2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
\r
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.RNAInteractionColourScheme;
\r
56 import jalview.schemes.ResidueProperties;
\r
57 import jalview.schemes.StrandColourScheme;
\r
58 import jalview.schemes.TCoffeeColourScheme;
\r
59 import jalview.schemes.TaylorColourScheme;
\r
60 import jalview.schemes.TurnColourScheme;
\r
61 import jalview.schemes.ZappoColourScheme;
\r
62 import jalview.structure.StructureSelectionManager;
\r
64 import java.awt.BorderLayout;
\r
65 import java.awt.Canvas;
\r
66 import java.awt.CheckboxMenuItem;
\r
67 import java.awt.Color;
\r
68 import java.awt.Font;
\r
69 import java.awt.FontMetrics;
\r
70 import java.awt.Frame;
\r
71 import java.awt.Graphics;
\r
72 import java.awt.Label;
\r
73 import java.awt.Menu;
\r
74 import java.awt.MenuBar;
\r
75 import java.awt.MenuItem;
\r
76 import java.awt.event.ActionEvent;
\r
77 import java.awt.event.ActionListener;
\r
78 import java.awt.event.FocusEvent;
\r
79 import java.awt.event.FocusListener;
\r
80 import java.awt.event.ItemEvent;
\r
81 import java.awt.event.ItemListener;
\r
82 import java.awt.event.KeyEvent;
\r
83 import java.awt.event.KeyListener;
\r
84 import java.awt.event.WindowAdapter;
\r
85 import java.awt.event.WindowEvent;
\r
86 import java.io.IOException;
\r
87 import java.io.InputStreamReader;
\r
88 import java.net.URL;
\r
89 import java.net.URLEncoder;
\r
90 import java.util.Enumeration;
\r
91 import java.util.Hashtable;
\r
92 import java.util.List;
\r
93 import java.util.StringTokenizer;
\r
94 import java.util.Vector;
\r
96 import javax.xml.parsers.ParserConfigurationException;
\r
98 import org.xml.sax.SAXException;
\r
100 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
\r
101 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
\r
102 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
\r
103 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
\r
105 public class AlignFrame extends EmbmenuFrame implements ActionListener,
\r
106 ItemListener, KeyListener
\r
108 public AlignmentPanel alignPanel;
\r
110 public AlignViewport viewport;
\r
112 int DEFAULT_WIDTH = 700;
\r
114 int DEFAULT_HEIGHT = 500;
\r
116 String jalviewServletURL;
\r
118 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
\r
119 String title, boolean embedded)
\r
121 if (applet != null)
\r
123 jalviewServletURL = applet.getParameter("APPLICATION_URL");
\r
129 } catch (Exception ex)
\r
131 ex.printStackTrace();
\r
134 viewport = new AlignViewport(al, applet);
\r
135 alignPanel = new AlignmentPanel(this, viewport);
\r
137 viewport.updateConservation(alignPanel);
\r
138 viewport.updateConsensus(alignPanel);
\r
140 annotationPanelMenuItem.setState(viewport.showAnnotation);
\r
141 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
\r
142 followMouseOverFlag.setState(viewport.getFollowHighlight());
\r
143 showGroupConsensus.setState(viewport.isShowGroupConsensus());
\r
144 showGroupConservation.setState(viewport.isShowGroupConservation());
\r
145 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
\r
146 showSequenceLogo.setState(viewport.isShowSequenceLogo());
\r
147 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
\r
149 seqLimits.setState(viewport.showJVSuffix);
\r
151 if (applet != null)
\r
153 String param = applet.getParameter("sortBy");
\r
156 if (param.equalsIgnoreCase("Id"))
\r
158 sortIDMenuItem_actionPerformed();
\r
160 else if (param.equalsIgnoreCase("Pairwise Identity"))
\r
162 sortPairwiseMenuItem_actionPerformed();
\r
164 else if (param.equalsIgnoreCase("Length"))
\r
166 sortLengthMenuItem_actionPerformed();
\r
170 param = applet.getParameter("wrap");
\r
173 if (param.equalsIgnoreCase("true"))
\r
175 wrapMenuItem.setState(true);
\r
176 wrapMenuItem_actionPerformed();
\r
179 param = applet.getParameter("centrecolumnlabels");
\r
182 centreColumnLabelFlag.setState(true);
\r
183 centreColumnLabelFlag_stateChanged();
\r
187 param = applet.getParameter("windowWidth");
\r
190 int width = Integer.parseInt(param);
\r
191 DEFAULT_WIDTH = width;
\r
193 param = applet.getParameter("windowHeight");
\r
196 int height = Integer.parseInt(param);
\r
197 DEFAULT_HEIGHT = height;
\r
199 } catch (Exception ex)
\r
204 if (viewport.getAlignment().isNucleotide())
\r
206 viewport.updateStrucConsensus(alignPanel);
\r
207 if (viewport.getAlignment().hasRNAStructure())
\r
209 RNAHelixColour.setEnabled(true);
\r
213 RNAHelixColour.setEnabled(false);
\r
218 RNAHelixColour.setEnabled(false);
\r
219 purinePyrimidineColour.setEnabled(false);
\r
222 // Some JVMS send keyevents to Top frame or lowest panel,
\r
223 // Havent worked out why yet. So add to both this frame and seqCanvas for
\r
225 this.addKeyListener(this);
\r
226 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
\r
227 alignPanel.idPanel.idCanvas.addKeyListener(this);
\r
228 alignPanel.scalePanel.addKeyListener(this);
\r
229 alignPanel.annotationPanel.addKeyListener(this);
\r
230 alignPanel.annotationPanelHolder.addKeyListener(this);
\r
231 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
\r
232 alignPanel.alabels.addKeyListener(this);
\r
233 createAlignFrameWindow(embedded, title);
\r
236 alignPanel.adjustAnnotationHeight();
\r
237 alignPanel.paintAlignment(true);
\r
240 public AlignViewport getAlignViewport()
\r
245 public SeqCanvas getSeqcanvas()
\r
247 return alignPanel.seqPanel.seqCanvas;
\r
251 * Load a features file onto the alignment
\r
254 * file URL, content, or other resolvable path
\r
256 * is protocol for accessing data referred to by file
\r
259 public boolean parseFeaturesFile(String file, String type)
\r
261 return parseFeaturesFile(file, type, true);
\r
265 * Load a features file onto the alignment
\r
268 * file URL, content, or other resolvable path
\r
270 * is protocol for accessing data referred to by file
\r
271 * @param autoenabledisplay
\r
272 * when true, display features flag will be automatically enabled if
\r
273 * features are loaded
\r
274 * @return true if data parsed as a features file
\r
276 public boolean parseFeaturesFile(String file, String type,
\r
277 boolean autoenabledisplay)
\r
279 // TODO: test if importing a features file onto an alignment which already
\r
280 // has features with links overwrites the original links.
\r
282 Hashtable featureLinks = new Hashtable();
\r
283 boolean featuresFile = false;
\r
286 featuresFile = new jalview.io.FeaturesFile(file, type)
\r
287 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
\r
288 .getFeatureRenderer().featureColours, featureLinks,
\r
289 true, viewport.applet.getDefaultParameter(
\r
290 "relaxedidmatch", false));
\r
291 } catch (Exception ex)
\r
293 ex.printStackTrace();
\r
298 if (featureLinks.size() > 0)
\r
300 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
\r
302 if (autoenabledisplay)
\r
304 viewport.showSequenceFeatures = true;
\r
305 sequenceFeatures.setState(true);
\r
307 if (viewport.featureSettings != null)
\r
309 viewport.featureSettings.refreshTable();
\r
311 alignPanel.paintAlignment(true);
\r
312 statusBar.setText("Successfully added features to alignment.");
\r
314 return featuresFile;
\r
318 public void keyPressed(KeyEvent evt)
\r
320 if (viewport.cursorMode
\r
321 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
\r
322 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
\r
323 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
\r
324 && Character.isDigit(evt.getKeyChar()))
\r
325 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
\r
327 switch (evt.getKeyCode())
\r
329 case 27: // escape key
\r
330 deselectAllSequenceMenuItem_actionPerformed();
\r
332 alignPanel.alabels.cancelDrag();
\r
334 case KeyEvent.VK_X:
\r
335 if (evt.isControlDown() || evt.isMetaDown())
\r
337 cut_actionPerformed();
\r
340 case KeyEvent.VK_C:
\r
341 if (viewport.cursorMode && !evt.isControlDown())
\r
343 alignPanel.seqPanel.setCursorColumn();
\r
345 if (evt.isControlDown() || evt.isMetaDown())
\r
347 copy_actionPerformed();
\r
350 case KeyEvent.VK_V:
\r
351 if (evt.isControlDown())
\r
353 paste(evt.isShiftDown());
\r
356 case KeyEvent.VK_A:
\r
357 if (evt.isControlDown() || evt.isMetaDown())
\r
359 selectAllSequenceMenuItem_actionPerformed();
\r
362 case KeyEvent.VK_DOWN:
\r
363 if (viewport.cursorMode)
\r
365 alignPanel.seqPanel.moveCursor(0, 1);
\r
369 moveSelectedSequences(false);
\r
373 case KeyEvent.VK_UP:
\r
374 if (viewport.cursorMode)
\r
376 alignPanel.seqPanel.moveCursor(0, -1);
\r
380 moveSelectedSequences(true);
\r
384 case KeyEvent.VK_LEFT:
\r
385 if (evt.isAltDown() || !viewport.cursorMode)
\r
386 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
\r
388 alignPanel.seqPanel.moveCursor(-1, 0);
\r
391 case KeyEvent.VK_RIGHT:
\r
392 if (evt.isAltDown() || !viewport.cursorMode)
\r
393 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
\r
395 alignPanel.seqPanel.moveCursor(1, 0);
\r
398 case KeyEvent.VK_SPACE:
\r
399 if (viewport.cursorMode)
\r
401 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
\r
402 || evt.isShiftDown() || evt.isAltDown());
\r
406 case KeyEvent.VK_DELETE:
\r
407 case KeyEvent.VK_BACK_SPACE:
\r
408 if (viewport.cursorMode)
\r
410 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
\r
411 || evt.isShiftDown() || evt.isAltDown());
\r
415 cut_actionPerformed();
\r
416 alignPanel.seqPanel.seqCanvas.repaint();
\r
420 case KeyEvent.VK_S:
\r
421 if (viewport.cursorMode)
\r
423 alignPanel.seqPanel.setCursorRow();
\r
426 case KeyEvent.VK_P:
\r
427 if (viewport.cursorMode)
\r
429 alignPanel.seqPanel.setCursorPosition();
\r
433 case KeyEvent.VK_ENTER:
\r
434 case KeyEvent.VK_COMMA:
\r
435 if (viewport.cursorMode)
\r
437 alignPanel.seqPanel.setCursorRowAndColumn();
\r
441 case KeyEvent.VK_Q:
\r
442 if (viewport.cursorMode)
\r
444 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
\r
447 case KeyEvent.VK_M:
\r
448 if (viewport.cursorMode)
\r
450 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
\r
454 case KeyEvent.VK_F2:
\r
455 viewport.cursorMode = !viewport.cursorMode;
\r
456 statusBar.setText("Keyboard editing mode is "
\r
457 + (viewport.cursorMode ? "on" : "off"));
\r
458 if (viewport.cursorMode)
\r
460 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
\r
461 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
\r
465 case KeyEvent.VK_F:
\r
466 if (evt.isControlDown())
\r
468 findMenuItem_actionPerformed();
\r
472 case KeyEvent.VK_H:
\r
474 boolean toggleSeqs = !evt.isControlDown();
\r
475 boolean toggleCols = !evt.isShiftDown();
\r
476 toggleHiddenRegions(toggleSeqs, toggleCols);
\r
480 case KeyEvent.VK_PAGE_UP:
\r
481 if (viewport.wrapAlignment)
\r
483 alignPanel.scrollUp(true);
\r
487 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
\r
488 - viewport.endSeq + viewport.startSeq);
\r
492 case KeyEvent.VK_PAGE_DOWN:
\r
493 if (viewport.wrapAlignment)
\r
495 alignPanel.scrollUp(false);
\r
499 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
\r
500 + viewport.endSeq - viewport.startSeq);
\r
504 case KeyEvent.VK_Z:
\r
505 if (evt.isControlDown())
\r
507 undoMenuItem_actionPerformed();
\r
511 case KeyEvent.VK_Y:
\r
512 if (evt.isControlDown())
\r
514 redoMenuItem_actionPerformed();
\r
518 case KeyEvent.VK_L:
\r
519 if (evt.isControlDown())
\r
521 trimAlignment(true);
\r
525 case KeyEvent.VK_R:
\r
526 if (evt.isControlDown())
\r
528 trimAlignment(false);
\r
532 case KeyEvent.VK_E:
\r
533 if (evt.isControlDown())
\r
535 if (evt.isShiftDown())
\r
537 this.removeAllGapsMenuItem_actionPerformed();
\r
541 removeGappedColumnMenuItem_actionPerformed();
\r
545 case KeyEvent.VK_I:
\r
546 if (evt.isControlDown())
\r
548 if (evt.isAltDown())
\r
550 invertColSel_actionPerformed();
\r
554 invertSequenceMenuItem_actionPerformed();
\r
559 case KeyEvent.VK_U:
\r
560 if (evt.isControlDown())
\r
562 this.deleteGroups_actionPerformed();
\r
566 case KeyEvent.VK_T:
\r
567 if (evt.isControlDown())
\r
574 alignPanel.paintAlignment(true);
\r
578 * called by key handler and the hide all/show all menu items
\r
580 * @param toggleSeqs
\r
581 * @param toggleCols
\r
583 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
\r
585 boolean hide = false;
\r
586 SequenceGroup sg = viewport.getSelectionGroup();
\r
587 if (!toggleSeqs && !toggleCols)
\r
589 // Hide everything by the current selection - this is a hack - we do the
\r
590 // invert and then hide
\r
591 // first check that there will be visible columns after the invert.
\r
592 if ((viewport.getColumnSelection() != null
\r
593 && viewport.getColumnSelection().getSelected() != null && viewport
\r
594 .getColumnSelection().getSelected().size() > 0)
\r
595 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
\r
598 // now invert the sequence set, if required - empty selection implies
\r
599 // that no hiding is required.
\r
602 invertSequenceMenuItem_actionPerformed();
\r
603 sg = viewport.getSelectionGroup();
\r
607 viewport.expandColSelection(sg, true);
\r
608 // finally invert the column selection and get the new sequence
\r
609 // selection and indicate it should be hidden.
\r
610 invertColSel_actionPerformed();
\r
617 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
\r
620 viewport.hideAllSelectedSeqs();
\r
622 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
\r
625 viewport.showAllHiddenSeqs();
\r
631 if (viewport.getColumnSelection().getSelected().size() > 0)
\r
633 viewport.hideSelectedColumns();
\r
636 viewport.setSelectionGroup(sg);
\r
641 viewport.showAllHiddenColumns();
\r
647 public void keyReleased(KeyEvent evt)
\r
652 public void keyTyped(KeyEvent evt)
\r
657 public void itemStateChanged(ItemEvent evt)
\r
659 if (evt.getSource() == displayNonconservedMenuItem)
\r
661 displayNonconservedMenuItem_actionPerformed();
\r
663 else if (evt.getSource() == colourTextMenuItem)
\r
665 colourTextMenuItem_actionPerformed();
\r
667 else if (evt.getSource() == wrapMenuItem)
\r
669 wrapMenuItem_actionPerformed();
\r
671 else if (evt.getSource() == scaleAbove)
\r
673 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
675 else if (evt.getSource() == scaleLeft)
\r
677 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
679 else if (evt.getSource() == scaleRight)
\r
681 viewport.setScaleRightWrapped(scaleRight.getState());
\r
683 else if (evt.getSource() == seqLimits)
\r
685 seqLimits_itemStateChanged();
\r
687 else if (evt.getSource() == viewBoxesMenuItem)
\r
689 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
691 else if (evt.getSource() == viewTextMenuItem)
\r
693 viewport.setShowText(viewTextMenuItem.getState());
\r
695 else if (evt.getSource() == renderGapsMenuItem)
\r
697 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
699 else if (evt.getSource() == annotationPanelMenuItem)
\r
701 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
702 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
704 else if (evt.getSource() == sequenceFeatures)
\r
706 viewport.showSequenceFeatures(sequenceFeatures.getState());
\r
707 alignPanel.seqPanel.seqCanvas.repaint();
\r
709 else if (evt.getSource() == conservationMenuItem)
\r
711 conservationMenuItem_actionPerformed();
\r
713 else if (evt.getSource() == abovePIDThreshold)
\r
715 abovePIDThreshold_actionPerformed();
\r
717 else if (evt.getSource() == applyToAllGroups)
\r
719 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
721 else if (evt.getSource() == autoCalculate)
\r
723 viewport.autoCalculateConsensus = autoCalculate.getState();
\r
725 else if (evt.getSource() == sortByTree)
\r
727 viewport.sortByTree = sortByTree.getState();
\r
729 else if (evt.getSource() == this.centreColumnLabelFlag)
\r
731 centreColumnLabelFlag_stateChanged();
\r
733 else if (evt.getSource() == this.followMouseOverFlag)
\r
735 mouseOverFlag_stateChanged();
\r
737 else if (evt.getSource() == showGroupConsensus)
\r
739 showGroupConsensus_actionPerformed();
\r
741 else if (evt.getSource() == showGroupConservation)
\r
743 showGroupConservation_actionPerformed();
\r
745 else if (evt.getSource() == showSequenceLogo)
\r
747 showSequenceLogo_actionPerformed();
\r
749 else if (evt.getSource() == normSequenceLogo)
\r
751 normSequenceLogo_actionPerformed();
\r
753 else if (evt.getSource() == showConsensusHistogram)
\r
755 showConsensusHistogram_actionPerformed();
\r
757 else if (evt.getSource() == applyAutoAnnotationSettings)
\r
759 applyAutoAnnotationSettings_actionPerformed();
\r
761 alignPanel.paintAlignment(true);
\r
764 private void mouseOverFlag_stateChanged()
\r
766 viewport.followHighlight = followMouseOverFlag.getState();
\r
767 // TODO: could kick the scrollTo mechanism to reset view for current
\r
771 private void centreColumnLabelFlag_stateChanged()
\r
773 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
\r
774 this.alignPanel.annotationPanel.repaint();
\r
778 public void actionPerformed(ActionEvent evt)
\r
780 Object source = evt.getSource();
\r
782 if (source == inputText)
\r
784 inputText_actionPerformed();
\r
786 else if (source == loadTree)
\r
788 loadTree_actionPerformed();
\r
790 else if (source == loadApplication)
\r
792 launchFullApplication();
\r
794 else if (source == loadAnnotations)
\r
798 else if (source == outputAnnotations)
\r
800 outputAnnotations(true);
\r
802 else if (source == outputFeatures)
\r
804 outputFeatures(true, "Jalview");
\r
806 else if (source == closeMenuItem)
\r
808 closeMenuItem_actionPerformed();
\r
810 else if (source == copy)
\r
812 copy_actionPerformed();
\r
814 else if (source == undoMenuItem)
\r
816 undoMenuItem_actionPerformed();
\r
818 else if (source == redoMenuItem)
\r
820 redoMenuItem_actionPerformed();
\r
822 else if (source == inputText)
\r
824 inputText_actionPerformed();
\r
826 else if (source == closeMenuItem)
\r
828 closeMenuItem_actionPerformed();
\r
830 else if (source == undoMenuItem)
\r
832 undoMenuItem_actionPerformed();
\r
834 else if (source == redoMenuItem)
\r
836 redoMenuItem_actionPerformed();
\r
838 else if (source == copy)
\r
840 copy_actionPerformed();
\r
842 else if (source == pasteNew)
\r
844 pasteNew_actionPerformed();
\r
846 else if (source == pasteThis)
\r
848 pasteThis_actionPerformed();
\r
850 else if (source == cut)
\r
852 cut_actionPerformed();
\r
854 else if (source == delete)
\r
856 delete_actionPerformed();
\r
858 else if (source == grpsFromSelection)
\r
860 makeGrpsFromSelection_actionPerformed();
\r
862 else if (source == deleteGroups)
\r
864 deleteGroups_actionPerformed();
\r
866 else if (source == selectAllSequenceMenuItem)
\r
868 selectAllSequenceMenuItem_actionPerformed();
\r
870 else if (source == deselectAllSequenceMenuItem)
\r
872 deselectAllSequenceMenuItem_actionPerformed();
\r
874 else if (source == invertSequenceMenuItem)
\r
876 invertSequenceMenuItem_actionPerformed();
\r
878 else if (source == invertColSel)
\r
880 viewport.invertColumnSelection();
\r
881 alignPanel.paintAlignment(true);
\r
883 else if (source == remove2LeftMenuItem)
\r
885 trimAlignment(true);
\r
887 else if (source == remove2RightMenuItem)
\r
889 trimAlignment(false);
\r
891 else if (source == removeGappedColumnMenuItem)
\r
893 removeGappedColumnMenuItem_actionPerformed();
\r
895 else if (source == removeAllGapsMenuItem)
\r
897 removeAllGapsMenuItem_actionPerformed();
\r
899 else if (source == findMenuItem)
\r
901 findMenuItem_actionPerformed();
\r
903 else if (source == font)
\r
905 new FontChooser(alignPanel);
\r
907 else if (source == newView)
\r
911 else if (source == showColumns)
\r
913 viewport.showAllHiddenColumns();
\r
914 alignPanel.paintAlignment(true);
\r
916 else if (source == showSeqs)
\r
918 viewport.showAllHiddenSeqs();
\r
919 alignPanel.paintAlignment(true);
\r
921 else if (source == hideColumns)
\r
923 viewport.hideSelectedColumns();
\r
924 alignPanel.paintAlignment(true);
\r
926 else if (source == hideSequences
\r
927 && viewport.getSelectionGroup() != null)
\r
929 viewport.hideAllSelectedSeqs();
\r
930 alignPanel.paintAlignment(true);
\r
932 else if (source == hideAllButSelection)
\r
934 toggleHiddenRegions(false, false);
\r
935 alignPanel.paintAlignment(true);
\r
937 else if (source == hideAllSelection)
\r
939 SequenceGroup sg = viewport.getSelectionGroup();
\r
940 viewport.expandColSelection(sg, false);
\r
941 viewport.hideAllSelectedSeqs();
\r
942 viewport.hideSelectedColumns();
\r
943 alignPanel.paintAlignment(true);
\r
945 else if (source == showAllHidden)
\r
947 viewport.showAllHiddenColumns();
\r
948 viewport.showAllHiddenSeqs();
\r
949 alignPanel.paintAlignment(true);
\r
951 else if (source == showGroupConsensus)
\r
953 showGroupConsensus_actionPerformed();
\r
955 else if (source == showGroupConservation)
\r
957 showGroupConservation_actionPerformed();
\r
959 else if (source == showSequenceLogo)
\r
961 showSequenceLogo_actionPerformed();
\r
963 else if (source == normSequenceLogo)
\r
965 normSequenceLogo_actionPerformed();
\r
967 else if (source == showConsensusHistogram)
\r
969 showConsensusHistogram_actionPerformed();
\r
971 else if (source == applyAutoAnnotationSettings)
\r
973 applyAutoAnnotationSettings_actionPerformed();
\r
975 else if (source == featureSettings)
\r
977 new FeatureSettings(alignPanel);
\r
979 else if (source == alProperties)
\r
981 StringBuffer contents = new jalview.io.AlignmentProperties(
\r
982 viewport.getAlignment()).formatAsString();
\r
983 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
984 cap.setText(contents.toString());
\r
985 Frame frame = new Frame();
\r
987 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
\r
988 + getTitle(), 400, 250);
\r
990 else if (source == overviewMenuItem)
\r
992 overviewMenuItem_actionPerformed();
\r
994 else if (source == noColourmenuItem)
\r
996 changeColour(null);
\r
998 else if (source == clustalColour)
\r
1000 abovePIDThreshold.setState(false);
\r
1001 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
\r
1003 else if (source == zappoColour)
\r
1005 changeColour(new ZappoColourScheme());
\r
1007 else if (source == taylorColour)
\r
1009 changeColour(new TaylorColourScheme());
\r
1011 else if (source == hydrophobicityColour)
\r
1013 changeColour(new HydrophobicColourScheme());
\r
1015 else if (source == helixColour)
\r
1017 changeColour(new HelixColourScheme());
\r
1019 else if (source == strandColour)
\r
1021 changeColour(new StrandColourScheme());
\r
1023 else if (source == turnColour)
\r
1025 changeColour(new TurnColourScheme());
\r
1027 else if (source == buriedColour)
\r
1029 changeColour(new BuriedColourScheme());
\r
1031 else if (source == nucleotideColour)
\r
1033 changeColour(new NucleotideColourScheme());
\r
1035 else if (source == purinePyrimidineColour)
\r
1037 changeColour(new PurinePyrimidineColourScheme());
\r
1040 else if (source == RNAHelixColour)
\r
1042 new RNAHelicesColourChooser(viewport, alignPanel);
\r
1044 else if (source == modifyPID)
\r
1046 modifyPID_actionPerformed();
\r
1048 else if (source == modifyConservation)
\r
1050 modifyConservation_actionPerformed();
\r
1052 else if (source == userDefinedColour)
\r
1054 new UserDefinedColours(alignPanel, null);
\r
1056 else if (source == PIDColour)
\r
1058 changeColour(new PIDColourScheme());
\r
1060 else if (source == BLOSUM62Colour)
\r
1062 changeColour(new Blosum62ColourScheme());
\r
1064 else if (source == tcoffeeColour)
\r
1066 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
1068 else if (source == annotationColour)
\r
1070 new AnnotationColourChooser(viewport, alignPanel);
\r
1072 else if (source == sortPairwiseMenuItem)
\r
1074 sortPairwiseMenuItem_actionPerformed();
\r
1076 else if (source == sortIDMenuItem)
\r
1078 sortIDMenuItem_actionPerformed();
\r
1080 else if (source == sortLengthMenuItem)
\r
1082 sortLengthMenuItem_actionPerformed();
\r
1084 else if (source == sortGroupMenuItem)
\r
1086 sortGroupMenuItem_actionPerformed();
\r
1088 else if (source == removeRedundancyMenuItem)
\r
1090 removeRedundancyMenuItem_actionPerformed();
\r
1092 else if (source == pairwiseAlignmentMenuItem)
\r
1094 pairwiseAlignmentMenuItem_actionPerformed();
\r
1096 else if (source == PCAMenuItem)
\r
1098 PCAMenuItem_actionPerformed();
\r
1100 else if (source == averageDistanceTreeMenuItem)
\r
1102 averageDistanceTreeMenuItem_actionPerformed();
\r
1104 else if (source == neighbourTreeMenuItem)
\r
1106 neighbourTreeMenuItem_actionPerformed();
\r
1108 else if (source == njTreeBlosumMenuItem)
\r
1110 njTreeBlosumMenuItem_actionPerformed();
\r
1112 else if (source == avDistanceTreeBlosumMenuItem)
\r
1114 avTreeBlosumMenuItem_actionPerformed();
\r
1116 else if (source == documentation)
\r
1118 documentation_actionPerformed();
\r
1120 else if (source == about)
\r
1122 about_actionPerformed();
\r
1127 public void inputText_actionPerformed()
\r
1129 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1130 Frame frame = new Frame();
\r
1132 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
1135 protected void outputText_actionPerformed(ActionEvent e)
\r
1137 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1138 Frame frame = new Frame();
\r
1140 jalview.bin.JalviewLite.addFrame(frame,
\r
1141 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
1142 cap.setText(new AppletFormatAdapter().formatSequences(
\r
1143 e.getActionCommand(), viewport.getAlignment(),
\r
1144 viewport.showJVSuffix));
\r
1147 public void loadAnnotations()
\r
1149 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
1150 cap.setText("Paste your features / annotations / T-coffee score file here.");
\r
1151 cap.setAnnotationImport();
\r
1152 Frame frame = new Frame();
\r
1154 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
\r
1158 public String outputAnnotations(boolean displayTextbox)
\r
1160 String annotation = new AnnotationFile().printAnnotations(
\r
1161 viewport.showAnnotation ? viewport.getAlignment()
\r
1162 .getAlignmentAnnotation() : null, viewport
\r
1163 .getAlignment().getGroups(), ((Alignment) viewport
\r
1164 .getAlignment()).alignmentProperties);
\r
1166 if (displayTextbox)
\r
1168 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
\r
1169 Frame frame = new Frame();
\r
1171 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
\r
1172 cap.setText(annotation);
\r
1175 return annotation;
\r
1178 private Hashtable getDisplayedFeatureCols()
\r
1180 if (alignPanel.getFeatureRenderer() != null
\r
1181 && viewport.featuresDisplayed != null)
\r
1183 FeatureRenderer fr = alignPanel.getFeatureRenderer();
\r
1184 Hashtable fcols = new Hashtable();
\r
1185 Enumeration en = viewport.featuresDisplayed.keys();
\r
1186 while (en.hasMoreElements())
\r
1188 Object col = en.nextElement();
\r
1189 fcols.put(col, fr.featureColours.get(col));
\r
1196 public String outputFeatures(boolean displayTextbox, String format)
\r
1199 if (format.equalsIgnoreCase("Jalview"))
\r
1201 features = new FeaturesFile().printJalviewFormat(viewport
\r
1202 .getAlignment().getSequencesArray(),
\r
1203 getDisplayedFeatureCols());
\r
1207 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
\r
1208 .getSequencesArray(), getDisplayedFeatureCols());
\r
1211 if (displayTextbox)
\r
1213 boolean frimport = false;
\r
1214 if (features == null || features.equals("No Features Visible"))
\r
1216 features = "# No features visible - paste some and import them here.";
\r
1220 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
\r
1223 cap.setAnnotationImport();
\r
1225 Frame frame = new Frame();
\r
1227 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
\r
1228 cap.setText(features);
\r
1232 if (features == null)
\r
1239 void launchFullApplication()
\r
1241 StringBuffer url = new StringBuffer(jalviewServletURL);
\r
1243 url.append("?open="
\r
1244 + appendProtocol(viewport.applet.getParameter("file")));
\r
1246 if (viewport.applet.getParameter("features") != null)
\r
1248 url.append("&features=");
\r
1249 url.append(appendProtocol(viewport.applet.getParameter("features")));
\r
1252 if (viewport.applet.getParameter("annotations") != null)
\r
1254 url.append("&annotations=");
\r
1255 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
\r
1258 if (viewport.applet.getParameter("jnetfile") != null)
\r
1260 url.append("&annotations=");
\r
1261 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
\r
1264 if (viewport.applet.getParameter("defaultColour") != null)
\r
1266 url.append("&colour="
\r
1267 + removeWhiteSpace(viewport.applet
\r
1268 .getParameter("defaultColour")));
\r
1271 if (viewport.applet.getParameter("userDefinedColour") != null)
\r
1273 url.append("&colour="
\r
1274 + removeWhiteSpace(viewport.applet
\r
1275 .getParameter("userDefinedColour")));
\r
1277 if (viewport.applet.getParameter("tree") != null)
\r
1279 url.append("&tree="
\r
1280 + appendProtocol(viewport.applet.getParameter("tree")));
\r
1282 if (viewport.applet.getParameter("treeFile") != null)
\r
1284 url.append("&tree="
\r
1285 + appendProtocol(viewport.applet.getParameter("treeFile")));
\r
1288 showURL(url.toString(), "FULL_APP");
\r
1291 String removeWhiteSpace(String colour)
\r
1293 StringBuffer sb = new StringBuffer();
\r
1294 for (int i = 0; i < colour.length(); i++)
\r
1296 if (Character.isWhitespace(colour.charAt(i)))
\r
1302 sb.append(colour.charAt(i));
\r
1306 return sb.toString();
\r
1309 String appendProtocol(String url)
\r
1314 url = URLEncoder.encode(url);
\r
1317 * When we finally deprecate 1.1 compatibility, we can start to use
\r
1318 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
\r
1319 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
\r
1320 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
\r
1321 * ex.printStackTrace(); }
\r
1323 catch (java.net.MalformedURLException ex)
\r
1325 url = viewport.applet.getCodeBase() + url;
\r
1330 public void closeMenuItem_actionPerformed()
\r
1332 PaintRefresher.RemoveComponent(alignPanel);
\r
1333 if (alignPanel.seqPanel != null
\r
1334 && alignPanel.seqPanel.seqCanvas != null)
\r
1336 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
\r
1338 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
\r
1340 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
\r
1343 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
\r
1351 alignPanel = null;
\r
1358 void updateEditMenuBar()
\r
1361 if (viewport.historyList.size() > 0)
\r
1363 undoMenuItem.setEnabled(true);
\r
1364 CommandI command = (CommandI) viewport.historyList.peek();
\r
1365 undoMenuItem.setLabel("Undo " + command.getDescription());
\r
1369 undoMenuItem.setEnabled(false);
\r
1370 undoMenuItem.setLabel("Undo");
\r
1373 if (viewport.redoList.size() > 0)
\r
1375 redoMenuItem.setEnabled(true);
\r
1377 CommandI command = (CommandI) viewport.redoList.peek();
\r
1378 redoMenuItem.setLabel("Redo " + command.getDescription());
\r
1382 redoMenuItem.setEnabled(false);
\r
1383 redoMenuItem.setLabel("Redo");
\r
1390 public void addHistoryItem(CommandI command)
\r
1392 if (command.getSize() > 0)
\r
1394 viewport.historyList.push(command);
\r
1395 viewport.redoList.removeAllElements();
\r
1396 updateEditMenuBar();
\r
1397 viewport.updateHiddenColumns();
\r
1402 * TODO: JAL-1104 DOCUMENT ME!
\r
1407 protected void undoMenuItem_actionPerformed()
\r
1409 if (viewport.historyList.size() < 1)
\r
1414 CommandI command = (CommandI) viewport.historyList.pop();
\r
1415 viewport.redoList.push(command);
\r
1416 command.undoCommand(null);
\r
1418 AlignViewport originalSource = getOriginatingSource(command);
\r
1420 if (originalSource != viewport)
\r
1423 .println("Warning: Viewport object mismatch whilst undoing");
\r
1425 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
\r
1426 // viewport.getColumnSelection().getHiddenColumns()
\r
1428 updateEditMenuBar();
\r
1429 originalSource.firePropertyChange("alignment", null, originalSource
\r
1430 .getAlignment().getSequences());
\r
1434 * TODO: JAL-1104 DOCUMENT ME!
\r
1439 protected void redoMenuItem_actionPerformed()
\r
1441 if (viewport.redoList.size() < 1)
\r
1446 CommandI command = (CommandI) viewport.redoList.pop();
\r
1447 viewport.historyList.push(command);
\r
1448 command.doCommand(null);
\r
1450 AlignViewport originalSource = getOriginatingSource(command);
\r
1452 if (originalSource != viewport)
\r
1455 .println("Warning: Viewport object mismatch whilst re-doing");
\r
1457 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
\r
1458 // viewport.getColumnSelection().getHiddenColumns()
\r
1461 updateEditMenuBar();
\r
1462 originalSource.firePropertyChange("alignment", null, originalSource
\r
1463 .getAlignment().getSequences());
\r
1466 AlignViewport getOriginatingSource(CommandI command)
\r
1468 AlignViewport originalSource = null;
\r
1469 // For sequence removal and addition, we need to fire
\r
1470 // the property change event FROM the viewport where the
\r
1471 // original alignment was altered
\r
1472 AlignmentI al = null;
\r
1473 if (command instanceof EditCommand)
\r
1475 EditCommand editCommand = (EditCommand) command;
\r
1476 al = editCommand.getAlignment();
\r
1477 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
1478 .getSequenceSetId());
\r
1479 for (int i = 0; i < comps.size(); i++)
\r
1481 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
1483 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
\r
1485 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
\r
1492 if (originalSource == null)
\r
1494 // The original view is closed, we must validate
\r
1495 // the current view against the closed view first
\r
1498 PaintRefresher.validateSequences(al, viewport.getAlignment());
\r
1501 originalSource = viewport;
\r
1504 return originalSource;
\r
1507 public void moveSelectedSequences(boolean up)
\r
1509 SequenceGroup sg = viewport.getSelectionGroup();
\r
1514 viewport.getAlignment().moveSelectedSequencesByOne(sg,
\r
1515 up ? null : viewport.getHiddenRepSequences(), up);
\r
1516 alignPanel.paintAlignment(true);
\r
1519 synchronized void slideSequences(boolean right, int size)
\r
1521 List<SequenceI> sg = new Vector<SequenceI>();
\r
1522 if (viewport.cursorMode)
\r
1524 sg.add(viewport.getAlignment().getSequenceAt(
\r
1525 alignPanel.seqPanel.seqCanvas.cursorY));
\r
1527 else if (viewport.getSelectionGroup() != null
\r
1528 && viewport.getSelectionGroup().getSize() != viewport
\r
1529 .getAlignment().getHeight())
\r
1531 sg = viewport.getSelectionGroup().getSequences(
\r
1532 viewport.getHiddenRepSequences());
\r
1535 if (sg.size() < 1)
\r
1540 Vector<SequenceI> invertGroup = new Vector();
\r
1542 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
1544 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
\r
1545 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
\r
1548 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
\r
1550 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
\r
1552 for (int i = 0; i < invertGroup.size(); i++)
\r
1553 seqs2[i] = invertGroup.elementAt(i);
\r
1555 SlideSequencesCommand ssc;
\r
1557 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
\r
1558 size, viewport.getGapCharacter());
\r
1560 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
\r
1561 size, viewport.getGapCharacter());
\r
1563 int groupAdjustment = 0;
\r
1564 if (ssc.getGapsInsertedBegin() && right)
\r
1566 if (viewport.cursorMode)
\r
1567 alignPanel.seqPanel.moveCursor(size, 0);
\r
1569 groupAdjustment = size;
\r
1571 else if (!ssc.getGapsInsertedBegin() && !right)
\r
1573 if (viewport.cursorMode)
\r
1574 alignPanel.seqPanel.moveCursor(-size, 0);
\r
1576 groupAdjustment = -size;
\r
1579 if (groupAdjustment != 0)
\r
1581 viewport.getSelectionGroup().setStartRes(
\r
1582 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
\r
1583 viewport.getSelectionGroup().setEndRes(
\r
1584 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
\r
1587 boolean appendHistoryItem = false;
\r
1588 if (viewport.historyList != null && viewport.historyList.size() > 0
\r
1589 && viewport.historyList.peek() instanceof SlideSequencesCommand)
\r
1591 appendHistoryItem = ssc
\r
1592 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
\r
1596 if (!appendHistoryItem)
\r
1597 addHistoryItem(ssc);
\r
1602 static StringBuffer copiedSequences;
\r
1604 static Vector copiedHiddenColumns;
\r
1606 protected void copy_actionPerformed()
\r
1608 if (viewport.getSelectionGroup() == null)
\r
1613 SequenceGroup sg = viewport.getSelectionGroup();
\r
1614 copiedSequences = new StringBuffer();
\r
1615 Hashtable orderedSeqs = new Hashtable();
\r
1616 for (int i = 0; i < sg.getSize(); i++)
\r
1618 SequenceI seq = sg.getSequenceAt(i);
\r
1619 int index = viewport.getAlignment().findIndex(seq);
\r
1620 orderedSeqs.put(index + "", seq);
\r
1623 int index = 0, startRes, endRes;
\r
1626 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
\r
1628 copiedHiddenColumns = new Vector();
\r
1629 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
\r
1630 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
\r
1633 int[] region = (int[]) viewport.getColumnSelection()
\r
1634 .getHiddenColumns().elementAt(i);
\r
1636 copiedHiddenColumns.addElement(new int[]
\r
1637 { region[0] - hiddenOffset, region[1] - hiddenOffset });
\r
1642 copiedHiddenColumns = null;
\r
1645 for (int i = 0; i < sg.getSize(); i++)
\r
1647 SequenceI seq = null;
\r
1649 while (seq == null)
\r
1651 if (orderedSeqs.containsKey(index + ""))
\r
1653 seq = (SequenceI) orderedSeqs.get(index + "");
\r
1665 // Returns residue following index if gap
\r
1666 startRes = seq.findPosition(sg.getStartRes());
\r
1669 // Need to find the residue preceeding index if gap
\r
1672 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
1674 ch = seq.getCharAt(j);
\r
1675 if (!jalview.util.Comparison.isGap((ch)))
\r
1683 endRes += seq.getStart() - 1;
\r
1686 copiedSequences.append(seq.getName()
\r
1692 + seq.getSequenceAsString(sg.getStartRes(),
\r
1693 sg.getEndRes() + 1) + "\n");
\r
1698 protected void pasteNew_actionPerformed()
\r
1703 protected void pasteThis_actionPerformed()
\r
1708 void paste(boolean newAlignment)
\r
1713 if (copiedSequences == null)
\r
1718 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
1719 Vector seqs = new Vector();
\r
1720 while (st.hasMoreElements())
\r
1722 String name = st.nextToken();
\r
1723 int start = Integer.parseInt(st.nextToken());
\r
1724 int end = Integer.parseInt(st.nextToken());
\r
1725 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
\r
1727 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
1728 for (int i = 0; i < seqs.size(); i++)
\r
1730 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
1735 String newtitle = new String("Copied sequences");
\r
1736 if (getTitle().startsWith("Copied sequences"))
\r
1738 newtitle = getTitle();
\r
1742 newtitle = newtitle.concat("- from " + getTitle());
\r
1744 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
\r
1745 viewport.applet, newtitle, false);
\r
1746 if (copiedHiddenColumns != null)
\r
1748 for (int i = 0; i < copiedHiddenColumns.size(); i++)
\r
1750 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
\r
1751 af.viewport.hideColumns(region[0], region[1]);
\r
1755 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
\r
1760 addSequences(newSeqs);
\r
1763 } catch (Exception ex)
\r
1765 } // could be anything being pasted in here
\r
1769 void addSequences(SequenceI[] seqs)
\r
1771 for (int i = 0; i < seqs.length; i++)
\r
1773 viewport.getAlignment().addSequence(seqs[i]);
\r
1777 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
\r
1778 seqs, 0, viewport.getAlignment().getWidth(),
\r
1779 viewport.getAlignment()));
\r
1781 viewport.setEndSeq(viewport.getAlignment().getHeight());
\r
1782 viewport.getAlignment().getWidth();
\r
1783 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1788 protected void cut_actionPerformed()
\r
1790 copy_actionPerformed();
\r
1791 delete_actionPerformed();
\r
1794 protected void delete_actionPerformed()
\r
1797 SequenceGroup sg = viewport.getSelectionGroup();
\r
1803 Vector seqs = new Vector();
\r
1805 for (int i = 0; i < sg.getSize(); i++)
\r
1807 seq = sg.getSequenceAt(i);
\r
1808 seqs.addElement(seq);
\r
1811 // If the cut affects all sequences, remove highlighted columns
\r
1812 if (sg.getSize() == viewport.getAlignment().getHeight())
\r
1814 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
1815 sg.getEndRes() + 1);
\r
1818 SequenceI[] cut = new SequenceI[seqs.size()];
\r
1819 for (int i = 0; i < seqs.size(); i++)
\r
1821 cut[i] = (SequenceI) seqs.elementAt(i);
\r
1825 * //ADD HISTORY ITEM
\r
1827 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
\r
1828 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
\r
1829 viewport.getAlignment()));
\r
1831 viewport.setSelectionGroup(null);
\r
1832 viewport.getAlignment().deleteGroup(sg);
\r
1834 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
1837 if (viewport.getAlignment().getHeight() < 1)
\r
1839 this.setVisible(false);
\r
1841 viewport.sendSelection();
\r
1845 * group consensus toggled
\r
1848 protected void showGroupConsensus_actionPerformed()
\r
1850 viewport.setShowGroupConsensus(showGroupConsensus.getState());
\r
1851 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1856 * group conservation toggled.
\r
1858 protected void showGroupConservation_actionPerformed()
\r
1860 viewport.setShowGroupConservation(showGroupConservation.getState());
\r
1861 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1868 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
\r
1869 * .event.ActionEvent)
\r
1871 protected void showConsensusHistogram_actionPerformed()
\r
1873 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
\r
1874 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1881 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
\r
1882 * .event.ActionEvent)
\r
1884 protected void showSequenceLogo_actionPerformed()
\r
1886 viewport.setShowSequenceLogo(showSequenceLogo.getState());
\r
1887 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1890 protected void normSequenceLogo_actionPerformed()
\r
1892 showSequenceLogo.setState(true);
\r
1893 viewport.setShowSequenceLogo(true);
\r
1894 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
\r
1895 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1898 protected void applyAutoAnnotationSettings_actionPerformed()
\r
1900 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
\r
1903 protected void makeGrpsFromSelection_actionPerformed()
\r
1905 if (viewport.getSelectionGroup() != null)
\r
1907 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
\r
1908 viewport.getSequenceSelection(),
\r
1909 viewport.getAlignmentView(true).getSequenceStrings(
\r
1910 viewport.getGapCharacter()), viewport.getAlignment()
\r
1912 viewport.getAlignment().deleteAllGroups();
\r
1913 viewport.sequenceColours = null;
\r
1914 viewport.setSelectionGroup(null);
\r
1915 // set view properties for each group
\r
1916 for (int g = 0; g < gps.length; g++)
\r
1918 // gps[g].setShowunconserved(viewport.getShowUnconserved());
\r
1919 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
\r
1920 viewport.getAlignment().addGroup(gps[g]);
\r
1921 Color col = new Color((int) (Math.random() * 255),
\r
1922 (int) (Math.random() * 255), (int) (Math.random() * 255));
\r
1923 col = col.brighter();
\r
1924 for (SequenceI sq : gps[g].getSequences(null))
\r
1925 viewport.setSequenceColour(sq, col);
\r
1927 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
\r
1928 alignPanel.updateAnnotation();
\r
1929 alignPanel.paintAlignment(true);
\r
1933 protected void deleteGroups_actionPerformed()
\r
1935 viewport.getAlignment().deleteAllGroups();
\r
1936 viewport.sequenceColours = null;
\r
1937 viewport.setSelectionGroup(null);
\r
1939 alignPanel.paintAlignment(true);
\r
1942 public void selectAllSequenceMenuItem_actionPerformed()
\r
1944 SequenceGroup sg = new SequenceGroup();
\r
1945 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1947 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
1949 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
\r
1950 viewport.setSelectionGroup(sg);
\r
1951 alignPanel.paintAlignment(true);
\r
1952 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1953 viewport.sendSelection();
\r
1956 public void deselectAllSequenceMenuItem_actionPerformed()
\r
1958 if (viewport.cursorMode)
\r
1960 alignPanel.seqPanel.keyboardNo1 = null;
\r
1961 alignPanel.seqPanel.keyboardNo2 = null;
\r
1963 viewport.setSelectionGroup(null);
\r
1964 viewport.getColumnSelection().clear();
\r
1965 viewport.setSelectionGroup(null);
\r
1966 alignPanel.idPanel.idCanvas.searchResults = null;
\r
1967 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
1968 alignPanel.paintAlignment(true);
\r
1969 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1970 viewport.sendSelection();
\r
1973 public void invertSequenceMenuItem_actionPerformed()
\r
1975 SequenceGroup sg = viewport.getSelectionGroup();
\r
1976 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
1978 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
1981 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1982 viewport.sendSelection();
\r
1985 public void invertColSel_actionPerformed()
\r
1987 viewport.invertColumnSelection();
\r
1988 alignPanel.paintAlignment(true);
\r
1989 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
\r
1990 viewport.sendSelection();
\r
1993 void trimAlignment(boolean trimLeft)
\r
1995 ColumnSelection colSel = viewport.getColumnSelection();
\r
1998 if (colSel.size() > 0)
\r
2002 column = colSel.getMin();
\r
2006 column = colSel.getMax();
\r
2010 if (viewport.getSelectionGroup() != null)
\r
2012 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2013 viewport.getHiddenRepSequences());
\r
2017 seqs = viewport.getAlignment().getSequencesArray();
\r
2020 TrimRegionCommand trimRegion;
\r
2023 trimRegion = new TrimRegionCommand("Remove Left",
\r
2024 TrimRegionCommand.TRIM_LEFT, seqs, column,
\r
2025 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2026 viewport.getSelectionGroup());
\r
2027 viewport.setStartRes(0);
\r
2031 trimRegion = new TrimRegionCommand("Remove Right",
\r
2032 TrimRegionCommand.TRIM_RIGHT, seqs, column,
\r
2033 viewport.getAlignment(), viewport.getColumnSelection(),
\r
2034 viewport.getSelectionGroup());
\r
2037 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
\r
2039 addHistoryItem(trimRegion);
\r
2041 for (SequenceGroup sg : viewport.getAlignment().getGroups())
\r
2043 if ((trimLeft && !sg.adjustForRemoveLeft(column))
\r
2044 || (!trimLeft && !sg.adjustForRemoveRight(column)))
\r
2046 viewport.getAlignment().deleteGroup(sg);
\r
2050 viewport.firePropertyChange("alignment", null, viewport
\r
2051 .getAlignment().getSequences());
\r
2055 public void removeGappedColumnMenuItem_actionPerformed()
\r
2057 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2060 if (viewport.getSelectionGroup() != null)
\r
2062 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2063 viewport.getHiddenRepSequences());
\r
2064 start = viewport.getSelectionGroup().getStartRes();
\r
2065 end = viewport.getSelectionGroup().getEndRes();
\r
2069 seqs = viewport.getAlignment().getSequencesArray();
\r
2072 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
\r
2073 "Remove Gapped Columns", seqs, start, end,
\r
2074 viewport.getAlignment());
\r
2076 addHistoryItem(removeGapCols);
\r
2078 statusBar.setText("Removed " + removeGapCols.getSize()
\r
2079 + " empty columns.");
\r
2081 // This is to maintain viewport position on first residue
\r
2082 // of first sequence
\r
2083 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2084 int startRes = seq.findPosition(viewport.startRes);
\r
2085 // ShiftList shifts;
\r
2086 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
\r
2087 // edit.alColumnChanges=shifts.getInverse();
\r
2088 // if (viewport.hasHiddenColumns)
\r
2089 // viewport.getColumnSelection().compensateForEdits(shifts);
\r
2090 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2091 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2096 public void removeAllGapsMenuItem_actionPerformed()
\r
2098 int start = 0, end = viewport.getAlignment().getWidth() - 1;
\r
2101 if (viewport.getSelectionGroup() != null)
\r
2103 seqs = viewport.getSelectionGroup().getSequencesAsArray(
\r
2104 viewport.getHiddenRepSequences());
\r
2105 start = viewport.getSelectionGroup().getStartRes();
\r
2106 end = viewport.getSelectionGroup().getEndRes();
\r
2110 seqs = viewport.getAlignment().getSequencesArray();
\r
2113 // This is to maintain viewport position on first residue
\r
2114 // of first sequence
\r
2115 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
\r
2116 int startRes = seq.findPosition(viewport.startRes);
\r
2118 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
\r
2119 viewport.getAlignment()));
\r
2121 viewport.setStartRes(seq.findIndex(startRes) - 1);
\r
2123 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
\r
2128 public void findMenuItem_actionPerformed()
\r
2130 new Finder(alignPanel);
\r
2134 * create a new view derived from the current view
\r
2136 * @param viewtitle
\r
2137 * @return frame for the new view
\r
2139 public AlignFrame newView(String viewtitle)
\r
2142 if (viewport.hasHiddenRows())
\r
2144 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
\r
2145 .getFullAlignment().getSequencesArray());
\r
2149 newal = new Alignment(viewport.getAlignment().getSequencesArray());
\r
2152 if (viewport.getAlignment().getAlignmentAnnotation() != null)
\r
2154 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
\r
2156 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
\r
2158 newal.addAnnotation(viewport.getAlignment()
\r
2159 .getAlignmentAnnotation()[i]);
\r
2164 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
\r
2166 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
\r
2167 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
\r
2168 PaintRefresher.Register(newaf.alignPanel,
\r
2169 newaf.alignPanel.av.getSequenceSetId());
\r
2171 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
\r
2172 newaf.alignPanel.av.getSequenceSetId());
\r
2173 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
\r
2174 newaf.alignPanel.av.getSequenceSetId());
\r
2176 Vector comps = (Vector) PaintRefresher.components.get(viewport
\r
2177 .getSequenceSetId());
\r
2178 int viewSize = -1;
\r
2179 for (int i = 0; i < comps.size(); i++)
\r
2181 if (comps.elementAt(i) instanceof AlignmentPanel)
\r
2187 String title = new String(this.getTitle());
\r
2188 if (viewtitle != null)
\r
2190 title = viewtitle + " ( " + title + ")";
\r
2194 if (title.indexOf("(View") > -1)
\r
2196 title = title.substring(0, title.indexOf("(View"));
\r
2198 title += "(View " + viewSize + ")";
\r
2201 newaf.setTitle(title.toString());
\r
2203 newaf.viewport.historyList = viewport.historyList;
\r
2204 newaf.viewport.redoList = viewport.redoList;
\r
2210 * @return list of feature groups on the view
\r
2212 public String[] getFeatureGroups()
\r
2214 FeatureRenderer fr = null;
\r
2215 if (alignPanel != null
\r
2216 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2218 return fr.getGroups();
\r
2224 * get sequence feature groups that are hidden or shown
\r
2230 public String[] getFeatureGroupsOfState(boolean visible)
\r
2232 FeatureRenderer fr = null;
\r
2233 if (alignPanel != null
\r
2234 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2236 return fr.getGroups(visible);
\r
2242 * Change the display state for the given feature groups
\r
2245 * list of group strings
\r
2247 * visible or invisible
\r
2249 public void setFeatureGroupState(String[] groups, boolean state)
\r
2251 FeatureRenderer fr = null;
\r
2252 this.sequenceFeatures.setState(true);
\r
2253 viewport.showSequenceFeatures(true);
\r
2254 if (alignPanel != null
\r
2255 && (fr = alignPanel.getFeatureRenderer()) != null)
\r
2257 fr.setGroupState(groups, state);
\r
2258 alignPanel.seqPanel.seqCanvas.repaint();
\r
2259 if (alignPanel.overviewPanel != null)
\r
2261 alignPanel.overviewPanel.updateOverviewImage();
\r
2266 public void seqLimits_itemStateChanged()
\r
2268 viewport.setShowJVSuffix(seqLimits.getState());
\r
2269 alignPanel.fontChanged();
\r
2270 alignPanel.paintAlignment(true);
\r
2273 protected void colourTextMenuItem_actionPerformed()
\r
2275 viewport.setColourText(colourTextMenuItem.getState());
\r
2276 alignPanel.paintAlignment(true);
\r
2279 protected void displayNonconservedMenuItem_actionPerformed()
\r
2281 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
\r
2282 alignPanel.paintAlignment(true);
\r
2285 protected void wrapMenuItem_actionPerformed()
\r
2287 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
2288 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
2289 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
2290 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
2291 scaleRight.setEnabled(wrapMenuItem.getState());
\r
2292 alignPanel.paintAlignment(true);
\r
2295 public void overviewMenuItem_actionPerformed()
\r
2297 if (alignPanel.overviewPanel != null)
\r
2302 Frame frame = new Frame();
\r
2303 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
2304 frame.add(overview);
\r
2305 // +50 must allow for applet frame window
\r
2306 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
2307 overview.getPreferredSize().width,
\r
2308 overview.getPreferredSize().height + 50);
\r
2311 final AlignmentPanel ap = alignPanel;
\r
2312 frame.addWindowListener(new WindowAdapter()
\r
2315 public void windowClosing(WindowEvent e)
\r
2319 ap.setOverviewPanel(null);
\r
2324 alignPanel.setOverviewPanel(overview);
\r
2328 void changeColour(ColourSchemeI cs)
\r
2330 int threshold = 0;
\r
2334 if (viewport.getAbovePIDThreshold())
\r
2336 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
2339 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
2341 viewport.setGlobalColourScheme(cs);
\r
2345 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
2348 if (viewport.getConservationSelected())
\r
2351 Alignment al = (Alignment) viewport.getAlignment();
\r
2352 Conservation c = new Conservation("All",
\r
2353 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
2354 al.getWidth() - 1);
\r
2357 c.verdict(false, viewport.getConsPercGaps());
\r
2359 cs.setConservation(c);
\r
2361 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
\r
2362 cs, "Background"));
\r
2367 cs.setConservation(null);
\r
2370 cs.setConsensus(viewport.getSequenceConsensusHash());
\r
2373 viewport.setGlobalColourScheme(cs);
\r
2375 if (alignPanel.getOverviewPanel() != null)
\r
2377 alignPanel.getOverviewPanel().updateOverviewImage();
\r
2380 jalview.structure.StructureSelectionManager
\r
2381 .getStructureSelectionManager(viewport.applet)
\r
2382 .sequenceColoursChanged(alignPanel);
\r
2384 alignPanel.paintAlignment(true);
\r
2387 protected void modifyPID_actionPerformed()
\r
2389 if (viewport.getAbovePIDThreshold()
\r
2390 && viewport.getGlobalColourScheme() != null)
\r
2392 SliderPanel.setPIDSliderSource(alignPanel,
\r
2393 viewport.getGlobalColourScheme(), "Background");
\r
2394 SliderPanel.showPIDSlider();
\r
2398 protected void modifyConservation_actionPerformed()
\r
2400 if (viewport.getConservationSelected()
\r
2401 && viewport.getGlobalColourScheme() != null)
\r
2403 SliderPanel.setConservationSlider(alignPanel,
\r
2404 viewport.getGlobalColourScheme(), "Background");
\r
2405 SliderPanel.showConservationSlider();
\r
2409 protected void conservationMenuItem_actionPerformed()
\r
2411 viewport.setConservationSelected(conservationMenuItem.getState());
\r
2413 viewport.setAbovePIDThreshold(false);
\r
2414 abovePIDThreshold.setState(false);
\r
2416 changeColour(viewport.getGlobalColourScheme());
\r
2418 modifyConservation_actionPerformed();
\r
2421 public void abovePIDThreshold_actionPerformed()
\r
2423 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
2425 conservationMenuItem.setState(false);
\r
2426 viewport.setConservationSelected(false);
\r
2428 changeColour(viewport.getGlobalColourScheme());
\r
2430 modifyPID_actionPerformed();
\r
2433 public void sortPairwiseMenuItem_actionPerformed()
\r
2435 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2436 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
\r
2437 .getAlignment().getSequenceAt(0), null);
\r
2439 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
\r
2440 viewport.getAlignment()));
\r
2441 alignPanel.paintAlignment(true);
\r
2444 public void sortIDMenuItem_actionPerformed()
\r
2446 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2447 AlignmentSorter.sortByID(viewport.getAlignment());
\r
2448 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
\r
2449 viewport.getAlignment()));
\r
2450 alignPanel.paintAlignment(true);
\r
2453 public void sortLengthMenuItem_actionPerformed()
\r
2455 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2456 AlignmentSorter.sortByLength(viewport.getAlignment());
\r
2457 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
\r
2458 viewport.getAlignment()));
\r
2459 alignPanel.paintAlignment(true);
\r
2462 public void sortGroupMenuItem_actionPerformed()
\r
2464 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2465 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
2466 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
\r
2467 viewport.getAlignment()));
\r
2468 alignPanel.paintAlignment(true);
\r
2472 public void removeRedundancyMenuItem_actionPerformed()
\r
2474 new RedundancyPanel(alignPanel);
\r
2477 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
2479 if (viewport.getSelectionGroup() != null
\r
2480 && viewport.getSelectionGroup().getSize() > 1)
\r
2482 Frame frame = new Frame();
\r
2483 frame.add(new PairwiseAlignPanel(alignPanel));
\r
2484 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
\r
2489 public void PCAMenuItem_actionPerformed()
\r
2491 // are the sequences aligned?
\r
2492 if (!viewport.getAlignment().isAligned(false))
\r
2494 SequenceI current;
\r
2495 int Width = viewport.getAlignment().getWidth();
\r
2497 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2499 current = viewport.getAlignment().getSequenceAt(i);
\r
2501 if (current.getLength() < Width)
\r
2503 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2506 alignPanel.paintAlignment(true);
\r
2509 if ((viewport.getSelectionGroup() != null
\r
2510 && viewport.getSelectionGroup().getSize() < 4 && viewport
\r
2511 .getSelectionGroup().getSize() > 0)
\r
2512 || viewport.getAlignment().getHeight() < 4)
\r
2519 new PCAPanel(viewport);
\r
2520 } catch (java.lang.OutOfMemoryError ex)
\r
2526 public void averageDistanceTreeMenuItem_actionPerformed()
\r
2528 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2531 public void neighbourTreeMenuItem_actionPerformed()
\r
2533 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2536 protected void njTreeBlosumMenuItem_actionPerformed()
\r
2538 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2541 protected void avTreeBlosumMenuItem_actionPerformed()
\r
2543 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2546 void NewTreePanel(String type, String pwType, String title)
\r
2548 // are the sequences aligned?
\r
2549 if (!viewport.getAlignment().isAligned(false))
\r
2551 SequenceI current;
\r
2552 int Width = viewport.getAlignment().getWidth();
\r
2554 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
2556 current = viewport.getAlignment().getSequenceAt(i);
\r
2558 if (current.getLength() < Width)
\r
2560 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
2563 alignPanel.paintAlignment(true);
\r
2567 if ((viewport.getSelectionGroup() != null && viewport
\r
2568 .getSelectionGroup().getSize() > 1)
\r
2569 || (viewport.getAlignment().getHeight() > 1))
\r
2571 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
\r
2573 addTreeMenuItem(tp, title);
\r
2575 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
2579 void loadTree_actionPerformed()
\r
2581 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
\r
2582 cap.setText("Paste your Newick tree file here.");
\r
2583 cap.setTreeImport();
\r
2584 Frame frame = new Frame();
\r
2586 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
\r
2589 public void loadTree(jalview.io.NewickFile tree, String treeFile)
\r
2591 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
\r
2592 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
2593 addTreeMenuItem(tp, treeFile);
\r
2597 * sort the alignment using the given treePanel
\r
2599 * @param treePanel
\r
2600 * tree used to sort view
\r
2602 * string used for undo event name
\r
2604 public void sortByTree(TreePanel treePanel, String title)
\r
2606 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2608 .sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
2609 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2610 // HistoryItem.SORT));
\r
2611 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
\r
2612 viewport.getAlignment()));
\r
2613 alignPanel.paintAlignment(true);
\r
2617 * Do any automatic reordering of the alignment and add the necessary bits to
\r
2618 * the menu structure for the new tree
\r
2620 * @param treePanel
\r
2623 protected void addTreeMenuItem(final TreePanel treePanel,
\r
2624 final String title)
\r
2626 final MenuItem item = new MenuItem(title);
\r
2627 sortByTreeMenu.add(item);
\r
2628 item.addActionListener(new java.awt.event.ActionListener()
\r
2631 public void actionPerformed(ActionEvent evt)
\r
2633 sortByTree(treePanel, title); // treePanel.getTitle());
\r
2637 treePanel.addWindowListener(new WindowAdapter()
\r
2640 public void windowOpened(WindowEvent e)
\r
2642 if (viewport.sortByTree)
\r
2644 sortByTree(treePanel, title);
\r
2646 super.windowOpened(e);
\r
2650 public void windowClosing(WindowEvent e)
\r
2652 sortByTreeMenu.remove(item);
\r
2657 public boolean sortBy(AlignmentOrder alorder, String undoname)
\r
2659 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
\r
2660 if (viewport.applet.debug)
\r
2662 System.err.println("Sorting " + alorder.getOrder().size()
\r
2663 + " in alignment '" + getTitle() + "'");
\r
2665 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
\r
2666 if (undoname != null)
\r
2668 addHistoryItem(new OrderCommand(undoname, oldOrder,
\r
2669 viewport.getAlignment()));
\r
2671 alignPanel.paintAlignment(true);
\r
2675 protected void documentation_actionPerformed()
\r
2677 alignPanel.av.applet.openJalviewHelpUrl();
\r
2680 protected void about_actionPerformed()
\r
2683 class AboutPanel extends Canvas
\r
2689 public AboutPanel(String version, String builddate)
\r
2691 this.version = version;
\r
2692 this.builddate = builddate;
\r
2696 public void paint(Graphics g)
\r
2698 g.setColor(Color.white);
\r
2699 g.fillRect(0, 0, getSize().width, getSize().height);
\r
2700 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2701 FontMetrics fm = g.getFontMetrics();
\r
2702 int fh = fm.getHeight();
\r
2704 g.setColor(Color.black);
\r
2705 // TODO: update this text for each release or centrally store it for
\r
2706 // lite and application
\r
2707 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
2708 g.drawString("JalviewLite - Release " + version, x, y += fh);
\r
2709 g.setFont(new Font("Helvetica", Font.BOLD, 12));
\r
2710 g.drawString("Build date: " + builddate, x, y += fh);
\r
2711 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
2713 "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
\r
2714 x, y += fh * 1.5);
\r
2716 "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",
\r
2717 x + 50, y += fh + 8);
\r
2719 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
\r
2722 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
\r
2724 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
\r
2726 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
\r
2729 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
\r
2731 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
\r
2736 Frame frame = new Frame();
\r
2737 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
\r
2738 .getBuildDate()));
\r
2739 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
\r
2743 public void showURL(String url, String target)
\r
2745 if (viewport.applet == null)
\r
2747 System.out.println("Not running as applet - no browser available.");
\r
2751 viewport.applet.showURL(url, target);
\r
2755 // ////////////////////////////////////////////////////////////////////////////////
\r
2756 // JBuilder Graphics here
\r
2758 MenuBar alignFrameMenuBar = new MenuBar();
\r
2760 Menu fileMenu = new Menu("File");
\r
2762 MenuItem loadApplication = new MenuItem("View in Full Application");
\r
2764 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
\r
2766 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
\r
2768 MenuItem outputFeatures = new MenuItem("Export Features ...");
\r
2770 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
\r
2772 MenuItem closeMenuItem = new MenuItem("Close");
\r
2774 Menu editMenu = new Menu("Edit");
\r
2776 Menu viewMenu = new Menu("View");
\r
2778 Menu colourMenu = new Menu("Colour");
\r
2780 Menu calculateMenu = new Menu("Calculate");
\r
2782 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
\r
2784 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
\r
2786 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
\r
2788 MenuItem remove2LeftMenuItem = new MenuItem();
\r
2790 MenuItem remove2RightMenuItem = new MenuItem();
\r
2792 MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
2794 MenuItem removeAllGapsMenuItem = new MenuItem();
\r
2796 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
2798 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
2800 MenuItem sortPairwiseMenuItem = new MenuItem();
\r
2802 MenuItem sortIDMenuItem = new MenuItem();
\r
2804 MenuItem sortLengthMenuItem = new MenuItem();
\r
2806 MenuItem sortGroupMenuItem = new MenuItem();
\r
2808 MenuItem removeRedundancyMenuItem = new MenuItem();
\r
2810 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
2812 MenuItem PCAMenuItem = new MenuItem();
\r
2814 MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
2816 MenuItem neighbourTreeMenuItem = new MenuItem();
\r
2818 BorderLayout borderLayout1 = new BorderLayout();
\r
2820 public Label statusBar = new Label();
\r
2822 Menu outputTextboxMenu = new Menu();
\r
2824 MenuItem clustalColour = new MenuItem();
\r
2826 MenuItem zappoColour = new MenuItem();
\r
2828 MenuItem taylorColour = new MenuItem();
\r
2830 MenuItem hydrophobicityColour = new MenuItem();
\r
2832 MenuItem helixColour = new MenuItem();
\r
2834 MenuItem strandColour = new MenuItem();
\r
2836 MenuItem turnColour = new MenuItem();
\r
2838 MenuItem buriedColour = new MenuItem();
\r
2840 MenuItem purinePyrimidineColour = new MenuItem();
\r
2842 MenuItem RNAInteractionColour = new MenuItem();
\r
2844 MenuItem RNAHelixColour = new MenuItem();
\r
2846 MenuItem userDefinedColour = new MenuItem();
\r
2848 MenuItem PIDColour = new MenuItem();
\r
2850 MenuItem BLOSUM62Colour = new MenuItem();
\r
2852 MenuItem tcoffeeColour = new MenuItem();
\r
2854 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
2856 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
2858 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
2860 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
2862 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
\r
2864 MenuItem alProperties = new MenuItem("Alignment Properties...");
\r
2866 MenuItem overviewMenuItem = new MenuItem();
\r
2868 MenuItem undoMenuItem = new MenuItem();
\r
2870 MenuItem redoMenuItem = new MenuItem();
\r
2872 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
2874 MenuItem noColourmenuItem = new MenuItem();
\r
2876 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
2878 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
2880 MenuItem findMenuItem = new MenuItem();
\r
2882 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
2884 MenuItem nucleotideColour = new MenuItem();
\r
2886 MenuItem deleteGroups = new MenuItem();
\r
2888 MenuItem grpsFromSelection = new MenuItem();
\r
2890 MenuItem delete = new MenuItem();
\r
2892 MenuItem copy = new MenuItem();
\r
2894 MenuItem cut = new MenuItem();
\r
2896 Menu pasteMenu = new Menu();
\r
2898 MenuItem pasteNew = new MenuItem();
\r
2900 MenuItem pasteThis = new MenuItem();
\r
2902 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
2904 MenuItem font = new MenuItem();
\r
2906 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
2908 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
2910 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
2912 MenuItem modifyPID = new MenuItem();
\r
2914 MenuItem modifyConservation = new MenuItem();
\r
2916 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
\r
2917 "Autocalculate Consensus", true);
\r
2919 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
\r
2920 "Sort Alignment With New Tree", true);
\r
2922 Menu sortByTreeMenu = new Menu();
\r
2924 Menu sort = new Menu();
\r
2926 Menu calculate = new Menu();
\r
2928 MenuItem inputText = new MenuItem();
\r
2930 Menu helpMenu = new Menu();
\r
2932 MenuItem documentation = new MenuItem();
\r
2934 MenuItem about = new MenuItem();
\r
2936 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
2938 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
\r
2940 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
\r
2942 Menu autoAnnMenu = new Menu();
\r
2944 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
\r
2946 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
\r
2948 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
\r
2950 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
\r
2952 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
\r
2954 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
\r
2956 private void jbInit() throws Exception
\r
2959 setMenuBar(alignFrameMenuBar);
\r
2963 // dynamically fill save as menu with available formats
\r
2964 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
2967 item = new MenuItem(
\r
2968 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
2970 item.addActionListener(new java.awt.event.ActionListener()
\r
2973 public void actionPerformed(ActionEvent e)
\r
2975 outputText_actionPerformed(e);
\r
2979 outputTextboxMenu.add(item);
\r
2981 closeMenuItem.addActionListener(this);
\r
2982 loadApplication.addActionListener(this);
\r
2984 loadTree.addActionListener(this);
\r
2985 loadAnnotations.addActionListener(this);
\r
2986 outputFeatures.addActionListener(this);
\r
2987 outputAnnotations.addActionListener(this);
\r
2988 selectAllSequenceMenuItem.addActionListener(this);
\r
2989 deselectAllSequenceMenuItem.addActionListener(this);
\r
2990 invertSequenceMenuItem.addActionListener(this);
\r
2991 remove2LeftMenuItem.setLabel("Remove Left");
\r
2992 remove2LeftMenuItem.addActionListener(this);
\r
2993 remove2RightMenuItem.setLabel("Remove Right");
\r
2994 remove2RightMenuItem.addActionListener(this);
\r
2995 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
2996 removeGappedColumnMenuItem.addActionListener(this);
\r
2997 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
2998 removeAllGapsMenuItem.addActionListener(this);
\r
2999 viewBoxesMenuItem.setLabel("Boxes");
\r
3000 viewBoxesMenuItem.setState(true);
\r
3001 viewBoxesMenuItem.addItemListener(this);
\r
3002 viewTextMenuItem.setLabel("Text");
\r
3003 viewTextMenuItem.setState(true);
\r
3004 viewTextMenuItem.addItemListener(this);
\r
3005 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
3006 sortPairwiseMenuItem.addActionListener(this);
\r
3007 sortIDMenuItem.setLabel("by ID");
\r
3008 sortIDMenuItem.addActionListener(this);
\r
3009 sortLengthMenuItem.setLabel("by Length");
\r
3010 sortLengthMenuItem.addActionListener(this);
\r
3011 sortGroupMenuItem.setLabel("by Group");
\r
3012 sortGroupMenuItem.addActionListener(this);
\r
3013 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
3014 removeRedundancyMenuItem.addActionListener(this);
\r
3015 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
3016 pairwiseAlignmentMenuItem.addActionListener(this);
\r
3017 PCAMenuItem.setLabel("Principal Component Analysis");
\r
3018 PCAMenuItem.addActionListener(this);
\r
3019 averageDistanceTreeMenuItem
\r
3020 .setLabel("Average Distance Using % Identity");
\r
3021 averageDistanceTreeMenuItem.addActionListener(this);
\r
3022 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
3023 neighbourTreeMenuItem.addActionListener(this);
\r
3024 statusBar.setBackground(Color.white);
\r
3025 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
3026 statusBar.setText("Status bar");
\r
3027 outputTextboxMenu.setLabel("Output to Textbox");
\r
3028 clustalColour.setLabel("Clustalx");
\r
3030 clustalColour.addActionListener(this);
\r
3031 zappoColour.setLabel("Zappo");
\r
3032 zappoColour.addActionListener(this);
\r
3033 taylorColour.setLabel("Taylor");
\r
3034 taylorColour.addActionListener(this);
\r
3035 hydrophobicityColour.setLabel("Hydrophobicity");
\r
3036 hydrophobicityColour.addActionListener(this);
\r
3037 helixColour.setLabel("Helix Propensity");
\r
3038 helixColour.addActionListener(this);
\r
3039 strandColour.setLabel("Strand Propensity");
\r
3040 strandColour.addActionListener(this);
\r
3041 turnColour.setLabel("Turn Propensity");
\r
3042 turnColour.addActionListener(this);
\r
3043 buriedColour.setLabel("Buried Index");
\r
3044 buriedColour.addActionListener(this);
\r
3045 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
\r
3046 purinePyrimidineColour.addActionListener(this);
\r
3047 RNAInteractionColour.setLabel("Purine/Pyrimidine");
\r
3048 RNAInteractionColour.addActionListener(this);
\r
3049 RNAHelixColour.setLabel("by RNA Helices");
\r
3050 RNAHelixColour.addActionListener(this);
\r
3051 userDefinedColour.setLabel("User Defined...");
\r
3052 userDefinedColour.addActionListener(this);
\r
3053 PIDColour.setLabel("Percentage Identity");
\r
3054 PIDColour.addActionListener(this);
\r
3055 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
3056 BLOSUM62Colour.addActionListener(this);
\r
3057 tcoffeeColour.setLabel("T-Coffee Scores");
\r
3058 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
\r
3060 tcoffeeColour.addActionListener(this);
\r
3061 avDistanceTreeBlosumMenuItem
\r
3062 .setLabel("Average Distance Using BLOSUM62");
\r
3063 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
3064 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
3065 njTreeBlosumMenuItem.addActionListener(this);
\r
3066 annotationPanelMenuItem.setLabel("Show Annotations");
\r
3067 annotationPanelMenuItem.addItemListener(this);
\r
3068 colourTextMenuItem.setLabel("Colour Text");
\r
3069 colourTextMenuItem.addItemListener(this);
\r
3070 displayNonconservedMenuItem.setLabel("Show nonconserved");
\r
3071 displayNonconservedMenuItem.addItemListener(this);
\r
3072 alProperties.addActionListener(this);
\r
3073 overviewMenuItem.setLabel("Overview Window");
\r
3074 overviewMenuItem.addActionListener(this);
\r
3075 undoMenuItem.setEnabled(false);
\r
3076 undoMenuItem.setLabel("Undo");
\r
3077 undoMenuItem.addActionListener(this);
\r
3078 redoMenuItem.setEnabled(false);
\r
3079 redoMenuItem.setLabel("Redo");
\r
3080 redoMenuItem.addActionListener(this);
\r
3081 conservationMenuItem.setLabel("by Conservation");
\r
3082 conservationMenuItem.addItemListener(this);
\r
3083 noColourmenuItem.setLabel("None");
\r
3084 noColourmenuItem.addActionListener(this);
\r
3085 wrapMenuItem.setLabel("Wrap");
\r
3086 wrapMenuItem.addItemListener(this);
\r
3087 renderGapsMenuItem.setLabel("Show Gaps");
\r
3088 renderGapsMenuItem.setState(true);
\r
3089 renderGapsMenuItem.addItemListener(this);
\r
3090 findMenuItem.setLabel("Find...");
\r
3091 findMenuItem.addActionListener(this);
\r
3092 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
3093 abovePIDThreshold.addItemListener(this);
\r
3094 nucleotideColour.setLabel("Nucleotide");
\r
3095 nucleotideColour.addActionListener(this);
\r
3096 deleteGroups.setLabel("Undefine Groups");
\r
3097 deleteGroups.addActionListener(this);
\r
3098 grpsFromSelection.setLabel("Make Groups for selection");
\r
3099 grpsFromSelection.addActionListener(this);
\r
3100 copy.setLabel("Copy");
\r
3101 copy.addActionListener(this);
\r
3102 cut.setLabel("Cut");
\r
3103 cut.addActionListener(this);
\r
3104 delete.setLabel("Delete");
\r
3105 delete.addActionListener(this);
\r
3106 pasteMenu.setLabel("Paste");
\r
3107 pasteNew.setLabel("To New Alignment");
\r
3108 pasteNew.addActionListener(this);
\r
3109 pasteThis.setLabel("Add To This Alignment");
\r
3110 pasteThis.addActionListener(this);
\r
3111 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
3112 applyToAllGroups.setState(true);
\r
3113 applyToAllGroups.addItemListener(this);
\r
3114 font.setLabel("Font...");
\r
3115 font.addActionListener(this);
\r
3116 scaleAbove.setLabel("Scale Above");
\r
3117 scaleAbove.setState(true);
\r
3118 scaleAbove.setEnabled(false);
\r
3119 scaleAbove.addItemListener(this);
\r
3120 scaleLeft.setEnabled(false);
\r
3121 scaleLeft.setState(true);
\r
3122 scaleLeft.setLabel("Scale Left");
\r
3123 scaleLeft.addItemListener(this);
\r
3124 scaleRight.setEnabled(false);
\r
3125 scaleRight.setState(true);
\r
3126 scaleRight.setLabel("Scale Right");
\r
3127 scaleRight.addItemListener(this);
\r
3128 modifyPID.setLabel("Modify Identity Threshold...");
\r
3129 modifyPID.addActionListener(this);
\r
3130 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
3131 modifyConservation.addActionListener(this);
\r
3132 sortByTreeMenu.setLabel("By Tree Order");
\r
3133 sort.setLabel("Sort");
\r
3134 calculate.setLabel("Calculate Tree");
\r
3135 autoCalculate.addItemListener(this);
\r
3136 sortByTree.addItemListener(this);
\r
3137 inputText.setLabel("Input from textbox");
\r
3138 inputText.addActionListener(this);
\r
3139 centreColumnLabelFlag.setLabel("Centre column labels");
\r
3140 centreColumnLabelFlag.addItemListener(this);
\r
3141 followMouseOverFlag.setLabel("Automatic Scrolling");
\r
3142 followMouseOverFlag.addItemListener(this);
\r
3143 helpMenu.setLabel("Help");
\r
3144 documentation.setLabel("Documentation");
\r
3145 documentation.addActionListener(this);
\r
3147 about.setLabel("About...");
\r
3148 about.addActionListener(this);
\r
3149 seqLimits.setState(true);
\r
3150 seqLimits.setLabel("Show Sequence Limits");
\r
3151 seqLimits.addItemListener(this);
\r
3152 featureSettings.setLabel("Feature Settings...");
\r
3153 featureSettings.addActionListener(this);
\r
3154 sequenceFeatures.setLabel("Sequence Features");
\r
3155 sequenceFeatures.addItemListener(this);
\r
3156 sequenceFeatures.setState(false);
\r
3157 annotationColour.setLabel("by Annotation...");
\r
3158 annotationColour.addActionListener(this);
\r
3159 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
\r
3160 invertColSel.setLabel("Invert Column Selection");
\r
3161 menu1.setLabel("Show");
\r
3162 showColumns.setLabel("All Columns ");
\r
3163 showSeqs.setLabel("All Sequences");
\r
3164 menu2.setLabel("Hide");
\r
3165 hideColumns.setLabel("Selected Columns");
\r
3166 hideSequences.setLabel("Selected Sequences");
\r
3167 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
\r
3168 hideAllSelection.setLabel("Selected Region");
\r
3169 showAllHidden.setLabel("All Sequences and Columns");
\r
3170 showGroupConsensus.setLabel("Group Consensus");
\r
3171 showGroupConservation.setLabel("Group Conservation");
\r
3172 showConsensusHistogram.setLabel("Show Consensus Histogram");
\r
3173 showSequenceLogo.setLabel("Show Consensus Logo");
\r
3174 normSequenceLogo.setLabel("Normalise Consensus Logo");
\r
3175 applyAutoAnnotationSettings.setLabel("Apply to all groups");
\r
3176 applyAutoAnnotationSettings.setState(true);
\r
3177 autoAnnMenu.setLabel("Autocalculated Annotation");
\r
3179 invertColSel.addActionListener(this);
\r
3180 showColumns.addActionListener(this);
\r
3181 showSeqs.addActionListener(this);
\r
3182 hideColumns.addActionListener(this);
\r
3183 hideSequences.addActionListener(this);
\r
3184 hideAllButSelection.addActionListener(this);
\r
3185 hideAllSelection.addActionListener(this);
\r
3186 showAllHidden.addActionListener(this);
\r
3187 showGroupConsensus.addItemListener(this);
\r
3188 showGroupConservation.addItemListener(this);
\r
3189 showConsensusHistogram.addItemListener(this);
\r
3190 showSequenceLogo.addItemListener(this);
\r
3191 applyAutoAnnotationSettings.addItemListener(this);
\r
3192 formatMenu.setLabel("Format");
\r
3193 selectMenu.setLabel("Select");
\r
3194 newView.setLabel("New View");
\r
3195 newView.addActionListener(this);
\r
3196 alignFrameMenuBar.add(fileMenu);
\r
3197 alignFrameMenuBar.add(editMenu);
\r
3198 alignFrameMenuBar.add(selectMenu);
\r
3199 alignFrameMenuBar.add(viewMenu);
\r
3200 alignFrameMenuBar.add(formatMenu);
\r
3201 alignFrameMenuBar.add(colourMenu);
\r
3202 alignFrameMenuBar.add(calculateMenu);
\r
3203 alignFrameMenuBar.add(helpMenu);
\r
3205 fileMenu.add(inputText);
\r
3206 fileMenu.add(loadTree);
\r
3207 fileMenu.add(loadAnnotations);
\r
3209 fileMenu.addSeparator();
\r
3210 fileMenu.add(outputTextboxMenu);
\r
3211 fileMenu.add(outputFeatures);
\r
3212 fileMenu.add(outputAnnotations);
\r
3214 if (jalviewServletURL != null)
\r
3216 fileMenu.add(loadApplication);
\r
3219 fileMenu.addSeparator();
\r
3220 fileMenu.add(closeMenuItem);
\r
3222 editMenu.add(undoMenuItem);
\r
3223 editMenu.add(redoMenuItem);
\r
3224 editMenu.add(cut);
\r
3225 editMenu.add(copy);
\r
3226 editMenu.add(pasteMenu);
\r
3227 editMenu.add(delete);
\r
3228 editMenu.addSeparator();
\r
3229 editMenu.add(remove2LeftMenuItem);
\r
3230 editMenu.add(remove2RightMenuItem);
\r
3231 editMenu.add(removeGappedColumnMenuItem);
\r
3232 editMenu.add(removeAllGapsMenuItem);
\r
3233 editMenu.add(removeRedundancyMenuItem);
\r
3234 viewMenu.add(newView);
\r
3235 viewMenu.addSeparator();
\r
3236 viewMenu.add(menu1);
\r
3237 viewMenu.add(menu2);
\r
3238 viewMenu.addSeparator();
\r
3239 viewMenu.add(followMouseOverFlag);
\r
3240 viewMenu.add(annotationPanelMenuItem);
\r
3241 autoAnnMenu.add(applyAutoAnnotationSettings);
\r
3242 autoAnnMenu.add(showConsensusHistogram);
\r
3243 autoAnnMenu.add(showSequenceLogo);
\r
3244 autoAnnMenu.add(normSequenceLogo);
\r
3245 autoAnnMenu.addSeparator();
\r
3246 autoAnnMenu.add(showGroupConservation);
\r
3247 autoAnnMenu.add(showGroupConsensus);
\r
3248 viewMenu.add(autoAnnMenu);
\r
3249 viewMenu.addSeparator();
\r
3250 viewMenu.add(sequenceFeatures);
\r
3251 viewMenu.add(featureSettings);
\r
3252 viewMenu.addSeparator();
\r
3253 viewMenu.add(alProperties);
\r
3254 viewMenu.addSeparator();
\r
3255 viewMenu.add(overviewMenuItem);
\r
3256 colourMenu.add(applyToAllGroups);
\r
3257 colourMenu.addSeparator();
\r
3258 colourMenu.add(noColourmenuItem);
\r
3259 colourMenu.add(clustalColour);
\r
3260 colourMenu.add(BLOSUM62Colour);
\r
3261 colourMenu.add(PIDColour);
\r
3262 colourMenu.add(zappoColour);
\r
3263 colourMenu.add(taylorColour);
\r
3264 colourMenu.add(hydrophobicityColour);
\r
3265 colourMenu.add(helixColour);
\r
3266 colourMenu.add(strandColour);
\r
3267 colourMenu.add(turnColour);
\r
3268 colourMenu.add(buriedColour);
\r
3269 colourMenu.add(nucleotideColour);
\r
3270 colourMenu.add(purinePyrimidineColour);
\r
3271 // colourMenu.add(RNAInteractionColour);
\r
3272 colourMenu.add(tcoffeeColour);
\r
3273 colourMenu.add(userDefinedColour);
\r
3274 colourMenu.addSeparator();
\r
3275 colourMenu.add(conservationMenuItem);
\r
3276 colourMenu.add(modifyConservation);
\r
3277 colourMenu.add(abovePIDThreshold);
\r
3278 colourMenu.add(modifyPID);
\r
3279 colourMenu.add(annotationColour);
\r
3280 colourMenu.add(RNAHelixColour);
\r
3281 calculateMenu.add(sort);
\r
3282 calculateMenu.add(calculate);
\r
3283 calculateMenu.addSeparator();
\r
3284 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
3285 calculateMenu.add(PCAMenuItem);
\r
3286 calculateMenu.add(autoCalculate);
\r
3287 calculateMenu.add(sortByTree);
\r
3288 this.add(statusBar, BorderLayout.SOUTH);
\r
3289 pasteMenu.add(pasteNew);
\r
3290 pasteMenu.add(pasteThis);
\r
3291 sort.add(sortIDMenuItem);
\r
3292 sort.add(sortLengthMenuItem);
\r
3293 sort.add(sortByTreeMenu);
\r
3294 sort.add(sortGroupMenuItem);
\r
3295 sort.add(sortPairwiseMenuItem);
\r
3296 calculate.add(averageDistanceTreeMenuItem);
\r
3297 calculate.add(neighbourTreeMenuItem);
\r
3298 calculate.add(avDistanceTreeBlosumMenuItem);
\r
3299 calculate.add(njTreeBlosumMenuItem);
\r
3300 helpMenu.add(documentation);
\r
3301 helpMenu.add(about);
\r
3302 menu1.add(showColumns);
\r
3303 menu1.add(showSeqs);
\r
3304 menu1.add(showAllHidden);
\r
3305 menu2.add(hideColumns);
\r
3306 menu2.add(hideSequences);
\r
3307 menu2.add(hideAllSelection);
\r
3308 menu2.add(hideAllButSelection);
\r
3309 formatMenu.add(font);
\r
3310 formatMenu.add(seqLimits);
\r
3311 formatMenu.add(wrapMenuItem);
\r
3312 formatMenu.add(scaleAbove);
\r
3313 formatMenu.add(scaleLeft);
\r
3314 formatMenu.add(scaleRight);
\r
3315 formatMenu.add(viewBoxesMenuItem);
\r
3316 formatMenu.add(viewTextMenuItem);
\r
3317 formatMenu.add(colourTextMenuItem);
\r
3318 formatMenu.add(displayNonconservedMenuItem);
\r
3319 formatMenu.add(renderGapsMenuItem);
\r
3320 formatMenu.add(centreColumnLabelFlag);
\r
3321 selectMenu.add(findMenuItem);
\r
3322 selectMenu.addSeparator();
\r
3323 selectMenu.add(selectAllSequenceMenuItem);
\r
3324 selectMenu.add(deselectAllSequenceMenuItem);
\r
3325 selectMenu.add(invertSequenceMenuItem);
\r
3326 selectMenu.add(invertColSel);
\r
3327 selectMenu.add(grpsFromSelection);
\r
3328 selectMenu.add(deleteGroups);
\r
3332 MenuItem featureSettings = new MenuItem();
\r
3334 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
3336 MenuItem annotationColour = new MenuItem();
\r
3338 MenuItem invertColSel = new MenuItem();
\r
3340 Menu menu1 = new Menu();
\r
3342 MenuItem showColumns = new MenuItem();
\r
3344 MenuItem showSeqs = new MenuItem();
\r
3346 Menu menu2 = new Menu();
\r
3348 MenuItem hideColumns = new MenuItem();
\r
3350 MenuItem hideSequences = new MenuItem();
\r
3352 MenuItem hideAllButSelection = new MenuItem();
\r
3354 MenuItem hideAllSelection = new MenuItem();
\r
3356 MenuItem showAllHidden = new MenuItem();
\r
3358 Menu formatMenu = new Menu();
\r
3360 Menu selectMenu = new Menu();
\r
3362 MenuItem newView = new MenuItem();
\r
3365 * Attach the alignFrame panels after embedding menus, if necessary. This used
\r
3366 * to be called setEmbedded, but is now creates the dropdown menus in a
\r
3367 * platform independent manner to avoid OSX/Mac menu appendage daftness.
\r
3369 * @param reallyEmbedded
\r
3370 * true to attach the view to the applet area on the page rather than
\r
3373 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
\r
3375 if (reallyEmbedded)
\r
3378 // Explicly build the embedded menu panel for the on-page applet
\r
3380 // view cannot be closed if its actually on the page
\r
3381 fileMenu.remove(closeMenuItem);
\r
3382 fileMenu.remove(3); // Remove Seperator
\r
3383 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
\r
3384 Font.PLAIN, 10, false); // use our own fonts.
\r
3385 // and actually add the components to the applet area
\r
3386 viewport.applet.setLayout(new BorderLayout());
\r
3387 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
\r
3388 viewport.applet.add(statusBar, BorderLayout.SOUTH);
\r
3389 alignPanel.setSize(viewport.applet.getSize().width,
\r
3390 viewport.applet.getSize().height - embeddedMenu.HEIGHT
\r
3391 - statusBar.HEIGHT);
\r
3392 viewport.applet.add(alignPanel, BorderLayout.CENTER);
\r
3393 final AlignFrame me = this;
\r
3394 viewport.applet.addFocusListener(new FocusListener()
\r
3398 public void focusLost(FocusEvent e)
\r
3400 if (me.viewport.applet.currentAlignFrame == me)
\r
3402 me.viewport.applet.currentAlignFrame = null;
\r
3407 public void focusGained(FocusEvent e)
\r
3409 me.viewport.applet.currentAlignFrame = me;
\r
3412 viewport.applet.validate();
\r
3417 // test and embed menu bar if necessary.
\r
3419 if (embedMenuIfNeeded(alignPanel))
\r
3421 // adjust for status bar height too
\r
3422 alignPanel.setSize(getSize().width, getSize().height
\r
3423 - statusBar.HEIGHT);
\r
3425 add(statusBar, BorderLayout.SOUTH);
\r
3426 add(alignPanel, BorderLayout.CENTER);
\r
3427 // and register with the applet so it can pass external API calls to us
\r
3428 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
\r
3434 * create a new binding between structures in an existing jmol viewer instance
\r
3435 * and an alignpanel with sequences that have existing PDBFile entries. Note,
\r
3436 * this does not open a new Jmol window, or modify the display of the
\r
3437 * structures in the original jmol window. Note This method doesn't work
\r
3438 * without an additional javascript library to exchange messages between the
\r
3439 * distinct applets. See http://issues.jalview.org/browse/JAL-621
\r
3442 * JmolViewer instance
\r
3443 * @param sequenceIds
\r
3444 * - sequence Ids to search for associations
\r
3446 public SequenceStructureBinding addStructureViewInstance(
\r
3447 Object jmolviewer, String[] sequenceIds)
\r
3449 org.jmol.api.JmolViewer viewer = null;
\r
3452 viewer = (org.jmol.api.JmolViewer) jmolviewer;
\r
3453 } catch (ClassCastException ex)
\r
3455 System.err.println("Unsupported viewer object :"
\r
3456 + jmolviewer.getClass());
\r
3458 if (viewer == null)
\r
3460 System.err.println("Can't use this object as a structure viewer:"
\r
3461 + jmolviewer.getClass());
\r
3464 SequenceI[] seqs = null;
\r
3465 if (sequenceIds == null || sequenceIds.length == 0)
\r
3467 seqs = viewport.getAlignment().getSequencesArray();
\r
3471 Vector sqi = new Vector();
\r
3472 AlignmentI al = viewport.getAlignment();
\r
3473 for (int sid = 0; sid < sequenceIds.length; sid++)
\r
3475 SequenceI sq = al.findName(sequenceIds[sid]);
\r
3478 sqi.addElement(sq);
\r
3481 if (sqi.size() > 0)
\r
3483 seqs = new SequenceI[sqi.size()];
\r
3484 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
\r
3486 seqs[sid] = (SequenceI) sqi.elementAt(sid);
\r
3494 ExtJmol jmv = null;
\r
3495 // TODO: search for a jmv that involves viewer
\r
3497 { // create a new viewer/jalview binding.
\r
3498 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
\r
3506 * bind a pdb file to a sequence in the current view
\r
3508 * @param sequenceId
\r
3509 * - sequenceId within the dataset.
\r
3510 * @param pdbEntryString
\r
3511 * - the short name for the PDB file
\r
3513 * - pdb file - either a URL or a valid PDB file.
\r
3514 * @return true if binding was as success TODO: consider making an exception
\r
3515 * structure for indicating when PDB parsing or sequenceId location
\r
3518 public boolean addPdbFile(String sequenceId, String pdbEntryString,
\r
3521 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
\r
3522 boolean needtoadd = false;
\r
3523 if (toaddpdb != null)
\r
3525 Vector pdbe = toaddpdb.getPDBId();
\r
3526 PDBEntry pdbentry = null;
\r
3527 if (pdbe != null && pdbe.size() > 0)
\r
3529 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
\r
3531 pdbentry = (PDBEntry) pdbe.elementAt(pe);
\r
3532 if (!pdbentry.getId().equals(pdbEntryString)
\r
3533 && !pdbentry.getFile().equals(pdbFile))
\r
3543 if (pdbentry == null)
\r
3545 pdbentry = new PDBEntry();
\r
3546 pdbentry.setId(pdbEntryString);
\r
3547 pdbentry.setFile(pdbFile);
\r
3548 needtoadd = true; // add this new entry to sequence.
\r
3550 // resolve data source
\r
3551 // TODO: this code should be a refactored to an io package
\r
3552 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
\r
3553 if (protocol == null)
\r
3559 // make a note of the access mode and add
\r
3560 if (pdbentry.getProperty() == null)
\r
3562 pdbentry.setProperty(new Hashtable());
\r
3564 pdbentry.getProperty().put("protocol", protocol);
\r
3565 toaddpdb.addPDBId(pdbentry);
\r
3571 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
\r
3575 Vector sequences = new Vector();
\r
3576 for (int i = 0; i < seqs.length; i++)
\r
3578 if (seqs[i] != null)
\r
3580 sequences.addElement(new Object[]
\r
3581 { seqs[i], (chains != null) ? chains[i] : null });
\r
3584 seqs = new SequenceI[sequences.size()];
\r
3585 chains = new String[sequences.size()];
\r
3586 for (int i = 0, isize = sequences.size(); i < isize; i++)
\r
3588 Object[] oj = (Object[]) sequences.elementAt(i);
\r
3590 seqs[i] = (SequenceI) oj[0];
\r
3591 chains[i] = (String) oj[1];
\r
3594 return new Object[]
\r
3599 public void newStructureView(JalviewLite applet, PDBEntry pdb,
\r
3600 SequenceI[] seqs, String[] chains, String protocol)
\r
3602 // Scrub any null sequences from the array
\r
3603 Object[] sqch = cleanSeqChainArrays(seqs, chains);
\r
3604 seqs = (SequenceI[]) sqch[0];
\r
3605 chains = (String[]) sqch[1];
\r
3606 if (seqs == null || seqs.length == 0)
\r
3609 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
3611 if (protocol == null || protocol.trim().length() == 0
\r
3612 || protocol.equals("null"))
\r
3614 protocol = (String) pdb.getProperty().get("protocol");
\r
3615 if (protocol == null)
\r
3617 System.err.println("Couldn't work out protocol to open structure: "
\r
3622 if (applet.useXtrnalSviewer)
\r
3624 // register the association(s) and quit, don't create any windows.
\r
3625 if (StructureSelectionManager.getStructureSelectionManager(applet)
\r
3626 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
\r
3628 System.err.println("Failed to map " + pdb.getFile() + " ("
\r
3629 + protocol + ") to any sequences");
\r
3633 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
\r
3635 // can only do alignments with Jmol
\r
3636 // find the last jmol window assigned to this alignment
\r
3637 jalview.appletgui.AppletJmol ajm = null, tajm;
\r
3638 Vector jmols = applet
\r
3639 .getAppletWindow(jalview.appletgui.AppletJmol.class);
\r
3640 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
\r
3642 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
\r
3643 if (tajm.ap.alignFrame == this)
\r
3652 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
3653 // try and add the pdb structure
\r
3658 // otherwise, create a new window
\r
3659 if (applet.jmolAvailable)
\r
3661 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
\r
3663 applet.lastFrameX += 40;
\r
3664 applet.lastFrameY += 40;
\r
3668 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
\r
3673 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
\r
3674 SequenceI[][] seqs, String[][] chains, String[] protocols)
\r
3676 // TODO Auto-generated method stub
\r
3677 System.err.println("Aligned Structure View: Not yet implemented.");
\r
3681 * modify the current selection, providing the user has not made a selection
\r
3685 * - sequences from this alignment
\r
3687 * - columns to be selected on the alignment
\r
3689 public void select(SequenceGroup sel, ColumnSelection csel)
\r
3691 alignPanel.seqPanel.selection(sel, csel, null);
\r
3694 public void scrollTo(int row, int column)
\r
3696 alignPanel.seqPanel.scrollTo(row, column);
\r
3699 public void scrollToRow(int row)
\r
3701 alignPanel.seqPanel.scrollToRow(row);
\r
3704 public void scrollToColumn(int column)
\r
3706 alignPanel.seqPanel.scrollToColumn(column);
\r
3710 * @return the alignments unique ID.
\r
3712 public String getSequenceSetId()
\r
3714 return viewport.getSequenceSetId();
\r
3718 * Load the (T-Coffee) score file from the specified url
\r
3721 * File/URL/T-COFFEE score file contents
\r
3722 * @throws IOException
\r
3723 * @return true if alignment was annotated with data from source
\r
3724 * @throws SAXException
\r
3725 * @throws ParserConfigurationException
\r
3726 * @throws ExceptionFileFormatOrSyntax
\r
3727 * @throws ExceptionLoadingFailed
\r
3728 * @throws ExceptionPermissionDenied
\r
3729 * @throws InterruptedException
\r
3730 * @throws ExceptionUnmatchedClosingParentheses
\r
3732 public boolean loadScoreFile(String source) throws Exception
\r
3735 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
\r
3736 AppletFormatAdapter.checkProtocol(source));
\r
3737 if (!file.isValid())
\r
3739 // TODO: raise dialog for gui
\r
3740 System.err.println("Problems parsing T-Coffee scores: "
\r
3741 + file.getWarningMessage());
\r
3742 System.err.println("Origin was:\n" + source);
\r
3747 * check that the score matrix matches the alignment dimensions
\r
3750 if ((aln = viewport.getAlignment()) != null
\r
3751 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
\r
3754 // TODO: raise a dialog box here rather than bomb out.
\r
3756 .println("The scores matrix does not match the alignment dimensions");
\r
3760 // TODO add parameter to indicate if matching should be done
\r
3761 if (file.annotateAlignment(alignPanel.getAlignment(), false))
\r
3763 alignPanel.fontChanged();
\r
3764 tcoffeeColour.setEnabled(true);
\r
3765 // switch to this color
\r
3766 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
\r
3771 System.err.println("Problems resolving T-Coffee scores:");
\r
3772 if (file.getWarningMessage() != null)
\r
3774 System.err.println(file.getWarningMessage());
\r