2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import java.awt.BorderLayout;
24 import java.awt.Canvas;
25 import java.awt.CheckboxMenuItem;
26 import java.awt.Color;
27 import java.awt.FlowLayout;
29 import java.awt.FontMetrics;
30 import java.awt.Frame;
31 import java.awt.Graphics;
32 import java.awt.Label;
34 import java.awt.MenuBar;
35 import java.awt.MenuItem;
36 import java.awt.Panel;
37 import java.awt.Rectangle;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.event.FocusEvent;
41 import java.awt.event.FocusListener;
42 import java.awt.event.ItemEvent;
43 import java.awt.event.ItemListener;
44 import java.awt.event.KeyEvent;
45 import java.awt.event.KeyListener;
46 import java.awt.event.WindowAdapter;
47 import java.awt.event.WindowEvent;
48 import java.io.IOException;
49 import java.io.UnsupportedEncodingException;
51 import java.net.URLEncoder;
52 import java.util.Arrays;
53 import java.util.Deque;
54 import java.util.HashMap;
55 import java.util.List;
57 import java.util.StringTokenizer;
58 import java.util.Vector;
60 import org.jmol.viewer.Viewer;
62 import jalview.analysis.AlignmentSorter;
63 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
64 import jalview.analysis.TreeBuilder;
65 import jalview.analysis.scoremodels.PIDModel;
66 import jalview.analysis.scoremodels.ScoreModels;
67 import jalview.api.AlignViewControllerGuiI;
68 import jalview.api.AlignViewControllerI;
69 import jalview.api.AlignViewportI;
70 import jalview.api.FeatureColourI;
71 import jalview.api.FeatureRenderer;
72 import jalview.api.FeatureSettingsControllerI;
73 import jalview.api.SequenceStructureBinding;
74 import jalview.bin.JalviewLite;
75 import jalview.commands.CommandI;
76 import jalview.commands.EditCommand;
77 import jalview.commands.EditCommand.Action;
78 import jalview.commands.OrderCommand;
79 import jalview.commands.RemoveGapColCommand;
80 import jalview.commands.RemoveGapsCommand;
81 import jalview.commands.SlideSequencesCommand;
82 import jalview.commands.TrimRegionCommand;
83 import jalview.datamodel.Alignment;
84 import jalview.datamodel.AlignmentAnnotation;
85 import jalview.datamodel.AlignmentI;
86 import jalview.datamodel.AlignmentOrder;
87 import jalview.datamodel.ColumnSelection;
88 import jalview.datamodel.HiddenColumns;
89 import jalview.datamodel.PDBEntry;
90 import jalview.datamodel.Sequence;
91 import jalview.datamodel.SequenceGroup;
92 import jalview.datamodel.SequenceI;
93 import jalview.io.AnnotationFile;
94 import jalview.io.AppletFormatAdapter;
95 import jalview.io.DataSourceType;
96 import jalview.io.FeaturesFile;
97 import jalview.io.FileFormat;
98 import jalview.io.FileFormatI;
99 import jalview.io.FileFormats;
100 import jalview.io.TCoffeeScoreFile;
101 import jalview.schemes.Blosum62ColourScheme;
102 import jalview.schemes.BuriedColourScheme;
103 import jalview.schemes.ClustalxColourScheme;
104 import jalview.schemes.ColourSchemeI;
105 import jalview.schemes.HelixColourScheme;
106 import jalview.schemes.HydrophobicColourScheme;
107 import jalview.schemes.NucleotideColourScheme;
108 import jalview.schemes.PIDColourScheme;
109 import jalview.schemes.PurinePyrimidineColourScheme;
110 import jalview.schemes.RNAHelicesColour;
111 import jalview.schemes.StrandColourScheme;
112 import jalview.schemes.TCoffeeColourScheme;
113 import jalview.schemes.TaylorColourScheme;
114 import jalview.schemes.TurnColourScheme;
115 import jalview.schemes.ZappoColourScheme;
116 import jalview.structure.StructureSelectionManager;
117 import jalview.structures.models.AAStructureBindingModel;
118 import jalview.util.MappingUtils;
119 import jalview.util.MessageManager;
120 import jalview.viewmodel.AlignmentViewport;
121 import jalview.viewmodel.ViewportRanges;
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.formatMessage("label.keyboard_editing_mode",
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.autoCalculateConsensus = 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(
1457 viewport.getAlignment().getSequencesArray(),
1458 alignPanel.getFeatureRenderer(), true, false);
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;
1587 } catch (UnsupportedEncodingException ex)
1590 "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1592 ex.printStackTrace();
1597 public void closeMenuItem_actionPerformed()
1599 PaintRefresher.RemoveComponent(alignPanel);
1600 if (alignPanel.seqPanel != null
1601 && alignPanel.seqPanel.seqCanvas != null)
1603 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1605 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1607 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1610 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1616 if (alignPanel != null && alignPanel.overviewPanel != null)
1618 alignPanel.overviewPanel.dispose();
1627 void updateEditMenuBar()
1630 if (viewport.getHistoryList().size() > 0)
1632 undoMenuItem.setEnabled(true);
1633 CommandI command = viewport.getHistoryList().peek();
1634 undoMenuItem.setLabel(MessageManager
1635 .formatMessage("label.undo_command", new Object[]
1636 { command.getDescription() }));
1640 undoMenuItem.setEnabled(false);
1641 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1644 if (viewport.getRedoList().size() > 0)
1646 redoMenuItem.setEnabled(true);
1648 CommandI command = viewport.getRedoList().peek();
1649 redoMenuItem.setLabel(MessageManager
1650 .formatMessage("label.redo_command", new Object[]
1651 { command.getDescription() }));
1655 redoMenuItem.setEnabled(false);
1656 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1664 public void addHistoryItem(CommandI command)
1666 if (command.getSize() > 0)
1668 viewport.addToHistoryList(command);
1669 viewport.clearRedoList();
1670 updateEditMenuBar();
1671 viewport.updateHiddenColumns();
1676 * TODO: JAL-1104 DOCUMENT ME!
1681 protected void undoMenuItem_actionPerformed()
1683 if (viewport.getHistoryList().isEmpty())
1688 CommandI command = viewport.getHistoryList().pop();
1689 viewport.addToRedoList(command);
1690 command.undoCommand(null);
1692 AlignmentViewport originalSource = getOriginatingSource(command);
1694 if (originalSource != viewport)
1697 .println("Warning: Viewport object mismatch whilst undoing");
1699 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1700 // viewport.getColumnSelection().getHiddenColumns()
1702 updateEditMenuBar();
1703 originalSource.firePropertyChange("alignment", null,
1704 originalSource.getAlignment().getSequences());
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.firePropertyChange("alignment", null,
1737 originalSource.getAlignment().getSequences());
1740 AlignmentViewport getOriginatingSource(CommandI command)
1742 AlignmentViewport originalSource = null;
1743 // For sequence removal and addition, we need to fire
1744 // the property change event FROM the viewport where the
1745 // original alignment was altered
1746 AlignmentI al = null;
1747 if (command instanceof EditCommand)
1749 EditCommand editCommand = (EditCommand) command;
1750 al = editCommand.getAlignment();
1751 Vector comps = PaintRefresher.components
1752 .get(viewport.getSequenceSetId());
1753 for (int i = 0; i < comps.size(); i++)
1755 if (comps.elementAt(i) instanceof AlignmentPanel)
1757 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1759 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1766 if (originalSource == null)
1768 // The original view is closed, we must validate
1769 // the current view against the closed view first
1772 PaintRefresher.validateSequences(al, viewport.getAlignment());
1775 originalSource = viewport;
1778 return originalSource;
1782 * Move the currently selected sequences up or down one position in the
1787 public void moveSelectedSequences(boolean up)
1789 SequenceGroup sg = viewport.getSelectionGroup();
1794 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1795 up ? null : viewport.getHiddenRepSequences(), up);
1796 alignPanel.paintAlignment(true, false);
1799 * Also move cDNA/protein complement sequences
1801 AlignViewportI complement = viewport.getCodingComplement();
1802 if (complement != null)
1804 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1805 viewport, complement);
1806 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1807 up ? null : complement.getHiddenRepSequences(), up);
1808 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1813 synchronized void slideSequences(boolean right, int size)
1815 List<SequenceI> sg = new Vector<>();
1816 if (viewport.cursorMode)
1818 sg.add(viewport.getAlignment()
1819 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1821 else if (viewport.getSelectionGroup() != null
1822 && viewport.getSelectionGroup().getSize() != viewport
1823 .getAlignment().getHeight())
1825 sg = viewport.getSelectionGroup()
1826 .getSequences(viewport.getHiddenRepSequences());
1834 Vector<SequenceI> invertGroup = new Vector();
1836 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1838 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1840 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1844 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1846 SequenceI[] seqs2 = invertGroup
1847 .toArray(new SequenceI[invertGroup.size()]);
1848 for (int i = 0; i < invertGroup.size(); i++)
1850 seqs2[i] = invertGroup.elementAt(i);
1853 SlideSequencesCommand ssc;
1856 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1857 viewport.getGapCharacter());
1861 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1862 viewport.getGapCharacter());
1865 int groupAdjustment = 0;
1866 if (ssc.getGapsInsertedBegin() && right)
1868 if (viewport.cursorMode)
1870 alignPanel.seqPanel.moveCursor(size, 0);
1874 groupAdjustment = size;
1877 else if (!ssc.getGapsInsertedBegin() && !right)
1879 if (viewport.cursorMode)
1881 alignPanel.seqPanel.moveCursor(-size, 0);
1885 groupAdjustment = -size;
1889 if (groupAdjustment != 0)
1891 viewport.getSelectionGroup().setStartRes(
1892 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1893 viewport.getSelectionGroup().setEndRes(
1894 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1897 boolean appendHistoryItem = false;
1898 Deque<CommandI> historyList = viewport.getHistoryList();
1899 if (historyList != null && historyList.size() > 0
1900 && historyList.peek() instanceof SlideSequencesCommand)
1902 appendHistoryItem = ssc.appendSlideCommand(
1903 (SlideSequencesCommand) historyList.peek());
1906 if (!appendHistoryItem)
1908 addHistoryItem(ssc);
1914 static StringBuffer copiedSequences;
1916 static HiddenColumns copiedHiddenColumns;
1918 protected void copy_actionPerformed()
1920 if (viewport.getSelectionGroup() == null)
1925 SequenceGroup sg = viewport.getSelectionGroup();
1926 copiedSequences = new StringBuffer();
1927 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1928 for (int i = 0; i < sg.getSize(); i++)
1930 SequenceI seq = sg.getSequenceAt(i);
1931 int index = viewport.getAlignment().findIndex(seq);
1932 orderedSeqs.put(index, seq);
1935 int index = 0, startRes, endRes;
1938 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1940 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1941 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1943 // create new HiddenColumns object with copy of hidden regions
1944 // between startRes and endRes, offset by startRes
1945 copiedHiddenColumns = new HiddenColumns(
1946 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1947 hiddenCutoff, hiddenOffset);
1951 copiedHiddenColumns = null;
1954 for (int i = 0; i < sg.getSize(); i++)
1956 SequenceI seq = null;
1960 if (orderedSeqs.containsKey(index))
1962 seq = orderedSeqs.get(index);
1973 // Returns residue following index if gap
1974 startRes = seq.findPosition(sg.getStartRes());
1977 // Need to find the residue preceeding index if gap
1980 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1982 ch = seq.getCharAt(j);
1983 if (!jalview.util.Comparison.isGap((ch)))
1991 endRes += seq.getStart() - 1;
1994 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1995 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
2002 protected void pasteNew_actionPerformed()
2007 protected void pasteThis_actionPerformed()
2012 void paste(boolean newAlignment)
2016 if (copiedSequences == null)
2021 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2023 Vector seqs = new Vector();
2024 while (st.hasMoreElements())
2026 String name = st.nextToken();
2027 int start = Integer.parseInt(st.nextToken());
2028 int end = Integer.parseInt(st.nextToken());
2029 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2031 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2032 for (int i = 0; i < seqs.size(); i++)
2034 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2039 String newtitle = MessageManager
2040 .getString("label.copied_sequences");
2041 if (getTitle().startsWith(
2042 MessageManager.getString("label.copied_sequences")))
2044 newtitle = getTitle();
2048 newtitle = newtitle.concat(MessageManager
2049 .formatMessage("label.from_msname", new String[]
2052 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2053 viewport.applet, newtitle, false);
2054 af.viewport.setHiddenColumns(copiedHiddenColumns);
2056 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2061 addSequences(newSeqs);
2064 } catch (Exception ex)
2066 } // could be anything being pasted in here
2070 void addSequences(SequenceI[] seqs)
2072 for (int i = 0; i < seqs.length; i++)
2074 viewport.getAlignment().addSequence(seqs[i]);
2078 addHistoryItem(new EditCommand(
2079 MessageManager.getString("label.add_sequences"), Action.PASTE,
2080 seqs, 0, viewport.getAlignment().getWidth(),
2081 viewport.getAlignment()));
2083 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2085 viewport.getAlignment().getWidth();
2086 viewport.firePropertyChange("alignment", null,
2087 viewport.getAlignment().getSequences());
2091 protected void cut_actionPerformed()
2093 copy_actionPerformed();
2094 delete_actionPerformed();
2097 protected void delete_actionPerformed()
2100 SequenceGroup sg = viewport.getSelectionGroup();
2106 Vector seqs = new Vector();
2108 for (int i = 0; i < sg.getSize(); i++)
2110 seq = sg.getSequenceAt(i);
2111 seqs.addElement(seq);
2115 * If the cut affects all sequences, warn, remove highlighted columns
2117 if (sg.getSize() == viewport.getAlignment().getHeight())
2119 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2120 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2121 if (isEntireAlignWidth)
2123 String title = MessageManager.getString("label.delete_all");
2124 Panel infoPanel = new Panel();
2125 infoPanel.setLayout(new FlowLayout());
2127 new Label(MessageManager.getString("warn.delete_all")));
2129 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2130 dialog.setMainPanel(infoPanel);
2131 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2132 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2133 dialog.setVisible(true);
2140 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2141 sg.getEndRes() + 1);
2144 SequenceI[] cut = new SequenceI[seqs.size()];
2145 for (int i = 0; i < seqs.size(); i++)
2147 cut[i] = (SequenceI) seqs.elementAt(i);
2151 * //ADD HISTORY ITEM
2153 addHistoryItem(new EditCommand(
2154 MessageManager.getString("label.cut_sequences"), Action.CUT,
2155 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2156 viewport.getAlignment()));
2158 viewport.setSelectionGroup(null);
2159 viewport.getAlignment().deleteGroup(sg);
2161 viewport.firePropertyChange("alignment", null,
2162 viewport.getAlignment().getSequences());
2164 if (viewport.getAlignment().getHeight() < 1)
2166 this.setVisible(false);
2168 viewport.sendSelection();
2172 * group consensus toggled
2175 protected void showGroupConsensus_actionPerformed()
2177 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2178 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183 * group conservation toggled.
2185 protected void showGroupConservation_actionPerformed()
2187 viewport.setShowGroupConservation(showGroupConservation.getState());
2188 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2196 * .event.ActionEvent)
2198 protected void showConsensusHistogram_actionPerformed()
2200 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2201 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2208 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2209 * .event.ActionEvent)
2211 protected void showSequenceLogo_actionPerformed()
2213 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2214 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2217 protected void normSequenceLogo_actionPerformed()
2219 showSequenceLogo.setState(true);
2220 viewport.setShowSequenceLogo(true);
2221 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2222 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2225 protected void applyAutoAnnotationSettings_actionPerformed()
2227 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2230 protected void makeGrpsFromSelection_actionPerformed()
2232 if (avc.makeGroupsFromSelection())
2234 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2235 alignPanel.updateAnnotation();
2236 alignPanel.paintAlignment(true, true);
2240 protected void createGroup_actionPerformed()
2245 protected void unGroup_actionPerformed()
2249 alignPanel.alignmentChanged();
2253 protected void deleteGroups_actionPerformed()
2255 if (avc.deleteGroups())
2257 alignPanel.alignmentChanged();
2261 public void selectAllSequenceMenuItem_actionPerformed()
2263 SequenceGroup sg = new SequenceGroup();
2264 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2266 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2268 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2269 viewport.setSelectionGroup(sg);
2270 // JAL-2034 - should delegate to
2271 // alignPanel to decide if overview needs
2273 alignPanel.paintAlignment(false, false);
2274 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2275 viewport.sendSelection();
2278 public void deselectAllSequenceMenuItem_actionPerformed()
2280 if (viewport.cursorMode)
2282 alignPanel.seqPanel.keyboardNo1 = null;
2283 alignPanel.seqPanel.keyboardNo2 = null;
2285 viewport.setSelectionGroup(null);
2286 viewport.getColumnSelection().clear();
2287 viewport.setSelectionGroup(null);
2288 alignPanel.idPanel.idCanvas.searchResults = null;
2289 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2290 // JAL-2034 - should delegate to
2291 // alignPanel to decide if overview needs
2293 alignPanel.paintAlignment(false, false);
2294 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2295 viewport.sendSelection();
2298 public void invertSequenceMenuItem_actionPerformed()
2300 SequenceGroup sg = viewport.getSelectionGroup();
2301 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2303 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2306 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2307 viewport.sendSelection();
2310 public void invertColSel_actionPerformed()
2312 viewport.invertColumnSelection();
2313 alignPanel.paintAlignment(true, false);
2314 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2315 viewport.sendSelection();
2318 void trimAlignment(boolean trimLeft)
2320 AlignmentI al = viewport.getAlignment();
2321 ViewportRanges ranges = viewport.getRanges();
2322 ColumnSelection colSel = viewport.getColumnSelection();
2325 if (!colSel.isEmpty())
2329 column = colSel.getMin();
2333 column = colSel.getMax();
2337 if (viewport.getSelectionGroup() != null)
2339 seqs = viewport.getSelectionGroup()
2340 .getSequencesAsArray(viewport.getHiddenRepSequences());
2344 seqs = al.getSequencesArray();
2347 TrimRegionCommand trimRegion;
2350 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2352 ranges.setStartRes(0);
2356 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2360 setStatus(MessageManager.formatMessage("label.removed_columns",
2362 { Integer.valueOf(trimRegion.getSize()).toString() }));
2363 addHistoryItem(trimRegion);
2365 for (SequenceGroup sg : al.getGroups())
2367 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2368 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2374 viewport.firePropertyChange("alignment", null, al.getSequences());
2378 public void removeGappedColumnMenuItem_actionPerformed()
2380 AlignmentI al = viewport.getAlignment();
2381 ViewportRanges ranges = viewport.getRanges();
2383 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2386 if (viewport.getSelectionGroup() != null)
2388 seqs = viewport.getSelectionGroup()
2389 .getSequencesAsArray(viewport.getHiddenRepSequences());
2390 start = viewport.getSelectionGroup().getStartRes();
2391 end = viewport.getSelectionGroup().getEndRes();
2395 seqs = viewport.getAlignment().getSequencesArray();
2398 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2399 "Remove Gapped Columns", seqs, start, end,
2400 viewport.getAlignment());
2402 addHistoryItem(removeGapCols);
2404 setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2406 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2408 // This is to maintain viewport position on first residue
2409 // of first sequence
2410 SequenceI seq = al.getSequenceAt(0);
2411 int startRes = seq.findPosition(ranges.getStartRes());
2412 // ShiftList shifts;
2413 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2414 // edit.alColumnChanges=shifts.getInverse();
2415 // if (viewport.hasHiddenColumns)
2416 // viewport.getColumnSelection().compensateForEdits(shifts);
2417 ranges.setStartRes(seq.findIndex(startRes) - 1);
2418 viewport.firePropertyChange("alignment", null, al.getSequences());
2422 public void removeAllGapsMenuItem_actionPerformed()
2424 AlignmentI al = viewport.getAlignment();
2425 ViewportRanges ranges = viewport.getRanges();
2427 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2430 if (viewport.getSelectionGroup() != null)
2432 seqs = viewport.getSelectionGroup()
2433 .getSequencesAsArray(viewport.getHiddenRepSequences());
2434 start = viewport.getSelectionGroup().getStartRes();
2435 end = viewport.getSelectionGroup().getEndRes();
2439 seqs = viewport.getAlignment().getSequencesArray();
2442 // This is to maintain viewport position on first residue
2443 // of first sequence
2444 SequenceI seq = al.getSequenceAt(0);
2445 int startRes = seq.findPosition(ranges.getStartRes());
2448 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2450 ranges.setStartRes(seq.findIndex(startRes) - 1);
2452 viewport.firePropertyChange("alignment", null, al.getSequences());
2456 public void findMenuItem_actionPerformed()
2458 new Finder(alignPanel);
2462 * create a new view derived from the current view
2465 * @return frame for the new view
2467 public AlignFrame newView(String viewtitle)
2470 if (viewport.hasHiddenRows())
2472 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2473 .getFullAlignment().getSequencesArray());
2477 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2480 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2482 for (int i = 0; i < viewport.getAlignment()
2483 .getAlignmentAnnotation().length; i++)
2485 if (!viewport.getAlignment()
2486 .getAlignmentAnnotation()[i].autoCalculated)
2488 newal.addAnnotation(
2489 viewport.getAlignment().getAlignmentAnnotation()[i]);
2494 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2496 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2497 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2498 PaintRefresher.Register(newaf.alignPanel,
2499 newaf.alignPanel.av.getSequenceSetId());
2501 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2502 newaf.alignPanel.av.getSequenceSetId());
2503 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2504 newaf.alignPanel.av.getSequenceSetId());
2506 Vector comps = PaintRefresher.components
2507 .get(viewport.getSequenceSetId());
2509 for (int i = 0; i < comps.size(); i++)
2511 if (comps.elementAt(i) instanceof AlignmentPanel)
2517 String title = new String(this.getTitle());
2518 if (viewtitle != null)
2520 title = viewtitle + " ( " + title + ")";
2524 if (title.indexOf("(View") > -1)
2526 title = title.substring(0, title.indexOf("(View"));
2528 title += "(View " + viewSize + ")";
2531 newaf.setTitle(title.toString());
2533 newaf.viewport.setHistoryList(viewport.getHistoryList());
2534 newaf.viewport.setRedoList(viewport.getRedoList());
2540 * @return list of feature groups on the view
2542 public String[] getFeatureGroups()
2544 FeatureRenderer fr = null;
2545 if (alignPanel != null
2546 && (fr = alignPanel.getFeatureRenderer()) != null)
2548 List<String> gps = fr.getFeatureGroups();
2549 String[] _gps = gps.toArray(new String[gps.size()]);
2556 * get sequence feature groups that are hidden or shown
2562 public String[] getFeatureGroupsOfState(boolean visible)
2564 FeatureRenderer fr = null;
2565 if (alignPanel != null
2566 && (fr = alignPanel.getFeatureRenderer()) != null)
2568 List<String> gps = fr.getGroups(visible);
2569 String[] _gps = gps.toArray(new String[gps.size()]);
2576 * Change the display state for the given feature groups
2579 * list of group strings
2581 * visible or invisible
2583 public void setFeatureGroupState(String[] groups, boolean state)
2585 FeatureRenderer fr = null;
2586 this.sequenceFeatures.setState(true);
2587 viewport.setShowSequenceFeatures(true);
2588 if (alignPanel != null
2589 && (fr = alignPanel.getFeatureRenderer()) != null)
2592 fr.setGroupVisibility(Arrays.asList(groups), state);
2593 alignPanel.seqPanel.seqCanvas.repaint();
2594 if (alignPanel.overviewPanel != null)
2596 alignPanel.overviewPanel.updateOverviewImage();
2601 public void seqLimits_itemStateChanged()
2603 viewport.setShowJVSuffix(seqLimits.getState());
2604 alignPanel.fontChanged();
2605 alignPanel.paintAlignment(true, false);
2608 protected void colourTextMenuItem_actionPerformed()
2610 viewport.setColourText(colourTextMenuItem.getState());
2611 alignPanel.paintAlignment(false, false);
2614 protected void displayNonconservedMenuItem_actionPerformed()
2616 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2617 alignPanel.paintAlignment(false, false);
2620 protected void wrapMenuItem_actionPerformed()
2622 viewport.setWrapAlignment(wrapMenuItem.getState());
2623 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2624 scaleAbove.setEnabled(wrapMenuItem.getState());
2625 scaleLeft.setEnabled(wrapMenuItem.getState());
2626 scaleRight.setEnabled(wrapMenuItem.getState());
2627 alignPanel.paintAlignment(true, false);
2630 public void overviewMenuItem_actionPerformed()
2632 if (alignPanel.overviewPanel != null)
2637 Frame frame = new Frame();
2638 final OverviewPanel overview = new OverviewPanel(alignPanel);
2639 frame.add(overview);
2640 // +50 must allow for applet frame window
2641 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2642 .formatMessage("label.overview_params", new String[]
2643 { this.getTitle() }), overview.getPreferredSize().width,
2644 overview.getPreferredSize().height + 50);
2647 final AlignmentPanel ap = alignPanel;
2648 frame.addWindowListener(new WindowAdapter()
2651 public void windowClosing(WindowEvent e)
2656 ap.setOverviewPanel(null);
2661 alignPanel.setOverviewPanel(overview);
2666 public void changeColour(ColourSchemeI cs)
2668 viewport.setGlobalColourScheme(cs);
2670 alignPanel.paintAlignment(true, true);
2673 protected void modifyPID_actionPerformed()
2675 if (viewport.getAbovePIDThreshold()
2676 && viewport.getGlobalColourScheme() != null)
2678 SliderPanel.setPIDSliderSource(alignPanel,
2679 viewport.getResidueShading(), alignPanel.getViewName());
2680 SliderPanel.showPIDSlider();
2684 protected void modifyConservation_actionPerformed()
2686 if (viewport.getConservationSelected()
2687 && viewport.getGlobalColourScheme() != null)
2689 SliderPanel.setConservationSlider(alignPanel,
2690 viewport.getResidueShading(), alignPanel.getViewName());
2691 SliderPanel.showConservationSlider();
2695 protected void conservationMenuItem_actionPerformed()
2697 boolean selected = conservationMenuItem.getState();
2698 modifyConservation.setEnabled(selected);
2699 viewport.setConservationSelected(selected);
2700 viewport.getResidueShading().setConservationApplied(selected);
2702 changeColour(viewport.getGlobalColourScheme());
2706 modifyConservation_actionPerformed();
2710 SliderPanel.hideConservationSlider();
2714 public void abovePIDThreshold_actionPerformed()
2716 boolean selected = abovePIDThreshold.getState();
2717 modifyPID.setEnabled(selected);
2718 viewport.setAbovePIDThreshold(selected);
2721 viewport.getResidueShading().setThreshold(0,
2722 viewport.isIgnoreGapsConsensus());
2725 changeColour(viewport.getGlobalColourScheme());
2729 modifyPID_actionPerformed();
2733 SliderPanel.hidePIDSlider();
2737 public void sortPairwiseMenuItem_actionPerformed()
2739 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2740 AlignmentSorter.sortByPID(viewport.getAlignment(),
2741 viewport.getAlignment().getSequenceAt(0));
2743 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2744 viewport.getAlignment()));
2745 alignPanel.paintAlignment(true, false);
2748 public void sortIDMenuItem_actionPerformed()
2750 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2751 AlignmentSorter.sortByID(viewport.getAlignment());
2753 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2754 alignPanel.paintAlignment(true, false);
2757 public void sortLengthMenuItem_actionPerformed()
2759 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2760 AlignmentSorter.sortByLength(viewport.getAlignment());
2761 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2762 viewport.getAlignment()));
2763 alignPanel.paintAlignment(true, false);
2766 public void sortGroupMenuItem_actionPerformed()
2768 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2769 AlignmentSorter.sortByGroup(viewport.getAlignment());
2770 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2771 viewport.getAlignment()));
2772 alignPanel.paintAlignment(true, false);
2776 public void removeRedundancyMenuItem_actionPerformed()
2778 new RedundancyPanel(alignPanel);
2781 public void pairwiseAlignmentMenuItem_actionPerformed()
2783 if (viewport.getSelectionGroup() != null
2784 && viewport.getSelectionGroup().getSize() > 1)
2786 Frame frame = new Frame();
2787 frame.add(new PairwiseAlignPanel(alignPanel));
2788 jalview.bin.JalviewLite.addFrame(frame,
2789 MessageManager.getString("action.pairwise_alignment"), 600,
2794 public void PCAMenuItem_actionPerformed()
2796 // are the sequences aligned?
2797 if (!viewport.getAlignment().isAligned(false))
2800 int Width = viewport.getAlignment().getWidth();
2802 for (int i = 0; i < viewport.getAlignment().getSequences()
2805 current = viewport.getAlignment().getSequenceAt(i);
2807 if (current.getLength() < Width)
2809 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2812 alignPanel.paintAlignment(false, false);
2815 if ((viewport.getSelectionGroup() != null
2816 && viewport.getSelectionGroup().getSize() < 4
2817 && viewport.getSelectionGroup().getSize() > 0)
2818 || viewport.getAlignment().getHeight() < 4)
2825 new PCAPanel(viewport);
2826 } catch (java.lang.OutOfMemoryError ex)
2832 public void averageDistanceTreeMenuItem_actionPerformed()
2834 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2835 "Average distance tree using PID");
2838 public void neighbourTreeMenuItem_actionPerformed()
2840 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2841 "Neighbour joining tree using PID");
2844 protected void njTreeBlosumMenuItem_actionPerformed()
2846 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2847 ScoreModels.getInstance().getBlosum62().getName(),
2848 "Neighbour joining tree using BLOSUM62");
2851 protected void avTreeBlosumMenuItem_actionPerformed()
2853 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2854 ScoreModels.getInstance().getBlosum62().getName(),
2855 "Average distance tree using BLOSUM62");
2858 void newTreePanel(String type, String pwType, String title)
2860 // are the sequences aligned?
2861 if (!viewport.getAlignment().isAligned(false))
2864 int Width = viewport.getAlignment().getWidth();
2866 for (int i = 0; i < viewport.getAlignment().getSequences()
2869 current = viewport.getAlignment().getSequenceAt(i);
2871 if (current.getLength() < Width)
2873 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2876 alignPanel.paintAlignment(false, false);
2880 if ((viewport.getSelectionGroup() != null
2881 && viewport.getSelectionGroup().getSize() > 1)
2882 || (viewport.getAlignment().getHeight() > 1))
2884 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2886 addTreeMenuItem(tp, title);
2888 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2892 void loadTree_actionPerformed()
2894 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2895 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2896 cap.setTreeImport();
2897 Frame frame = new Frame();
2899 jalview.bin.JalviewLite.addFrame(frame,
2900 MessageManager.getString("label.paste_newick_file"), 400, 300);
2903 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2905 TreePanel tp = new TreePanel(alignPanel, treeFile,
2906 MessageManager.getString("label.load_tree_from_file"), tree);
2907 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2908 addTreeMenuItem(tp, treeFile);
2912 * sort the alignment using the given treePanel
2915 * tree used to sort view
2917 * string used for undo event name
2919 public void sortByTree(TreePanel treePanel, String title)
2921 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2922 AlignmentSorter.sortByTree(viewport.getAlignment(),
2923 treePanel.getTree());
2924 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2925 // HistoryItem.SORT));
2926 addHistoryItem(new OrderCommand(MessageManager
2927 .formatMessage("label.order_by_params", new String[]
2928 { title }), oldOrder, viewport.getAlignment()));
2929 alignPanel.paintAlignment(true, false);
2933 * Do any automatic reordering of the alignment and add the necessary bits to
2934 * the menu structure for the new tree
2939 protected void addTreeMenuItem(final TreePanel treePanel,
2942 final MenuItem item = new MenuItem(title);
2943 sortByTreeMenu.add(item);
2944 item.addActionListener(new java.awt.event.ActionListener()
2947 public void actionPerformed(ActionEvent evt)
2949 sortByTree(treePanel, title); // treePanel.getTitle());
2953 treePanel.addWindowListener(new WindowAdapter()
2956 public void windowOpened(WindowEvent e)
2958 if (viewport.sortByTree)
2960 sortByTree(treePanel, title);
2962 super.windowOpened(e);
2966 public void windowClosing(WindowEvent e)
2968 sortByTreeMenu.remove(item);
2973 public boolean sortBy(AlignmentOrder alorder, String undoname)
2975 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2976 if (viewport.applet.debug)
2978 System.err.println("Sorting " + alorder.getOrder().size()
2979 + " in alignment '" + getTitle() + "'");
2981 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2982 if (undoname != null)
2984 addHistoryItem(new OrderCommand(undoname, oldOrder,
2985 viewport.getAlignment()));
2987 alignPanel.paintAlignment(true, false);
2991 protected void documentation_actionPerformed()
2993 alignPanel.av.applet.openJalviewHelpUrl();
2996 protected void about_actionPerformed()
2999 class AboutPanel extends Canvas
3005 public AboutPanel(String version, String builddate)
3007 this.version = version;
3008 this.builddate = builddate;
3012 public void paint(Graphics g)
3014 g.setColor(Color.white);
3015 g.fillRect(0, 0, getSize().width, getSize().height);
3016 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3017 FontMetrics fm = g.getFontMetrics();
3018 int fh = fm.getHeight();
3020 g.setColor(Color.black);
3021 // TODO: update this text for each release or centrally store it for
3022 // lite and application
3023 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3024 g.drawString(MessageManager
3025 .formatMessage("label.jalviewLite_release", new String[]
3026 { version }), x, y += fh);
3027 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3028 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3030 { builddate }), x, y += fh);
3031 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3032 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3034 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3035 x + 50, y += fh + 8);
3036 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3038 g.drawString(MessageManager
3039 .getString("label.jalview_distribution_lists"), x, y += fh);
3040 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3043 MessageManager.getString("label.jalview_cite_1_authors"), x,
3045 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3047 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3052 Frame frame = new Frame();
3053 frame.add(new AboutPanel(JalviewLite.getVersion(),
3054 JalviewLite.getBuildDate()));
3055 jalview.bin.JalviewLite.addFrame(frame,
3056 MessageManager.getString("label.jalview"), 580, 220);
3060 public void showURL(String url, String target)
3062 if (viewport.applet == null)
3064 System.out.println("Not running as applet - no browser available.");
3068 viewport.applet.showURL(url, target);
3072 // ////////////////////////////////////////////////////////////////////////////////
3073 // JBuilder Graphics here
3075 MenuBar alignFrameMenuBar = new MenuBar();
3077 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3079 MenuItem loadApplication = new MenuItem(
3080 MessageManager.getString("label.view_full_application"));
3082 MenuItem loadTree = new MenuItem(
3083 MessageManager.getString("label.load_associated_tree"));
3085 MenuItem loadAnnotations = new MenuItem(
3086 MessageManager.getString("label.load_features_annotations"));
3088 MenuItem outputFeatures = new MenuItem(
3089 MessageManager.getString("label.export_features"));
3091 MenuItem outputAnnotations = new MenuItem(
3092 MessageManager.getString("label.export_annotations"));
3094 MenuItem closeMenuItem = new MenuItem(
3095 MessageManager.getString("action.close"));
3097 MenuItem selectAllSequenceMenuItem = new MenuItem(
3098 MessageManager.getString("action.select_all"));
3100 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3101 MessageManager.getString("action.deselect_all"));
3103 MenuItem invertSequenceMenuItem = new MenuItem(
3104 MessageManager.getString("action.invert_selection"));
3106 MenuItem remove2LeftMenuItem = new MenuItem();
3108 MenuItem remove2RightMenuItem = new MenuItem();
3110 MenuItem removeGappedColumnMenuItem = new MenuItem();
3112 MenuItem removeAllGapsMenuItem = new MenuItem();
3114 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3116 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3118 MenuItem sortPairwiseMenuItem = new MenuItem();
3120 MenuItem sortIDMenuItem = new MenuItem();
3122 MenuItem sortLengthMenuItem = new MenuItem();
3124 MenuItem sortGroupMenuItem = new MenuItem();
3126 MenuItem removeRedundancyMenuItem = new MenuItem();
3128 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3130 MenuItem PCAMenuItem = new MenuItem();
3132 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3134 MenuItem neighbourTreeMenuItem = new MenuItem();
3136 BorderLayout borderLayout1 = new BorderLayout();
3138 public Label statusBar = new Label();
3140 MenuItem clustalColour = new MenuItem();
3142 MenuItem zappoColour = new MenuItem();
3144 MenuItem taylorColour = new MenuItem();
3146 MenuItem hydrophobicityColour = new MenuItem();
3148 MenuItem helixColour = new MenuItem();
3150 MenuItem strandColour = new MenuItem();
3152 MenuItem turnColour = new MenuItem();
3154 MenuItem buriedColour = new MenuItem();
3156 MenuItem purinePyrimidineColour = new MenuItem();
3158 // MenuItem RNAInteractionColour = new MenuItem();
3160 MenuItem RNAHelixColour = new MenuItem();
3162 MenuItem userDefinedColour = new MenuItem();
3164 MenuItem PIDColour = new MenuItem();
3166 MenuItem BLOSUM62Colour = new MenuItem();
3168 MenuItem tcoffeeColour = new MenuItem();
3170 MenuItem njTreeBlosumMenuItem = new MenuItem();
3172 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3174 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3176 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3178 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3180 MenuItem alProperties = new MenuItem(
3181 MessageManager.getString("label.alignment_props"));
3183 MenuItem overviewMenuItem = new MenuItem();
3185 MenuItem undoMenuItem = new MenuItem();
3187 MenuItem redoMenuItem = new MenuItem();
3189 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3191 MenuItem noColourmenuItem = new MenuItem();
3193 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3195 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3197 MenuItem findMenuItem = new MenuItem();
3199 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3201 MenuItem nucleotideColour = new MenuItem();
3203 MenuItem deleteGroups = new MenuItem();
3205 MenuItem grpsFromSelection = new MenuItem();
3207 MenuItem createGroup = new MenuItem();
3209 MenuItem unGroup = new MenuItem();
3211 MenuItem delete = new MenuItem();
3213 MenuItem copy = new MenuItem();
3215 MenuItem cut = new MenuItem();
3217 Menu pasteMenu = new Menu();
3219 MenuItem pasteNew = new MenuItem();
3221 MenuItem pasteThis = new MenuItem();
3223 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3225 MenuItem font = new MenuItem();
3227 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3229 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3231 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3233 MenuItem modifyPID = new MenuItem();
3235 MenuItem modifyConservation = new MenuItem();
3237 CheckboxMenuItem autoCalculate = null;
3239 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3240 "Sort Alignment With New Tree", true);
3242 Menu sortByTreeMenu = new Menu();
3244 MenuItem inputText = new MenuItem();
3246 MenuItem documentation = new MenuItem();
3248 MenuItem about = new MenuItem();
3250 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3252 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3254 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3256 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3258 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3260 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3262 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3264 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3266 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3269 * Initialise menus and other items
3273 private void jbInit() throws Exception
3275 setMenuBar(alignFrameMenuBar);
3278 * Configure File menu items and actions
3281 .setLabel(MessageManager.getString("label.input_from_textbox"));
3282 inputText.addActionListener(this);
3283 Menu outputTextboxMenu = new Menu(
3284 MessageManager.getString("label.out_to_textbox"));
3285 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3287 MenuItem item = new MenuItem(ff);
3289 item.addActionListener(new java.awt.event.ActionListener()
3292 public void actionPerformed(ActionEvent e)
3294 outputText_actionPerformed(e);
3298 outputTextboxMenu.add(item);
3300 closeMenuItem.addActionListener(this);
3301 loadApplication.addActionListener(this);
3302 loadTree.addActionListener(this);
3303 loadAnnotations.addActionListener(this);
3304 outputFeatures.addActionListener(this);
3305 outputAnnotations.addActionListener(this);
3308 * Configure Edit menu items and actions
3310 undoMenuItem.setEnabled(false);
3311 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3312 undoMenuItem.addActionListener(this);
3313 redoMenuItem.setEnabled(false);
3314 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3315 redoMenuItem.addActionListener(this);
3316 copy.setLabel(MessageManager.getString("action.copy"));
3317 copy.addActionListener(this);
3318 cut.setLabel(MessageManager.getString("action.cut"));
3319 cut.addActionListener(this);
3320 delete.setLabel(MessageManager.getString("action.delete"));
3321 delete.addActionListener(this);
3322 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3323 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3324 pasteNew.addActionListener(this);
3325 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3326 pasteThis.addActionListener(this);
3328 .setLabel(MessageManager.getString("action.remove_left"));
3329 remove2LeftMenuItem.addActionListener(this);
3330 remove2RightMenuItem
3331 .setLabel(MessageManager.getString("action.remove_right"));
3332 remove2RightMenuItem.addActionListener(this);
3333 removeGappedColumnMenuItem.setLabel(
3334 MessageManager.getString("action.remove_empty_columns"));
3335 removeGappedColumnMenuItem.addActionListener(this);
3336 removeAllGapsMenuItem
3337 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3338 removeAllGapsMenuItem.addActionListener(this);
3339 removeRedundancyMenuItem
3340 .setLabel(MessageManager.getString("action.remove_redundancy"));
3341 removeRedundancyMenuItem.addActionListener(this);
3344 * Configure Select menu items and actions
3346 findMenuItem.setLabel(MessageManager.getString("action.find"));
3347 findMenuItem.addActionListener(this);
3348 selectAllSequenceMenuItem.addActionListener(this);
3349 deselectAllSequenceMenuItem.addActionListener(this);
3350 invertSequenceMenuItem.setLabel(
3351 MessageManager.getString("action.invert_sequence_selection"));
3352 invertSequenceMenuItem.addActionListener(this);
3353 invertColSel.setLabel(
3354 MessageManager.getString("action.invert_column_selection"));
3355 invertColSel.addActionListener(this);
3357 .setLabel(MessageManager.getString("action.undefine_groups"));
3358 deleteGroups.addActionListener(this);
3359 grpsFromSelection.setLabel(
3360 MessageManager.getString("action.make_groups_selection"));
3361 grpsFromSelection.addActionListener(this);
3362 createGroup.setLabel(MessageManager.getString("action.create_group"));
3363 createGroup.addActionListener(this);
3364 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3365 unGroup.addActionListener(this);
3367 annotationColumnSelection.setLabel(
3368 MessageManager.getString("action.select_by_annotation"));
3369 annotationColumnSelection.addActionListener(this);
3372 * Configure View menu items and actions
3374 newView.setLabel(MessageManager.getString("action.new_view"));
3375 newView.addActionListener(this);
3376 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3377 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3378 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3379 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3381 .setLabel(MessageManager.getString("label.selected_columns"));
3383 .setLabel(MessageManager.getString("label.selected_sequences"));
3384 hideAllButSelection.setLabel(
3385 MessageManager.getString("label.all_but_selected_region"));
3387 .setLabel(MessageManager.getString("label.selected_region"));
3388 showAllHidden.setLabel(
3389 MessageManager.getString("label.all_sequences_columns"));
3390 showColumns.addActionListener(this);
3391 showSeqs.addActionListener(this);
3392 hideColumns.addActionListener(this);
3393 hideSequences.addActionListener(this);
3394 hideAllButSelection.addActionListener(this);
3395 hideAllSelection.addActionListener(this);
3396 showAllHidden.addActionListener(this);
3398 .setLabel(MessageManager.getString("action.feature_settings"));
3399 featureSettings.addActionListener(this);
3400 sequenceFeatures.setLabel(
3401 MessageManager.getString("label.show_sequence_features"));
3402 sequenceFeatures.addItemListener(this);
3403 sequenceFeatures.setState(false);
3404 followMouseOverFlag.setLabel(
3405 MessageManager.getString("label.automatic_scrolling"));
3406 followMouseOverFlag.addItemListener(this);
3407 alProperties.addActionListener(this);
3409 .setLabel(MessageManager.getString("label.overview_window"));
3410 overviewMenuItem.addActionListener(this);
3413 * Configure Annotations menu items and actions
3415 annotationPanelMenuItem
3416 .setLabel(MessageManager.getString("label.show_annotations"));
3417 annotationPanelMenuItem.addItemListener(this);
3419 .setLabel(MessageManager.getString("label.group_consensus"));
3420 showGroupConservation
3421 .setLabel(MessageManager.getString("label.group_conservation"));
3422 showConsensusHistogram.setLabel(
3423 MessageManager.getString("label.show_consensus_histogram"));
3424 showSequenceLogo.setLabel(
3425 MessageManager.getString("label.show_consensus_logo"));
3426 normSequenceLogo.setLabel(
3427 MessageManager.getString("label.norm_consensus_logo"));
3428 applyAutoAnnotationSettings
3429 .setLabel(MessageManager.getString("label.apply_all_groups"));
3430 applyAutoAnnotationSettings.setState(true);
3431 Menu autoAnnMenu = new Menu(
3432 MessageManager.getString("label.autocalculated_annotation"));
3433 showGroupConsensus.addItemListener(this);
3434 showGroupConservation.addItemListener(this);
3435 showConsensusHistogram.addItemListener(this);
3436 showSequenceLogo.addItemListener(this);
3437 normSequenceLogo.addItemListener(this);
3438 applyAutoAnnotationSettings.addItemListener(this);
3439 showAlignmentAnnotations = new CheckboxMenuItem(
3440 MessageManager.getString("label.show_all_al_annotations"));
3441 showSequenceAnnotations = new CheckboxMenuItem(
3442 MessageManager.getString("label.show_all_seq_annotations"));
3443 sortAnnBySequence = new CheckboxMenuItem(
3444 MessageManager.getString("label.sort_annotations_by_sequence"));
3445 sortAnnByLabel = new CheckboxMenuItem(
3446 MessageManager.getString("label.sort_annotations_by_label"));
3447 showAutoFirst = new CheckboxMenuItem(
3448 MessageManager.getString("label.show_first"));
3449 showAutoFirst.setState(false); // pending applet parameter
3450 setShowAutoCalculatedAbove(showAutoFirst.getState());
3451 showAutoLast = new CheckboxMenuItem(
3452 MessageManager.getString("label.show_last"));
3453 showAutoLast.setState(!showAutoFirst.getState());
3454 showAlignmentAnnotations.addItemListener(this);
3455 showSequenceAnnotations.addItemListener(this);
3456 sortAnnBySequence.addItemListener(this);
3457 sortAnnByLabel.addItemListener(this);
3458 showAutoFirst.addItemListener(this);
3459 showAutoLast.addItemListener(this);
3462 * Configure Format menu items and actions
3464 font.setLabel(MessageManager.getString("action.font"));
3465 font.addActionListener(this);
3466 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3467 scaleAbove.setState(true);
3468 scaleAbove.setEnabled(false);
3469 scaleAbove.addItemListener(this);
3470 scaleLeft.setEnabled(false);
3471 scaleLeft.setState(true);
3472 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3473 scaleLeft.addItemListener(this);
3474 scaleRight.setEnabled(false);
3475 scaleRight.setState(true);
3476 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3477 scaleRight.addItemListener(this);
3478 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3479 viewBoxesMenuItem.setState(true);
3480 viewBoxesMenuItem.addItemListener(this);
3481 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3482 viewTextMenuItem.setState(true);
3483 viewTextMenuItem.addItemListener(this);
3485 .setLabel(MessageManager.getString("label.colour_text"));
3486 colourTextMenuItem.addItemListener(this);
3487 displayNonconservedMenuItem
3488 .setLabel(MessageManager.getString("label.show_non_conserved"));
3489 displayNonconservedMenuItem.addItemListener(this);
3490 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3491 wrapMenuItem.addItemListener(this);
3493 .setLabel(MessageManager.getString("action.show_gaps"));
3494 renderGapsMenuItem.setState(true);
3495 renderGapsMenuItem.addItemListener(this);
3496 centreColumnLabelFlag.setLabel(
3497 MessageManager.getString("label.centre_column_labels"));
3498 centreColumnLabelFlag.addItemListener(this);
3499 seqLimits.setState(true);
3501 MessageManager.getString("label.show_sequence_limits"));
3502 seqLimits.addItemListener(this);
3505 * Configure Colour menu items and actions
3507 applyToAllGroups.setLabel(
3508 MessageManager.getString("label.apply_colour_to_all_groups"));
3509 applyToAllGroups.setState(true);
3510 applyToAllGroups.addItemListener(this);
3511 clustalColour.setLabel(
3512 MessageManager.getString("label.colourScheme_clustal"));
3513 clustalColour.addActionListener(this);
3515 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3516 zappoColour.addActionListener(this);
3517 taylorColour.setLabel(
3518 MessageManager.getString("label.colourScheme_taylor"));
3519 taylorColour.addActionListener(this);
3520 hydrophobicityColour.setLabel(
3521 MessageManager.getString("label.colourScheme_hydrophobic"));
3522 hydrophobicityColour.addActionListener(this);
3523 helixColour.setLabel(
3524 MessageManager.getString("label.colourScheme_helixpropensity"));
3525 helixColour.addActionListener(this);
3526 strandColour.setLabel(MessageManager
3527 .getString("label.colourScheme_strandpropensity"));
3528 strandColour.addActionListener(this);
3529 turnColour.setLabel(
3530 MessageManager.getString("label.colourScheme_turnpropensity"));
3531 turnColour.addActionListener(this);
3532 buriedColour.setLabel(
3533 MessageManager.getString("label.colourScheme_buriedindex"));
3534 buriedColour.addActionListener(this);
3535 purinePyrimidineColour.setLabel(MessageManager
3536 .getString("label.colourScheme_purine/pyrimidine"));
3537 purinePyrimidineColour.addActionListener(this);
3538 // RNAInteractionColour.setLabel(MessageManager
3539 // .getString("label.rna_interaction"));
3540 // RNAInteractionColour.addActionListener(this);
3541 RNAHelixColour.setLabel(
3542 MessageManager.getString("label.colourScheme_rnahelices"));
3543 RNAHelixColour.addActionListener(this);
3545 .setLabel(MessageManager.getString("action.user_defined"));
3546 userDefinedColour.addActionListener(this);
3548 MessageManager.getString("label.colourScheme_%identity"));
3549 PIDColour.addActionListener(this);
3550 BLOSUM62Colour.setLabel(
3551 MessageManager.getString("label.colourScheme_blosum62"));
3552 BLOSUM62Colour.addActionListener(this);
3553 tcoffeeColour.setLabel(
3554 MessageManager.getString("label.colourScheme_t-coffeescores"));
3555 // it will be enabled only if a score file is provided
3556 tcoffeeColour.setEnabled(false);
3557 tcoffeeColour.addActionListener(this);
3558 conservationMenuItem
3559 .setLabel(MessageManager.getString("action.by_conservation"));
3560 conservationMenuItem.addItemListener(this);
3561 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3562 noColourmenuItem.addActionListener(this);
3563 abovePIDThreshold.setLabel(
3564 MessageManager.getString("label.above_identity_threshold"));
3565 abovePIDThreshold.addItemListener(this);
3566 nucleotideColour.setLabel(
3567 MessageManager.getString("label.colourScheme_nucleotide"));
3568 nucleotideColour.addActionListener(this);
3570 MessageManager.getString("label.modify_identity_threshold"));
3571 modifyPID.setEnabled(abovePIDThreshold.getState());
3572 modifyPID.addActionListener(this);
3573 modifyConservation.setLabel(MessageManager
3574 .getString("label.modify_conservation_threshold"));
3575 modifyConservation.setEnabled(conservationMenuItem.getState());
3576 modifyConservation.addActionListener(this);
3578 .setLabel(MessageManager.getString("action.by_annotation"));
3579 annotationColour.addActionListener(this);
3582 * Configure Calculate menu items and actions
3584 sortPairwiseMenuItem
3585 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3586 sortPairwiseMenuItem.addActionListener(this);
3587 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3588 sortIDMenuItem.addActionListener(this);
3590 .setLabel(MessageManager.getString("action.by_length"));
3591 sortLengthMenuItem.addActionListener(this);
3592 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3593 sortGroupMenuItem.addActionListener(this);
3594 pairwiseAlignmentMenuItem.setLabel(
3595 MessageManager.getString("action.pairwise_alignment"));
3596 pairwiseAlignmentMenuItem.addActionListener(this);
3597 PCAMenuItem.setLabel(
3598 MessageManager.getString("label.principal_component_analysis"));
3599 PCAMenuItem.addActionListener(this);
3600 autoCalculate = new CheckboxMenuItem(
3601 MessageManager.getString("label.autocalculate_consensus"),
3603 averageDistanceTreeMenuItem.setLabel(
3604 MessageManager.getString("label.average_distance_identity"));
3605 averageDistanceTreeMenuItem.addActionListener(this);
3606 neighbourTreeMenuItem.setLabel(
3607 MessageManager.getString("label.neighbour_joining_identity"));
3608 neighbourTreeMenuItem.addActionListener(this);
3609 avDistanceTreeBlosumMenuItem.setLabel(
3610 MessageManager.getString("label.average_distance_blosum62"));
3611 avDistanceTreeBlosumMenuItem.addActionListener(this);
3612 njTreeBlosumMenuItem
3613 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3614 njTreeBlosumMenuItem.addActionListener(this);
3616 .setLabel(MessageManager.getString("action.by_tree_order"));
3617 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3618 Menu calculateTreeMenu = new Menu(
3619 MessageManager.getString("action.calculate_tree"));
3620 autoCalculate.addItemListener(this);
3621 sortByTree.addItemListener(this);
3624 * Configure Help menu items and actions
3626 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3627 documentation.setLabel(MessageManager.getString("label.documentation"));
3628 documentation.addActionListener(this);
3629 about.setLabel(MessageManager.getString("label.about"));
3630 about.addActionListener(this);
3633 * Add top level menus to frame
3635 alignFrameMenuBar.add(fileMenu);
3636 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3637 alignFrameMenuBar.add(editMenu);
3638 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3639 alignFrameMenuBar.add(selectMenu);
3640 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3641 alignFrameMenuBar.add(viewMenu);
3642 Menu annotationsMenu = new Menu(
3643 MessageManager.getString("action.annotations"));
3644 alignFrameMenuBar.add(annotationsMenu);
3645 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3646 alignFrameMenuBar.add(formatMenu);
3647 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3648 alignFrameMenuBar.add(colourMenu);
3649 Menu calculateMenu = new Menu(
3650 MessageManager.getString("action.calculate"));
3651 alignFrameMenuBar.add(calculateMenu);
3652 alignFrameMenuBar.add(helpMenu);
3657 fileMenu.add(inputText);
3658 fileMenu.add(loadTree);
3659 fileMenu.add(loadAnnotations);
3660 fileMenu.addSeparator();
3661 fileMenu.add(outputTextboxMenu);
3662 fileMenu.add(outputFeatures);
3663 fileMenu.add(outputAnnotations);
3664 if (jalviewServletURL != null)
3666 fileMenu.add(loadApplication);
3668 fileMenu.addSeparator();
3669 fileMenu.add(closeMenuItem);
3674 editMenu.add(undoMenuItem);
3675 editMenu.add(redoMenuItem);
3678 pasteMenu.add(pasteNew);
3679 pasteMenu.add(pasteThis);
3680 editMenu.add(pasteMenu);
3681 editMenu.add(delete);
3682 editMenu.addSeparator();
3683 editMenu.add(remove2LeftMenuItem);
3684 editMenu.add(remove2RightMenuItem);
3685 editMenu.add(removeGappedColumnMenuItem);
3686 editMenu.add(removeAllGapsMenuItem);
3687 editMenu.add(removeRedundancyMenuItem);
3692 selectMenu.add(findMenuItem);
3693 selectMenu.addSeparator();
3694 selectMenu.add(selectAllSequenceMenuItem);
3695 selectMenu.add(deselectAllSequenceMenuItem);
3696 selectMenu.add(invertSequenceMenuItem);
3697 selectMenu.add(invertColSel);
3698 selectMenu.add(createGroup);
3699 selectMenu.add(unGroup);
3700 selectMenu.add(grpsFromSelection);
3701 selectMenu.add(deleteGroups);
3702 selectMenu.add(annotationColumnSelection);
3707 viewMenu.add(newView);
3708 viewMenu.addSeparator();
3709 showMenu.add(showColumns);
3710 showMenu.add(showSeqs);
3711 showMenu.add(showAllHidden);
3712 viewMenu.add(showMenu);
3713 hideMenu.add(hideColumns);
3714 hideMenu.add(hideSequences);
3715 hideMenu.add(hideAllSelection);
3716 hideMenu.add(hideAllButSelection);
3717 viewMenu.add(hideMenu);
3718 viewMenu.addSeparator();
3719 viewMenu.add(followMouseOverFlag);
3720 viewMenu.addSeparator();
3721 viewMenu.add(sequenceFeatures);
3722 viewMenu.add(featureSettings);
3723 viewMenu.addSeparator();
3724 viewMenu.add(alProperties);
3725 viewMenu.addSeparator();
3726 viewMenu.add(overviewMenuItem);
3731 annotationsMenu.add(annotationPanelMenuItem);
3732 annotationsMenu.addSeparator();
3733 annotationsMenu.add(showAlignmentAnnotations);
3734 annotationsMenu.add(showSequenceAnnotations);
3735 annotationsMenu.add(sortAnnBySequence);
3736 annotationsMenu.add(sortAnnByLabel);
3737 annotationsMenu.addSeparator();
3738 autoAnnMenu.add(showAutoFirst);
3739 autoAnnMenu.add(showAutoLast);
3740 autoAnnMenu.addSeparator();
3741 autoAnnMenu.add(applyAutoAnnotationSettings);
3742 autoAnnMenu.add(showConsensusHistogram);
3743 autoAnnMenu.add(showSequenceLogo);
3744 autoAnnMenu.add(normSequenceLogo);
3745 autoAnnMenu.addSeparator();
3746 autoAnnMenu.add(showGroupConservation);
3747 autoAnnMenu.add(showGroupConsensus);
3748 annotationsMenu.add(autoAnnMenu);
3753 formatMenu.add(font);
3754 formatMenu.add(seqLimits);
3755 formatMenu.add(wrapMenuItem);
3756 formatMenu.add(scaleAbove);
3757 formatMenu.add(scaleLeft);
3758 formatMenu.add(scaleRight);
3759 formatMenu.add(viewBoxesMenuItem);
3760 formatMenu.add(viewTextMenuItem);
3761 formatMenu.add(colourTextMenuItem);
3762 formatMenu.add(displayNonconservedMenuItem);
3763 formatMenu.add(renderGapsMenuItem);
3764 formatMenu.add(centreColumnLabelFlag);
3769 colourMenu.add(applyToAllGroups);
3770 colourMenu.addSeparator();
3771 colourMenu.add(noColourmenuItem);
3772 colourMenu.add(clustalColour);
3773 colourMenu.add(BLOSUM62Colour);
3774 colourMenu.add(PIDColour);
3775 colourMenu.add(zappoColour);
3776 colourMenu.add(taylorColour);
3777 colourMenu.add(hydrophobicityColour);
3778 colourMenu.add(helixColour);
3779 colourMenu.add(strandColour);
3780 colourMenu.add(turnColour);
3781 colourMenu.add(buriedColour);
3782 colourMenu.add(nucleotideColour);
3783 colourMenu.add(purinePyrimidineColour);
3784 // colourMenu.add(RNAInteractionColour);
3785 colourMenu.add(tcoffeeColour);
3786 colourMenu.add(userDefinedColour);
3787 colourMenu.addSeparator();
3788 colourMenu.add(conservationMenuItem);
3789 colourMenu.add(modifyConservation);
3790 colourMenu.add(abovePIDThreshold);
3791 colourMenu.add(modifyPID);
3792 colourMenu.add(annotationColour);
3793 colourMenu.add(RNAHelixColour);
3798 sortMenu.add(sortIDMenuItem);
3799 sortMenu.add(sortLengthMenuItem);
3800 sortMenu.add(sortByTreeMenu);
3801 sortMenu.add(sortGroupMenuItem);
3802 sortMenu.add(sortPairwiseMenuItem);
3803 calculateMenu.add(sortMenu);
3804 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3805 calculateTreeMenu.add(neighbourTreeMenuItem);
3806 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3807 calculateTreeMenu.add(njTreeBlosumMenuItem);
3808 calculateMenu.add(calculateTreeMenu);
3809 calculateMenu.addSeparator();
3810 calculateMenu.add(pairwiseAlignmentMenuItem);
3811 calculateMenu.add(PCAMenuItem);
3812 calculateMenu.add(autoCalculate);
3813 calculateMenu.add(sortByTree);
3818 helpMenu.add(documentation);
3819 helpMenu.add(about);
3824 statusBar.setBackground(Color.white);
3825 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3826 setStatus(MessageManager.getString("label.status_bar"));
3827 this.add(statusBar, BorderLayout.SOUTH);
3831 public void setStatus(String string)
3833 statusBar.setText(string);
3836 MenuItem featureSettings = new MenuItem();
3838 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3840 MenuItem annotationColour = new MenuItem();
3842 MenuItem annotationColumnSelection = new MenuItem();
3844 MenuItem invertColSel = new MenuItem();
3846 MenuItem showColumns = new MenuItem();
3848 MenuItem showSeqs = new MenuItem();
3850 MenuItem hideColumns = new MenuItem();
3852 MenuItem hideSequences = new MenuItem();
3854 MenuItem hideAllButSelection = new MenuItem();
3856 MenuItem hideAllSelection = new MenuItem();
3858 MenuItem showAllHidden = new MenuItem();
3860 MenuItem newView = new MenuItem();
3862 private CheckboxMenuItem showAlignmentAnnotations;
3864 private CheckboxMenuItem showSequenceAnnotations;
3866 private CheckboxMenuItem sortAnnBySequence;
3868 private CheckboxMenuItem sortAnnByLabel;
3870 private CheckboxMenuItem showAutoFirst;
3872 private CheckboxMenuItem showAutoLast;
3874 private SplitFrame splitFrame;
3877 * Attach the alignFrame panels after embedding menus, if necessary. This used
3878 * to be called setEmbedded, but is now creates the dropdown menus in a
3879 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3881 * @param reallyEmbedded
3882 * true to attach the view to the applet area on the page rather than
3885 public void createAlignFrameWindow(boolean reallyEmbedded)
3889 embedAlignFrameInApplet(viewport.applet);
3894 // test and embed menu bar if necessary.
3896 if (embedMenuIfNeeded(alignPanel))
3899 * adjust for status bar height too. ? pointless as overridden by layout
3902 alignPanel.setSize(getSize().width,
3903 getSize().height - statusBar.getHeight());
3905 add(statusBar, BorderLayout.SOUTH);
3906 add(alignPanel, BorderLayout.CENTER);
3907 // and register with the applet so it can pass external API calls to us
3908 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3914 * Add the components of this AlignFrame to the applet container.
3918 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3921 // Explicitly build the embedded menu panel for the on-page applet
3923 // view cannot be closed if its actually on the page
3924 fileMenu.remove(closeMenuItem);
3925 fileMenu.remove(3); // Remove Separator
3926 // construct embedded menu, using default font
3927 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3928 // and actually add the components to the applet area
3929 theApplet.setLayout(new BorderLayout());
3930 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3931 theApplet.add(statusBar, BorderLayout.SOUTH);
3932 // TODO should size be left to the layout manager?
3933 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3934 - embeddedMenu.getHeight() - statusBar.getHeight());
3935 theApplet.add(alignPanel, BorderLayout.CENTER);
3936 final AlignFrame me = this;
3937 theApplet.addFocusListener(new FocusListener()
3941 public void focusLost(FocusEvent e)
3943 if (theApplet.currentAlignFrame == me)
3945 theApplet.currentAlignFrame = null;
3950 public void focusGained(FocusEvent e)
3952 theApplet.currentAlignFrame = me;
3955 theApplet.validate();
3959 * create a new binding between structures in an existing jmol viewer instance
3960 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3961 * this does not open a new Jmol window, or modify the display of the
3962 * structures in the original jmol window. Note This method doesn't work
3963 * without an additional javascript library to exchange messages between the
3964 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3967 * JmolViewer instance
3968 * @param sequenceIds
3969 * - sequence Ids to search for associations
3971 public SequenceStructureBinding addStructureViewInstance(
3972 Object jmolviewer, String[] sequenceIds)
3974 Viewer viewer = null;
3977 viewer = (Viewer) jmolviewer;
3978 } catch (ClassCastException ex)
3981 "Unsupported viewer object :" + jmolviewer.getClass());
3985 System.err.println("Can't use this object as a structure viewer:"
3986 + jmolviewer.getClass());
3989 SequenceI[] seqs = null;
3990 if (sequenceIds == null || sequenceIds.length == 0)
3992 seqs = viewport.getAlignment().getSequencesArray();
3996 Vector sqi = new Vector();
3997 AlignmentI al = viewport.getAlignment();
3998 for (int sid = 0; sid < sequenceIds.length; sid++)
4000 SequenceI sq = al.findName(sequenceIds[sid]);
4008 seqs = new SequenceI[sqi.size()];
4009 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4011 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4019 AAStructureBindingModel jmv = null;
4020 // TODO: search for a jmv that involves viewer
4022 { // create a new viewer/jalview binding.
4023 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4030 * bind a pdb file to a sequence in the current view
4033 * - sequenceId within the dataset.
4034 * @param pdbEntryString
4035 * - the short name for the PDB file
4037 * - pdb file - either a URL or a valid PDB file.
4038 * @return true if binding was as success TODO: consider making an exception
4039 * structure for indicating when PDB parsing or sequenceId location
4042 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4045 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4046 boolean needtoadd = false;
4047 if (toaddpdb != null)
4049 Vector pdbe = toaddpdb.getAllPDBEntries();
4050 PDBEntry pdbentry = null;
4051 if (pdbe != null && pdbe.size() > 0)
4053 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4055 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4056 if (!pdbentry.getId().equals(pdbEntryString)
4057 && !pdbentry.getFile().equals(pdbFile))
4067 if (pdbentry == null)
4069 pdbentry = new PDBEntry();
4070 pdbentry.setId(pdbEntryString);
4071 pdbentry.setFile(pdbFile);
4072 needtoadd = true; // add this new entry to sequence.
4074 // resolve data source
4075 // TODO: this code should be a refactored to an io package
4076 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4078 if (protocol == null)
4084 pdbentry.setProperty("protocol", protocol);
4085 toaddpdb.addPDBId(pdbentry);
4086 alignPanel.getStructureSelectionManager()
4087 .registerPDBEntry(pdbentry);
4093 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4097 Vector sequences = new Vector();
4098 for (int i = 0; i < seqs.length; i++)
4100 if (seqs[i] != null)
4103 .addElement(new Object[]
4104 { seqs[i], (chains != null) ? chains[i] : null });
4107 seqs = new SequenceI[sequences.size()];
4108 chains = new String[sequences.size()];
4109 for (int i = 0, isize = sequences.size(); i < isize; i++)
4111 Object[] oj = (Object[]) sequences.elementAt(i);
4113 seqs[i] = (SequenceI) oj[0];
4114 chains[i] = (String) oj[1];
4117 return new Object[] { seqs, chains };
4121 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4122 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4124 // Scrub any null sequences from the array
4125 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4126 seqs = (SequenceI[]) sqch[0];
4127 chains = (String[]) sqch[1];
4128 if (seqs == null || seqs.length == 0)
4131 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4133 if (protocol == null)
4135 String sourceType = (String) pdb.getProperty("protocol");
4138 protocol = DataSourceType.valueOf(sourceType);
4139 } catch (IllegalArgumentException e)
4143 if (protocol == null)
4145 System.err.println("Couldn't work out protocol to open structure: "
4150 if (applet.useXtrnalSviewer)
4152 // register the association(s) and quit, don't create any windows.
4153 if (StructureSelectionManager.getStructureSelectionManager(applet)
4154 .setMapping(seqs, chains, pdb.getFile(), protocol,
4157 System.err.println("Failed to map " + pdb.getFile() + " ("
4158 + protocol + ") to any sequences");
4162 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4164 // can only do alignments with Jmol
4165 // find the last jmol window assigned to this alignment
4166 AppletJmol ajm = null, tajm;
4167 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4168 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4170 tajm = (AppletJmol) jmols.elementAt(i);
4171 if (tajm.ap.alignFrame == this)
4180 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4181 // try and add the pdb structure
4186 // otherwise, create a new window
4187 if (applet.jmolAvailable)
4189 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4190 applet.lastFrameX += 40;
4191 applet.lastFrameY += 40;
4195 new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4200 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4201 SequenceI[][] seqs, String[][] chains, String[] protocols)
4203 // TODO Auto-generated method stub
4204 System.err.println("Aligned Structure View: Not yet implemented.");
4208 * modify the current selection, providing the user has not made a selection
4212 * - sequences from this alignment
4214 * - columns to be selected on the alignment
4216 public void select(SequenceGroup sel, ColumnSelection csel,
4217 HiddenColumns hidden)
4219 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4222 public void scrollTo(int row, int column)
4224 alignPanel.seqPanel.scrollTo(row, column);
4227 public void scrollToRow(int row)
4229 alignPanel.seqPanel.scrollToRow(row);
4232 public void scrollToColumn(int column)
4234 alignPanel.seqPanel.scrollToColumn(column);
4238 * @return the alignments unique ID.
4240 public String getSequenceSetId()
4242 return viewport.getSequenceSetId();
4246 * Load the (T-Coffee) score file from the specified url
4249 * File/URL/T-COFFEE score file contents
4250 * @throws IOException
4251 * @return true if alignment was annotated with data from source
4253 public boolean loadScoreFile(String source) throws IOException
4256 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4257 AppletFormatAdapter.checkProtocol(source));
4258 if (!file.isValid())
4260 // TODO: raise dialog for gui
4261 System.err.println("Problems parsing T-Coffee scores: "
4262 + file.getWarningMessage());
4263 System.err.println("Origin was:\n" + source);
4268 * check that the score matrix matches the alignment dimensions
4271 if ((aln = viewport.getAlignment()) != null
4272 && (aln.getHeight() != file.getHeight()
4273 || aln.getWidth() != file.getWidth()))
4275 // TODO: raise a dialog box here rather than bomb out.
4277 "The scores matrix does not match the alignment dimensions");
4281 // TODO add parameter to indicate if matching should be done
4282 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4284 alignPanel.fontChanged();
4285 tcoffeeColour.setEnabled(true);
4286 // switch to this color
4287 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4292 System.err.println("Problems resolving T-Coffee scores:");
4293 if (file.getWarningMessage() != null)
4295 System.err.println(file.getWarningMessage());
4301 public SplitFrame getSplitFrame()
4303 return this.splitFrame;
4306 public void setSplitFrame(SplitFrame sf)
4308 this.splitFrame = sf;
4311 // may not need this
4313 public void setShowSeqFeatures(boolean b)
4315 // showSeqFeatures.setSelected(b);
4316 viewport.setShowSequenceFeatures(b);
4321 public void setMenusForViewport()
4323 // setMenusFromViewport(viewport);
4328 public void refreshFeatureUI(boolean enableIfNecessary)
4330 if (enableIfNecessary)
4332 sequenceFeatures.setState(true);
4333 alignPanel.av.setShowSequenceFeatures(true);
4338 public FeatureSettingsControllerI getFeatureSettingsUI()
4340 return alignPanel.av.featureSettings;
4344 public FeatureSettingsControllerI showFeatureSettingsUI()
4346 return new FeatureSettings(alignPanel);
4349 private Rectangle fs_bounds = null;
4352 public void setFeatureSettingsGeometry(Rectangle bounds)
4358 public Rectangle getFeatureSettingsGeometry()