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.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureRenderer;
29 import jalview.api.FeatureSettingsControllerI;
30 import jalview.api.SequenceStructureBinding;
31 import jalview.bin.JalviewLite;
32 import jalview.commands.CommandI;
33 import jalview.commands.EditCommand;
34 import jalview.commands.EditCommand.Action;
35 import jalview.commands.OrderCommand;
36 import jalview.commands.RemoveGapColCommand;
37 import jalview.commands.RemoveGapsCommand;
38 import jalview.commands.SlideSequencesCommand;
39 import jalview.commands.TrimRegionCommand;
40 import jalview.datamodel.Alignment;
41 import jalview.datamodel.AlignmentAnnotation;
42 import jalview.datamodel.AlignmentI;
43 import jalview.datamodel.AlignmentOrder;
44 import jalview.datamodel.ColumnSelection;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.Sequence;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.io.AnnotationFile;
50 import jalview.io.AppletFormatAdapter;
51 import jalview.io.FeaturesFile;
52 import jalview.io.TCoffeeScoreFile;
53 import jalview.schemes.Blosum62ColourScheme;
54 import jalview.schemes.BuriedColourScheme;
55 import jalview.schemes.ClustalxColourScheme;
56 import jalview.schemes.ColourSchemeI;
57 import jalview.schemes.HelixColourScheme;
58 import jalview.schemes.HydrophobicColourScheme;
59 import jalview.schemes.NucleotideColourScheme;
60 import jalview.schemes.PIDColourScheme;
61 import jalview.schemes.PurinePyrimidineColourScheme;
62 import jalview.schemes.RNAHelicesColourChooser;
63 import jalview.schemes.StrandColourScheme;
64 import jalview.schemes.TCoffeeColourScheme;
65 import jalview.schemes.TaylorColourScheme;
66 import jalview.schemes.TurnColourScheme;
67 import jalview.schemes.ZappoColourScheme;
68 import jalview.structure.StructureSelectionManager;
69 import jalview.structures.models.AAStructureBindingModel;
70 import jalview.util.MappingUtils;
71 import jalview.util.MessageManager;
72 import jalview.viewmodel.AlignmentViewport;
74 import java.awt.BorderLayout;
75 import java.awt.Canvas;
76 import java.awt.CheckboxMenuItem;
77 import java.awt.Color;
79 import java.awt.FontMetrics;
80 import java.awt.Frame;
81 import java.awt.Graphics;
82 import java.awt.Label;
84 import java.awt.MenuBar;
85 import java.awt.MenuItem;
86 import java.awt.event.ActionEvent;
87 import java.awt.event.ActionListener;
88 import java.awt.event.FocusEvent;
89 import java.awt.event.FocusListener;
90 import java.awt.event.ItemEvent;
91 import java.awt.event.ItemListener;
92 import java.awt.event.KeyEvent;
93 import java.awt.event.KeyListener;
94 import java.awt.event.WindowAdapter;
95 import java.awt.event.WindowEvent;
96 import java.io.IOException;
98 import java.net.URLEncoder;
99 import java.util.Arrays;
100 import java.util.Deque;
101 import java.util.HashMap;
102 import java.util.Hashtable;
103 import java.util.List;
104 import java.util.Map;
105 import java.util.StringTokenizer;
106 import java.util.Vector;
108 import org.jmol.viewer.Viewer;
110 public class AlignFrame extends EmbmenuFrame implements ActionListener,
111 ItemListener, KeyListener, AlignViewControllerGuiI
113 public AlignViewControllerI avc;
115 public AlignmentPanel alignPanel;
117 public AlignViewport viewport;
119 // width and height may be overridden by applet parameters
120 int frameWidth = 700;
122 int frameHeight = 500;
124 String jalviewServletURL;
127 * Flag for showing autocalculated consensus above or below other consensus
130 private boolean showAutoCalculatedAbove;
132 private SequenceAnnotationOrder annotationSortOrder;
135 * Constructor that creates the frame and adds it to the display.
142 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
145 this(al, applet, title, embedded, true);
149 * Constructor that optionally allows the frame to be displayed or only
156 * @param addToDisplay
158 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
159 boolean embedded, boolean addToDisplay)
161 this(al, null, null, applet, title, embedded, addToDisplay);
164 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
165 ColumnSelection columnSelection, JalviewLite applet,
166 String title, boolean embedded)
168 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
171 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
172 ColumnSelection columnSelection, JalviewLite applet,
173 String title, boolean embedded, boolean addToDisplay)
177 jalviewServletURL = applet.getParameter("APPLICATION_URL");
183 } catch (Exception ex)
185 ex.printStackTrace();
187 // need to get window geometry before we calculate alignment layout
193 param = applet.getParameter("windowWidth");
196 int width = Integer.parseInt(param);
199 param = applet.getParameter("windowHeight");
202 int height = Integer.parseInt(param);
203 frameHeight = height;
205 } catch (Exception ex)
209 viewport = new AlignViewport(al, applet);
211 if (hiddenSeqs != null && hiddenSeqs.length > 0)
213 viewport.hideSequence(hiddenSeqs);
215 if (columnSelection != null)
217 viewport.setColumnSelection(columnSelection);
220 alignPanel = new AlignmentPanel(this, viewport);
221 avc = new jalview.controller.AlignViewController(this, viewport,
223 viewport.updateConservation(alignPanel);
224 viewport.updateConsensus(alignPanel);
226 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
227 followMouseOverFlag.setState(viewport.isFollowHighlight());
228 showGroupConsensus.setState(viewport.isShowGroupConsensus());
229 showGroupConservation.setState(viewport.isShowGroupConservation());
230 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
231 showSequenceLogo.setState(viewport.isShowSequenceLogo());
232 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
233 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
234 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
235 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
236 showSequenceAnnotations.setState(viewport.isShowAnnotation());
238 seqLimits.setState(viewport.getShowJVSuffix());
242 String param = applet.getParameter("sortBy");
245 if (param.equalsIgnoreCase("Id"))
247 sortIDMenuItem_actionPerformed();
249 else if (param.equalsIgnoreCase("Pairwise Identity"))
251 sortPairwiseMenuItem_actionPerformed();
253 else if (param.equalsIgnoreCase("Length"))
255 sortLengthMenuItem_actionPerformed();
259 param = applet.getParameter("wrap");
262 if (param.equalsIgnoreCase("true"))
264 wrapMenuItem.setState(true);
265 wrapMenuItem_actionPerformed();
268 param = applet.getParameter("centrecolumnlabels");
271 centreColumnLabelFlag.setState(true);
272 centreColumnLabelFlag_stateChanged();
276 if (viewport.getAlignment().isNucleotide())
278 viewport.updateStrucConsensus(alignPanel);
279 if (viewport.getAlignment().hasRNAStructure())
281 RNAHelixColour.setEnabled(true);
285 RNAHelixColour.setEnabled(false);
290 RNAHelixColour.setEnabled(false);
291 purinePyrimidineColour.setEnabled(false);
293 // Some JVMS send keyevents to Top frame or lowest panel,
294 // Havent worked out why yet. So add to both this frame and seqCanvas for
296 this.addKeyListener(this);
297 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
298 alignPanel.idPanel.idCanvas.addKeyListener(this);
299 alignPanel.scalePanel.addKeyListener(this);
300 alignPanel.annotationPanel.addKeyListener(this);
301 alignPanel.annotationPanelHolder.addKeyListener(this);
302 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
303 alignPanel.alabels.addKeyListener(this);
305 setAnnotationsVisibility();
309 addToDisplay(embedded);
316 public void addToDisplay(boolean embedded)
318 createAlignFrameWindow(embedded);
320 alignPanel.adjustAnnotationHeight();
321 alignPanel.paintAlignment(true);
324 public AlignViewport getAlignViewport()
329 public SeqCanvas getSeqcanvas()
331 return alignPanel.seqPanel.seqCanvas;
335 * Load a features file onto the alignment
338 * file URL, content, or other resolvable path
340 * is protocol for accessing data referred to by file
343 public boolean parseFeaturesFile(String file, String type)
345 return parseFeaturesFile(file, type, true);
349 * Load a features file onto the alignment
352 * file URL, content, or other resolvable path
354 * is protocol for accessing data referred to by file
355 * @param autoenabledisplay
356 * when true, display features flag will be automatically enabled if
357 * features are loaded
358 * @return true if data parsed as a features file
360 public boolean parseFeaturesFile(String file, String type,
361 boolean autoenabledisplay)
363 // TODO: test if importing a features file onto an alignment which already
364 // has features with links overwrites the original links.
366 Hashtable featureLinks = new Hashtable();
367 boolean featuresFile = false;
370 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
371 .getAlignment(), alignPanel.seqPanel.seqCanvas
372 .getFeatureRenderer().getFeatureColours(), featureLinks,
373 true, viewport.applet.getDefaultParameter("relaxedidmatch",
375 } catch (Exception ex)
377 ex.printStackTrace();
382 if (featureLinks.size() > 0)
384 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
386 if (autoenabledisplay)
388 viewport.setShowSequenceFeatures(true);
389 sequenceFeatures.setState(true);
391 if (alignPanel.seqPanel.seqCanvas.fr != null)
393 // update the min/max ranges where necessary
394 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
396 if (viewport.featureSettings != null)
398 viewport.featureSettings.refreshTable();
400 alignPanel.paintAlignment(true);
401 statusBar.setText(MessageManager
402 .getString("label.successfully_added_features_alignment"));
408 public void keyPressed(KeyEvent evt)
410 if (viewport.cursorMode
411 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
412 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
413 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
414 && Character.isDigit(evt.getKeyChar()))
416 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
419 switch (evt.getKeyCode())
421 case 27: // escape key
422 deselectAllSequenceMenuItem_actionPerformed();
424 alignPanel.alabels.cancelDrag();
427 if (evt.isControlDown() || evt.isMetaDown())
429 cut_actionPerformed();
433 if (viewport.cursorMode && !evt.isControlDown())
435 alignPanel.seqPanel.setCursorColumn();
437 if (evt.isControlDown() || evt.isMetaDown())
439 copy_actionPerformed();
443 if (evt.isControlDown())
445 paste(evt.isShiftDown());
449 if (evt.isControlDown() || evt.isMetaDown())
451 selectAllSequenceMenuItem_actionPerformed();
454 case KeyEvent.VK_DOWN:
455 if (viewport.cursorMode)
457 alignPanel.seqPanel.moveCursor(0, 1);
461 moveSelectedSequences(false);
466 if (viewport.cursorMode)
468 alignPanel.seqPanel.moveCursor(0, -1);
472 moveSelectedSequences(true);
476 case KeyEvent.VK_LEFT:
477 if (evt.isAltDown() || !viewport.cursorMode)
479 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
483 alignPanel.seqPanel.moveCursor(-1, 0);
487 case KeyEvent.VK_RIGHT:
488 if (evt.isAltDown() || !viewport.cursorMode)
490 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
494 alignPanel.seqPanel.moveCursor(1, 0);
498 case KeyEvent.VK_SPACE:
499 if (viewport.cursorMode)
501 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
502 || evt.isShiftDown() || evt.isAltDown());
506 case KeyEvent.VK_DELETE:
507 case KeyEvent.VK_BACK_SPACE:
508 if (viewport.cursorMode)
510 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
511 || evt.isShiftDown() || evt.isAltDown());
515 cut_actionPerformed();
516 alignPanel.seqPanel.seqCanvas.repaint();
521 if (viewport.cursorMode)
523 alignPanel.seqPanel.setCursorRow();
527 if (viewport.cursorMode)
529 alignPanel.seqPanel.setCursorPosition();
533 case KeyEvent.VK_ENTER:
534 case KeyEvent.VK_COMMA:
535 if (viewport.cursorMode)
537 alignPanel.seqPanel.setCursorRowAndColumn();
542 if (viewport.cursorMode)
544 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
548 if (viewport.cursorMode)
550 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
555 viewport.cursorMode = !viewport.cursorMode;
556 statusBar.setText(MessageManager.formatMessage(
557 "label.keyboard_editing_mode",
558 new String[] { (viewport.cursorMode ? "on" : "off") }));
559 if (viewport.cursorMode)
561 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
562 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
567 if (evt.isControlDown())
569 findMenuItem_actionPerformed();
575 boolean toggleSeqs = !evt.isControlDown();
576 boolean toggleCols = !evt.isShiftDown();
577 toggleHiddenRegions(toggleSeqs, toggleCols);
581 case KeyEvent.VK_PAGE_UP:
582 if (viewport.getWrapAlignment())
584 alignPanel.scrollUp(true);
588 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
589 - viewport.endSeq + viewport.startSeq);
593 case KeyEvent.VK_PAGE_DOWN:
594 if (viewport.getWrapAlignment())
596 alignPanel.scrollUp(false);
600 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
601 + viewport.endSeq - viewport.startSeq);
606 if (evt.isControlDown())
608 undoMenuItem_actionPerformed();
613 if (evt.isControlDown())
615 redoMenuItem_actionPerformed();
620 if (evt.isControlDown())
627 if (evt.isControlDown())
629 trimAlignment(false);
634 if (evt.isControlDown())
636 if (evt.isShiftDown())
638 this.removeAllGapsMenuItem_actionPerformed();
642 removeGappedColumnMenuItem_actionPerformed();
647 if (evt.isControlDown())
651 invertColSel_actionPerformed();
655 invertSequenceMenuItem_actionPerformed();
661 if (evt.isControlDown())
663 if (evt.isShiftDown())
665 this.unGroup_actionPerformed();
669 this.createGroup_actionPerformed();
675 if (evt.isControlDown())
677 this.deleteGroups_actionPerformed();
682 if (evt.isControlDown())
689 alignPanel.paintAlignment(true);
693 * called by key handler and the hide all/show all menu items
698 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
700 boolean hide = false;
701 SequenceGroup sg = viewport.getSelectionGroup();
702 if (!toggleSeqs && !toggleCols)
704 // Hide everything by the current selection - this is a hack - we do the
705 // invert and then hide
706 // first check that there will be visible columns after the invert.
707 if ((viewport.getColumnSelection() != null
708 && viewport.getColumnSelection().getSelected() != null && viewport
709 .getColumnSelection().getSelected().size() > 0)
710 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
713 // now invert the sequence set, if required - empty selection implies
714 // that no hiding is required.
717 invertSequenceMenuItem_actionPerformed();
718 sg = viewport.getSelectionGroup();
722 viewport.expandColSelection(sg, true);
723 // finally invert the column selection and get the new sequence
724 // selection and indicate it should be hidden.
725 invertColSel_actionPerformed();
732 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
735 viewport.hideAllSelectedSeqs();
737 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
740 viewport.showAllHiddenSeqs();
746 if (viewport.getColumnSelection().getSelected().size() > 0)
748 viewport.hideSelectedColumns();
751 viewport.setSelectionGroup(sg);
756 viewport.showAllHiddenColumns();
762 public void keyReleased(KeyEvent evt)
767 public void keyTyped(KeyEvent evt)
772 public void itemStateChanged(ItemEvent evt)
774 final Object source = evt.getSource();
775 if (source == displayNonconservedMenuItem)
777 displayNonconservedMenuItem_actionPerformed();
779 else if (source == colourTextMenuItem)
781 colourTextMenuItem_actionPerformed();
783 else if (source == wrapMenuItem)
785 wrapMenuItem_actionPerformed();
787 else if (source == scaleAbove)
789 viewport.setScaleAboveWrapped(scaleAbove.getState());
791 else if (source == scaleLeft)
793 viewport.setScaleLeftWrapped(scaleLeft.getState());
795 else if (source == scaleRight)
797 viewport.setScaleRightWrapped(scaleRight.getState());
799 else if (source == seqLimits)
801 seqLimits_itemStateChanged();
803 else if (source == viewBoxesMenuItem)
805 viewport.setShowBoxes(viewBoxesMenuItem.getState());
807 else if (source == viewTextMenuItem)
809 viewport.setShowText(viewTextMenuItem.getState());
811 else if (source == renderGapsMenuItem)
813 viewport.setRenderGaps(renderGapsMenuItem.getState());
815 else if (source == annotationPanelMenuItem)
817 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
818 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
820 else if (source == sequenceFeatures)
822 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
823 alignPanel.seqPanel.seqCanvas.repaint();
825 else if (source == showAlignmentAnnotations)
827 setAnnotationsVisibility();
829 else if (source == showSequenceAnnotations)
831 setAnnotationsVisibility();
833 else if (source == sortAnnBySequence)
835 boolean newState = sortAnnBySequence.getState();
836 sortAnnByLabel.setState(false);
837 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
838 : SequenceAnnotationOrder.NONE);
839 setViewportAnnotationOrder();
841 else if (source == sortAnnByLabel)
843 boolean newState = sortAnnByLabel.getState();
844 sortAnnBySequence.setState(false);
845 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
846 : SequenceAnnotationOrder.NONE);
847 setViewportAnnotationOrder();
849 else if (source == showAutoFirst)
851 showAutoLast.setState(!showAutoFirst.getState());
852 setShowAutoCalculatedAbove(showAutoFirst.getState());
853 setViewportAnnotationOrder();
855 else if (source == showAutoLast)
857 showAutoFirst.setState(!showAutoLast.getState());
858 setShowAutoCalculatedAbove(showAutoFirst.getState());
859 setViewportAnnotationOrder();
861 else if (source == conservationMenuItem)
863 conservationMenuItem_actionPerformed();
865 else if (source == abovePIDThreshold)
867 abovePIDThreshold_actionPerformed();
869 else if (source == applyToAllGroups)
871 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
873 else if (source == autoCalculate)
875 viewport.autoCalculateConsensus = autoCalculate.getState();
877 else if (source == sortByTree)
879 viewport.sortByTree = sortByTree.getState();
881 else if (source == this.centreColumnLabelFlag)
883 centreColumnLabelFlag_stateChanged();
885 else if (source == this.followMouseOverFlag)
887 mouseOverFlag_stateChanged();
889 else if (source == showGroupConsensus)
891 showGroupConsensus_actionPerformed();
893 else if (source == showGroupConservation)
895 showGroupConservation_actionPerformed();
897 else if (source == showSequenceLogo)
899 showSequenceLogo_actionPerformed();
901 else if (source == normSequenceLogo)
903 normSequenceLogo_actionPerformed();
905 else if (source == showConsensusHistogram)
907 showConsensusHistogram_actionPerformed();
909 else if (source == applyAutoAnnotationSettings)
911 applyAutoAnnotationSettings_actionPerformed();
913 alignPanel.paintAlignment(true);
917 * Set the visibility state of sequence-related and/or alignment-related
918 * annotations depending on checkbox selections, and repaint.
922 private void setAnnotationsVisibility()
924 boolean showForAlignment = showAlignmentAnnotations.getState();
925 boolean showForSequences = showSequenceAnnotations.getState();
926 for (AlignmentAnnotation aa : alignPanel.getAlignment()
927 .getAlignmentAnnotation())
929 boolean visible = (aa.sequenceRef == null ? showForAlignment
931 aa.visible = visible;
933 alignPanel.validateAnnotationDimensions(true);
938 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
940 this.annotationSortOrder = order;
944 * Set flags on the viewport that control annotation ordering
946 private void setViewportAnnotationOrder()
948 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
950 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
953 private void setShowAutoCalculatedAbove(boolean showAbove)
955 this.showAutoCalculatedAbove = showAbove;
958 private void mouseOverFlag_stateChanged()
960 viewport.setFollowHighlight(followMouseOverFlag.getState());
961 // TODO: could kick the scrollTo mechanism to reset view for current
965 private void centreColumnLabelFlag_stateChanged()
967 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
968 this.alignPanel.annotationPanel.repaint();
972 public void actionPerformed(ActionEvent evt)
974 viewport.applet.currentAlignFrame = this;
976 Object source = evt.getSource();
978 if (source == inputText)
980 inputText_actionPerformed();
982 else if (source == loadTree)
984 loadTree_actionPerformed();
986 else if (source == loadApplication)
988 launchFullApplication();
990 else if (source == loadAnnotations)
994 else if (source == outputAnnotations)
996 outputAnnotations(true);
998 else if (source == outputFeatures)
1000 outputFeatures(true, "Jalview");
1002 else if (source == closeMenuItem)
1004 closeMenuItem_actionPerformed();
1006 else if (source == copy)
1008 copy_actionPerformed();
1010 else if (source == undoMenuItem)
1012 undoMenuItem_actionPerformed();
1014 else if (source == redoMenuItem)
1016 redoMenuItem_actionPerformed();
1018 else if (source == inputText)
1020 inputText_actionPerformed();
1022 else if (source == closeMenuItem)
1024 closeMenuItem_actionPerformed();
1026 else if (source == undoMenuItem)
1028 undoMenuItem_actionPerformed();
1030 else if (source == redoMenuItem)
1032 redoMenuItem_actionPerformed();
1034 else if (source == copy)
1036 copy_actionPerformed();
1038 else if (source == pasteNew)
1040 pasteNew_actionPerformed();
1042 else if (source == pasteThis)
1044 pasteThis_actionPerformed();
1046 else if (source == cut)
1048 cut_actionPerformed();
1050 else if (source == delete)
1052 delete_actionPerformed();
1054 else if (source == grpsFromSelection)
1056 makeGrpsFromSelection_actionPerformed();
1058 else if (source == deleteGroups)
1060 deleteGroups_actionPerformed();
1062 else if (source == selectAllSequenceMenuItem)
1064 selectAllSequenceMenuItem_actionPerformed();
1066 else if (source == deselectAllSequenceMenuItem)
1068 deselectAllSequenceMenuItem_actionPerformed();
1070 else if (source == invertSequenceMenuItem)
1072 invertSequenceMenuItem_actionPerformed();
1074 else if (source == invertColSel)
1076 viewport.invertColumnSelection();
1077 alignPanel.paintAlignment(true);
1079 else if (source == remove2LeftMenuItem)
1081 trimAlignment(true);
1083 else if (source == remove2RightMenuItem)
1085 trimAlignment(false);
1087 else if (source == removeGappedColumnMenuItem)
1089 removeGappedColumnMenuItem_actionPerformed();
1091 else if (source == removeAllGapsMenuItem)
1093 removeAllGapsMenuItem_actionPerformed();
1095 else if (source == findMenuItem)
1097 findMenuItem_actionPerformed();
1099 else if (source == font)
1101 new FontChooser(alignPanel);
1103 else if (source == newView)
1107 else if (source == showColumns)
1109 viewport.showAllHiddenColumns();
1110 alignPanel.paintAlignment(true);
1112 else if (source == showSeqs)
1114 viewport.showAllHiddenSeqs();
1115 alignPanel.paintAlignment(true);
1117 else if (source == hideColumns)
1119 viewport.hideSelectedColumns();
1120 alignPanel.paintAlignment(true);
1122 else if (source == hideSequences
1123 && viewport.getSelectionGroup() != null)
1125 viewport.hideAllSelectedSeqs();
1126 alignPanel.paintAlignment(true);
1128 else if (source == hideAllButSelection)
1130 toggleHiddenRegions(false, false);
1131 alignPanel.paintAlignment(true);
1133 else if (source == hideAllSelection)
1135 SequenceGroup sg = viewport.getSelectionGroup();
1136 viewport.expandColSelection(sg, false);
1137 viewport.hideAllSelectedSeqs();
1138 viewport.hideSelectedColumns();
1139 alignPanel.paintAlignment(true);
1141 else if (source == showAllHidden)
1143 viewport.showAllHiddenColumns();
1144 viewport.showAllHiddenSeqs();
1145 alignPanel.paintAlignment(true);
1147 else if (source == showGroupConsensus)
1149 showGroupConsensus_actionPerformed();
1151 else if (source == showGroupConservation)
1153 showGroupConservation_actionPerformed();
1155 else if (source == showSequenceLogo)
1157 showSequenceLogo_actionPerformed();
1159 else if (source == normSequenceLogo)
1161 normSequenceLogo_actionPerformed();
1163 else if (source == showConsensusHistogram)
1165 showConsensusHistogram_actionPerformed();
1167 else if (source == applyAutoAnnotationSettings)
1169 applyAutoAnnotationSettings_actionPerformed();
1171 else if (source == featureSettings)
1173 new FeatureSettings(alignPanel);
1175 else if (source == alProperties)
1177 StringBuffer contents = new jalview.io.AlignmentProperties(
1178 viewport.getAlignment()).formatAsString();
1179 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1180 cap.setText(contents.toString());
1181 Frame frame = new Frame();
1183 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1184 "label.alignment_properties", new String[] { getTitle() }),
1187 else if (source == overviewMenuItem)
1189 overviewMenuItem_actionPerformed();
1191 else if (source == noColourmenuItem)
1195 else if (source == clustalColour)
1197 abovePIDThreshold.setState(false);
1198 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1200 else if (source == zappoColour)
1202 changeColour(new ZappoColourScheme());
1204 else if (source == taylorColour)
1206 changeColour(new TaylorColourScheme());
1208 else if (source == hydrophobicityColour)
1210 changeColour(new HydrophobicColourScheme());
1212 else if (source == helixColour)
1214 changeColour(new HelixColourScheme());
1216 else if (source == strandColour)
1218 changeColour(new StrandColourScheme());
1220 else if (source == turnColour)
1222 changeColour(new TurnColourScheme());
1224 else if (source == buriedColour)
1226 changeColour(new BuriedColourScheme());
1228 else if (source == nucleotideColour)
1230 changeColour(new NucleotideColourScheme());
1232 else if (source == purinePyrimidineColour)
1234 changeColour(new PurinePyrimidineColourScheme());
1236 // else if (source == RNAInteractionColour)
1238 // changeColour(new RNAInteractionColourScheme());
1240 else if (source == RNAHelixColour)
1242 new RNAHelicesColourChooser(viewport, alignPanel);
1244 else if (source == modifyPID)
1246 modifyPID_actionPerformed();
1248 else if (source == modifyConservation)
1250 modifyConservation_actionPerformed();
1252 else if (source == userDefinedColour)
1254 new UserDefinedColours(alignPanel, null);
1256 else if (source == PIDColour)
1258 changeColour(new PIDColourScheme());
1260 else if (source == BLOSUM62Colour)
1262 changeColour(new Blosum62ColourScheme());
1264 else if (source == tcoffeeColour)
1266 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1268 else if (source == annotationColour)
1270 new AnnotationColourChooser(viewport, alignPanel);
1272 else if (source == annotationColumnSelection)
1274 new AnnotationColumnChooser(viewport, alignPanel);
1276 else if (source == sortPairwiseMenuItem)
1278 sortPairwiseMenuItem_actionPerformed();
1280 else if (source == sortIDMenuItem)
1282 sortIDMenuItem_actionPerformed();
1284 else if (source == sortLengthMenuItem)
1286 sortLengthMenuItem_actionPerformed();
1288 else if (source == sortGroupMenuItem)
1290 sortGroupMenuItem_actionPerformed();
1292 else if (source == removeRedundancyMenuItem)
1294 removeRedundancyMenuItem_actionPerformed();
1296 else if (source == pairwiseAlignmentMenuItem)
1298 pairwiseAlignmentMenuItem_actionPerformed();
1300 else if (source == PCAMenuItem)
1302 PCAMenuItem_actionPerformed();
1304 else if (source == averageDistanceTreeMenuItem)
1306 averageDistanceTreeMenuItem_actionPerformed();
1308 else if (source == neighbourTreeMenuItem)
1310 neighbourTreeMenuItem_actionPerformed();
1312 else if (source == njTreeBlosumMenuItem)
1314 njTreeBlosumMenuItem_actionPerformed();
1316 else if (source == avDistanceTreeBlosumMenuItem)
1318 avTreeBlosumMenuItem_actionPerformed();
1320 else if (source == documentation)
1322 documentation_actionPerformed();
1324 else if (source == about)
1326 about_actionPerformed();
1331 public void inputText_actionPerformed()
1333 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1334 Frame frame = new Frame();
1336 jalview.bin.JalviewLite.addFrame(frame,
1337 MessageManager.getString("label.input_cut_paste"), 500, 500);
1340 protected void outputText_actionPerformed(ActionEvent e)
1342 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1343 Frame frame = new Frame();
1345 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1346 "label.alignment_output_command",
1347 new Object[] { e.getActionCommand() }), 600, 500);
1349 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1350 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1351 e.getActionCommand(), viewport.getAlignment(),
1352 viewport.getShowJVSuffix()));
1355 public void loadAnnotations()
1357 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1358 cap.setText(MessageManager
1359 .getString("label.paste_features_annotations_Tcoffee_here"));
1360 cap.setAnnotationImport();
1361 Frame frame = new Frame();
1363 jalview.bin.JalviewLite.addFrame(frame,
1364 MessageManager.getString("action.paste_annotations"), 400, 300);
1368 public String outputAnnotations(boolean displayTextbox)
1370 String annotation = new AnnotationFile()
1371 .printAnnotationsForView(viewport);
1375 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1376 Frame frame = new Frame();
1378 jalview.bin.JalviewLite.addFrame(frame,
1379 MessageManager.getString("label.annotations"), 600, 500);
1380 cap.setText(annotation);
1386 private Map<String, Object> getDisplayedFeatureCols()
1388 if (alignPanel.getFeatureRenderer() != null
1389 && viewport.getFeaturesDisplayed() != null)
1391 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1397 public String outputFeatures(boolean displayTextbox, String format)
1400 if (format.equalsIgnoreCase("Jalview"))
1402 features = new FeaturesFile().printJalviewFormat(viewport
1403 .getAlignment().getSequencesArray(),
1404 getDisplayedFeatureCols());
1408 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1409 .getSequencesArray(), getDisplayedFeatureCols());
1414 boolean frimport = false;
1415 if (features == null || features.equals("No Features Visible"))
1417 features = "# No features visible - paste some and import them here.";
1421 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1424 cap.setAnnotationImport();
1426 Frame frame = new Frame();
1428 jalview.bin.JalviewLite.addFrame(frame,
1429 MessageManager.getString("label.features"), 600, 500);
1430 cap.setText(features);
1434 if (features == null)
1443 void launchFullApplication()
1445 StringBuffer url = new StringBuffer(jalviewServletURL);
1447 // allow servlet parameters to be passed in applet parameter
1448 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1450 url.append(firstSep);
1453 + appendProtocol(viewport.applet.getParameter("file")));
1455 if (viewport.applet.getParameter("features") != null)
1457 url.append("&features=");
1458 url.append(appendProtocol(viewport.applet.getParameter("features")));
1461 if (viewport.applet.getParameter("annotations") != null)
1463 url.append("&annotations=");
1464 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1467 if (viewport.applet.getParameter("jnetfile") != null)
1469 url.append("&annotations=");
1470 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1473 if (viewport.applet.getParameter("defaultColour") != null)
1475 url.append("&colour="
1476 + removeWhiteSpace(viewport.applet
1477 .getParameter("defaultColour")));
1480 if (viewport.applet.getParameter("userDefinedColour") != null)
1482 url.append("&colour="
1483 + removeWhiteSpace(viewport.applet
1484 .getParameter("userDefinedColour")));
1486 if (viewport.applet.getParameter("tree") != null)
1489 + appendProtocol(viewport.applet.getParameter("tree")));
1491 if (viewport.applet.getParameter("treeFile") != null)
1494 + appendProtocol(viewport.applet.getParameter("treeFile")));
1497 showURL(url.toString(), "FULL_APP");
1500 String removeWhiteSpace(String colour)
1502 StringBuffer sb = new StringBuffer();
1503 for (int i = 0; i < colour.length(); i++)
1505 if (Character.isWhitespace(colour.charAt(i)))
1511 sb.append(colour.charAt(i));
1515 return sb.toString();
1518 String appendProtocol(String url)
1523 url = URLEncoder.encode(url);
1526 * When we finally deprecate 1.1 compatibility, we can start to use
1527 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1528 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1529 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1530 * ex.printStackTrace(); }
1532 catch (java.net.MalformedURLException ex)
1534 url = viewport.applet.getCodeBase() + url;
1539 public void closeMenuItem_actionPerformed()
1541 PaintRefresher.RemoveComponent(alignPanel);
1542 if (alignPanel.seqPanel != null
1543 && alignPanel.seqPanel.seqCanvas != null)
1545 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1547 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1549 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1552 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1567 void updateEditMenuBar()
1570 if (viewport.getHistoryList().size() > 0)
1572 undoMenuItem.setEnabled(true);
1573 CommandI command = viewport.getHistoryList().peek();
1574 undoMenuItem.setLabel(MessageManager.formatMessage(
1575 "label.undo_command",
1576 new Object[] { command.getDescription() }));
1580 undoMenuItem.setEnabled(false);
1581 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1584 if (viewport.getRedoList().size() > 0)
1586 redoMenuItem.setEnabled(true);
1588 CommandI command = viewport.getRedoList().peek();
1589 redoMenuItem.setLabel(MessageManager.formatMessage(
1590 "label.redo_command",
1591 new Object[] { command.getDescription() }));
1595 redoMenuItem.setEnabled(false);
1596 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1604 public void addHistoryItem(CommandI command)
1606 if (command.getSize() > 0)
1608 viewport.addToHistoryList(command);
1609 viewport.clearRedoList();
1610 updateEditMenuBar();
1611 viewport.updateHiddenColumns();
1616 * TODO: JAL-1104 DOCUMENT ME!
1621 protected void undoMenuItem_actionPerformed()
1623 if (viewport.getHistoryList().isEmpty())
1628 CommandI command = viewport.getHistoryList().pop();
1629 viewport.addToRedoList(command);
1630 command.undoCommand(null);
1632 AlignmentViewport originalSource = getOriginatingSource(command);
1634 if (originalSource != viewport)
1637 .println("Warning: Viewport object mismatch whilst undoing");
1639 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1640 // viewport.getColumnSelection().getHiddenColumns()
1642 updateEditMenuBar();
1643 originalSource.firePropertyChange("alignment", null, originalSource
1644 .getAlignment().getSequences());
1648 * TODO: JAL-1104 DOCUMENT ME!
1653 protected void redoMenuItem_actionPerformed()
1655 if (viewport.getRedoList().isEmpty())
1660 CommandI command = viewport.getRedoList().pop();
1661 viewport.addToHistoryList(command);
1662 command.doCommand(null);
1664 AlignmentViewport originalSource = getOriginatingSource(command);
1666 if (originalSource != viewport)
1669 .println("Warning: Viewport object mismatch whilst re-doing");
1671 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1672 // viewport.getColumnSelection().getHiddenColumns()
1675 updateEditMenuBar();
1676 originalSource.firePropertyChange("alignment", null, originalSource
1677 .getAlignment().getSequences());
1680 AlignmentViewport getOriginatingSource(CommandI command)
1682 AlignmentViewport originalSource = null;
1683 // For sequence removal and addition, we need to fire
1684 // the property change event FROM the viewport where the
1685 // original alignment was altered
1686 AlignmentI al = null;
1687 if (command instanceof EditCommand)
1689 EditCommand editCommand = (EditCommand) command;
1690 al = editCommand.getAlignment();
1691 Vector comps = (Vector) PaintRefresher.components.get(viewport
1692 .getSequenceSetId());
1693 for (int i = 0; i < comps.size(); i++)
1695 if (comps.elementAt(i) instanceof AlignmentPanel)
1697 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1699 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1706 if (originalSource == null)
1708 // The original view is closed, we must validate
1709 // the current view against the closed view first
1712 PaintRefresher.validateSequences(al, viewport.getAlignment());
1715 originalSource = viewport;
1718 return originalSource;
1722 * Move the currently selected sequences up or down one position in the
1727 public void moveSelectedSequences(boolean up)
1729 SequenceGroup sg = viewport.getSelectionGroup();
1734 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1735 up ? null : viewport.getHiddenRepSequences(), up);
1736 alignPanel.paintAlignment(true);
1739 * Also move cDNA/protein complement sequences
1741 AlignViewportI complement = viewport.getCodingComplement();
1742 if (complement != null)
1744 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1745 viewport, complement);
1746 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1747 up ? null : complement.getHiddenRepSequences(), up);
1748 // TODO need to trigger a repaint of the complementary panel - how?
1749 // would prefer to handle in SplitFrame but it is not overriding key
1754 synchronized void slideSequences(boolean right, int size)
1756 List<SequenceI> sg = new Vector<SequenceI>();
1757 if (viewport.cursorMode)
1759 sg.add(viewport.getAlignment().getSequenceAt(
1760 alignPanel.seqPanel.seqCanvas.cursorY));
1762 else if (viewport.getSelectionGroup() != null
1763 && viewport.getSelectionGroup().getSize() != viewport
1764 .getAlignment().getHeight())
1766 sg = viewport.getSelectionGroup().getSequences(
1767 viewport.getHiddenRepSequences());
1775 Vector<SequenceI> invertGroup = new Vector();
1777 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1779 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1781 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1785 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1787 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1789 for (int i = 0; i < invertGroup.size(); i++)
1791 seqs2[i] = invertGroup.elementAt(i);
1794 SlideSequencesCommand ssc;
1797 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1798 size, viewport.getGapCharacter());
1802 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1803 size, viewport.getGapCharacter());
1806 int groupAdjustment = 0;
1807 if (ssc.getGapsInsertedBegin() && right)
1809 if (viewport.cursorMode)
1811 alignPanel.seqPanel.moveCursor(size, 0);
1815 groupAdjustment = size;
1818 else if (!ssc.getGapsInsertedBegin() && !right)
1820 if (viewport.cursorMode)
1822 alignPanel.seqPanel.moveCursor(-size, 0);
1826 groupAdjustment = -size;
1830 if (groupAdjustment != 0)
1832 viewport.getSelectionGroup().setStartRes(
1833 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1834 viewport.getSelectionGroup().setEndRes(
1835 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1838 boolean appendHistoryItem = false;
1839 Deque<CommandI> historyList = viewport.getHistoryList();
1840 if (historyList != null && historyList.size() > 0
1841 && historyList.peek() instanceof SlideSequencesCommand)
1843 appendHistoryItem = ssc
1844 .appendSlideCommand((SlideSequencesCommand) historyList
1848 if (!appendHistoryItem)
1850 addHistoryItem(ssc);
1856 static StringBuffer copiedSequences;
1858 static Vector copiedHiddenColumns;
1860 protected void copy_actionPerformed()
1862 if (viewport.getSelectionGroup() == null)
1867 SequenceGroup sg = viewport.getSelectionGroup();
1868 copiedSequences = new StringBuffer();
1869 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1870 for (int i = 0; i < sg.getSize(); i++)
1872 SequenceI seq = sg.getSequenceAt(i);
1873 int index = viewport.getAlignment().findIndex(seq);
1874 orderedSeqs.put(index, seq);
1877 int index = 0, startRes, endRes;
1880 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1882 copiedHiddenColumns = new Vector();
1883 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1884 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1886 copiedHiddenColumns.addElement(new int[] {
1887 region[0] - hiddenOffset, region[1] - hiddenOffset });
1892 copiedHiddenColumns = null;
1895 for (int i = 0; i < sg.getSize(); i++)
1897 SequenceI seq = null;
1901 if (orderedSeqs.containsKey(index))
1903 seq = orderedSeqs.get(index);
1914 // Returns residue following index if gap
1915 startRes = seq.findPosition(sg.getStartRes());
1918 // Need to find the residue preceeding index if gap
1921 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1923 ch = seq.getCharAt(j);
1924 if (!jalview.util.Comparison.isGap((ch)))
1932 endRes += seq.getStart() - 1;
1935 copiedSequences.append(seq.getName()
1941 + seq.getSequenceAsString(sg.getStartRes(),
1942 sg.getEndRes() + 1) + "\n");
1947 protected void pasteNew_actionPerformed()
1952 protected void pasteThis_actionPerformed()
1957 void paste(boolean newAlignment)
1962 if (copiedSequences == null)
1967 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1968 Vector seqs = new Vector();
1969 while (st.hasMoreElements())
1971 String name = st.nextToken();
1972 int start = Integer.parseInt(st.nextToken());
1973 int end = Integer.parseInt(st.nextToken());
1974 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1976 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1977 for (int i = 0; i < seqs.size(); i++)
1979 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1984 String newtitle = MessageManager
1985 .getString("label.copied_sequences");
1986 if (getTitle().startsWith(
1987 MessageManager.getString("label.copied_sequences")))
1989 newtitle = getTitle();
1993 newtitle = newtitle.concat(MessageManager.formatMessage(
1994 "label.from_msname", new String[] { getTitle() }));
1996 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1997 viewport.applet, newtitle, false);
1998 if (copiedHiddenColumns != null)
2000 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2002 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2003 af.viewport.hideColumns(region[0], region[1]);
2007 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2012 addSequences(newSeqs);
2015 } catch (Exception ex)
2017 } // could be anything being pasted in here
2021 void addSequences(SequenceI[] seqs)
2023 for (int i = 0; i < seqs.length; i++)
2025 viewport.getAlignment().addSequence(seqs[i]);
2029 addHistoryItem(new EditCommand(
2030 MessageManager.getString("label.add_sequences"), Action.PASTE,
2031 seqs, 0, viewport.getAlignment().getWidth(),
2032 viewport.getAlignment()));
2034 viewport.setEndSeq(viewport.getAlignment().getHeight());
2035 viewport.getAlignment().getWidth();
2036 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2041 protected void cut_actionPerformed()
2043 copy_actionPerformed();
2044 delete_actionPerformed();
2047 protected void delete_actionPerformed()
2050 SequenceGroup sg = viewport.getSelectionGroup();
2056 Vector seqs = new Vector();
2058 for (int i = 0; i < sg.getSize(); i++)
2060 seq = sg.getSequenceAt(i);
2061 seqs.addElement(seq);
2064 // If the cut affects all sequences, remove highlighted columns
2065 if (sg.getSize() == viewport.getAlignment().getHeight())
2067 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2068 sg.getEndRes() + 1);
2071 SequenceI[] cut = new SequenceI[seqs.size()];
2072 for (int i = 0; i < seqs.size(); i++)
2074 cut[i] = (SequenceI) seqs.elementAt(i);
2078 * //ADD HISTORY ITEM
2080 addHistoryItem(new EditCommand(
2081 MessageManager.getString("label.cut_sequences"), Action.CUT,
2082 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2083 viewport.getAlignment()));
2085 viewport.setSelectionGroup(null);
2086 viewport.getAlignment().deleteGroup(sg);
2088 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2091 if (viewport.getAlignment().getHeight() < 1)
2093 this.setVisible(false);
2095 viewport.sendSelection();
2099 * group consensus toggled
2102 protected void showGroupConsensus_actionPerformed()
2104 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2105 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2110 * group conservation toggled.
2112 protected void showGroupConservation_actionPerformed()
2114 viewport.setShowGroupConservation(showGroupConservation.getState());
2115 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2122 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2123 * .event.ActionEvent)
2125 protected void showConsensusHistogram_actionPerformed()
2127 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2128 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2135 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2136 * .event.ActionEvent)
2138 protected void showSequenceLogo_actionPerformed()
2140 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2141 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2144 protected void normSequenceLogo_actionPerformed()
2146 showSequenceLogo.setState(true);
2147 viewport.setShowSequenceLogo(true);
2148 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2149 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2152 protected void applyAutoAnnotationSettings_actionPerformed()
2154 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2157 protected void makeGrpsFromSelection_actionPerformed()
2159 if (avc.makeGroupsFromSelection())
2161 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2162 alignPanel.updateAnnotation();
2163 alignPanel.paintAlignment(true);
2167 protected void createGroup_actionPerformed()
2172 protected void unGroup_actionPerformed()
2176 alignPanel.alignmentChanged();
2180 protected void deleteGroups_actionPerformed()
2182 if (avc.deleteGroups())
2184 alignPanel.alignmentChanged();
2188 public void selectAllSequenceMenuItem_actionPerformed()
2190 SequenceGroup sg = new SequenceGroup();
2191 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2193 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2195 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2196 viewport.setSelectionGroup(sg);
2197 alignPanel.paintAlignment(true);
2198 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2199 viewport.sendSelection();
2202 public void deselectAllSequenceMenuItem_actionPerformed()
2204 if (viewport.cursorMode)
2206 alignPanel.seqPanel.keyboardNo1 = null;
2207 alignPanel.seqPanel.keyboardNo2 = null;
2209 viewport.setSelectionGroup(null);
2210 viewport.getColumnSelection().clear();
2211 viewport.setSelectionGroup(null);
2212 alignPanel.idPanel.idCanvas.searchResults = null;
2213 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2214 alignPanel.paintAlignment(true);
2215 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2216 viewport.sendSelection();
2219 public void invertSequenceMenuItem_actionPerformed()
2221 SequenceGroup sg = viewport.getSelectionGroup();
2222 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2224 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2227 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2228 viewport.sendSelection();
2231 public void invertColSel_actionPerformed()
2233 viewport.invertColumnSelection();
2234 alignPanel.paintAlignment(true);
2235 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2236 viewport.sendSelection();
2239 void trimAlignment(boolean trimLeft)
2241 ColumnSelection colSel = viewport.getColumnSelection();
2244 if (colSel.size() > 0)
2248 column = colSel.getMin();
2252 column = colSel.getMax();
2256 if (viewport.getSelectionGroup() != null)
2258 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2259 viewport.getHiddenRepSequences());
2263 seqs = viewport.getAlignment().getSequencesArray();
2266 TrimRegionCommand trimRegion;
2269 trimRegion = new TrimRegionCommand("Remove Left",
2270 TrimRegionCommand.TRIM_LEFT, seqs, column,
2271 viewport.getAlignment(), viewport.getColumnSelection(),
2272 viewport.getSelectionGroup());
2273 viewport.setStartRes(0);
2277 trimRegion = new TrimRegionCommand("Remove Right",
2278 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2279 viewport.getAlignment(), viewport.getColumnSelection(),
2280 viewport.getSelectionGroup());
2283 statusBar.setText(MessageManager.formatMessage(
2284 "label.removed_columns",
2285 new String[] { Integer.valueOf(trimRegion.getSize())
2287 addHistoryItem(trimRegion);
2289 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2291 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2292 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2294 viewport.getAlignment().deleteGroup(sg);
2298 viewport.firePropertyChange("alignment", null, viewport
2299 .getAlignment().getSequences());
2303 public void removeGappedColumnMenuItem_actionPerformed()
2305 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2308 if (viewport.getSelectionGroup() != null)
2310 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2311 viewport.getHiddenRepSequences());
2312 start = viewport.getSelectionGroup().getStartRes();
2313 end = viewport.getSelectionGroup().getEndRes();
2317 seqs = viewport.getAlignment().getSequencesArray();
2320 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2321 "Remove Gapped Columns", seqs, start, end,
2322 viewport.getAlignment());
2324 addHistoryItem(removeGapCols);
2326 statusBar.setText(MessageManager.formatMessage(
2327 "label.removed_empty_columns",
2328 new String[] { Integer.valueOf(removeGapCols.getSize())
2331 // This is to maintain viewport position on first residue
2332 // of first sequence
2333 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2334 int startRes = seq.findPosition(viewport.startRes);
2335 // ShiftList shifts;
2336 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2337 // edit.alColumnChanges=shifts.getInverse();
2338 // if (viewport.hasHiddenColumns)
2339 // viewport.getColumnSelection().compensateForEdits(shifts);
2340 viewport.setStartRes(seq.findIndex(startRes) - 1);
2341 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2346 public void removeAllGapsMenuItem_actionPerformed()
2348 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2351 if (viewport.getSelectionGroup() != null)
2353 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2354 viewport.getHiddenRepSequences());
2355 start = viewport.getSelectionGroup().getStartRes();
2356 end = viewport.getSelectionGroup().getEndRes();
2360 seqs = viewport.getAlignment().getSequencesArray();
2363 // This is to maintain viewport position on first residue
2364 // of first sequence
2365 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2366 int startRes = seq.findPosition(viewport.startRes);
2368 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2369 viewport.getAlignment()));
2371 viewport.setStartRes(seq.findIndex(startRes) - 1);
2373 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2378 public void findMenuItem_actionPerformed()
2380 new Finder(alignPanel);
2384 * create a new view derived from the current view
2387 * @return frame for the new view
2389 public AlignFrame newView(String viewtitle)
2392 if (viewport.hasHiddenRows())
2394 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2395 .getFullAlignment().getSequencesArray());
2399 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2402 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2404 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2406 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2408 newal.addAnnotation(viewport.getAlignment()
2409 .getAlignmentAnnotation()[i]);
2414 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2416 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2417 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2418 PaintRefresher.Register(newaf.alignPanel,
2419 newaf.alignPanel.av.getSequenceSetId());
2421 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2422 newaf.alignPanel.av.getSequenceSetId());
2423 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2424 newaf.alignPanel.av.getSequenceSetId());
2426 Vector comps = (Vector) PaintRefresher.components.get(viewport
2427 .getSequenceSetId());
2429 for (int i = 0; i < comps.size(); i++)
2431 if (comps.elementAt(i) instanceof AlignmentPanel)
2437 String title = new String(this.getTitle());
2438 if (viewtitle != null)
2440 title = viewtitle + " ( " + title + ")";
2444 if (title.indexOf("(View") > -1)
2446 title = title.substring(0, title.indexOf("(View"));
2448 title += "(View " + viewSize + ")";
2451 newaf.setTitle(title.toString());
2453 newaf.viewport.setHistoryList(viewport.getHistoryList());
2454 newaf.viewport.setRedoList(viewport.getRedoList());
2460 * @return list of feature groups on the view
2462 public String[] getFeatureGroups()
2464 FeatureRenderer fr = null;
2465 if (alignPanel != null
2466 && (fr = alignPanel.getFeatureRenderer()) != null)
2468 List<String> gps = fr.getFeatureGroups();
2469 String[] _gps = gps.toArray(new String[gps.size()]);
2476 * get sequence feature groups that are hidden or shown
2482 public String[] getFeatureGroupsOfState(boolean visible)
2484 FeatureRenderer fr = null;
2485 if (alignPanel != null
2486 && (fr = alignPanel.getFeatureRenderer()) != null)
2488 List<String> gps = fr.getGroups(visible);
2489 String[] _gps = gps.toArray(new String[gps.size()]);
2496 * Change the display state for the given feature groups
2499 * list of group strings
2501 * visible or invisible
2503 public void setFeatureGroupState(String[] groups, boolean state)
2505 FeatureRenderer fr = null;
2506 this.sequenceFeatures.setState(true);
2507 viewport.setShowSequenceFeatures(true);
2508 if (alignPanel != null
2509 && (fr = alignPanel.getFeatureRenderer()) != null)
2512 fr.setGroupVisibility(Arrays.asList(groups), state);
2513 alignPanel.seqPanel.seqCanvas.repaint();
2514 if (alignPanel.overviewPanel != null)
2516 alignPanel.overviewPanel.updateOverviewImage();
2521 public void seqLimits_itemStateChanged()
2523 viewport.setShowJVSuffix(seqLimits.getState());
2524 alignPanel.fontChanged();
2525 alignPanel.paintAlignment(true);
2528 protected void colourTextMenuItem_actionPerformed()
2530 viewport.setColourText(colourTextMenuItem.getState());
2531 alignPanel.paintAlignment(true);
2534 protected void displayNonconservedMenuItem_actionPerformed()
2536 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2537 alignPanel.paintAlignment(true);
2540 protected void wrapMenuItem_actionPerformed()
2542 viewport.setWrapAlignment(wrapMenuItem.getState());
2543 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2544 scaleAbove.setEnabled(wrapMenuItem.getState());
2545 scaleLeft.setEnabled(wrapMenuItem.getState());
2546 scaleRight.setEnabled(wrapMenuItem.getState());
2547 alignPanel.paintAlignment(true);
2550 public void overviewMenuItem_actionPerformed()
2552 if (alignPanel.overviewPanel != null)
2557 Frame frame = new Frame();
2558 OverviewPanel overview = new OverviewPanel(alignPanel);
2559 frame.add(overview);
2560 // +50 must allow for applet frame window
2561 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2562 "label.overview_params", new String[] { this.getTitle() }),
2563 overview.getPreferredSize().width,
2564 overview.getPreferredSize().height + 50);
2567 final AlignmentPanel ap = alignPanel;
2568 frame.addWindowListener(new WindowAdapter()
2571 public void windowClosing(WindowEvent e)
2575 ap.setOverviewPanel(null);
2580 alignPanel.setOverviewPanel(overview);
2584 public void changeColour(ColourSchemeI cs)
2589 if (viewport.getAbovePIDThreshold())
2591 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2595 if (viewport.getConservationSelected())
2597 cs.setConservationApplied(true);
2598 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2603 cs.setConservationApplied(false);
2606 viewport.setGlobalColourScheme(cs);
2608 alignPanel.paintAlignment(true);
2611 protected void modifyPID_actionPerformed()
2613 if (viewport.getAbovePIDThreshold()
2614 && viewport.getGlobalColourScheme() != null)
2616 SliderPanel.setPIDSliderSource(alignPanel,
2617 viewport.getGlobalColourScheme(), "Background");
2618 SliderPanel.showPIDSlider();
2622 protected void modifyConservation_actionPerformed()
2624 if (viewport.getConservationSelected()
2625 && viewport.getGlobalColourScheme() != null)
2627 SliderPanel.setConservationSlider(alignPanel,
2628 viewport.getGlobalColourScheme(), "Background");
2629 SliderPanel.showConservationSlider();
2633 protected void conservationMenuItem_actionPerformed()
2635 viewport.setConservationSelected(conservationMenuItem.getState());
2637 viewport.setAbovePIDThreshold(false);
2638 abovePIDThreshold.setState(false);
2640 changeColour(viewport.getGlobalColourScheme());
2642 modifyConservation_actionPerformed();
2645 public void abovePIDThreshold_actionPerformed()
2647 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2649 conservationMenuItem.setState(false);
2650 viewport.setConservationSelected(false);
2652 changeColour(viewport.getGlobalColourScheme());
2654 modifyPID_actionPerformed();
2657 public void sortPairwiseMenuItem_actionPerformed()
2659 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2660 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2661 .getAlignment().getSequenceAt(0), null);
2663 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2664 viewport.getAlignment()));
2665 alignPanel.paintAlignment(true);
2668 public void sortIDMenuItem_actionPerformed()
2670 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2671 AlignmentSorter.sortByID(viewport.getAlignment());
2672 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2673 viewport.getAlignment()));
2674 alignPanel.paintAlignment(true);
2677 public void sortLengthMenuItem_actionPerformed()
2679 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2680 AlignmentSorter.sortByLength(viewport.getAlignment());
2681 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2682 viewport.getAlignment()));
2683 alignPanel.paintAlignment(true);
2686 public void sortGroupMenuItem_actionPerformed()
2688 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2689 AlignmentSorter.sortByGroup(viewport.getAlignment());
2690 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2691 viewport.getAlignment()));
2692 alignPanel.paintAlignment(true);
2696 public void removeRedundancyMenuItem_actionPerformed()
2698 new RedundancyPanel(alignPanel);
2701 public void pairwiseAlignmentMenuItem_actionPerformed()
2703 if (viewport.getSelectionGroup() != null
2704 && viewport.getSelectionGroup().getSize() > 1)
2706 Frame frame = new Frame();
2707 frame.add(new PairwiseAlignPanel(alignPanel));
2708 jalview.bin.JalviewLite.addFrame(frame,
2709 MessageManager.getString("action.pairwise_alignment"), 600,
2714 public void PCAMenuItem_actionPerformed()
2716 // are the sequences aligned?
2717 if (!viewport.getAlignment().isAligned(false))
2720 int Width = viewport.getAlignment().getWidth();
2722 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2724 current = viewport.getAlignment().getSequenceAt(i);
2726 if (current.getLength() < Width)
2728 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2731 alignPanel.paintAlignment(true);
2734 if ((viewport.getSelectionGroup() != null
2735 && viewport.getSelectionGroup().getSize() < 4 && viewport
2736 .getSelectionGroup().getSize() > 0)
2737 || viewport.getAlignment().getHeight() < 4)
2744 new PCAPanel(viewport);
2745 } catch (java.lang.OutOfMemoryError ex)
2751 public void averageDistanceTreeMenuItem_actionPerformed()
2753 NewTreePanel("AV", "PID", "Average distance tree using PID");
2756 public void neighbourTreeMenuItem_actionPerformed()
2758 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2761 protected void njTreeBlosumMenuItem_actionPerformed()
2763 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2766 protected void avTreeBlosumMenuItem_actionPerformed()
2768 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2771 void NewTreePanel(String type, String pwType, String title)
2773 // are the sequences aligned?
2774 if (!viewport.getAlignment().isAligned(false))
2777 int Width = viewport.getAlignment().getWidth();
2779 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2781 current = viewport.getAlignment().getSequenceAt(i);
2783 if (current.getLength() < Width)
2785 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2788 alignPanel.paintAlignment(true);
2792 if ((viewport.getSelectionGroup() != null && viewport
2793 .getSelectionGroup().getSize() > 1)
2794 || (viewport.getAlignment().getHeight() > 1))
2796 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2798 addTreeMenuItem(tp, title);
2800 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2804 void loadTree_actionPerformed()
2806 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2807 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2808 cap.setTreeImport();
2809 Frame frame = new Frame();
2811 jalview.bin.JalviewLite.addFrame(frame,
2812 MessageManager.getString("label.paste_newick_file"), 400, 300);
2815 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2817 TreePanel tp = new TreePanel(alignPanel, treeFile,
2818 MessageManager.getString("label.load_tree_from_file"), tree);
2819 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2820 addTreeMenuItem(tp, treeFile);
2824 * sort the alignment using the given treePanel
2827 * tree used to sort view
2829 * string used for undo event name
2831 public void sortByTree(TreePanel treePanel, String title)
2833 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2835 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2836 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2837 // HistoryItem.SORT));
2838 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2839 "label.order_by_params", new String[] { title }), oldOrder,
2840 viewport.getAlignment()));
2841 alignPanel.paintAlignment(true);
2845 * Do any automatic reordering of the alignment and add the necessary bits to
2846 * the menu structure for the new tree
2851 protected void addTreeMenuItem(final TreePanel treePanel,
2854 final MenuItem item = new MenuItem(title);
2855 sortByTreeMenu.add(item);
2856 item.addActionListener(new java.awt.event.ActionListener()
2859 public void actionPerformed(ActionEvent evt)
2861 sortByTree(treePanel, title); // treePanel.getTitle());
2865 treePanel.addWindowListener(new WindowAdapter()
2868 public void windowOpened(WindowEvent e)
2870 if (viewport.sortByTree)
2872 sortByTree(treePanel, title);
2874 super.windowOpened(e);
2878 public void windowClosing(WindowEvent e)
2880 sortByTreeMenu.remove(item);
2885 public boolean sortBy(AlignmentOrder alorder, String undoname)
2887 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2888 if (viewport.applet.debug)
2890 System.err.println("Sorting " + alorder.getOrder().size()
2891 + " in alignment '" + getTitle() + "'");
2893 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2894 if (undoname != null)
2896 addHistoryItem(new OrderCommand(undoname, oldOrder,
2897 viewport.getAlignment()));
2899 alignPanel.paintAlignment(true);
2903 protected void documentation_actionPerformed()
2905 alignPanel.av.applet.openJalviewHelpUrl();
2908 protected void about_actionPerformed()
2911 class AboutPanel extends Canvas
2917 public AboutPanel(String version, String builddate)
2919 this.version = version;
2920 this.builddate = builddate;
2924 public void paint(Graphics g)
2926 g.setColor(Color.white);
2927 g.fillRect(0, 0, getSize().width, getSize().height);
2928 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2929 FontMetrics fm = g.getFontMetrics();
2930 int fh = fm.getHeight();
2932 g.setColor(Color.black);
2933 // TODO: update this text for each release or centrally store it for
2934 // lite and application
2935 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2936 g.drawString(MessageManager.formatMessage(
2937 "label.jalviewLite_release", new String[] { version }), x,
2939 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2940 g.drawString(MessageManager.formatMessage(
2941 "label.jaview_build_date", new String[] { builddate }), x,
2943 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2944 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2946 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2947 x + 50, y += fh + 8);
2949 MessageManager.getString("label.jalview_dev_managers"), x,
2951 g.drawString(MessageManager
2952 .getString("label.jalview_distribution_lists"), x, y += fh);
2953 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2956 MessageManager.getString("label.jalview_cite_1_authors"),
2959 MessageManager.getString("label.jalview_cite_1_title"), x,
2961 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2966 Frame frame = new Frame();
2967 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2969 jalview.bin.JalviewLite.addFrame(frame,
2970 MessageManager.getString("label.jalview"), 580, 220);
2974 public void showURL(String url, String target)
2976 if (viewport.applet == null)
2978 System.out.println("Not running as applet - no browser available.");
2982 viewport.applet.showURL(url, target);
2986 // ////////////////////////////////////////////////////////////////////////////////
2987 // JBuilder Graphics here
2989 MenuBar alignFrameMenuBar = new MenuBar();
2991 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2993 MenuItem loadApplication = new MenuItem(
2994 MessageManager.getString("label.view_full_application"));
2996 MenuItem loadTree = new MenuItem(
2997 MessageManager.getString("label.load_associated_tree"));
2999 MenuItem loadAnnotations = new MenuItem(
3000 MessageManager.getString("label.load_features_annotations"));
3002 MenuItem outputFeatures = new MenuItem(
3003 MessageManager.getString("label.export_features"));
3005 MenuItem outputAnnotations = new MenuItem(
3006 MessageManager.getString("label.export_annotations"));
3008 MenuItem closeMenuItem = new MenuItem(
3009 MessageManager.getString("action.close"));
3011 MenuItem selectAllSequenceMenuItem = new MenuItem(
3012 MessageManager.getString("action.select_all"));
3014 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3015 MessageManager.getString("action.deselect_all"));
3017 MenuItem invertSequenceMenuItem = new MenuItem(
3018 MessageManager.getString("action.invert_selection"));
3020 MenuItem remove2LeftMenuItem = new MenuItem();
3022 MenuItem remove2RightMenuItem = new MenuItem();
3024 MenuItem removeGappedColumnMenuItem = new MenuItem();
3026 MenuItem removeAllGapsMenuItem = new MenuItem();
3028 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3030 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3032 MenuItem sortPairwiseMenuItem = new MenuItem();
3034 MenuItem sortIDMenuItem = new MenuItem();
3036 MenuItem sortLengthMenuItem = new MenuItem();
3038 MenuItem sortGroupMenuItem = new MenuItem();
3040 MenuItem removeRedundancyMenuItem = new MenuItem();
3042 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3044 MenuItem PCAMenuItem = new MenuItem();
3046 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3048 MenuItem neighbourTreeMenuItem = new MenuItem();
3050 BorderLayout borderLayout1 = new BorderLayout();
3052 public Label statusBar = new Label();
3054 MenuItem clustalColour = new MenuItem();
3056 MenuItem zappoColour = new MenuItem();
3058 MenuItem taylorColour = new MenuItem();
3060 MenuItem hydrophobicityColour = new MenuItem();
3062 MenuItem helixColour = new MenuItem();
3064 MenuItem strandColour = new MenuItem();
3066 MenuItem turnColour = new MenuItem();
3068 MenuItem buriedColour = new MenuItem();
3070 MenuItem purinePyrimidineColour = new MenuItem();
3072 // MenuItem RNAInteractionColour = new MenuItem();
3074 MenuItem RNAHelixColour = new MenuItem();
3076 MenuItem userDefinedColour = new MenuItem();
3078 MenuItem PIDColour = new MenuItem();
3080 MenuItem BLOSUM62Colour = new MenuItem();
3082 MenuItem tcoffeeColour = new MenuItem();
3084 MenuItem njTreeBlosumMenuItem = new MenuItem();
3086 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3088 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3090 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3092 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3094 MenuItem alProperties = new MenuItem(
3095 MessageManager.getString("label.alignment_props"));
3097 MenuItem overviewMenuItem = new MenuItem();
3099 MenuItem undoMenuItem = new MenuItem();
3101 MenuItem redoMenuItem = new MenuItem();
3103 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3105 MenuItem noColourmenuItem = new MenuItem();
3107 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3109 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3111 MenuItem findMenuItem = new MenuItem();
3113 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3115 MenuItem nucleotideColour = new MenuItem();
3117 MenuItem deleteGroups = new MenuItem();
3119 MenuItem grpsFromSelection = new MenuItem();
3121 MenuItem createGroup = new MenuItem();
3123 MenuItem unGroup = new MenuItem();
3125 MenuItem delete = new MenuItem();
3127 MenuItem copy = new MenuItem();
3129 MenuItem cut = new MenuItem();
3131 Menu pasteMenu = new Menu();
3133 MenuItem pasteNew = new MenuItem();
3135 MenuItem pasteThis = new MenuItem();
3137 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3139 MenuItem font = new MenuItem();
3141 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3143 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3145 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3147 MenuItem modifyPID = new MenuItem();
3149 MenuItem modifyConservation = new MenuItem();
3151 CheckboxMenuItem autoCalculate = null;
3153 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3154 "Sort Alignment With New Tree", true);
3156 Menu sortByTreeMenu = new Menu();
3158 MenuItem inputText = new MenuItem();
3160 MenuItem documentation = new MenuItem();
3162 MenuItem about = new MenuItem();
3164 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3166 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3168 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3170 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3172 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3174 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3176 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3178 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3180 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3183 * Initialise menus and other items
3187 private void jbInit() throws Exception
3189 setMenuBar(alignFrameMenuBar);
3192 * Configure File menu items and actions
3195 .setLabel(MessageManager.getString("label.input_from_textbox"));
3196 inputText.addActionListener(this);
3197 Menu outputTextboxMenu = new Menu(
3198 MessageManager.getString("label.out_to_textbox"));
3199 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3202 MenuItem item = new MenuItem(
3203 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3205 item.addActionListener(new java.awt.event.ActionListener()
3208 public void actionPerformed(ActionEvent e)
3210 outputText_actionPerformed(e);
3214 outputTextboxMenu.add(item);
3216 closeMenuItem.addActionListener(this);
3217 loadApplication.addActionListener(this);
3218 loadTree.addActionListener(this);
3219 loadAnnotations.addActionListener(this);
3220 outputFeatures.addActionListener(this);
3221 outputAnnotations.addActionListener(this);
3224 * Configure Edit menu items and actions
3226 undoMenuItem.setEnabled(false);
3227 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3228 undoMenuItem.addActionListener(this);
3229 redoMenuItem.setEnabled(false);
3230 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3231 redoMenuItem.addActionListener(this);
3232 copy.setLabel(MessageManager.getString("action.copy"));
3233 copy.addActionListener(this);
3234 cut.setLabel(MessageManager.getString("action.cut"));
3235 cut.addActionListener(this);
3236 delete.setLabel(MessageManager.getString("action.delete"));
3237 delete.addActionListener(this);
3238 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3239 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3240 pasteNew.addActionListener(this);
3241 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3242 pasteThis.addActionListener(this);
3243 remove2LeftMenuItem.setLabel(MessageManager
3244 .getString("action.remove_left"));
3245 remove2LeftMenuItem.addActionListener(this);
3246 remove2RightMenuItem.setLabel(MessageManager
3247 .getString("action.remove_right"));
3248 remove2RightMenuItem.addActionListener(this);
3249 removeGappedColumnMenuItem.setLabel(MessageManager
3250 .getString("action.remove_empty_columns"));
3251 removeGappedColumnMenuItem.addActionListener(this);
3252 removeAllGapsMenuItem.setLabel(MessageManager
3253 .getString("action.remove_all_gaps"));
3254 removeAllGapsMenuItem.addActionListener(this);
3255 removeRedundancyMenuItem.setLabel(MessageManager
3256 .getString("action.remove_redundancy"));
3257 removeRedundancyMenuItem.addActionListener(this);
3260 * Configure Select menu items and actions
3262 findMenuItem.setLabel(MessageManager.getString("action.find"));
3263 findMenuItem.addActionListener(this);
3264 selectAllSequenceMenuItem.addActionListener(this);
3265 deselectAllSequenceMenuItem.addActionListener(this);
3266 invertSequenceMenuItem.setLabel(MessageManager
3267 .getString("action.invert_sequence_selection"));
3268 invertSequenceMenuItem.addActionListener(this);
3269 invertColSel.setLabel(MessageManager
3270 .getString("action.invert_column_selection"));
3271 invertColSel.addActionListener(this);
3272 deleteGroups.setLabel(MessageManager
3273 .getString("action.undefine_groups"));
3274 deleteGroups.addActionListener(this);
3275 grpsFromSelection.setLabel(MessageManager
3276 .getString("action.make_groups_selection"));
3277 grpsFromSelection.addActionListener(this);
3278 createGroup.setLabel(MessageManager.getString("action.create_group"));
3279 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3280 annotationColumnSelection.setLabel(MessageManager
3281 .getString("action.select_by_annotation"));
3282 annotationColumnSelection.addActionListener(this);
3285 * Configure View menu items and actions
3287 newView.setLabel(MessageManager.getString("action.new_view"));
3288 newView.addActionListener(this);
3289 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3290 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3291 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3292 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3294 .setLabel(MessageManager.getString("label.selected_columns"));
3295 hideSequences.setLabel(MessageManager
3296 .getString("label.selected_sequences"));
3297 hideAllButSelection.setLabel(MessageManager
3298 .getString("label.all_but_selected_region"));
3299 hideAllSelection.setLabel(MessageManager
3300 .getString("label.selected_region"));
3301 showAllHidden.setLabel(MessageManager
3302 .getString("label.all_sequences_columns"));
3303 showColumns.addActionListener(this);
3304 showSeqs.addActionListener(this);
3305 hideColumns.addActionListener(this);
3306 hideSequences.addActionListener(this);
3307 hideAllButSelection.addActionListener(this);
3308 hideAllSelection.addActionListener(this);
3309 showAllHidden.addActionListener(this);
3310 featureSettings.setLabel(MessageManager
3311 .getString("action.feature_settings"));
3312 featureSettings.addActionListener(this);
3313 sequenceFeatures.setLabel(MessageManager
3314 .getString("label.show_sequence_features"));
3315 sequenceFeatures.addItemListener(this);
3316 sequenceFeatures.setState(false);
3317 followMouseOverFlag.setLabel(MessageManager
3318 .getString("label.automatic_scrolling"));
3319 followMouseOverFlag.addItemListener(this);
3320 alProperties.addActionListener(this);
3321 overviewMenuItem.setLabel(MessageManager
3322 .getString("label.overview_window"));
3323 overviewMenuItem.addActionListener(this);
3326 * Configure Annotations menu items and actions
3328 annotationPanelMenuItem.setLabel(MessageManager
3329 .getString("label.show_annotations"));
3330 annotationPanelMenuItem.addItemListener(this);
3331 showGroupConsensus.setLabel(MessageManager
3332 .getString("label.group_consensus"));
3333 showGroupConservation.setLabel(MessageManager
3334 .getString("label.group_conservation"));
3335 showConsensusHistogram.setLabel(MessageManager
3336 .getString("label.show_consensus_histogram"));
3337 showSequenceLogo.setLabel(MessageManager
3338 .getString("label.show_consensus_logo"));
3339 normSequenceLogo.setLabel(MessageManager
3340 .getString("label.norm_consensus_logo"));
3341 applyAutoAnnotationSettings.setLabel(MessageManager
3342 .getString("label.apply_all_groups"));
3343 applyAutoAnnotationSettings.setState(true);
3344 Menu autoAnnMenu = new Menu(
3345 MessageManager.getString("label.autocalculated_annotation"));
3346 showGroupConsensus.addItemListener(this);
3347 showGroupConservation.addItemListener(this);
3348 showConsensusHistogram.addItemListener(this);
3349 showSequenceLogo.addItemListener(this);
3350 normSequenceLogo.addItemListener(this);
3351 applyAutoAnnotationSettings.addItemListener(this);
3352 showAlignmentAnnotations = new CheckboxMenuItem(
3353 MessageManager.getString("label.show_all_al_annotations"));
3354 showSequenceAnnotations = new CheckboxMenuItem(
3355 MessageManager.getString("label.show_all_seq_annotations"));
3356 sortAnnBySequence = new CheckboxMenuItem(
3357 MessageManager.getString("label.sort_annotations_by_sequence"));
3358 sortAnnByLabel = new CheckboxMenuItem(
3359 MessageManager.getString("label.sort_annotations_by_label"));
3360 showAutoFirst = new CheckboxMenuItem(
3361 MessageManager.getString("label.show_first"));
3362 showAutoFirst.setState(false); // pending applet parameter
3363 setShowAutoCalculatedAbove(showAutoFirst.getState());
3364 showAutoLast = new CheckboxMenuItem(
3365 MessageManager.getString("label.show_last"));
3366 showAutoLast.setState(!showAutoFirst.getState());
3367 showAlignmentAnnotations.addItemListener(this);
3368 showSequenceAnnotations.addItemListener(this);
3369 sortAnnBySequence.addItemListener(this);
3370 sortAnnByLabel.addItemListener(this);
3371 showAutoFirst.addItemListener(this);
3372 showAutoLast.addItemListener(this);
3375 * Configure Format menu items and actions
3377 font.setLabel(MessageManager.getString("action.font"));
3378 font.addActionListener(this);
3379 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3380 scaleAbove.setState(true);
3381 scaleAbove.setEnabled(false);
3382 scaleAbove.addItemListener(this);
3383 scaleLeft.setEnabled(false);
3384 scaleLeft.setState(true);
3385 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3386 scaleLeft.addItemListener(this);
3387 scaleRight.setEnabled(false);
3388 scaleRight.setState(true);
3389 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3390 scaleRight.addItemListener(this);
3391 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3392 viewBoxesMenuItem.setState(true);
3393 viewBoxesMenuItem.addItemListener(this);
3394 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3395 viewTextMenuItem.setState(true);
3396 viewTextMenuItem.addItemListener(this);
3397 colourTextMenuItem.setLabel(MessageManager
3398 .getString("label.colour_text"));
3399 colourTextMenuItem.addItemListener(this);
3400 displayNonconservedMenuItem.setLabel(MessageManager
3401 .getString("label.show_non_conversed"));
3402 displayNonconservedMenuItem.addItemListener(this);
3403 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3404 wrapMenuItem.addItemListener(this);
3405 renderGapsMenuItem.setLabel(MessageManager
3406 .getString("action.show_gaps"));
3407 renderGapsMenuItem.setState(true);
3408 renderGapsMenuItem.addItemListener(this);
3409 centreColumnLabelFlag.setLabel(MessageManager
3410 .getString("label.centre_column_labels"));
3411 centreColumnLabelFlag.addItemListener(this);
3412 seqLimits.setState(true);
3413 seqLimits.setLabel(MessageManager
3414 .getString("label.show_sequence_limits"));
3415 seqLimits.addItemListener(this);
3418 * Configure Colour menu items and actions
3420 applyToAllGroups.setLabel(MessageManager
3421 .getString("label.apply_colour_to_all_groups"));
3422 applyToAllGroups.setState(true);
3423 applyToAllGroups.addItemListener(this);
3424 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3425 clustalColour.addActionListener(this);
3426 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3427 zappoColour.addActionListener(this);
3428 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3429 taylorColour.addActionListener(this);
3430 hydrophobicityColour.setLabel(MessageManager
3431 .getString("label.hydrophobicity"));
3432 hydrophobicityColour.addActionListener(this);
3434 .setLabel(MessageManager.getString("label.helix_propensity"));
3435 helixColour.addActionListener(this);
3436 strandColour.setLabel(MessageManager
3437 .getString("label.strand_propensity"));
3438 strandColour.addActionListener(this);
3439 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3440 turnColour.addActionListener(this);
3441 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3442 buriedColour.addActionListener(this);
3443 purinePyrimidineColour.setLabel(MessageManager
3444 .getString("label.purine_pyrimidine"));
3445 purinePyrimidineColour.addActionListener(this);
3446 // RNAInteractionColour.setLabel(MessageManager
3447 // .getString("label.rna_interaction"));
3448 // RNAInteractionColour.addActionListener(this);
3449 RNAHelixColour.setLabel(MessageManager
3450 .getString("action.by_rna_helixes"));
3451 RNAHelixColour.addActionListener(this);
3452 userDefinedColour.setLabel(MessageManager
3453 .getString("action.user_defined"));
3454 userDefinedColour.addActionListener(this);
3455 PIDColour.setLabel(MessageManager
3456 .getString("label.percentage_identity"));
3457 PIDColour.addActionListener(this);
3458 BLOSUM62Colour.setLabel(MessageManager
3459 .getString("label.blosum62_score"));
3460 BLOSUM62Colour.addActionListener(this);
3462 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3463 // it will be enabled only if a score file is provided
3464 tcoffeeColour.setEnabled(false);
3465 tcoffeeColour.addActionListener(this);
3466 conservationMenuItem.setLabel(MessageManager
3467 .getString("action.by_conservation"));
3468 conservationMenuItem.addItemListener(this);
3469 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3470 noColourmenuItem.addActionListener(this);
3471 abovePIDThreshold.setLabel(MessageManager
3472 .getString("label.above_identity_threshold"));
3473 abovePIDThreshold.addItemListener(this);
3474 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3475 nucleotideColour.addActionListener(this);
3476 modifyPID.setLabel(MessageManager
3477 .getString("label.modify_identity_thereshold"));
3478 modifyPID.addActionListener(this);
3479 modifyConservation.setLabel(MessageManager
3480 .getString("label.modify_conservation_thereshold"));
3481 modifyConservation.addActionListener(this);
3482 annotationColour.setLabel(MessageManager
3483 .getString("action.by_annotation"));
3484 annotationColour.addActionListener(this);
3487 * Configure Calculate menu items and actions
3489 sortPairwiseMenuItem.setLabel(MessageManager
3490 .getString("action.by_pairwise_id"));
3491 sortPairwiseMenuItem.addActionListener(this);
3492 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3493 sortIDMenuItem.addActionListener(this);
3494 sortLengthMenuItem.setLabel(MessageManager
3495 .getString("action.by_length"));
3496 sortLengthMenuItem.addActionListener(this);
3497 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3498 sortGroupMenuItem.addActionListener(this);
3499 pairwiseAlignmentMenuItem.setLabel(MessageManager
3500 .getString("action.pairwise_alignment"));
3501 pairwiseAlignmentMenuItem.addActionListener(this);
3502 PCAMenuItem.setLabel(MessageManager
3503 .getString("label.principal_component_analysis"));
3504 PCAMenuItem.addActionListener(this);
3505 autoCalculate = new CheckboxMenuItem(
3506 MessageManager.getString("label.autocalculate_consensus"), true);
3507 averageDistanceTreeMenuItem.setLabel(MessageManager
3508 .getString("label.average_distance_identity"));
3509 averageDistanceTreeMenuItem.addActionListener(this);
3510 neighbourTreeMenuItem.setLabel(MessageManager
3511 .getString("label.neighbour_joining_identity"));
3512 neighbourTreeMenuItem.addActionListener(this);
3513 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3514 .getString("label.average_distance_bloslum62"));
3515 avDistanceTreeBlosumMenuItem.addActionListener(this);
3516 njTreeBlosumMenuItem.setLabel(MessageManager
3517 .getString("label.neighbour_blosum62"));
3518 njTreeBlosumMenuItem.addActionListener(this);
3519 sortByTreeMenu.setLabel(MessageManager
3520 .getString("action.by_tree_order"));
3521 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3522 Menu calculateTreeMenu = new Menu(
3523 MessageManager.getString("action.calculate_tree"));
3524 autoCalculate.addItemListener(this);
3525 sortByTree.addItemListener(this);
3528 * Configure Help menu items and actions
3530 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3531 documentation.setLabel(MessageManager.getString("label.documentation"));
3532 documentation.addActionListener(this);
3533 about.setLabel(MessageManager.getString("label.about"));
3534 about.addActionListener(this);
3537 * Add top level menus to frame
3539 alignFrameMenuBar.add(fileMenu);
3540 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3541 alignFrameMenuBar.add(editMenu);
3542 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3543 alignFrameMenuBar.add(selectMenu);
3544 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3545 alignFrameMenuBar.add(viewMenu);
3546 Menu annotationsMenu = new Menu(
3547 MessageManager.getString("action.annotations"));
3548 alignFrameMenuBar.add(annotationsMenu);
3549 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3550 alignFrameMenuBar.add(formatMenu);
3551 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3552 alignFrameMenuBar.add(colourMenu);
3553 Menu calculateMenu = new Menu(
3554 MessageManager.getString("action.calculate"));
3555 alignFrameMenuBar.add(calculateMenu);
3556 alignFrameMenuBar.add(helpMenu);
3561 fileMenu.add(inputText);
3562 fileMenu.add(loadTree);
3563 fileMenu.add(loadAnnotations);
3564 fileMenu.addSeparator();
3565 fileMenu.add(outputTextboxMenu);
3566 fileMenu.add(outputFeatures);
3567 fileMenu.add(outputAnnotations);
3568 if (jalviewServletURL != null)
3570 fileMenu.add(loadApplication);
3572 fileMenu.addSeparator();
3573 fileMenu.add(closeMenuItem);
3578 editMenu.add(undoMenuItem);
3579 editMenu.add(redoMenuItem);
3582 pasteMenu.add(pasteNew);
3583 pasteMenu.add(pasteThis);
3584 editMenu.add(pasteMenu);
3585 editMenu.add(delete);
3586 editMenu.addSeparator();
3587 editMenu.add(remove2LeftMenuItem);
3588 editMenu.add(remove2RightMenuItem);
3589 editMenu.add(removeGappedColumnMenuItem);
3590 editMenu.add(removeAllGapsMenuItem);
3591 editMenu.add(removeRedundancyMenuItem);
3596 selectMenu.add(findMenuItem);
3597 selectMenu.addSeparator();
3598 selectMenu.add(selectAllSequenceMenuItem);
3599 selectMenu.add(deselectAllSequenceMenuItem);
3600 selectMenu.add(invertSequenceMenuItem);
3601 selectMenu.add(invertColSel);
3602 selectMenu.add(createGroup);
3603 selectMenu.add(unGroup);
3604 selectMenu.add(grpsFromSelection);
3605 selectMenu.add(deleteGroups);
3606 selectMenu.add(annotationColumnSelection);
3611 viewMenu.add(newView);
3612 viewMenu.addSeparator();
3613 showMenu.add(showColumns);
3614 showMenu.add(showSeqs);
3615 showMenu.add(showAllHidden);
3616 viewMenu.add(showMenu);
3617 hideMenu.add(hideColumns);
3618 hideMenu.add(hideSequences);
3619 hideMenu.add(hideAllSelection);
3620 hideMenu.add(hideAllButSelection);
3621 viewMenu.add(hideMenu);
3622 viewMenu.addSeparator();
3623 viewMenu.add(followMouseOverFlag);
3624 viewMenu.addSeparator();
3625 viewMenu.add(sequenceFeatures);
3626 viewMenu.add(featureSettings);
3627 viewMenu.addSeparator();
3628 viewMenu.add(alProperties);
3629 viewMenu.addSeparator();
3630 viewMenu.add(overviewMenuItem);
3635 annotationsMenu.add(annotationPanelMenuItem);
3636 annotationsMenu.addSeparator();
3637 annotationsMenu.add(showAlignmentAnnotations);
3638 annotationsMenu.add(showSequenceAnnotations);
3639 annotationsMenu.add(sortAnnBySequence);
3640 annotationsMenu.add(sortAnnByLabel);
3641 annotationsMenu.addSeparator();
3642 autoAnnMenu.add(showAutoFirst);
3643 autoAnnMenu.add(showAutoLast);
3644 autoAnnMenu.addSeparator();
3645 autoAnnMenu.add(applyAutoAnnotationSettings);
3646 autoAnnMenu.add(showConsensusHistogram);
3647 autoAnnMenu.add(showSequenceLogo);
3648 autoAnnMenu.add(normSequenceLogo);
3649 autoAnnMenu.addSeparator();
3650 autoAnnMenu.add(showGroupConservation);
3651 autoAnnMenu.add(showGroupConsensus);
3652 annotationsMenu.add(autoAnnMenu);
3657 formatMenu.add(font);
3658 formatMenu.add(seqLimits);
3659 formatMenu.add(wrapMenuItem);
3660 formatMenu.add(scaleAbove);
3661 formatMenu.add(scaleLeft);
3662 formatMenu.add(scaleRight);
3663 formatMenu.add(viewBoxesMenuItem);
3664 formatMenu.add(viewTextMenuItem);
3665 formatMenu.add(colourTextMenuItem);
3666 formatMenu.add(displayNonconservedMenuItem);
3667 formatMenu.add(renderGapsMenuItem);
3668 formatMenu.add(centreColumnLabelFlag);
3673 colourMenu.add(applyToAllGroups);
3674 colourMenu.addSeparator();
3675 colourMenu.add(noColourmenuItem);
3676 colourMenu.add(clustalColour);
3677 colourMenu.add(BLOSUM62Colour);
3678 colourMenu.add(PIDColour);
3679 colourMenu.add(zappoColour);
3680 colourMenu.add(taylorColour);
3681 colourMenu.add(hydrophobicityColour);
3682 colourMenu.add(helixColour);
3683 colourMenu.add(strandColour);
3684 colourMenu.add(turnColour);
3685 colourMenu.add(buriedColour);
3686 colourMenu.add(nucleotideColour);
3687 colourMenu.add(purinePyrimidineColour);
3688 // colourMenu.add(RNAInteractionColour);
3689 colourMenu.add(tcoffeeColour);
3690 colourMenu.add(userDefinedColour);
3691 colourMenu.addSeparator();
3692 colourMenu.add(conservationMenuItem);
3693 colourMenu.add(modifyConservation);
3694 colourMenu.add(abovePIDThreshold);
3695 colourMenu.add(modifyPID);
3696 colourMenu.add(annotationColour);
3697 colourMenu.add(RNAHelixColour);
3702 sortMenu.add(sortIDMenuItem);
3703 sortMenu.add(sortLengthMenuItem);
3704 sortMenu.add(sortByTreeMenu);
3705 sortMenu.add(sortGroupMenuItem);
3706 sortMenu.add(sortPairwiseMenuItem);
3707 calculateMenu.add(sortMenu);
3708 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3709 calculateTreeMenu.add(neighbourTreeMenuItem);
3710 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3711 calculateTreeMenu.add(njTreeBlosumMenuItem);
3712 calculateMenu.add(calculateTreeMenu);
3713 calculateMenu.addSeparator();
3714 calculateMenu.add(pairwiseAlignmentMenuItem);
3715 calculateMenu.add(PCAMenuItem);
3716 calculateMenu.add(autoCalculate);
3717 calculateMenu.add(sortByTree);
3722 helpMenu.add(documentation);
3723 helpMenu.add(about);
3728 statusBar.setBackground(Color.white);
3729 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3730 statusBar.setText(MessageManager.getString("label.status_bar"));
3731 this.add(statusBar, BorderLayout.SOUTH);
3734 public void setStatus(String string)
3736 statusBar.setText(string);
3739 MenuItem featureSettings = new MenuItem();
3741 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3743 MenuItem annotationColour = new MenuItem();
3745 MenuItem annotationColumnSelection = new MenuItem();
3747 MenuItem invertColSel = new MenuItem();
3749 MenuItem showColumns = new MenuItem();
3751 MenuItem showSeqs = new MenuItem();
3753 MenuItem hideColumns = new MenuItem();
3755 MenuItem hideSequences = new MenuItem();
3757 MenuItem hideAllButSelection = new MenuItem();
3759 MenuItem hideAllSelection = new MenuItem();
3761 MenuItem showAllHidden = new MenuItem();
3763 MenuItem newView = new MenuItem();
3765 private CheckboxMenuItem showAlignmentAnnotations;
3767 private CheckboxMenuItem showSequenceAnnotations;
3769 private CheckboxMenuItem sortAnnBySequence;
3771 private CheckboxMenuItem sortAnnByLabel;
3773 private CheckboxMenuItem showAutoFirst;
3775 private CheckboxMenuItem showAutoLast;
3777 private SplitFrame splitFrame;
3780 * Attach the alignFrame panels after embedding menus, if necessary. This used
3781 * to be called setEmbedded, but is now creates the dropdown menus in a
3782 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3784 * @param reallyEmbedded
3785 * true to attach the view to the applet area on the page rather than
3788 public void createAlignFrameWindow(boolean reallyEmbedded)
3792 embedAlignFrameInApplet(viewport.applet);
3797 // test and embed menu bar if necessary.
3799 if (embedMenuIfNeeded(alignPanel))
3802 * adjust for status bar height too. ? pointless as overridden by layout
3805 alignPanel.setSize(getSize().width,
3806 getSize().height - statusBar.getHeight());
3808 add(statusBar, BorderLayout.SOUTH);
3809 add(alignPanel, BorderLayout.CENTER);
3810 // and register with the applet so it can pass external API calls to us
3811 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3817 * Add the components of this AlignFrame to the applet container.
3821 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3824 // Explicitly build the embedded menu panel for the on-page applet
3826 // view cannot be closed if its actually on the page
3827 fileMenu.remove(closeMenuItem);
3828 fileMenu.remove(3); // Remove Separator
3829 // construct embedded menu, using default font
3830 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3831 // and actually add the components to the applet area
3832 theApplet.setLayout(new BorderLayout());
3833 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3834 theApplet.add(statusBar, BorderLayout.SOUTH);
3835 // TODO should size be left to the layout manager?
3836 alignPanel.setSize(theApplet.getSize().width,
3837 theApplet.getSize().height - embeddedMenu.getHeight()
3838 - statusBar.getHeight());
3839 theApplet.add(alignPanel, BorderLayout.CENTER);
3840 final AlignFrame me = this;
3841 theApplet.addFocusListener(new FocusListener()
3845 public void focusLost(FocusEvent e)
3847 if (theApplet.currentAlignFrame == me)
3849 theApplet.currentAlignFrame = null;
3854 public void focusGained(FocusEvent e)
3856 theApplet.currentAlignFrame = me;
3859 theApplet.validate();
3863 * create a new binding between structures in an existing jmol viewer instance
3864 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3865 * this does not open a new Jmol window, or modify the display of the
3866 * structures in the original jmol window. Note This method doesn't work
3867 * without an additional javascript library to exchange messages between the
3868 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3871 * JmolViewer instance
3872 * @param sequenceIds
3873 * - sequence Ids to search for associations
3875 public SequenceStructureBinding addStructureViewInstance(
3876 Object jmolviewer, String[] sequenceIds)
3878 Viewer viewer = null;
3881 viewer = (Viewer) jmolviewer;
3882 } catch (ClassCastException ex)
3884 System.err.println("Unsupported viewer object :"
3885 + jmolviewer.getClass());
3889 System.err.println("Can't use this object as a structure viewer:"
3890 + jmolviewer.getClass());
3893 SequenceI[] seqs = null;
3894 if (sequenceIds == null || sequenceIds.length == 0)
3896 seqs = viewport.getAlignment().getSequencesArray();
3900 Vector sqi = new Vector();
3901 AlignmentI al = viewport.getAlignment();
3902 for (int sid = 0; sid < sequenceIds.length; sid++)
3904 SequenceI sq = al.findName(sequenceIds[sid]);
3912 seqs = new SequenceI[sqi.size()];
3913 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3915 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3923 AAStructureBindingModel jmv = null;
3924 // TODO: search for a jmv that involves viewer
3926 { // create a new viewer/jalview binding.
3927 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3934 * bind a pdb file to a sequence in the current view
3937 * - sequenceId within the dataset.
3938 * @param pdbEntryString
3939 * - the short name for the PDB file
3941 * - pdb file - either a URL or a valid PDB file.
3942 * @return true if binding was as success TODO: consider making an exception
3943 * structure for indicating when PDB parsing or sequenceId location
3946 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3949 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3950 boolean needtoadd = false;
3951 if (toaddpdb != null)
3953 Vector pdbe = toaddpdb.getAllPDBEntries();
3954 PDBEntry pdbentry = null;
3955 if (pdbe != null && pdbe.size() > 0)
3957 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3959 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3960 if (!pdbentry.getId().equals(pdbEntryString)
3961 && !pdbentry.getFile().equals(pdbFile))
3971 if (pdbentry == null)
3973 pdbentry = new PDBEntry();
3974 pdbentry.setId(pdbEntryString);
3975 pdbentry.setFile(pdbFile);
3976 needtoadd = true; // add this new entry to sequence.
3978 // resolve data source
3979 // TODO: this code should be a refactored to an io package
3980 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3981 if (protocol == null)
3987 // make a note of the access mode and add
3988 if (pdbentry.getProperty() == null)
3990 pdbentry.setProperty(new Hashtable());
3992 pdbentry.getProperty().put("protocol", protocol);
3993 toaddpdb.addPDBId(pdbentry);
3994 alignPanel.getStructureSelectionManager()
3995 .registerPDBEntry(pdbentry);
4001 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4005 Vector sequences = new Vector();
4006 for (int i = 0; i < seqs.length; i++)
4008 if (seqs[i] != null)
4010 sequences.addElement(new Object[] { seqs[i],
4011 (chains != null) ? chains[i] : null });
4014 seqs = new SequenceI[sequences.size()];
4015 chains = new String[sequences.size()];
4016 for (int i = 0, isize = sequences.size(); i < isize; i++)
4018 Object[] oj = (Object[]) sequences.elementAt(i);
4020 seqs[i] = (SequenceI) oj[0];
4021 chains[i] = (String) oj[1];
4024 return new Object[] { seqs, chains };
4028 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4029 SequenceI[] seqs, String[] chains, String protocol)
4031 // Scrub any null sequences from the array
4032 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4033 seqs = (SequenceI[]) sqch[0];
4034 chains = (String[]) sqch[1];
4035 if (seqs == null || seqs.length == 0)
4038 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4040 if (protocol == null || protocol.trim().length() == 0
4041 || protocol.equals("null"))
4043 protocol = (String) pdb.getProperty().get("protocol");
4044 if (protocol == null)
4046 System.err.println("Couldn't work out protocol to open structure: "
4051 if (applet.useXtrnalSviewer)
4053 // register the association(s) and quit, don't create any windows.
4054 if (StructureSelectionManager.getStructureSelectionManager(applet)
4055 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4057 System.err.println("Failed to map " + pdb.getFile() + " ("
4058 + protocol + ") to any sequences");
4062 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4064 // can only do alignments with Jmol
4065 // find the last jmol window assigned to this alignment
4066 jalview.appletgui.AppletJmol ajm = null, tajm;
4067 Vector jmols = applet
4068 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4069 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4071 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4072 if (tajm.ap.alignFrame == this)
4081 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4082 // try and add the pdb structure
4087 // otherwise, create a new window
4088 if (applet.jmolAvailable)
4090 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4092 applet.lastFrameX += 40;
4093 applet.lastFrameY += 40;
4097 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4102 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4103 SequenceI[][] seqs, String[][] chains, String[] protocols)
4105 // TODO Auto-generated method stub
4106 System.err.println("Aligned Structure View: Not yet implemented.");
4110 * modify the current selection, providing the user has not made a selection
4114 * - sequences from this alignment
4116 * - columns to be selected on the alignment
4118 public void select(SequenceGroup sel, ColumnSelection csel)
4120 alignPanel.seqPanel.selection(sel, csel, null);
4123 public void scrollTo(int row, int column)
4125 alignPanel.seqPanel.scrollTo(row, column);
4128 public void scrollToRow(int row)
4130 alignPanel.seqPanel.scrollToRow(row);
4133 public void scrollToColumn(int column)
4135 alignPanel.seqPanel.scrollToColumn(column);
4139 * @return the alignments unique ID.
4141 public String getSequenceSetId()
4143 return viewport.getSequenceSetId();
4147 * Load the (T-Coffee) score file from the specified url
4150 * File/URL/T-COFFEE score file contents
4151 * @throws IOException
4152 * @return true if alignment was annotated with data from source
4154 public boolean loadScoreFile(String source) throws IOException
4157 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4158 AppletFormatAdapter.checkProtocol(source));
4159 if (!file.isValid())
4161 // TODO: raise dialog for gui
4162 System.err.println("Problems parsing T-Coffee scores: "
4163 + file.getWarningMessage());
4164 System.err.println("Origin was:\n" + source);
4169 * check that the score matrix matches the alignment dimensions
4172 if ((aln = viewport.getAlignment()) != null
4173 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4176 // TODO: raise a dialog box here rather than bomb out.
4178 .println("The scores matrix does not match the alignment dimensions");
4182 // TODO add parameter to indicate if matching should be done
4183 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4185 alignPanel.fontChanged();
4186 tcoffeeColour.setEnabled(true);
4187 // switch to this color
4188 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4193 System.err.println("Problems resolving T-Coffee scores:");
4194 if (file.getWarningMessage() != null)
4196 System.err.println(file.getWarningMessage());
4202 public SplitFrame getSplitFrame()
4204 return this.splitFrame;
4207 public void setSplitFrame(SplitFrame sf)
4209 this.splitFrame = sf;
4212 // may not need this
4214 public void setShowSeqFeatures(boolean b)
4216 // showSeqFeatures.setSelected(b);
4217 viewport.setShowSequenceFeatures(b);
4222 public void setMenusForViewport()
4224 // setMenusFromViewport(viewport);
4229 public void refreshFeatureUI(boolean enableIfNecessary)
4231 if (enableIfNecessary)
4233 sequenceFeatures.setState(true);
4234 alignPanel.av.setShowSequenceFeatures(true);
4239 public FeatureSettingsControllerI getFeatureSettingsUI()
4241 return alignPanel.av.featureSettings;