewMenuItem.setLabel("Overview Window");
\r
3013 overviewMenuItem.addActionListener(this);
\r
3014 undoMenuItem.setEnabled(false);
\r
3015 undoMenuItem.setLabel("Undo");
\r
3016 undoMenuItem.addActionListener(this);
\r
3017 redoMenuItem.setEnabled(false);
\r
3018 redoMenuItem.setLabel("Redo");
\r
3019 redoMenuItem.addActionListener(this);
\r
3020 conservationMenuItem.setLabel("by Conservation");
\r
3021 conservationMenuItem.addItemListener(this);
\r
3022 noColourmenuItem.setLabel("None");
\r
3023 noColourmenuItem.addActionListener(this);
\r
3024 wrapMenuItem.setLabel("Wrap");
\r
3025 wrapMenuItem.addItemListener(this);
\r
3026 renderGapsMenuItem.setLabel("Show Gaps");
\r
3027 renderGapsMenuItem.setState(true);
\r
3028 renderGapsMenuItem.addItemListener(this);
\r
3029 findMenuItem.setLabel("Find...");
\r
3030 findMenuItem.addActionListener(this);
\r
3031 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3032 abovePIDThreshold.addItemListener(this);
\r
3033 nucleotideColour.setLabel("Nucleotide");
\r
3034 nucleotideColour.addActionListener(this);
\r
3035 deleteGroups.setLabel("Undefine Groups");
\r
3036 deleteGroups.addActionListener(this);
\r
3037 grpsFromSelection.setLabel("Make Groups for selection");
\r
3038 grpsFromSelection.addActionListener(this);
\r
3039 copy.setLabel("Copy");
\r
3040 copy.addActionListener(this);
\r
3041 cut.setLabel("Cut");
\r
3042 cut.addActionListener(this);
\r
3043 delete.setLabel("Delete");
\r
3044 delete.addActionListener(this);
\r
3045 pasteMenu.setLabel("Paste");
\r
3046 pasteNew.setLabel("To New Alignment");
\r
3047 pasteNew.addActionListener(this);
\r
3048 pasteThis.setLabel("Add To This Alignment");
\r
3049 pasteThis.addActionListener(this);
\r
3050 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3051 applyToAllGroups.setState(true);
\r
3052 applyToAllGroups.addItemListener(this);
\r
3053 font.setLabel("Font...");
\r
3054 font.addActionListener(this);
\r
3055 scaleAbove.setLabel("Scale Above");
\r
3056 scaleAbove.setState(true);
\r
3057 scaleAbove.setEnabled(false);
\r
3058 scaleAbove.addItemListener(this);
\r
3059 scaleLeft.setEnabled(false);
\r
3060 scaleLeft.setState(true);
\r
3061 scaleLeft.setLabel("Scale Left");
\r
3062 scaleLeft.addItemListener(this);
\r
3063 scaleRight.setEnabled(false);
\r
3064 scaleRight.setState(true);
\r
3065 scaleRight.setLabel("Scale Right");
\r
3066 scaleRight.addItemListener(this);
\r
3067 modifyPID.setLabel("Modify Identity Threshold...");
\r
3068 modifyPID.addActionListener(this);
\r
3069 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3070 modifyConservation.addActionListener(this);
\r
3071 sortByTreeMenu.setLabel("By Tree Order");
\r
3072 sort.setLabel("Sort");
\r
3073 calculate.setLabel("Calculate Tree");
\r
3074 autoCalculate.addItemListener(this);
\r
3075 sortByTree.addItemListener(this);
\r
3076 inputText.setLabel("Input from textbox");
\r
3077 inputText.addActionListener(this);
\r
3078 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3079 centreColumnLabelFlag.addItemListener(this);
\r
3080 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3081 followMouseOverFlag.addItemListener(this);
\r
3082 helpMenu.setLabel("Help");
\r
3083 documentation.setLabel("Documentation");
\r
3084 documentation.addActionListener(this);
\r
3086 about.setLabel("About...");
\r
3087 about.addActionListener(this);
\r
3088 seqLimits.setState(true);
\r
3089 seqLimits.setLabel("Show Sequence Limits");
\r
3090 seqLimits.addItemListener(this);
\r
3091 featureSettings.setLabel("Feature Settings...");
\r
3092 featureSettings.addActionListener(this);
\r
3093 sequenceFeatures.setLabel("Sequence Features");
\r
3094 sequenceFeatures.addItemListener(this);
\r
3095 sequenceFeatures.setState(false);
\r
3096 annotationColour.setLabel("by Annotation...");
\r
3097 annotationColour.addActionListener(this);
\r
3098 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3099 invertColSel.setLabel("Invert Column Selection");
\r
3100 menu1.setLabel("Show");
\r
3101 showColumns.setLabel("All Columns ");
\r
3102 showSeqs.setLabel("All Sequences");
\r
3103 menu2.setLabel("Hide");
\r
3104 hideColumns.setLabel("Selected Columns");
\r
3105 hideSequences.setLabel("Selected Sequences");
\r
3106 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3107 hideAllSelection.setLabel("Selected Region");
\r
3108 showAllHidden.setLabel("All Sequences and Columns");
\r
3109 showGroupConsensus.setLabel("Group Consensus");
\r
3110 showGroupConservation.setLabel("Group Conservation");
\r
3111 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3112 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3113 normSequenceLogo.setLabel("Normalise Consensus Logo");
\r
3114 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3115 applyAutoAnnotationSettings.setState(true);
\r
3116 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3118 invertColSel.addActionListener(this);
\r
3119 showColumns.addActionListener(this);
\r
3120 showSeqs.addActionListener(this);
\r
3121 hideColumns.addActionListener(this);
\r
3122 hideSequences.addActionListener(this);
\r
3123 hideAllButSelection.addActionListener(this);
\r
3124 hideAllSelection.addActionListener(this);
\r
3125 showAllHidden.addActionListener(this);
\r
3126 showGroupConsensus.addItemListener(this);
\r
3127 showGroupConservation.addItemListener(this);
\r
3128 showConsensusHistogram.addItemListener(this);
\r
3129 showSequenceLogo.addItemListener(this);
\r
3130 normSequenceLogo.addItemListener(this);
\r
3132 applyAutoAnnotationSettings.addItemListener(this);
\r
3133 formatMenu.setLabel("Format");
\r
3134 selectMenu.setLabel("Select");
\r
3135 newView.setLabel("New View");
\r
3136 newView.addActionListener(this);
\r
3137 alignFrameMenuBar.add(fileMenu);
\r
3138 alignFrameMenuBar.add(editMenu);
\r
3139 alignFrameMenuBar.add(selectMenu);
\r
3140 alignFrameMenuBar.add(viewMenu);
\r
3141 alignFrameMenuBar.add(formatMenu);
\r
3142 alignFrameMenuBar.add(colourMenu);
\r
3143 alignFrameMenuBar.add(calculateMenu);
\r
3144 alignFrameMenuBar.add(helpMenu);
\r
3146 fileMenu.add(inputText);
\r
3147 fileMenu.add(loadTree);
\r
3148 fileMenu.add(loadAnnotations);
\r
3150 fileMenu.addSeparator();
\r
3151 fileMenu.add(outputTextboxMenu);
\r
3152 fileMenu.add(outputFeatures);
\r
3153 fileMenu.add(outputAnnotations);
\r
3155 if (jalviewServletURL != null)
\r
3157 fileMenu.add(loadApplication);
\r
3160 fileMenu.addSeparator();
\r
3161 fileMenu.add(closeMenuItem);
\r
3163 editMenu.add(undoMenuItem);
\r
3164 editMenu.add(redoMenuItem);
\r
3165 editMenu.add(cut);
\r
3166 editMenu.add(copy);
\r
3167 editMenu.add(pasteMenu);
\r
3168 editMenu.add(delete);
\r
3169 editMenu.addSeparator();
\r
3170 editMenu.add(remove2LeftMenuItem);
\r
3171 editMenu.add(remove2RightMenuItem);
\r
3172 editMenu.add(removeGappedColumnMenuItem);
\r
3173 editMenu.add(removeAllGapsMenuItem);
\r
3174 editMenu.add(removeRedundancyMenuItem);
\r
3175 viewMenu.add(newView);
\r
3176 viewMenu.addSeparator();
\r
3177 viewMenu.add(menu1);
\r
3178 viewMenu.add(menu2);
\r
3179 viewMenu.addSeparator();
\r
3180 viewMenu.add(followMouseOverFlag);
\r
3181 viewMenu.add(annotationPanelMenuItem);
\r
3182 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3183 autoAnnMenu.add(showConsensusHistogram);
\r
3184 autoAnnMenu.add(showSequenceLogo);
\r
3185 autoAnnMenu.add(normSequenceLogo);
\r
3186 autoAnnMenu.addSeparator();
\r
3187 autoAnnMenu.add(showGroupConservation);
\r
3188 autoAnnMenu.add(showGroupConsensus);
\r
3189 viewMenu.add(autoAnnMenu);
\r
3190 viewMenu.addSeparator();
\r
3191 viewMenu.add(sequenceFeatures);
\r
3192 viewMenu.add(featureSettings);
\r
3193 viewMenu.addSeparator();
\r
3194 viewMenu.add(alProperties);
\r
3195 viewMenu.addSeparator();
\r
3196 viewMenu.add(overviewMenuItem);
\r
3197 colourMenu.add(applyToAllGroups);
\r
3198 colourMenu.addSeparator();
\r
3199 colourMenu.add(noColourmenuItem);
\r
3200 colourMenu.add(clustalColour);
\r
3201 colourMenu.add(BLOSUM62Colour);
\r
3202 colourMenu.add(PIDColour);
\r
3203 colourMenu.add(zappoColour);
\r
3204 colourMenu.add(taylorColour);
\r
3205 colourMenu.add(hydrophobicityColour);
\r
3206 colourMenu.add(helixColour);
\r
3207 colourMenu.add(strandColour);
\r
3208 colourMenu.add(turnColour);
\r
3209 colourMenu.add(buriedColour);
\r
3210 colourMenu.add(nucleotideColour);
\r
3211 colourMenu.add(purinePyrimidineColour);
\r
3212 colourMenu.add(tcoffeeColour);
\r
3213 colourMenu.add(userDefinedColour);
\r
3214 colourMenu.addSeparator();
\r
3215 colourMenu.add(conservationMenuItem);
\r
3216 colourMenu.add(modifyConservation);
\r
3217 colourMenu.add(abovePIDThreshold);
\r
3218 colourMenu.add(modifyPID);
\r
3219 colourMenu.add(annotationColour);
\r
3220 colourMenu.add(RNAHelixColour);
\r
3221 calculateMenu.add(sort);
\r
3222 calculateMenu.add(calculate);
\r
3223 calculateMenu.addSeparator();
\r
3224 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3225 calculateMenu.add(PCAMenuItem);
\r
3226 calculateMenu.add(autoCalculate);
\r
3227 calculateMenu.add(sortByTree);
\r
3228 this.add(statusBar, BorderLayout.SOUTH);
\r
3229 pasteMenu.add(pasteNew);
\r
3230 pasteMenu.add(pasteThis);
\r
3231 sort.add(sortIDMenuItem);
\r
3232 sort.add(sortLengthMenuItem);
\r
3233 sort.add(sortByTreeMenu);
\r
3234 sort.add(sortGroupMenuItem);
\r
3235 sort.add(sortPairwiseMenuItem);
\r
3236 calculate.add(averageDistanceTreeMenuItem);
\r
3237 calculate.add(neighbourTreeMenuItem);
\r
3238 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3239 calculate.add(njTreeBlosumMenuItem);
\r
3240 helpMenu.add(documentation);
\r
3241 helpMenu.add(about);
\r
3242 menu1.add(showColumns);
\r
3243 menu1.add(showSeqs);
\r
3244 menu1.add(showAllHidden);
\r
3245 menu2.add(hideColumns);
\r
3246 menu2.add(hideSequences);
\r
3247 menu2.add(hideAllSelection);
\r
3248 menu2.add(hideAllButSelection);
\r
3249 formatMenu.add(font);
\r
3250 formatMenu.add(seqLimits);
\r
3251 formatMenu.add(wrapMenuItem);
\r
3252 formatMenu.add(scaleAbove);
\r
3253 formatMenu.add(scaleLeft);
\r
3254 formatMenu.add(scaleRight);
\r
3255 formatMenu.add(viewBoxesMenuItem);
\r
3256 formatMenu.add(viewTextMenuItem);
\r
3257 formatMenu.add(colourTextMenuItem);
\r
3258 formatMenu.add(displayNonconservedMenuItem);
\r
3259 formatMenu.add(renderGapsMenuItem);
\r
3260 formatMenu.add(centreColumnLabelFlag);
\r
3261 selectMenu.add(findMenuItem);
\r
3262 selectMenu.addSeparator();
\r
3263 selectMenu.add(selectAllSequenceMenuItem);
\r
3264 selectMenu.add(deselectAllSequenceMenuItem);
\r
3265 selectMenu.add(invertSequenceMenuItem);
\r
3266 selectMenu.add(invertColSel);
\r
3267 selectMenu.add(grpsFromSelection);
\r
3268 selectMenu.add(deleteGroups);
\r
3272 MenuItem featureSettings = new MenuItem();
\r
3274 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3276 MenuItem annotationColour = new MenuItem();
\r
3278 MenuItem invertColSel = new MenuItem();
\r
3280 Menu menu1 = new Menu();
\r
3282 MenuItem showColumns = new MenuItem();
\r
3284 MenuItem showSeqs = new MenuItem();
\r
3286 Menu menu2 = new Menu();
\r
3288 MenuItem hideColumns = new MenuItem();
\r
3290 MenuItem hideSequences = new MenuItem();
\r
3292 MenuItem hideAllButSelection = new MenuItem();
\r
3294 MenuItem hideAllSelection = new MenuItem();
\r
3296 MenuItem showAllHidden = new MenuItem();
\r
3298 Menu formatMenu = new Menu();
\r
3300 Menu selectMenu = new Menu();
\r
3302 MenuItem newView = new MenuItem();
\r
3305 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3306 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3307 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3309 * @param reallyEmbedded
\r
3310 * true to attach the view to the applet area on the page rather than
\r
3313 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3315 if (reallyEmbedded)
\r
3318 // Explicly build the embedded menu panel for the on-page applet
\r
3320 // view cannot be closed if its actually on the page
\r
3321 fileMenu.remove(closeMenuItem);
\r
3322 fileMenu.remove(3); // Remove Seperator
\r
3323 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3324 Font.PLAIN, 10, false); // use our own fonts.
\r
3325 // and actually add the components to the applet area
\r
3326 viewport.applet.setLayout(new BorderLayout());
\r
3327 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3328 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3329 alignPanel.setSize(viewport.applet.getSize().width,
\r
3330 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3331 - statusBar.HEIGHT);
\r
3332 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3333 final AlignFrame me = this;
\r
3334 viewport.applet.addFocusListener(new FocusListener()
\r
3338 public void focusLost(FocusEvent e)
\r
3340 if (me.viewport.applet.currentAlignFrame==me) {
\r
3341 me.viewport.applet.currentAlignFrame = null;
\r
3345 public void focusGained(FocusEvent e)
\r
3347 me.viewport.applet.currentAlignFrame = me;
\r
3350 viewport.applet.validate();
\r
3355 // test and embed menu bar if necessary.
\r
3357 if (embedMenuIfNeeded(alignPanel))
\r
3359 // adjust for status bar height too
\r
3360 alignPanel.setSize(getSize().width, getSize().height
\r
3361 - statusBar.HEIGHT);
\r
3363 add(statusBar, BorderLayout.SOUTH);
\r
3364 add(alignPanel, BorderLayout.CENTER);
\r
3365 // and register with the applet so it can pass external API calls to us
\r
3366 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3372 * create a new binding between structures in an existing jmol viewer instance
\r
3373 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3374 * this does not open a new Jmol window, or modify the display of the
\r
3375 * structures in the original jmol window. Note This method doesn't work
\r
3376 * without an additional javascript library to exchange messages between the
\r
3377 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3380 * JmolViewer instance
\r
3381 * @param sequenceIds
\r
3382 * - sequence Ids to search for associations
\r
3384 public SequenceStructureBinding addStructureViewInstance(
\r
3385 Object jmolviewer, String[] sequenceIds)
\r
3387 org.jmol.api.JmolViewer viewer = null;
\r
3390 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3391 } catch (ClassCastException ex)
\r
3393 System.err.println("Unsupported viewer object :"
\r
3394 + jmolviewer.getClass());
\r
3396 if (viewer == null)
\r
3398 System.err.println("Can't use this object as a structure viewer:"
\r
3399 + jmolviewer.getClass());
\r
3402 SequenceI[] seqs = null;
\r
3403 if (sequenceIds == null || sequenceIds.length == 0)
\r
3405 seqs = viewport.getAlignment().getSequencesArray();
\r
3409 Vector sqi = new Vector();
\r
3410 AlignmentI al = viewport.getAlignment();
\r
3411 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3413 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3416 sqi.addElement(sq);
\r
3419 if (sqi.size() > 0)
\r
3421 seqs = new SequenceI[sqi.size()];
\r
3422 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3424 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3432 ExtJmol jmv = null;
\r
3433 // TODO: search for a jmv that involves viewer
\r
3435 { // create a new viewer/jalview binding.
\r
3436 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
\r
3442 * bind a pdb file to a sequence in the current view
\r
3444 * @param sequenceId
\r
3445 * - sequenceId within the dataset.
\r
3446 * @param pdbEntryString
\r
3447 * - the short name for the PDB file
\r
3449 * - pdb file - either a URL or a valid PDB file.
\r
3450 * @return true if binding was as success TODO: consider making an exception
\r
3451 * structure for indicating when PDB parsing or sequenceId location
\r
3454 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3457 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3458 boolean needtoadd = false;
\r
3459 if (toaddpdb != null)
\r
3461 Vector pdbe = toaddpdb.getPDBId();
\r
3462 PDBEntry pdbentry = null;
\r
3463 if (pdbe != null && pdbe.size() > 0)
\r
3465 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3467 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3468 if (!pdbentry.getId().equals(pdbEntryString)
\r
3469 && !pdbentry.getFile().equals(pdbFile))
\r
3479 if (pdbentry == null)
\r
3481 pdbentry = new PDBEntry();
\r
3482 pdbentry.setId(pdbEntryString);
\r
3483 pdbentry.setFile(pdbFile);
\r
3484 needtoadd = true; // add this new entry to sequence.
\r
3486 // resolve data source
\r
3487 // TODO: this code should be a refactored to an io package
\r
3488 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3489 if (protocol == null)
\r
3495 // make a note of the access mode and add
\r
3496 if (pdbentry.getProperty() == null)
\r
3498 pdbentry.setProperty(new Hashtable());
\r
3500 pdbentry.getProperty().put("protocol", protocol);
\r
3501 toaddpdb.addPDBId(pdbentry);
\r
3507 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3511 Vector sequences = new Vector();
\r
3512 for (int i = 0; i < seqs.length; i++)
\r
3514 if (seqs[i] != null)
\r
3516 sequences.addElement(new Object[]
\r
3517 { seqs[i], (chains != null) ? chains[i] : null });
\r
3520 seqs = new SequenceI[sequences.size()];
\r
3521 chains = new String[sequences.size()];
\r
3522 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3524 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3526 seqs[i] = (SequenceI) oj[0];
\r
3527 chains[i] = (String) oj[1];
\r
3530 return new Object[]
\r
3535 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3536 SequenceI[] seqs, String[] chains, String protocol)
\r
3538 // Scrub any null sequences from the array
\r
3539 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3540 seqs = (SequenceI[]) sqch[0];
\r
3541 chains = (String[]) sqch[1];
\r
3542 if (seqs == null || seqs.length == 0)
\r
3545 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3547 if (protocol == null || protocol.trim().length() == 0
\r
3548 || protocol.equals("null"))
\r
3550 protocol = (String) pdb.getProperty().get("protocol");
\r
3551 if (protocol == null)
\r
3553 System.err.println("Couldn't work out protocol to open structure: "
\r
3558 if (applet.useXtrnalSviewer)
\r
3560 // register the association(s) and quit, don't create any windows.
\r
3561 if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
\r
3562 System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
\r
3566 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3568 // can only do alignments with Jmol
\r
3569 // find the last jmol window assigned to this alignment
\r
3570 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3571 Vector jmols = applet
\r
3572 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3573 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3575 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3576 if (tajm.ap.alignFrame == this)
\r
3585 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3586 // try and add the pdb structure
\r
3591 // otherwise, create a new window
\r
3592 if (applet.jmolAvailable)
\r
3594 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3596 applet.lastFrameX += 40;
\r
3597 applet.lastFrameY += 40;
\r
3601 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3606 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3607 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3609 // TODO Auto-generated method stub
\r
3610 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3614 * modify the current selection, providing the user has not made a selection already.
\r
3615 * @param sel - sequences from this alignment
\r
3616 * @param csel - columns to be selected on the alignment
\r
3618 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3620 alignPanel.seqPanel.selection(sel, csel, null);
\r
3623 public void scrollTo(int row, int column)
\r
3625 alignPanel.seqPanel.scrollTo(row, column);
\r
3627 public void scrollToRow(int row)
\r
3629 alignPanel.seqPanel.scrollToRow(row);
\r
3631 public void scrollToColumn(int column)
\r
3633 alignPanel.seqPanel.scrollToColumn(column);
\r
3636 * @return the alignments unique ID.
\r
3638 public String getSequenceSetId() {
\r
3639 return viewport.getSequenceSetId();
\r
3644 * Load the (T-Coffee) score file from the specified url
\r
3646 * @param source File/URL/T-COFFEE score file contents
\r
3647 * @throws IOException
\r
3648 * @return true if alignment was annotated with data from source
\r
3650 public boolean loadScoreFile( String source ) throws IOException {
\r
3652 TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
\r
3653 if( !file.isValid()) {
\r
3654 // TODO: raise dialog for gui
\r
3655 System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
\r
3656 System.err.println("Origin was:\n"+source);
\r
3661 * check that the score matrix matches the alignment dimensions
\r
3664 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
\r
3665 // TODO: raise a dialog box here rather than bomb out.
\r
3666 System.err.println("The scores matrix does not match the alignment dimensions");
\r
3670 // TODO add parameter to indicate if matching should be done
\r
3671 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3673 alignPanel.fontChanged();
\r
3674 tcoffeeColour.setEnabled(true);
\r
3675 // switch to this color
\r
3676 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3679 System.err.println("Problems resolving T-Coffee scores:");
\r
3680 if (file.getWarningMessage()!=null) {
\r
3681 System.err.println(file.getWarningMessage());
\r