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 jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.Rectangle;
99 import java.awt.event.ActionEvent;
100 import java.awt.event.ActionListener;
101 import java.awt.event.FocusEvent;
102 import java.awt.event.FocusListener;
103 import java.awt.event.ItemEvent;
104 import java.awt.event.ItemListener;
105 import java.awt.event.KeyEvent;
106 import java.awt.event.KeyListener;
107 import java.awt.event.WindowAdapter;
108 import java.awt.event.WindowEvent;
109 import java.io.IOException;
110 import java.io.UnsupportedEncodingException;
112 import java.net.URLEncoder;
113 import java.util.Arrays;
114 import java.util.Deque;
115 import java.util.HashMap;
116 import java.util.List;
117 import java.util.Map;
118 import java.util.StringTokenizer;
119 import java.util.Vector;
121 import org.jmol.viewer.Viewer;
123 public class AlignFrame extends EmbmenuFrame implements ActionListener,
124 ItemListener, KeyListener, AlignViewControllerGuiI
126 public AlignViewControllerI avc;
128 public AlignmentPanel alignPanel;
130 public AlignViewport viewport;
132 // width and height may be overridden by applet parameters
133 int frameWidth = 700;
135 int frameHeight = 500;
137 String jalviewServletURL;
140 * Flag for showing autocalculated consensus above or below other consensus
143 private boolean showAutoCalculatedAbove;
145 private SequenceAnnotationOrder annotationSortOrder;
148 * Constructor that creates the frame and adds it to the display.
155 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
158 this(al, applet, title, embedded, true);
162 * Constructor that optionally allows the frame to be displayed or only
169 * @param addToDisplay
171 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
172 boolean embedded, boolean addToDisplay)
174 this(al, null, null, applet, title, embedded, addToDisplay);
177 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
178 HiddenColumns hidden, JalviewLite applet, String title,
181 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
184 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
185 HiddenColumns hidden, JalviewLite applet, String title,
186 boolean embedded, boolean addToDisplay)
190 jalviewServletURL = applet.getParameter("APPLICATION_URL");
196 } catch (Exception ex)
198 ex.printStackTrace();
200 // need to get window geometry before we calculate alignment layout
206 param = applet.getParameter("windowWidth");
209 int width = Integer.parseInt(param);
212 param = applet.getParameter("windowHeight");
215 int height = Integer.parseInt(param);
216 frameHeight = height;
218 } catch (Exception ex)
222 viewport = new AlignViewport(al, applet);
224 if (hiddenSeqs != null && hiddenSeqs.length > 0)
226 viewport.hideSequence(hiddenSeqs);
230 viewport.getAlignment().setHiddenColumns(hidden);
232 viewport.setScaleAboveWrapped(scaleAbove.getState());
234 alignPanel = new AlignmentPanel(this, viewport);
235 avc = new jalview.controller.AlignViewController(this, viewport,
237 viewport.updateConservation(alignPanel);
238 viewport.updateConsensus(alignPanel);
240 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
241 followMouseOverFlag.setState(viewport.isFollowHighlight());
242 showGroupConsensus.setState(viewport.isShowGroupConsensus());
243 showGroupConservation.setState(viewport.isShowGroupConservation());
244 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
245 showSequenceLogo.setState(viewport.isShowSequenceLogo());
246 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
247 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
248 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
249 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
250 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
251 showAlignmentAnnotations.setState(true);
252 showSequenceAnnotations.setState(false);
254 seqLimits.setState(viewport.getShowJVSuffix());
258 String param = applet.getParameter("sortBy");
261 if (param.equalsIgnoreCase("Id"))
263 sortIDMenuItem_actionPerformed();
265 else if (param.equalsIgnoreCase("Pairwise Identity"))
267 sortPairwiseMenuItem_actionPerformed();
269 else if (param.equalsIgnoreCase("Length"))
271 sortLengthMenuItem_actionPerformed();
275 param = applet.getParameter("wrap");
278 if (param.equalsIgnoreCase("true"))
280 wrapMenuItem.setState(true);
281 wrapMenuItem_actionPerformed();
284 param = applet.getParameter("centrecolumnlabels");
287 centreColumnLabelFlag.setState(true);
288 centreColumnLabelFlag_stateChanged();
292 if (viewport.getAlignment().isNucleotide())
294 conservationMenuItem.setEnabled(false);
295 clustalColour.setEnabled(false);
296 BLOSUM62Colour.setEnabled(false);
297 zappoColour.setEnabled(false);
298 taylorColour.setEnabled(false);
299 hydrophobicityColour.setEnabled(false);
300 helixColour.setEnabled(false);
301 strandColour.setEnabled(false);
302 turnColour.setEnabled(false);
303 buriedColour.setEnabled(false);
304 viewport.updateStrucConsensus(alignPanel);
305 if (viewport.getAlignment().hasRNAStructure())
307 RNAHelixColour.setEnabled(true);
311 RNAHelixColour.setEnabled(false);
316 RNAHelixColour.setEnabled(false);
317 purinePyrimidineColour.setEnabled(false);
318 nucleotideColour.setEnabled(false);
320 // Some JVMS send keyevents to Top frame or lowest panel,
321 // Havent worked out why yet. So add to both this frame and seqCanvas for
323 this.addKeyListener(this);
324 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
325 alignPanel.idPanel.idCanvas.addKeyListener(this);
326 alignPanel.scalePanel.addKeyListener(this);
327 alignPanel.annotationPanel.addKeyListener(this);
328 alignPanel.annotationPanelHolder.addKeyListener(this);
329 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
330 alignPanel.alabels.addKeyListener(this);
332 setAnnotationsVisibility();
336 addToDisplay(embedded);
343 public void addToDisplay(boolean embedded)
345 createAlignFrameWindow(embedded);
347 alignPanel.adjustAnnotationHeight();
348 alignPanel.paintAlignment(true, true);
351 public AlignViewport getAlignViewport()
356 public SeqCanvas getSeqcanvas()
358 return alignPanel.seqPanel.seqCanvas;
362 * Load a features file onto the alignment
365 * file URL, content, or other resolvable path
367 * is protocol for accessing data referred to by file
370 public boolean parseFeaturesFile(String file, DataSourceType type)
372 return parseFeaturesFile(file, type, true);
376 * Load a features file onto the alignment
379 * file URL, content, or other resolvable path
381 * is protocol for accessing data referred to by file
382 * @param autoenabledisplay
383 * when true, display features flag will be automatically enabled if
384 * features are loaded
385 * @return true if data parsed as a features file
387 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
388 boolean autoenabledisplay)
390 boolean featuresFile = false;
393 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
394 .getFeatureRenderer().getFeatureColours();
395 boolean relaxedIdMatching = viewport.applet
396 .getDefaultParameter("relaxedidmatch", false);
397 featuresFile = new FeaturesFile(file, sourceType).parse(
398 viewport.getAlignment(), colours, true, relaxedIdMatching);
399 } catch (Exception ex)
401 ex.printStackTrace();
406 if (autoenabledisplay)
408 viewport.setShowSequenceFeatures(true);
409 sequenceFeatures.setState(true);
411 if (alignPanel.seqPanel.seqCanvas.fr != null)
413 // update the min/max ranges where necessary
414 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
416 if (viewport.featureSettings != null)
418 viewport.featureSettings.refreshTable();
420 alignPanel.paintAlignment(true, true);
421 setStatus(MessageManager
422 .getString("label.successfully_added_features_alignment"));
428 public void keyPressed(KeyEvent evt)
430 ViewportRanges ranges = viewport.getRanges();
432 if (viewport.cursorMode
433 && ((evt.getKeyCode() >= KeyEvent.VK_0
434 && evt.getKeyCode() <= KeyEvent.VK_9)
435 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
436 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
437 && Character.isDigit(evt.getKeyChar()))
439 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
442 switch (evt.getKeyCode())
444 case 27: // escape key
445 deselectAllSequenceMenuItem_actionPerformed();
447 alignPanel.alabels.cancelDrag();
450 if (evt.isControlDown() || evt.isMetaDown())
452 cut_actionPerformed();
456 if (viewport.cursorMode && !evt.isControlDown())
458 alignPanel.seqPanel.setCursorColumn();
460 if (evt.isControlDown() || evt.isMetaDown())
462 copy_actionPerformed();
466 if (evt.isControlDown())
468 paste(evt.isShiftDown());
472 if (evt.isControlDown() || evt.isMetaDown())
474 selectAllSequenceMenuItem_actionPerformed();
477 case KeyEvent.VK_DOWN:
478 if (viewport.cursorMode)
480 alignPanel.seqPanel.moveCursor(0, 1);
484 moveSelectedSequences(false);
489 if (viewport.cursorMode)
491 alignPanel.seqPanel.moveCursor(0, -1);
495 moveSelectedSequences(true);
499 case KeyEvent.VK_LEFT:
500 if (evt.isAltDown() || !viewport.cursorMode)
502 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
506 alignPanel.seqPanel.moveCursor(-1, 0);
510 case KeyEvent.VK_RIGHT:
511 if (evt.isAltDown() || !viewport.cursorMode)
513 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
517 alignPanel.seqPanel.moveCursor(1, 0);
521 case KeyEvent.VK_SPACE:
522 if (viewport.cursorMode)
524 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
525 || evt.isShiftDown() || evt.isAltDown());
529 case KeyEvent.VK_DELETE:
530 case KeyEvent.VK_BACK_SPACE:
531 if (viewport.cursorMode)
533 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
534 || evt.isShiftDown() || evt.isAltDown());
538 cut_actionPerformed();
539 alignPanel.seqPanel.seqCanvas.repaint();
544 if (viewport.cursorMode)
546 alignPanel.seqPanel.setCursorRow();
550 if (viewport.cursorMode)
552 alignPanel.seqPanel.setCursorPosition();
556 case KeyEvent.VK_ENTER:
557 case KeyEvent.VK_COMMA:
558 if (viewport.cursorMode)
560 alignPanel.seqPanel.setCursorRowAndColumn();
565 if (viewport.cursorMode)
567 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
571 if (viewport.cursorMode)
573 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
578 viewport.cursorMode = !viewport.cursorMode;
579 setStatus(MessageManager
580 .formatMessage("label.keyboard_editing_mode", new String[]
581 { (viewport.cursorMode ? "on" : "off") }));
582 if (viewport.cursorMode)
584 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
585 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
590 if (evt.isControlDown())
592 findMenuItem_actionPerformed();
598 boolean toggleSeqs = !evt.isControlDown();
599 boolean toggleCols = !evt.isShiftDown();
600 toggleHiddenRegions(toggleSeqs, toggleCols);
604 case KeyEvent.VK_PAGE_UP:
608 case KeyEvent.VK_PAGE_DOWN:
613 if (evt.isControlDown())
615 undoMenuItem_actionPerformed();
620 if (evt.isControlDown())
622 redoMenuItem_actionPerformed();
627 if (evt.isControlDown())
634 if (evt.isControlDown())
636 trimAlignment(false);
641 if (evt.isControlDown())
643 if (evt.isShiftDown())
645 this.removeAllGapsMenuItem_actionPerformed();
649 removeGappedColumnMenuItem_actionPerformed();
654 if (evt.isControlDown())
658 invertColSel_actionPerformed();
662 invertSequenceMenuItem_actionPerformed();
668 if (evt.isControlDown())
670 if (evt.isShiftDown())
672 this.unGroup_actionPerformed();
676 this.createGroup_actionPerformed();
682 if (evt.isControlDown())
684 this.deleteGroups_actionPerformed();
689 if (evt.isControlDown())
696 // TODO: repaint flags set only if the keystroke warrants it
697 alignPanel.paintAlignment(true, true);
701 * called by key handler and the hide all/show all menu items
706 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
708 boolean hide = false;
709 SequenceGroup sg = viewport.getSelectionGroup();
710 if (!toggleSeqs && !toggleCols)
712 // Hide everything by the current selection - this is a hack - we do the
713 // invert and then hide
714 // first check that there will be visible columns after the invert.
715 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
716 && sg.getStartRes() <= sg.getEndRes()))
718 // now invert the sequence set, if required - empty selection implies
719 // that no hiding is required.
722 invertSequenceMenuItem_actionPerformed();
723 sg = viewport.getSelectionGroup();
727 viewport.expandColSelection(sg, true);
728 // finally invert the column selection and get the new sequence
729 // selection and indicate it should be hidden.
730 invertColSel_actionPerformed();
737 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
740 viewport.hideAllSelectedSeqs();
742 else if (!(toggleCols && viewport.hasSelectedColumns()))
744 viewport.showAllHiddenSeqs();
750 if (viewport.hasSelectedColumns())
752 viewport.hideSelectedColumns();
755 viewport.setSelectionGroup(sg);
760 viewport.showAllHiddenColumns();
762 viewport.sendSelection();
767 public void keyReleased(KeyEvent evt)
772 public void keyTyped(KeyEvent evt)
777 public void itemStateChanged(ItemEvent evt)
779 final Object source = evt.getSource();
780 if (source == displayNonconservedMenuItem)
782 displayNonconservedMenuItem_actionPerformed();
784 else if (source == colourTextMenuItem)
786 colourTextMenuItem_actionPerformed();
788 else if (source == wrapMenuItem)
790 wrapMenuItem_actionPerformed();
792 else if (source == scaleAbove)
794 viewport.setScaleAboveWrapped(scaleAbove.getState());
796 else if (source == scaleLeft)
798 viewport.setScaleLeftWrapped(scaleLeft.getState());
800 else if (source == scaleRight)
802 viewport.setScaleRightWrapped(scaleRight.getState());
804 else if (source == seqLimits)
806 seqLimits_itemStateChanged();
808 else if (source == viewBoxesMenuItem)
810 viewport.setShowBoxes(viewBoxesMenuItem.getState());
812 else if (source == viewTextMenuItem)
814 viewport.setShowText(viewTextMenuItem.getState());
816 else if (source == renderGapsMenuItem)
818 viewport.setRenderGaps(renderGapsMenuItem.getState());
820 else if (source == annotationPanelMenuItem)
822 boolean showAnnotations = annotationPanelMenuItem.getState();
823 showAlignmentAnnotations.setEnabled(showAnnotations);
824 showSequenceAnnotations.setEnabled(showAnnotations);
825 viewport.setShowAnnotation(showAnnotations);
826 alignPanel.setAnnotationVisible(showAnnotations);
828 else if (source == sequenceFeatures)
830 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
831 alignPanel.seqPanel.seqCanvas.repaint();
833 else if (source == showAlignmentAnnotations)
835 setAnnotationsVisibility();
837 else if (source == showSequenceAnnotations)
839 setAnnotationsVisibility();
841 else if (source == sortAnnBySequence)
843 boolean newState = sortAnnBySequence.getState();
844 sortAnnByLabel.setState(false);
845 setAnnotationSortOrder(
846 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
847 : SequenceAnnotationOrder.NONE);
848 setViewportAnnotationOrder();
850 else if (source == sortAnnByLabel)
852 boolean newState = sortAnnByLabel.getState();
853 sortAnnBySequence.setState(false);
854 setAnnotationSortOrder(
855 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
856 : SequenceAnnotationOrder.NONE);
857 setViewportAnnotationOrder();
859 else if (source == showAutoFirst)
861 showAutoLast.setState(!showAutoFirst.getState());
862 setShowAutoCalculatedAbove(showAutoFirst.getState());
863 setViewportAnnotationOrder();
865 else if (source == showAutoLast)
867 showAutoFirst.setState(!showAutoLast.getState());
868 setShowAutoCalculatedAbove(showAutoFirst.getState());
869 setViewportAnnotationOrder();
871 else if (source == conservationMenuItem)
873 conservationMenuItem_actionPerformed();
875 else if (source == abovePIDThreshold)
877 abovePIDThreshold_actionPerformed();
879 else if (source == applyToAllGroups)
881 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
883 else if (source == autoCalculate)
885 viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
887 else if (source == sortByTree)
889 viewport.sortByTree = sortByTree.getState();
891 else if (source == this.centreColumnLabelFlag)
893 centreColumnLabelFlag_stateChanged();
895 else if (source == this.followMouseOverFlag)
897 mouseOverFlag_stateChanged();
899 else if (source == showGroupConsensus)
901 showGroupConsensus_actionPerformed();
903 else if (source == showGroupConservation)
905 showGroupConservation_actionPerformed();
907 else if (source == showSequenceLogo)
909 showSequenceLogo_actionPerformed();
911 else if (source == normSequenceLogo)
913 normSequenceLogo_actionPerformed();
915 else if (source == showConsensusHistogram)
917 showConsensusHistogram_actionPerformed();
919 else if (source == applyAutoAnnotationSettings)
921 applyAutoAnnotationSettings_actionPerformed();
923 // TODO: repaint flags set only if warranted
924 alignPanel.paintAlignment(true, true);
928 * Set the visibility state of sequence-related and/or alignment-related
929 * annotations depending on checkbox selections, and repaint.
933 private void setAnnotationsVisibility()
935 boolean showForAlignment = showAlignmentAnnotations.getState();
936 boolean showForSequences = showSequenceAnnotations.getState();
937 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
939 for (AlignmentAnnotation aa : alignPanel.getAlignment()
940 .getAlignmentAnnotation())
942 boolean visible = (aa.sequenceRef == null ? showForAlignment
944 aa.visible = visible;
947 alignPanel.validateAnnotationDimensions(true);
952 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
954 this.annotationSortOrder = order;
958 * Set flags on the viewport that control annotation ordering
960 private void setViewportAnnotationOrder()
962 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
964 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
967 private void setShowAutoCalculatedAbove(boolean showAbove)
969 this.showAutoCalculatedAbove = showAbove;
972 private void mouseOverFlag_stateChanged()
974 viewport.setFollowHighlight(followMouseOverFlag.getState());
975 // TODO: could kick the scrollTo mechanism to reset view for current
979 private void centreColumnLabelFlag_stateChanged()
981 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
982 this.alignPanel.annotationPanel.repaint();
986 public void actionPerformed(ActionEvent evt)
988 viewport.applet.currentAlignFrame = this;
990 Object source = evt.getSource();
992 if (source == inputText)
994 inputText_actionPerformed();
996 else if (source == loadTree)
998 loadTree_actionPerformed();
1000 else if (source == loadApplication)
1002 launchFullApplication();
1004 else if (source == loadAnnotations)
1008 else if (source == outputAnnotations)
1010 outputAnnotations(true);
1012 else if (source == outputFeatures)
1014 outputFeatures(true, "Jalview");
1016 else if (source == closeMenuItem)
1018 closeMenuItem_actionPerformed();
1020 else if (source == copy)
1022 copy_actionPerformed();
1024 else if (source == undoMenuItem)
1026 undoMenuItem_actionPerformed();
1028 else if (source == redoMenuItem)
1030 redoMenuItem_actionPerformed();
1032 else if (source == inputText)
1034 inputText_actionPerformed();
1036 else if (source == closeMenuItem)
1038 closeMenuItem_actionPerformed();
1040 else if (source == undoMenuItem)
1042 undoMenuItem_actionPerformed();
1044 else if (source == redoMenuItem)
1046 redoMenuItem_actionPerformed();
1048 else if (source == copy)
1050 copy_actionPerformed();
1052 else if (source == pasteNew)
1054 pasteNew_actionPerformed();
1056 else if (source == pasteThis)
1058 pasteThis_actionPerformed();
1060 else if (source == cut)
1062 cut_actionPerformed();
1064 else if (source == delete)
1066 delete_actionPerformed();
1068 else if (source == createGroup)
1070 createGroup_actionPerformed();
1072 else if (source == unGroup)
1074 unGroup_actionPerformed();
1076 else if (source == grpsFromSelection)
1078 makeGrpsFromSelection_actionPerformed();
1080 else if (source == deleteGroups)
1082 deleteGroups_actionPerformed();
1084 else if (source == selectAllSequenceMenuItem)
1086 selectAllSequenceMenuItem_actionPerformed();
1088 else if (source == deselectAllSequenceMenuItem)
1090 deselectAllSequenceMenuItem_actionPerformed();
1092 else if (source == invertSequenceMenuItem)
1094 invertSequenceMenuItem_actionPerformed();
1095 // uncomment to slave sequence selections in split frame
1096 // viewport.sendSelection();
1098 else if (source == invertColSel)
1100 viewport.invertColumnSelection();
1101 alignPanel.paintAlignment(false, false);
1102 viewport.sendSelection();
1104 else if (source == remove2LeftMenuItem)
1106 trimAlignment(true);
1108 else if (source == remove2RightMenuItem)
1110 trimAlignment(false);
1112 else if (source == removeGappedColumnMenuItem)
1114 removeGappedColumnMenuItem_actionPerformed();
1116 else if (source == removeAllGapsMenuItem)
1118 removeAllGapsMenuItem_actionPerformed();
1120 else if (source == findMenuItem)
1122 findMenuItem_actionPerformed();
1124 else if (source == font)
1126 new FontChooser(alignPanel);
1128 else if (source == newView)
1132 else if (source == showColumns)
1134 viewport.showAllHiddenColumns();
1135 alignPanel.paintAlignment(true, true);
1136 viewport.sendSelection();
1138 else if (source == showSeqs)
1140 viewport.showAllHiddenSeqs();
1141 alignPanel.paintAlignment(true, true);
1142 // uncomment if we want to slave sequence selections in split frame
1143 // viewport.sendSelection();
1145 else if (source == hideColumns)
1147 viewport.hideSelectedColumns();
1148 alignPanel.paintAlignment(true, true);
1149 viewport.sendSelection();
1151 else if (source == hideSequences
1152 && viewport.getSelectionGroup() != null)
1154 viewport.hideAllSelectedSeqs();
1155 alignPanel.paintAlignment(true, true);
1156 // uncomment if we want to slave sequence selections in split frame
1157 // viewport.sendSelection();
1159 else if (source == hideAllButSelection)
1161 toggleHiddenRegions(false, false);
1162 alignPanel.paintAlignment(true, true);
1163 viewport.sendSelection();
1165 else if (source == hideAllSelection)
1167 SequenceGroup sg = viewport.getSelectionGroup();
1168 viewport.expandColSelection(sg, false);
1169 viewport.hideAllSelectedSeqs();
1170 viewport.hideSelectedColumns();
1171 alignPanel.paintAlignment(true, true);
1172 viewport.sendSelection();
1174 else if (source == showAllHidden)
1176 viewport.showAllHiddenColumns();
1177 viewport.showAllHiddenSeqs();
1178 alignPanel.paintAlignment(true, true);
1179 viewport.sendSelection();
1181 else if (source == showGroupConsensus)
1183 showGroupConsensus_actionPerformed();
1185 else if (source == showGroupConservation)
1187 showGroupConservation_actionPerformed();
1189 else if (source == showSequenceLogo)
1191 showSequenceLogo_actionPerformed();
1193 else if (source == normSequenceLogo)
1195 normSequenceLogo_actionPerformed();
1197 else if (source == showConsensusHistogram)
1199 showConsensusHistogram_actionPerformed();
1201 else if (source == applyAutoAnnotationSettings)
1203 applyAutoAnnotationSettings_actionPerformed();
1205 else if (source == featureSettings)
1207 showFeatureSettingsUI();
1209 else if (source == alProperties)
1211 StringBuffer contents = new jalview.io.AlignmentProperties(
1212 viewport.getAlignment()).formatAsString();
1213 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214 cap.setText(contents.toString());
1215 Frame frame = new Frame();
1217 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1218 .formatMessage("label.alignment_properties", new String[]
1219 { getTitle() }), 400, 250);
1221 else if (source == overviewMenuItem)
1223 overviewMenuItem_actionPerformed();
1225 else if (source == noColourmenuItem)
1229 else if (source == clustalColour)
1231 abovePIDThreshold.setState(false);
1232 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1234 else if (source == zappoColour)
1236 changeColour(new ZappoColourScheme());
1238 else if (source == taylorColour)
1240 changeColour(new TaylorColourScheme());
1242 else if (source == hydrophobicityColour)
1244 changeColour(new HydrophobicColourScheme());
1246 else if (source == helixColour)
1248 changeColour(new HelixColourScheme());
1250 else if (source == strandColour)
1252 changeColour(new StrandColourScheme());
1254 else if (source == turnColour)
1256 changeColour(new TurnColourScheme());
1258 else if (source == buriedColour)
1260 changeColour(new BuriedColourScheme());
1262 else if (source == nucleotideColour)
1264 changeColour(new NucleotideColourScheme());
1266 else if (source == purinePyrimidineColour)
1268 changeColour(new PurinePyrimidineColourScheme());
1270 // else if (source == RNAInteractionColour)
1272 // changeColour(new RNAInteractionColourScheme());
1274 else if (source == RNAHelixColour)
1276 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1277 // new RNAHelicesColourChooser(viewport, alignPanel);
1279 else if (source == modifyPID)
1281 modifyPID_actionPerformed();
1283 else if (source == modifyConservation)
1285 modifyConservation_actionPerformed();
1287 else if (source == userDefinedColour)
1289 new UserDefinedColours(alignPanel, null);
1291 else if (source == PIDColour)
1293 changeColour(new PIDColourScheme());
1295 else if (source == BLOSUM62Colour)
1297 changeColour(new Blosum62ColourScheme());
1299 else if (source == tcoffeeColour)
1301 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1303 else if (source == annotationColour)
1305 new AnnotationColourChooser(viewport, alignPanel);
1307 else if (source == annotationColumnSelection)
1309 new AnnotationColumnChooser(viewport, alignPanel);
1311 else if (source == sortPairwiseMenuItem)
1313 sortPairwiseMenuItem_actionPerformed();
1315 else if (source == sortIDMenuItem)
1317 sortIDMenuItem_actionPerformed();
1319 else if (source == sortLengthMenuItem)
1321 sortLengthMenuItem_actionPerformed();
1323 else if (source == sortGroupMenuItem)
1325 sortGroupMenuItem_actionPerformed();
1327 else if (source == removeRedundancyMenuItem)
1329 removeRedundancyMenuItem_actionPerformed();
1331 else if (source == pairwiseAlignmentMenuItem)
1333 pairwiseAlignmentMenuItem_actionPerformed();
1335 else if (source == PCAMenuItem)
1337 PCAMenuItem_actionPerformed();
1339 else if (source == averageDistanceTreeMenuItem)
1341 averageDistanceTreeMenuItem_actionPerformed();
1343 else if (source == neighbourTreeMenuItem)
1345 neighbourTreeMenuItem_actionPerformed();
1347 else if (source == njTreeBlosumMenuItem)
1349 njTreeBlosumMenuItem_actionPerformed();
1351 else if (source == avDistanceTreeBlosumMenuItem)
1353 avTreeBlosumMenuItem_actionPerformed();
1355 else if (source == documentation)
1357 documentation_actionPerformed();
1359 else if (source == about)
1361 about_actionPerformed();
1366 public void inputText_actionPerformed()
1368 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1369 Frame frame = new Frame();
1371 jalview.bin.JalviewLite.addFrame(frame,
1372 MessageManager.getString("label.input_cut_paste"), 500, 500);
1375 protected void outputText_actionPerformed(ActionEvent e)
1377 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378 Frame frame = new Frame();
1380 JalviewLite.addFrame(frame, MessageManager
1381 .formatMessage("label.alignment_output_command", new Object[]
1382 { e.getActionCommand() }), 600, 500);
1384 FileFormatI fileFormat = FileFormats.getInstance()
1385 .forName(e.getActionCommand());
1387 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1388 viewport.getAlignment(), viewport.getShowJVSuffix()));
1391 public void loadAnnotations()
1393 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1394 cap.setText(MessageManager
1395 .getString("label.paste_features_annotations_Tcoffee_here"));
1396 cap.setAnnotationImport();
1397 Frame frame = new Frame();
1399 jalview.bin.JalviewLite.addFrame(frame,
1400 MessageManager.getString("action.paste_annotations"), 400, 300);
1404 public String outputAnnotations(boolean displayTextbox)
1406 String annotation = new AnnotationFile()
1407 .printAnnotationsForView(viewport);
1411 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1412 Frame frame = new Frame();
1414 jalview.bin.JalviewLite.addFrame(frame,
1415 MessageManager.getString("label.annotations"), 600, 500);
1416 cap.setText(annotation);
1422 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1424 if (alignPanel.getFeatureRenderer() != null
1425 && viewport.getFeaturesDisplayed() != null)
1427 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1433 private List<String> getDisplayedFeatureGroups()
1435 if (alignPanel.getFeatureRenderer() != null
1436 && viewport.getFeaturesDisplayed() != null)
1438 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1444 public String outputFeatures(boolean displayTextbox, String format)
1447 FeaturesFile formatter = new FeaturesFile();
1448 if (format.equalsIgnoreCase("Jalview"))
1450 features = formatter.printJalviewFormat(
1451 viewport.getAlignment().getSequencesArray(),
1452 alignPanel.getFeatureRenderer(), true, false);
1456 features = formatter.printGffFormat(viewport.getAlignment()
1457 .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1463 boolean frimport = false;
1464 if (features == null || features.equals("No Features Visible"))
1466 features = "# No features visible - paste some and import them here.";
1470 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1473 cap.setAnnotationImport();
1475 Frame frame = new Frame();
1477 jalview.bin.JalviewLite.addFrame(frame,
1478 MessageManager.getString("label.features"), 600, 500);
1479 cap.setText(features);
1483 if (features == null)
1492 void launchFullApplication()
1494 StringBuffer url = new StringBuffer(jalviewServletURL);
1496 // allow servlet parameters to be passed in applet parameter
1497 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1499 url.append(firstSep);
1502 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1504 if (viewport.applet.getParameter("features") != null)
1506 url.append("&features=");
1507 url.append(appendProtocol(viewport.applet.getParameter("features")));
1510 if (viewport.applet.getParameter("annotations") != null)
1512 url.append("&annotations=");
1514 appendProtocol(viewport.applet.getParameter("annotations")));
1517 if (viewport.applet.getParameter("jnetfile") != null
1518 || viewport.applet.getParameter("jpredfile") != null)
1520 url.append("&annotations=");
1521 url.append(appendProtocol(
1522 viewport.applet.getParameter("jnetfile") != null
1523 ? viewport.applet.getParameter("jnetfile")
1524 : viewport.applet.getParameter("jpredfile")));
1527 if (viewport.applet.getParameter("defaultColour") != null)
1529 url.append("&colour=" + removeWhiteSpace(
1530 viewport.applet.getParameter("defaultColour")));
1533 if (viewport.applet.getParameter("userDefinedColour") != null)
1535 url.append("&colour=" + removeWhiteSpace(
1536 viewport.applet.getParameter("userDefinedColour")));
1538 if (viewport.applet.getParameter("tree") != null)
1541 + appendProtocol(viewport.applet.getParameter("tree")));
1543 if (viewport.applet.getParameter("treeFile") != null)
1546 + appendProtocol(viewport.applet.getParameter("treeFile")));
1549 showURL(url.toString(), "FULL_APP");
1552 String removeWhiteSpace(String colour)
1554 StringBuffer sb = new StringBuffer();
1555 for (int i = 0; i < colour.length(); i++)
1557 if (Character.isWhitespace(colour.charAt(i)))
1563 sb.append(colour.charAt(i));
1567 return sb.toString();
1570 String appendProtocol(String url)
1575 url = URLEncoder.encode(url, "UTF-8");
1578 * When we finally deprecate 1.1 compatibility, we can start to use
1579 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1580 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1581 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1582 * ex.printStackTrace(); }
1584 catch (java.net.MalformedURLException ex)
1586 url = viewport.applet.getCodeBase() + url;
1588 catch (UnsupportedEncodingException ex)
1591 "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1593 ex.printStackTrace();
1598 public void closeMenuItem_actionPerformed()
1600 PaintRefresher.RemoveComponent(alignPanel);
1601 if (alignPanel.seqPanel != null
1602 && alignPanel.seqPanel.seqCanvas != null)
1604 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1606 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1608 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1611 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1617 if (alignPanel != null && alignPanel.overviewPanel != null)
1619 alignPanel.overviewPanel.dispose();
1628 void updateEditMenuBar()
1631 if (viewport.getHistoryList().size() > 0)
1633 undoMenuItem.setEnabled(true);
1634 CommandI command = viewport.getHistoryList().peek();
1635 undoMenuItem.setLabel(MessageManager
1636 .formatMessage("label.undo_command", new Object[]
1637 { command.getDescription() }));
1641 undoMenuItem.setEnabled(false);
1642 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1645 if (viewport.getRedoList().size() > 0)
1647 redoMenuItem.setEnabled(true);
1649 CommandI command = viewport.getRedoList().peek();
1650 redoMenuItem.setLabel(MessageManager
1651 .formatMessage("label.redo_command", new Object[]
1652 { command.getDescription() }));
1656 redoMenuItem.setEnabled(false);
1657 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1665 public void addHistoryItem(CommandI command)
1667 if (command.getSize() > 0)
1669 viewport.addToHistoryList(command);
1670 viewport.clearRedoList();
1671 updateEditMenuBar();
1672 viewport.updateHiddenColumns();
1677 * TODO: JAL-1104 DOCUMENT ME!
1682 protected void undoMenuItem_actionPerformed()
1684 if (viewport.getHistoryList().isEmpty())
1689 CommandI command = viewport.getHistoryList().pop();
1690 viewport.addToRedoList(command);
1691 command.undoCommand(null);
1693 AlignmentViewport originalSource = getOriginatingSource(command);
1695 if (originalSource != viewport)
1698 .println("Warning: Viewport object mismatch whilst undoing");
1700 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1701 // viewport.getColumnSelection().getHiddenColumns()
1703 updateEditMenuBar();
1704 originalSource.notifyAlignment();
1708 * TODO: JAL-1104 DOCUMENT ME!
1713 protected void redoMenuItem_actionPerformed()
1715 if (viewport.getRedoList().isEmpty())
1720 CommandI command = viewport.getRedoList().pop();
1721 viewport.addToHistoryList(command);
1722 command.doCommand(null);
1724 AlignmentViewport originalSource = getOriginatingSource(command);
1726 if (originalSource != viewport)
1729 .println("Warning: Viewport object mismatch whilst re-doing");
1731 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1732 // viewport.getColumnSelection().getHiddenColumns()
1735 updateEditMenuBar();
1736 originalSource.notifyAlignment();
1739 AlignmentViewport getOriginatingSource(CommandI command)
1741 AlignmentViewport originalSource = null;
1742 // For sequence removal and addition, we need to fire
1743 // the property change event FROM the viewport where the
1744 // original alignment was altered
1745 AlignmentI al = null;
1746 if (command instanceof EditCommand)
1748 EditCommand editCommand = (EditCommand) command;
1749 al = editCommand.getAlignment();
1750 Vector comps = PaintRefresher.components
1751 .get(viewport.getSequenceSetId());
1752 for (int i = 0; i < comps.size(); i++)
1754 if (comps.elementAt(i) instanceof AlignmentPanel)
1756 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1758 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1765 if (originalSource == null)
1767 // The original view is closed, we must validate
1768 // the current view against the closed view first
1771 PaintRefresher.validateSequences(al, viewport.getAlignment());
1774 originalSource = viewport;
1777 return originalSource;
1781 * Move the currently selected sequences up or down one position in the
1786 public void moveSelectedSequences(boolean up)
1788 SequenceGroup sg = viewport.getSelectionGroup();
1793 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1794 up ? null : viewport.getHiddenRepSequences(), up);
1795 alignPanel.paintAlignment(true, false);
1798 * Also move cDNA/protein complement sequences
1800 AlignViewportI complement = viewport.getCodingComplement();
1801 if (complement != null)
1803 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1804 viewport, complement);
1805 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1806 up ? null : complement.getHiddenRepSequences(), up);
1807 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1812 synchronized void slideSequences(boolean right, int size)
1814 List<SequenceI> sg = new Vector<>();
1815 if (viewport.cursorMode)
1817 sg.add(viewport.getAlignment()
1818 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1820 else if (viewport.getSelectionGroup() != null
1821 && viewport.getSelectionGroup().getSize() != viewport
1822 .getAlignment().getHeight())
1824 sg = viewport.getSelectionGroup()
1825 .getSequences(viewport.getHiddenRepSequences());
1833 Vector<SequenceI> invertGroup = new Vector();
1835 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1837 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1839 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1843 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1845 SequenceI[] seqs2 = invertGroup
1846 .toArray(new SequenceI[invertGroup.size()]);
1847 for (int i = 0; i < invertGroup.size(); i++)
1849 seqs2[i] = invertGroup.elementAt(i);
1852 SlideSequencesCommand ssc;
1855 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1856 viewport.getGapCharacter());
1860 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1861 viewport.getGapCharacter());
1864 int groupAdjustment = 0;
1865 if (ssc.getGapsInsertedBegin() && right)
1867 if (viewport.cursorMode)
1869 alignPanel.seqPanel.moveCursor(size, 0);
1873 groupAdjustment = size;
1876 else if (!ssc.getGapsInsertedBegin() && !right)
1878 if (viewport.cursorMode)
1880 alignPanel.seqPanel.moveCursor(-size, 0);
1884 groupAdjustment = -size;
1888 if (groupAdjustment != 0)
1890 viewport.getSelectionGroup().setStartRes(
1891 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1892 viewport.getSelectionGroup().setEndRes(
1893 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1896 boolean appendHistoryItem = false;
1897 Deque<CommandI> historyList = viewport.getHistoryList();
1898 if (historyList != null && historyList.size() > 0
1899 && historyList.peek() instanceof SlideSequencesCommand)
1901 appendHistoryItem = ssc.appendSlideCommand(
1902 (SlideSequencesCommand) historyList.peek());
1905 if (!appendHistoryItem)
1907 addHistoryItem(ssc);
1913 static StringBuffer copiedSequences;
1915 static HiddenColumns copiedHiddenColumns;
1917 protected void copy_actionPerformed()
1919 if (viewport.getSelectionGroup() == null)
1924 SequenceGroup sg = viewport.getSelectionGroup();
1925 copiedSequences = new StringBuffer();
1926 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1927 for (int i = 0; i < sg.getSize(); i++)
1929 SequenceI seq = sg.getSequenceAt(i);
1930 int index = viewport.getAlignment().findIndex(seq);
1931 orderedSeqs.put(index, seq);
1934 int index = 0, startRes, endRes;
1937 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1939 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1940 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1942 // create new HiddenColumns object with copy of hidden regions
1943 // between startRes and endRes, offset by startRes
1944 copiedHiddenColumns = new HiddenColumns(
1945 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1946 hiddenCutoff, hiddenOffset);
1950 copiedHiddenColumns = null;
1953 for (int i = 0; i < sg.getSize(); i++)
1955 SequenceI seq = null;
1959 if (orderedSeqs.containsKey(index))
1961 seq = orderedSeqs.get(index);
1972 // Returns residue following index if gap
1973 startRes = seq.findPosition(sg.getStartRes());
1976 // Need to find the residue preceeding index if gap
1979 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1981 ch = seq.getCharAt(j);
1982 if (!jalview.util.Comparison.isGap((ch)))
1990 endRes += seq.getStart() - 1;
1993 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1994 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
2001 protected void pasteNew_actionPerformed()
2006 protected void pasteThis_actionPerformed()
2011 void paste(boolean newAlignment)
2015 if (copiedSequences == null)
2020 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2022 Vector seqs = new Vector();
2023 while (st.hasMoreElements())
2025 String name = st.nextToken();
2026 int start = Integer.parseInt(st.nextToken());
2027 int end = Integer.parseInt(st.nextToken());
2028 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2030 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2031 for (int i = 0; i < seqs.size(); i++)
2033 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2038 String newtitle = MessageManager
2039 .getString("label.copied_sequences");
2040 if (getTitle().startsWith(
2041 MessageManager.getString("label.copied_sequences")))
2043 newtitle = getTitle();
2047 newtitle = newtitle.concat(MessageManager
2048 .formatMessage("label.from_msname", new String[]
2051 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2052 viewport.applet, newtitle, false);
2053 af.viewport.setHiddenColumns(copiedHiddenColumns);
2055 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2060 addSequences(newSeqs);
2063 } catch (Exception ex)
2065 } // could be anything being pasted in here
2069 void addSequences(SequenceI[] seqs)
2071 for (int i = 0; i < seqs.length; i++)
2073 viewport.getAlignment().addSequence(seqs[i]);
2077 addHistoryItem(new EditCommand(
2078 MessageManager.getString("label.add_sequences"), Action.PASTE,
2079 seqs, 0, viewport.getAlignment().getWidth(),
2080 viewport.getAlignment()));
2082 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2084 viewport.getAlignment().getWidth();
2085 viewport.notifyAlignment();
2089 protected void cut_actionPerformed()
2091 copy_actionPerformed();
2092 delete_actionPerformed();
2095 protected void delete_actionPerformed()
2098 SequenceGroup sg = viewport.getSelectionGroup();
2104 Vector seqs = new Vector();
2106 for (int i = 0; i < sg.getSize(); i++)
2108 seq = sg.getSequenceAt(i);
2109 seqs.addElement(seq);
2113 * If the cut affects all sequences, warn, remove highlighted columns
2115 if (sg.getSize() == viewport.getAlignment().getHeight())
2117 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2118 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2119 if (isEntireAlignWidth)
2121 String title = MessageManager.getString("label.delete_all");
2122 Panel infoPanel = new Panel();
2123 infoPanel.setLayout(new FlowLayout());
2125 new Label(MessageManager.getString("warn.delete_all")));
2127 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2128 dialog.setMainPanel(infoPanel);
2129 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2130 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2131 dialog.setVisible(true);
2138 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2139 sg.getEndRes() + 1);
2142 SequenceI[] cut = new SequenceI[seqs.size()];
2143 for (int i = 0; i < seqs.size(); i++)
2145 cut[i] = (SequenceI) seqs.elementAt(i);
2149 * //ADD HISTORY ITEM
2151 addHistoryItem(new EditCommand(
2152 MessageManager.getString("label.cut_sequences"), Action.CUT,
2153 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2154 viewport.getAlignment()));
2156 viewport.setSelectionGroup(null);
2157 viewport.getAlignment().deleteGroup(sg);
2159 viewport.notifyAlignment();
2161 if (viewport.getAlignment().getHeight() < 1)
2163 this.setVisible(false);
2165 viewport.sendSelection();
2169 * group consensus toggled
2172 protected void showGroupConsensus_actionPerformed()
2174 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2175 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180 * group conservation toggled.
2182 protected void showGroupConservation_actionPerformed()
2184 viewport.setShowGroupConservation(showGroupConservation.getState());
2185 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2193 * .event.ActionEvent)
2195 protected void showConsensusHistogram_actionPerformed()
2197 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2198 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2205 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2206 * .event.ActionEvent)
2208 protected void showSequenceLogo_actionPerformed()
2210 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2211 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2214 protected void normSequenceLogo_actionPerformed()
2216 showSequenceLogo.setState(true);
2217 viewport.setShowSequenceLogo(true);
2218 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2219 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2222 protected void applyAutoAnnotationSettings_actionPerformed()
2224 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2227 protected void makeGrpsFromSelection_actionPerformed()
2229 if (avc.makeGroupsFromSelection())
2231 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2232 alignPanel.updateAnnotation();
2233 alignPanel.paintAlignment(true, true);
2237 protected void createGroup_actionPerformed()
2242 protected void unGroup_actionPerformed()
2246 alignPanel.alignmentChanged();
2250 protected void deleteGroups_actionPerformed()
2252 if (avc.deleteGroups())
2254 alignPanel.alignmentChanged();
2258 public void selectAllSequenceMenuItem_actionPerformed()
2260 SequenceGroup sg = new SequenceGroup();
2261 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2263 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2265 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2266 viewport.setSelectionGroup(sg);
2267 // JAL-2034 - should delegate to
2268 // alignPanel to decide if overview needs
2270 alignPanel.paintAlignment(false, false);
2271 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2272 viewport.sendSelection();
2275 public void deselectAllSequenceMenuItem_actionPerformed()
2277 if (viewport.cursorMode)
2279 alignPanel.seqPanel.keyboardNo1 = null;
2280 alignPanel.seqPanel.keyboardNo2 = null;
2282 viewport.setSelectionGroup(null);
2283 viewport.getColumnSelection().clear();
2284 viewport.setSelectionGroup(null);
2285 alignPanel.idPanel.idCanvas.searchResults = null;
2286 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2287 // JAL-2034 - should delegate to
2288 // alignPanel to decide if overview needs
2290 alignPanel.paintAlignment(false, false);
2291 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2292 viewport.sendSelection();
2295 public void invertSequenceMenuItem_actionPerformed()
2297 SequenceGroup sg = viewport.getSelectionGroup();
2298 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2300 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2303 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2304 viewport.sendSelection();
2307 public void invertColSel_actionPerformed()
2309 viewport.invertColumnSelection();
2310 alignPanel.paintAlignment(true, false);
2311 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2312 viewport.sendSelection();
2315 void trimAlignment(boolean trimLeft)
2317 AlignmentI al = viewport.getAlignment();
2318 ViewportRanges ranges = viewport.getRanges();
2319 ColumnSelection colSel = viewport.getColumnSelection();
2322 if (!colSel.isEmpty())
2326 column = colSel.getMin();
2330 column = colSel.getMax();
2334 if (viewport.getSelectionGroup() != null)
2336 seqs = viewport.getSelectionGroup()
2337 .getSequencesAsArray(viewport.getHiddenRepSequences());
2341 seqs = al.getSequencesArray();
2344 TrimRegionCommand trimRegion;
2347 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2349 ranges.setStartRes(0);
2353 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2357 setStatus(MessageManager
2358 .formatMessage("label.removed_columns", new String[]
2359 { Integer.valueOf(trimRegion.getSize()).toString() }));
2360 addHistoryItem(trimRegion);
2362 for (SequenceGroup sg : al.getGroups())
2364 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2365 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2371 viewport.notifyAlignment();
2375 public void removeGappedColumnMenuItem_actionPerformed()
2377 AlignmentI al = viewport.getAlignment();
2378 ViewportRanges ranges = viewport.getRanges();
2380 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2383 if (viewport.getSelectionGroup() != null)
2385 seqs = viewport.getSelectionGroup()
2386 .getSequencesAsArray(viewport.getHiddenRepSequences());
2387 start = viewport.getSelectionGroup().getStartRes();
2388 end = viewport.getSelectionGroup().getEndRes();
2392 seqs = viewport.getAlignment().getSequencesArray();
2395 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2396 "Remove Gapped Columns", seqs, start, end,
2397 viewport.getAlignment());
2399 addHistoryItem(removeGapCols);
2401 setStatus(MessageManager
2402 .formatMessage("label.removed_empty_columns", new String[]
2403 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2405 // This is to maintain viewport position on first residue
2406 // of first sequence
2407 SequenceI seq = al.getSequenceAt(0);
2408 int startRes = seq.findPosition(ranges.getStartRes());
2409 // ShiftList shifts;
2410 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2411 // edit.alColumnChanges=shifts.getInverse();
2412 // if (viewport.hasHiddenColumns)
2413 // viewport.getColumnSelection().compensateForEdits(shifts);
2414 ranges.setStartRes(seq.findIndex(startRes) - 1);
2415 viewport.notifyAlignment();
2419 public void removeAllGapsMenuItem_actionPerformed()
2421 AlignmentI al = viewport.getAlignment();
2422 ViewportRanges ranges = viewport.getRanges();
2424 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2427 if (viewport.getSelectionGroup() != null)
2429 seqs = viewport.getSelectionGroup()
2430 .getSequencesAsArray(viewport.getHiddenRepSequences());
2431 start = viewport.getSelectionGroup().getStartRes();
2432 end = viewport.getSelectionGroup().getEndRes();
2436 seqs = viewport.getAlignment().getSequencesArray();
2439 // This is to maintain viewport position on first residue
2440 // of first sequence
2441 SequenceI seq = al.getSequenceAt(0);
2442 int startRes = seq.findPosition(ranges.getStartRes());
2445 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2447 ranges.setStartRes(seq.findIndex(startRes) - 1);
2449 viewport.notifyAlignment();
2453 public void findMenuItem_actionPerformed()
2455 new Finder(alignPanel);
2459 * create a new view derived from the current view
2462 * @return frame for the new view
2464 public AlignFrame newView(String viewtitle)
2467 if (viewport.hasHiddenRows())
2469 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2470 .getFullAlignment().getSequencesArray());
2474 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2477 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2479 for (int i = 0; i < viewport.getAlignment()
2480 .getAlignmentAnnotation().length; i++)
2482 if (!viewport.getAlignment()
2483 .getAlignmentAnnotation()[i].autoCalculated)
2485 newal.addAnnotation(
2486 viewport.getAlignment().getAlignmentAnnotation()[i]);
2491 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2493 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2494 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2495 PaintRefresher.Register(newaf.alignPanel,
2496 newaf.alignPanel.av.getSequenceSetId());
2498 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2499 newaf.alignPanel.av.getSequenceSetId());
2500 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2501 newaf.alignPanel.av.getSequenceSetId());
2503 Vector comps = PaintRefresher.components
2504 .get(viewport.getSequenceSetId());
2506 for (int i = 0; i < comps.size(); i++)
2508 if (comps.elementAt(i) instanceof AlignmentPanel)
2514 String title = new String(this.getTitle());
2515 if (viewtitle != null)
2517 title = viewtitle + " ( " + title + ")";
2521 if (title.indexOf("(View") > -1)
2523 title = title.substring(0, title.indexOf("(View"));
2525 title += "(View " + viewSize + ")";
2528 newaf.setTitle(title.toString());
2530 newaf.viewport.setHistoryList(viewport.getHistoryList());
2531 newaf.viewport.setRedoList(viewport.getRedoList());
2537 * @return list of feature groups on the view
2539 public String[] getFeatureGroups()
2541 FeatureRenderer fr = null;
2542 if (alignPanel != null
2543 && (fr = alignPanel.getFeatureRenderer()) != null)
2545 List<String> gps = fr.getFeatureGroups();
2546 String[] _gps = gps.toArray(new String[gps.size()]);
2553 * get sequence feature groups that are hidden or shown
2559 public String[] getFeatureGroupsOfState(boolean visible)
2561 FeatureRenderer fr = null;
2562 if (alignPanel != null
2563 && (fr = alignPanel.getFeatureRenderer()) != null)
2565 List<String> gps = fr.getGroups(visible);
2566 String[] _gps = gps.toArray(new String[gps.size()]);
2573 * Change the display state for the given feature groups
2576 * list of group strings
2578 * visible or invisible
2580 public void setFeatureGroupState(String[] groups, boolean state)
2582 FeatureRenderer fr = null;
2583 this.sequenceFeatures.setState(true);
2584 viewport.setShowSequenceFeatures(true);
2585 if (alignPanel != null
2586 && (fr = alignPanel.getFeatureRenderer()) != null)
2589 fr.setGroupVisibility(Arrays.asList(groups), state);
2590 alignPanel.seqPanel.seqCanvas.repaint();
2591 if (alignPanel.overviewPanel != null)
2593 alignPanel.overviewPanel.updateOverviewImage();
2598 public void seqLimits_itemStateChanged()
2600 viewport.setShowJVSuffix(seqLimits.getState());
2601 alignPanel.fontChanged();
2602 alignPanel.paintAlignment(true, false);
2605 protected void colourTextMenuItem_actionPerformed()
2607 viewport.setColourText(colourTextMenuItem.getState());
2608 alignPanel.paintAlignment(false, false);
2611 protected void displayNonconservedMenuItem_actionPerformed()
2613 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2614 alignPanel.paintAlignment(false, false);
2617 protected void wrapMenuItem_actionPerformed()
2619 viewport.setWrapAlignment(wrapMenuItem.getState());
2620 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2621 scaleAbove.setEnabled(wrapMenuItem.getState());
2622 scaleLeft.setEnabled(wrapMenuItem.getState());
2623 scaleRight.setEnabled(wrapMenuItem.getState());
2624 alignPanel.paintAlignment(true, false);
2627 public void overviewMenuItem_actionPerformed()
2629 if (alignPanel.overviewPanel != null)
2634 Frame frame = new Frame();
2635 final OverviewPanel overview = new OverviewPanel(alignPanel);
2636 frame.add(overview);
2637 // +50 must allow for applet frame window
2638 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2639 .formatMessage("label.overview_params", new String[]
2640 { this.getTitle() }), overview.getPreferredSize().width,
2641 overview.getPreferredSize().height + 50);
2644 final AlignmentPanel ap = alignPanel;
2645 frame.addWindowListener(new WindowAdapter()
2648 public void windowClosing(WindowEvent e)
2653 ap.setOverviewPanel(null);
2658 alignPanel.setOverviewPanel(overview);
2663 public void changeColour(ColourSchemeI cs)
2665 viewport.setGlobalColourScheme(cs);
2667 alignPanel.paintAlignment(true, true);
2670 protected void modifyPID_actionPerformed()
2672 if (viewport.getAbovePIDThreshold()
2673 && viewport.getGlobalColourScheme() != null)
2675 SliderPanel.setPIDSliderSource(alignPanel,
2676 viewport.getResidueShading(), alignPanel.getViewName());
2677 SliderPanel.showPIDSlider();
2681 protected void modifyConservation_actionPerformed()
2683 if (viewport.getConservationSelected()
2684 && viewport.getGlobalColourScheme() != null)
2686 SliderPanel.setConservationSlider(alignPanel,
2687 viewport.getResidueShading(), alignPanel.getViewName());
2688 SliderPanel.showConservationSlider();
2692 protected void conservationMenuItem_actionPerformed()
2694 boolean selected = conservationMenuItem.getState();
2695 modifyConservation.setEnabled(selected);
2696 viewport.setConservationSelected(selected);
2697 viewport.getResidueShading().setConservationApplied(selected);
2699 changeColour(viewport.getGlobalColourScheme());
2703 modifyConservation_actionPerformed();
2707 SliderPanel.hideConservationSlider();
2711 public void abovePIDThreshold_actionPerformed()
2713 boolean selected = abovePIDThreshold.getState();
2714 modifyPID.setEnabled(selected);
2715 viewport.setAbovePIDThreshold(selected);
2718 viewport.getResidueShading().setThreshold(0,
2719 viewport.isIgnoreGapsConsensus());
2722 changeColour(viewport.getGlobalColourScheme());
2726 modifyPID_actionPerformed();
2730 SliderPanel.hidePIDSlider();
2734 public void sortPairwiseMenuItem_actionPerformed()
2736 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2737 AlignmentSorter.sortByPID(viewport.getAlignment(),
2738 viewport.getAlignment().getSequenceAt(0));
2740 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2741 viewport.getAlignment()));
2742 alignPanel.paintAlignment(true, false);
2745 public void sortIDMenuItem_actionPerformed()
2747 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2748 AlignmentSorter.sortByID(viewport.getAlignment());
2750 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2751 alignPanel.paintAlignment(true, false);
2754 public void sortLengthMenuItem_actionPerformed()
2756 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2757 AlignmentSorter.sortByLength(viewport.getAlignment());
2758 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2759 viewport.getAlignment()));
2760 alignPanel.paintAlignment(true, false);
2763 public void sortGroupMenuItem_actionPerformed()
2765 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2766 AlignmentSorter.sortByGroup(viewport.getAlignment());
2767 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2768 viewport.getAlignment()));
2769 alignPanel.paintAlignment(true, false);
2773 public void removeRedundancyMenuItem_actionPerformed()
2775 new RedundancyPanel(alignPanel);
2778 public void pairwiseAlignmentMenuItem_actionPerformed()
2780 if (viewport.getSelectionGroup() != null
2781 && viewport.getSelectionGroup().getSize() > 1)
2783 Frame frame = new Frame();
2784 frame.add(new PairwiseAlignPanel(alignPanel));
2785 jalview.bin.JalviewLite.addFrame(frame,
2786 MessageManager.getString("action.pairwise_alignment"), 600,
2791 public void PCAMenuItem_actionPerformed()
2793 // are the sequences aligned?
2794 if (!viewport.getAlignment().isAligned(false))
2797 int Width = viewport.getAlignment().getWidth();
2799 for (int i = 0; i < viewport.getAlignment().getSequences()
2802 current = viewport.getAlignment().getSequenceAt(i);
2804 if (current.getLength() < Width)
2806 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2809 alignPanel.paintAlignment(false, false);
2812 if ((viewport.getSelectionGroup() != null
2813 && viewport.getSelectionGroup().getSize() < 4
2814 && viewport.getSelectionGroup().getSize() > 0)
2815 || viewport.getAlignment().getHeight() < 4)
2822 new PCAPanel(viewport);
2823 } catch (java.lang.OutOfMemoryError ex)
2829 public void averageDistanceTreeMenuItem_actionPerformed()
2831 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2832 "Average distance tree using PID");
2835 public void neighbourTreeMenuItem_actionPerformed()
2837 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2838 "Neighbour joining tree using PID");
2841 protected void njTreeBlosumMenuItem_actionPerformed()
2843 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2844 ScoreModels.getInstance().getBlosum62().getName(),
2845 "Neighbour joining tree using BLOSUM62");
2848 protected void avTreeBlosumMenuItem_actionPerformed()
2850 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2851 ScoreModels.getInstance().getBlosum62().getName(),
2852 "Average distance tree using BLOSUM62");
2855 void newTreePanel(String type, String pwType, String title)
2857 // are the sequences aligned?
2858 if (!viewport.getAlignment().isAligned(false))
2861 int Width = viewport.getAlignment().getWidth();
2863 for (int i = 0; i < viewport.getAlignment().getSequences()
2866 current = viewport.getAlignment().getSequenceAt(i);
2868 if (current.getLength() < Width)
2870 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2873 alignPanel.paintAlignment(false, false);
2877 if ((viewport.getSelectionGroup() != null
2878 && viewport.getSelectionGroup().getSize() > 1)
2879 || (viewport.getAlignment().getHeight() > 1))
2881 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2883 addTreeMenuItem(tp, title);
2885 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2889 void loadTree_actionPerformed()
2891 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2892 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2893 cap.setTreeImport();
2894 Frame frame = new Frame();
2896 jalview.bin.JalviewLite.addFrame(frame,
2897 MessageManager.getString("label.paste_newick_file"), 400, 300);
2900 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2902 TreePanel tp = new TreePanel(alignPanel, treeFile,
2903 MessageManager.getString("label.load_tree_from_file"), tree);
2904 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2905 addTreeMenuItem(tp, treeFile);
2909 * sort the alignment using the given treePanel
2912 * tree used to sort view
2914 * string used for undo event name
2916 public void sortByTree(TreePanel treePanel, String title)
2918 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2919 AlignmentSorter.sortByTree(viewport.getAlignment(),
2920 treePanel.getTree());
2921 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2922 // HistoryItem.SORT));
2923 addHistoryItem(new OrderCommand(MessageManager
2924 .formatMessage("label.order_by_params", new String[]
2925 { title }), oldOrder, viewport.getAlignment()));
2926 alignPanel.paintAlignment(true, false);
2930 * Do any automatic reordering of the alignment and add the necessary bits to
2931 * the menu structure for the new tree
2936 protected void addTreeMenuItem(final TreePanel treePanel,
2939 final MenuItem item = new MenuItem(title);
2940 sortByTreeMenu.add(item);
2941 item.addActionListener(new java.awt.event.ActionListener()
2944 public void actionPerformed(ActionEvent evt)
2946 sortByTree(treePanel, title); // treePanel.getTitle());
2950 treePanel.addWindowListener(new WindowAdapter()
2953 public void windowOpened(WindowEvent e)
2955 if (viewport.sortByTree)
2957 sortByTree(treePanel, title);
2959 super.windowOpened(e);
2963 public void windowClosing(WindowEvent e)
2965 sortByTreeMenu.remove(item);
2970 public boolean sortBy(AlignmentOrder alorder, String undoname)
2972 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2973 if (viewport.applet.debug)
2975 System.err.println("Sorting " + alorder.getOrder().size()
2976 + " in alignment '" + getTitle() + "'");
2978 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2979 if (undoname != null)
2981 addHistoryItem(new OrderCommand(undoname, oldOrder,
2982 viewport.getAlignment()));
2984 alignPanel.paintAlignment(true, false);
2988 protected void documentation_actionPerformed()
2990 alignPanel.av.applet.openJalviewHelpUrl();
2993 protected void about_actionPerformed()
2996 class AboutPanel extends Canvas
3002 public AboutPanel(String version, String builddate)
3004 this.version = version;
3005 this.builddate = builddate;
3009 public void paint(Graphics g)
3011 g.setColor(Color.white);
3012 g.fillRect(0, 0, getSize().width, getSize().height);
3013 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3014 FontMetrics fm = g.getFontMetrics();
3015 int fh = fm.getHeight();
3017 g.setColor(Color.black);
3018 // TODO: update this text for each release or centrally store it for
3019 // lite and application
3020 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3021 g.drawString(MessageManager
3022 .formatMessage("label.jalviewLite_release", new String[]
3023 { version }), x, y += fh);
3024 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3025 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3027 { builddate }), x, y += fh);
3028 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3029 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3031 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3032 x + 50, y += fh + 8);
3033 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3035 g.drawString(MessageManager
3036 .getString("label.jalview_distribution_lists"), x, y += fh);
3037 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3040 MessageManager.getString("label.jalview_cite_1_authors"), x,
3042 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3044 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3049 Frame frame = new Frame();
3050 frame.add(new AboutPanel(JalviewLite.getVersion(),
3051 JalviewLite.getBuildDate()));
3052 jalview.bin.JalviewLite.addFrame(frame,
3053 MessageManager.getString("label.jalview"), 580, 220);
3057 public void showURL(String url, String target)
3059 if (viewport.applet == null)
3061 System.out.println("Not running as applet - no browser available.");
3065 viewport.applet.showURL(url, target);
3069 // ////////////////////////////////////////////////////////////////////////////////
3070 // JBuilder Graphics here
3072 MenuBar alignFrameMenuBar = new MenuBar();
3074 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3076 MenuItem loadApplication = new MenuItem(
3077 MessageManager.getString("label.view_full_application"));
3079 MenuItem loadTree = new MenuItem(
3080 MessageManager.getString("label.load_associated_tree"));
3082 MenuItem loadAnnotations = new MenuItem(
3083 MessageManager.getString("label.load_features_annotations"));
3085 MenuItem outputFeatures = new MenuItem(
3086 MessageManager.getString("label.export_features"));
3088 MenuItem outputAnnotations = new MenuItem(
3089 MessageManager.getString("label.export_annotations"));
3091 MenuItem closeMenuItem = new MenuItem(
3092 MessageManager.getString("action.close"));
3094 MenuItem selectAllSequenceMenuItem = new MenuItem(
3095 MessageManager.getString("action.select_all"));
3097 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3098 MessageManager.getString("action.deselect_all"));
3100 MenuItem invertSequenceMenuItem = new MenuItem(
3101 MessageManager.getString("action.invert_selection"));
3103 MenuItem remove2LeftMenuItem = new MenuItem();
3105 MenuItem remove2RightMenuItem = new MenuItem();
3107 MenuItem removeGappedColumnMenuItem = new MenuItem();
3109 MenuItem removeAllGapsMenuItem = new MenuItem();
3111 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3113 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3115 MenuItem sortPairwiseMenuItem = new MenuItem();
3117 MenuItem sortIDMenuItem = new MenuItem();
3119 MenuItem sortLengthMenuItem = new MenuItem();
3121 MenuItem sortGroupMenuItem = new MenuItem();
3123 MenuItem removeRedundancyMenuItem = new MenuItem();
3125 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3127 MenuItem PCAMenuItem = new MenuItem();
3129 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3131 MenuItem neighbourTreeMenuItem = new MenuItem();
3133 BorderLayout borderLayout1 = new BorderLayout();
3135 public Label statusBar = new Label();
3137 MenuItem clustalColour = new MenuItem();
3139 MenuItem zappoColour = new MenuItem();
3141 MenuItem taylorColour = new MenuItem();
3143 MenuItem hydrophobicityColour = new MenuItem();
3145 MenuItem helixColour = new MenuItem();
3147 MenuItem strandColour = new MenuItem();
3149 MenuItem turnColour = new MenuItem();
3151 MenuItem buriedColour = new MenuItem();
3153 MenuItem purinePyrimidineColour = new MenuItem();
3155 // MenuItem RNAInteractionColour = new MenuItem();
3157 MenuItem RNAHelixColour = new MenuItem();
3159 MenuItem userDefinedColour = new MenuItem();
3161 MenuItem PIDColour = new MenuItem();
3163 MenuItem BLOSUM62Colour = new MenuItem();
3165 MenuItem tcoffeeColour = new MenuItem();
3167 MenuItem njTreeBlosumMenuItem = new MenuItem();
3169 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3171 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3173 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3175 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3177 MenuItem alProperties = new MenuItem(
3178 MessageManager.getString("label.alignment_props"));
3180 MenuItem overviewMenuItem = new MenuItem();
3182 MenuItem undoMenuItem = new MenuItem();
3184 MenuItem redoMenuItem = new MenuItem();
3186 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3188 MenuItem noColourmenuItem = new MenuItem();
3190 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3192 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3194 MenuItem findMenuItem = new MenuItem();
3196 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3198 MenuItem nucleotideColour = new MenuItem();
3200 MenuItem deleteGroups = new MenuItem();
3202 MenuItem grpsFromSelection = new MenuItem();
3204 MenuItem createGroup = new MenuItem();
3206 MenuItem unGroup = new MenuItem();
3208 MenuItem delete = new MenuItem();
3210 MenuItem copy = new MenuItem();
3212 MenuItem cut = new MenuItem();
3214 Menu pasteMenu = new Menu();
3216 MenuItem pasteNew = new MenuItem();
3218 MenuItem pasteThis = new MenuItem();
3220 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3222 MenuItem font = new MenuItem();
3224 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3226 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3228 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3230 MenuItem modifyPID = new MenuItem();
3232 MenuItem modifyConservation = new MenuItem();
3234 CheckboxMenuItem autoCalculate = null;
3236 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3237 "Sort Alignment With New Tree", true);
3239 Menu sortByTreeMenu = new Menu();
3241 MenuItem inputText = new MenuItem();
3243 MenuItem documentation = new MenuItem();
3245 MenuItem about = new MenuItem();
3247 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3249 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3251 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3253 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3255 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3257 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3259 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3261 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3263 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3266 * Initialise menus and other items
3270 private void jbInit() throws Exception
3272 setMenuBar(alignFrameMenuBar);
3275 * Configure File menu items and actions
3278 .setLabel(MessageManager.getString("label.input_from_textbox"));
3279 inputText.addActionListener(this);
3280 Menu outputTextboxMenu = new Menu(
3281 MessageManager.getString("label.out_to_textbox"));
3282 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3284 MenuItem item = new MenuItem(ff);
3286 item.addActionListener(new java.awt.event.ActionListener()
3289 public void actionPerformed(ActionEvent e)
3291 outputText_actionPerformed(e);
3295 outputTextboxMenu.add(item);
3297 closeMenuItem.addActionListener(this);
3298 loadApplication.addActionListener(this);
3299 loadTree.addActionListener(this);
3300 loadAnnotations.addActionListener(this);
3301 outputFeatures.addActionListener(this);
3302 outputAnnotations.addActionListener(this);
3305 * Configure Edit menu items and actions
3307 undoMenuItem.setEnabled(false);
3308 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3309 undoMenuItem.addActionListener(this);
3310 redoMenuItem.setEnabled(false);
3311 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3312 redoMenuItem.addActionListener(this);
3313 copy.setLabel(MessageManager.getString("action.copy"));
3314 copy.addActionListener(this);
3315 cut.setLabel(MessageManager.getString("action.cut"));
3316 cut.addActionListener(this);
3317 delete.setLabel(MessageManager.getString("action.delete"));
3318 delete.addActionListener(this);
3319 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3320 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3321 pasteNew.addActionListener(this);
3322 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3323 pasteThis.addActionListener(this);
3325 .setLabel(MessageManager.getString("action.remove_left"));
3326 remove2LeftMenuItem.addActionListener(this);
3327 remove2RightMenuItem
3328 .setLabel(MessageManager.getString("action.remove_right"));
3329 remove2RightMenuItem.addActionListener(this);
3330 removeGappedColumnMenuItem.setLabel(
3331 MessageManager.getString("action.remove_empty_columns"));
3332 removeGappedColumnMenuItem.addActionListener(this);
3333 removeAllGapsMenuItem
3334 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3335 removeAllGapsMenuItem.addActionListener(this);
3336 removeRedundancyMenuItem
3337 .setLabel(MessageManager.getString("action.remove_redundancy"));
3338 removeRedundancyMenuItem.addActionListener(this);
3341 * Configure Select menu items and actions
3343 findMenuItem.setLabel(MessageManager.getString("action.find"));
3344 findMenuItem.addActionListener(this);
3345 selectAllSequenceMenuItem.addActionListener(this);
3346 deselectAllSequenceMenuItem.addActionListener(this);
3347 invertSequenceMenuItem.setLabel(
3348 MessageManager.getString("action.invert_sequence_selection"));
3349 invertSequenceMenuItem.addActionListener(this);
3350 invertColSel.setLabel(
3351 MessageManager.getString("action.invert_column_selection"));
3352 invertColSel.addActionListener(this);
3354 .setLabel(MessageManager.getString("action.undefine_groups"));
3355 deleteGroups.addActionListener(this);
3356 grpsFromSelection.setLabel(
3357 MessageManager.getString("action.make_groups_selection"));
3358 grpsFromSelection.addActionListener(this);
3359 createGroup.setLabel(MessageManager.getString("action.create_group"));
3360 createGroup.addActionListener(this);
3361 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3362 unGroup.addActionListener(this);
3364 annotationColumnSelection.setLabel(
3365 MessageManager.getString("action.select_by_annotation"));
3366 annotationColumnSelection.addActionListener(this);
3369 * Configure View menu items and actions
3371 newView.setLabel(MessageManager.getString("action.new_view"));
3372 newView.addActionListener(this);
3373 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3374 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3375 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3376 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3378 .setLabel(MessageManager.getString("label.selected_columns"));
3380 .setLabel(MessageManager.getString("label.selected_sequences"));
3381 hideAllButSelection.setLabel(
3382 MessageManager.getString("label.all_but_selected_region"));
3384 .setLabel(MessageManager.getString("label.selected_region"));
3385 showAllHidden.setLabel(
3386 MessageManager.getString("label.all_sequences_columns"));
3387 showColumns.addActionListener(this);
3388 showSeqs.addActionListener(this);
3389 hideColumns.addActionListener(this);
3390 hideSequences.addActionListener(this);
3391 hideAllButSelection.addActionListener(this);
3392 hideAllSelection.addActionListener(this);
3393 showAllHidden.addActionListener(this);
3395 .setLabel(MessageManager.getString("action.feature_settings"));
3396 featureSettings.addActionListener(this);
3397 sequenceFeatures.setLabel(
3398 MessageManager.getString("label.show_sequence_features"));
3399 sequenceFeatures.addItemListener(this);
3400 sequenceFeatures.setState(false);
3401 followMouseOverFlag.setLabel(
3402 MessageManager.getString("label.automatic_scrolling"));
3403 followMouseOverFlag.addItemListener(this);
3404 alProperties.addActionListener(this);
3406 .setLabel(MessageManager.getString("label.overview_window"));
3407 overviewMenuItem.addActionListener(this);
3410 * Configure Annotations menu items and actions
3412 annotationPanelMenuItem
3413 .setLabel(MessageManager.getString("label.show_annotations"));
3414 annotationPanelMenuItem.addItemListener(this);
3416 .setLabel(MessageManager.getString("label.group_consensus"));
3417 showGroupConservation
3418 .setLabel(MessageManager.getString("label.group_conservation"));
3419 showConsensusHistogram.setLabel(
3420 MessageManager.getString("label.show_consensus_histogram"));
3421 showSequenceLogo.setLabel(
3422 MessageManager.getString("label.show_consensus_logo"));
3423 normSequenceLogo.setLabel(
3424 MessageManager.getString("label.norm_consensus_logo"));
3425 applyAutoAnnotationSettings
3426 .setLabel(MessageManager.getString("label.apply_all_groups"));
3427 applyAutoAnnotationSettings.setState(true);
3428 Menu autoAnnMenu = new Menu(
3429 MessageManager.getString("label.autocalculated_annotation"));
3430 showGroupConsensus.addItemListener(this);
3431 showGroupConservation.addItemListener(this);
3432 showConsensusHistogram.addItemListener(this);
3433 showSequenceLogo.addItemListener(this);
3434 normSequenceLogo.addItemListener(this);
3435 applyAutoAnnotationSettings.addItemListener(this);
3436 showAlignmentAnnotations = new CheckboxMenuItem(
3437 MessageManager.getString("label.show_all_al_annotations"));
3438 showSequenceAnnotations = new CheckboxMenuItem(
3439 MessageManager.getString("label.show_all_seq_annotations"));
3440 sortAnnBySequence = new CheckboxMenuItem(
3441 MessageManager.getString("label.sort_annotations_by_sequence"));
3442 sortAnnByLabel = new CheckboxMenuItem(
3443 MessageManager.getString("label.sort_annotations_by_label"));
3444 showAutoFirst = new CheckboxMenuItem(
3445 MessageManager.getString("label.show_first"));
3446 showAutoFirst.setState(false); // pending applet parameter
3447 setShowAutoCalculatedAbove(showAutoFirst.getState());
3448 showAutoLast = new CheckboxMenuItem(
3449 MessageManager.getString("label.show_last"));
3450 showAutoLast.setState(!showAutoFirst.getState());
3451 showAlignmentAnnotations.addItemListener(this);
3452 showSequenceAnnotations.addItemListener(this);
3453 sortAnnBySequence.addItemListener(this);
3454 sortAnnByLabel.addItemListener(this);
3455 showAutoFirst.addItemListener(this);
3456 showAutoLast.addItemListener(this);
3459 * Configure Format menu items and actions
3461 font.setLabel(MessageManager.getString("action.font"));
3462 font.addActionListener(this);
3463 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3464 scaleAbove.setState(true);
3465 scaleAbove.setEnabled(false);
3466 scaleAbove.addItemListener(this);
3467 scaleLeft.setEnabled(false);
3468 scaleLeft.setState(true);
3469 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3470 scaleLeft.addItemListener(this);
3471 scaleRight.setEnabled(false);
3472 scaleRight.setState(true);
3473 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3474 scaleRight.addItemListener(this);
3475 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3476 viewBoxesMenuItem.setState(true);
3477 viewBoxesMenuItem.addItemListener(this);
3478 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3479 viewTextMenuItem.setState(true);
3480 viewTextMenuItem.addItemListener(this);
3482 .setLabel(MessageManager.getString("label.colour_text"));
3483 colourTextMenuItem.addItemListener(this);
3484 displayNonconservedMenuItem
3485 .setLabel(MessageManager.getString("label.show_non_conserved"));
3486 displayNonconservedMenuItem.addItemListener(this);
3487 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3488 wrapMenuItem.addItemListener(this);
3490 .setLabel(MessageManager.getString("action.show_gaps"));
3491 renderGapsMenuItem.setState(true);
3492 renderGapsMenuItem.addItemListener(this);
3493 centreColumnLabelFlag.setLabel(
3494 MessageManager.getString("label.centre_column_labels"));
3495 centreColumnLabelFlag.addItemListener(this);
3496 seqLimits.setState(true);
3498 MessageManager.getString("label.show_sequence_limits"));
3499 seqLimits.addItemListener(this);
3502 * Configure Colour menu items and actions
3504 applyToAllGroups.setLabel(
3505 MessageManager.getString("label.apply_colour_to_all_groups"));
3506 applyToAllGroups.setState(true);
3507 applyToAllGroups.addItemListener(this);
3508 clustalColour.setLabel(
3509 MessageManager.getString("label.colourScheme_clustal"));
3510 clustalColour.addActionListener(this);
3512 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3513 zappoColour.addActionListener(this);
3514 taylorColour.setLabel(
3515 MessageManager.getString("label.colourScheme_taylor"));
3516 taylorColour.addActionListener(this);
3517 hydrophobicityColour.setLabel(
3518 MessageManager.getString("label.colourScheme_hydrophobic"));
3519 hydrophobicityColour.addActionListener(this);
3520 helixColour.setLabel(MessageManager
3521 .getString("label.colourScheme_helix_propensity"));
3522 helixColour.addActionListener(this);
3523 strandColour.setLabel(MessageManager
3524 .getString("label.colourScheme_strand_propensity"));
3525 strandColour.addActionListener(this);
3526 turnColour.setLabel(
3527 MessageManager.getString("label.colourScheme_turn_propensity"));
3528 turnColour.addActionListener(this);
3529 buriedColour.setLabel(
3530 MessageManager.getString("label.colourScheme_buried_index"));
3531 buriedColour.addActionListener(this);
3532 purinePyrimidineColour.setLabel(MessageManager
3533 .getString("label.colourScheme_purine/pyrimidine"));
3534 purinePyrimidineColour.addActionListener(this);
3535 // RNAInteractionColour.setLabel(MessageManager
3536 // .getString("label.rna_interaction"));
3537 // RNAInteractionColour.addActionListener(this);
3538 RNAHelixColour.setLabel(
3539 MessageManager.getString("label.colourScheme_rna_helices"));
3540 RNAHelixColour.addActionListener(this);
3542 .setLabel(MessageManager.getString("action.user_defined"));
3543 userDefinedColour.addActionListener(this);
3545 MessageManager.getString("label.colourScheme_%_identity"));
3546 PIDColour.addActionListener(this);
3547 BLOSUM62Colour.setLabel(
3548 MessageManager.getString("label.colourScheme_blosum62"));
3549 BLOSUM62Colour.addActionListener(this);
3550 tcoffeeColour.setLabel(
3551 MessageManager.getString("label.colourScheme_t-coffee_scores"));
3552 // it will be enabled only if a score file is provided
3553 tcoffeeColour.setEnabled(false);
3554 tcoffeeColour.addActionListener(this);
3555 conservationMenuItem
3556 .setLabel(MessageManager.getString("action.by_conservation"));
3557 conservationMenuItem.addItemListener(this);
3558 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3559 noColourmenuItem.addActionListener(this);
3560 abovePIDThreshold.setLabel(
3561 MessageManager.getString("label.above_identity_threshold"));
3562 abovePIDThreshold.addItemListener(this);
3563 nucleotideColour.setLabel(
3564 MessageManager.getString("label.colourScheme_nucleotide"));
3565 nucleotideColour.addActionListener(this);
3567 MessageManager.getString("label.modify_identity_threshold"));
3568 modifyPID.setEnabled(abovePIDThreshold.getState());
3569 modifyPID.addActionListener(this);
3570 modifyConservation.setLabel(MessageManager
3571 .getString("label.modify_conservation_threshold"));
3572 modifyConservation.setEnabled(conservationMenuItem.getState());
3573 modifyConservation.addActionListener(this);
3575 .setLabel(MessageManager.getString("action.by_annotation"));
3576 annotationColour.addActionListener(this);
3579 * Configure Calculate menu items and actions
3581 sortPairwiseMenuItem
3582 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3583 sortPairwiseMenuItem.addActionListener(this);
3584 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3585 sortIDMenuItem.addActionListener(this);
3587 .setLabel(MessageManager.getString("action.by_length"));
3588 sortLengthMenuItem.addActionListener(this);
3589 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3590 sortGroupMenuItem.addActionListener(this);
3591 pairwiseAlignmentMenuItem.setLabel(
3592 MessageManager.getString("action.pairwise_alignment"));
3593 pairwiseAlignmentMenuItem.addActionListener(this);
3594 PCAMenuItem.setLabel(
3595 MessageManager.getString("label.principal_component_analysis"));
3596 PCAMenuItem.addActionListener(this);
3597 autoCalculate = new CheckboxMenuItem(
3598 MessageManager.getString("label.autocalculate_consensus"),
3600 averageDistanceTreeMenuItem.setLabel(
3601 MessageManager.getString("label.average_distance_identity"));
3602 averageDistanceTreeMenuItem.addActionListener(this);
3603 neighbourTreeMenuItem.setLabel(
3604 MessageManager.getString("label.neighbour_joining_identity"));
3605 neighbourTreeMenuItem.addActionListener(this);
3606 avDistanceTreeBlosumMenuItem.setLabel(
3607 MessageManager.getString("label.average_distance_blosum62"));
3608 avDistanceTreeBlosumMenuItem.addActionListener(this);
3609 njTreeBlosumMenuItem
3610 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3611 njTreeBlosumMenuItem.addActionListener(this);
3613 .setLabel(MessageManager.getString("action.by_tree_order"));
3614 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3615 Menu calculateTreeMenu = new Menu(
3616 MessageManager.getString("action.calculate_tree"));
3617 autoCalculate.addItemListener(this);
3618 sortByTree.addItemListener(this);
3621 * Configure Help menu items and actions
3623 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3624 documentation.setLabel(MessageManager.getString("label.documentation"));
3625 documentation.addActionListener(this);
3626 about.setLabel(MessageManager.getString("label.about"));
3627 about.addActionListener(this);
3630 * Add top level menus to frame
3632 alignFrameMenuBar.add(fileMenu);
3633 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3634 alignFrameMenuBar.add(editMenu);
3635 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3636 alignFrameMenuBar.add(selectMenu);
3637 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3638 alignFrameMenuBar.add(viewMenu);
3639 Menu annotationsMenu = new Menu(
3640 MessageManager.getString("action.annotations"));
3641 alignFrameMenuBar.add(annotationsMenu);
3642 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3643 alignFrameMenuBar.add(formatMenu);
3644 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3645 alignFrameMenuBar.add(colourMenu);
3646 Menu calculateMenu = new Menu(
3647 MessageManager.getString("action.calculate"));
3648 alignFrameMenuBar.add(calculateMenu);
3649 alignFrameMenuBar.add(helpMenu);
3654 fileMenu.add(inputText);
3655 fileMenu.add(loadTree);
3656 fileMenu.add(loadAnnotations);
3657 fileMenu.addSeparator();
3658 fileMenu.add(outputTextboxMenu);
3659 fileMenu.add(outputFeatures);
3660 fileMenu.add(outputAnnotations);
3661 if (jalviewServletURL != null)
3663 fileMenu.add(loadApplication);
3665 fileMenu.addSeparator();
3666 fileMenu.add(closeMenuItem);
3671 editMenu.add(undoMenuItem);
3672 editMenu.add(redoMenuItem);
3675 pasteMenu.add(pasteNew);
3676 pasteMenu.add(pasteThis);
3677 editMenu.add(pasteMenu);
3678 editMenu.add(delete);
3679 editMenu.addSeparator();
3680 editMenu.add(remove2LeftMenuItem);
3681 editMenu.add(remove2RightMenuItem);
3682 editMenu.add(removeGappedColumnMenuItem);
3683 editMenu.add(removeAllGapsMenuItem);
3684 editMenu.add(removeRedundancyMenuItem);
3689 selectMenu.add(findMenuItem);
3690 selectMenu.addSeparator();
3691 selectMenu.add(selectAllSequenceMenuItem);
3692 selectMenu.add(deselectAllSequenceMenuItem);
3693 selectMenu.add(invertSequenceMenuItem);
3694 selectMenu.add(invertColSel);
3695 selectMenu.add(createGroup);
3696 selectMenu.add(unGroup);
3697 selectMenu.add(grpsFromSelection);
3698 selectMenu.add(deleteGroups);
3699 selectMenu.add(annotationColumnSelection);
3704 viewMenu.add(newView);
3705 viewMenu.addSeparator();
3706 showMenu.add(showColumns);
3707 showMenu.add(showSeqs);
3708 showMenu.add(showAllHidden);
3709 viewMenu.add(showMenu);
3710 hideMenu.add(hideColumns);
3711 hideMenu.add(hideSequences);
3712 hideMenu.add(hideAllSelection);
3713 hideMenu.add(hideAllButSelection);
3714 viewMenu.add(hideMenu);
3715 viewMenu.addSeparator();
3716 viewMenu.add(followMouseOverFlag);
3717 viewMenu.addSeparator();
3718 viewMenu.add(sequenceFeatures);
3719 viewMenu.add(featureSettings);
3720 viewMenu.addSeparator();
3721 viewMenu.add(alProperties);
3722 viewMenu.addSeparator();
3723 viewMenu.add(overviewMenuItem);
3728 annotationsMenu.add(annotationPanelMenuItem);
3729 annotationsMenu.addSeparator();
3730 annotationsMenu.add(showAlignmentAnnotations);
3731 annotationsMenu.add(showSequenceAnnotations);
3732 annotationsMenu.add(sortAnnBySequence);
3733 annotationsMenu.add(sortAnnByLabel);
3734 annotationsMenu.addSeparator();
3735 autoAnnMenu.add(showAutoFirst);
3736 autoAnnMenu.add(showAutoLast);
3737 autoAnnMenu.addSeparator();
3738 autoAnnMenu.add(applyAutoAnnotationSettings);
3739 autoAnnMenu.add(showConsensusHistogram);
3740 autoAnnMenu.add(showSequenceLogo);
3741 autoAnnMenu.add(normSequenceLogo);
3742 autoAnnMenu.addSeparator();
3743 autoAnnMenu.add(showGroupConservation);
3744 autoAnnMenu.add(showGroupConsensus);
3745 annotationsMenu.add(autoAnnMenu);
3750 formatMenu.add(font);
3751 formatMenu.add(seqLimits);
3752 formatMenu.add(wrapMenuItem);
3753 formatMenu.add(scaleAbove);
3754 formatMenu.add(scaleLeft);
3755 formatMenu.add(scaleRight);
3756 formatMenu.add(viewBoxesMenuItem);
3757 formatMenu.add(viewTextMenuItem);
3758 formatMenu.add(colourTextMenuItem);
3759 formatMenu.add(displayNonconservedMenuItem);
3760 formatMenu.add(renderGapsMenuItem);
3761 formatMenu.add(centreColumnLabelFlag);
3766 colourMenu.add(applyToAllGroups);
3767 colourMenu.addSeparator();
3768 colourMenu.add(noColourmenuItem);
3769 colourMenu.add(clustalColour);
3770 colourMenu.add(BLOSUM62Colour);
3771 colourMenu.add(PIDColour);
3772 colourMenu.add(zappoColour);
3773 colourMenu.add(taylorColour);
3774 colourMenu.add(hydrophobicityColour);
3775 colourMenu.add(helixColour);
3776 colourMenu.add(strandColour);
3777 colourMenu.add(turnColour);
3778 colourMenu.add(buriedColour);
3779 colourMenu.add(nucleotideColour);
3780 colourMenu.add(purinePyrimidineColour);
3781 // colourMenu.add(RNAInteractionColour);
3782 colourMenu.add(tcoffeeColour);
3783 colourMenu.add(userDefinedColour);
3784 colourMenu.addSeparator();
3785 colourMenu.add(conservationMenuItem);
3786 colourMenu.add(modifyConservation);
3787 colourMenu.add(abovePIDThreshold);
3788 colourMenu.add(modifyPID);
3789 colourMenu.add(annotationColour);
3790 colourMenu.add(RNAHelixColour);
3795 sortMenu.add(sortIDMenuItem);
3796 sortMenu.add(sortLengthMenuItem);
3797 sortMenu.add(sortByTreeMenu);
3798 sortMenu.add(sortGroupMenuItem);
3799 sortMenu.add(sortPairwiseMenuItem);
3800 calculateMenu.add(sortMenu);
3801 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3802 calculateTreeMenu.add(neighbourTreeMenuItem);
3803 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3804 calculateTreeMenu.add(njTreeBlosumMenuItem);
3805 calculateMenu.add(calculateTreeMenu);
3806 calculateMenu.addSeparator();
3807 calculateMenu.add(pairwiseAlignmentMenuItem);
3808 calculateMenu.add(PCAMenuItem);
3809 calculateMenu.add(autoCalculate);
3810 calculateMenu.add(sortByTree);
3815 helpMenu.add(documentation);
3816 helpMenu.add(about);
3821 statusBar.setBackground(Color.white);
3822 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3823 setStatus(MessageManager.getString("label.status_bar"));
3824 this.add(statusBar, BorderLayout.SOUTH);
3828 public void setStatus(String string)
3830 statusBar.setText(string);
3833 MenuItem featureSettings = new MenuItem();
3835 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3837 MenuItem annotationColour = new MenuItem();
3839 MenuItem annotationColumnSelection = new MenuItem();
3841 MenuItem invertColSel = new MenuItem();
3843 MenuItem showColumns = new MenuItem();
3845 MenuItem showSeqs = new MenuItem();
3847 MenuItem hideColumns = new MenuItem();
3849 MenuItem hideSequences = new MenuItem();
3851 MenuItem hideAllButSelection = new MenuItem();
3853 MenuItem hideAllSelection = new MenuItem();
3855 MenuItem showAllHidden = new MenuItem();
3857 MenuItem newView = new MenuItem();
3859 private CheckboxMenuItem showAlignmentAnnotations;
3861 private CheckboxMenuItem showSequenceAnnotations;
3863 private CheckboxMenuItem sortAnnBySequence;
3865 private CheckboxMenuItem sortAnnByLabel;
3867 private CheckboxMenuItem showAutoFirst;
3869 private CheckboxMenuItem showAutoLast;
3871 private SplitFrame splitFrame;
3874 * Attach the alignFrame panels after embedding menus, if necessary. This used
3875 * to be called setEmbedded, but is now creates the dropdown menus in a
3876 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3878 * @param reallyEmbedded
3879 * true to attach the view to the applet area on the page rather than
3882 public void createAlignFrameWindow(boolean reallyEmbedded)
3886 embedAlignFrameInApplet(viewport.applet);
3891 // test and embed menu bar if necessary.
3893 if (embedMenuIfNeeded(alignPanel))
3896 * adjust for status bar height too. ? pointless as overridden by layout
3899 alignPanel.setSize(getSize().width,
3900 getSize().height - statusBar.getHeight());
3902 add(statusBar, BorderLayout.SOUTH);
3903 add(alignPanel, BorderLayout.CENTER);
3904 // and register with the applet so it can pass external API calls to us
3905 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3911 * Add the components of this AlignFrame to the applet container.
3915 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3918 // Explicitly build the embedded menu panel for the on-page applet
3920 // view cannot be closed if its actually on the page
3921 fileMenu.remove(closeMenuItem);
3922 fileMenu.remove(3); // Remove Separator
3923 // construct embedded menu, using default font
3924 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3925 // and actually add the components to the applet area
3926 theApplet.setLayout(new BorderLayout());
3927 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3928 theApplet.add(statusBar, BorderLayout.SOUTH);
3929 // TODO should size be left to the layout manager?
3930 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3931 - embeddedMenu.getHeight() - statusBar.getHeight());
3932 theApplet.add(alignPanel, BorderLayout.CENTER);
3933 final AlignFrame me = this;
3934 theApplet.addFocusListener(new FocusListener()
3938 public void focusLost(FocusEvent e)
3940 if (theApplet.currentAlignFrame == me)
3942 theApplet.currentAlignFrame = null;
3947 public void focusGained(FocusEvent e)
3949 theApplet.currentAlignFrame = me;
3952 theApplet.validate();
3956 * create a new binding between structures in an existing jmol viewer instance
3957 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3958 * this does not open a new Jmol window, or modify the display of the
3959 * structures in the original jmol window. Note This method doesn't work
3960 * without an additional javascript library to exchange messages between the
3961 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3964 * JmolViewer instance
3965 * @param sequenceIds
3966 * - sequence Ids to search for associations
3968 public SequenceStructureBinding addStructureViewInstance(
3969 Object jmolviewer, String[] sequenceIds)
3971 Viewer viewer = null;
3974 viewer = (Viewer) jmolviewer;
3975 } catch (ClassCastException ex)
3978 "Unsupported viewer object :" + jmolviewer.getClass());
3982 System.err.println("Can't use this object as a structure viewer:"
3983 + jmolviewer.getClass());
3986 SequenceI[] seqs = null;
3987 if (sequenceIds == null || sequenceIds.length == 0)
3989 seqs = viewport.getAlignment().getSequencesArray();
3993 Vector sqi = new Vector();
3994 AlignmentI al = viewport.getAlignment();
3995 for (int sid = 0; sid < sequenceIds.length; sid++)
3997 SequenceI sq = al.findName(sequenceIds[sid]);
4005 seqs = new SequenceI[sqi.size()];
4006 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4008 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4016 AAStructureBindingModel jmv = null;
4017 // TODO: search for a jmv that involves viewer
4019 { // create a new viewer/jalview binding.
4020 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4027 * bind a pdb file to a sequence in the current view
4030 * - sequenceId within the dataset.
4031 * @param pdbEntryString
4032 * - the short name for the PDB file
4034 * - pdb file - either a URL or a valid PDB file.
4035 * @return true if binding was as success TODO: consider making an exception
4036 * structure for indicating when PDB parsing or sequenceId location
4039 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4042 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4043 boolean needtoadd = false;
4044 if (toaddpdb != null)
4046 Vector pdbe = toaddpdb.getAllPDBEntries();
4047 PDBEntry pdbentry = null;
4048 if (pdbe != null && pdbe.size() > 0)
4050 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4052 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4053 if (!pdbentry.getId().equals(pdbEntryString)
4054 && !pdbentry.getFile().equals(pdbFile))
4064 if (pdbentry == null)
4066 pdbentry = new PDBEntry();
4067 pdbentry.setId(pdbEntryString);
4068 pdbentry.setFile(pdbFile);
4069 needtoadd = true; // add this new entry to sequence.
4071 // resolve data source
4072 // TODO: this code should be a refactored to an io package
4073 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4075 if (protocol == null)
4081 pdbentry.setProperty("protocol", protocol);
4082 toaddpdb.addPDBId(pdbentry);
4083 alignPanel.getStructureSelectionManager()
4084 .registerPDBEntry(pdbentry);
4090 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4094 Vector sequences = new Vector();
4095 for (int i = 0; i < seqs.length; i++)
4097 if (seqs[i] != null)
4100 .addElement(new Object[]
4101 { seqs[i], (chains != null) ? chains[i] : null });
4104 seqs = new SequenceI[sequences.size()];
4105 chains = new String[sequences.size()];
4106 for (int i = 0, isize = sequences.size(); i < isize; i++)
4108 Object[] oj = (Object[]) sequences.elementAt(i);
4110 seqs[i] = (SequenceI) oj[0];
4111 chains[i] = (String) oj[1];
4114 return new Object[] { seqs, chains };
4118 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4119 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4121 // Scrub any null sequences from the array
4122 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4123 seqs = (SequenceI[]) sqch[0];
4124 chains = (String[]) sqch[1];
4125 if (seqs == null || seqs.length == 0)
4128 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4130 if (protocol == null)
4132 String sourceType = (String) pdb.getProperty("protocol");
4135 protocol = DataSourceType.valueOf(sourceType);
4136 } catch (IllegalArgumentException e)
4140 if (protocol == null)
4142 System.err.println("Couldn't work out protocol to open structure: "
4147 if (applet.useXtrnalSviewer)
4149 // register the association(s) and quit, don't create any windows.
4150 if (StructureSelectionManager.getStructureSelectionManager(applet)
4151 .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4153 System.err.println("Failed to map " + pdb.getFile() + " ("
4154 + protocol + ") to any sequences");
4158 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4160 // can only do alignments with Jmol
4161 // find the last jmol window assigned to this alignment
4162 AppletJmol ajm = null, tajm;
4163 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4164 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4166 tajm = (AppletJmol) jmols.elementAt(i);
4167 if (tajm.ap.alignFrame == this)
4176 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4177 // try and add the pdb structure
4182 // otherwise, create a new window
4183 if (applet.jmolAvailable)
4185 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4186 applet.lastFrameX += 40;
4187 applet.lastFrameY += 40;
4191 new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4196 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4197 SequenceI[][] seqs, String[][] chains, String[] protocols)
4199 // TODO Auto-generated method stub
4200 System.err.println("Aligned Structure View: Not yet implemented.");
4204 * modify the current selection, providing the user has not made a selection
4208 * - sequences from this alignment
4210 * - columns to be selected on the alignment
4212 public void select(SequenceGroup sel, ColumnSelection csel,
4213 HiddenColumns hidden)
4215 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4218 public void scrollTo(int row, int column)
4220 alignPanel.seqPanel.scrollTo(row, column);
4223 public void scrollToRow(int row)
4225 alignPanel.seqPanel.scrollToRow(row);
4228 public void scrollToColumn(int column)
4230 alignPanel.seqPanel.scrollToColumn(column);
4234 * @return the alignments unique ID.
4236 public String getSequenceSetId()
4238 return viewport.getSequenceSetId();
4242 * Load the (T-Coffee) score file from the specified url
4245 * File/URL/T-COFFEE score file contents
4246 * @throws IOException
4247 * @return true if alignment was annotated with data from source
4249 public boolean loadScoreFile(String source) throws IOException
4252 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4253 AppletFormatAdapter.checkProtocol(source));
4254 if (!file.isValid())
4256 // TODO: raise dialog for gui
4257 System.err.println("Problems parsing T-Coffee scores: "
4258 + file.getWarningMessage());
4259 System.err.println("Origin was:\n" + source);
4264 * check that the score matrix matches the alignment dimensions
4267 if ((aln = viewport.getAlignment()) != null
4268 && (aln.getHeight() != file.getHeight()
4269 || aln.getWidth() != file.getWidth()))
4271 // TODO: raise a dialog box here rather than bomb out.
4273 "The scores matrix does not match the alignment dimensions");
4277 // TODO add parameter to indicate if matching should be done
4278 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4280 alignPanel.fontChanged();
4281 tcoffeeColour.setEnabled(true);
4282 // switch to this color
4283 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4288 System.err.println("Problems resolving T-Coffee scores:");
4289 if (file.getWarningMessage() != null)
4291 System.err.println(file.getWarningMessage());
4297 public SplitFrame getSplitFrame()
4299 return this.splitFrame;
4302 public void setSplitFrame(SplitFrame sf)
4304 this.splitFrame = sf;
4307 // may not need this
4309 public void setShowSeqFeatures(boolean b)
4311 // showSeqFeatures.setSelected(b);
4312 viewport.setShowSequenceFeatures(b);
4317 public void setMenusForViewport()
4319 // setMenusFromViewport(viewport);
4324 public void refreshFeatureUI(boolean enableIfNecessary)
4326 if (enableIfNecessary)
4328 sequenceFeatures.setState(true);
4329 alignPanel.av.setShowSequenceFeatures(true);
4334 public FeatureSettingsControllerI getFeatureSettingsUI()
4336 return alignPanel.av.featureSettings;
4340 public FeatureSettingsControllerI showFeatureSettingsUI()
4342 return new FeatureSettings(alignPanel);
4345 private Rectangle fs_bounds = null;
4348 public void setFeatureSettingsGeometry(Rectangle bounds)
4354 public Rectangle getFeatureSettingsGeometry()