2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.appletgui;
20 import jalview.analysis.AlignmentSorter;
21 import jalview.analysis.Conservation;
22 import jalview.api.AlignViewControllerI;
23 import jalview.api.SequenceStructureBinding;
24 import jalview.bin.JalviewLite;
25 import jalview.commands.CommandI;
26 import jalview.commands.EditCommand;
27 import jalview.commands.OrderCommand;
28 import jalview.commands.RemoveGapColCommand;
29 import jalview.commands.RemoveGapsCommand;
30 import jalview.commands.SlideSequencesCommand;
31 import jalview.commands.TrimRegionCommand;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.AlignmentOrder;
35 import jalview.datamodel.ColumnSelection;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.io.AnnotationFile;
41 import jalview.io.AppletFormatAdapter;
42 import jalview.io.FeaturesFile;
43 import jalview.io.TCoffeeScoreFile;
44 import jalview.schemes.Blosum62ColourScheme;
45 import jalview.schemes.BuriedColourScheme;
46 import jalview.schemes.ClustalxColourScheme;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.HelixColourScheme;
49 import jalview.schemes.HydrophobicColourScheme;
50 import jalview.schemes.NucleotideColourScheme;
51 import jalview.schemes.PIDColourScheme;
52 import jalview.schemes.PurinePyrimidineColourScheme;
53 import jalview.schemes.RNAHelicesColourChooser;
54 import jalview.schemes.ResidueProperties;
55 import jalview.schemes.StrandColourScheme;
56 import jalview.schemes.TCoffeeColourScheme;
57 import jalview.schemes.TaylorColourScheme;
58 import jalview.schemes.TurnColourScheme;
59 import jalview.schemes.ZappoColourScheme;
60 import jalview.structure.StructureSelectionManager;
62 import java.awt.BorderLayout;
63 import java.awt.Canvas;
64 import java.awt.CheckboxMenuItem;
65 import java.awt.Color;
67 import java.awt.FontMetrics;
68 import java.awt.Frame;
69 import java.awt.Graphics;
70 import java.awt.Label;
72 import java.awt.MenuBar;
73 import java.awt.MenuItem;
74 import java.awt.event.ActionEvent;
75 import java.awt.event.ActionListener;
76 import java.awt.event.FocusEvent;
77 import java.awt.event.FocusListener;
78 import java.awt.event.ItemEvent;
79 import java.awt.event.ItemListener;
80 import java.awt.event.KeyEvent;
81 import java.awt.event.KeyListener;
82 import java.awt.event.WindowAdapter;
83 import java.awt.event.WindowEvent;
84 import java.io.IOException;
86 import java.net.URLEncoder;
87 import java.util.Enumeration;
88 import java.util.Hashtable;
89 import java.util.List;
90 import java.util.StringTokenizer;
91 import java.util.Vector;
93 public class AlignFrame extends EmbmenuFrame implements ActionListener,
94 ItemListener, KeyListener
96 public AlignViewControllerI avc;
97 public AlignmentPanel alignPanel;
99 public AlignViewport viewport;
101 int DEFAULT_WIDTH = 700;
103 int DEFAULT_HEIGHT = 500;
105 String jalviewServletURL;
107 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
108 String title, boolean embedded)
112 jalviewServletURL = applet.getParameter("APPLICATION_URL");
118 } catch (Exception ex)
120 ex.printStackTrace();
123 viewport = new AlignViewport(al, applet);
124 alignPanel = new AlignmentPanel(this, viewport);
125 avc = new jalview.controller.AlignViewController(viewport, alignPanel);
126 viewport.updateConservation(alignPanel);
127 viewport.updateConsensus(alignPanel);
129 annotationPanelMenuItem.setState(viewport.showAnnotation);
130 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
131 followMouseOverFlag.setState(viewport.getFollowHighlight());
132 showGroupConsensus.setState(viewport.isShowGroupConsensus());
133 showGroupConservation.setState(viewport.isShowGroupConservation());
134 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
135 showSequenceLogo.setState(viewport.isShowSequenceLogo());
136 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
138 seqLimits.setState(viewport.showJVSuffix);
142 String param = applet.getParameter("sortBy");
145 if (param.equalsIgnoreCase("Id"))
147 sortIDMenuItem_actionPerformed();
149 else if (param.equalsIgnoreCase("Pairwise Identity"))
151 sortPairwiseMenuItem_actionPerformed();
153 else if (param.equalsIgnoreCase("Length"))
155 sortLengthMenuItem_actionPerformed();
159 param = applet.getParameter("wrap");
162 if (param.equalsIgnoreCase("true"))
164 wrapMenuItem.setState(true);
165 wrapMenuItem_actionPerformed();
168 param = applet.getParameter("centrecolumnlabels");
171 centreColumnLabelFlag.setState(true);
172 centreColumnLabelFlag_stateChanged();
176 param = applet.getParameter("windowWidth");
179 int width = Integer.parseInt(param);
180 DEFAULT_WIDTH = width;
182 param = applet.getParameter("windowHeight");
185 int height = Integer.parseInt(param);
186 DEFAULT_HEIGHT = height;
188 } catch (Exception ex)
193 if (viewport.getAlignment().isNucleotide())
195 viewport.updateStrucConsensus(alignPanel);
196 if (viewport.getAlignment().hasRNAStructure())
198 RNAHelixColour.setEnabled(true);
202 RNAHelixColour.setEnabled(false);
207 RNAHelixColour.setEnabled(false);
208 purinePyrimidineColour.setEnabled(false);
210 // Some JVMS send keyevents to Top frame or lowest panel,
211 // Havent worked out why yet. So add to both this frame and seqCanvas for
213 this.addKeyListener(this);
214 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
215 alignPanel.idPanel.idCanvas.addKeyListener(this);
216 alignPanel.scalePanel.addKeyListener(this);
217 alignPanel.annotationPanel.addKeyListener(this);
218 alignPanel.annotationPanelHolder.addKeyListener(this);
219 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
220 alignPanel.alabels.addKeyListener(this);
221 createAlignFrameWindow(embedded, title);
224 alignPanel.adjustAnnotationHeight();
225 alignPanel.paintAlignment(true);
228 public AlignViewport getAlignViewport()
233 public SeqCanvas getSeqcanvas()
235 return alignPanel.seqPanel.seqCanvas;
239 * Load a features file onto the alignment
242 * file URL, content, or other resolvable path
244 * is protocol for accessing data referred to by file
247 public boolean parseFeaturesFile(String file, String type)
249 return parseFeaturesFile(file, type, true);
253 * Load a features file onto the alignment
256 * file URL, content, or other resolvable path
258 * is protocol for accessing data referred to by file
259 * @param autoenabledisplay
260 * when true, display features flag will be automatically enabled if
261 * features are loaded
262 * @return true if data parsed as a features file
264 public boolean parseFeaturesFile(String file, String type,
265 boolean autoenabledisplay)
267 // TODO: test if importing a features file onto an alignment which already
268 // has features with links overwrites the original links.
270 Hashtable featureLinks = new Hashtable();
271 boolean featuresFile = false;
274 featuresFile = new jalview.io.FeaturesFile(file, type)
275 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
276 .getFeatureRenderer().featureColours, featureLinks,
277 true, viewport.applet.getDefaultParameter(
278 "relaxedidmatch", false));
279 } catch (Exception ex)
281 ex.printStackTrace();
286 if (featureLinks.size() > 0)
288 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
290 if (autoenabledisplay)
292 viewport.showSequenceFeatures = true;
293 sequenceFeatures.setState(true);
295 if (viewport.featureSettings != null)
297 viewport.featureSettings.refreshTable();
299 alignPanel.paintAlignment(true);
300 statusBar.setText("Successfully added features to alignment.");
306 public void keyPressed(KeyEvent evt)
308 if (viewport.cursorMode
309 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
310 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
311 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
312 && Character.isDigit(evt.getKeyChar()))
313 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
315 switch (evt.getKeyCode())
317 case 27: // escape key
318 deselectAllSequenceMenuItem_actionPerformed();
320 alignPanel.alabels.cancelDrag();
323 if (evt.isControlDown() || evt.isMetaDown())
325 cut_actionPerformed();
329 if (viewport.cursorMode && !evt.isControlDown())
331 alignPanel.seqPanel.setCursorColumn();
333 if (evt.isControlDown() || evt.isMetaDown())
335 copy_actionPerformed();
339 if (evt.isControlDown())
341 paste(evt.isShiftDown());
345 if (evt.isControlDown() || evt.isMetaDown())
347 selectAllSequenceMenuItem_actionPerformed();
350 case KeyEvent.VK_DOWN:
351 if (viewport.cursorMode)
353 alignPanel.seqPanel.moveCursor(0, 1);
357 moveSelectedSequences(false);
362 if (viewport.cursorMode)
364 alignPanel.seqPanel.moveCursor(0, -1);
368 moveSelectedSequences(true);
372 case KeyEvent.VK_LEFT:
373 if (evt.isAltDown() || !viewport.cursorMode)
374 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
376 alignPanel.seqPanel.moveCursor(-1, 0);
379 case KeyEvent.VK_RIGHT:
380 if (evt.isAltDown() || !viewport.cursorMode)
381 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
383 alignPanel.seqPanel.moveCursor(1, 0);
386 case KeyEvent.VK_SPACE:
387 if (viewport.cursorMode)
389 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
390 || evt.isShiftDown() || evt.isAltDown());
394 case KeyEvent.VK_DELETE:
395 case KeyEvent.VK_BACK_SPACE:
396 if (viewport.cursorMode)
398 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
399 || evt.isShiftDown() || evt.isAltDown());
403 cut_actionPerformed();
404 alignPanel.seqPanel.seqCanvas.repaint();
409 if (viewport.cursorMode)
411 alignPanel.seqPanel.setCursorRow();
415 if (viewport.cursorMode)
417 alignPanel.seqPanel.setCursorPosition();
421 case KeyEvent.VK_ENTER:
422 case KeyEvent.VK_COMMA:
423 if (viewport.cursorMode)
425 alignPanel.seqPanel.setCursorRowAndColumn();
430 if (viewport.cursorMode)
432 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
436 if (viewport.cursorMode)
438 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
443 viewport.cursorMode = !viewport.cursorMode;
444 statusBar.setText("Keyboard editing mode is "
445 + (viewport.cursorMode ? "on" : "off"));
446 if (viewport.cursorMode)
448 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
449 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
454 if (evt.isControlDown())
456 findMenuItem_actionPerformed();
462 boolean toggleSeqs = !evt.isControlDown();
463 boolean toggleCols = !evt.isShiftDown();
464 toggleHiddenRegions(toggleSeqs, toggleCols);
468 case KeyEvent.VK_PAGE_UP:
469 if (viewport.wrapAlignment)
471 alignPanel.scrollUp(true);
475 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
476 - viewport.endSeq + viewport.startSeq);
480 case KeyEvent.VK_PAGE_DOWN:
481 if (viewport.wrapAlignment)
483 alignPanel.scrollUp(false);
487 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
488 + viewport.endSeq - viewport.startSeq);
493 if (evt.isControlDown())
495 undoMenuItem_actionPerformed();
500 if (evt.isControlDown())
502 redoMenuItem_actionPerformed();
507 if (evt.isControlDown())
514 if (evt.isControlDown())
516 trimAlignment(false);
521 if (evt.isControlDown())
523 if (evt.isShiftDown())
525 this.removeAllGapsMenuItem_actionPerformed();
529 removeGappedColumnMenuItem_actionPerformed();
534 if (evt.isControlDown())
538 invertColSel_actionPerformed();
542 invertSequenceMenuItem_actionPerformed();
548 if (evt.isControlDown())
550 if (evt.isShiftDown())
552 this.unGroup_actionPerformed();
556 this.createGroup_actionPerformed();
562 if (evt.isControlDown())
564 this.deleteGroups_actionPerformed();
569 if (evt.isControlDown())
576 alignPanel.paintAlignment(true);
580 * called by key handler and the hide all/show all menu items
585 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
587 boolean hide = false;
588 SequenceGroup sg = viewport.getSelectionGroup();
589 if (!toggleSeqs && !toggleCols)
591 // Hide everything by the current selection - this is a hack - we do the
592 // invert and then hide
593 // first check that there will be visible columns after the invert.
594 if ((viewport.getColumnSelection() != null
595 && viewport.getColumnSelection().getSelected() != null && viewport
596 .getColumnSelection().getSelected().size() > 0)
597 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
600 // now invert the sequence set, if required - empty selection implies
601 // that no hiding is required.
604 invertSequenceMenuItem_actionPerformed();
605 sg = viewport.getSelectionGroup();
609 viewport.expandColSelection(sg, true);
610 // finally invert the column selection and get the new sequence
611 // selection and indicate it should be hidden.
612 invertColSel_actionPerformed();
619 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
622 viewport.hideAllSelectedSeqs();
624 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
627 viewport.showAllHiddenSeqs();
633 if (viewport.getColumnSelection().getSelected().size() > 0)
635 viewport.hideSelectedColumns();
638 viewport.setSelectionGroup(sg);
643 viewport.showAllHiddenColumns();
649 public void keyReleased(KeyEvent evt)
654 public void keyTyped(KeyEvent evt)
659 public void itemStateChanged(ItemEvent evt)
661 if (evt.getSource() == displayNonconservedMenuItem)
663 displayNonconservedMenuItem_actionPerformed();
665 else if (evt.getSource() == colourTextMenuItem)
667 colourTextMenuItem_actionPerformed();
669 else if (evt.getSource() == wrapMenuItem)
671 wrapMenuItem_actionPerformed();
673 else if (evt.getSource() == scaleAbove)
675 viewport.setScaleAboveWrapped(scaleAbove.getState());
677 else if (evt.getSource() == scaleLeft)
679 viewport.setScaleLeftWrapped(scaleLeft.getState());
681 else if (evt.getSource() == scaleRight)
683 viewport.setScaleRightWrapped(scaleRight.getState());
685 else if (evt.getSource() == seqLimits)
687 seqLimits_itemStateChanged();
689 else if (evt.getSource() == viewBoxesMenuItem)
691 viewport.setShowBoxes(viewBoxesMenuItem.getState());
693 else if (evt.getSource() == viewTextMenuItem)
695 viewport.setShowText(viewTextMenuItem.getState());
697 else if (evt.getSource() == renderGapsMenuItem)
699 viewport.setRenderGaps(renderGapsMenuItem.getState());
701 else if (evt.getSource() == annotationPanelMenuItem)
703 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
704 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
706 else if (evt.getSource() == sequenceFeatures)
708 viewport.showSequenceFeatures(sequenceFeatures.getState());
709 alignPanel.seqPanel.seqCanvas.repaint();
711 else if (evt.getSource() == conservationMenuItem)
713 conservationMenuItem_actionPerformed();
715 else if (evt.getSource() == abovePIDThreshold)
717 abovePIDThreshold_actionPerformed();
719 else if (evt.getSource() == applyToAllGroups)
721 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
723 else if (evt.getSource() == autoCalculate)
725 viewport.autoCalculateConsensus = autoCalculate.getState();
727 else if (evt.getSource() == sortByTree)
729 viewport.sortByTree = sortByTree.getState();
731 else if (evt.getSource() == this.centreColumnLabelFlag)
733 centreColumnLabelFlag_stateChanged();
735 else if (evt.getSource() == this.followMouseOverFlag)
737 mouseOverFlag_stateChanged();
739 else if (evt.getSource() == showGroupConsensus)
741 showGroupConsensus_actionPerformed();
743 else if (evt.getSource() == showGroupConservation)
745 showGroupConservation_actionPerformed();
747 else if (evt.getSource() == showSequenceLogo)
749 showSequenceLogo_actionPerformed();
751 else if (evt.getSource() == normSequenceLogo)
753 normSequenceLogo_actionPerformed();
755 else if (evt.getSource() == showConsensusHistogram)
757 showConsensusHistogram_actionPerformed();
759 else if (evt.getSource() == applyAutoAnnotationSettings)
761 applyAutoAnnotationSettings_actionPerformed();
763 alignPanel.paintAlignment(true);
766 private void mouseOverFlag_stateChanged()
768 viewport.followHighlight = followMouseOverFlag.getState();
769 // TODO: could kick the scrollTo mechanism to reset view for current
773 private void centreColumnLabelFlag_stateChanged()
775 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
776 this.alignPanel.annotationPanel.repaint();
780 public void actionPerformed(ActionEvent evt)
782 Object source = evt.getSource();
784 if (source == inputText)
786 inputText_actionPerformed();
788 else if (source == loadTree)
790 loadTree_actionPerformed();
792 else if (source == loadApplication)
794 launchFullApplication();
796 else if (source == loadAnnotations)
800 else if (source == outputAnnotations)
802 outputAnnotations(true);
804 else if (source == outputFeatures)
806 outputFeatures(true, "Jalview");
808 else if (source == closeMenuItem)
810 closeMenuItem_actionPerformed();
812 else if (source == copy)
814 copy_actionPerformed();
816 else if (source == undoMenuItem)
818 undoMenuItem_actionPerformed();
820 else if (source == redoMenuItem)
822 redoMenuItem_actionPerformed();
824 else if (source == inputText)
826 inputText_actionPerformed();
828 else if (source == closeMenuItem)
830 closeMenuItem_actionPerformed();
832 else if (source == undoMenuItem)
834 undoMenuItem_actionPerformed();
836 else if (source == redoMenuItem)
838 redoMenuItem_actionPerformed();
840 else if (source == copy)
842 copy_actionPerformed();
844 else if (source == pasteNew)
846 pasteNew_actionPerformed();
848 else if (source == pasteThis)
850 pasteThis_actionPerformed();
852 else if (source == cut)
854 cut_actionPerformed();
856 else if (source == delete)
858 delete_actionPerformed();
860 else if (source == grpsFromSelection)
862 makeGrpsFromSelection_actionPerformed();
864 else if (source == deleteGroups)
866 deleteGroups_actionPerformed();
868 else if (source == selectAllSequenceMenuItem)
870 selectAllSequenceMenuItem_actionPerformed();
872 else if (source == deselectAllSequenceMenuItem)
874 deselectAllSequenceMenuItem_actionPerformed();
876 else if (source == invertSequenceMenuItem)
878 invertSequenceMenuItem_actionPerformed();
880 else if (source == invertColSel)
882 viewport.invertColumnSelection();
883 alignPanel.paintAlignment(true);
885 else if (source == remove2LeftMenuItem)
889 else if (source == remove2RightMenuItem)
891 trimAlignment(false);
893 else if (source == removeGappedColumnMenuItem)
895 removeGappedColumnMenuItem_actionPerformed();
897 else if (source == removeAllGapsMenuItem)
899 removeAllGapsMenuItem_actionPerformed();
901 else if (source == findMenuItem)
903 findMenuItem_actionPerformed();
905 else if (source == font)
907 new FontChooser(alignPanel);
909 else if (source == newView)
913 else if (source == showColumns)
915 viewport.showAllHiddenColumns();
916 alignPanel.paintAlignment(true);
918 else if (source == showSeqs)
920 viewport.showAllHiddenSeqs();
921 alignPanel.paintAlignment(true);
923 else if (source == hideColumns)
925 viewport.hideSelectedColumns();
926 alignPanel.paintAlignment(true);
928 else if (source == hideSequences
929 && viewport.getSelectionGroup() != null)
931 viewport.hideAllSelectedSeqs();
932 alignPanel.paintAlignment(true);
934 else if (source == hideAllButSelection)
936 toggleHiddenRegions(false, false);
937 alignPanel.paintAlignment(true);
939 else if (source == hideAllSelection)
941 SequenceGroup sg = viewport.getSelectionGroup();
942 viewport.expandColSelection(sg, false);
943 viewport.hideAllSelectedSeqs();
944 viewport.hideSelectedColumns();
945 alignPanel.paintAlignment(true);
947 else if (source == showAllHidden)
949 viewport.showAllHiddenColumns();
950 viewport.showAllHiddenSeqs();
951 alignPanel.paintAlignment(true);
953 else if (source == showGroupConsensus)
955 showGroupConsensus_actionPerformed();
957 else if (source == showGroupConservation)
959 showGroupConservation_actionPerformed();
961 else if (source == showSequenceLogo)
963 showSequenceLogo_actionPerformed();
965 else if (source == normSequenceLogo)
967 normSequenceLogo_actionPerformed();
969 else if (source == showConsensusHistogram)
971 showConsensusHistogram_actionPerformed();
973 else if (source == applyAutoAnnotationSettings)
975 applyAutoAnnotationSettings_actionPerformed();
977 else if (source == featureSettings)
979 new FeatureSettings(alignPanel);
981 else if (source == alProperties)
983 StringBuffer contents = new jalview.io.AlignmentProperties(
984 viewport.getAlignment()).formatAsString();
985 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
986 cap.setText(contents.toString());
987 Frame frame = new Frame();
989 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
990 + getTitle(), 400, 250);
992 else if (source == overviewMenuItem)
994 overviewMenuItem_actionPerformed();
996 else if (source == noColourmenuItem)
1000 else if (source == clustalColour)
1002 abovePIDThreshold.setState(false);
1003 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1005 else if (source == zappoColour)
1007 changeColour(new ZappoColourScheme());
1009 else if (source == taylorColour)
1011 changeColour(new TaylorColourScheme());
1013 else if (source == hydrophobicityColour)
1015 changeColour(new HydrophobicColourScheme());
1017 else if (source == helixColour)
1019 changeColour(new HelixColourScheme());
1021 else if (source == strandColour)
1023 changeColour(new StrandColourScheme());
1025 else if (source == turnColour)
1027 changeColour(new TurnColourScheme());
1029 else if (source == buriedColour)
1031 changeColour(new BuriedColourScheme());
1033 else if (source == nucleotideColour)
1035 changeColour(new NucleotideColourScheme());
1037 else if (source == purinePyrimidineColour)
1039 changeColour(new PurinePyrimidineColourScheme());
1041 else if (source == RNAHelixColour)
1043 new RNAHelicesColourChooser(viewport, alignPanel);
1045 else if (source == modifyPID)
1047 modifyPID_actionPerformed();
1049 else if (source == modifyConservation)
1051 modifyConservation_actionPerformed();
1053 else if (source == userDefinedColour)
1055 new UserDefinedColours(alignPanel, null);
1057 else if (source == PIDColour)
1059 changeColour(new PIDColourScheme());
1061 else if (source == BLOSUM62Colour)
1063 changeColour(new Blosum62ColourScheme());
1065 else if (source == tcoffeeColour)
1067 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1069 else if (source == annotationColour)
1071 new AnnotationColourChooser(viewport, alignPanel);
1073 else if (source == sortPairwiseMenuItem)
1075 sortPairwiseMenuItem_actionPerformed();
1077 else if (source == sortIDMenuItem)
1079 sortIDMenuItem_actionPerformed();
1081 else if (source == sortLengthMenuItem)
1083 sortLengthMenuItem_actionPerformed();
1085 else if (source == sortGroupMenuItem)
1087 sortGroupMenuItem_actionPerformed();
1089 else if (source == removeRedundancyMenuItem)
1091 removeRedundancyMenuItem_actionPerformed();
1093 else if (source == pairwiseAlignmentMenuItem)
1095 pairwiseAlignmentMenuItem_actionPerformed();
1097 else if (source == PCAMenuItem)
1099 PCAMenuItem_actionPerformed();
1101 else if (source == averageDistanceTreeMenuItem)
1103 averageDistanceTreeMenuItem_actionPerformed();
1105 else if (source == neighbourTreeMenuItem)
1107 neighbourTreeMenuItem_actionPerformed();
1109 else if (source == njTreeBlosumMenuItem)
1111 njTreeBlosumMenuItem_actionPerformed();
1113 else if (source == avDistanceTreeBlosumMenuItem)
1115 avTreeBlosumMenuItem_actionPerformed();
1117 else if (source == documentation)
1119 documentation_actionPerformed();
1121 else if (source == about)
1123 about_actionPerformed();
1128 public void inputText_actionPerformed()
1130 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1131 Frame frame = new Frame();
1133 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
1136 protected void outputText_actionPerformed(ActionEvent e)
1138 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1139 Frame frame = new Frame();
1141 jalview.bin.JalviewLite.addFrame(frame,
1142 "Alignment output - " + e.getActionCommand(), 600, 500);
1143 cap.setText(new AppletFormatAdapter().formatSequences(
1144 e.getActionCommand(), viewport.getAlignment(),
1145 viewport.showJVSuffix));
1148 public void loadAnnotations()
1150 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1151 cap.setText("Paste your features / annotations / T-coffee score file here.");
1152 cap.setAnnotationImport();
1153 Frame frame = new Frame();
1155 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
1159 public String outputAnnotations(boolean displayTextbox)
1161 String annotation = new AnnotationFile().printAnnotations(
1162 viewport.showAnnotation ? viewport.getAlignment()
1163 .getAlignmentAnnotation() : null, viewport
1164 .getAlignment().getGroups(), ((Alignment) viewport
1165 .getAlignment()).alignmentProperties);
1169 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1170 Frame frame = new Frame();
1172 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
1173 cap.setText(annotation);
1179 private Hashtable getDisplayedFeatureCols()
1181 if (alignPanel.getFeatureRenderer() != null
1182 && viewport.featuresDisplayed != null)
1184 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1185 Hashtable fcols = new Hashtable();
1186 Enumeration en = viewport.featuresDisplayed.keys();
1187 while (en.hasMoreElements())
1189 Object col = en.nextElement();
1190 fcols.put(col, fr.featureColours.get(col));
1197 public String outputFeatures(boolean displayTextbox, String format)
1200 if (format.equalsIgnoreCase("Jalview"))
1202 features = new FeaturesFile().printJalviewFormat(viewport
1203 .getAlignment().getSequencesArray(),
1204 getDisplayedFeatureCols());
1208 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1209 .getSequencesArray(), getDisplayedFeatureCols());
1214 boolean frimport = false;
1215 if (features == null || features.equals("No Features Visible"))
1217 features = "# No features visible - paste some and import them here.";
1221 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1224 cap.setAnnotationImport();
1226 Frame frame = new Frame();
1228 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1229 cap.setText(features);
1233 if (features == null)
1240 void launchFullApplication()
1242 StringBuffer url = new StringBuffer(jalviewServletURL);
1245 + appendProtocol(viewport.applet.getParameter("file")));
1247 if (viewport.applet.getParameter("features") != null)
1249 url.append("&features=");
1250 url.append(appendProtocol(viewport.applet.getParameter("features")));
1253 if (viewport.applet.getParameter("annotations") != null)
1255 url.append("&annotations=");
1256 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1259 if (viewport.applet.getParameter("jnetfile") != null)
1261 url.append("&annotations=");
1262 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1265 if (viewport.applet.getParameter("defaultColour") != null)
1267 url.append("&colour="
1268 + removeWhiteSpace(viewport.applet
1269 .getParameter("defaultColour")));
1272 if (viewport.applet.getParameter("userDefinedColour") != null)
1274 url.append("&colour="
1275 + removeWhiteSpace(viewport.applet
1276 .getParameter("userDefinedColour")));
1278 if (viewport.applet.getParameter("tree") != null)
1281 + appendProtocol(viewport.applet.getParameter("tree")));
1283 if (viewport.applet.getParameter("treeFile") != null)
1286 + appendProtocol(viewport.applet.getParameter("treeFile")));
1289 showURL(url.toString(), "FULL_APP");
1292 String removeWhiteSpace(String colour)
1294 StringBuffer sb = new StringBuffer();
1295 for (int i = 0; i < colour.length(); i++)
1297 if (Character.isWhitespace(colour.charAt(i)))
1303 sb.append(colour.charAt(i));
1307 return sb.toString();
1310 String appendProtocol(String url)
1315 url = URLEncoder.encode(url);
1318 * When we finally deprecate 1.1 compatibility, we can start to use
1319 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1320 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1321 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1322 * ex.printStackTrace(); }
1324 catch (java.net.MalformedURLException ex)
1326 url = viewport.applet.getCodeBase() + url;
1331 public void closeMenuItem_actionPerformed()
1333 PaintRefresher.RemoveComponent(alignPanel);
1334 if (alignPanel.seqPanel != null
1335 && alignPanel.seqPanel.seqCanvas != null)
1337 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1339 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1341 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1344 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1359 void updateEditMenuBar()
1362 if (viewport.historyList.size() > 0)
1364 undoMenuItem.setEnabled(true);
1365 CommandI command = (CommandI) viewport.historyList.peek();
1366 undoMenuItem.setLabel("Undo " + command.getDescription());
1370 undoMenuItem.setEnabled(false);
1371 undoMenuItem.setLabel("Undo");
1374 if (viewport.redoList.size() > 0)
1376 redoMenuItem.setEnabled(true);
1378 CommandI command = (CommandI) viewport.redoList.peek();
1379 redoMenuItem.setLabel("Redo " + command.getDescription());
1383 redoMenuItem.setEnabled(false);
1384 redoMenuItem.setLabel("Redo");
1391 public void addHistoryItem(CommandI command)
1393 if (command.getSize() > 0)
1395 viewport.historyList.push(command);
1396 viewport.redoList.removeAllElements();
1397 updateEditMenuBar();
1398 viewport.updateHiddenColumns();
1403 * TODO: JAL-1104 DOCUMENT ME!
1408 protected void undoMenuItem_actionPerformed()
1410 if (viewport.historyList.size() < 1)
1415 CommandI command = (CommandI) viewport.historyList.pop();
1416 viewport.redoList.push(command);
1417 command.undoCommand(null);
1419 AlignViewport originalSource = getOriginatingSource(command);
1421 if (originalSource != viewport)
1424 .println("Warning: Viewport object mismatch whilst undoing");
1426 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1427 // viewport.getColumnSelection().getHiddenColumns()
1429 updateEditMenuBar();
1430 originalSource.firePropertyChange("alignment", null, originalSource
1431 .getAlignment().getSequences());
1435 * TODO: JAL-1104 DOCUMENT ME!
1440 protected void redoMenuItem_actionPerformed()
1442 if (viewport.redoList.size() < 1)
1447 CommandI command = (CommandI) viewport.redoList.pop();
1448 viewport.historyList.push(command);
1449 command.doCommand(null);
1451 AlignViewport originalSource = getOriginatingSource(command);
1453 if (originalSource != viewport)
1456 .println("Warning: Viewport object mismatch whilst re-doing");
1458 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1459 // viewport.getColumnSelection().getHiddenColumns()
1462 updateEditMenuBar();
1463 originalSource.firePropertyChange("alignment", null, originalSource
1464 .getAlignment().getSequences());
1467 AlignViewport getOriginatingSource(CommandI command)
1469 AlignViewport originalSource = null;
1470 // For sequence removal and addition, we need to fire
1471 // the property change event FROM the viewport where the
1472 // original alignment was altered
1473 AlignmentI al = null;
1474 if (command instanceof EditCommand)
1476 EditCommand editCommand = (EditCommand) command;
1477 al = editCommand.getAlignment();
1478 Vector comps = (Vector) PaintRefresher.components.get(viewport
1479 .getSequenceSetId());
1480 for (int i = 0; i < comps.size(); i++)
1482 if (comps.elementAt(i) instanceof AlignmentPanel)
1484 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1486 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1493 if (originalSource == null)
1495 // The original view is closed, we must validate
1496 // the current view against the closed view first
1499 PaintRefresher.validateSequences(al, viewport.getAlignment());
1502 originalSource = viewport;
1505 return originalSource;
1508 public void moveSelectedSequences(boolean up)
1510 SequenceGroup sg = viewport.getSelectionGroup();
1515 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1516 up ? null : viewport.getHiddenRepSequences(), up);
1517 alignPanel.paintAlignment(true);
1520 synchronized void slideSequences(boolean right, int size)
1522 List<SequenceI> sg = new Vector<SequenceI>();
1523 if (viewport.cursorMode)
1525 sg.add(viewport.getAlignment().getSequenceAt(
1526 alignPanel.seqPanel.seqCanvas.cursorY));
1528 else if (viewport.getSelectionGroup() != null
1529 && viewport.getSelectionGroup().getSize() != viewport
1530 .getAlignment().getHeight())
1532 sg = viewport.getSelectionGroup().getSequences(
1533 viewport.getHiddenRepSequences());
1541 Vector<SequenceI> invertGroup = new Vector();
1543 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1545 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1546 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1549 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1551 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1553 for (int i = 0; i < invertGroup.size(); i++)
1554 seqs2[i] = invertGroup.elementAt(i);
1556 SlideSequencesCommand ssc;
1558 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1559 size, viewport.getGapCharacter());
1561 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1562 size, viewport.getGapCharacter());
1564 int groupAdjustment = 0;
1565 if (ssc.getGapsInsertedBegin() && right)
1567 if (viewport.cursorMode)
1568 alignPanel.seqPanel.moveCursor(size, 0);
1570 groupAdjustment = size;
1572 else if (!ssc.getGapsInsertedBegin() && !right)
1574 if (viewport.cursorMode)
1575 alignPanel.seqPanel.moveCursor(-size, 0);
1577 groupAdjustment = -size;
1580 if (groupAdjustment != 0)
1582 viewport.getSelectionGroup().setStartRes(
1583 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1584 viewport.getSelectionGroup().setEndRes(
1585 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1588 boolean appendHistoryItem = false;
1589 if (viewport.historyList != null && viewport.historyList.size() > 0
1590 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1592 appendHistoryItem = ssc
1593 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1597 if (!appendHistoryItem)
1598 addHistoryItem(ssc);
1603 static StringBuffer copiedSequences;
1605 static Vector copiedHiddenColumns;
1607 protected void copy_actionPerformed()
1609 if (viewport.getSelectionGroup() == null)
1614 SequenceGroup sg = viewport.getSelectionGroup();
1615 copiedSequences = new StringBuffer();
1616 Hashtable orderedSeqs = new Hashtable();
1617 for (int i = 0; i < sg.getSize(); i++)
1619 SequenceI seq = sg.getSequenceAt(i);
1620 int index = viewport.getAlignment().findIndex(seq);
1621 orderedSeqs.put(index + "", seq);
1624 int index = 0, startRes, endRes;
1627 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1629 copiedHiddenColumns = new Vector();
1630 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1631 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1634 int[] region = (int[]) viewport.getColumnSelection()
1635 .getHiddenColumns().elementAt(i);
1637 copiedHiddenColumns.addElement(new int[]
1638 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1643 copiedHiddenColumns = null;
1646 for (int i = 0; i < sg.getSize(); i++)
1648 SequenceI seq = null;
1652 if (orderedSeqs.containsKey(index + ""))
1654 seq = (SequenceI) orderedSeqs.get(index + "");
1666 // Returns residue following index if gap
1667 startRes = seq.findPosition(sg.getStartRes());
1670 // Need to find the residue preceeding index if gap
1673 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1675 ch = seq.getCharAt(j);
1676 if (!jalview.util.Comparison.isGap((ch)))
1684 endRes += seq.getStart() - 1;
1687 copiedSequences.append(seq.getName()
1693 + seq.getSequenceAsString(sg.getStartRes(),
1694 sg.getEndRes() + 1) + "\n");
1699 protected void pasteNew_actionPerformed()
1704 protected void pasteThis_actionPerformed()
1709 void paste(boolean newAlignment)
1714 if (copiedSequences == null)
1719 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1720 Vector seqs = new Vector();
1721 while (st.hasMoreElements())
1723 String name = st.nextToken();
1724 int start = Integer.parseInt(st.nextToken());
1725 int end = Integer.parseInt(st.nextToken());
1726 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1728 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1729 for (int i = 0; i < seqs.size(); i++)
1731 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1736 String newtitle = new String("Copied sequences");
1737 if (getTitle().startsWith("Copied sequences"))
1739 newtitle = getTitle();
1743 newtitle = newtitle.concat("- from " + getTitle());
1745 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1746 viewport.applet, newtitle, false);
1747 if (copiedHiddenColumns != null)
1749 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1751 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1752 af.viewport.hideColumns(region[0], region[1]);
1756 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1761 addSequences(newSeqs);
1764 } catch (Exception ex)
1766 } // could be anything being pasted in here
1770 void addSequences(SequenceI[] seqs)
1772 for (int i = 0; i < seqs.length; i++)
1774 viewport.getAlignment().addSequence(seqs[i]);
1778 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1779 seqs, 0, viewport.getAlignment().getWidth(),
1780 viewport.getAlignment()));
1782 viewport.setEndSeq(viewport.getAlignment().getHeight());
1783 viewport.getAlignment().getWidth();
1784 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1789 protected void cut_actionPerformed()
1791 copy_actionPerformed();
1792 delete_actionPerformed();
1795 protected void delete_actionPerformed()
1798 SequenceGroup sg = viewport.getSelectionGroup();
1804 Vector seqs = new Vector();
1806 for (int i = 0; i < sg.getSize(); i++)
1808 seq = sg.getSequenceAt(i);
1809 seqs.addElement(seq);
1812 // If the cut affects all sequences, remove highlighted columns
1813 if (sg.getSize() == viewport.getAlignment().getHeight())
1815 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1816 sg.getEndRes() + 1);
1819 SequenceI[] cut = new SequenceI[seqs.size()];
1820 for (int i = 0; i < seqs.size(); i++)
1822 cut[i] = (SequenceI) seqs.elementAt(i);
1826 * //ADD HISTORY ITEM
1828 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1829 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1830 viewport.getAlignment()));
1832 viewport.setSelectionGroup(null);
1833 viewport.getAlignment().deleteGroup(sg);
1835 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1838 if (viewport.getAlignment().getHeight() < 1)
1840 this.setVisible(false);
1842 viewport.sendSelection();
1846 * group consensus toggled
1849 protected void showGroupConsensus_actionPerformed()
1851 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1852 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1857 * group conservation toggled.
1859 protected void showGroupConservation_actionPerformed()
1861 viewport.setShowGroupConservation(showGroupConservation.getState());
1862 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1869 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1870 * .event.ActionEvent)
1872 protected void showConsensusHistogram_actionPerformed()
1874 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1875 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1882 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1883 * .event.ActionEvent)
1885 protected void showSequenceLogo_actionPerformed()
1887 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1888 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1891 protected void normSequenceLogo_actionPerformed()
1893 showSequenceLogo.setState(true);
1894 viewport.setShowSequenceLogo(true);
1895 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1896 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1899 protected void applyAutoAnnotationSettings_actionPerformed()
1901 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1904 protected void makeGrpsFromSelection_actionPerformed()
1906 if (avc.makeGroupsFromSelection()) {
1907 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1908 alignPanel.updateAnnotation();
1909 alignPanel.paintAlignment(true);
1913 protected void createGroup_actionPerformed()
1917 protected void unGroup_actionPerformed()
1921 alignPanel.alignmentChanged();
1924 protected void deleteGroups_actionPerformed()
1926 if (avc.deleteGroups())
1928 alignPanel.alignmentChanged();
1932 public void selectAllSequenceMenuItem_actionPerformed()
1934 SequenceGroup sg = new SequenceGroup();
1935 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1937 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1939 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1940 viewport.setSelectionGroup(sg);
1941 alignPanel.paintAlignment(true);
1942 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1943 viewport.sendSelection();
1946 public void deselectAllSequenceMenuItem_actionPerformed()
1948 if (viewport.cursorMode)
1950 alignPanel.seqPanel.keyboardNo1 = null;
1951 alignPanel.seqPanel.keyboardNo2 = null;
1953 viewport.setSelectionGroup(null);
1954 viewport.getColumnSelection().clear();
1955 viewport.setSelectionGroup(null);
1956 alignPanel.idPanel.idCanvas.searchResults = null;
1957 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1958 alignPanel.paintAlignment(true);
1959 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1960 viewport.sendSelection();
1963 public void invertSequenceMenuItem_actionPerformed()
1965 SequenceGroup sg = viewport.getSelectionGroup();
1966 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1968 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1971 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1972 viewport.sendSelection();
1975 public void invertColSel_actionPerformed()
1977 viewport.invertColumnSelection();
1978 alignPanel.paintAlignment(true);
1979 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1980 viewport.sendSelection();
1983 void trimAlignment(boolean trimLeft)
1985 ColumnSelection colSel = viewport.getColumnSelection();
1988 if (colSel.size() > 0)
1992 column = colSel.getMin();
1996 column = colSel.getMax();
2000 if (viewport.getSelectionGroup() != null)
2002 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2003 viewport.getHiddenRepSequences());
2007 seqs = viewport.getAlignment().getSequencesArray();
2010 TrimRegionCommand trimRegion;
2013 trimRegion = new TrimRegionCommand("Remove Left",
2014 TrimRegionCommand.TRIM_LEFT, seqs, column,
2015 viewport.getAlignment(), viewport.getColumnSelection(),
2016 viewport.getSelectionGroup());
2017 viewport.setStartRes(0);
2021 trimRegion = new TrimRegionCommand("Remove Right",
2022 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2023 viewport.getAlignment(), viewport.getColumnSelection(),
2024 viewport.getSelectionGroup());
2027 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2029 addHistoryItem(trimRegion);
2031 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2033 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2034 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2036 viewport.getAlignment().deleteGroup(sg);
2040 viewport.firePropertyChange("alignment", null, viewport
2041 .getAlignment().getSequences());
2045 public void removeGappedColumnMenuItem_actionPerformed()
2047 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2050 if (viewport.getSelectionGroup() != null)
2052 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2053 viewport.getHiddenRepSequences());
2054 start = viewport.getSelectionGroup().getStartRes();
2055 end = viewport.getSelectionGroup().getEndRes();
2059 seqs = viewport.getAlignment().getSequencesArray();
2062 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2063 "Remove Gapped Columns", seqs, start, end,
2064 viewport.getAlignment());
2066 addHistoryItem(removeGapCols);
2068 statusBar.setText("Removed " + removeGapCols.getSize()
2069 + " empty columns.");
2071 // This is to maintain viewport position on first residue
2072 // of first sequence
2073 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2074 int startRes = seq.findPosition(viewport.startRes);
2075 // ShiftList shifts;
2076 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2077 // edit.alColumnChanges=shifts.getInverse();
2078 // if (viewport.hasHiddenColumns)
2079 // viewport.getColumnSelection().compensateForEdits(shifts);
2080 viewport.setStartRes(seq.findIndex(startRes) - 1);
2081 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2086 public void removeAllGapsMenuItem_actionPerformed()
2088 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2091 if (viewport.getSelectionGroup() != null)
2093 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2094 viewport.getHiddenRepSequences());
2095 start = viewport.getSelectionGroup().getStartRes();
2096 end = viewport.getSelectionGroup().getEndRes();
2100 seqs = viewport.getAlignment().getSequencesArray();
2103 // This is to maintain viewport position on first residue
2104 // of first sequence
2105 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2106 int startRes = seq.findPosition(viewport.startRes);
2108 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2109 viewport.getAlignment()));
2111 viewport.setStartRes(seq.findIndex(startRes) - 1);
2113 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2118 public void findMenuItem_actionPerformed()
2120 new Finder(alignPanel);
2124 * create a new view derived from the current view
2127 * @return frame for the new view
2129 public AlignFrame newView(String viewtitle)
2132 if (viewport.hasHiddenRows())
2134 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2135 .getFullAlignment().getSequencesArray());
2139 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2142 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2144 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2146 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2148 newal.addAnnotation(viewport.getAlignment()
2149 .getAlignmentAnnotation()[i]);
2154 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2156 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2157 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2158 PaintRefresher.Register(newaf.alignPanel,
2159 newaf.alignPanel.av.getSequenceSetId());
2161 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2162 newaf.alignPanel.av.getSequenceSetId());
2163 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2164 newaf.alignPanel.av.getSequenceSetId());
2166 Vector comps = (Vector) PaintRefresher.components.get(viewport
2167 .getSequenceSetId());
2169 for (int i = 0; i < comps.size(); i++)
2171 if (comps.elementAt(i) instanceof AlignmentPanel)
2177 String title = new String(this.getTitle());
2178 if (viewtitle != null)
2180 title = viewtitle + " ( " + title + ")";
2184 if (title.indexOf("(View") > -1)
2186 title = title.substring(0, title.indexOf("(View"));
2188 title += "(View " + viewSize + ")";
2191 newaf.setTitle(title.toString());
2193 newaf.viewport.historyList = viewport.historyList;
2194 newaf.viewport.redoList = viewport.redoList;
2200 * @return list of feature groups on the view
2202 public String[] getFeatureGroups()
2204 FeatureRenderer fr = null;
2205 if (alignPanel != null
2206 && (fr = alignPanel.getFeatureRenderer()) != null)
2208 return fr.getGroups();
2214 * get sequence feature groups that are hidden or shown
2220 public String[] getFeatureGroupsOfState(boolean visible)
2222 FeatureRenderer fr = null;
2223 if (alignPanel != null
2224 && (fr = alignPanel.getFeatureRenderer()) != null)
2226 return fr.getGroups(visible);
2232 * Change the display state for the given feature groups
2235 * list of group strings
2237 * visible or invisible
2239 public void setFeatureGroupState(String[] groups, boolean state)
2241 FeatureRenderer fr = null;
2242 this.sequenceFeatures.setState(true);
2243 viewport.showSequenceFeatures(true);
2244 if (alignPanel != null
2245 && (fr = alignPanel.getFeatureRenderer()) != null)
2247 fr.setGroupState(groups, state);
2248 alignPanel.seqPanel.seqCanvas.repaint();
2249 if (alignPanel.overviewPanel != null)
2251 alignPanel.overviewPanel.updateOverviewImage();
2256 public void seqLimits_itemStateChanged()
2258 viewport.setShowJVSuffix(seqLimits.getState());
2259 alignPanel.fontChanged();
2260 alignPanel.paintAlignment(true);
2263 protected void colourTextMenuItem_actionPerformed()
2265 viewport.setColourText(colourTextMenuItem.getState());
2266 alignPanel.paintAlignment(true);
2269 protected void displayNonconservedMenuItem_actionPerformed()
2271 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2272 alignPanel.paintAlignment(true);
2275 protected void wrapMenuItem_actionPerformed()
2277 viewport.setWrapAlignment(wrapMenuItem.getState());
2278 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2279 scaleAbove.setEnabled(wrapMenuItem.getState());
2280 scaleLeft.setEnabled(wrapMenuItem.getState());
2281 scaleRight.setEnabled(wrapMenuItem.getState());
2282 alignPanel.paintAlignment(true);
2285 public void overviewMenuItem_actionPerformed()
2287 if (alignPanel.overviewPanel != null)
2292 Frame frame = new Frame();
2293 OverviewPanel overview = new OverviewPanel(alignPanel);
2294 frame.add(overview);
2295 // +50 must allow for applet frame window
2296 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2297 overview.getPreferredSize().width,
2298 overview.getPreferredSize().height + 50);
2301 final AlignmentPanel ap = alignPanel;
2302 frame.addWindowListener(new WindowAdapter()
2305 public void windowClosing(WindowEvent e)
2309 ap.setOverviewPanel(null);
2314 alignPanel.setOverviewPanel(overview);
2318 void changeColour(ColourSchemeI cs)
2324 if (viewport.getAbovePIDThreshold())
2326 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2329 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2331 viewport.setGlobalColourScheme(cs);
2335 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2338 if (viewport.getConservationSelected())
2341 Alignment al = (Alignment) viewport.getAlignment();
2342 Conservation c = new Conservation("All",
2343 ResidueProperties.propHash, 3, al.getSequences(), 0,
2347 c.verdict(false, viewport.getConsPercGaps());
2349 cs.setConservation(c);
2351 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2357 cs.setConservation(null);
2360 cs.setConsensus(viewport.getSequenceConsensusHash());
2363 viewport.setGlobalColourScheme(cs);
2365 if (alignPanel.getOverviewPanel() != null)
2367 alignPanel.getOverviewPanel().updateOverviewImage();
2370 jalview.structure.StructureSelectionManager
2371 .getStructureSelectionManager(viewport.applet)
2372 .sequenceColoursChanged(alignPanel);
2374 alignPanel.paintAlignment(true);
2377 protected void modifyPID_actionPerformed()
2379 if (viewport.getAbovePIDThreshold()
2380 && viewport.getGlobalColourScheme() != null)
2382 SliderPanel.setPIDSliderSource(alignPanel,
2383 viewport.getGlobalColourScheme(), "Background");
2384 SliderPanel.showPIDSlider();
2388 protected void modifyConservation_actionPerformed()
2390 if (viewport.getConservationSelected()
2391 && viewport.getGlobalColourScheme() != null)
2393 SliderPanel.setConservationSlider(alignPanel,
2394 viewport.getGlobalColourScheme(), "Background");
2395 SliderPanel.showConservationSlider();
2399 protected void conservationMenuItem_actionPerformed()
2401 viewport.setConservationSelected(conservationMenuItem.getState());
2403 viewport.setAbovePIDThreshold(false);
2404 abovePIDThreshold.setState(false);
2406 changeColour(viewport.getGlobalColourScheme());
2408 modifyConservation_actionPerformed();
2411 public void abovePIDThreshold_actionPerformed()
2413 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2415 conservationMenuItem.setState(false);
2416 viewport.setConservationSelected(false);
2418 changeColour(viewport.getGlobalColourScheme());
2420 modifyPID_actionPerformed();
2423 public void sortPairwiseMenuItem_actionPerformed()
2425 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2426 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2427 .getAlignment().getSequenceAt(0), null);
2429 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2430 viewport.getAlignment()));
2431 alignPanel.paintAlignment(true);
2434 public void sortIDMenuItem_actionPerformed()
2436 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2437 AlignmentSorter.sortByID(viewport.getAlignment());
2438 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2439 viewport.getAlignment()));
2440 alignPanel.paintAlignment(true);
2443 public void sortLengthMenuItem_actionPerformed()
2445 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2446 AlignmentSorter.sortByLength(viewport.getAlignment());
2447 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2448 viewport.getAlignment()));
2449 alignPanel.paintAlignment(true);
2452 public void sortGroupMenuItem_actionPerformed()
2454 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2455 AlignmentSorter.sortByGroup(viewport.getAlignment());
2456 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2457 viewport.getAlignment()));
2458 alignPanel.paintAlignment(true);
2462 public void removeRedundancyMenuItem_actionPerformed()
2464 new RedundancyPanel(alignPanel);
2467 public void pairwiseAlignmentMenuItem_actionPerformed()
2469 if (viewport.getSelectionGroup() != null
2470 && viewport.getSelectionGroup().getSize() > 1)
2472 Frame frame = new Frame();
2473 frame.add(new PairwiseAlignPanel(alignPanel));
2474 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2479 public void PCAMenuItem_actionPerformed()
2481 // are the sequences aligned?
2482 if (!viewport.getAlignment().isAligned(false))
2485 int Width = viewport.getAlignment().getWidth();
2487 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2489 current = viewport.getAlignment().getSequenceAt(i);
2491 if (current.getLength() < Width)
2493 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2496 alignPanel.paintAlignment(true);
2499 if ((viewport.getSelectionGroup() != null
2500 && viewport.getSelectionGroup().getSize() < 4 && viewport
2501 .getSelectionGroup().getSize() > 0)
2502 || viewport.getAlignment().getHeight() < 4)
2509 new PCAPanel(viewport);
2510 } catch (java.lang.OutOfMemoryError ex)
2516 public void averageDistanceTreeMenuItem_actionPerformed()
2518 NewTreePanel("AV", "PID", "Average distance tree using PID");
2521 public void neighbourTreeMenuItem_actionPerformed()
2523 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2526 protected void njTreeBlosumMenuItem_actionPerformed()
2528 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2531 protected void avTreeBlosumMenuItem_actionPerformed()
2533 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2536 void NewTreePanel(String type, String pwType, String title)
2538 // are the sequences aligned?
2539 if (!viewport.getAlignment().isAligned(false))
2542 int Width = viewport.getAlignment().getWidth();
2544 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2546 current = viewport.getAlignment().getSequenceAt(i);
2548 if (current.getLength() < Width)
2550 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2553 alignPanel.paintAlignment(true);
2557 if ((viewport.getSelectionGroup() != null && viewport
2558 .getSelectionGroup().getSize() > 1)
2559 || (viewport.getAlignment().getHeight() > 1))
2561 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2563 addTreeMenuItem(tp, title);
2565 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2569 void loadTree_actionPerformed()
2571 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2572 cap.setText("Paste your Newick tree file here.");
2573 cap.setTreeImport();
2574 Frame frame = new Frame();
2576 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2579 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2581 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
2582 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2583 addTreeMenuItem(tp, treeFile);
2587 * sort the alignment using the given treePanel
2590 * tree used to sort view
2592 * string used for undo event name
2594 public void sortByTree(TreePanel treePanel, String title)
2596 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2598 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2599 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2600 // HistoryItem.SORT));
2601 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2602 viewport.getAlignment()));
2603 alignPanel.paintAlignment(true);
2607 * Do any automatic reordering of the alignment and add the necessary bits to
2608 * the menu structure for the new tree
2613 protected void addTreeMenuItem(final TreePanel treePanel,
2616 final MenuItem item = new MenuItem(title);
2617 sortByTreeMenu.add(item);
2618 item.addActionListener(new java.awt.event.ActionListener()
2621 public void actionPerformed(ActionEvent evt)
2623 sortByTree(treePanel, title); // treePanel.getTitle());
2627 treePanel.addWindowListener(new WindowAdapter()
2630 public void windowOpened(WindowEvent e)
2632 if (viewport.sortByTree)
2634 sortByTree(treePanel, title);
2636 super.windowOpened(e);
2640 public void windowClosing(WindowEvent e)
2642 sortByTreeMenu.remove(item);
2647 public boolean sortBy(AlignmentOrder alorder, String undoname)
2649 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2650 if (viewport.applet.debug)
2652 System.err.println("Sorting " + alorder.getOrder().size()
2653 + " in alignment '" + getTitle() + "'");
2655 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2656 if (undoname != null)
2658 addHistoryItem(new OrderCommand(undoname, oldOrder,
2659 viewport.getAlignment()));
2661 alignPanel.paintAlignment(true);
2665 protected void documentation_actionPerformed()
2667 alignPanel.av.applet.openJalviewHelpUrl();
2670 protected void about_actionPerformed()
2673 class AboutPanel extends Canvas
2679 public AboutPanel(String version, String builddate)
2681 this.version = version;
2682 this.builddate = builddate;
2686 public void paint(Graphics g)
2688 g.setColor(Color.white);
2689 g.fillRect(0, 0, getSize().width, getSize().height);
2690 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2691 FontMetrics fm = g.getFontMetrics();
2692 int fh = fm.getHeight();
2694 g.setColor(Color.black);
2695 // TODO: update this text for each release or centrally store it for
2696 // lite and application
2697 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2698 g.drawString("JalviewLite - Release " + version, x, y += fh);
2699 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2700 g.drawString("Build date: " + builddate, x, y += fh);
2701 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2703 "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
2705 g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
2707 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2710 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2712 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2714 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2717 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2719 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2724 Frame frame = new Frame();
2725 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2727 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2731 public void showURL(String url, String target)
2733 if (viewport.applet == null)
2735 System.out.println("Not running as applet - no browser available.");
2739 viewport.applet.showURL(url, target);
2743 // ////////////////////////////////////////////////////////////////////////////////
2744 // JBuilder Graphics here
2746 MenuBar alignFrameMenuBar = new MenuBar();
2748 Menu fileMenu = new Menu("File");
2750 MenuItem loadApplication = new MenuItem("View in Full Application");
2752 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2754 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2756 MenuItem outputFeatures = new MenuItem("Export Features ...");
2758 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2760 MenuItem closeMenuItem = new MenuItem("Close");
2762 Menu editMenu = new Menu("Edit");
2764 Menu viewMenu = new Menu("View");
2766 Menu colourMenu = new Menu("Colour");
2768 Menu calculateMenu = new Menu("Calculate");
2770 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2772 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2774 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2776 MenuItem remove2LeftMenuItem = new MenuItem();
2778 MenuItem remove2RightMenuItem = new MenuItem();
2780 MenuItem removeGappedColumnMenuItem = new MenuItem();
2782 MenuItem removeAllGapsMenuItem = new MenuItem();
2784 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2786 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2788 MenuItem sortPairwiseMenuItem = new MenuItem();
2790 MenuItem sortIDMenuItem = new MenuItem();
2792 MenuItem sortLengthMenuItem = new MenuItem();
2794 MenuItem sortGroupMenuItem = new MenuItem();
2796 MenuItem removeRedundancyMenuItem = new MenuItem();
2798 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2800 MenuItem PCAMenuItem = new MenuItem();
2802 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2804 MenuItem neighbourTreeMenuItem = new MenuItem();
2806 BorderLayout borderLayout1 = new BorderLayout();
2808 public Label statusBar = new Label();
2810 Menu outputTextboxMenu = new Menu();
2812 MenuItem clustalColour = new MenuItem();
2814 MenuItem zappoColour = new MenuItem();
2816 MenuItem taylorColour = new MenuItem();
2818 MenuItem hydrophobicityColour = new MenuItem();
2820 MenuItem helixColour = new MenuItem();
2822 MenuItem strandColour = new MenuItem();
2824 MenuItem turnColour = new MenuItem();
2826 MenuItem buriedColour = new MenuItem();
2828 MenuItem purinePyrimidineColour = new MenuItem();
2830 MenuItem RNAHelixColour = new MenuItem();
2832 MenuItem userDefinedColour = new MenuItem();
2834 MenuItem PIDColour = new MenuItem();
2836 MenuItem BLOSUM62Colour = new MenuItem();
2838 MenuItem tcoffeeColour = new MenuItem();
2840 MenuItem njTreeBlosumMenuItem = new MenuItem();
2842 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2844 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2846 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2848 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2850 MenuItem alProperties = new MenuItem("Alignment Properties...");
2852 MenuItem overviewMenuItem = new MenuItem();
2854 MenuItem undoMenuItem = new MenuItem();
2856 MenuItem redoMenuItem = new MenuItem();
2858 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2860 MenuItem noColourmenuItem = new MenuItem();
2862 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2864 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2866 MenuItem findMenuItem = new MenuItem();
2868 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2870 MenuItem nucleotideColour = new MenuItem();
2872 MenuItem deleteGroups = new MenuItem();
2874 MenuItem grpsFromSelection = new MenuItem();
2876 MenuItem createGroup = new MenuItem();
2878 MenuItem unGroup = new MenuItem();
2880 MenuItem delete = new MenuItem();
2882 MenuItem copy = new MenuItem();
2884 MenuItem cut = new MenuItem();
2886 Menu pasteMenu = new Menu();
2888 MenuItem pasteNew = new MenuItem();
2890 MenuItem pasteThis = new MenuItem();
2892 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2894 MenuItem font = new MenuItem();
2896 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2898 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2900 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2902 MenuItem modifyPID = new MenuItem();
2904 MenuItem modifyConservation = new MenuItem();
2906 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2907 "Autocalculate Consensus", true);
2909 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2910 "Sort Alignment With New Tree", true);
2912 Menu sortByTreeMenu = new Menu();
2914 Menu sort = new Menu();
2916 Menu calculate = new Menu();
2918 MenuItem inputText = new MenuItem();
2920 Menu helpMenu = new Menu();
2922 MenuItem documentation = new MenuItem();
2924 MenuItem about = new MenuItem();
2926 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2928 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2930 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2932 Menu autoAnnMenu = new Menu();
2934 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2936 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2938 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2940 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2942 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2944 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2946 private void jbInit() throws Exception
2949 setMenuBar(alignFrameMenuBar);
2953 // dynamically fill save as menu with available formats
2954 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2957 item = new MenuItem(
2958 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2960 item.addActionListener(new java.awt.event.ActionListener()
2963 public void actionPerformed(ActionEvent e)
2965 outputText_actionPerformed(e);
2969 outputTextboxMenu.add(item);
2971 closeMenuItem.addActionListener(this);
2972 loadApplication.addActionListener(this);
2974 loadTree.addActionListener(this);
2975 loadAnnotations.addActionListener(this);
2976 outputFeatures.addActionListener(this);
2977 outputAnnotations.addActionListener(this);
2978 selectAllSequenceMenuItem.addActionListener(this);
2979 deselectAllSequenceMenuItem.addActionListener(this);
2980 invertSequenceMenuItem.addActionListener(this);
2981 remove2LeftMenuItem.setLabel("Remove Left");
2982 remove2LeftMenuItem.addActionListener(this);
2983 remove2RightMenuItem.setLabel("Remove Right");
2984 remove2RightMenuItem.addActionListener(this);
2985 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2986 removeGappedColumnMenuItem.addActionListener(this);
2987 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2988 removeAllGapsMenuItem.addActionListener(this);
2989 viewBoxesMenuItem.setLabel("Boxes");
2990 viewBoxesMenuItem.setState(true);
2991 viewBoxesMenuItem.addItemListener(this);
2992 viewTextMenuItem.setLabel("Text");
2993 viewTextMenuItem.setState(true);
2994 viewTextMenuItem.addItemListener(this);
2995 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2996 sortPairwiseMenuItem.addActionListener(this);
2997 sortIDMenuItem.setLabel("by ID");
2998 sortIDMenuItem.addActionListener(this);
2999 sortLengthMenuItem.setLabel("by Length");
3000 sortLengthMenuItem.addActionListener(this);
3001 sortGroupMenuItem.setLabel("by Group");
3002 sortGroupMenuItem.addActionListener(this);
3003 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
3004 removeRedundancyMenuItem.addActionListener(this);
3005 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
3006 pairwiseAlignmentMenuItem.addActionListener(this);
3007 PCAMenuItem.setLabel("Principal Component Analysis");
3008 PCAMenuItem.addActionListener(this);
3009 averageDistanceTreeMenuItem
3010 .setLabel("Average Distance Using % Identity");
3011 averageDistanceTreeMenuItem.addActionListener(this);
3012 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
3013 neighbourTreeMenuItem.addActionListener(this);
3014 statusBar.setBackground(Color.white);
3015 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3016 statusBar.setText("Status bar");
3017 outputTextboxMenu.setLabel("Output to Textbox");
3018 clustalColour.setLabel("Clustalx");
3020 clustalColour.addActionListener(this);
3021 zappoColour.setLabel("Zappo");
3022 zappoColour.addActionListener(this);
3023 taylorColour.setLabel("Taylor");
3024 taylorColour.addActionListener(this);
3025 hydrophobicityColour.setLabel("Hydrophobicity");
3026 hydrophobicityColour.addActionListener(this);
3027 helixColour.setLabel("Helix Propensity");
3028 helixColour.addActionListener(this);
3029 strandColour.setLabel("Strand Propensity");
3030 strandColour.addActionListener(this);
3031 turnColour.setLabel("Turn Propensity");
3032 turnColour.addActionListener(this);
3033 buriedColour.setLabel("Buried Index");
3034 buriedColour.addActionListener(this);
3035 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
3036 purinePyrimidineColour.addActionListener(this);
3037 RNAHelixColour.setLabel("by RNA Helices");
3038 RNAHelixColour.addActionListener(this);
3039 userDefinedColour.setLabel("User Defined...");
3040 userDefinedColour.addActionListener(this);
3041 PIDColour.setLabel("Percentage Identity");
3042 PIDColour.addActionListener(this);
3043 BLOSUM62Colour.setLabel("BLOSUM62 Score");
3044 BLOSUM62Colour.addActionListener(this);
3045 tcoffeeColour.setLabel("T-Coffee Scores");
3046 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3048 tcoffeeColour.addActionListener(this);
3049 avDistanceTreeBlosumMenuItem
3050 .setLabel("Average Distance Using BLOSUM62");
3051 avDistanceTreeBlosumMenuItem.addActionListener(this);
3052 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
3053 njTreeBlosumMenuItem.addActionListener(this);
3054 annotationPanelMenuItem.setLabel("Show Annotations");
3055 annotationPanelMenuItem.addItemListener(this);
3056 colourTextMenuItem.setLabel("Colour Text");
3057 colourTextMenuItem.addItemListener(this);
3058 displayNonconservedMenuItem.setLabel("Show nonconserved");
3059 displayNonconservedMenuItem.addItemListener(this);
3060 alProperties.addActionListener(this);
3061 overviewMenuItem.setLabel("Overview Window");
3062 overviewMenuItem.addActionListener(this);
3063 undoMenuItem.setEnabled(false);
3064 undoMenuItem.setLabel("Undo");
3065 undoMenuItem.addActionListener(this);
3066 redoMenuItem.setEnabled(false);
3067 redoMenuItem.setLabel("Redo");
3068 redoMenuItem.addActionListener(this);
3069 conservationMenuItem.setLabel("by Conservation");
3070 conservationMenuItem.addItemListener(this);
3071 noColourmenuItem.setLabel("None");
3072 noColourmenuItem.addActionListener(this);
3073 wrapMenuItem.setLabel("Wrap");
3074 wrapMenuItem.addItemListener(this);
3075 renderGapsMenuItem.setLabel("Show Gaps");
3076 renderGapsMenuItem.setState(true);
3077 renderGapsMenuItem.addItemListener(this);
3078 findMenuItem.setLabel("Find...");
3079 findMenuItem.addActionListener(this);
3080 abovePIDThreshold.setLabel("Above Identity Threshold");
3081 abovePIDThreshold.addItemListener(this);
3082 nucleotideColour.setLabel("Nucleotide");
3083 nucleotideColour.addActionListener(this);
3084 deleteGroups.setLabel("Undefine Groups");
3085 deleteGroups.addActionListener(this);
3086 grpsFromSelection.setLabel("Make Groups For Selection");
3087 grpsFromSelection.addActionListener(this);
3088 createGroup.setLabel("Create Group");
3089 unGroup.setLabel("Remove Group");
3090 copy.setLabel("Copy");
3091 copy.addActionListener(this);
3092 cut.setLabel("Cut");
3093 cut.addActionListener(this);
3094 delete.setLabel("Delete");
3095 delete.addActionListener(this);
3096 pasteMenu.setLabel("Paste");
3097 pasteNew.setLabel("To New Alignment");
3098 pasteNew.addActionListener(this);
3099 pasteThis.setLabel("Add To This Alignment");
3100 pasteThis.addActionListener(this);
3101 applyToAllGroups.setLabel("Apply Colour To All Groups");
3102 applyToAllGroups.setState(true);
3103 applyToAllGroups.addItemListener(this);
3104 font.setLabel("Font...");
3105 font.addActionListener(this);
3106 scaleAbove.setLabel("Scale Above");
3107 scaleAbove.setState(true);
3108 scaleAbove.setEnabled(false);
3109 scaleAbove.addItemListener(this);
3110 scaleLeft.setEnabled(false);
3111 scaleLeft.setState(true);
3112 scaleLeft.setLabel("Scale Left");
3113 scaleLeft.addItemListener(this);
3114 scaleRight.setEnabled(false);
3115 scaleRight.setState(true);
3116 scaleRight.setLabel("Scale Right");
3117 scaleRight.addItemListener(this);
3118 modifyPID.setLabel("Modify Identity Threshold...");
3119 modifyPID.addActionListener(this);
3120 modifyConservation.setLabel("Modify Conservation Threshold...");
3121 modifyConservation.addActionListener(this);
3122 sortByTreeMenu.setLabel("By Tree Order");
3123 sort.setLabel("Sort");
3124 calculate.setLabel("Calculate Tree");
3125 autoCalculate.addItemListener(this);
3126 sortByTree.addItemListener(this);
3127 inputText.setLabel("Input from textbox");
3128 inputText.addActionListener(this);
3129 centreColumnLabelFlag.setLabel("Centre column labels");
3130 centreColumnLabelFlag.addItemListener(this);
3131 followMouseOverFlag.setLabel("Automatic Scrolling");
3132 followMouseOverFlag.addItemListener(this);
3133 helpMenu.setLabel("Help");
3134 documentation.setLabel("Documentation");
3135 documentation.addActionListener(this);
3137 about.setLabel("About...");
3138 about.addActionListener(this);
3139 seqLimits.setState(true);
3140 seqLimits.setLabel("Show Sequence Limits");
3141 seqLimits.addItemListener(this);
3142 featureSettings.setLabel("Feature Settings...");
3143 featureSettings.addActionListener(this);
3144 sequenceFeatures.setLabel("Sequence Features");
3145 sequenceFeatures.addItemListener(this);
3146 sequenceFeatures.setState(false);
3147 annotationColour.setLabel("by Annotation...");
3148 annotationColour.addActionListener(this);
3149 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
3150 invertColSel.setLabel("Invert Column Selection");
3151 menu1.setLabel("Show");
3152 showColumns.setLabel("All Columns ");
3153 showSeqs.setLabel("All Sequences");
3154 menu2.setLabel("Hide");
3155 hideColumns.setLabel("Selected Columns");
3156 hideSequences.setLabel("Selected Sequences");
3157 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
3158 hideAllSelection.setLabel("Selected Region");
3159 showAllHidden.setLabel("All Sequences and Columns");
3160 showGroupConsensus.setLabel("Group Consensus");
3161 showGroupConservation.setLabel("Group Conservation");
3162 showConsensusHistogram.setLabel("Show Consensus Histogram");
3163 showSequenceLogo.setLabel("Show Consensus Logo");
3164 normSequenceLogo.setLabel("Normalise Consensus Logo");
3165 applyAutoAnnotationSettings.setLabel("Apply to all groups");
3166 applyAutoAnnotationSettings.setState(true);
3167 autoAnnMenu.setLabel("Autocalculated Annotation");
3169 invertColSel.addActionListener(this);
3170 showColumns.addActionListener(this);
3171 showSeqs.addActionListener(this);
3172 hideColumns.addActionListener(this);
3173 hideSequences.addActionListener(this);
3174 hideAllButSelection.addActionListener(this);
3175 hideAllSelection.addActionListener(this);
3176 showAllHidden.addActionListener(this);
3177 showGroupConsensus.addItemListener(this);
3178 showGroupConservation.addItemListener(this);
3179 showConsensusHistogram.addItemListener(this);
3180 showSequenceLogo.addItemListener(this);
3181 normSequenceLogo.addItemListener(this);
3183 applyAutoAnnotationSettings.addItemListener(this);
3184 formatMenu.setLabel("Format");
3185 selectMenu.setLabel("Select");
3186 newView.setLabel("New View");
3187 newView.addActionListener(this);
3188 alignFrameMenuBar.add(fileMenu);
3189 alignFrameMenuBar.add(editMenu);
3190 alignFrameMenuBar.add(selectMenu);
3191 alignFrameMenuBar.add(viewMenu);
3192 alignFrameMenuBar.add(formatMenu);
3193 alignFrameMenuBar.add(colourMenu);
3194 alignFrameMenuBar.add(calculateMenu);
3195 alignFrameMenuBar.add(helpMenu);
3197 fileMenu.add(inputText);
3198 fileMenu.add(loadTree);
3199 fileMenu.add(loadAnnotations);
3201 fileMenu.addSeparator();
3202 fileMenu.add(outputTextboxMenu);
3203 fileMenu.add(outputFeatures);
3204 fileMenu.add(outputAnnotations);
3206 if (jalviewServletURL != null)
3208 fileMenu.add(loadApplication);
3211 fileMenu.addSeparator();
3212 fileMenu.add(closeMenuItem);
3214 editMenu.add(undoMenuItem);
3215 editMenu.add(redoMenuItem);
3218 editMenu.add(pasteMenu);
3219 editMenu.add(delete);
3220 editMenu.addSeparator();
3221 editMenu.add(remove2LeftMenuItem);
3222 editMenu.add(remove2RightMenuItem);
3223 editMenu.add(removeGappedColumnMenuItem);
3224 editMenu.add(removeAllGapsMenuItem);
3225 editMenu.add(removeRedundancyMenuItem);
3226 viewMenu.add(newView);
3227 viewMenu.addSeparator();
3228 viewMenu.add(menu1);
3229 viewMenu.add(menu2);
3230 viewMenu.addSeparator();
3231 viewMenu.add(followMouseOverFlag);
3232 viewMenu.add(annotationPanelMenuItem);
3233 autoAnnMenu.add(applyAutoAnnotationSettings);
3234 autoAnnMenu.add(showConsensusHistogram);
3235 autoAnnMenu.add(showSequenceLogo);
3236 autoAnnMenu.add(normSequenceLogo);
3237 autoAnnMenu.addSeparator();
3238 autoAnnMenu.add(showGroupConservation);
3239 autoAnnMenu.add(showGroupConsensus);
3240 viewMenu.add(autoAnnMenu);
3241 viewMenu.addSeparator();
3242 viewMenu.add(sequenceFeatures);
3243 viewMenu.add(featureSettings);
3244 viewMenu.addSeparator();
3245 viewMenu.add(alProperties);
3246 viewMenu.addSeparator();
3247 viewMenu.add(overviewMenuItem);
3248 colourMenu.add(applyToAllGroups);
3249 colourMenu.addSeparator();
3250 colourMenu.add(noColourmenuItem);
3251 colourMenu.add(clustalColour);
3252 colourMenu.add(BLOSUM62Colour);
3253 colourMenu.add(PIDColour);
3254 colourMenu.add(zappoColour);
3255 colourMenu.add(taylorColour);
3256 colourMenu.add(hydrophobicityColour);
3257 colourMenu.add(helixColour);
3258 colourMenu.add(strandColour);
3259 colourMenu.add(turnColour);
3260 colourMenu.add(buriedColour);
3261 colourMenu.add(nucleotideColour);
3262 colourMenu.add(purinePyrimidineColour);
3263 colourMenu.add(tcoffeeColour);
3264 colourMenu.add(userDefinedColour);
3265 colourMenu.addSeparator();
3266 colourMenu.add(conservationMenuItem);
3267 colourMenu.add(modifyConservation);
3268 colourMenu.add(abovePIDThreshold);
3269 colourMenu.add(modifyPID);
3270 colourMenu.add(annotationColour);
3271 colourMenu.add(RNAHelixColour);
3272 calculateMenu.add(sort);
3273 calculateMenu.add(calculate);
3274 calculateMenu.addSeparator();
3275 calculateMenu.add(pairwiseAlignmentMenuItem);
3276 calculateMenu.add(PCAMenuItem);
3277 calculateMenu.add(autoCalculate);
3278 calculateMenu.add(sortByTree);
3279 this.add(statusBar, BorderLayout.SOUTH);
3280 pasteMenu.add(pasteNew);
3281 pasteMenu.add(pasteThis);
3282 sort.add(sortIDMenuItem);
3283 sort.add(sortLengthMenuItem);
3284 sort.add(sortByTreeMenu);
3285 sort.add(sortGroupMenuItem);
3286 sort.add(sortPairwiseMenuItem);
3287 calculate.add(averageDistanceTreeMenuItem);
3288 calculate.add(neighbourTreeMenuItem);
3289 calculate.add(avDistanceTreeBlosumMenuItem);
3290 calculate.add(njTreeBlosumMenuItem);
3291 helpMenu.add(documentation);
3292 helpMenu.add(about);
3293 menu1.add(showColumns);
3294 menu1.add(showSeqs);
3295 menu1.add(showAllHidden);
3296 menu2.add(hideColumns);
3297 menu2.add(hideSequences);
3298 menu2.add(hideAllSelection);
3299 menu2.add(hideAllButSelection);
3300 formatMenu.add(font);
3301 formatMenu.add(seqLimits);
3302 formatMenu.add(wrapMenuItem);
3303 formatMenu.add(scaleAbove);
3304 formatMenu.add(scaleLeft);
3305 formatMenu.add(scaleRight);
3306 formatMenu.add(viewBoxesMenuItem);
3307 formatMenu.add(viewTextMenuItem);
3308 formatMenu.add(colourTextMenuItem);
3309 formatMenu.add(displayNonconservedMenuItem);
3310 formatMenu.add(renderGapsMenuItem);
3311 formatMenu.add(centreColumnLabelFlag);
3312 selectMenu.add(findMenuItem);
3313 selectMenu.addSeparator();
3314 selectMenu.add(selectAllSequenceMenuItem);
3315 selectMenu.add(deselectAllSequenceMenuItem);
3316 selectMenu.add(invertSequenceMenuItem);
3317 selectMenu.add(invertColSel);
3318 selectMenu.add(createGroup);
3319 selectMenu.add(unGroup);
3320 selectMenu.add(grpsFromSelection);
3321 selectMenu.add(deleteGroups);
3325 MenuItem featureSettings = new MenuItem();
3327 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3329 MenuItem annotationColour = new MenuItem();
3331 MenuItem invertColSel = new MenuItem();
3333 Menu menu1 = new Menu();
3335 MenuItem showColumns = new MenuItem();
3337 MenuItem showSeqs = new MenuItem();
3339 Menu menu2 = new Menu();
3341 MenuItem hideColumns = new MenuItem();
3343 MenuItem hideSequences = new MenuItem();
3345 MenuItem hideAllButSelection = new MenuItem();
3347 MenuItem hideAllSelection = new MenuItem();
3349 MenuItem showAllHidden = new MenuItem();
3351 Menu formatMenu = new Menu();
3353 Menu selectMenu = new Menu();
3355 MenuItem newView = new MenuItem();
3358 * Attach the alignFrame panels after embedding menus, if necessary. This used
3359 * to be called setEmbedded, but is now creates the dropdown menus in a
3360 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3362 * @param reallyEmbedded
3363 * true to attach the view to the applet area on the page rather than
3366 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3371 // Explicly build the embedded menu panel for the on-page applet
3373 // view cannot be closed if its actually on the page
3374 fileMenu.remove(closeMenuItem);
3375 fileMenu.remove(3); // Remove Seperator
3376 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3377 Font.PLAIN, 10, false); // use our own fonts.
3378 // and actually add the components to the applet area
3379 viewport.applet.setLayout(new BorderLayout());
3380 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3381 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3382 alignPanel.setSize(viewport.applet.getSize().width,
3383 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3384 - statusBar.HEIGHT);
3385 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3386 final AlignFrame me = this;
3387 viewport.applet.addFocusListener(new FocusListener()
3391 public void focusLost(FocusEvent e)
3393 if (me.viewport.applet.currentAlignFrame == me)
3395 me.viewport.applet.currentAlignFrame = null;
3400 public void focusGained(FocusEvent e)
3402 me.viewport.applet.currentAlignFrame = me;
3405 viewport.applet.validate();
3410 // test and embed menu bar if necessary.
3412 if (embedMenuIfNeeded(alignPanel))
3414 // adjust for status bar height too
3415 alignPanel.setSize(getSize().width, getSize().height
3416 - statusBar.HEIGHT);
3418 add(statusBar, BorderLayout.SOUTH);
3419 add(alignPanel, BorderLayout.CENTER);
3420 // and register with the applet so it can pass external API calls to us
3421 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3427 * create a new binding between structures in an existing jmol viewer instance
3428 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3429 * this does not open a new Jmol window, or modify the display of the
3430 * structures in the original jmol window. Note This method doesn't work
3431 * without an additional javascript library to exchange messages between the
3432 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3435 * JmolViewer instance
3436 * @param sequenceIds
3437 * - sequence Ids to search for associations
3439 public SequenceStructureBinding addStructureViewInstance(
3440 Object jmolviewer, String[] sequenceIds)
3442 org.jmol.api.JmolViewer viewer = null;
3445 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3446 } catch (ClassCastException ex)
3448 System.err.println("Unsupported viewer object :"
3449 + jmolviewer.getClass());
3453 System.err.println("Can't use this object as a structure viewer:"
3454 + jmolviewer.getClass());
3457 SequenceI[] seqs = null;
3458 if (sequenceIds == null || sequenceIds.length == 0)
3460 seqs = viewport.getAlignment().getSequencesArray();
3464 Vector sqi = new Vector();
3465 AlignmentI al = viewport.getAlignment();
3466 for (int sid = 0; sid < sequenceIds.length; sid++)
3468 SequenceI sq = al.findName(sequenceIds[sid]);
3476 seqs = new SequenceI[sqi.size()];
3477 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3479 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3488 // TODO: search for a jmv that involves viewer
3490 { // create a new viewer/jalview binding.
3491 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3499 * bind a pdb file to a sequence in the current view
3502 * - sequenceId within the dataset.
3503 * @param pdbEntryString
3504 * - the short name for the PDB file
3506 * - pdb file - either a URL or a valid PDB file.
3507 * @return true if binding was as success TODO: consider making an exception
3508 * structure for indicating when PDB parsing or sequenceId location
3511 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3514 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3515 boolean needtoadd = false;
3516 if (toaddpdb != null)
3518 Vector pdbe = toaddpdb.getPDBId();
3519 PDBEntry pdbentry = null;
3520 if (pdbe != null && pdbe.size() > 0)
3522 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3524 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3525 if (!pdbentry.getId().equals(pdbEntryString)
3526 && !pdbentry.getFile().equals(pdbFile))
3536 if (pdbentry == null)
3538 pdbentry = new PDBEntry();
3539 pdbentry.setId(pdbEntryString);
3540 pdbentry.setFile(pdbFile);
3541 needtoadd = true; // add this new entry to sequence.
3543 // resolve data source
3544 // TODO: this code should be a refactored to an io package
3545 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3546 if (protocol == null)
3552 // make a note of the access mode and add
3553 if (pdbentry.getProperty() == null)
3555 pdbentry.setProperty(new Hashtable());
3557 pdbentry.getProperty().put("protocol", protocol);
3558 toaddpdb.addPDBId(pdbentry);
3564 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3568 Vector sequences = new Vector();
3569 for (int i = 0; i < seqs.length; i++)
3571 if (seqs[i] != null)
3573 sequences.addElement(new Object[]
3574 { seqs[i], (chains != null) ? chains[i] : null });
3577 seqs = new SequenceI[sequences.size()];
3578 chains = new String[sequences.size()];
3579 for (int i = 0, isize = sequences.size(); i < isize; i++)
3581 Object[] oj = (Object[]) sequences.elementAt(i);
3583 seqs[i] = (SequenceI) oj[0];
3584 chains[i] = (String) oj[1];
3592 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3593 SequenceI[] seqs, String[] chains, String protocol)
3595 // Scrub any null sequences from the array
3596 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3597 seqs = (SequenceI[]) sqch[0];
3598 chains = (String[]) sqch[1];
3599 if (seqs == null || seqs.length == 0)
3602 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3604 if (protocol == null || protocol.trim().length() == 0
3605 || protocol.equals("null"))
3607 protocol = (String) pdb.getProperty().get("protocol");
3608 if (protocol == null)
3610 System.err.println("Couldn't work out protocol to open structure: "
3615 if (applet.useXtrnalSviewer)
3617 // register the association(s) and quit, don't create any windows.
3618 if (StructureSelectionManager.getStructureSelectionManager(applet)
3619 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3621 System.err.println("Failed to map " + pdb.getFile() + " ("
3622 + protocol + ") to any sequences");
3626 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3628 // can only do alignments with Jmol
3629 // find the last jmol window assigned to this alignment
3630 jalview.appletgui.AppletJmol ajm = null, tajm;
3631 Vector jmols = applet
3632 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3633 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3635 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3636 if (tajm.ap.alignFrame == this)
3645 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3646 // try and add the pdb structure
3651 // otherwise, create a new window
3652 if (applet.jmolAvailable)
3654 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3656 applet.lastFrameX += 40;
3657 applet.lastFrameY += 40;
3661 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3666 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3667 SequenceI[][] seqs, String[][] chains, String[] protocols)
3669 // TODO Auto-generated method stub
3670 System.err.println("Aligned Structure View: Not yet implemented.");
3674 * modify the current selection, providing the user has not made a selection
3678 * - sequences from this alignment
3680 * - columns to be selected on the alignment
3682 public void select(SequenceGroup sel, ColumnSelection csel)
3684 alignPanel.seqPanel.selection(sel, csel, null);
3687 public void scrollTo(int row, int column)
3689 alignPanel.seqPanel.scrollTo(row, column);
3692 public void scrollToRow(int row)
3694 alignPanel.seqPanel.scrollToRow(row);
3697 public void scrollToColumn(int column)
3699 alignPanel.seqPanel.scrollToColumn(column);
3703 * @return the alignments unique ID.
3705 public String getSequenceSetId()
3707 return viewport.getSequenceSetId();
3711 * Load the (T-Coffee) score file from the specified url
3714 * File/URL/T-COFFEE score file contents
3715 * @throws IOException
3716 * @return true if alignment was annotated with data from source
3718 public boolean loadScoreFile(String source) throws IOException
3721 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3722 AppletFormatAdapter.checkProtocol(source));
3723 if (!file.isValid())
3725 // TODO: raise dialog for gui
3726 System.err.println("Problems parsing T-Coffee scores: "
3727 + file.getWarningMessage());
3728 System.err.println("Origin was:\n" + source);
3733 * check that the score matrix matches the alignment dimensions
3736 if ((aln = viewport.getAlignment()) != null
3737 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3740 // TODO: raise a dialog box here rather than bomb out.
3742 .println("The scores matrix does not match the alignment dimensions");
3746 // TODO add parameter to indicate if matching should be done
3747 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3749 alignPanel.fontChanged();
3750 tcoffeeColour.setEnabled(true);
3751 // switch to this color
3752 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3757 System.err.println("Problems resolving T-Coffee scores:");
3758 if (file.getWarningMessage() != null)
3760 System.err.println(file.getWarningMessage());