2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import java.awt.BorderLayout;
24 import java.awt.Canvas;
25 import java.awt.CheckboxMenuItem;
26 import java.awt.Color;
28 import java.awt.FontMetrics;
29 import java.awt.Frame;
30 import java.awt.Graphics;
31 import java.awt.Label;
33 import java.awt.MenuBar;
34 import java.awt.MenuItem;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.ActionListener;
37 import java.awt.event.FocusEvent;
38 import java.awt.event.FocusListener;
39 import java.awt.event.ItemEvent;
40 import java.awt.event.ItemListener;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.KeyListener;
43 import java.awt.event.WindowAdapter;
44 import java.awt.event.WindowEvent;
45 import java.io.IOException;
47 import java.net.URLEncoder;
48 import java.util.Arrays;
49 import java.util.Deque;
50 import java.util.HashMap;
51 import java.util.Hashtable;
52 import java.util.List;
54 import java.util.StringTokenizer;
55 import java.util.Vector;
57 import jalview.analysis.AlignmentSorter;
58 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
59 import jalview.api.AlignViewControllerGuiI;
60 import jalview.api.AlignViewControllerI;
61 import jalview.api.AlignViewportI;
62 import jalview.api.FeatureRenderer;
63 import jalview.api.SequenceStructureBinding;
64 import jalview.bin.JalviewLite;
65 import jalview.commands.CommandI;
66 import jalview.commands.EditCommand;
67 import jalview.commands.EditCommand.Action;
68 import jalview.commands.OrderCommand;
69 import jalview.commands.RemoveGapColCommand;
70 import jalview.commands.RemoveGapsCommand;
71 import jalview.commands.SlideSequencesCommand;
72 import jalview.commands.TrimRegionCommand;
73 import jalview.datamodel.Alignment;
74 import jalview.datamodel.AlignmentAnnotation;
75 import jalview.datamodel.AlignmentI;
76 import jalview.datamodel.AlignmentOrder;
77 import jalview.datamodel.ColumnSelection;
78 import jalview.datamodel.PDBEntry;
79 import jalview.datamodel.Sequence;
80 import jalview.datamodel.SequenceGroup;
81 import jalview.datamodel.SequenceI;
82 import jalview.io.AnnotationFile;
83 import jalview.io.AppletFormatAdapter;
84 import jalview.io.FeaturesFile;
85 import jalview.io.TCoffeeScoreFile;
86 import jalview.schemes.Blosum62ColourScheme;
87 import jalview.schemes.BuriedColourScheme;
88 import jalview.schemes.ClustalxColourScheme;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.HelixColourScheme;
91 import jalview.schemes.HydrophobicColourScheme;
92 import jalview.schemes.NucleotideColourScheme;
93 import jalview.schemes.PIDColourScheme;
94 import jalview.schemes.PurinePyrimidineColourScheme;
95 import jalview.schemes.RNAHelicesColourChooser;
96 import jalview.schemes.RNAInteractionColourScheme;
97 import jalview.schemes.StrandColourScheme;
98 import jalview.schemes.TCoffeeColourScheme;
99 import jalview.schemes.TaylorColourScheme;
100 import jalview.schemes.TurnColourScheme;
101 import jalview.schemes.ZappoColourScheme;
102 import jalview.structure.StructureSelectionManager;
103 import jalview.structures.models.AAStructureBindingModel;
104 import jalview.util.MappingUtils;
105 import jalview.util.MessageManager;
107 public class AlignFrame extends EmbmenuFrame implements ActionListener,
108 ItemListener, KeyListener, AlignViewControllerGuiI
110 public AlignViewControllerI avc;
112 public AlignmentPanel alignPanel;
114 public AlignViewport viewport;
116 // width and height may be overridden by applet parameters
117 int frameWidth = 700;
119 int frameHeight = 500;
121 String jalviewServletURL;
124 * Flag for showing autocalculated consensus above or below other consensus
127 private boolean showAutoCalculatedAbove;
129 private SequenceAnnotationOrder annotationSortOrder;
132 * Constructor that creates the frame and adds it to the display.
139 public AlignFrame(AlignmentI al, JalviewLite applet,
140 String title, boolean embedded)
142 this(al, applet, title, embedded, true);
146 * Constructor that optionally allows the frame to be displayed or only
153 * @param addToDisplay
155 public AlignFrame(AlignmentI al, JalviewLite applet,
156 String title, boolean embedded, boolean addToDisplay)
160 jalviewServletURL = applet.getParameter("APPLICATION_URL");
166 } catch (Exception ex)
168 ex.printStackTrace();
170 // need to get window geometry before we calculate alignment layout
176 param = applet.getParameter("windowWidth");
179 int width = Integer.parseInt(param);
182 param = applet.getParameter("windowHeight");
185 int height = Integer.parseInt(param);
186 frameHeight = height;
188 } catch (Exception ex)
192 viewport = new AlignViewport(al, applet);
193 alignPanel = new AlignmentPanel(this, viewport);
194 avc = new jalview.controller.AlignViewController(this, viewport,
196 viewport.updateConservation(alignPanel);
197 viewport.updateConsensus(alignPanel);
199 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
200 followMouseOverFlag.setState(viewport.getFollowHighlight());
201 showGroupConsensus.setState(viewport.isShowGroupConsensus());
202 showGroupConservation.setState(viewport.isShowGroupConservation());
203 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
204 showSequenceLogo.setState(viewport.isShowSequenceLogo());
205 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
206 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
207 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
208 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
209 showSequenceAnnotations.setState(viewport.isShowAnnotation());
211 seqLimits.setState(viewport.getShowJVSuffix());
215 String param = applet.getParameter("sortBy");
218 if (param.equalsIgnoreCase("Id"))
220 sortIDMenuItem_actionPerformed();
222 else if (param.equalsIgnoreCase("Pairwise Identity"))
224 sortPairwiseMenuItem_actionPerformed();
226 else if (param.equalsIgnoreCase("Length"))
228 sortLengthMenuItem_actionPerformed();
232 param = applet.getParameter("wrap");
235 if (param.equalsIgnoreCase("true"))
237 wrapMenuItem.setState(true);
238 wrapMenuItem_actionPerformed();
241 param = applet.getParameter("centrecolumnlabels");
244 centreColumnLabelFlag.setState(true);
245 centreColumnLabelFlag_stateChanged();
249 if (viewport.getAlignment().isNucleotide())
251 viewport.updateStrucConsensus(alignPanel);
252 if (viewport.getAlignment().hasRNAStructure())
254 RNAHelixColour.setEnabled(true);
258 RNAHelixColour.setEnabled(false);
263 RNAHelixColour.setEnabled(false);
264 purinePyrimidineColour.setEnabled(false);
266 // Some JVMS send keyevents to Top frame or lowest panel,
267 // Havent worked out why yet. So add to both this frame and seqCanvas for
269 this.addKeyListener(this);
270 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
271 alignPanel.idPanel.idCanvas.addKeyListener(this);
272 alignPanel.scalePanel.addKeyListener(this);
273 alignPanel.annotationPanel.addKeyListener(this);
274 alignPanel.annotationPanelHolder.addKeyListener(this);
275 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
276 alignPanel.alabels.addKeyListener(this);
280 addToDisplay(embedded);
287 public void addToDisplay(boolean embedded)
289 createAlignFrameWindow(embedded);
291 alignPanel.adjustAnnotationHeight();
292 alignPanel.paintAlignment(true);
295 public AlignViewport getAlignViewport()
300 public SeqCanvas getSeqcanvas()
302 return alignPanel.seqPanel.seqCanvas;
306 * Load a features file onto the alignment
309 * file URL, content, or other resolvable path
311 * is protocol for accessing data referred to by file
314 public boolean parseFeaturesFile(String file, String type)
316 return parseFeaturesFile(file, type, true);
320 * Load a features file onto the alignment
323 * file URL, content, or other resolvable path
325 * is protocol for accessing data referred to by file
326 * @param autoenabledisplay
327 * when true, display features flag will be automatically enabled if
328 * features are loaded
329 * @return true if data parsed as a features file
331 public boolean parseFeaturesFile(String file, String type,
332 boolean autoenabledisplay)
334 // TODO: test if importing a features file onto an alignment which already
335 // has features with links overwrites the original links.
337 Hashtable featureLinks = new Hashtable();
338 boolean featuresFile = false;
341 featuresFile = new jalview.io.FeaturesFile(file, type)
342 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
343 .getFeatureRenderer().getFeatureColours(), featureLinks,
344 true, viewport.applet.getDefaultParameter(
345 "relaxedidmatch", false));
346 } catch (Exception ex)
348 ex.printStackTrace();
353 if (featureLinks.size() > 0)
355 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
357 if (autoenabledisplay)
359 viewport.setShowSequenceFeatures(true);
360 sequenceFeatures.setState(true);
362 if (alignPanel.seqPanel.seqCanvas.fr != null)
364 // update the min/max ranges where necessary
365 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
367 if (viewport.featureSettings != null)
369 viewport.featureSettings.refreshTable();
371 alignPanel.paintAlignment(true);
372 statusBar.setText(MessageManager
373 .getString("label.successfully_added_features_alignment"));
379 public void keyPressed(KeyEvent evt)
381 if (viewport.cursorMode
382 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
383 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
384 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
385 && Character.isDigit(evt.getKeyChar()))
387 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
390 switch (evt.getKeyCode())
392 case 27: // escape key
393 deselectAllSequenceMenuItem_actionPerformed();
395 alignPanel.alabels.cancelDrag();
398 if (evt.isControlDown() || evt.isMetaDown())
400 cut_actionPerformed();
404 if (viewport.cursorMode && !evt.isControlDown())
406 alignPanel.seqPanel.setCursorColumn();
408 if (evt.isControlDown() || evt.isMetaDown())
410 copy_actionPerformed();
414 if (evt.isControlDown())
416 paste(evt.isShiftDown());
420 if (evt.isControlDown() || evt.isMetaDown())
422 selectAllSequenceMenuItem_actionPerformed();
425 case KeyEvent.VK_DOWN:
426 if (viewport.cursorMode)
428 alignPanel.seqPanel.moveCursor(0, 1);
432 moveSelectedSequences(false);
437 if (viewport.cursorMode)
439 alignPanel.seqPanel.moveCursor(0, -1);
443 moveSelectedSequences(true);
447 case KeyEvent.VK_LEFT:
448 if (evt.isAltDown() || !viewport.cursorMode)
450 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
454 alignPanel.seqPanel.moveCursor(-1, 0);
458 case KeyEvent.VK_RIGHT:
459 if (evt.isAltDown() || !viewport.cursorMode)
461 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
465 alignPanel.seqPanel.moveCursor(1, 0);
469 case KeyEvent.VK_SPACE:
470 if (viewport.cursorMode)
472 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
473 || evt.isShiftDown() || evt.isAltDown());
477 case KeyEvent.VK_DELETE:
478 case KeyEvent.VK_BACK_SPACE:
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
482 || evt.isShiftDown() || evt.isAltDown());
486 cut_actionPerformed();
487 alignPanel.seqPanel.seqCanvas.repaint();
492 if (viewport.cursorMode)
494 alignPanel.seqPanel.setCursorRow();
498 if (viewport.cursorMode)
500 alignPanel.seqPanel.setCursorPosition();
504 case KeyEvent.VK_ENTER:
505 case KeyEvent.VK_COMMA:
506 if (viewport.cursorMode)
508 alignPanel.seqPanel.setCursorRowAndColumn();
513 if (viewport.cursorMode)
515 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
526 viewport.cursorMode = !viewport.cursorMode;
527 statusBar.setText(MessageManager.formatMessage(
528 "label.keyboard_editing_mode", new String[]
529 { (viewport.cursorMode ? "on" : "off") }));
530 if (viewport.cursorMode)
532 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
533 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
538 if (evt.isControlDown())
540 findMenuItem_actionPerformed();
546 boolean toggleSeqs = !evt.isControlDown();
547 boolean toggleCols = !evt.isShiftDown();
548 toggleHiddenRegions(toggleSeqs, toggleCols);
552 case KeyEvent.VK_PAGE_UP:
553 if (viewport.getWrapAlignment())
555 alignPanel.scrollUp(true);
559 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
560 - viewport.endSeq + viewport.startSeq);
564 case KeyEvent.VK_PAGE_DOWN:
565 if (viewport.getWrapAlignment())
567 alignPanel.scrollUp(false);
571 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
572 + viewport.endSeq - viewport.startSeq);
577 if (evt.isControlDown())
579 undoMenuItem_actionPerformed();
584 if (evt.isControlDown())
586 redoMenuItem_actionPerformed();
591 if (evt.isControlDown())
598 if (evt.isControlDown())
600 trimAlignment(false);
605 if (evt.isControlDown())
607 if (evt.isShiftDown())
609 this.removeAllGapsMenuItem_actionPerformed();
613 removeGappedColumnMenuItem_actionPerformed();
618 if (evt.isControlDown())
622 invertColSel_actionPerformed();
626 invertSequenceMenuItem_actionPerformed();
632 if (evt.isControlDown())
634 if (evt.isShiftDown())
636 this.unGroup_actionPerformed();
640 this.createGroup_actionPerformed();
646 if (evt.isControlDown())
648 this.deleteGroups_actionPerformed();
653 if (evt.isControlDown())
660 alignPanel.paintAlignment(true);
664 * called by key handler and the hide all/show all menu items
669 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
671 boolean hide = false;
672 SequenceGroup sg = viewport.getSelectionGroup();
673 if (!toggleSeqs && !toggleCols)
675 // Hide everything by the current selection - this is a hack - we do the
676 // invert and then hide
677 // first check that there will be visible columns after the invert.
678 if ((viewport.getColumnSelection() != null
679 && viewport.getColumnSelection().getSelected() != null && viewport
680 .getColumnSelection().getSelected().size() > 0)
681 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
684 // now invert the sequence set, if required - empty selection implies
685 // that no hiding is required.
688 invertSequenceMenuItem_actionPerformed();
689 sg = viewport.getSelectionGroup();
693 viewport.expandColSelection(sg, true);
694 // finally invert the column selection and get the new sequence
695 // selection and indicate it should be hidden.
696 invertColSel_actionPerformed();
703 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
706 viewport.hideAllSelectedSeqs();
708 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
711 viewport.showAllHiddenSeqs();
717 if (viewport.getColumnSelection().getSelected().size() > 0)
719 viewport.hideSelectedColumns();
722 viewport.setSelectionGroup(sg);
727 viewport.showAllHiddenColumns();
733 public void keyReleased(KeyEvent evt)
738 public void keyTyped(KeyEvent evt)
743 public void itemStateChanged(ItemEvent evt)
745 final Object source = evt.getSource();
746 if (source == displayNonconservedMenuItem)
748 displayNonconservedMenuItem_actionPerformed();
750 else if (source == colourTextMenuItem)
752 colourTextMenuItem_actionPerformed();
754 else if (source == wrapMenuItem)
756 wrapMenuItem_actionPerformed();
758 else if (source == scaleAbove)
760 viewport.setScaleAboveWrapped(scaleAbove.getState());
762 else if (source == scaleLeft)
764 viewport.setScaleLeftWrapped(scaleLeft.getState());
766 else if (source == scaleRight)
768 viewport.setScaleRightWrapped(scaleRight.getState());
770 else if (source == seqLimits)
772 seqLimits_itemStateChanged();
774 else if (source == viewBoxesMenuItem)
776 viewport.setShowBoxes(viewBoxesMenuItem.getState());
778 else if (source == viewTextMenuItem)
780 viewport.setShowText(viewTextMenuItem.getState());
782 else if (source == renderGapsMenuItem)
784 viewport.setRenderGaps(renderGapsMenuItem.getState());
786 else if (source == annotationPanelMenuItem)
788 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
789 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
791 else if (source == sequenceFeatures)
793 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
794 alignPanel.seqPanel.seqCanvas.repaint();
796 else if (source == showAlignmentAnnotations)
798 setAnnotationsVisibility();
800 else if (source == showSequenceAnnotations)
802 setAnnotationsVisibility();
804 else if (source == sortAnnBySequence)
806 boolean newState = sortAnnBySequence.getState();
807 sortAnnByLabel.setState(false);
808 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
809 : SequenceAnnotationOrder.NONE);
810 setViewportAnnotationOrder();
812 else if (source == sortAnnByLabel)
814 boolean newState = sortAnnByLabel.getState();
815 sortAnnBySequence.setState(false);
816 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
817 : SequenceAnnotationOrder.NONE);
818 setViewportAnnotationOrder();
820 else if (source == showAutoFirst)
822 showAutoLast.setState(!showAutoFirst.getState());
823 setShowAutoCalculatedAbove(showAutoFirst.getState());
824 setViewportAnnotationOrder();
826 else if (source == showAutoLast)
828 showAutoFirst.setState(!showAutoLast.getState());
829 setShowAutoCalculatedAbove(showAutoFirst.getState());
830 setViewportAnnotationOrder();
832 else if (source == conservationMenuItem)
834 conservationMenuItem_actionPerformed();
836 else if (source == abovePIDThreshold)
838 abovePIDThreshold_actionPerformed();
840 else if (source == applyToAllGroups)
842 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
844 else if (source == autoCalculate)
846 viewport.autoCalculateConsensus = autoCalculate.getState();
848 else if (source == sortByTree)
850 viewport.sortByTree = sortByTree.getState();
852 else if (source == this.centreColumnLabelFlag)
854 centreColumnLabelFlag_stateChanged();
856 else if (source == this.followMouseOverFlag)
858 mouseOverFlag_stateChanged();
860 else if (source == showGroupConsensus)
862 showGroupConsensus_actionPerformed();
864 else if (source == showGroupConservation)
866 showGroupConservation_actionPerformed();
868 else if (source == showSequenceLogo)
870 showSequenceLogo_actionPerformed();
872 else if (source == normSequenceLogo)
874 normSequenceLogo_actionPerformed();
876 else if (source == showConsensusHistogram)
878 showConsensusHistogram_actionPerformed();
880 else if (source == applyAutoAnnotationSettings)
882 applyAutoAnnotationSettings_actionPerformed();
884 alignPanel.paintAlignment(true);
888 * Set the visibility state of sequence-related and/or alignment-related
889 * annotations depending on checkbox selections. Repaint after calling.
893 private void setAnnotationsVisibility()
895 boolean showForAlignment = showAlignmentAnnotations.getState();
896 boolean showForSequences = showSequenceAnnotations.getState();
897 for (AlignmentAnnotation aa : alignPanel.getAlignment()
898 .getAlignmentAnnotation())
900 boolean visible = (aa.sequenceRef == null ? showForAlignment
902 aa.visible = visible;
904 alignPanel.validateAnnotationDimensions(false);
907 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
909 this.annotationSortOrder = order;
913 * Set flags on the viewport that control annotation ordering
915 private void setViewportAnnotationOrder()
917 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
919 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
922 private void setShowAutoCalculatedAbove(boolean showAbove)
924 this.showAutoCalculatedAbove = showAbove;
927 private void mouseOverFlag_stateChanged()
929 viewport.followHighlight = followMouseOverFlag.getState();
930 // TODO: could kick the scrollTo mechanism to reset view for current
934 private void centreColumnLabelFlag_stateChanged()
936 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
937 this.alignPanel.annotationPanel.repaint();
941 public void actionPerformed(ActionEvent evt)
943 Object source = evt.getSource();
945 if (source == inputText)
947 inputText_actionPerformed();
949 else if (source == loadTree)
951 loadTree_actionPerformed();
953 else if (source == loadApplication)
955 launchFullApplication();
957 else if (source == loadAnnotations)
961 else if (source == outputAnnotations)
963 outputAnnotations(true);
965 else if (source == outputFeatures)
967 outputFeatures(true, "Jalview");
969 else if (source == closeMenuItem)
971 closeMenuItem_actionPerformed();
973 else if (source == copy)
975 copy_actionPerformed();
977 else if (source == undoMenuItem)
979 undoMenuItem_actionPerformed();
981 else if (source == redoMenuItem)
983 redoMenuItem_actionPerformed();
985 else if (source == inputText)
987 inputText_actionPerformed();
989 else if (source == closeMenuItem)
991 closeMenuItem_actionPerformed();
993 else if (source == undoMenuItem)
995 undoMenuItem_actionPerformed();
997 else if (source == redoMenuItem)
999 redoMenuItem_actionPerformed();
1001 else if (source == copy)
1003 copy_actionPerformed();
1005 else if (source == pasteNew)
1007 pasteNew_actionPerformed();
1009 else if (source == pasteThis)
1011 pasteThis_actionPerformed();
1013 else if (source == cut)
1015 cut_actionPerformed();
1017 else if (source == delete)
1019 delete_actionPerformed();
1021 else if (source == grpsFromSelection)
1023 makeGrpsFromSelection_actionPerformed();
1025 else if (source == deleteGroups)
1027 deleteGroups_actionPerformed();
1029 else if (source == selectAllSequenceMenuItem)
1031 selectAllSequenceMenuItem_actionPerformed();
1033 else if (source == deselectAllSequenceMenuItem)
1035 deselectAllSequenceMenuItem_actionPerformed();
1037 else if (source == invertSequenceMenuItem)
1039 invertSequenceMenuItem_actionPerformed();
1041 else if (source == invertColSel)
1043 viewport.invertColumnSelection();
1044 alignPanel.paintAlignment(true);
1046 else if (source == remove2LeftMenuItem)
1048 trimAlignment(true);
1050 else if (source == remove2RightMenuItem)
1052 trimAlignment(false);
1054 else if (source == removeGappedColumnMenuItem)
1056 removeGappedColumnMenuItem_actionPerformed();
1058 else if (source == removeAllGapsMenuItem)
1060 removeAllGapsMenuItem_actionPerformed();
1062 else if (source == findMenuItem)
1064 findMenuItem_actionPerformed();
1066 else if (source == font)
1068 new FontChooser(alignPanel);
1070 else if (source == newView)
1074 else if (source == showColumns)
1076 viewport.showAllHiddenColumns();
1077 alignPanel.paintAlignment(true);
1079 else if (source == showSeqs)
1081 viewport.showAllHiddenSeqs();
1082 alignPanel.paintAlignment(true);
1084 else if (source == hideColumns)
1086 viewport.hideSelectedColumns();
1087 alignPanel.paintAlignment(true);
1089 else if (source == hideSequences
1090 && viewport.getSelectionGroup() != null)
1092 viewport.hideAllSelectedSeqs();
1093 alignPanel.paintAlignment(true);
1095 else if (source == hideAllButSelection)
1097 toggleHiddenRegions(false, false);
1098 alignPanel.paintAlignment(true);
1100 else if (source == hideAllSelection)
1102 SequenceGroup sg = viewport.getSelectionGroup();
1103 viewport.expandColSelection(sg, false);
1104 viewport.hideAllSelectedSeqs();
1105 viewport.hideSelectedColumns();
1106 alignPanel.paintAlignment(true);
1108 else if (source == showAllHidden)
1110 viewport.showAllHiddenColumns();
1111 viewport.showAllHiddenSeqs();
1112 alignPanel.paintAlignment(true);
1114 else if (source == showGroupConsensus)
1116 showGroupConsensus_actionPerformed();
1118 else if (source == showGroupConservation)
1120 showGroupConservation_actionPerformed();
1122 else if (source == showSequenceLogo)
1124 showSequenceLogo_actionPerformed();
1126 else if (source == normSequenceLogo)
1128 normSequenceLogo_actionPerformed();
1130 else if (source == showConsensusHistogram)
1132 showConsensusHistogram_actionPerformed();
1134 else if (source == applyAutoAnnotationSettings)
1136 applyAutoAnnotationSettings_actionPerformed();
1138 else if (source == featureSettings)
1140 new FeatureSettings(alignPanel);
1142 else if (source == alProperties)
1144 StringBuffer contents = new jalview.io.AlignmentProperties(
1145 viewport.getAlignment()).formatAsString();
1146 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1147 cap.setText(contents.toString());
1148 Frame frame = new Frame();
1150 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1151 "label.alignment_properties", new String[]
1152 { getTitle() }), 400, 250);
1154 else if (source == overviewMenuItem)
1156 overviewMenuItem_actionPerformed();
1158 else if (source == noColourmenuItem)
1162 else if (source == clustalColour)
1164 abovePIDThreshold.setState(false);
1165 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1167 else if (source == zappoColour)
1169 changeColour(new ZappoColourScheme());
1171 else if (source == taylorColour)
1173 changeColour(new TaylorColourScheme());
1175 else if (source == hydrophobicityColour)
1177 changeColour(new HydrophobicColourScheme());
1179 else if (source == helixColour)
1181 changeColour(new HelixColourScheme());
1183 else if (source == strandColour)
1185 changeColour(new StrandColourScheme());
1187 else if (source == turnColour)
1189 changeColour(new TurnColourScheme());
1191 else if (source == buriedColour)
1193 changeColour(new BuriedColourScheme());
1195 else if (source == nucleotideColour)
1197 changeColour(new NucleotideColourScheme());
1199 else if (source == purinePyrimidineColour)
1201 changeColour(new PurinePyrimidineColourScheme());
1203 else if (source == RNAInteractionColour)
1205 changeColour(new RNAInteractionColourScheme());
1207 else if (source == RNAHelixColour)
1209 new RNAHelicesColourChooser(viewport, alignPanel);
1211 else if (source == modifyPID)
1213 modifyPID_actionPerformed();
1215 else if (source == modifyConservation)
1217 modifyConservation_actionPerformed();
1219 else if (source == userDefinedColour)
1221 new UserDefinedColours(alignPanel, null);
1223 else if (source == PIDColour)
1225 changeColour(new PIDColourScheme());
1227 else if (source == BLOSUM62Colour)
1229 changeColour(new Blosum62ColourScheme());
1231 else if (source == tcoffeeColour)
1233 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1235 else if (source == annotationColour)
1237 new AnnotationColourChooser(viewport, alignPanel);
1239 else if (source == annotationColumnSelection)
1241 new AnnotationColumnChooser(viewport, alignPanel);
1243 else if (source == sortPairwiseMenuItem)
1245 sortPairwiseMenuItem_actionPerformed();
1247 else if (source == sortIDMenuItem)
1249 sortIDMenuItem_actionPerformed();
1251 else if (source == sortLengthMenuItem)
1253 sortLengthMenuItem_actionPerformed();
1255 else if (source == sortGroupMenuItem)
1257 sortGroupMenuItem_actionPerformed();
1259 else if (source == removeRedundancyMenuItem)
1261 removeRedundancyMenuItem_actionPerformed();
1263 else if (source == pairwiseAlignmentMenuItem)
1265 pairwiseAlignmentMenuItem_actionPerformed();
1267 else if (source == PCAMenuItem)
1269 PCAMenuItem_actionPerformed();
1271 else if (source == averageDistanceTreeMenuItem)
1273 averageDistanceTreeMenuItem_actionPerformed();
1275 else if (source == neighbourTreeMenuItem)
1277 neighbourTreeMenuItem_actionPerformed();
1279 else if (source == njTreeBlosumMenuItem)
1281 njTreeBlosumMenuItem_actionPerformed();
1283 else if (source == avDistanceTreeBlosumMenuItem)
1285 avTreeBlosumMenuItem_actionPerformed();
1287 else if (source == documentation)
1289 documentation_actionPerformed();
1291 else if (source == about)
1293 about_actionPerformed();
1298 public void inputText_actionPerformed()
1300 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1301 Frame frame = new Frame();
1303 jalview.bin.JalviewLite.addFrame(frame,
1304 MessageManager.getString("label.input_cut_paste"), 500, 500);
1307 protected void outputText_actionPerformed(ActionEvent e)
1309 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1310 Frame frame = new Frame();
1312 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1313 "label.alignment_output_command", new Object[]
1314 { e.getActionCommand() }), 600, 500);
1315 cap.setText(new AppletFormatAdapter().formatSequences(
1316 e.getActionCommand(), viewport.getAlignment(),
1317 viewport.getShowJVSuffix()));
1320 public void loadAnnotations()
1322 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1323 cap.setText(MessageManager
1324 .getString("label.paste_features_annotations_Tcoffee_here"));
1325 cap.setAnnotationImport();
1326 Frame frame = new Frame();
1328 jalview.bin.JalviewLite.addFrame(frame,
1329 MessageManager.getString("action.paste_annotations"), 400, 300);
1333 public String outputAnnotations(boolean displayTextbox)
1335 String annotation = new AnnotationFile()
1336 .printAnnotationsForView(viewport);
1340 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1341 Frame frame = new Frame();
1343 jalview.bin.JalviewLite.addFrame(frame,
1344 MessageManager.getString("label.annotations"), 600, 500);
1345 cap.setText(annotation);
1351 private Map<String,Object> getDisplayedFeatureCols()
1353 if (alignPanel.getFeatureRenderer() != null
1354 && viewport.getFeaturesDisplayed()!= null)
1356 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1362 public String outputFeatures(boolean displayTextbox, String format)
1365 if (format.equalsIgnoreCase("Jalview"))
1367 features = new FeaturesFile().printJalviewFormat(viewport
1368 .getAlignment().getSequencesArray(),
1369 getDisplayedFeatureCols());
1373 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1374 .getSequencesArray(), getDisplayedFeatureCols());
1379 boolean frimport = false;
1380 if (features == null || features.equals("No Features Visible"))
1382 features = "# No features visible - paste some and import them here.";
1386 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1389 cap.setAnnotationImport();
1391 Frame frame = new Frame();
1393 jalview.bin.JalviewLite.addFrame(frame,
1394 MessageManager.getString("label.features"), 600, 500);
1395 cap.setText(features);
1399 if (features == null)
1408 void launchFullApplication()
1410 StringBuffer url = new StringBuffer(jalviewServletURL);
1412 // allow servlet parameters to be passed in applet parameter
1413 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1415 url.append(firstSep);
1418 + appendProtocol(viewport.applet.getParameter("file")));
1420 if (viewport.applet.getParameter("features") != null)
1422 url.append("&features=");
1423 url.append(appendProtocol(viewport.applet.getParameter("features")));
1426 if (viewport.applet.getParameter("annotations") != null)
1428 url.append("&annotations=");
1429 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1432 if (viewport.applet.getParameter("jnetfile") != null)
1434 url.append("&annotations=");
1435 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1438 if (viewport.applet.getParameter("defaultColour") != null)
1440 url.append("&colour="
1441 + removeWhiteSpace(viewport.applet
1442 .getParameter("defaultColour")));
1445 if (viewport.applet.getParameter("userDefinedColour") != null)
1447 url.append("&colour="
1448 + removeWhiteSpace(viewport.applet
1449 .getParameter("userDefinedColour")));
1451 if (viewport.applet.getParameter("tree") != null)
1454 + appendProtocol(viewport.applet.getParameter("tree")));
1456 if (viewport.applet.getParameter("treeFile") != null)
1459 + appendProtocol(viewport.applet.getParameter("treeFile")));
1462 showURL(url.toString(), "FULL_APP");
1465 String removeWhiteSpace(String colour)
1467 StringBuffer sb = new StringBuffer();
1468 for (int i = 0; i < colour.length(); i++)
1470 if (Character.isWhitespace(colour.charAt(i)))
1476 sb.append(colour.charAt(i));
1480 return sb.toString();
1483 String appendProtocol(String url)
1488 url = URLEncoder.encode(url);
1491 * When we finally deprecate 1.1 compatibility, we can start to use
1492 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1493 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1494 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1495 * ex.printStackTrace(); }
1497 catch (java.net.MalformedURLException ex)
1499 url = viewport.applet.getCodeBase() + url;
1504 public void closeMenuItem_actionPerformed()
1506 PaintRefresher.RemoveComponent(alignPanel);
1507 if (alignPanel.seqPanel != null
1508 && alignPanel.seqPanel.seqCanvas != null)
1510 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1512 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1514 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1517 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1532 void updateEditMenuBar()
1535 if (viewport.getHistoryList().size() > 0)
1537 undoMenuItem.setEnabled(true);
1538 CommandI command = viewport.getHistoryList().peek();
1539 undoMenuItem.setLabel(MessageManager.formatMessage(
1540 "label.undo_command", new Object[]
1541 { command.getDescription() }));
1545 undoMenuItem.setEnabled(false);
1546 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1549 if (viewport.getRedoList().size() > 0)
1551 redoMenuItem.setEnabled(true);
1553 CommandI command = viewport.getRedoList().peek();
1554 redoMenuItem.setLabel(MessageManager.formatMessage(
1555 "label.redo_command", new Object[]
1556 { command.getDescription() }));
1560 redoMenuItem.setEnabled(false);
1561 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1569 public void addHistoryItem(CommandI command)
1571 if (command.getSize() > 0)
1573 viewport.addToHistoryList(command);
1574 viewport.clearRedoList();
1575 updateEditMenuBar();
1576 viewport.updateHiddenColumns();
1581 * TODO: JAL-1104 DOCUMENT ME!
1586 protected void undoMenuItem_actionPerformed()
1588 if (viewport.getHistoryList().isEmpty())
1593 CommandI command = viewport.getHistoryList().pop();
1594 viewport.addToRedoList(command);
1595 command.undoCommand(null);
1597 AlignViewport originalSource = getOriginatingSource(command);
1599 if (originalSource != viewport)
1602 .println("Warning: Viewport object mismatch whilst undoing");
1604 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1605 // viewport.getColumnSelection().getHiddenColumns()
1607 updateEditMenuBar();
1608 originalSource.firePropertyChange("alignment", null, originalSource
1609 .getAlignment().getSequences());
1613 * TODO: JAL-1104 DOCUMENT ME!
1618 protected void redoMenuItem_actionPerformed()
1620 if (viewport.getRedoList().isEmpty())
1625 CommandI command = viewport.getRedoList().pop();
1626 viewport.addToHistoryList(command);
1627 command.doCommand(null);
1629 AlignViewport originalSource = getOriginatingSource(command);
1631 if (originalSource != viewport)
1634 .println("Warning: Viewport object mismatch whilst re-doing");
1636 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1637 // viewport.getColumnSelection().getHiddenColumns()
1640 updateEditMenuBar();
1641 originalSource.firePropertyChange("alignment", null, originalSource
1642 .getAlignment().getSequences());
1645 AlignViewport getOriginatingSource(CommandI command)
1647 AlignViewport originalSource = null;
1648 // For sequence removal and addition, we need to fire
1649 // the property change event FROM the viewport where the
1650 // original alignment was altered
1651 AlignmentI al = null;
1652 if (command instanceof EditCommand)
1654 EditCommand editCommand = (EditCommand) command;
1655 al = editCommand.getAlignment();
1656 Vector comps = (Vector) PaintRefresher.components.get(viewport
1657 .getSequenceSetId());
1658 for (int i = 0; i < comps.size(); i++)
1660 if (comps.elementAt(i) instanceof AlignmentPanel)
1662 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1664 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1671 if (originalSource == null)
1673 // The original view is closed, we must validate
1674 // the current view against the closed view first
1677 PaintRefresher.validateSequences(al, viewport.getAlignment());
1680 originalSource = viewport;
1683 return originalSource;
1687 * Move the currently selected sequences up or down one position in the
1692 public void moveSelectedSequences(boolean up)
1694 SequenceGroup sg = viewport.getSelectionGroup();
1699 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1700 up ? null : viewport.getHiddenRepSequences(), up);
1701 alignPanel.paintAlignment(true);
1704 * Also move cDNA/protein complement sequences
1706 AlignViewportI complement = viewport.getCodingComplement();
1707 if (complement != null)
1709 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1710 viewport, complement);
1711 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1712 up ? null : complement.getHiddenRepSequences(), up);
1713 // TODO need to trigger a repaint of the complementary panel - how?
1714 // would prefer to handle in SplitFrame but it is not overriding key
1719 synchronized void slideSequences(boolean right, int size)
1721 List<SequenceI> sg = new Vector<SequenceI>();
1722 if (viewport.cursorMode)
1724 sg.add(viewport.getAlignment().getSequenceAt(
1725 alignPanel.seqPanel.seqCanvas.cursorY));
1727 else if (viewport.getSelectionGroup() != null
1728 && viewport.getSelectionGroup().getSize() != viewport
1729 .getAlignment().getHeight())
1731 sg = viewport.getSelectionGroup().getSequences(
1732 viewport.getHiddenRepSequences());
1740 Vector<SequenceI> invertGroup = new Vector();
1742 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1744 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1746 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1750 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1752 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1754 for (int i = 0; i < invertGroup.size(); i++)
1756 seqs2[i] = invertGroup.elementAt(i);
1759 SlideSequencesCommand ssc;
1762 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1763 size, viewport.getGapCharacter());
1767 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1768 size, viewport.getGapCharacter());
1771 int groupAdjustment = 0;
1772 if (ssc.getGapsInsertedBegin() && right)
1774 if (viewport.cursorMode)
1776 alignPanel.seqPanel.moveCursor(size, 0);
1780 groupAdjustment = size;
1783 else if (!ssc.getGapsInsertedBegin() && !right)
1785 if (viewport.cursorMode)
1787 alignPanel.seqPanel.moveCursor(-size, 0);
1791 groupAdjustment = -size;
1795 if (groupAdjustment != 0)
1797 viewport.getSelectionGroup().setStartRes(
1798 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1799 viewport.getSelectionGroup().setEndRes(
1800 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1803 boolean appendHistoryItem = false;
1804 Deque<CommandI> historyList = viewport.getHistoryList();
1805 if (historyList != null && historyList.size() > 0
1806 && historyList.peek() instanceof SlideSequencesCommand)
1808 appendHistoryItem = ssc
1809 .appendSlideCommand((SlideSequencesCommand) historyList
1813 if (!appendHistoryItem)
1815 addHistoryItem(ssc);
1821 static StringBuffer copiedSequences;
1823 static Vector copiedHiddenColumns;
1825 protected void copy_actionPerformed()
1827 if (viewport.getSelectionGroup() == null)
1832 SequenceGroup sg = viewport.getSelectionGroup();
1833 copiedSequences = new StringBuffer();
1834 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1835 for (int i = 0; i < sg.getSize(); i++)
1837 SequenceI seq = sg.getSequenceAt(i);
1838 int index = viewport.getAlignment().findIndex(seq);
1839 orderedSeqs.put(index, seq);
1842 int index = 0, startRes, endRes;
1845 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1847 copiedHiddenColumns = new Vector();
1848 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1849 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1851 copiedHiddenColumns.addElement(new int[]
1852 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1857 copiedHiddenColumns = null;
1860 for (int i = 0; i < sg.getSize(); i++)
1862 SequenceI seq = null;
1866 if (orderedSeqs.containsKey(index))
1868 seq = orderedSeqs.get(index);
1879 // Returns residue following index if gap
1880 startRes = seq.findPosition(sg.getStartRes());
1883 // Need to find the residue preceeding index if gap
1886 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1888 ch = seq.getCharAt(j);
1889 if (!jalview.util.Comparison.isGap((ch)))
1897 endRes += seq.getStart() - 1;
1900 copiedSequences.append(seq.getName()
1906 + seq.getSequenceAsString(sg.getStartRes(),
1907 sg.getEndRes() + 1) + "\n");
1912 protected void pasteNew_actionPerformed()
1917 protected void pasteThis_actionPerformed()
1922 void paste(boolean newAlignment)
1927 if (copiedSequences == null)
1932 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1933 Vector seqs = new Vector();
1934 while (st.hasMoreElements())
1936 String name = st.nextToken();
1937 int start = Integer.parseInt(st.nextToken());
1938 int end = Integer.parseInt(st.nextToken());
1939 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1941 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1942 for (int i = 0; i < seqs.size(); i++)
1944 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1949 String newtitle = MessageManager.getString("label.copied_sequences");
1950 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1952 newtitle = getTitle();
1956 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1958 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1959 viewport.applet, newtitle, false);
1960 if (copiedHiddenColumns != null)
1962 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1964 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1965 af.viewport.hideColumns(region[0], region[1]);
1969 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
1974 addSequences(newSeqs);
1977 } catch (Exception ex)
1979 } // could be anything being pasted in here
1983 void addSequences(SequenceI[] seqs)
1985 for (int i = 0; i < seqs.length; i++)
1987 viewport.getAlignment().addSequence(seqs[i]);
1991 addHistoryItem(new EditCommand(
1992 MessageManager.getString("label.add_sequences"), Action.PASTE,
1993 seqs, 0, viewport.getAlignment().getWidth(),
1994 viewport.getAlignment()));
1996 viewport.setEndSeq(viewport.getAlignment().getHeight());
1997 viewport.getAlignment().getWidth();
1998 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2003 protected void cut_actionPerformed()
2005 copy_actionPerformed();
2006 delete_actionPerformed();
2009 protected void delete_actionPerformed()
2012 SequenceGroup sg = viewport.getSelectionGroup();
2018 Vector seqs = new Vector();
2020 for (int i = 0; i < sg.getSize(); i++)
2022 seq = sg.getSequenceAt(i);
2023 seqs.addElement(seq);
2026 // If the cut affects all sequences, remove highlighted columns
2027 if (sg.getSize() == viewport.getAlignment().getHeight())
2029 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2030 sg.getEndRes() + 1);
2033 SequenceI[] cut = new SequenceI[seqs.size()];
2034 for (int i = 0; i < seqs.size(); i++)
2036 cut[i] = (SequenceI) seqs.elementAt(i);
2040 * //ADD HISTORY ITEM
2042 addHistoryItem(new EditCommand(
2043 MessageManager.getString("label.cut_sequences"), Action.CUT,
2044 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2045 viewport.getAlignment()));
2047 viewport.setSelectionGroup(null);
2048 viewport.getAlignment().deleteGroup(sg);
2050 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2053 if (viewport.getAlignment().getHeight() < 1)
2055 this.setVisible(false);
2057 viewport.sendSelection();
2061 * group consensus toggled
2064 protected void showGroupConsensus_actionPerformed()
2066 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2067 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2072 * group conservation toggled.
2074 protected void showGroupConservation_actionPerformed()
2076 viewport.setShowGroupConservation(showGroupConservation.getState());
2077 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2084 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2085 * .event.ActionEvent)
2087 protected void showConsensusHistogram_actionPerformed()
2089 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2090 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2097 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2098 * .event.ActionEvent)
2100 protected void showSequenceLogo_actionPerformed()
2102 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2103 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2106 protected void normSequenceLogo_actionPerformed()
2108 showSequenceLogo.setState(true);
2109 viewport.setShowSequenceLogo(true);
2110 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2111 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2114 protected void applyAutoAnnotationSettings_actionPerformed()
2116 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2119 protected void makeGrpsFromSelection_actionPerformed()
2121 if (avc.makeGroupsFromSelection())
2123 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2124 alignPanel.updateAnnotation();
2125 alignPanel.paintAlignment(true);
2129 protected void createGroup_actionPerformed()
2134 protected void unGroup_actionPerformed()
2138 alignPanel.alignmentChanged();
2142 protected void deleteGroups_actionPerformed()
2144 if (avc.deleteGroups())
2146 alignPanel.alignmentChanged();
2150 public void selectAllSequenceMenuItem_actionPerformed()
2152 SequenceGroup sg = new SequenceGroup();
2153 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2155 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2157 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2158 viewport.setSelectionGroup(sg);
2159 alignPanel.paintAlignment(true);
2160 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2161 viewport.sendSelection();
2164 public void deselectAllSequenceMenuItem_actionPerformed()
2166 if (viewport.cursorMode)
2168 alignPanel.seqPanel.keyboardNo1 = null;
2169 alignPanel.seqPanel.keyboardNo2 = null;
2171 viewport.setSelectionGroup(null);
2172 viewport.getColumnSelection().clear();
2173 viewport.setSelectionGroup(null);
2174 alignPanel.idPanel.idCanvas.searchResults = null;
2175 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2176 alignPanel.paintAlignment(true);
2177 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2178 viewport.sendSelection();
2181 public void invertSequenceMenuItem_actionPerformed()
2183 SequenceGroup sg = viewport.getSelectionGroup();
2184 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2186 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2189 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2190 viewport.sendSelection();
2193 public void invertColSel_actionPerformed()
2195 viewport.invertColumnSelection();
2196 alignPanel.paintAlignment(true);
2197 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2198 viewport.sendSelection();
2201 void trimAlignment(boolean trimLeft)
2203 ColumnSelection colSel = viewport.getColumnSelection();
2206 if (colSel.size() > 0)
2210 column = colSel.getMin();
2214 column = colSel.getMax();
2218 if (viewport.getSelectionGroup() != null)
2220 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2221 viewport.getHiddenRepSequences());
2225 seqs = viewport.getAlignment().getSequencesArray();
2228 TrimRegionCommand trimRegion;
2231 trimRegion = new TrimRegionCommand("Remove Left",
2232 TrimRegionCommand.TRIM_LEFT, seqs, column,
2233 viewport.getAlignment(), viewport.getColumnSelection(),
2234 viewport.getSelectionGroup());
2235 viewport.setStartRes(0);
2239 trimRegion = new TrimRegionCommand("Remove Right",
2240 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2241 viewport.getAlignment(), viewport.getColumnSelection(),
2242 viewport.getSelectionGroup());
2245 statusBar.setText(MessageManager.formatMessage(
2246 "label.removed_columns", new String[]
2247 { Integer.valueOf(trimRegion.getSize()).toString() }));
2248 addHistoryItem(trimRegion);
2250 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2252 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2253 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2255 viewport.getAlignment().deleteGroup(sg);
2259 viewport.firePropertyChange("alignment", null, viewport
2260 .getAlignment().getSequences());
2264 public void removeGappedColumnMenuItem_actionPerformed()
2266 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2269 if (viewport.getSelectionGroup() != null)
2271 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2272 viewport.getHiddenRepSequences());
2273 start = viewport.getSelectionGroup().getStartRes();
2274 end = viewport.getSelectionGroup().getEndRes();
2278 seqs = viewport.getAlignment().getSequencesArray();
2281 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2282 "Remove Gapped Columns", seqs, start, end,
2283 viewport.getAlignment());
2285 addHistoryItem(removeGapCols);
2287 statusBar.setText(MessageManager.formatMessage(
2288 "label.removed_empty_columns", new String[]
2289 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2291 // This is to maintain viewport position on first residue
2292 // of first sequence
2293 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2294 int startRes = seq.findPosition(viewport.startRes);
2295 // ShiftList shifts;
2296 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2297 // edit.alColumnChanges=shifts.getInverse();
2298 // if (viewport.hasHiddenColumns)
2299 // viewport.getColumnSelection().compensateForEdits(shifts);
2300 viewport.setStartRes(seq.findIndex(startRes) - 1);
2301 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2306 public void removeAllGapsMenuItem_actionPerformed()
2308 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2311 if (viewport.getSelectionGroup() != null)
2313 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2314 viewport.getHiddenRepSequences());
2315 start = viewport.getSelectionGroup().getStartRes();
2316 end = viewport.getSelectionGroup().getEndRes();
2320 seqs = viewport.getAlignment().getSequencesArray();
2323 // This is to maintain viewport position on first residue
2324 // of first sequence
2325 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2326 int startRes = seq.findPosition(viewport.startRes);
2328 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2329 viewport.getAlignment()));
2331 viewport.setStartRes(seq.findIndex(startRes) - 1);
2333 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2338 public void findMenuItem_actionPerformed()
2340 new Finder(alignPanel);
2344 * create a new view derived from the current view
2347 * @return frame for the new view
2349 public AlignFrame newView(String viewtitle)
2352 if (viewport.hasHiddenRows())
2354 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2355 .getFullAlignment().getSequencesArray());
2359 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2362 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2364 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2366 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2368 newal.addAnnotation(viewport.getAlignment()
2369 .getAlignmentAnnotation()[i]);
2374 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2376 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2377 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2378 PaintRefresher.Register(newaf.alignPanel,
2379 newaf.alignPanel.av.getSequenceSetId());
2381 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2382 newaf.alignPanel.av.getSequenceSetId());
2383 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2384 newaf.alignPanel.av.getSequenceSetId());
2386 Vector comps = (Vector) PaintRefresher.components.get(viewport
2387 .getSequenceSetId());
2389 for (int i = 0; i < comps.size(); i++)
2391 if (comps.elementAt(i) instanceof AlignmentPanel)
2397 String title = new String(this.getTitle());
2398 if (viewtitle != null)
2400 title = viewtitle + " ( " + title + ")";
2404 if (title.indexOf("(View") > -1)
2406 title = title.substring(0, title.indexOf("(View"));
2408 title += "(View " + viewSize + ")";
2411 newaf.setTitle(title.toString());
2413 newaf.viewport.setHistoryList(viewport.getHistoryList());
2414 newaf.viewport.setRedoList(viewport.getRedoList());
2420 * @return list of feature groups on the view
2422 public String[] getFeatureGroups()
2424 FeatureRenderer fr = null;
2425 if (alignPanel != null
2426 && (fr = alignPanel.getFeatureRenderer()) != null)
2428 List<String> gps = fr.getFeatureGroups();
2429 String[] _gps = gps.toArray(new String[gps.size()]);
2436 * get sequence feature groups that are hidden or shown
2442 public String[] getFeatureGroupsOfState(boolean visible)
2444 FeatureRenderer fr = null;
2445 if (alignPanel != null
2446 && (fr = alignPanel.getFeatureRenderer()) != null)
2448 List<String> gps = fr.getGroups(visible);
2449 String[] _gps = gps.toArray(new String[gps.size()]);
2456 * Change the display state for the given feature groups
2459 * list of group strings
2461 * visible or invisible
2463 public void setFeatureGroupState(String[] groups, boolean state)
2465 FeatureRenderer fr = null;
2466 this.sequenceFeatures.setState(true);
2467 viewport.setShowSequenceFeatures(true);
2468 if (alignPanel != null
2469 && (fr = alignPanel.getFeatureRenderer()) != null)
2472 fr.setGroupVisibility(Arrays.asList(groups), state);
2473 alignPanel.seqPanel.seqCanvas.repaint();
2474 if (alignPanel.overviewPanel != null)
2476 alignPanel.overviewPanel.updateOverviewImage();
2481 public void seqLimits_itemStateChanged()
2483 viewport.setShowJVSuffix(seqLimits.getState());
2484 alignPanel.fontChanged();
2485 alignPanel.paintAlignment(true);
2488 protected void colourTextMenuItem_actionPerformed()
2490 viewport.setColourText(colourTextMenuItem.getState());
2491 alignPanel.paintAlignment(true);
2494 protected void displayNonconservedMenuItem_actionPerformed()
2496 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2497 alignPanel.paintAlignment(true);
2500 protected void wrapMenuItem_actionPerformed()
2502 viewport.setWrapAlignment(wrapMenuItem.getState());
2503 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2504 scaleAbove.setEnabled(wrapMenuItem.getState());
2505 scaleLeft.setEnabled(wrapMenuItem.getState());
2506 scaleRight.setEnabled(wrapMenuItem.getState());
2507 alignPanel.paintAlignment(true);
2510 public void overviewMenuItem_actionPerformed()
2512 if (alignPanel.overviewPanel != null)
2517 Frame frame = new Frame();
2518 OverviewPanel overview = new OverviewPanel(alignPanel);
2519 frame.add(overview);
2520 // +50 must allow for applet frame window
2521 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2522 "label.overview_params", new String[]
2523 { this.getTitle() }), overview.getPreferredSize().width,
2524 overview.getPreferredSize().height + 50);
2527 final AlignmentPanel ap = alignPanel;
2528 frame.addWindowListener(new WindowAdapter()
2531 public void windowClosing(WindowEvent e)
2535 ap.setOverviewPanel(null);
2540 alignPanel.setOverviewPanel(overview);
2544 void changeColour(ColourSchemeI cs)
2550 if (viewport.getAbovePIDThreshold())
2552 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2556 if (viewport.getConservationSelected())
2558 cs.setConservationApplied(true);
2559 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2564 cs.setConservationApplied(false);
2567 viewport.setGlobalColourScheme(cs);
2569 if (alignPanel.getOverviewPanel() != null)
2571 alignPanel.getOverviewPanel().updateOverviewImage();
2574 jalview.structure.StructureSelectionManager
2575 .getStructureSelectionManager(viewport.applet)
2576 .sequenceColoursChanged(alignPanel);
2578 alignPanel.paintAlignment(true);
2581 protected void modifyPID_actionPerformed()
2583 if (viewport.getAbovePIDThreshold()
2584 && viewport.getGlobalColourScheme() != null)
2586 SliderPanel.setPIDSliderSource(alignPanel,
2587 viewport.getGlobalColourScheme(), "Background");
2588 SliderPanel.showPIDSlider();
2592 protected void modifyConservation_actionPerformed()
2594 if (viewport.getConservationSelected()
2595 && viewport.getGlobalColourScheme() != null)
2597 SliderPanel.setConservationSlider(alignPanel,
2598 viewport.getGlobalColourScheme(), "Background");
2599 SliderPanel.showConservationSlider();
2603 protected void conservationMenuItem_actionPerformed()
2605 viewport.setConservationSelected(conservationMenuItem.getState());
2607 viewport.setAbovePIDThreshold(false);
2608 abovePIDThreshold.setState(false);
2610 changeColour(viewport.getGlobalColourScheme());
2612 modifyConservation_actionPerformed();
2615 public void abovePIDThreshold_actionPerformed()
2617 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2619 conservationMenuItem.setState(false);
2620 viewport.setConservationSelected(false);
2622 changeColour(viewport.getGlobalColourScheme());
2624 modifyPID_actionPerformed();
2627 public void sortPairwiseMenuItem_actionPerformed()
2629 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2630 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2631 .getAlignment().getSequenceAt(0), null);
2633 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2634 viewport.getAlignment()));
2635 alignPanel.paintAlignment(true);
2638 public void sortIDMenuItem_actionPerformed()
2640 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2641 AlignmentSorter.sortByID(viewport.getAlignment());
2642 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2643 viewport.getAlignment()));
2644 alignPanel.paintAlignment(true);
2647 public void sortLengthMenuItem_actionPerformed()
2649 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2650 AlignmentSorter.sortByLength(viewport.getAlignment());
2651 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2652 viewport.getAlignment()));
2653 alignPanel.paintAlignment(true);
2656 public void sortGroupMenuItem_actionPerformed()
2658 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2659 AlignmentSorter.sortByGroup(viewport.getAlignment());
2660 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2661 viewport.getAlignment()));
2662 alignPanel.paintAlignment(true);
2666 public void removeRedundancyMenuItem_actionPerformed()
2668 new RedundancyPanel(alignPanel);
2671 public void pairwiseAlignmentMenuItem_actionPerformed()
2673 if (viewport.getSelectionGroup() != null
2674 && viewport.getSelectionGroup().getSize() > 1)
2676 Frame frame = new Frame();
2677 frame.add(new PairwiseAlignPanel(alignPanel));
2678 jalview.bin.JalviewLite.addFrame(frame,
2679 MessageManager.getString("action.pairwise_alignment"), 600,
2684 public void PCAMenuItem_actionPerformed()
2686 // are the sequences aligned?
2687 if (!viewport.getAlignment().isAligned(false))
2690 int Width = viewport.getAlignment().getWidth();
2692 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2694 current = viewport.getAlignment().getSequenceAt(i);
2696 if (current.getLength() < Width)
2698 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2701 alignPanel.paintAlignment(true);
2704 if ((viewport.getSelectionGroup() != null
2705 && viewport.getSelectionGroup().getSize() < 4 && viewport
2706 .getSelectionGroup().getSize() > 0)
2707 || viewport.getAlignment().getHeight() < 4)
2714 new PCAPanel(viewport);
2715 } catch (java.lang.OutOfMemoryError ex)
2721 public void averageDistanceTreeMenuItem_actionPerformed()
2723 NewTreePanel("AV", "PID", "Average distance tree using PID");
2726 public void neighbourTreeMenuItem_actionPerformed()
2728 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2731 protected void njTreeBlosumMenuItem_actionPerformed()
2733 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2736 protected void avTreeBlosumMenuItem_actionPerformed()
2738 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2741 void NewTreePanel(String type, String pwType, String title)
2743 // are the sequences aligned?
2744 if (!viewport.getAlignment().isAligned(false))
2747 int Width = viewport.getAlignment().getWidth();
2749 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2751 current = viewport.getAlignment().getSequenceAt(i);
2753 if (current.getLength() < Width)
2755 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2758 alignPanel.paintAlignment(true);
2762 if ((viewport.getSelectionGroup() != null && viewport
2763 .getSelectionGroup().getSize() > 1)
2764 || (viewport.getAlignment().getHeight() > 1))
2766 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2768 addTreeMenuItem(tp, title);
2770 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2774 void loadTree_actionPerformed()
2776 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2777 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2778 cap.setTreeImport();
2779 Frame frame = new Frame();
2781 jalview.bin.JalviewLite.addFrame(frame,
2782 MessageManager.getString("label.paste_newick_file"), 400, 300);
2785 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2787 TreePanel tp = new TreePanel(alignPanel, treeFile,
2788 MessageManager.getString("label.load_tree_from_file"), tree);
2789 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2790 addTreeMenuItem(tp, treeFile);
2794 * sort the alignment using the given treePanel
2797 * tree used to sort view
2799 * string used for undo event name
2801 public void sortByTree(TreePanel treePanel, String title)
2803 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2805 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2806 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2807 // HistoryItem.SORT));
2808 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2809 "label.order_by_params", new String[]
2810 { title }), oldOrder, viewport.getAlignment()));
2811 alignPanel.paintAlignment(true);
2815 * Do any automatic reordering of the alignment and add the necessary bits to
2816 * the menu structure for the new tree
2821 protected void addTreeMenuItem(final TreePanel treePanel,
2824 final MenuItem item = new MenuItem(title);
2825 sortByTreeMenu.add(item);
2826 item.addActionListener(new java.awt.event.ActionListener()
2829 public void actionPerformed(ActionEvent evt)
2831 sortByTree(treePanel, title); // treePanel.getTitle());
2835 treePanel.addWindowListener(new WindowAdapter()
2838 public void windowOpened(WindowEvent e)
2840 if (viewport.sortByTree)
2842 sortByTree(treePanel, title);
2844 super.windowOpened(e);
2848 public void windowClosing(WindowEvent e)
2850 sortByTreeMenu.remove(item);
2855 public boolean sortBy(AlignmentOrder alorder, String undoname)
2857 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2858 if (viewport.applet.debug)
2860 System.err.println("Sorting " + alorder.getOrder().size()
2861 + " in alignment '" + getTitle() + "'");
2863 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2864 if (undoname != null)
2866 addHistoryItem(new OrderCommand(undoname, oldOrder,
2867 viewport.getAlignment()));
2869 alignPanel.paintAlignment(true);
2873 protected void documentation_actionPerformed()
2875 alignPanel.av.applet.openJalviewHelpUrl();
2878 protected void about_actionPerformed()
2881 class AboutPanel extends Canvas
2887 public AboutPanel(String version, String builddate)
2889 this.version = version;
2890 this.builddate = builddate;
2894 public void paint(Graphics g)
2896 g.setColor(Color.white);
2897 g.fillRect(0, 0, getSize().width, getSize().height);
2898 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2899 FontMetrics fm = g.getFontMetrics();
2900 int fh = fm.getHeight();
2902 g.setColor(Color.black);
2903 // TODO: update this text for each release or centrally store it for
2904 // lite and application
2905 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2906 g.drawString(MessageManager.formatMessage(
2907 "label.jalviewLite_release", new String[]
2908 { version }), x, y += fh);
2909 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2910 g.drawString(MessageManager.formatMessage(
2911 "label.jaview_build_date", new String[]
2912 { builddate }), x, y += fh);
2913 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2914 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2916 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2917 x + 50, y += fh + 8);
2919 MessageManager.getString("label.jalview_dev_managers"), x,
2921 g.drawString(MessageManager
2922 .getString("label.jalview_distribution_lists"), x, y += fh);
2923 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2926 MessageManager.getString("label.jalview_cite_1_authors"),
2929 MessageManager.getString("label.jalview_cite_1_title"), x,
2931 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2936 Frame frame = new Frame();
2937 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2939 jalview.bin.JalviewLite.addFrame(frame,
2940 MessageManager.getString("label.jalview"), 580, 220);
2944 public void showURL(String url, String target)
2946 if (viewport.applet == null)
2948 System.out.println("Not running as applet - no browser available.");
2952 viewport.applet.showURL(url, target);
2956 // ////////////////////////////////////////////////////////////////////////////////
2957 // JBuilder Graphics here
2959 MenuBar alignFrameMenuBar = new MenuBar();
2961 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2963 MenuItem loadApplication = new MenuItem(
2964 MessageManager.getString("label.view_full_application"));
2966 MenuItem loadTree = new MenuItem(
2967 MessageManager.getString("label.load_associated_tree"));
2969 MenuItem loadAnnotations = new MenuItem(
2970 MessageManager.getString("label.load_features_annotations"));
2972 MenuItem outputFeatures = new MenuItem(
2973 MessageManager.getString("label.export_features").concat("..."));
2975 MenuItem outputAnnotations = new MenuItem(
2976 MessageManager.getString("label.export_annotations").concat("..."));
2978 MenuItem closeMenuItem = new MenuItem(
2979 MessageManager.getString("action.close"));
2981 MenuItem selectAllSequenceMenuItem = new MenuItem(
2982 MessageManager.getString("action.select_all"));
2984 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2985 MessageManager.getString("action.deselect_all"));
2987 MenuItem invertSequenceMenuItem = new MenuItem(
2988 MessageManager.getString("action.invert_selection"));
2990 MenuItem remove2LeftMenuItem = new MenuItem();
2992 MenuItem remove2RightMenuItem = new MenuItem();
2994 MenuItem removeGappedColumnMenuItem = new MenuItem();
2996 MenuItem removeAllGapsMenuItem = new MenuItem();
2998 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3000 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3002 MenuItem sortPairwiseMenuItem = new MenuItem();
3004 MenuItem sortIDMenuItem = new MenuItem();
3006 MenuItem sortLengthMenuItem = new MenuItem();
3008 MenuItem sortGroupMenuItem = new MenuItem();
3010 MenuItem removeRedundancyMenuItem = new MenuItem();
3012 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3014 MenuItem PCAMenuItem = new MenuItem();
3016 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3018 MenuItem neighbourTreeMenuItem = new MenuItem();
3020 BorderLayout borderLayout1 = new BorderLayout();
3022 public Label statusBar = new Label();
3024 MenuItem clustalColour = new MenuItem();
3026 MenuItem zappoColour = new MenuItem();
3028 MenuItem taylorColour = new MenuItem();
3030 MenuItem hydrophobicityColour = new MenuItem();
3032 MenuItem helixColour = new MenuItem();
3034 MenuItem strandColour = new MenuItem();
3036 MenuItem turnColour = new MenuItem();
3038 MenuItem buriedColour = new MenuItem();
3040 MenuItem purinePyrimidineColour = new MenuItem();
3042 MenuItem RNAInteractionColour = new MenuItem();
3044 MenuItem RNAHelixColour = new MenuItem();
3046 MenuItem userDefinedColour = new MenuItem();
3048 MenuItem PIDColour = new MenuItem();
3050 MenuItem BLOSUM62Colour = new MenuItem();
3052 MenuItem tcoffeeColour = new MenuItem();
3054 MenuItem njTreeBlosumMenuItem = new MenuItem();
3056 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3058 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3060 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3062 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3064 MenuItem alProperties = new MenuItem(
3065 MessageManager.getString("label.alignment_props"));
3067 MenuItem overviewMenuItem = new MenuItem();
3069 MenuItem undoMenuItem = new MenuItem();
3071 MenuItem redoMenuItem = new MenuItem();
3073 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3075 MenuItem noColourmenuItem = new MenuItem();
3077 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3079 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3081 MenuItem findMenuItem = new MenuItem();
3083 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3085 MenuItem nucleotideColour = new MenuItem();
3087 MenuItem deleteGroups = new MenuItem();
3089 MenuItem grpsFromSelection = new MenuItem();
3091 MenuItem createGroup = new MenuItem();
3093 MenuItem unGroup = new MenuItem();
3095 MenuItem delete = new MenuItem();
3097 MenuItem copy = new MenuItem();
3099 MenuItem cut = new MenuItem();
3101 Menu pasteMenu = new Menu();
3103 MenuItem pasteNew = new MenuItem();
3105 MenuItem pasteThis = new MenuItem();
3107 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3109 MenuItem font = new MenuItem();
3111 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3113 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3115 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3117 MenuItem modifyPID = new MenuItem();
3119 MenuItem modifyConservation = new MenuItem();
3121 CheckboxMenuItem autoCalculate = null;
3123 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3124 "Sort Alignment With New Tree", true);
3126 Menu sortByTreeMenu = new Menu();
3128 MenuItem inputText = new MenuItem();
3130 MenuItem documentation = new MenuItem();
3132 MenuItem about = new MenuItem();
3134 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3136 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3138 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3140 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3142 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3144 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3146 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3148 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3150 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3153 * Initialise menus and other items
3157 private void jbInit() throws Exception
3159 setMenuBar(alignFrameMenuBar);
3162 * Configure File menu items and actions
3165 .setLabel(MessageManager.getString("label.input_from_textbox"));
3166 inputText.addActionListener(this);
3167 Menu outputTextboxMenu = new Menu(
3168 MessageManager.getString("label.out_to_textbox"));
3169 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3172 MenuItem item = new MenuItem(
3173 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3175 item.addActionListener(new java.awt.event.ActionListener()
3178 public void actionPerformed(ActionEvent e)
3180 outputText_actionPerformed(e);
3184 outputTextboxMenu.add(item);
3186 closeMenuItem.addActionListener(this);
3187 loadApplication.addActionListener(this);
3188 loadTree.addActionListener(this);
3189 loadAnnotations.addActionListener(this);
3190 outputFeatures.addActionListener(this);
3191 outputAnnotations.addActionListener(this);
3194 * Configure Edit menu items and actions
3196 undoMenuItem.setEnabled(false);
3197 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3198 undoMenuItem.addActionListener(this);
3199 redoMenuItem.setEnabled(false);
3200 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3201 redoMenuItem.addActionListener(this);
3202 copy.setLabel(MessageManager.getString("action.copy"));
3203 copy.addActionListener(this);
3204 cut.setLabel(MessageManager.getString("action.cut"));
3205 cut.addActionListener(this);
3206 delete.setLabel(MessageManager.getString("action.delete"));
3207 delete.addActionListener(this);
3208 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3209 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3210 pasteNew.addActionListener(this);
3211 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3212 pasteThis.addActionListener(this);
3213 remove2LeftMenuItem.setLabel(MessageManager
3214 .getString("action.remove_left"));
3215 remove2LeftMenuItem.addActionListener(this);
3216 remove2RightMenuItem.setLabel(MessageManager
3217 .getString("action.remove_right"));
3218 remove2RightMenuItem.addActionListener(this);
3219 removeGappedColumnMenuItem.setLabel(MessageManager
3220 .getString("action.remove_empty_columns"));
3221 removeGappedColumnMenuItem.addActionListener(this);
3222 removeAllGapsMenuItem.setLabel(MessageManager
3223 .getString("action.remove_all_gaps"));
3224 removeAllGapsMenuItem.addActionListener(this);
3225 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3226 "action.remove_redundancy").concat("..."));
3227 removeRedundancyMenuItem.addActionListener(this);
3230 * Configure Select menu items and actions
3232 findMenuItem.setLabel(MessageManager.getString("action.find"));
3233 findMenuItem.addActionListener(this);
3234 selectAllSequenceMenuItem.addActionListener(this);
3235 deselectAllSequenceMenuItem.addActionListener(this);
3236 invertSequenceMenuItem.setLabel(MessageManager
3237 .getString("action.invert_sequence_selection"));
3238 invertSequenceMenuItem.addActionListener(this);
3239 invertColSel.setLabel(MessageManager
3240 .getString("action.invert_column_selection"));
3241 invertColSel.addActionListener(this);
3242 deleteGroups.setLabel(MessageManager
3243 .getString("action.undefine_groups"));
3244 deleteGroups.addActionListener(this);
3245 grpsFromSelection.setLabel(MessageManager
3246 .getString("action.make_groups_selection"));
3247 grpsFromSelection.addActionListener(this);
3248 createGroup.setLabel(MessageManager.getString("action.create_group"));
3249 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3250 annotationColumnSelection.setLabel("Select by Annotation");
3251 annotationColumnSelection.addActionListener(this);
3254 * Configure View menu items and actions
3256 newView.setLabel(MessageManager.getString("action.new_view"));
3257 newView.addActionListener(this);
3258 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3259 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3260 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3261 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3263 .setLabel(MessageManager.getString("label.selected_columns"));
3264 hideSequences.setLabel(MessageManager
3265 .getString("label.selected_sequences"));
3266 hideAllButSelection.setLabel(MessageManager
3267 .getString("label.all_but_selected_region"));
3268 hideAllSelection.setLabel(MessageManager
3269 .getString("label.selected_region"));
3270 showAllHidden.setLabel(MessageManager
3271 .getString("label.all_sequences_columns"));
3272 showColumns.addActionListener(this);
3273 showSeqs.addActionListener(this);
3274 hideColumns.addActionListener(this);
3275 hideSequences.addActionListener(this);
3276 hideAllButSelection.addActionListener(this);
3277 hideAllSelection.addActionListener(this);
3278 showAllHidden.addActionListener(this);
3279 featureSettings.setLabel(MessageManager
3280 .getString("label.feature_settings"));
3281 featureSettings.addActionListener(this);
3282 sequenceFeatures.setLabel(MessageManager
3283 .getString("label.show_sequence_features"));
3284 sequenceFeatures.addItemListener(this);
3285 sequenceFeatures.setState(false);
3286 followMouseOverFlag.setLabel(MessageManager
3287 .getString("label.automatic_scrolling"));
3288 followMouseOverFlag.addItemListener(this);
3289 alProperties.addActionListener(this);
3290 overviewMenuItem.setLabel(MessageManager
3291 .getString("label.overview_window"));
3292 overviewMenuItem.addActionListener(this);
3295 * Configure Annotations menu items and actions
3297 annotationPanelMenuItem.setLabel(MessageManager
3298 .getString("label.show_annotations"));
3299 annotationPanelMenuItem.addItemListener(this);
3300 showGroupConsensus.setLabel(MessageManager
3301 .getString("label.group_consensus"));
3302 showGroupConservation.setLabel(MessageManager
3303 .getString("label.group_conservation"));
3304 showConsensusHistogram.setLabel(MessageManager
3305 .getString("label.show_consensus_histogram"));
3306 showSequenceLogo.setLabel(MessageManager
3307 .getString("label.show_consensus_logo"));
3308 normSequenceLogo.setLabel(MessageManager
3309 .getString("label.norm_consensus_logo"));
3310 applyAutoAnnotationSettings.setLabel(MessageManager
3311 .getString("label.apply_all_groups"));
3312 applyAutoAnnotationSettings.setState(true);
3313 Menu autoAnnMenu = new Menu(
3314 MessageManager.getString("label.autocalculated_annotation"));
3315 showGroupConsensus.addItemListener(this);
3316 showGroupConservation.addItemListener(this);
3317 showConsensusHistogram.addItemListener(this);
3318 showSequenceLogo.addItemListener(this);
3319 normSequenceLogo.addItemListener(this);
3320 applyAutoAnnotationSettings.addItemListener(this);
3321 showAlignmentAnnotations = new CheckboxMenuItem(
3322 MessageManager.getString("label.show_all_al_annotations"));
3323 showSequenceAnnotations = new CheckboxMenuItem(
3324 MessageManager.getString("label.show_all_seq_annotations"));
3325 sortAnnBySequence = new CheckboxMenuItem(
3326 MessageManager.getString("label.sort_annotations_by_sequence"));
3327 sortAnnByLabel = new CheckboxMenuItem(
3328 MessageManager.getString("label.sort_annotations_by_label"));
3329 showAutoFirst = new CheckboxMenuItem(
3330 MessageManager.getString("label.show_first"));
3331 showAutoLast = new CheckboxMenuItem(
3332 MessageManager.getString("label.show_last"));
3333 showAlignmentAnnotations.addItemListener(this);
3334 showSequenceAnnotations.addItemListener(this);
3335 sortAnnBySequence.addItemListener(this);
3336 sortAnnByLabel.addItemListener(this);
3337 showAutoFirst.addItemListener(this);
3338 showAutoLast.addItemListener(this);
3341 * Configure Format menu items and actions
3343 font.setLabel(MessageManager.getString("action.font"));
3344 font.addActionListener(this);
3345 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3346 scaleAbove.setState(true);
3347 scaleAbove.setEnabled(false);
3348 scaleAbove.addItemListener(this);
3349 scaleLeft.setEnabled(false);
3350 scaleLeft.setState(true);
3351 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3352 scaleLeft.addItemListener(this);
3353 scaleRight.setEnabled(false);
3354 scaleRight.setState(true);
3355 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3356 scaleRight.addItemListener(this);
3357 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3358 viewBoxesMenuItem.setState(true);
3359 viewBoxesMenuItem.addItemListener(this);
3360 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3361 viewTextMenuItem.setState(true);
3362 viewTextMenuItem.addItemListener(this);
3363 colourTextMenuItem.setLabel(MessageManager
3364 .getString("label.colour_text"));
3365 colourTextMenuItem.addItemListener(this);
3366 displayNonconservedMenuItem.setLabel(MessageManager
3367 .getString("label.show_non_conversed"));
3368 displayNonconservedMenuItem.addItemListener(this);
3369 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3370 wrapMenuItem.addItemListener(this);
3371 renderGapsMenuItem.setLabel(MessageManager
3372 .getString("action.show_gaps"));
3373 renderGapsMenuItem.setState(true);
3374 renderGapsMenuItem.addItemListener(this);
3375 centreColumnLabelFlag.setLabel(MessageManager
3376 .getString("label.centre_column_labels"));
3377 centreColumnLabelFlag.addItemListener(this);
3378 seqLimits.setState(true);
3379 seqLimits.setLabel(MessageManager
3380 .getString("label.show_sequence_limits"));
3381 seqLimits.addItemListener(this);
3384 * Configure Colour menu items and actions
3386 applyToAllGroups.setLabel(MessageManager
3387 .getString("label.apply_colour_to_all_groups"));
3388 applyToAllGroups.setState(true);
3389 applyToAllGroups.addItemListener(this);
3390 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3391 clustalColour.addActionListener(this);
3392 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3393 zappoColour.addActionListener(this);
3394 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3395 taylorColour.addActionListener(this);
3396 hydrophobicityColour.setLabel(MessageManager
3397 .getString("label.hydrophobicity"));
3398 hydrophobicityColour.addActionListener(this);
3400 .setLabel(MessageManager.getString("label.helix_propensity"));
3401 helixColour.addActionListener(this);
3402 strandColour.setLabel(MessageManager
3403 .getString("label.strand_propensity"));
3404 strandColour.addActionListener(this);
3405 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3406 turnColour.addActionListener(this);
3407 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3408 buriedColour.addActionListener(this);
3409 purinePyrimidineColour.setLabel(MessageManager
3410 .getString("label.purine_pyrimidine"));
3411 purinePyrimidineColour.addActionListener(this);
3412 RNAInteractionColour.setLabel(MessageManager
3413 .getString("label.rna_interaction"));
3414 RNAInteractionColour.addActionListener(this);
3415 RNAHelixColour.setLabel(MessageManager
3416 .getString("action.by_rna_helixes"));
3417 RNAHelixColour.addActionListener(this);
3418 userDefinedColour.setLabel(MessageManager
3419 .getString("action.user_defined"));
3420 userDefinedColour.addActionListener(this);
3421 PIDColour.setLabel(MessageManager
3422 .getString("label.percentage_identity"));
3423 PIDColour.addActionListener(this);
3424 BLOSUM62Colour.setLabel(MessageManager
3425 .getString("label.blosum62_score"));
3426 BLOSUM62Colour.addActionListener(this);
3428 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3429 // it will be enabled only if a score file is provided
3430 tcoffeeColour.setEnabled(false);
3431 tcoffeeColour.addActionListener(this);
3432 conservationMenuItem.setLabel(MessageManager
3433 .getString("action.by_conservation"));
3434 conservationMenuItem.addItemListener(this);
3435 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3436 noColourmenuItem.addActionListener(this);
3437 abovePIDThreshold.setLabel(MessageManager
3438 .getString("label.above_identity_threshold"));
3439 abovePIDThreshold.addItemListener(this);
3440 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3441 nucleotideColour.addActionListener(this);
3442 modifyPID.setLabel(MessageManager
3443 .getString("label.modify_identity_thereshold"));
3444 modifyPID.addActionListener(this);
3445 modifyConservation.setLabel(MessageManager
3446 .getString("label.modify_conservation_thereshold"));
3447 modifyConservation.addActionListener(this);
3448 annotationColour.setLabel(MessageManager
3449 .getString("action.by_annotation"));
3450 annotationColour.addActionListener(this);
3453 * Configure Calculate menu items and actions
3455 sortPairwiseMenuItem.setLabel(MessageManager
3456 .getString("action.by_pairwise_id"));
3457 sortPairwiseMenuItem.addActionListener(this);
3458 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3459 sortIDMenuItem.addActionListener(this);
3460 sortLengthMenuItem.setLabel(MessageManager
3461 .getString("action.by_length"));
3462 sortLengthMenuItem.addActionListener(this);
3463 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3464 sortGroupMenuItem.addActionListener(this);
3465 pairwiseAlignmentMenuItem.setLabel(MessageManager
3466 .getString("action.pairwise_alignment"));
3467 pairwiseAlignmentMenuItem.addActionListener(this);
3468 PCAMenuItem.setLabel(MessageManager
3469 .getString("label.principal_component_analysis"));
3470 PCAMenuItem.addActionListener(this);
3471 autoCalculate = new CheckboxMenuItem(
3472 MessageManager.getString("label.autocalculate_consensus"), true);
3473 averageDistanceTreeMenuItem.setLabel(MessageManager
3474 .getString("label.average_distance_identity"));
3475 averageDistanceTreeMenuItem.addActionListener(this);
3476 neighbourTreeMenuItem.setLabel(MessageManager
3477 .getString("label.neighbour_joining_identity"));
3478 neighbourTreeMenuItem.addActionListener(this);
3479 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3480 .getString("label.average_distance_bloslum62"));
3481 avDistanceTreeBlosumMenuItem.addActionListener(this);
3482 njTreeBlosumMenuItem.setLabel(MessageManager
3483 .getString("label.neighbour_blosum62"));
3484 njTreeBlosumMenuItem.addActionListener(this);
3485 sortByTreeMenu.setLabel(MessageManager
3486 .getString("action.by_tree_order"));
3487 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3488 Menu calculateTreeMenu = new Menu(
3489 MessageManager.getString("action.calculate_tree"));
3490 autoCalculate.addItemListener(this);
3491 sortByTree.addItemListener(this);
3494 * Configure Help menu items and actions
3496 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3497 documentation.setLabel(MessageManager.getString("label.documentation"));
3498 documentation.addActionListener(this);
3499 about.setLabel(MessageManager.getString("label.about"));
3500 about.addActionListener(this);
3503 * Add top level menus to frame
3505 alignFrameMenuBar.add(fileMenu);
3506 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3507 alignFrameMenuBar.add(editMenu);
3508 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3509 alignFrameMenuBar.add(selectMenu);
3510 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3511 alignFrameMenuBar.add(viewMenu);
3512 Menu annotationsMenu = new Menu(
3513 MessageManager.getString("action.annotations"));
3514 alignFrameMenuBar.add(annotationsMenu);
3515 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3516 alignFrameMenuBar.add(formatMenu);
3517 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3518 alignFrameMenuBar.add(colourMenu);
3519 Menu calculateMenu = new Menu(
3520 MessageManager.getString("action.calculate"));
3521 alignFrameMenuBar.add(calculateMenu);
3522 alignFrameMenuBar.add(helpMenu);
3527 fileMenu.add(inputText);
3528 fileMenu.add(loadTree);
3529 fileMenu.add(loadAnnotations);
3530 fileMenu.addSeparator();
3531 fileMenu.add(outputTextboxMenu);
3532 fileMenu.add(outputFeatures);
3533 fileMenu.add(outputAnnotations);
3534 if (jalviewServletURL != null)
3536 fileMenu.add(loadApplication);
3538 fileMenu.addSeparator();
3539 fileMenu.add(closeMenuItem);
3544 editMenu.add(undoMenuItem);
3545 editMenu.add(redoMenuItem);
3548 pasteMenu.add(pasteNew);
3549 pasteMenu.add(pasteThis);
3550 editMenu.add(pasteMenu);
3551 editMenu.add(delete);
3552 editMenu.addSeparator();
3553 editMenu.add(remove2LeftMenuItem);
3554 editMenu.add(remove2RightMenuItem);
3555 editMenu.add(removeGappedColumnMenuItem);
3556 editMenu.add(removeAllGapsMenuItem);
3557 editMenu.add(removeRedundancyMenuItem);
3562 selectMenu.add(findMenuItem);
3563 selectMenu.addSeparator();
3564 selectMenu.add(selectAllSequenceMenuItem);
3565 selectMenu.add(deselectAllSequenceMenuItem);
3566 selectMenu.add(invertSequenceMenuItem);
3567 selectMenu.add(invertColSel);
3568 selectMenu.add(createGroup);
3569 selectMenu.add(unGroup);
3570 selectMenu.add(grpsFromSelection);
3571 selectMenu.add(deleteGroups);
3572 selectMenu.add(annotationColumnSelection);
3577 viewMenu.add(newView);
3578 viewMenu.addSeparator();
3579 showMenu.add(showColumns);
3580 showMenu.add(showSeqs);
3581 showMenu.add(showAllHidden);
3582 viewMenu.add(showMenu);
3583 hideMenu.add(hideColumns);
3584 hideMenu.add(hideSequences);
3585 hideMenu.add(hideAllSelection);
3586 hideMenu.add(hideAllButSelection);
3587 viewMenu.add(hideMenu);
3588 viewMenu.addSeparator();
3589 viewMenu.add(followMouseOverFlag);
3590 viewMenu.addSeparator();
3591 viewMenu.add(sequenceFeatures);
3592 viewMenu.add(featureSettings);
3593 viewMenu.addSeparator();
3594 viewMenu.add(alProperties);
3595 viewMenu.addSeparator();
3596 viewMenu.add(overviewMenuItem);
3601 annotationsMenu.add(annotationPanelMenuItem);
3602 annotationsMenu.addSeparator();
3603 annotationsMenu.add(showAlignmentAnnotations);
3604 annotationsMenu.add(showSequenceAnnotations);
3605 annotationsMenu.add(sortAnnBySequence);
3606 annotationsMenu.add(sortAnnByLabel);
3607 annotationsMenu.addSeparator();
3608 autoAnnMenu.add(showAutoFirst);
3609 autoAnnMenu.add(showAutoLast);
3610 autoAnnMenu.addSeparator();
3611 autoAnnMenu.add(applyAutoAnnotationSettings);
3612 autoAnnMenu.add(showConsensusHistogram);
3613 autoAnnMenu.add(showSequenceLogo);
3614 autoAnnMenu.add(normSequenceLogo);
3615 autoAnnMenu.addSeparator();
3616 autoAnnMenu.add(showGroupConservation);
3617 autoAnnMenu.add(showGroupConsensus);
3618 annotationsMenu.add(autoAnnMenu);
3623 formatMenu.add(font);
3624 formatMenu.add(seqLimits);
3625 formatMenu.add(wrapMenuItem);
3626 formatMenu.add(scaleAbove);
3627 formatMenu.add(scaleLeft);
3628 formatMenu.add(scaleRight);
3629 formatMenu.add(viewBoxesMenuItem);
3630 formatMenu.add(viewTextMenuItem);
3631 formatMenu.add(colourTextMenuItem);
3632 formatMenu.add(displayNonconservedMenuItem);
3633 formatMenu.add(renderGapsMenuItem);
3634 formatMenu.add(centreColumnLabelFlag);
3639 colourMenu.add(applyToAllGroups);
3640 colourMenu.addSeparator();
3641 colourMenu.add(noColourmenuItem);
3642 colourMenu.add(clustalColour);
3643 colourMenu.add(BLOSUM62Colour);
3644 colourMenu.add(PIDColour);
3645 colourMenu.add(zappoColour);
3646 colourMenu.add(taylorColour);
3647 colourMenu.add(hydrophobicityColour);
3648 colourMenu.add(helixColour);
3649 colourMenu.add(strandColour);
3650 colourMenu.add(turnColour);
3651 colourMenu.add(buriedColour);
3652 colourMenu.add(nucleotideColour);
3653 colourMenu.add(purinePyrimidineColour);
3654 // colourMenu.add(RNAInteractionColour);
3655 colourMenu.add(tcoffeeColour);
3656 colourMenu.add(userDefinedColour);
3657 colourMenu.addSeparator();
3658 colourMenu.add(conservationMenuItem);
3659 colourMenu.add(modifyConservation);
3660 colourMenu.add(abovePIDThreshold);
3661 colourMenu.add(modifyPID);
3662 colourMenu.add(annotationColour);
3663 colourMenu.add(RNAHelixColour);
3668 sortMenu.add(sortIDMenuItem);
3669 sortMenu.add(sortLengthMenuItem);
3670 sortMenu.add(sortByTreeMenu);
3671 sortMenu.add(sortGroupMenuItem);
3672 sortMenu.add(sortPairwiseMenuItem);
3673 calculateMenu.add(sortMenu);
3674 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3675 calculateTreeMenu.add(neighbourTreeMenuItem);
3676 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3677 calculateTreeMenu.add(njTreeBlosumMenuItem);
3678 calculateMenu.add(calculateTreeMenu);
3679 calculateMenu.addSeparator();
3680 calculateMenu.add(pairwiseAlignmentMenuItem);
3681 calculateMenu.add(PCAMenuItem);
3682 calculateMenu.add(autoCalculate);
3683 calculateMenu.add(sortByTree);
3688 helpMenu.add(documentation);
3689 helpMenu.add(about);
3694 statusBar.setBackground(Color.white);
3695 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3696 statusBar.setText(MessageManager.getString("label.status_bar"));
3697 this.add(statusBar, BorderLayout.SOUTH);
3700 public void setStatus(String string)
3702 statusBar.setText(string);
3705 MenuItem featureSettings = new MenuItem();
3707 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3709 MenuItem annotationColour = new MenuItem();
3711 MenuItem annotationColumnSelection = new MenuItem();
3713 MenuItem invertColSel = new MenuItem();
3715 MenuItem showColumns = new MenuItem();
3717 MenuItem showSeqs = new MenuItem();
3719 MenuItem hideColumns = new MenuItem();
3721 MenuItem hideSequences = new MenuItem();
3723 MenuItem hideAllButSelection = new MenuItem();
3725 MenuItem hideAllSelection = new MenuItem();
3727 MenuItem showAllHidden = new MenuItem();
3729 MenuItem newView = new MenuItem();
3731 private CheckboxMenuItem showAlignmentAnnotations;
3733 private CheckboxMenuItem showSequenceAnnotations;
3735 private CheckboxMenuItem sortAnnBySequence;
3737 private CheckboxMenuItem sortAnnByLabel;
3739 private CheckboxMenuItem showAutoFirst;
3741 private CheckboxMenuItem showAutoLast;
3744 * Attach the alignFrame panels after embedding menus, if necessary. This used
3745 * to be called setEmbedded, but is now creates the dropdown menus in a
3746 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3748 * @param reallyEmbedded
3749 * true to attach the view to the applet area on the page rather than
3752 public void createAlignFrameWindow(boolean reallyEmbedded)
3756 embedAlignFrameInApplet(viewport.applet);
3761 // test and embed menu bar if necessary.
3763 if (embedMenuIfNeeded(alignPanel))
3766 * adjust for status bar height too. ? pointless as overridden by layout
3769 alignPanel.setSize(getSize().width,
3770 getSize().height - statusBar.getHeight());
3772 add(statusBar, BorderLayout.SOUTH);
3773 add(alignPanel, BorderLayout.CENTER);
3774 // and register with the applet so it can pass external API calls to us
3775 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3782 * Add the components of this AlignFrame to the applet container.
3786 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3789 // Explicitly build the embedded menu panel for the on-page applet
3791 // view cannot be closed if its actually on the page
3792 fileMenu.remove(closeMenuItem);
3793 fileMenu.remove(3); // Remove Separator
3794 // construct embedded menu, using default font
3795 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3796 // and actually add the components to the applet area
3797 theApplet.setLayout(new BorderLayout());
3798 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3799 theApplet.add(statusBar, BorderLayout.SOUTH);
3800 // TODO should size be left to the layout manager?
3801 alignPanel.setSize(theApplet.getSize().width,
3802 theApplet.getSize().height - embeddedMenu.getHeight()
3803 - statusBar.getHeight());
3804 theApplet.add(alignPanel, BorderLayout.CENTER);
3805 final AlignFrame me = this;
3806 theApplet.addFocusListener(new FocusListener()
3810 public void focusLost(FocusEvent e)
3812 if (theApplet.currentAlignFrame == me)
3814 theApplet.currentAlignFrame = null;
3819 public void focusGained(FocusEvent e)
3821 theApplet.currentAlignFrame = me;
3824 theApplet.validate();
3828 * create a new binding between structures in an existing jmol viewer instance
3829 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3830 * this does not open a new Jmol window, or modify the display of the
3831 * structures in the original jmol window. Note This method doesn't work
3832 * without an additional javascript library to exchange messages between the
3833 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3836 * JmolViewer instance
3837 * @param sequenceIds
3838 * - sequence Ids to search for associations
3840 public SequenceStructureBinding addStructureViewInstance(
3841 Object jmolviewer, String[] sequenceIds)
3843 org.jmol.api.JmolViewer viewer = null;
3846 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3847 } catch (ClassCastException ex)
3849 System.err.println("Unsupported viewer object :"
3850 + jmolviewer.getClass());
3854 System.err.println("Can't use this object as a structure viewer:"
3855 + jmolviewer.getClass());
3858 SequenceI[] seqs = null;
3859 if (sequenceIds == null || sequenceIds.length == 0)
3861 seqs = viewport.getAlignment().getSequencesArray();
3865 Vector sqi = new Vector();
3866 AlignmentI al = viewport.getAlignment();
3867 for (int sid = 0; sid < sequenceIds.length; sid++)
3869 SequenceI sq = al.findName(sequenceIds[sid]);
3877 seqs = new SequenceI[sqi.size()];
3878 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3880 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3888 AAStructureBindingModel jmv = null;
3889 // TODO: search for a jmv that involves viewer
3891 { // create a new viewer/jalview binding.
3892 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3900 * bind a pdb file to a sequence in the current view
3903 * - sequenceId within the dataset.
3904 * @param pdbEntryString
3905 * - the short name for the PDB file
3907 * - pdb file - either a URL or a valid PDB file.
3908 * @return true if binding was as success TODO: consider making an exception
3909 * structure for indicating when PDB parsing or sequenceId location
3912 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3915 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3916 boolean needtoadd = false;
3917 if (toaddpdb != null)
3919 Vector pdbe = toaddpdb.getPDBId();
3920 PDBEntry pdbentry = null;
3921 if (pdbe != null && pdbe.size() > 0)
3923 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3925 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3926 if (!pdbentry.getId().equals(pdbEntryString)
3927 && !pdbentry.getFile().equals(pdbFile))
3937 if (pdbentry == null)
3939 pdbentry = new PDBEntry();
3940 pdbentry.setId(pdbEntryString);
3941 pdbentry.setFile(pdbFile);
3942 needtoadd = true; // add this new entry to sequence.
3944 // resolve data source
3945 // TODO: this code should be a refactored to an io package
3946 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3947 if (protocol == null)
3953 // make a note of the access mode and add
3954 if (pdbentry.getProperty() == null)
3956 pdbentry.setProperty(new Hashtable());
3958 pdbentry.getProperty().put("protocol", protocol);
3959 toaddpdb.addPDBId(pdbentry);
3960 alignPanel.getStructureSelectionManager()
3961 .registerPDBEntry(pdbentry);
3967 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3971 Vector sequences = new Vector();
3972 for (int i = 0; i < seqs.length; i++)
3974 if (seqs[i] != null)
3976 sequences.addElement(new Object[]
3977 { seqs[i], (chains != null) ? chains[i] : null });
3980 seqs = new SequenceI[sequences.size()];
3981 chains = new String[sequences.size()];
3982 for (int i = 0, isize = sequences.size(); i < isize; i++)
3984 Object[] oj = (Object[]) sequences.elementAt(i);
3986 seqs[i] = (SequenceI) oj[0];
3987 chains[i] = (String) oj[1];
3995 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3996 SequenceI[] seqs, String[] chains, String protocol)
3998 // Scrub any null sequences from the array
3999 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4000 seqs = (SequenceI[]) sqch[0];
4001 chains = (String[]) sqch[1];
4002 if (seqs == null || seqs.length == 0)
4005 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4007 if (protocol == null || protocol.trim().length() == 0
4008 || protocol.equals("null"))
4010 protocol = (String) pdb.getProperty().get("protocol");
4011 if (protocol == null)
4013 System.err.println("Couldn't work out protocol to open structure: "
4018 if (applet.useXtrnalSviewer)
4020 // register the association(s) and quit, don't create any windows.
4021 if (StructureSelectionManager.getStructureSelectionManager(applet)
4022 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4024 System.err.println("Failed to map " + pdb.getFile() + " ("
4025 + protocol + ") to any sequences");
4029 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4031 // can only do alignments with Jmol
4032 // find the last jmol window assigned to this alignment
4033 jalview.appletgui.AppletJmol ajm = null, tajm;
4034 Vector jmols = applet
4035 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4036 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4038 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4039 if (tajm.ap.alignFrame == this)
4048 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4049 // try and add the pdb structure
4054 // otherwise, create a new window
4055 if (applet.jmolAvailable)
4057 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4059 applet.lastFrameX += 40;
4060 applet.lastFrameY += 40;
4064 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4069 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4070 SequenceI[][] seqs, String[][] chains, String[] protocols)
4072 // TODO Auto-generated method stub
4073 System.err.println("Aligned Structure View: Not yet implemented.");
4077 * modify the current selection, providing the user has not made a selection
4081 * - sequences from this alignment
4083 * - columns to be selected on the alignment
4085 public void select(SequenceGroup sel, ColumnSelection csel)
4087 alignPanel.seqPanel.selection(sel, csel, null);
4090 public void scrollTo(int row, int column)
4092 alignPanel.seqPanel.scrollTo(row, column);
4095 public void scrollToRow(int row)
4097 alignPanel.seqPanel.scrollToRow(row);
4100 public void scrollToColumn(int column)
4102 alignPanel.seqPanel.scrollToColumn(column);
4106 * @return the alignments unique ID.
4108 public String getSequenceSetId()
4110 return viewport.getSequenceSetId();
4114 * Load the (T-Coffee) score file from the specified url
4117 * File/URL/T-COFFEE score file contents
4118 * @throws IOException
4119 * @return true if alignment was annotated with data from source
4121 public boolean loadScoreFile(String source) throws IOException
4124 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4125 AppletFormatAdapter.checkProtocol(source));
4126 if (!file.isValid())
4128 // TODO: raise dialog for gui
4129 System.err.println("Problems parsing T-Coffee scores: "
4130 + file.getWarningMessage());
4131 System.err.println("Origin was:\n" + source);
4136 * check that the score matrix matches the alignment dimensions
4139 if ((aln = viewport.getAlignment()) != null
4140 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4143 // TODO: raise a dialog box here rather than bomb out.
4145 .println("The scores matrix does not match the alignment dimensions");
4149 // TODO add parameter to indicate if matching should be done
4150 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4152 alignPanel.fontChanged();
4153 tcoffeeColour.setEnabled(true);
4154 // switch to this color
4155 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4160 System.err.println("Problems resolving T-Coffee scores:");
4161 if (file.getWarningMessage() != null)
4163 System.err.println(file.getWarningMessage());