2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.event.ActionEvent;
99 import java.awt.event.ActionListener;
100 import java.awt.event.FocusEvent;
101 import java.awt.event.FocusListener;
102 import java.awt.event.ItemEvent;
103 import java.awt.event.ItemListener;
104 import java.awt.event.KeyEvent;
105 import java.awt.event.KeyListener;
106 import java.awt.event.WindowAdapter;
107 import java.awt.event.WindowEvent;
108 import java.io.IOException;
110 import java.net.URLEncoder;
111 import java.util.Arrays;
112 import java.util.Deque;
113 import java.util.HashMap;
114 import java.util.List;
115 import java.util.Map;
116 import java.util.StringTokenizer;
117 import java.util.Vector;
119 import org.jmol.viewer.Viewer;
121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
122 ItemListener, KeyListener, AlignViewControllerGuiI
124 public AlignViewControllerI avc;
126 public AlignmentPanel alignPanel;
128 public AlignViewport viewport;
130 // width and height may be overridden by applet parameters
131 int frameWidth = 700;
133 int frameHeight = 500;
135 String jalviewServletURL;
138 * Flag for showing autocalculated consensus above or below other consensus
141 private boolean showAutoCalculatedAbove;
143 private SequenceAnnotationOrder annotationSortOrder;
146 * Constructor that creates the frame and adds it to the display.
153 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
156 this(al, applet, title, embedded, true);
160 * Constructor that optionally allows the frame to be displayed or only
167 * @param addToDisplay
169 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
170 boolean embedded, boolean addToDisplay)
172 this(al, null, null, applet, title, embedded, addToDisplay);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 HiddenColumns hidden, JalviewLite applet,
177 String title, boolean embedded)
179 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
183 HiddenColumns hidden, JalviewLite applet,
184 String title, boolean embedded, boolean addToDisplay)
188 jalviewServletURL = applet.getParameter("APPLICATION_URL");
194 } catch (Exception ex)
196 ex.printStackTrace();
198 // need to get window geometry before we calculate alignment layout
204 param = applet.getParameter("windowWidth");
207 int width = Integer.parseInt(param);
210 param = applet.getParameter("windowHeight");
213 int height = Integer.parseInt(param);
214 frameHeight = height;
216 } catch (Exception ex)
220 viewport = new AlignViewport(al, applet);
222 if (hiddenSeqs != null && hiddenSeqs.length > 0)
224 viewport.hideSequence(hiddenSeqs);
228 viewport.getAlignment().setHiddenColumns(hidden);
230 viewport.setScaleAboveWrapped(scaleAbove.getState());
232 alignPanel = new AlignmentPanel(this, viewport);
233 avc = new jalview.controller.AlignViewController(this, viewport,
235 viewport.updateConservation(alignPanel);
236 viewport.updateConsensus(alignPanel);
237 viewport.updateInformation(alignPanel);
239 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
240 followMouseOverFlag.setState(viewport.isFollowHighlight());
241 showGroupConsensus.setState(viewport.isShowGroupConsensus());
242 showGroupConservation.setState(viewport.isShowGroupConservation());
243 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
244 showSequenceLogo.setState(viewport.isShowSequenceLogo());
245 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
246 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
247 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
248 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
249 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
250 showAlignmentAnnotations.setState(true);
251 showSequenceAnnotations.setState(false);
253 seqLimits.setState(viewport.getShowJVSuffix());
257 String param = applet.getParameter("sortBy");
260 if (param.equalsIgnoreCase("Id"))
262 sortIDMenuItem_actionPerformed();
264 else if (param.equalsIgnoreCase("Pairwise Identity"))
266 sortPairwiseMenuItem_actionPerformed();
268 else if (param.equalsIgnoreCase("Length"))
270 sortLengthMenuItem_actionPerformed();
274 param = applet.getParameter("wrap");
277 if (param.equalsIgnoreCase("true"))
279 wrapMenuItem.setState(true);
280 wrapMenuItem_actionPerformed();
283 param = applet.getParameter("centrecolumnlabels");
286 centreColumnLabelFlag.setState(true);
287 centreColumnLabelFlag_stateChanged();
291 if (viewport.getAlignment().isNucleotide())
293 conservationMenuItem.setEnabled(false);
294 clustalColour.setEnabled(false);
295 BLOSUM62Colour.setEnabled(false);
296 zappoColour.setEnabled(false);
297 taylorColour.setEnabled(false);
298 hydrophobicityColour.setEnabled(false);
299 helixColour.setEnabled(false);
300 strandColour.setEnabled(false);
301 turnColour.setEnabled(false);
302 buriedColour.setEnabled(false);
303 viewport.updateStrucConsensus(alignPanel);
304 if (viewport.getAlignment().hasRNAStructure())
306 RNAHelixColour.setEnabled(true);
310 RNAHelixColour.setEnabled(false);
315 RNAHelixColour.setEnabled(false);
316 purinePyrimidineColour.setEnabled(false);
317 nucleotideColour.setEnabled(false);
319 // Some JVMS send keyevents to Top frame or lowest panel,
320 // Havent worked out why yet. So add to both this frame and seqCanvas for
322 this.addKeyListener(this);
323 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
324 alignPanel.idPanel.idCanvas.addKeyListener(this);
325 alignPanel.scalePanel.addKeyListener(this);
326 alignPanel.annotationPanel.addKeyListener(this);
327 alignPanel.annotationPanelHolder.addKeyListener(this);
328 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
329 alignPanel.alabels.addKeyListener(this);
331 setAnnotationsVisibility();
335 addToDisplay(embedded);
342 public void addToDisplay(boolean embedded)
344 createAlignFrameWindow(embedded);
346 alignPanel.adjustAnnotationHeight();
347 alignPanel.paintAlignment(true);
350 public AlignViewport getAlignViewport()
355 public SeqCanvas getSeqcanvas()
357 return alignPanel.seqPanel.seqCanvas;
361 * Load a features file onto the alignment
364 * file URL, content, or other resolvable path
366 * is protocol for accessing data referred to by file
369 public boolean parseFeaturesFile(String file, DataSourceType type)
371 return parseFeaturesFile(file, type, true);
375 * Load a features file onto the alignment
378 * file URL, content, or other resolvable path
380 * is protocol for accessing data referred to by file
381 * @param autoenabledisplay
382 * when true, display features flag will be automatically enabled if
383 * features are loaded
384 * @return true if data parsed as a features file
386 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
387 boolean autoenabledisplay)
389 boolean featuresFile = false;
392 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
393 .getFeatureRenderer().getFeatureColours();
394 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
395 "relaxedidmatch", false);
396 featuresFile = new FeaturesFile(file, sourceType).parse(
397 viewport.getAlignment(), colours, true, relaxedIdMatching);
398 } catch (Exception ex)
400 ex.printStackTrace();
405 if (autoenabledisplay)
407 viewport.setShowSequenceFeatures(true);
408 sequenceFeatures.setState(true);
410 if (alignPanel.seqPanel.seqCanvas.fr != null)
412 // update the min/max ranges where necessary
413 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
415 if (viewport.featureSettings != null)
417 viewport.featureSettings.refreshTable();
419 alignPanel.paintAlignment(true);
420 statusBar.setText(MessageManager
421 .getString("label.successfully_added_features_alignment"));
427 public void keyPressed(KeyEvent evt)
429 ViewportRanges ranges = viewport.getRanges();
431 if (viewport.cursorMode
432 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
433 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
434 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
435 && Character.isDigit(evt.getKeyChar()))
437 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
440 switch (evt.getKeyCode())
442 case 27: // escape key
443 deselectAllSequenceMenuItem_actionPerformed();
445 alignPanel.alabels.cancelDrag();
448 if (evt.isControlDown() || evt.isMetaDown())
450 cut_actionPerformed();
454 if (viewport.cursorMode && !evt.isControlDown())
456 alignPanel.seqPanel.setCursorColumn();
458 if (evt.isControlDown() || evt.isMetaDown())
460 copy_actionPerformed();
464 if (evt.isControlDown())
466 paste(evt.isShiftDown());
470 if (evt.isControlDown() || evt.isMetaDown())
472 selectAllSequenceMenuItem_actionPerformed();
475 case KeyEvent.VK_DOWN:
476 if (viewport.cursorMode)
478 alignPanel.seqPanel.moveCursor(0, 1);
482 moveSelectedSequences(false);
487 if (viewport.cursorMode)
489 alignPanel.seqPanel.moveCursor(0, -1);
493 moveSelectedSequences(true);
497 case KeyEvent.VK_LEFT:
498 if (evt.isAltDown() || !viewport.cursorMode)
500 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
504 alignPanel.seqPanel.moveCursor(-1, 0);
508 case KeyEvent.VK_RIGHT:
509 if (evt.isAltDown() || !viewport.cursorMode)
511 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
515 alignPanel.seqPanel.moveCursor(1, 0);
519 case KeyEvent.VK_SPACE:
520 if (viewport.cursorMode)
522 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
523 || evt.isShiftDown() || evt.isAltDown());
527 case KeyEvent.VK_DELETE:
528 case KeyEvent.VK_BACK_SPACE:
529 if (viewport.cursorMode)
531 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
532 || evt.isShiftDown() || evt.isAltDown());
536 cut_actionPerformed();
537 alignPanel.seqPanel.seqCanvas.repaint();
542 if (viewport.cursorMode)
544 alignPanel.seqPanel.setCursorRow();
548 if (viewport.cursorMode)
550 alignPanel.seqPanel.setCursorPosition();
554 case KeyEvent.VK_ENTER:
555 case KeyEvent.VK_COMMA:
556 if (viewport.cursorMode)
558 alignPanel.seqPanel.setCursorRowAndColumn();
563 if (viewport.cursorMode)
565 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
569 if (viewport.cursorMode)
571 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
576 viewport.cursorMode = !viewport.cursorMode;
577 statusBar.setText(MessageManager.formatMessage(
578 "label.keyboard_editing_mode",
579 new String[] { (viewport.cursorMode ? "on" : "off") }));
580 if (viewport.cursorMode)
582 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
583 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
588 if (evt.isControlDown())
590 findMenuItem_actionPerformed();
596 boolean toggleSeqs = !evt.isControlDown();
597 boolean toggleCols = !evt.isShiftDown();
598 toggleHiddenRegions(toggleSeqs, toggleCols);
602 case KeyEvent.VK_PAGE_UP:
603 if (viewport.getWrapAlignment())
605 ranges.scrollUp(true);
613 case KeyEvent.VK_PAGE_DOWN:
614 if (viewport.getWrapAlignment())
616 ranges.scrollUp(false);
625 if (evt.isControlDown())
627 undoMenuItem_actionPerformed();
632 if (evt.isControlDown())
634 redoMenuItem_actionPerformed();
639 if (evt.isControlDown())
646 if (evt.isControlDown())
648 trimAlignment(false);
653 if (evt.isControlDown())
655 if (evt.isShiftDown())
657 this.removeAllGapsMenuItem_actionPerformed();
661 removeGappedColumnMenuItem_actionPerformed();
666 if (evt.isControlDown())
670 invertColSel_actionPerformed();
674 invertSequenceMenuItem_actionPerformed();
680 if (evt.isControlDown())
682 if (evt.isShiftDown())
684 this.unGroup_actionPerformed();
688 this.createGroup_actionPerformed();
694 if (evt.isControlDown())
696 this.deleteGroups_actionPerformed();
701 if (evt.isControlDown())
708 alignPanel.paintAlignment(true);
712 * called by key handler and the hide all/show all menu items
717 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
719 boolean hide = false;
720 SequenceGroup sg = viewport.getSelectionGroup();
721 if (!toggleSeqs && !toggleCols)
723 // Hide everything by the current selection - this is a hack - we do the
724 // invert and then hide
725 // first check that there will be visible columns after the invert.
726 if (viewport.hasSelectedColumns()
727 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
730 // now invert the sequence set, if required - empty selection implies
731 // that no hiding is required.
734 invertSequenceMenuItem_actionPerformed();
735 sg = viewport.getSelectionGroup();
739 viewport.expandColSelection(sg, true);
740 // finally invert the column selection and get the new sequence
741 // selection and indicate it should be hidden.
742 invertColSel_actionPerformed();
749 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
752 viewport.hideAllSelectedSeqs();
754 else if (!(toggleCols && viewport.hasSelectedColumns()))
756 viewport.showAllHiddenSeqs();
762 if (viewport.hasSelectedColumns())
764 viewport.hideSelectedColumns();
767 viewport.setSelectionGroup(sg);
772 viewport.showAllHiddenColumns();
774 viewport.sendSelection();
779 public void keyReleased(KeyEvent evt)
784 public void keyTyped(KeyEvent evt)
789 public void itemStateChanged(ItemEvent evt)
791 final Object source = evt.getSource();
792 if (source == displayNonconservedMenuItem)
794 displayNonconservedMenuItem_actionPerformed();
796 else if (source == colourTextMenuItem)
798 colourTextMenuItem_actionPerformed();
800 else if (source == wrapMenuItem)
802 wrapMenuItem_actionPerformed();
804 else if (source == scaleAbove)
806 viewport.setScaleAboveWrapped(scaleAbove.getState());
808 else if (source == scaleLeft)
810 viewport.setScaleLeftWrapped(scaleLeft.getState());
812 else if (source == scaleRight)
814 viewport.setScaleRightWrapped(scaleRight.getState());
816 else if (source == seqLimits)
818 seqLimits_itemStateChanged();
820 else if (source == viewBoxesMenuItem)
822 viewport.setShowBoxes(viewBoxesMenuItem.getState());
824 else if (source == viewTextMenuItem)
826 viewport.setShowText(viewTextMenuItem.getState());
828 else if (source == renderGapsMenuItem)
830 viewport.setRenderGaps(renderGapsMenuItem.getState());
832 else if (source == annotationPanelMenuItem)
834 boolean showAnnotations = annotationPanelMenuItem.getState();
835 showAlignmentAnnotations.setEnabled(showAnnotations);
836 showSequenceAnnotations.setEnabled(showAnnotations);
837 viewport.setShowAnnotation(showAnnotations);
838 alignPanel.setAnnotationVisible(showAnnotations);
840 else if (source == sequenceFeatures)
842 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
843 alignPanel.seqPanel.seqCanvas.repaint();
845 else if (source == showAlignmentAnnotations)
847 setAnnotationsVisibility();
849 else if (source == showSequenceAnnotations)
851 setAnnotationsVisibility();
853 else if (source == sortAnnBySequence)
855 boolean newState = sortAnnBySequence.getState();
856 sortAnnByLabel.setState(false);
857 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
858 : SequenceAnnotationOrder.NONE);
859 setViewportAnnotationOrder();
861 else if (source == sortAnnByLabel)
863 boolean newState = sortAnnByLabel.getState();
864 sortAnnBySequence.setState(false);
865 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
866 : SequenceAnnotationOrder.NONE);
867 setViewportAnnotationOrder();
869 else if (source == showAutoFirst)
871 showAutoLast.setState(!showAutoFirst.getState());
872 setShowAutoCalculatedAbove(showAutoFirst.getState());
873 setViewportAnnotationOrder();
875 else if (source == showAutoLast)
877 showAutoFirst.setState(!showAutoLast.getState());
878 setShowAutoCalculatedAbove(showAutoFirst.getState());
879 setViewportAnnotationOrder();
881 else if (source == conservationMenuItem)
883 conservationMenuItem_actionPerformed();
885 else if (source == abovePIDThreshold)
887 abovePIDThreshold_actionPerformed();
889 else if (source == applyToAllGroups)
891 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
893 else if (source == autoCalculate)
895 viewport.autoCalculateConsensus = autoCalculate.getState();
897 else if (source == sortByTree)
899 viewport.sortByTree = sortByTree.getState();
901 else if (source == this.centreColumnLabelFlag)
903 centreColumnLabelFlag_stateChanged();
905 else if (source == this.followMouseOverFlag)
907 mouseOverFlag_stateChanged();
909 else if (source == showGroupConsensus)
911 showGroupConsensus_actionPerformed();
913 else if (source == showGroupConservation)
915 showGroupConservation_actionPerformed();
917 else if (source == showSequenceLogo)
919 showSequenceLogo_actionPerformed();
921 else if (source == normSequenceLogo)
923 normSequenceLogo_actionPerformed();
925 else if (source == showConsensusHistogram)
927 showConsensusHistogram_actionPerformed();
929 else if (source == applyAutoAnnotationSettings)
931 applyAutoAnnotationSettings_actionPerformed();
933 alignPanel.paintAlignment(true);
937 * Set the visibility state of sequence-related and/or alignment-related
938 * annotations depending on checkbox selections, and repaint.
942 private void setAnnotationsVisibility()
944 boolean showForAlignment = showAlignmentAnnotations.getState();
945 boolean showForSequences = showSequenceAnnotations.getState();
946 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
948 for (AlignmentAnnotation aa : alignPanel.getAlignment()
949 .getAlignmentAnnotation())
951 boolean visible = (aa.sequenceRef == null ? showForAlignment
953 aa.visible = visible;
956 alignPanel.validateAnnotationDimensions(true);
961 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
963 this.annotationSortOrder = order;
967 * Set flags on the viewport that control annotation ordering
969 private void setViewportAnnotationOrder()
971 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
973 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
976 private void setShowAutoCalculatedAbove(boolean showAbove)
978 this.showAutoCalculatedAbove = showAbove;
981 private void mouseOverFlag_stateChanged()
983 viewport.setFollowHighlight(followMouseOverFlag.getState());
984 // TODO: could kick the scrollTo mechanism to reset view for current
988 private void centreColumnLabelFlag_stateChanged()
990 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
991 this.alignPanel.annotationPanel.repaint();
995 public void actionPerformed(ActionEvent evt)
997 viewport.applet.currentAlignFrame = this;
999 Object source = evt.getSource();
1001 if (source == inputText)
1003 inputText_actionPerformed();
1005 else if (source == loadTree)
1007 loadTree_actionPerformed();
1009 else if (source == loadApplication)
1011 launchFullApplication();
1013 else if (source == loadAnnotations)
1017 else if (source == outputAnnotations)
1019 outputAnnotations(true);
1021 else if (source == outputFeatures)
1023 outputFeatures(true, "Jalview");
1025 else if (source == closeMenuItem)
1027 closeMenuItem_actionPerformed();
1029 else if (source == copy)
1031 copy_actionPerformed();
1033 else if (source == undoMenuItem)
1035 undoMenuItem_actionPerformed();
1037 else if (source == redoMenuItem)
1039 redoMenuItem_actionPerformed();
1041 else if (source == inputText)
1043 inputText_actionPerformed();
1045 else if (source == closeMenuItem)
1047 closeMenuItem_actionPerformed();
1049 else if (source == undoMenuItem)
1051 undoMenuItem_actionPerformed();
1053 else if (source == redoMenuItem)
1055 redoMenuItem_actionPerformed();
1057 else if (source == copy)
1059 copy_actionPerformed();
1061 else if (source == pasteNew)
1063 pasteNew_actionPerformed();
1065 else if (source == pasteThis)
1067 pasteThis_actionPerformed();
1069 else if (source == cut)
1071 cut_actionPerformed();
1073 else if (source == delete)
1075 delete_actionPerformed();
1077 else if (source == createGroup)
1079 createGroup_actionPerformed();
1081 else if (source == unGroup)
1083 unGroup_actionPerformed();
1085 else if (source == grpsFromSelection)
1087 makeGrpsFromSelection_actionPerformed();
1089 else if (source == deleteGroups)
1091 deleteGroups_actionPerformed();
1093 else if (source == selectAllSequenceMenuItem)
1095 selectAllSequenceMenuItem_actionPerformed();
1097 else if (source == deselectAllSequenceMenuItem)
1099 deselectAllSequenceMenuItem_actionPerformed();
1101 else if (source == invertSequenceMenuItem)
1103 invertSequenceMenuItem_actionPerformed();
1104 // uncomment to slave sequence selections in split frame
1105 // viewport.sendSelection();
1107 else if (source == invertColSel)
1109 viewport.invertColumnSelection();
1110 alignPanel.paintAlignment(true);
1111 viewport.sendSelection();
1113 else if (source == remove2LeftMenuItem)
1115 trimAlignment(true);
1117 else if (source == remove2RightMenuItem)
1119 trimAlignment(false);
1121 else if (source == removeGappedColumnMenuItem)
1123 removeGappedColumnMenuItem_actionPerformed();
1125 else if (source == removeAllGapsMenuItem)
1127 removeAllGapsMenuItem_actionPerformed();
1129 else if (source == findMenuItem)
1131 findMenuItem_actionPerformed();
1133 else if (source == font)
1135 new FontChooser(alignPanel);
1137 else if (source == newView)
1141 else if (source == showColumns)
1143 viewport.showAllHiddenColumns();
1144 alignPanel.paintAlignment(true);
1145 viewport.sendSelection();
1147 else if (source == showSeqs)
1149 viewport.showAllHiddenSeqs();
1150 alignPanel.paintAlignment(true);
1151 // uncomment if we want to slave sequence selections in split frame
1152 // viewport.sendSelection();
1154 else if (source == hideColumns)
1156 viewport.hideSelectedColumns();
1157 alignPanel.paintAlignment(true);
1158 viewport.sendSelection();
1160 else if (source == hideSequences
1161 && viewport.getSelectionGroup() != null)
1163 viewport.hideAllSelectedSeqs();
1164 alignPanel.paintAlignment(true);
1165 // uncomment if we want to slave sequence selections in split frame
1166 // viewport.sendSelection();
1168 else if (source == hideAllButSelection)
1170 toggleHiddenRegions(false, false);
1171 alignPanel.paintAlignment(true);
1172 viewport.sendSelection();
1174 else if (source == hideAllSelection)
1176 SequenceGroup sg = viewport.getSelectionGroup();
1177 viewport.expandColSelection(sg, false);
1178 viewport.hideAllSelectedSeqs();
1179 viewport.hideSelectedColumns();
1180 alignPanel.paintAlignment(true);
1181 viewport.sendSelection();
1183 else if (source == showAllHidden)
1185 viewport.showAllHiddenColumns();
1186 viewport.showAllHiddenSeqs();
1187 alignPanel.paintAlignment(true);
1188 viewport.sendSelection();
1190 else if (source == showGroupConsensus)
1192 showGroupConsensus_actionPerformed();
1194 else if (source == showGroupConservation)
1196 showGroupConservation_actionPerformed();
1198 else if (source == showSequenceLogo)
1200 showSequenceLogo_actionPerformed();
1202 else if (source == normSequenceLogo)
1204 normSequenceLogo_actionPerformed();
1206 else if (source == showConsensusHistogram)
1208 showConsensusHistogram_actionPerformed();
1210 else if (source == applyAutoAnnotationSettings)
1212 applyAutoAnnotationSettings_actionPerformed();
1214 else if (source == featureSettings)
1216 new FeatureSettings(alignPanel);
1218 else if (source == alProperties)
1220 StringBuffer contents = new jalview.io.AlignmentProperties(
1221 viewport.getAlignment()).formatAsString();
1222 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1223 cap.setText(contents.toString());
1224 Frame frame = new Frame();
1226 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1227 "label.alignment_properties", new String[] { getTitle() }),
1230 else if (source == overviewMenuItem)
1232 overviewMenuItem_actionPerformed();
1234 else if (source == noColourmenuItem)
1238 else if (source == clustalColour)
1240 abovePIDThreshold.setState(false);
1241 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1243 else if (source == zappoColour)
1245 changeColour(new ZappoColourScheme());
1247 else if (source == taylorColour)
1249 changeColour(new TaylorColourScheme());
1251 else if (source == hydrophobicityColour)
1253 changeColour(new HydrophobicColourScheme());
1255 else if (source == helixColour)
1257 changeColour(new HelixColourScheme());
1259 else if (source == strandColour)
1261 changeColour(new StrandColourScheme());
1263 else if (source == turnColour)
1265 changeColour(new TurnColourScheme());
1267 else if (source == buriedColour)
1269 changeColour(new BuriedColourScheme());
1271 else if (source == nucleotideColour)
1273 changeColour(new NucleotideColourScheme());
1275 else if (source == purinePyrimidineColour)
1277 changeColour(new PurinePyrimidineColourScheme());
1279 // else if (source == RNAInteractionColour)
1281 // changeColour(new RNAInteractionColourScheme());
1283 else if (source == RNAHelixColour)
1285 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1286 // new RNAHelicesColourChooser(viewport, alignPanel);
1288 else if (source == modifyPID)
1290 modifyPID_actionPerformed();
1292 else if (source == modifyConservation)
1294 modifyConservation_actionPerformed();
1296 else if (source == userDefinedColour)
1298 new UserDefinedColours(alignPanel, null);
1300 else if (source == PIDColour)
1302 changeColour(new PIDColourScheme());
1304 else if (source == BLOSUM62Colour)
1306 changeColour(new Blosum62ColourScheme());
1308 else if (source == tcoffeeColour)
1310 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1312 else if (source == annotationColour)
1314 new AnnotationColourChooser(viewport, alignPanel);
1316 else if (source == annotationColumnSelection)
1318 new AnnotationColumnChooser(viewport, alignPanel);
1320 else if (source == sortPairwiseMenuItem)
1322 sortPairwiseMenuItem_actionPerformed();
1324 else if (source == sortIDMenuItem)
1326 sortIDMenuItem_actionPerformed();
1328 else if (source == sortLengthMenuItem)
1330 sortLengthMenuItem_actionPerformed();
1332 else if (source == sortGroupMenuItem)
1334 sortGroupMenuItem_actionPerformed();
1336 else if (source == removeRedundancyMenuItem)
1338 removeRedundancyMenuItem_actionPerformed();
1340 else if (source == pairwiseAlignmentMenuItem)
1342 pairwiseAlignmentMenuItem_actionPerformed();
1344 else if (source == PCAMenuItem)
1346 PCAMenuItem_actionPerformed();
1348 else if (source == averageDistanceTreeMenuItem)
1350 averageDistanceTreeMenuItem_actionPerformed();
1352 else if (source == neighbourTreeMenuItem)
1354 neighbourTreeMenuItem_actionPerformed();
1356 else if (source == njTreeBlosumMenuItem)
1358 njTreeBlosumMenuItem_actionPerformed();
1360 else if (source == avDistanceTreeBlosumMenuItem)
1362 avTreeBlosumMenuItem_actionPerformed();
1364 else if (source == documentation)
1366 documentation_actionPerformed();
1368 else if (source == about)
1370 about_actionPerformed();
1375 public void inputText_actionPerformed()
1377 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378 Frame frame = new Frame();
1380 jalview.bin.JalviewLite.addFrame(frame,
1381 MessageManager.getString("label.input_cut_paste"), 500, 500);
1384 protected void outputText_actionPerformed(ActionEvent e)
1386 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1387 Frame frame = new Frame();
1389 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1390 "label.alignment_output_command",
1391 new Object[] { e.getActionCommand() }), 600, 500);
1393 FileFormatI fileFormat = FileFormats.getInstance().forName(
1394 e.getActionCommand());
1395 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1396 fileFormat, viewport.getAlignment(),
1397 viewport.getShowJVSuffix()));
1400 public void loadAnnotations()
1402 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1403 cap.setText(MessageManager
1404 .getString("label.paste_features_annotations_Tcoffee_here"));
1405 cap.setAnnotationImport();
1406 Frame frame = new Frame();
1408 jalview.bin.JalviewLite.addFrame(frame,
1409 MessageManager.getString("action.paste_annotations"), 400, 300);
1413 public String outputAnnotations(boolean displayTextbox)
1415 String annotation = new AnnotationFile()
1416 .printAnnotationsForView(viewport);
1420 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1421 Frame frame = new Frame();
1423 jalview.bin.JalviewLite.addFrame(frame,
1424 MessageManager.getString("label.annotations"), 600, 500);
1425 cap.setText(annotation);
1431 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1433 if (alignPanel.getFeatureRenderer() != null
1434 && viewport.getFeaturesDisplayed() != null)
1436 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1442 public String outputFeatures(boolean displayTextbox, String format)
1445 FeaturesFile formatter = new FeaturesFile();
1446 if (format.equalsIgnoreCase("Jalview"))
1448 features = formatter.printJalviewFormat(viewport.getAlignment()
1449 .getSequencesArray(), getDisplayedFeatureCols());
1453 features = formatter.printGffFormat(viewport.getAlignment()
1454 .getSequencesArray(), getDisplayedFeatureCols());
1459 boolean frimport = false;
1460 if (features == null || features.equals("No Features Visible"))
1462 features = "# No features visible - paste some and import them here.";
1466 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1469 cap.setAnnotationImport();
1471 Frame frame = new Frame();
1473 jalview.bin.JalviewLite.addFrame(frame,
1474 MessageManager.getString("label.features"), 600, 500);
1475 cap.setText(features);
1479 if (features == null)
1488 void launchFullApplication()
1490 StringBuffer url = new StringBuffer(jalviewServletURL);
1492 // allow servlet parameters to be passed in applet parameter
1493 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1495 url.append(firstSep);
1498 + appendProtocol(viewport.applet.getParameter("file")));
1500 if (viewport.applet.getParameter("features") != null)
1502 url.append("&features=");
1503 url.append(appendProtocol(viewport.applet.getParameter("features")));
1506 if (viewport.applet.getParameter("annotations") != null)
1508 url.append("&annotations=");
1509 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1512 if (viewport.applet.getParameter("jnetfile") != null
1513 || viewport.applet.getParameter("jpredfile") != null)
1515 url.append("&annotations=");
1516 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1517 .getParameter("jnetfile") : viewport.applet
1518 .getParameter("jpredfile")));
1521 if (viewport.applet.getParameter("defaultColour") != null)
1523 url.append("&colour="
1524 + removeWhiteSpace(viewport.applet
1525 .getParameter("defaultColour")));
1528 if (viewport.applet.getParameter("userDefinedColour") != null)
1530 url.append("&colour="
1531 + removeWhiteSpace(viewport.applet
1532 .getParameter("userDefinedColour")));
1534 if (viewport.applet.getParameter("tree") != null)
1537 + appendProtocol(viewport.applet.getParameter("tree")));
1539 if (viewport.applet.getParameter("treeFile") != null)
1542 + appendProtocol(viewport.applet.getParameter("treeFile")));
1545 showURL(url.toString(), "FULL_APP");
1548 String removeWhiteSpace(String colour)
1550 StringBuffer sb = new StringBuffer();
1551 for (int i = 0; i < colour.length(); i++)
1553 if (Character.isWhitespace(colour.charAt(i)))
1559 sb.append(colour.charAt(i));
1563 return sb.toString();
1566 String appendProtocol(String url)
1571 url = URLEncoder.encode(url);
1574 * When we finally deprecate 1.1 compatibility, we can start to use
1575 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1576 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1577 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1578 * ex.printStackTrace(); }
1580 catch (java.net.MalformedURLException ex)
1582 url = viewport.applet.getCodeBase() + url;
1587 public void closeMenuItem_actionPerformed()
1589 PaintRefresher.RemoveComponent(alignPanel);
1590 if (alignPanel.seqPanel != null
1591 && alignPanel.seqPanel.seqCanvas != null)
1593 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1595 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1597 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1600 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1615 void updateEditMenuBar()
1618 if (viewport.getHistoryList().size() > 0)
1620 undoMenuItem.setEnabled(true);
1621 CommandI command = viewport.getHistoryList().peek();
1622 undoMenuItem.setLabel(MessageManager.formatMessage(
1623 "label.undo_command",
1624 new Object[] { command.getDescription() }));
1628 undoMenuItem.setEnabled(false);
1629 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1632 if (viewport.getRedoList().size() > 0)
1634 redoMenuItem.setEnabled(true);
1636 CommandI command = viewport.getRedoList().peek();
1637 redoMenuItem.setLabel(MessageManager.formatMessage(
1638 "label.redo_command",
1639 new Object[] { command.getDescription() }));
1643 redoMenuItem.setEnabled(false);
1644 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1652 public void addHistoryItem(CommandI command)
1654 if (command.getSize() > 0)
1656 viewport.addToHistoryList(command);
1657 viewport.clearRedoList();
1658 updateEditMenuBar();
1659 viewport.updateHiddenColumns();
1664 * TODO: JAL-1104 DOCUMENT ME!
1669 protected void undoMenuItem_actionPerformed()
1671 if (viewport.getHistoryList().isEmpty())
1676 CommandI command = viewport.getHistoryList().pop();
1677 viewport.addToRedoList(command);
1678 command.undoCommand(null);
1680 AlignmentViewport originalSource = getOriginatingSource(command);
1682 if (originalSource != viewport)
1685 .println("Warning: Viewport object mismatch whilst undoing");
1687 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1688 // viewport.getColumnSelection().getHiddenColumns()
1690 updateEditMenuBar();
1691 originalSource.firePropertyChange("alignment", null, originalSource
1692 .getAlignment().getSequences());
1696 * TODO: JAL-1104 DOCUMENT ME!
1701 protected void redoMenuItem_actionPerformed()
1703 if (viewport.getRedoList().isEmpty())
1708 CommandI command = viewport.getRedoList().pop();
1709 viewport.addToHistoryList(command);
1710 command.doCommand(null);
1712 AlignmentViewport originalSource = getOriginatingSource(command);
1714 if (originalSource != viewport)
1717 .println("Warning: Viewport object mismatch whilst re-doing");
1719 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1720 // viewport.getColumnSelection().getHiddenColumns()
1723 updateEditMenuBar();
1724 originalSource.firePropertyChange("alignment", null, originalSource
1725 .getAlignment().getSequences());
1728 AlignmentViewport getOriginatingSource(CommandI command)
1730 AlignmentViewport originalSource = null;
1731 // For sequence removal and addition, we need to fire
1732 // the property change event FROM the viewport where the
1733 // original alignment was altered
1734 AlignmentI al = null;
1735 if (command instanceof EditCommand)
1737 EditCommand editCommand = (EditCommand) command;
1738 al = editCommand.getAlignment();
1739 Vector comps = (Vector) PaintRefresher.components.get(viewport
1740 .getSequenceSetId());
1741 for (int i = 0; i < comps.size(); i++)
1743 if (comps.elementAt(i) instanceof AlignmentPanel)
1745 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1747 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1754 if (originalSource == null)
1756 // The original view is closed, we must validate
1757 // the current view against the closed view first
1760 PaintRefresher.validateSequences(al, viewport.getAlignment());
1763 originalSource = viewport;
1766 return originalSource;
1770 * Move the currently selected sequences up or down one position in the
1775 public void moveSelectedSequences(boolean up)
1777 SequenceGroup sg = viewport.getSelectionGroup();
1782 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1783 up ? null : viewport.getHiddenRepSequences(), up);
1784 alignPanel.paintAlignment(true);
1787 * Also move cDNA/protein complement sequences
1789 AlignViewportI complement = viewport.getCodingComplement();
1790 if (complement != null)
1792 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1793 viewport, complement);
1794 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1795 up ? null : complement.getHiddenRepSequences(), up);
1796 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1800 synchronized void slideSequences(boolean right, int size)
1802 List<SequenceI> sg = new Vector<>();
1803 if (viewport.cursorMode)
1805 sg.add(viewport.getAlignment().getSequenceAt(
1806 alignPanel.seqPanel.seqCanvas.cursorY));
1808 else if (viewport.getSelectionGroup() != null
1809 && viewport.getSelectionGroup().getSize() != viewport
1810 .getAlignment().getHeight())
1812 sg = viewport.getSelectionGroup().getSequences(
1813 viewport.getHiddenRepSequences());
1821 Vector<SequenceI> invertGroup = new Vector();
1823 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1825 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1827 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1831 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1833 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1835 for (int i = 0; i < invertGroup.size(); i++)
1837 seqs2[i] = invertGroup.elementAt(i);
1840 SlideSequencesCommand ssc;
1843 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1844 size, viewport.getGapCharacter());
1848 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1849 size, viewport.getGapCharacter());
1852 int groupAdjustment = 0;
1853 if (ssc.getGapsInsertedBegin() && right)
1855 if (viewport.cursorMode)
1857 alignPanel.seqPanel.moveCursor(size, 0);
1861 groupAdjustment = size;
1864 else if (!ssc.getGapsInsertedBegin() && !right)
1866 if (viewport.cursorMode)
1868 alignPanel.seqPanel.moveCursor(-size, 0);
1872 groupAdjustment = -size;
1876 if (groupAdjustment != 0)
1878 viewport.getSelectionGroup().setStartRes(
1879 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1880 viewport.getSelectionGroup().setEndRes(
1881 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1884 boolean appendHistoryItem = false;
1885 Deque<CommandI> historyList = viewport.getHistoryList();
1886 if (historyList != null && historyList.size() > 0
1887 && historyList.peek() instanceof SlideSequencesCommand)
1889 appendHistoryItem = ssc
1890 .appendSlideCommand((SlideSequencesCommand) historyList
1894 if (!appendHistoryItem)
1896 addHistoryItem(ssc);
1902 static StringBuffer copiedSequences;
1904 static Vector copiedHiddenColumns;
1906 protected void copy_actionPerformed()
1908 if (viewport.getSelectionGroup() == null)
1913 SequenceGroup sg = viewport.getSelectionGroup();
1914 copiedSequences = new StringBuffer();
1915 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1916 for (int i = 0; i < sg.getSize(); i++)
1918 SequenceI seq = sg.getSequenceAt(i);
1919 int index = viewport.getAlignment().findIndex(seq);
1920 orderedSeqs.put(index, seq);
1923 int index = 0, startRes, endRes;
1926 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1928 copiedHiddenColumns = new Vector();
1929 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1930 for (int[] region : viewport.getAlignment().getHiddenColumns()
1931 .getHiddenRegions())
1933 copiedHiddenColumns.addElement(new int[] {
1934 region[0] - hiddenOffset, region[1] - hiddenOffset });
1939 copiedHiddenColumns = null;
1942 for (int i = 0; i < sg.getSize(); i++)
1944 SequenceI seq = null;
1948 if (orderedSeqs.containsKey(index))
1950 seq = orderedSeqs.get(index);
1961 // Returns residue following index if gap
1962 startRes = seq.findPosition(sg.getStartRes());
1965 // Need to find the residue preceeding index if gap
1968 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1970 ch = seq.getCharAt(j);
1971 if (!jalview.util.Comparison.isGap((ch)))
1979 endRes += seq.getStart() - 1;
1982 copiedSequences.append(seq.getName()
1988 + seq.getSequenceAsString(sg.getStartRes(),
1989 sg.getEndRes() + 1) + "\n");
1994 protected void pasteNew_actionPerformed()
1999 protected void pasteThis_actionPerformed()
2004 void paste(boolean newAlignment)
2009 if (copiedSequences == null)
2014 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2015 Vector seqs = new Vector();
2016 while (st.hasMoreElements())
2018 String name = st.nextToken();
2019 int start = Integer.parseInt(st.nextToken());
2020 int end = Integer.parseInt(st.nextToken());
2021 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2023 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2024 for (int i = 0; i < seqs.size(); i++)
2026 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2031 String newtitle = MessageManager
2032 .getString("label.copied_sequences");
2033 if (getTitle().startsWith(
2034 MessageManager.getString("label.copied_sequences")))
2036 newtitle = getTitle();
2040 newtitle = newtitle.concat(MessageManager.formatMessage(
2041 "label.from_msname", new String[] { getTitle() }));
2043 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2044 viewport.applet, newtitle, false);
2045 if (copiedHiddenColumns != null)
2047 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2049 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2050 af.viewport.hideColumns(region[0], region[1]);
2054 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2059 addSequences(newSeqs);
2062 } catch (Exception ex)
2064 } // could be anything being pasted in here
2068 void addSequences(SequenceI[] seqs)
2070 for (int i = 0; i < seqs.length; i++)
2072 viewport.getAlignment().addSequence(seqs[i]);
2076 addHistoryItem(new EditCommand(
2077 MessageManager.getString("label.add_sequences"), Action.PASTE,
2078 seqs, 0, viewport.getAlignment().getWidth(),
2079 viewport.getAlignment()));
2081 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2082 viewport.getAlignment().getWidth();
2083 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2088 protected void cut_actionPerformed()
2090 copy_actionPerformed();
2091 delete_actionPerformed();
2094 protected void delete_actionPerformed()
2097 SequenceGroup sg = viewport.getSelectionGroup();
2103 Vector seqs = new Vector();
2105 for (int i = 0; i < sg.getSize(); i++)
2107 seq = sg.getSequenceAt(i);
2108 seqs.addElement(seq);
2112 * If the cut affects all sequences, warn, remove highlighted columns
2114 if (sg.getSize() == viewport.getAlignment().getHeight())
2116 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2117 .getAlignment().getWidth()) ? true : false;
2118 if (isEntireAlignWidth)
2120 String title = MessageManager.getString("label.delete_all");
2121 Panel infoPanel = new Panel();
2122 infoPanel.setLayout(new FlowLayout());
2124 .add(new Label(MessageManager.getString("warn.delete_all")));
2126 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2127 dialog.setMainPanel(infoPanel);
2128 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2129 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2130 dialog.setVisible(true);
2137 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2138 sg.getEndRes() + 1);
2141 SequenceI[] cut = new SequenceI[seqs.size()];
2142 for (int i = 0; i < seqs.size(); i++)
2144 cut[i] = (SequenceI) seqs.elementAt(i);
2148 * //ADD HISTORY ITEM
2150 addHistoryItem(new EditCommand(
2151 MessageManager.getString("label.cut_sequences"), Action.CUT,
2152 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2153 viewport.getAlignment()));
2155 viewport.setSelectionGroup(null);
2156 viewport.getAlignment().deleteGroup(sg);
2158 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2161 if (viewport.getAlignment().getHeight() < 1)
2163 this.setVisible(false);
2165 viewport.sendSelection();
2169 * group consensus toggled
2172 protected void showGroupConsensus_actionPerformed()
2174 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2175 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180 * group conservation toggled.
2182 protected void showGroupConservation_actionPerformed()
2184 viewport.setShowGroupConservation(showGroupConservation.getState());
2185 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2193 * .event.ActionEvent)
2195 protected void showConsensusHistogram_actionPerformed()
2197 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2198 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2205 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2206 * .event.ActionEvent)
2208 protected void showSequenceLogo_actionPerformed()
2210 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2211 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2214 protected void normSequenceLogo_actionPerformed()
2216 showSequenceLogo.setState(true);
2217 viewport.setShowSequenceLogo(true);
2218 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2219 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2222 protected void applyAutoAnnotationSettings_actionPerformed()
2224 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2227 protected void makeGrpsFromSelection_actionPerformed()
2229 if (avc.makeGroupsFromSelection())
2231 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2232 alignPanel.updateAnnotation();
2233 alignPanel.paintAlignment(true);
2237 protected void createGroup_actionPerformed()
2242 protected void unGroup_actionPerformed()
2246 alignPanel.alignmentChanged();
2250 protected void deleteGroups_actionPerformed()
2252 if (avc.deleteGroups())
2254 alignPanel.alignmentChanged();
2258 public void selectAllSequenceMenuItem_actionPerformed()
2260 SequenceGroup sg = new SequenceGroup();
2261 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2263 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2265 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2266 viewport.setSelectionGroup(sg);
2267 // JAL-2034 - should delegate to
2268 // alignPanel to decide if overview needs
2270 alignPanel.paintAlignment(false);
2271 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2272 viewport.sendSelection();
2275 public void deselectAllSequenceMenuItem_actionPerformed()
2277 if (viewport.cursorMode)
2279 alignPanel.seqPanel.keyboardNo1 = null;
2280 alignPanel.seqPanel.keyboardNo2 = null;
2282 viewport.setSelectionGroup(null);
2283 viewport.getColumnSelection().clear();
2284 viewport.setSelectionGroup(null);
2285 alignPanel.idPanel.idCanvas.searchResults = null;
2286 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2287 // JAL-2034 - should delegate to
2288 // alignPanel to decide if overview needs
2290 alignPanel.paintAlignment(false);
2291 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2292 viewport.sendSelection();
2295 public void invertSequenceMenuItem_actionPerformed()
2297 SequenceGroup sg = viewport.getSelectionGroup();
2298 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2300 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2303 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2304 viewport.sendSelection();
2307 public void invertColSel_actionPerformed()
2309 viewport.invertColumnSelection();
2310 alignPanel.paintAlignment(true);
2311 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2312 viewport.sendSelection();
2315 void trimAlignment(boolean trimLeft)
2317 AlignmentI al = viewport.getAlignment();
2318 ViewportRanges ranges = viewport.getRanges();
2319 ColumnSelection colSel = viewport.getColumnSelection();
2322 if (!colSel.isEmpty())
2326 column = colSel.getMin();
2330 column = colSel.getMax();
2334 if (viewport.getSelectionGroup() != null)
2336 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2337 viewport.getHiddenRepSequences());
2341 seqs = al.getSequencesArray();
2344 TrimRegionCommand trimRegion;
2347 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2349 ranges.setStartRes(0);
2353 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2357 statusBar.setText(MessageManager.formatMessage(
2358 "label.removed_columns",
2359 new String[] { Integer.valueOf(trimRegion.getSize())
2361 addHistoryItem(trimRegion);
2363 for (SequenceGroup sg : al.getGroups())
2365 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2366 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2372 viewport.firePropertyChange("alignment", null, al.getSequences());
2376 public void removeGappedColumnMenuItem_actionPerformed()
2378 AlignmentI al = viewport.getAlignment();
2379 ViewportRanges ranges = viewport.getRanges();
2381 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2384 if (viewport.getSelectionGroup() != null)
2386 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2387 viewport.getHiddenRepSequences());
2388 start = viewport.getSelectionGroup().getStartRes();
2389 end = viewport.getSelectionGroup().getEndRes();
2393 seqs = viewport.getAlignment().getSequencesArray();
2396 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2397 "Remove Gapped Columns", seqs, start, end,
2398 viewport.getAlignment());
2400 addHistoryItem(removeGapCols);
2402 statusBar.setText(MessageManager.formatMessage(
2403 "label.removed_empty_columns",
2404 new String[] { Integer.valueOf(removeGapCols.getSize())
2407 // This is to maintain viewport position on first residue
2408 // of first sequence
2409 SequenceI seq = al.getSequenceAt(0);
2410 int startRes = seq.findPosition(ranges.getStartRes());
2411 // ShiftList shifts;
2412 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2413 // edit.alColumnChanges=shifts.getInverse();
2414 // if (viewport.hasHiddenColumns)
2415 // viewport.getColumnSelection().compensateForEdits(shifts);
2416 ranges.setStartRes(seq.findIndex(startRes) - 1);
2417 viewport.firePropertyChange("alignment", null, al.getSequences());
2421 public void removeAllGapsMenuItem_actionPerformed()
2423 AlignmentI al = viewport.getAlignment();
2424 ViewportRanges ranges = viewport.getRanges();
2426 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2429 if (viewport.getSelectionGroup() != null)
2431 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2432 viewport.getHiddenRepSequences());
2433 start = viewport.getSelectionGroup().getStartRes();
2434 end = viewport.getSelectionGroup().getEndRes();
2438 seqs = viewport.getAlignment().getSequencesArray();
2441 // This is to maintain viewport position on first residue
2442 // of first sequence
2443 SequenceI seq = al.getSequenceAt(0);
2444 int startRes = seq.findPosition(ranges.getStartRes());
2446 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2449 ranges.setStartRes(seq.findIndex(startRes) - 1);
2451 viewport.firePropertyChange("alignment", null, al.getSequences());
2455 public void findMenuItem_actionPerformed()
2457 new Finder(alignPanel);
2461 * create a new view derived from the current view
2464 * @return frame for the new view
2466 public AlignFrame newView(String viewtitle)
2469 if (viewport.hasHiddenRows())
2471 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2472 .getFullAlignment().getSequencesArray());
2476 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2479 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2481 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2483 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2485 newal.addAnnotation(viewport.getAlignment()
2486 .getAlignmentAnnotation()[i]);
2491 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2493 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2494 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2495 PaintRefresher.Register(newaf.alignPanel,
2496 newaf.alignPanel.av.getSequenceSetId());
2498 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2499 newaf.alignPanel.av.getSequenceSetId());
2500 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2501 newaf.alignPanel.av.getSequenceSetId());
2503 Vector comps = (Vector) PaintRefresher.components.get(viewport
2504 .getSequenceSetId());
2506 for (int i = 0; i < comps.size(); i++)
2508 if (comps.elementAt(i) instanceof AlignmentPanel)
2514 String title = new String(this.getTitle());
2515 if (viewtitle != null)
2517 title = viewtitle + " ( " + title + ")";
2521 if (title.indexOf("(View") > -1)
2523 title = title.substring(0, title.indexOf("(View"));
2525 title += "(View " + viewSize + ")";
2528 newaf.setTitle(title.toString());
2530 newaf.viewport.setHistoryList(viewport.getHistoryList());
2531 newaf.viewport.setRedoList(viewport.getRedoList());
2537 * @return list of feature groups on the view
2539 public String[] getFeatureGroups()
2541 FeatureRenderer fr = null;
2542 if (alignPanel != null
2543 && (fr = alignPanel.getFeatureRenderer()) != null)
2545 List<String> gps = fr.getFeatureGroups();
2546 String[] _gps = gps.toArray(new String[gps.size()]);
2553 * get sequence feature groups that are hidden or shown
2559 public String[] getFeatureGroupsOfState(boolean visible)
2561 FeatureRenderer fr = null;
2562 if (alignPanel != null
2563 && (fr = alignPanel.getFeatureRenderer()) != null)
2565 List<String> gps = fr.getGroups(visible);
2566 String[] _gps = gps.toArray(new String[gps.size()]);
2573 * Change the display state for the given feature groups
2576 * list of group strings
2578 * visible or invisible
2580 public void setFeatureGroupState(String[] groups, boolean state)
2582 FeatureRenderer fr = null;
2583 this.sequenceFeatures.setState(true);
2584 viewport.setShowSequenceFeatures(true);
2585 if (alignPanel != null
2586 && (fr = alignPanel.getFeatureRenderer()) != null)
2589 fr.setGroupVisibility(Arrays.asList(groups), state);
2590 alignPanel.seqPanel.seqCanvas.repaint();
2591 if (alignPanel.overviewPanel != null)
2593 alignPanel.overviewPanel.updateOverviewImage();
2598 public void seqLimits_itemStateChanged()
2600 viewport.setShowJVSuffix(seqLimits.getState());
2601 alignPanel.fontChanged();
2602 alignPanel.paintAlignment(true);
2605 protected void colourTextMenuItem_actionPerformed()
2607 viewport.setColourText(colourTextMenuItem.getState());
2608 alignPanel.paintAlignment(true);
2611 protected void displayNonconservedMenuItem_actionPerformed()
2613 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2614 alignPanel.paintAlignment(true);
2617 protected void wrapMenuItem_actionPerformed()
2619 viewport.setWrapAlignment(wrapMenuItem.getState());
2620 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2621 scaleAbove.setEnabled(wrapMenuItem.getState());
2622 scaleLeft.setEnabled(wrapMenuItem.getState());
2623 scaleRight.setEnabled(wrapMenuItem.getState());
2624 alignPanel.paintAlignment(true);
2627 public void overviewMenuItem_actionPerformed()
2629 if (alignPanel.overviewPanel != null)
2634 Frame frame = new Frame();
2635 OverviewPanel overview = new OverviewPanel(alignPanel);
2636 frame.add(overview);
2637 // +50 must allow for applet frame window
2638 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2639 "label.overview_params", new String[] { this.getTitle() }),
2640 overview.getPreferredSize().width,
2641 overview.getPreferredSize().height + 50);
2644 final AlignmentPanel ap = alignPanel;
2645 frame.addWindowListener(new WindowAdapter()
2648 public void windowClosing(WindowEvent e)
2652 ap.setOverviewPanel(null);
2657 alignPanel.setOverviewPanel(overview);
2662 public void changeColour(ColourSchemeI cs)
2664 viewport.setGlobalColourScheme(cs);
2666 alignPanel.paintAlignment(true);
2669 protected void modifyPID_actionPerformed()
2671 if (viewport.getAbovePIDThreshold()
2672 && viewport.getGlobalColourScheme() != null)
2674 SliderPanel.setPIDSliderSource(alignPanel,
2675 viewport.getResidueShading(), alignPanel.getViewName());
2676 SliderPanel.showPIDSlider();
2680 protected void modifyConservation_actionPerformed()
2682 if (viewport.getConservationSelected()
2683 && viewport.getGlobalColourScheme() != null)
2685 SliderPanel.setConservationSlider(alignPanel,
2686 viewport.getResidueShading(), alignPanel.getViewName());
2687 SliderPanel.showConservationSlider();
2691 protected void conservationMenuItem_actionPerformed()
2693 boolean selected = conservationMenuItem.getState();
2694 modifyConservation.setEnabled(selected);
2695 viewport.setConservationSelected(selected);
2696 viewport.getResidueShading().setConservationApplied(selected);
2698 changeColour(viewport.getGlobalColourScheme());
2702 modifyConservation_actionPerformed();
2706 SliderPanel.hideConservationSlider();
2710 public void abovePIDThreshold_actionPerformed()
2712 boolean selected = abovePIDThreshold.getState();
2713 modifyPID.setEnabled(selected);
2714 viewport.setAbovePIDThreshold(selected);
2717 viewport.getResidueShading().setThreshold(0,
2718 viewport.isIgnoreGapsConsensus());
2721 changeColour(viewport.getGlobalColourScheme());
2725 modifyPID_actionPerformed();
2729 SliderPanel.hidePIDSlider();
2733 public void sortPairwiseMenuItem_actionPerformed()
2735 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2736 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2737 .getAlignment().getSequenceAt(0));
2739 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2740 viewport.getAlignment()));
2741 alignPanel.paintAlignment(true);
2744 public void sortIDMenuItem_actionPerformed()
2746 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2747 AlignmentSorter.sortByID(viewport.getAlignment());
2748 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2749 viewport.getAlignment()));
2750 alignPanel.paintAlignment(true);
2753 public void sortLengthMenuItem_actionPerformed()
2755 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2756 AlignmentSorter.sortByLength(viewport.getAlignment());
2757 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2758 viewport.getAlignment()));
2759 alignPanel.paintAlignment(true);
2762 public void sortGroupMenuItem_actionPerformed()
2764 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2765 AlignmentSorter.sortByGroup(viewport.getAlignment());
2766 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2767 viewport.getAlignment()));
2768 alignPanel.paintAlignment(true);
2772 public void removeRedundancyMenuItem_actionPerformed()
2774 new RedundancyPanel(alignPanel);
2777 public void pairwiseAlignmentMenuItem_actionPerformed()
2779 if (viewport.getSelectionGroup() != null
2780 && viewport.getSelectionGroup().getSize() > 1)
2782 Frame frame = new Frame();
2783 frame.add(new PairwiseAlignPanel(alignPanel));
2784 jalview.bin.JalviewLite.addFrame(frame,
2785 MessageManager.getString("action.pairwise_alignment"), 600,
2790 public void PCAMenuItem_actionPerformed()
2792 // are the sequences aligned?
2793 if (!viewport.getAlignment().isAligned(false))
2796 int Width = viewport.getAlignment().getWidth();
2798 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2800 current = viewport.getAlignment().getSequenceAt(i);
2802 if (current.getLength() < Width)
2804 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2807 alignPanel.paintAlignment(true);
2810 if ((viewport.getSelectionGroup() != null
2811 && viewport.getSelectionGroup().getSize() < 4 && viewport
2812 .getSelectionGroup().getSize() > 0)
2813 || viewport.getAlignment().getHeight() < 4)
2820 new PCAPanel(viewport);
2821 } catch (java.lang.OutOfMemoryError ex)
2827 public void averageDistanceTreeMenuItem_actionPerformed()
2829 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2830 "Average distance tree using PID");
2833 public void neighbourTreeMenuItem_actionPerformed()
2835 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2836 "Neighbour joining tree using PID");
2839 protected void njTreeBlosumMenuItem_actionPerformed()
2841 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2842 .getBlosum62().getName(),
2843 "Neighbour joining tree using BLOSUM62");
2846 protected void avTreeBlosumMenuItem_actionPerformed()
2848 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2849 .getBlosum62().getName(),
2850 "Average distance tree using BLOSUM62");
2853 void newTreePanel(String type, String pwType, String title)
2855 // are the sequences aligned?
2856 if (!viewport.getAlignment().isAligned(false))
2859 int Width = viewport.getAlignment().getWidth();
2861 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2863 current = viewport.getAlignment().getSequenceAt(i);
2865 if (current.getLength() < Width)
2867 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2870 alignPanel.paintAlignment(true);
2874 if ((viewport.getSelectionGroup() != null && viewport
2875 .getSelectionGroup().getSize() > 1)
2876 || (viewport.getAlignment().getHeight() > 1))
2878 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2880 addTreeMenuItem(tp, title);
2882 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2886 void loadTree_actionPerformed()
2888 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2889 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2890 cap.setTreeImport();
2891 Frame frame = new Frame();
2893 jalview.bin.JalviewLite.addFrame(frame,
2894 MessageManager.getString("label.paste_newick_file"), 400, 300);
2897 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2899 TreePanel tp = new TreePanel(alignPanel, treeFile,
2900 MessageManager.getString("label.load_tree_from_file"), tree);
2901 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2902 addTreeMenuItem(tp, treeFile);
2906 * sort the alignment using the given treePanel
2909 * tree used to sort view
2911 * string used for undo event name
2913 public void sortByTree(TreePanel treePanel, String title)
2915 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2917 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2918 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2919 // HistoryItem.SORT));
2920 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2921 "label.order_by_params", new String[] { title }), oldOrder,
2922 viewport.getAlignment()));
2923 alignPanel.paintAlignment(true);
2927 * Do any automatic reordering of the alignment and add the necessary bits to
2928 * the menu structure for the new tree
2933 protected void addTreeMenuItem(final TreePanel treePanel,
2936 final MenuItem item = new MenuItem(title);
2937 sortByTreeMenu.add(item);
2938 item.addActionListener(new java.awt.event.ActionListener()
2941 public void actionPerformed(ActionEvent evt)
2943 sortByTree(treePanel, title); // treePanel.getTitle());
2947 treePanel.addWindowListener(new WindowAdapter()
2950 public void windowOpened(WindowEvent e)
2952 if (viewport.sortByTree)
2954 sortByTree(treePanel, title);
2956 super.windowOpened(e);
2960 public void windowClosing(WindowEvent e)
2962 sortByTreeMenu.remove(item);
2967 public boolean sortBy(AlignmentOrder alorder, String undoname)
2969 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2970 if (viewport.applet.debug)
2972 System.err.println("Sorting " + alorder.getOrder().size()
2973 + " in alignment '" + getTitle() + "'");
2975 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2976 if (undoname != null)
2978 addHistoryItem(new OrderCommand(undoname, oldOrder,
2979 viewport.getAlignment()));
2981 alignPanel.paintAlignment(true);
2985 protected void documentation_actionPerformed()
2987 alignPanel.av.applet.openJalviewHelpUrl();
2990 protected void about_actionPerformed()
2993 class AboutPanel extends Canvas
2999 public AboutPanel(String version, String builddate)
3001 this.version = version;
3002 this.builddate = builddate;
3006 public void paint(Graphics g)
3008 g.setColor(Color.white);
3009 g.fillRect(0, 0, getSize().width, getSize().height);
3010 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3011 FontMetrics fm = g.getFontMetrics();
3012 int fh = fm.getHeight();
3014 g.setColor(Color.black);
3015 // TODO: update this text for each release or centrally store it for
3016 // lite and application
3017 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3018 g.drawString(MessageManager.formatMessage(
3019 "label.jalviewLite_release", new String[] { version }), x,
3021 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3022 g.drawString(MessageManager.formatMessage(
3023 "label.jaview_build_date", new String[] { builddate }), x,
3025 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3026 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3028 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3029 x + 50, y += fh + 8);
3031 MessageManager.getString("label.jalview_dev_managers"), x,
3033 g.drawString(MessageManager
3034 .getString("label.jalview_distribution_lists"), x, y += fh);
3035 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3038 MessageManager.getString("label.jalview_cite_1_authors"),
3041 MessageManager.getString("label.jalview_cite_1_title"), x,
3043 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3048 Frame frame = new Frame();
3049 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3051 jalview.bin.JalviewLite.addFrame(frame,
3052 MessageManager.getString("label.jalview"), 580, 220);
3056 public void showURL(String url, String target)
3058 if (viewport.applet == null)
3060 System.out.println("Not running as applet - no browser available.");
3064 viewport.applet.showURL(url, target);
3068 // ////////////////////////////////////////////////////////////////////////////////
3069 // JBuilder Graphics here
3071 MenuBar alignFrameMenuBar = new MenuBar();
3073 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3075 MenuItem loadApplication = new MenuItem(
3076 MessageManager.getString("label.view_full_application"));
3078 MenuItem loadTree = new MenuItem(
3079 MessageManager.getString("label.load_associated_tree"));
3081 MenuItem loadAnnotations = new MenuItem(
3082 MessageManager.getString("label.load_features_annotations"));
3084 MenuItem outputFeatures = new MenuItem(
3085 MessageManager.getString("label.export_features"));
3087 MenuItem outputAnnotations = new MenuItem(
3088 MessageManager.getString("label.export_annotations"));
3090 MenuItem closeMenuItem = new MenuItem(
3091 MessageManager.getString("action.close"));
3093 MenuItem selectAllSequenceMenuItem = new MenuItem(
3094 MessageManager.getString("action.select_all"));
3096 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3097 MessageManager.getString("action.deselect_all"));
3099 MenuItem invertSequenceMenuItem = new MenuItem(
3100 MessageManager.getString("action.invert_selection"));
3102 MenuItem remove2LeftMenuItem = new MenuItem();
3104 MenuItem remove2RightMenuItem = new MenuItem();
3106 MenuItem removeGappedColumnMenuItem = new MenuItem();
3108 MenuItem removeAllGapsMenuItem = new MenuItem();
3110 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3112 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3114 MenuItem sortPairwiseMenuItem = new MenuItem();
3116 MenuItem sortIDMenuItem = new MenuItem();
3118 MenuItem sortLengthMenuItem = new MenuItem();
3120 MenuItem sortGroupMenuItem = new MenuItem();
3122 MenuItem removeRedundancyMenuItem = new MenuItem();
3124 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3126 MenuItem PCAMenuItem = new MenuItem();
3128 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3130 MenuItem neighbourTreeMenuItem = new MenuItem();
3132 BorderLayout borderLayout1 = new BorderLayout();
3134 public Label statusBar = new Label();
3136 MenuItem clustalColour = new MenuItem();
3138 MenuItem zappoColour = new MenuItem();
3140 MenuItem taylorColour = new MenuItem();
3142 MenuItem hydrophobicityColour = new MenuItem();
3144 MenuItem helixColour = new MenuItem();
3146 MenuItem strandColour = new MenuItem();
3148 MenuItem turnColour = new MenuItem();
3150 MenuItem buriedColour = new MenuItem();
3152 MenuItem purinePyrimidineColour = new MenuItem();
3154 // MenuItem RNAInteractionColour = new MenuItem();
3156 MenuItem RNAHelixColour = new MenuItem();
3158 MenuItem userDefinedColour = new MenuItem();
3160 MenuItem PIDColour = new MenuItem();
3162 MenuItem BLOSUM62Colour = new MenuItem();
3164 MenuItem tcoffeeColour = new MenuItem();
3166 MenuItem njTreeBlosumMenuItem = new MenuItem();
3168 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3170 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3172 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3174 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3176 MenuItem alProperties = new MenuItem(
3177 MessageManager.getString("label.alignment_props"));
3179 MenuItem overviewMenuItem = new MenuItem();
3181 MenuItem undoMenuItem = new MenuItem();
3183 MenuItem redoMenuItem = new MenuItem();
3185 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3187 MenuItem noColourmenuItem = new MenuItem();
3189 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3191 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3193 MenuItem findMenuItem = new MenuItem();
3195 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3197 MenuItem nucleotideColour = new MenuItem();
3199 MenuItem deleteGroups = new MenuItem();
3201 MenuItem grpsFromSelection = new MenuItem();
3203 MenuItem createGroup = new MenuItem();
3205 MenuItem unGroup = new MenuItem();
3207 MenuItem delete = new MenuItem();
3209 MenuItem copy = new MenuItem();
3211 MenuItem cut = new MenuItem();
3213 Menu pasteMenu = new Menu();
3215 MenuItem pasteNew = new MenuItem();
3217 MenuItem pasteThis = new MenuItem();
3219 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3221 MenuItem font = new MenuItem();
3223 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3225 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3227 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3229 MenuItem modifyPID = new MenuItem();
3231 MenuItem modifyConservation = new MenuItem();
3233 CheckboxMenuItem autoCalculate = null;
3235 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3236 "Sort Alignment With New Tree", true);
3238 Menu sortByTreeMenu = new Menu();
3240 MenuItem inputText = new MenuItem();
3242 MenuItem documentation = new MenuItem();
3244 MenuItem about = new MenuItem();
3246 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3248 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3250 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3252 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3254 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3256 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3258 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3260 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3262 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3265 * Initialise menus and other items
3269 private void jbInit() throws Exception
3271 setMenuBar(alignFrameMenuBar);
3274 * Configure File menu items and actions
3277 .setLabel(MessageManager.getString("label.input_from_textbox"));
3278 inputText.addActionListener(this);
3279 Menu outputTextboxMenu = new Menu(
3280 MessageManager.getString("label.out_to_textbox"));
3281 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3283 MenuItem item = new MenuItem(ff);
3285 item.addActionListener(new java.awt.event.ActionListener()
3288 public void actionPerformed(ActionEvent e)
3290 outputText_actionPerformed(e);
3294 outputTextboxMenu.add(item);
3296 closeMenuItem.addActionListener(this);
3297 loadApplication.addActionListener(this);
3298 loadTree.addActionListener(this);
3299 loadAnnotations.addActionListener(this);
3300 outputFeatures.addActionListener(this);
3301 outputAnnotations.addActionListener(this);
3304 * Configure Edit menu items and actions
3306 undoMenuItem.setEnabled(false);
3307 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3308 undoMenuItem.addActionListener(this);
3309 redoMenuItem.setEnabled(false);
3310 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3311 redoMenuItem.addActionListener(this);
3312 copy.setLabel(MessageManager.getString("action.copy"));
3313 copy.addActionListener(this);
3314 cut.setLabel(MessageManager.getString("action.cut"));
3315 cut.addActionListener(this);
3316 delete.setLabel(MessageManager.getString("action.delete"));
3317 delete.addActionListener(this);
3318 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3319 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3320 pasteNew.addActionListener(this);
3321 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3322 pasteThis.addActionListener(this);
3323 remove2LeftMenuItem.setLabel(MessageManager
3324 .getString("action.remove_left"));
3325 remove2LeftMenuItem.addActionListener(this);
3326 remove2RightMenuItem.setLabel(MessageManager
3327 .getString("action.remove_right"));
3328 remove2RightMenuItem.addActionListener(this);
3329 removeGappedColumnMenuItem.setLabel(MessageManager
3330 .getString("action.remove_empty_columns"));
3331 removeGappedColumnMenuItem.addActionListener(this);
3332 removeAllGapsMenuItem.setLabel(MessageManager
3333 .getString("action.remove_all_gaps"));
3334 removeAllGapsMenuItem.addActionListener(this);
3335 removeRedundancyMenuItem.setLabel(MessageManager
3336 .getString("action.remove_redundancy"));
3337 removeRedundancyMenuItem.addActionListener(this);
3340 * Configure Select menu items and actions
3342 findMenuItem.setLabel(MessageManager.getString("action.find"));
3343 findMenuItem.addActionListener(this);
3344 selectAllSequenceMenuItem.addActionListener(this);
3345 deselectAllSequenceMenuItem.addActionListener(this);
3346 invertSequenceMenuItem.setLabel(MessageManager
3347 .getString("action.invert_sequence_selection"));
3348 invertSequenceMenuItem.addActionListener(this);
3349 invertColSel.setLabel(MessageManager
3350 .getString("action.invert_column_selection"));
3351 invertColSel.addActionListener(this);
3352 deleteGroups.setLabel(MessageManager
3353 .getString("action.undefine_groups"));
3354 deleteGroups.addActionListener(this);
3355 grpsFromSelection.setLabel(MessageManager
3356 .getString("action.make_groups_selection"));
3357 grpsFromSelection.addActionListener(this);
3358 createGroup.setLabel(MessageManager.getString("action.create_group"));
3359 createGroup.addActionListener(this);
3360 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3361 unGroup.addActionListener(this);
3363 annotationColumnSelection.setLabel(MessageManager
3364 .getString("action.select_by_annotation"));
3365 annotationColumnSelection.addActionListener(this);
3368 * Configure View menu items and actions
3370 newView.setLabel(MessageManager.getString("action.new_view"));
3371 newView.addActionListener(this);
3372 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3373 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3374 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3375 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3377 .setLabel(MessageManager.getString("label.selected_columns"));
3378 hideSequences.setLabel(MessageManager
3379 .getString("label.selected_sequences"));
3380 hideAllButSelection.setLabel(MessageManager
3381 .getString("label.all_but_selected_region"));
3382 hideAllSelection.setLabel(MessageManager
3383 .getString("label.selected_region"));
3384 showAllHidden.setLabel(MessageManager
3385 .getString("label.all_sequences_columns"));
3386 showColumns.addActionListener(this);
3387 showSeqs.addActionListener(this);
3388 hideColumns.addActionListener(this);
3389 hideSequences.addActionListener(this);
3390 hideAllButSelection.addActionListener(this);
3391 hideAllSelection.addActionListener(this);
3392 showAllHidden.addActionListener(this);
3393 featureSettings.setLabel(MessageManager
3394 .getString("action.feature_settings"));
3395 featureSettings.addActionListener(this);
3396 sequenceFeatures.setLabel(MessageManager
3397 .getString("label.show_sequence_features"));
3398 sequenceFeatures.addItemListener(this);
3399 sequenceFeatures.setState(false);
3400 followMouseOverFlag.setLabel(MessageManager
3401 .getString("label.automatic_scrolling"));
3402 followMouseOverFlag.addItemListener(this);
3403 alProperties.addActionListener(this);
3404 overviewMenuItem.setLabel(MessageManager
3405 .getString("label.overview_window"));
3406 overviewMenuItem.addActionListener(this);
3409 * Configure Annotations menu items and actions
3411 annotationPanelMenuItem.setLabel(MessageManager
3412 .getString("label.show_annotations"));
3413 annotationPanelMenuItem.addItemListener(this);
3414 showGroupConsensus.setLabel(MessageManager
3415 .getString("label.group_consensus"));
3416 showGroupConservation.setLabel(MessageManager
3417 .getString("label.group_conservation"));
3418 showConsensusHistogram.setLabel(MessageManager
3419 .getString("label.show_consensus_histogram"));
3420 showSequenceLogo.setLabel(MessageManager
3421 .getString("label.show_consensus_logo"));
3422 normSequenceLogo.setLabel(MessageManager
3423 .getString("label.norm_consensus_logo"));
3424 applyAutoAnnotationSettings.setLabel(MessageManager
3425 .getString("label.apply_all_groups"));
3426 applyAutoAnnotationSettings.setState(true);
3427 Menu autoAnnMenu = new Menu(
3428 MessageManager.getString("label.autocalculated_annotation"));
3429 showGroupConsensus.addItemListener(this);
3430 showGroupConservation.addItemListener(this);
3431 showConsensusHistogram.addItemListener(this);
3432 showSequenceLogo.addItemListener(this);
3433 normSequenceLogo.addItemListener(this);
3434 applyAutoAnnotationSettings.addItemListener(this);
3435 showAlignmentAnnotations = new CheckboxMenuItem(
3436 MessageManager.getString("label.show_all_al_annotations"));
3437 showSequenceAnnotations = new CheckboxMenuItem(
3438 MessageManager.getString("label.show_all_seq_annotations"));
3439 sortAnnBySequence = new CheckboxMenuItem(
3440 MessageManager.getString("label.sort_annotations_by_sequence"));
3441 sortAnnByLabel = new CheckboxMenuItem(
3442 MessageManager.getString("label.sort_annotations_by_label"));
3443 showAutoFirst = new CheckboxMenuItem(
3444 MessageManager.getString("label.show_first"));
3445 showAutoFirst.setState(false); // pending applet parameter
3446 setShowAutoCalculatedAbove(showAutoFirst.getState());
3447 showAutoLast = new CheckboxMenuItem(
3448 MessageManager.getString("label.show_last"));
3449 showAutoLast.setState(!showAutoFirst.getState());
3450 showAlignmentAnnotations.addItemListener(this);
3451 showSequenceAnnotations.addItemListener(this);
3452 sortAnnBySequence.addItemListener(this);
3453 sortAnnByLabel.addItemListener(this);
3454 showAutoFirst.addItemListener(this);
3455 showAutoLast.addItemListener(this);
3458 * Configure Format menu items and actions
3460 font.setLabel(MessageManager.getString("action.font"));
3461 font.addActionListener(this);
3462 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3463 scaleAbove.setState(true);
3464 scaleAbove.setEnabled(false);
3465 scaleAbove.addItemListener(this);
3466 scaleLeft.setEnabled(false);
3467 scaleLeft.setState(true);
3468 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3469 scaleLeft.addItemListener(this);
3470 scaleRight.setEnabled(false);
3471 scaleRight.setState(true);
3472 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3473 scaleRight.addItemListener(this);
3474 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3475 viewBoxesMenuItem.setState(true);
3476 viewBoxesMenuItem.addItemListener(this);
3477 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3478 viewTextMenuItem.setState(true);
3479 viewTextMenuItem.addItemListener(this);
3480 colourTextMenuItem.setLabel(MessageManager
3481 .getString("label.colour_text"));
3482 colourTextMenuItem.addItemListener(this);
3483 displayNonconservedMenuItem.setLabel(MessageManager
3484 .getString("label.show_non_conserved"));
3485 displayNonconservedMenuItem.addItemListener(this);
3486 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3487 wrapMenuItem.addItemListener(this);
3488 renderGapsMenuItem.setLabel(MessageManager
3489 .getString("action.show_gaps"));
3490 renderGapsMenuItem.setState(true);
3491 renderGapsMenuItem.addItemListener(this);
3492 centreColumnLabelFlag.setLabel(MessageManager
3493 .getString("label.centre_column_labels"));
3494 centreColumnLabelFlag.addItemListener(this);
3495 seqLimits.setState(true);
3496 seqLimits.setLabel(MessageManager
3497 .getString("label.show_sequence_limits"));
3498 seqLimits.addItemListener(this);
3501 * Configure Colour menu items and actions
3503 applyToAllGroups.setLabel(MessageManager
3504 .getString("label.apply_colour_to_all_groups"));
3505 applyToAllGroups.setState(true);
3506 applyToAllGroups.addItemListener(this);
3507 clustalColour.setLabel(MessageManager
3508 .getString("label.colourScheme_clustal"));
3509 clustalColour.addActionListener(this);
3510 zappoColour.setLabel(MessageManager
3511 .getString("label.colourScheme_zappo"));
3512 zappoColour.addActionListener(this);
3513 taylorColour.setLabel(MessageManager
3514 .getString("label.colourScheme_taylor"));
3515 taylorColour.addActionListener(this);
3516 hydrophobicityColour.setLabel(MessageManager
3517 .getString("label.colourScheme_hydrophobic"));
3518 hydrophobicityColour.addActionListener(this);
3519 helixColour.setLabel(MessageManager
3520 .getString("label.colourScheme_helix_propensity"));
3521 helixColour.addActionListener(this);
3522 strandColour.setLabel(MessageManager
3523 .getString("label.colourScheme_strand_propensity"));
3524 strandColour.addActionListener(this);
3525 turnColour.setLabel(MessageManager
3526 .getString("label.colourScheme_turn_propensity"));
3527 turnColour.addActionListener(this);
3528 buriedColour.setLabel(MessageManager
3529 .getString("label.colourScheme_buried_index"));
3530 buriedColour.addActionListener(this);
3531 purinePyrimidineColour.setLabel(MessageManager
3532 .getString("label.colourScheme_purine/pyrimidine"));
3533 purinePyrimidineColour.addActionListener(this);
3534 // RNAInteractionColour.setLabel(MessageManager
3535 // .getString("label.rna_interaction"));
3536 // RNAInteractionColour.addActionListener(this);
3537 RNAHelixColour.setLabel(MessageManager
3538 .getString("label.colourScheme_rna_helices"));
3539 RNAHelixColour.addActionListener(this);
3540 userDefinedColour.setLabel(MessageManager
3541 .getString("action.user_defined"));
3542 userDefinedColour.addActionListener(this);
3543 PIDColour.setLabel(MessageManager
3544 .getString("label.colourScheme_%_identity"));
3545 PIDColour.addActionListener(this);
3546 BLOSUM62Colour.setLabel(MessageManager
3547 .getString("label.colourScheme_blosum62"));
3548 BLOSUM62Colour.addActionListener(this);
3549 tcoffeeColour.setLabel(MessageManager
3550 .getString("label.colourScheme_t-coffee_scores"));
3551 // it will be enabled only if a score file is provided
3552 tcoffeeColour.setEnabled(false);
3553 tcoffeeColour.addActionListener(this);
3554 conservationMenuItem.setLabel(MessageManager
3555 .getString("action.by_conservation"));
3556 conservationMenuItem.addItemListener(this);
3557 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3558 noColourmenuItem.addActionListener(this);
3559 abovePIDThreshold.setLabel(MessageManager
3560 .getString("label.above_identity_threshold"));
3561 abovePIDThreshold.addItemListener(this);
3562 nucleotideColour.setLabel(MessageManager
3563 .getString("label.colourScheme_nucleotide"));
3564 nucleotideColour.addActionListener(this);
3565 modifyPID.setLabel(MessageManager
3566 .getString("label.modify_identity_threshold"));
3567 modifyPID.setEnabled(abovePIDThreshold.getState());
3568 modifyPID.addActionListener(this);
3569 modifyConservation.setLabel(MessageManager
3570 .getString("label.modify_conservation_threshold"));
3571 modifyConservation.setEnabled(conservationMenuItem.getState());
3572 modifyConservation.addActionListener(this);
3573 annotationColour.setLabel(MessageManager
3574 .getString("action.by_annotation"));
3575 annotationColour.addActionListener(this);
3578 * Configure Calculate menu items and actions
3580 sortPairwiseMenuItem.setLabel(MessageManager
3581 .getString("action.by_pairwise_id"));
3582 sortPairwiseMenuItem.addActionListener(this);
3583 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3584 sortIDMenuItem.addActionListener(this);
3585 sortLengthMenuItem.setLabel(MessageManager
3586 .getString("action.by_length"));
3587 sortLengthMenuItem.addActionListener(this);
3588 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3589 sortGroupMenuItem.addActionListener(this);
3590 pairwiseAlignmentMenuItem.setLabel(MessageManager
3591 .getString("action.pairwise_alignment"));
3592 pairwiseAlignmentMenuItem.addActionListener(this);
3593 PCAMenuItem.setLabel(MessageManager
3594 .getString("label.principal_component_analysis"));
3595 PCAMenuItem.addActionListener(this);
3596 autoCalculate = new CheckboxMenuItem(
3597 MessageManager.getString("label.autocalculate_consensus"), true);
3598 averageDistanceTreeMenuItem.setLabel(MessageManager
3599 .getString("label.average_distance_identity"));
3600 averageDistanceTreeMenuItem.addActionListener(this);
3601 neighbourTreeMenuItem.setLabel(MessageManager
3602 .getString("label.neighbour_joining_identity"));
3603 neighbourTreeMenuItem.addActionListener(this);
3604 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3605 .getString("label.average_distance_blosum62"));
3606 avDistanceTreeBlosumMenuItem.addActionListener(this);
3607 njTreeBlosumMenuItem.setLabel(MessageManager
3608 .getString("label.neighbour_blosum62"));
3609 njTreeBlosumMenuItem.addActionListener(this);
3610 sortByTreeMenu.setLabel(MessageManager
3611 .getString("action.by_tree_order"));
3612 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3613 Menu calculateTreeMenu = new Menu(
3614 MessageManager.getString("action.calculate_tree"));
3615 autoCalculate.addItemListener(this);
3616 sortByTree.addItemListener(this);
3619 * Configure Help menu items and actions
3621 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3622 documentation.setLabel(MessageManager.getString("label.documentation"));
3623 documentation.addActionListener(this);
3624 about.setLabel(MessageManager.getString("label.about"));
3625 about.addActionListener(this);
3628 * Add top level menus to frame
3630 alignFrameMenuBar.add(fileMenu);
3631 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3632 alignFrameMenuBar.add(editMenu);
3633 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3634 alignFrameMenuBar.add(selectMenu);
3635 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3636 alignFrameMenuBar.add(viewMenu);
3637 Menu annotationsMenu = new Menu(
3638 MessageManager.getString("action.annotations"));
3639 alignFrameMenuBar.add(annotationsMenu);
3640 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3641 alignFrameMenuBar.add(formatMenu);
3642 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3643 alignFrameMenuBar.add(colourMenu);
3644 Menu calculateMenu = new Menu(
3645 MessageManager.getString("action.calculate"));
3646 alignFrameMenuBar.add(calculateMenu);
3647 alignFrameMenuBar.add(helpMenu);
3652 fileMenu.add(inputText);
3653 fileMenu.add(loadTree);
3654 fileMenu.add(loadAnnotations);
3655 fileMenu.addSeparator();
3656 fileMenu.add(outputTextboxMenu);
3657 fileMenu.add(outputFeatures);
3658 fileMenu.add(outputAnnotations);
3659 if (jalviewServletURL != null)
3661 fileMenu.add(loadApplication);
3663 fileMenu.addSeparator();
3664 fileMenu.add(closeMenuItem);
3669 editMenu.add(undoMenuItem);
3670 editMenu.add(redoMenuItem);
3673 pasteMenu.add(pasteNew);
3674 pasteMenu.add(pasteThis);
3675 editMenu.add(pasteMenu);
3676 editMenu.add(delete);
3677 editMenu.addSeparator();
3678 editMenu.add(remove2LeftMenuItem);
3679 editMenu.add(remove2RightMenuItem);
3680 editMenu.add(removeGappedColumnMenuItem);
3681 editMenu.add(removeAllGapsMenuItem);
3682 editMenu.add(removeRedundancyMenuItem);
3687 selectMenu.add(findMenuItem);
3688 selectMenu.addSeparator();
3689 selectMenu.add(selectAllSequenceMenuItem);
3690 selectMenu.add(deselectAllSequenceMenuItem);
3691 selectMenu.add(invertSequenceMenuItem);
3692 selectMenu.add(invertColSel);
3693 selectMenu.add(createGroup);
3694 selectMenu.add(unGroup);
3695 selectMenu.add(grpsFromSelection);
3696 selectMenu.add(deleteGroups);
3697 selectMenu.add(annotationColumnSelection);
3702 viewMenu.add(newView);
3703 viewMenu.addSeparator();
3704 showMenu.add(showColumns);
3705 showMenu.add(showSeqs);
3706 showMenu.add(showAllHidden);
3707 viewMenu.add(showMenu);
3708 hideMenu.add(hideColumns);
3709 hideMenu.add(hideSequences);
3710 hideMenu.add(hideAllSelection);
3711 hideMenu.add(hideAllButSelection);
3712 viewMenu.add(hideMenu);
3713 viewMenu.addSeparator();
3714 viewMenu.add(followMouseOverFlag);
3715 viewMenu.addSeparator();
3716 viewMenu.add(sequenceFeatures);
3717 viewMenu.add(featureSettings);
3718 viewMenu.addSeparator();
3719 viewMenu.add(alProperties);
3720 viewMenu.addSeparator();
3721 viewMenu.add(overviewMenuItem);
3726 annotationsMenu.add(annotationPanelMenuItem);
3727 annotationsMenu.addSeparator();
3728 annotationsMenu.add(showAlignmentAnnotations);
3729 annotationsMenu.add(showSequenceAnnotations);
3730 annotationsMenu.add(sortAnnBySequence);
3731 annotationsMenu.add(sortAnnByLabel);
3732 annotationsMenu.addSeparator();
3733 autoAnnMenu.add(showAutoFirst);
3734 autoAnnMenu.add(showAutoLast);
3735 autoAnnMenu.addSeparator();
3736 autoAnnMenu.add(applyAutoAnnotationSettings);
3737 autoAnnMenu.add(showConsensusHistogram);
3738 autoAnnMenu.add(showSequenceLogo);
3739 autoAnnMenu.add(normSequenceLogo);
3740 autoAnnMenu.addSeparator();
3741 autoAnnMenu.add(showGroupConservation);
3742 autoAnnMenu.add(showGroupConsensus);
3743 annotationsMenu.add(autoAnnMenu);
3748 formatMenu.add(font);
3749 formatMenu.add(seqLimits);
3750 formatMenu.add(wrapMenuItem);
3751 formatMenu.add(scaleAbove);
3752 formatMenu.add(scaleLeft);
3753 formatMenu.add(scaleRight);
3754 formatMenu.add(viewBoxesMenuItem);
3755 formatMenu.add(viewTextMenuItem);
3756 formatMenu.add(colourTextMenuItem);
3757 formatMenu.add(displayNonconservedMenuItem);
3758 formatMenu.add(renderGapsMenuItem);
3759 formatMenu.add(centreColumnLabelFlag);
3764 colourMenu.add(applyToAllGroups);
3765 colourMenu.addSeparator();
3766 colourMenu.add(noColourmenuItem);
3767 colourMenu.add(clustalColour);
3768 colourMenu.add(BLOSUM62Colour);
3769 colourMenu.add(PIDColour);
3770 colourMenu.add(zappoColour);
3771 colourMenu.add(taylorColour);
3772 colourMenu.add(hydrophobicityColour);
3773 colourMenu.add(helixColour);
3774 colourMenu.add(strandColour);
3775 colourMenu.add(turnColour);
3776 colourMenu.add(buriedColour);
3777 colourMenu.add(nucleotideColour);
3778 colourMenu.add(purinePyrimidineColour);
3779 // colourMenu.add(RNAInteractionColour);
3780 colourMenu.add(tcoffeeColour);
3781 colourMenu.add(userDefinedColour);
3782 colourMenu.addSeparator();
3783 colourMenu.add(conservationMenuItem);
3784 colourMenu.add(modifyConservation);
3785 colourMenu.add(abovePIDThreshold);
3786 colourMenu.add(modifyPID);
3787 colourMenu.add(annotationColour);
3788 colourMenu.add(RNAHelixColour);
3793 sortMenu.add(sortIDMenuItem);
3794 sortMenu.add(sortLengthMenuItem);
3795 sortMenu.add(sortByTreeMenu);
3796 sortMenu.add(sortGroupMenuItem);
3797 sortMenu.add(sortPairwiseMenuItem);
3798 calculateMenu.add(sortMenu);
3799 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3800 calculateTreeMenu.add(neighbourTreeMenuItem);
3801 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3802 calculateTreeMenu.add(njTreeBlosumMenuItem);
3803 calculateMenu.add(calculateTreeMenu);
3804 calculateMenu.addSeparator();
3805 calculateMenu.add(pairwiseAlignmentMenuItem);
3806 calculateMenu.add(PCAMenuItem);
3807 calculateMenu.add(autoCalculate);
3808 calculateMenu.add(sortByTree);
3813 helpMenu.add(documentation);
3814 helpMenu.add(about);
3819 statusBar.setBackground(Color.white);
3820 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3821 statusBar.setText(MessageManager.getString("label.status_bar"));
3822 this.add(statusBar, BorderLayout.SOUTH);
3826 public void setStatus(String string)
3828 statusBar.setText(string);
3831 MenuItem featureSettings = new MenuItem();
3833 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3835 MenuItem annotationColour = new MenuItem();
3837 MenuItem annotationColumnSelection = new MenuItem();
3839 MenuItem invertColSel = new MenuItem();
3841 MenuItem showColumns = new MenuItem();
3843 MenuItem showSeqs = new MenuItem();
3845 MenuItem hideColumns = new MenuItem();
3847 MenuItem hideSequences = new MenuItem();
3849 MenuItem hideAllButSelection = new MenuItem();
3851 MenuItem hideAllSelection = new MenuItem();
3853 MenuItem showAllHidden = new MenuItem();
3855 MenuItem newView = new MenuItem();
3857 private CheckboxMenuItem showAlignmentAnnotations;
3859 private CheckboxMenuItem showSequenceAnnotations;
3861 private CheckboxMenuItem sortAnnBySequence;
3863 private CheckboxMenuItem sortAnnByLabel;
3865 private CheckboxMenuItem showAutoFirst;
3867 private CheckboxMenuItem showAutoLast;
3869 private SplitFrame splitFrame;
3872 * Attach the alignFrame panels after embedding menus, if necessary. This used
3873 * to be called setEmbedded, but is now creates the dropdown menus in a
3874 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3876 * @param reallyEmbedded
3877 * true to attach the view to the applet area on the page rather than
3880 public void createAlignFrameWindow(boolean reallyEmbedded)
3884 embedAlignFrameInApplet(viewport.applet);
3889 // test and embed menu bar if necessary.
3891 if (embedMenuIfNeeded(alignPanel))
3894 * adjust for status bar height too. ? pointless as overridden by layout
3897 alignPanel.setSize(getSize().width,
3898 getSize().height - statusBar.getHeight());
3900 add(statusBar, BorderLayout.SOUTH);
3901 add(alignPanel, BorderLayout.CENTER);
3902 // and register with the applet so it can pass external API calls to us
3903 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3909 * Add the components of this AlignFrame to the applet container.
3913 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3916 // Explicitly build the embedded menu panel for the on-page applet
3918 // view cannot be closed if its actually on the page
3919 fileMenu.remove(closeMenuItem);
3920 fileMenu.remove(3); // Remove Separator
3921 // construct embedded menu, using default font
3922 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3923 // and actually add the components to the applet area
3924 theApplet.setLayout(new BorderLayout());
3925 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3926 theApplet.add(statusBar, BorderLayout.SOUTH);
3927 // TODO should size be left to the layout manager?
3928 alignPanel.setSize(theApplet.getSize().width,
3929 theApplet.getSize().height - embeddedMenu.getHeight()
3930 - statusBar.getHeight());
3931 theApplet.add(alignPanel, BorderLayout.CENTER);
3932 final AlignFrame me = this;
3933 theApplet.addFocusListener(new FocusListener()
3937 public void focusLost(FocusEvent e)
3939 if (theApplet.currentAlignFrame == me)
3941 theApplet.currentAlignFrame = null;
3946 public void focusGained(FocusEvent e)
3948 theApplet.currentAlignFrame = me;
3951 theApplet.validate();
3955 * create a new binding between structures in an existing jmol viewer instance
3956 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3957 * this does not open a new Jmol window, or modify the display of the
3958 * structures in the original jmol window. Note This method doesn't work
3959 * without an additional javascript library to exchange messages between the
3960 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3963 * JmolViewer instance
3964 * @param sequenceIds
3965 * - sequence Ids to search for associations
3967 public SequenceStructureBinding addStructureViewInstance(
3968 Object jmolviewer, String[] sequenceIds)
3970 Viewer viewer = null;
3973 viewer = (Viewer) jmolviewer;
3974 } catch (ClassCastException ex)
3976 System.err.println("Unsupported viewer object :"
3977 + jmolviewer.getClass());
3981 System.err.println("Can't use this object as a structure viewer:"
3982 + jmolviewer.getClass());
3985 SequenceI[] seqs = null;
3986 if (sequenceIds == null || sequenceIds.length == 0)
3988 seqs = viewport.getAlignment().getSequencesArray();
3992 Vector sqi = new Vector();
3993 AlignmentI al = viewport.getAlignment();
3994 for (int sid = 0; sid < sequenceIds.length; sid++)
3996 SequenceI sq = al.findName(sequenceIds[sid]);
4004 seqs = new SequenceI[sqi.size()];
4005 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4007 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4015 AAStructureBindingModel jmv = null;
4016 // TODO: search for a jmv that involves viewer
4018 { // create a new viewer/jalview binding.
4019 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4026 * bind a pdb file to a sequence in the current view
4029 * - sequenceId within the dataset.
4030 * @param pdbEntryString
4031 * - the short name for the PDB file
4033 * - pdb file - either a URL or a valid PDB file.
4034 * @return true if binding was as success TODO: consider making an exception
4035 * structure for indicating when PDB parsing or sequenceId location
4038 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4041 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4042 boolean needtoadd = false;
4043 if (toaddpdb != null)
4045 Vector pdbe = toaddpdb.getAllPDBEntries();
4046 PDBEntry pdbentry = null;
4047 if (pdbe != null && pdbe.size() > 0)
4049 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4051 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4052 if (!pdbentry.getId().equals(pdbEntryString)
4053 && !pdbentry.getFile().equals(pdbFile))
4063 if (pdbentry == null)
4065 pdbentry = new PDBEntry();
4066 pdbentry.setId(pdbEntryString);
4067 pdbentry.setFile(pdbFile);
4068 needtoadd = true; // add this new entry to sequence.
4070 // resolve data source
4071 // TODO: this code should be a refactored to an io package
4072 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4073 pdbFile, FileFormat.PDB);
4074 if (protocol == null)
4080 pdbentry.setProperty("protocol", protocol);
4081 toaddpdb.addPDBId(pdbentry);
4082 alignPanel.getStructureSelectionManager()
4083 .registerPDBEntry(pdbentry);
4089 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4093 Vector sequences = new Vector();
4094 for (int i = 0; i < seqs.length; i++)
4096 if (seqs[i] != null)
4098 sequences.addElement(new Object[] { seqs[i],
4099 (chains != null) ? chains[i] : null });
4102 seqs = new SequenceI[sequences.size()];
4103 chains = new String[sequences.size()];
4104 for (int i = 0, isize = sequences.size(); i < isize; i++)
4106 Object[] oj = (Object[]) sequences.elementAt(i);
4108 seqs[i] = (SequenceI) oj[0];
4109 chains[i] = (String) oj[1];
4112 return new Object[] { seqs, chains };
4116 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4117 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4119 // Scrub any null sequences from the array
4120 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4121 seqs = (SequenceI[]) sqch[0];
4122 chains = (String[]) sqch[1];
4123 if (seqs == null || seqs.length == 0)
4126 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4128 if (protocol == null)
4130 String sourceType = (String) pdb.getProperty("protocol");
4133 protocol = DataSourceType.valueOf(sourceType);
4134 } catch (IllegalArgumentException e)
4138 if (protocol == null)
4140 System.err.println("Couldn't work out protocol to open structure: "
4145 if (applet.useXtrnalSviewer)
4147 // register the association(s) and quit, don't create any windows.
4148 if (StructureSelectionManager.getStructureSelectionManager(applet)
4149 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4151 System.err.println("Failed to map " + pdb.getFile() + " ("
4152 + protocol + ") to any sequences");
4156 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4158 // can only do alignments with Jmol
4159 // find the last jmol window assigned to this alignment
4160 AppletJmol ajm = null, tajm;
4161 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4162 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4164 tajm = (AppletJmol) jmols.elementAt(i);
4165 if (tajm.ap.alignFrame == this)
4174 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4175 // try and add the pdb structure
4180 // otherwise, create a new window
4181 if (applet.jmolAvailable)
4183 new AppletJmol(pdb, seqs, chains, alignPanel,
4185 applet.lastFrameX += 40;
4186 applet.lastFrameY += 40;
4190 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4195 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4196 SequenceI[][] seqs, String[][] chains, String[] protocols)
4198 // TODO Auto-generated method stub
4199 System.err.println("Aligned Structure View: Not yet implemented.");
4203 * modify the current selection, providing the user has not made a selection
4207 * - sequences from this alignment
4209 * - columns to be selected on the alignment
4211 public void select(SequenceGroup sel, ColumnSelection csel,
4212 HiddenColumns hidden)
4214 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4217 public void scrollTo(int row, int column)
4219 alignPanel.seqPanel.scrollTo(row, column);
4222 public void scrollToRow(int row)
4224 alignPanel.seqPanel.scrollToRow(row);
4227 public void scrollToColumn(int column)
4229 alignPanel.seqPanel.scrollToColumn(column);
4233 * @return the alignments unique ID.
4235 public String getSequenceSetId()
4237 return viewport.getSequenceSetId();
4241 * Load the (T-Coffee) score file from the specified url
4244 * File/URL/T-COFFEE score file contents
4245 * @throws IOException
4246 * @return true if alignment was annotated with data from source
4248 public boolean loadScoreFile(String source) throws IOException
4251 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4252 AppletFormatAdapter.checkProtocol(source));
4253 if (!file.isValid())
4255 // TODO: raise dialog for gui
4256 System.err.println("Problems parsing T-Coffee scores: "
4257 + file.getWarningMessage());
4258 System.err.println("Origin was:\n" + source);
4263 * check that the score matrix matches the alignment dimensions
4266 if ((aln = viewport.getAlignment()) != null
4267 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4270 // TODO: raise a dialog box here rather than bomb out.
4272 .println("The scores matrix does not match the alignment dimensions");
4276 // TODO add parameter to indicate if matching should be done
4277 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4279 alignPanel.fontChanged();
4280 tcoffeeColour.setEnabled(true);
4281 // switch to this color
4282 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4287 System.err.println("Problems resolving T-Coffee scores:");
4288 if (file.getWarningMessage() != null)
4290 System.err.println(file.getWarningMessage());
4296 public SplitFrame getSplitFrame()
4298 return this.splitFrame;
4301 public void setSplitFrame(SplitFrame sf)
4303 this.splitFrame = sf;
4306 // may not need this
4308 public void setShowSeqFeatures(boolean b)
4310 // showSeqFeatures.setSelected(b);
4311 viewport.setShowSequenceFeatures(b);
4316 public void setMenusForViewport()
4318 // setMenusFromViewport(viewport);
4323 public void refreshFeatureUI(boolean enableIfNecessary)
4325 if (enableIfNecessary)
4327 sequenceFeatures.setState(true);
4328 alignPanel.av.setShowSequenceFeatures(true);
4333 public FeatureSettingsControllerI getFeatureSettingsUI()
4335 return alignPanel.av.featureSettings;