2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import java.awt.BorderLayout;
24 import java.awt.Canvas;
25 import java.awt.CheckboxMenuItem;
26 import java.awt.Color;
28 import java.awt.FontMetrics;
29 import java.awt.Frame;
30 import java.awt.Graphics;
31 import java.awt.Label;
33 import java.awt.MenuBar;
34 import java.awt.MenuItem;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.ActionListener;
37 import java.awt.event.FocusEvent;
38 import java.awt.event.FocusListener;
39 import java.awt.event.ItemEvent;
40 import java.awt.event.ItemListener;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.KeyListener;
43 import java.awt.event.WindowAdapter;
44 import java.awt.event.WindowEvent;
45 import java.io.IOException;
47 import java.net.URLEncoder;
48 import java.util.Arrays;
49 import java.util.Deque;
50 import java.util.HashMap;
51 import java.util.Hashtable;
52 import java.util.List;
54 import java.util.StringTokenizer;
55 import java.util.Vector;
57 import jalview.analysis.AlignmentSorter;
58 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
59 import jalview.api.AlignViewControllerGuiI;
60 import jalview.api.AlignViewControllerI;
61 import jalview.api.AlignViewportI;
62 import jalview.api.FeatureRenderer;
63 import jalview.api.SequenceStructureBinding;
64 import jalview.bin.JalviewLite;
65 import jalview.commands.CommandI;
66 import jalview.commands.EditCommand;
67 import jalview.commands.EditCommand.Action;
68 import jalview.commands.OrderCommand;
69 import jalview.commands.RemoveGapColCommand;
70 import jalview.commands.RemoveGapsCommand;
71 import jalview.commands.SlideSequencesCommand;
72 import jalview.commands.TrimRegionCommand;
73 import jalview.datamodel.Alignment;
74 import jalview.datamodel.AlignmentAnnotation;
75 import jalview.datamodel.AlignmentI;
76 import jalview.datamodel.AlignmentOrder;
77 import jalview.datamodel.ColumnSelection;
78 import jalview.datamodel.PDBEntry;
79 import jalview.datamodel.Sequence;
80 import jalview.datamodel.SequenceGroup;
81 import jalview.datamodel.SequenceI;
82 import jalview.io.AnnotationFile;
83 import jalview.io.AppletFormatAdapter;
84 import jalview.io.FeaturesFile;
85 import jalview.io.TCoffeeScoreFile;
86 import jalview.schemes.Blosum62ColourScheme;
87 import jalview.schemes.BuriedColourScheme;
88 import jalview.schemes.ClustalxColourScheme;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.HelixColourScheme;
91 import jalview.schemes.HydrophobicColourScheme;
92 import jalview.schemes.NucleotideColourScheme;
93 import jalview.schemes.PIDColourScheme;
94 import jalview.schemes.PurinePyrimidineColourScheme;
95 import jalview.schemes.RNAHelicesColourChooser;
96 import jalview.schemes.RNAInteractionColourScheme;
97 import jalview.schemes.StrandColourScheme;
98 import jalview.schemes.TCoffeeColourScheme;
99 import jalview.schemes.TaylorColourScheme;
100 import jalview.schemes.TurnColourScheme;
101 import jalview.schemes.ZappoColourScheme;
102 import jalview.structure.StructureSelectionManager;
103 import jalview.structures.models.AAStructureBindingModel;
104 import jalview.util.MappingUtils;
105 import jalview.util.MessageManager;
107 public class AlignFrame extends EmbmenuFrame implements ActionListener,
108 ItemListener, KeyListener, AlignViewControllerGuiI
110 public AlignViewControllerI avc;
112 public AlignmentPanel alignPanel;
114 public AlignViewport viewport;
116 int DEFAULT_WIDTH = 700;
118 int DEFAULT_HEIGHT = 500;
120 String jalviewServletURL;
123 * Flag for showing autocalculated consensus above or below other consensus
126 private boolean showAutoCalculatedAbove;
128 private SequenceAnnotationOrder annotationSortOrder;
131 * Constructor that creates the frame and adds it to the display.
138 public AlignFrame(AlignmentI al, JalviewLite applet,
139 String title, boolean embedded)
141 this(al, applet, title, embedded, true);
145 * Constructor that optionally allows the frame to be displayed or only
152 * @param addToDisplay
154 public AlignFrame(AlignmentI al, JalviewLite applet,
155 String title, boolean embedded, boolean addToDisplay)
159 jalviewServletURL = applet.getParameter("APPLICATION_URL");
165 } catch (Exception ex)
167 ex.printStackTrace();
169 // need to get window geometry before we calculate alignment layout
175 param = applet.getParameter("windowWidth");
178 int width = Integer.parseInt(param);
179 DEFAULT_WIDTH = width;
181 param = applet.getParameter("windowHeight");
184 int height = Integer.parseInt(param);
185 DEFAULT_HEIGHT = height;
187 } catch (Exception ex)
191 viewport = new AlignViewport(al, applet);
192 alignPanel = new AlignmentPanel(this, viewport);
193 avc = new jalview.controller.AlignViewController(this, viewport,
195 viewport.updateConservation(alignPanel);
196 viewport.updateConsensus(alignPanel);
198 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
199 followMouseOverFlag.setState(viewport.getFollowHighlight());
200 showGroupConsensus.setState(viewport.isShowGroupConsensus());
201 showGroupConservation.setState(viewport.isShowGroupConservation());
202 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
203 showSequenceLogo.setState(viewport.isShowSequenceLogo());
204 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
205 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
206 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
207 showSequenceAnnotations.setState(viewport.isShowAnnotation());
209 seqLimits.setState(viewport.getShowJVSuffix());
213 String param = applet.getParameter("sortBy");
216 if (param.equalsIgnoreCase("Id"))
218 sortIDMenuItem_actionPerformed();
220 else if (param.equalsIgnoreCase("Pairwise Identity"))
222 sortPairwiseMenuItem_actionPerformed();
224 else if (param.equalsIgnoreCase("Length"))
226 sortLengthMenuItem_actionPerformed();
230 param = applet.getParameter("wrap");
233 if (param.equalsIgnoreCase("true"))
235 wrapMenuItem.setState(true);
236 wrapMenuItem_actionPerformed();
239 param = applet.getParameter("centrecolumnlabels");
242 centreColumnLabelFlag.setState(true);
243 centreColumnLabelFlag_stateChanged();
247 if (viewport.getAlignment().isNucleotide())
249 viewport.updateStrucConsensus(alignPanel);
250 if (viewport.getAlignment().hasRNAStructure())
252 RNAHelixColour.setEnabled(true);
256 RNAHelixColour.setEnabled(false);
261 RNAHelixColour.setEnabled(false);
262 purinePyrimidineColour.setEnabled(false);
264 // Some JVMS send keyevents to Top frame or lowest panel,
265 // Havent worked out why yet. So add to both this frame and seqCanvas for
267 this.addKeyListener(this);
268 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
269 alignPanel.idPanel.idCanvas.addKeyListener(this);
270 alignPanel.scalePanel.addKeyListener(this);
271 alignPanel.annotationPanel.addKeyListener(this);
272 alignPanel.annotationPanelHolder.addKeyListener(this);
273 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
274 alignPanel.alabels.addKeyListener(this);
278 addToDisplay(embedded);
285 public void addToDisplay(boolean embedded)
287 createAlignFrameWindow(embedded);
289 alignPanel.adjustAnnotationHeight();
290 alignPanel.paintAlignment(true);
293 public AlignViewport getAlignViewport()
298 public SeqCanvas getSeqcanvas()
300 return alignPanel.seqPanel.seqCanvas;
304 * Load a features file onto the alignment
307 * file URL, content, or other resolvable path
309 * is protocol for accessing data referred to by file
312 public boolean parseFeaturesFile(String file, String type)
314 return parseFeaturesFile(file, type, true);
318 * Load a features file onto the alignment
321 * file URL, content, or other resolvable path
323 * is protocol for accessing data referred to by file
324 * @param autoenabledisplay
325 * when true, display features flag will be automatically enabled if
326 * features are loaded
327 * @return true if data parsed as a features file
329 public boolean parseFeaturesFile(String file, String type,
330 boolean autoenabledisplay)
332 // TODO: test if importing a features file onto an alignment which already
333 // has features with links overwrites the original links.
335 Hashtable featureLinks = new Hashtable();
336 boolean featuresFile = false;
339 featuresFile = new jalview.io.FeaturesFile(file, type)
340 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
341 .getFeatureRenderer().getFeatureColours(), featureLinks,
342 true, viewport.applet.getDefaultParameter(
343 "relaxedidmatch", false));
344 } catch (Exception ex)
346 ex.printStackTrace();
351 if (featureLinks.size() > 0)
353 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
355 if (autoenabledisplay)
357 viewport.setShowSequenceFeatures(true);
358 sequenceFeatures.setState(true);
360 if (alignPanel.seqPanel.seqCanvas.fr != null)
362 // update the min/max ranges where necessary
363 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
365 if (viewport.featureSettings != null)
367 viewport.featureSettings.refreshTable();
369 alignPanel.paintAlignment(true);
370 statusBar.setText(MessageManager
371 .getString("label.successfully_added_features_alignment"));
377 public void keyPressed(KeyEvent evt)
379 if (viewport.cursorMode
380 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
381 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
382 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
383 && Character.isDigit(evt.getKeyChar()))
385 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
388 switch (evt.getKeyCode())
390 case 27: // escape key
391 deselectAllSequenceMenuItem_actionPerformed();
393 alignPanel.alabels.cancelDrag();
396 if (evt.isControlDown() || evt.isMetaDown())
398 cut_actionPerformed();
402 if (viewport.cursorMode && !evt.isControlDown())
404 alignPanel.seqPanel.setCursorColumn();
406 if (evt.isControlDown() || evt.isMetaDown())
408 copy_actionPerformed();
412 if (evt.isControlDown())
414 paste(evt.isShiftDown());
418 if (evt.isControlDown() || evt.isMetaDown())
420 selectAllSequenceMenuItem_actionPerformed();
423 case KeyEvent.VK_DOWN:
424 if (viewport.cursorMode)
426 alignPanel.seqPanel.moveCursor(0, 1);
430 moveSelectedSequences(false);
435 if (viewport.cursorMode)
437 alignPanel.seqPanel.moveCursor(0, -1);
441 moveSelectedSequences(true);
445 case KeyEvent.VK_LEFT:
446 if (evt.isAltDown() || !viewport.cursorMode)
448 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
452 alignPanel.seqPanel.moveCursor(-1, 0);
456 case KeyEvent.VK_RIGHT:
457 if (evt.isAltDown() || !viewport.cursorMode)
459 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
463 alignPanel.seqPanel.moveCursor(1, 0);
467 case KeyEvent.VK_SPACE:
468 if (viewport.cursorMode)
470 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
471 || evt.isShiftDown() || evt.isAltDown());
475 case KeyEvent.VK_DELETE:
476 case KeyEvent.VK_BACK_SPACE:
477 if (viewport.cursorMode)
479 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
480 || evt.isShiftDown() || evt.isAltDown());
484 cut_actionPerformed();
485 alignPanel.seqPanel.seqCanvas.repaint();
490 if (viewport.cursorMode)
492 alignPanel.seqPanel.setCursorRow();
496 if (viewport.cursorMode)
498 alignPanel.seqPanel.setCursorPosition();
502 case KeyEvent.VK_ENTER:
503 case KeyEvent.VK_COMMA:
504 if (viewport.cursorMode)
506 alignPanel.seqPanel.setCursorRowAndColumn();
511 if (viewport.cursorMode)
513 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
517 if (viewport.cursorMode)
519 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
524 viewport.cursorMode = !viewport.cursorMode;
525 statusBar.setText(MessageManager.formatMessage(
526 "label.keyboard_editing_mode", new String[]
527 { (viewport.cursorMode ? "on" : "off") }));
528 if (viewport.cursorMode)
530 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
531 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
536 if (evt.isControlDown())
538 findMenuItem_actionPerformed();
544 boolean toggleSeqs = !evt.isControlDown();
545 boolean toggleCols = !evt.isShiftDown();
546 toggleHiddenRegions(toggleSeqs, toggleCols);
550 case KeyEvent.VK_PAGE_UP:
551 if (viewport.getWrapAlignment())
553 alignPanel.scrollUp(true);
557 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
558 - viewport.endSeq + viewport.startSeq);
562 case KeyEvent.VK_PAGE_DOWN:
563 if (viewport.getWrapAlignment())
565 alignPanel.scrollUp(false);
569 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
570 + viewport.endSeq - viewport.startSeq);
575 if (evt.isControlDown())
577 undoMenuItem_actionPerformed();
582 if (evt.isControlDown())
584 redoMenuItem_actionPerformed();
589 if (evt.isControlDown())
596 if (evt.isControlDown())
598 trimAlignment(false);
603 if (evt.isControlDown())
605 if (evt.isShiftDown())
607 this.removeAllGapsMenuItem_actionPerformed();
611 removeGappedColumnMenuItem_actionPerformed();
616 if (evt.isControlDown())
620 invertColSel_actionPerformed();
624 invertSequenceMenuItem_actionPerformed();
630 if (evt.isControlDown())
632 if (evt.isShiftDown())
634 this.unGroup_actionPerformed();
638 this.createGroup_actionPerformed();
644 if (evt.isControlDown())
646 this.deleteGroups_actionPerformed();
651 if (evt.isControlDown())
658 alignPanel.paintAlignment(true);
662 * called by key handler and the hide all/show all menu items
667 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
669 boolean hide = false;
670 SequenceGroup sg = viewport.getSelectionGroup();
671 if (!toggleSeqs && !toggleCols)
673 // Hide everything by the current selection - this is a hack - we do the
674 // invert and then hide
675 // first check that there will be visible columns after the invert.
676 if ((viewport.getColumnSelection() != null
677 && viewport.getColumnSelection().getSelected() != null && viewport
678 .getColumnSelection().getSelected().size() > 0)
679 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
682 // now invert the sequence set, if required - empty selection implies
683 // that no hiding is required.
686 invertSequenceMenuItem_actionPerformed();
687 sg = viewport.getSelectionGroup();
691 viewport.expandColSelection(sg, true);
692 // finally invert the column selection and get the new sequence
693 // selection and indicate it should be hidden.
694 invertColSel_actionPerformed();
701 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
704 viewport.hideAllSelectedSeqs();
706 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
709 viewport.showAllHiddenSeqs();
715 if (viewport.getColumnSelection().getSelected().size() > 0)
717 viewport.hideSelectedColumns();
720 viewport.setSelectionGroup(sg);
725 viewport.showAllHiddenColumns();
731 public void keyReleased(KeyEvent evt)
736 public void keyTyped(KeyEvent evt)
741 public void itemStateChanged(ItemEvent evt)
743 final Object source = evt.getSource();
744 if (source == displayNonconservedMenuItem)
746 displayNonconservedMenuItem_actionPerformed();
748 else if (source == colourTextMenuItem)
750 colourTextMenuItem_actionPerformed();
752 else if (source == wrapMenuItem)
754 wrapMenuItem_actionPerformed();
756 else if (source == scaleAbove)
758 viewport.setScaleAboveWrapped(scaleAbove.getState());
760 else if (source == scaleLeft)
762 viewport.setScaleLeftWrapped(scaleLeft.getState());
764 else if (source == scaleRight)
766 viewport.setScaleRightWrapped(scaleRight.getState());
768 else if (source == seqLimits)
770 seqLimits_itemStateChanged();
772 else if (source == viewBoxesMenuItem)
774 viewport.setShowBoxes(viewBoxesMenuItem.getState());
776 else if (source == viewTextMenuItem)
778 viewport.setShowText(viewTextMenuItem.getState());
780 else if (source == renderGapsMenuItem)
782 viewport.setRenderGaps(renderGapsMenuItem.getState());
784 else if (source == annotationPanelMenuItem)
786 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
787 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
789 else if (source == sequenceFeatures)
791 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
792 alignPanel.seqPanel.seqCanvas.repaint();
794 else if (source == showAlignmentAnnotations)
796 setAnnotationsVisibility();
798 else if (source == showSequenceAnnotations)
800 setAnnotationsVisibility();
802 else if (source == sortAnnBySequence)
804 boolean newState = sortAnnBySequence.getState();
805 sortAnnByLabel.setState(false);
806 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
807 : SequenceAnnotationOrder.NONE);
808 setViewportAnnotationOrder();
810 else if (source == sortAnnByLabel)
812 boolean newState = sortAnnByLabel.getState();
813 sortAnnBySequence.setState(false);
814 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
815 : SequenceAnnotationOrder.NONE);
816 setViewportAnnotationOrder();
818 else if (source == showAutoFirst)
820 showAutoLast.setState(!showAutoFirst.getState());
821 setShowAutoCalculatedAbove(showAutoFirst.getState());
822 setViewportAnnotationOrder();
824 else if (source == showAutoLast)
826 showAutoFirst.setState(!showAutoLast.getState());
827 setShowAutoCalculatedAbove(showAutoFirst.getState());
828 setViewportAnnotationOrder();
830 else if (source == conservationMenuItem)
832 conservationMenuItem_actionPerformed();
834 else if (source == abovePIDThreshold)
836 abovePIDThreshold_actionPerformed();
838 else if (source == applyToAllGroups)
840 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
842 else if (source == autoCalculate)
844 viewport.autoCalculateConsensus = autoCalculate.getState();
846 else if (source == sortByTree)
848 viewport.sortByTree = sortByTree.getState();
850 else if (source == this.centreColumnLabelFlag)
852 centreColumnLabelFlag_stateChanged();
854 else if (source == this.followMouseOverFlag)
856 mouseOverFlag_stateChanged();
858 else if (source == showGroupConsensus)
860 showGroupConsensus_actionPerformed();
862 else if (source == showGroupConservation)
864 showGroupConservation_actionPerformed();
866 else if (source == showSequenceLogo)
868 showSequenceLogo_actionPerformed();
870 else if (source == normSequenceLogo)
872 normSequenceLogo_actionPerformed();
874 else if (source == showConsensusHistogram)
876 showConsensusHistogram_actionPerformed();
878 else if (source == applyAutoAnnotationSettings)
880 applyAutoAnnotationSettings_actionPerformed();
882 alignPanel.paintAlignment(true);
886 * Set the visibility state of sequence-related and/or alignment-related
887 * annotations depending on checkbox selections. Repaint after calling.
891 private void setAnnotationsVisibility()
893 boolean showForAlignment = showAlignmentAnnotations.getState();
894 boolean showForSequences = showSequenceAnnotations.getState();
895 for (AlignmentAnnotation aa : alignPanel.getAlignment()
896 .getAlignmentAnnotation())
898 boolean visible = (aa.sequenceRef == null ? showForAlignment
900 aa.visible = visible;
902 alignPanel.validateAnnotationDimensions(false);
905 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
907 this.annotationSortOrder = order;
911 * Set flags on the viewport that control annotation ordering
913 private void setViewportAnnotationOrder()
915 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
917 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
920 private void setShowAutoCalculatedAbove(boolean showAbove)
922 this.showAutoCalculatedAbove = showAbove;
925 private void mouseOverFlag_stateChanged()
927 viewport.followHighlight = followMouseOverFlag.getState();
928 // TODO: could kick the scrollTo mechanism to reset view for current
932 private void centreColumnLabelFlag_stateChanged()
934 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
935 this.alignPanel.annotationPanel.repaint();
939 public void actionPerformed(ActionEvent evt)
941 Object source = evt.getSource();
943 if (source == inputText)
945 inputText_actionPerformed();
947 else if (source == loadTree)
949 loadTree_actionPerformed();
951 else if (source == loadApplication)
953 launchFullApplication();
955 else if (source == loadAnnotations)
959 else if (source == outputAnnotations)
961 outputAnnotations(true);
963 else if (source == outputFeatures)
965 outputFeatures(true, "Jalview");
967 else if (source == closeMenuItem)
969 closeMenuItem_actionPerformed();
971 else if (source == copy)
973 copy_actionPerformed();
975 else if (source == undoMenuItem)
977 undoMenuItem_actionPerformed();
979 else if (source == redoMenuItem)
981 redoMenuItem_actionPerformed();
983 else if (source == inputText)
985 inputText_actionPerformed();
987 else if (source == closeMenuItem)
989 closeMenuItem_actionPerformed();
991 else if (source == undoMenuItem)
993 undoMenuItem_actionPerformed();
995 else if (source == redoMenuItem)
997 redoMenuItem_actionPerformed();
999 else if (source == copy)
1001 copy_actionPerformed();
1003 else if (source == pasteNew)
1005 pasteNew_actionPerformed();
1007 else if (source == pasteThis)
1009 pasteThis_actionPerformed();
1011 else if (source == cut)
1013 cut_actionPerformed();
1015 else if (source == delete)
1017 delete_actionPerformed();
1019 else if (source == grpsFromSelection)
1021 makeGrpsFromSelection_actionPerformed();
1023 else if (source == deleteGroups)
1025 deleteGroups_actionPerformed();
1027 else if (source == selectAllSequenceMenuItem)
1029 selectAllSequenceMenuItem_actionPerformed();
1031 else if (source == deselectAllSequenceMenuItem)
1033 deselectAllSequenceMenuItem_actionPerformed();
1035 else if (source == invertSequenceMenuItem)
1037 invertSequenceMenuItem_actionPerformed();
1039 else if (source == invertColSel)
1041 viewport.invertColumnSelection();
1042 alignPanel.paintAlignment(true);
1044 else if (source == remove2LeftMenuItem)
1046 trimAlignment(true);
1048 else if (source == remove2RightMenuItem)
1050 trimAlignment(false);
1052 else if (source == removeGappedColumnMenuItem)
1054 removeGappedColumnMenuItem_actionPerformed();
1056 else if (source == removeAllGapsMenuItem)
1058 removeAllGapsMenuItem_actionPerformed();
1060 else if (source == findMenuItem)
1062 findMenuItem_actionPerformed();
1064 else if (source == font)
1066 new FontChooser(alignPanel);
1068 else if (source == newView)
1072 else if (source == showColumns)
1074 viewport.showAllHiddenColumns();
1075 alignPanel.paintAlignment(true);
1077 else if (source == showSeqs)
1079 viewport.showAllHiddenSeqs();
1080 alignPanel.paintAlignment(true);
1082 else if (source == hideColumns)
1084 viewport.hideSelectedColumns();
1085 alignPanel.paintAlignment(true);
1087 else if (source == hideSequences
1088 && viewport.getSelectionGroup() != null)
1090 viewport.hideAllSelectedSeqs();
1091 alignPanel.paintAlignment(true);
1093 else if (source == hideAllButSelection)
1095 toggleHiddenRegions(false, false);
1096 alignPanel.paintAlignment(true);
1098 else if (source == hideAllSelection)
1100 SequenceGroup sg = viewport.getSelectionGroup();
1101 viewport.expandColSelection(sg, false);
1102 viewport.hideAllSelectedSeqs();
1103 viewport.hideSelectedColumns();
1104 alignPanel.paintAlignment(true);
1106 else if (source == showAllHidden)
1108 viewport.showAllHiddenColumns();
1109 viewport.showAllHiddenSeqs();
1110 alignPanel.paintAlignment(true);
1112 else if (source == showGroupConsensus)
1114 showGroupConsensus_actionPerformed();
1116 else if (source == showGroupConservation)
1118 showGroupConservation_actionPerformed();
1120 else if (source == showSequenceLogo)
1122 showSequenceLogo_actionPerformed();
1124 else if (source == normSequenceLogo)
1126 normSequenceLogo_actionPerformed();
1128 else if (source == showConsensusHistogram)
1130 showConsensusHistogram_actionPerformed();
1132 else if (source == applyAutoAnnotationSettings)
1134 applyAutoAnnotationSettings_actionPerformed();
1136 else if (source == featureSettings)
1138 new FeatureSettings(alignPanel);
1140 else if (source == alProperties)
1142 StringBuffer contents = new jalview.io.AlignmentProperties(
1143 viewport.getAlignment()).formatAsString();
1144 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1145 cap.setText(contents.toString());
1146 Frame frame = new Frame();
1148 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1149 "label.alignment_properties", new String[]
1150 { getTitle() }), 400, 250);
1152 else if (source == overviewMenuItem)
1154 overviewMenuItem_actionPerformed();
1156 else if (source == noColourmenuItem)
1160 else if (source == clustalColour)
1162 abovePIDThreshold.setState(false);
1163 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1165 else if (source == zappoColour)
1167 changeColour(new ZappoColourScheme());
1169 else if (source == taylorColour)
1171 changeColour(new TaylorColourScheme());
1173 else if (source == hydrophobicityColour)
1175 changeColour(new HydrophobicColourScheme());
1177 else if (source == helixColour)
1179 changeColour(new HelixColourScheme());
1181 else if (source == strandColour)
1183 changeColour(new StrandColourScheme());
1185 else if (source == turnColour)
1187 changeColour(new TurnColourScheme());
1189 else if (source == buriedColour)
1191 changeColour(new BuriedColourScheme());
1193 else if (source == nucleotideColour)
1195 changeColour(new NucleotideColourScheme());
1197 else if (source == purinePyrimidineColour)
1199 changeColour(new PurinePyrimidineColourScheme());
1201 else if (source == RNAInteractionColour)
1203 changeColour(new RNAInteractionColourScheme());
1205 else if (source == RNAHelixColour)
1207 new RNAHelicesColourChooser(viewport, alignPanel);
1209 else if (source == modifyPID)
1211 modifyPID_actionPerformed();
1213 else if (source == modifyConservation)
1215 modifyConservation_actionPerformed();
1217 else if (source == userDefinedColour)
1219 new UserDefinedColours(alignPanel, null);
1221 else if (source == PIDColour)
1223 changeColour(new PIDColourScheme());
1225 else if (source == BLOSUM62Colour)
1227 changeColour(new Blosum62ColourScheme());
1229 else if (source == tcoffeeColour)
1231 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1233 else if (source == annotationColour)
1235 new AnnotationColourChooser(viewport, alignPanel);
1237 else if (source == annotationColumnSelection)
1239 new AnnotationColumnChooser(viewport, alignPanel);
1241 else if (source == sortPairwiseMenuItem)
1243 sortPairwiseMenuItem_actionPerformed();
1245 else if (source == sortIDMenuItem)
1247 sortIDMenuItem_actionPerformed();
1249 else if (source == sortLengthMenuItem)
1251 sortLengthMenuItem_actionPerformed();
1253 else if (source == sortGroupMenuItem)
1255 sortGroupMenuItem_actionPerformed();
1257 else if (source == removeRedundancyMenuItem)
1259 removeRedundancyMenuItem_actionPerformed();
1261 else if (source == pairwiseAlignmentMenuItem)
1263 pairwiseAlignmentMenuItem_actionPerformed();
1265 else if (source == PCAMenuItem)
1267 PCAMenuItem_actionPerformed();
1269 else if (source == averageDistanceTreeMenuItem)
1271 averageDistanceTreeMenuItem_actionPerformed();
1273 else if (source == neighbourTreeMenuItem)
1275 neighbourTreeMenuItem_actionPerformed();
1277 else if (source == njTreeBlosumMenuItem)
1279 njTreeBlosumMenuItem_actionPerformed();
1281 else if (source == avDistanceTreeBlosumMenuItem)
1283 avTreeBlosumMenuItem_actionPerformed();
1285 else if (source == documentation)
1287 documentation_actionPerformed();
1289 else if (source == about)
1291 about_actionPerformed();
1296 public void inputText_actionPerformed()
1298 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1299 Frame frame = new Frame();
1301 jalview.bin.JalviewLite.addFrame(frame,
1302 MessageManager.getString("label.input_cut_paste"), 500, 500);
1305 protected void outputText_actionPerformed(ActionEvent e)
1307 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1308 Frame frame = new Frame();
1310 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1311 "label.alignment_output_command", new Object[]
1312 { e.getActionCommand() }), 600, 500);
1313 cap.setText(new AppletFormatAdapter().formatSequences(
1314 e.getActionCommand(), viewport.getAlignment(),
1315 viewport.getShowJVSuffix()));
1318 public void loadAnnotations()
1320 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1321 cap.setText(MessageManager
1322 .getString("label.paste_features_annotations_Tcoffee_here"));
1323 cap.setAnnotationImport();
1324 Frame frame = new Frame();
1326 jalview.bin.JalviewLite.addFrame(frame,
1327 MessageManager.getString("action.paste_annotations"), 400, 300);
1331 public String outputAnnotations(boolean displayTextbox)
1333 String annotation = new AnnotationFile()
1334 .printAnnotationsForView(viewport);
1338 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1339 Frame frame = new Frame();
1341 jalview.bin.JalviewLite.addFrame(frame,
1342 MessageManager.getString("label.annotations"), 600, 500);
1343 cap.setText(annotation);
1349 private Map<String,Object> getDisplayedFeatureCols()
1351 if (alignPanel.getFeatureRenderer() != null
1352 && viewport.getFeaturesDisplayed()!= null)
1354 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1360 public String outputFeatures(boolean displayTextbox, String format)
1363 if (format.equalsIgnoreCase("Jalview"))
1365 features = new FeaturesFile().printJalviewFormat(viewport
1366 .getAlignment().getSequencesArray(),
1367 getDisplayedFeatureCols());
1371 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1372 .getSequencesArray(), getDisplayedFeatureCols());
1377 boolean frimport = false;
1378 if (features == null || features.equals("No Features Visible"))
1380 features = "# No features visible - paste some and import them here.";
1384 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1387 cap.setAnnotationImport();
1389 Frame frame = new Frame();
1391 jalview.bin.JalviewLite.addFrame(frame,
1392 MessageManager.getString("label.features"), 600, 500);
1393 cap.setText(features);
1397 if (features == null)
1406 void launchFullApplication()
1408 StringBuffer url = new StringBuffer(jalviewServletURL);
1410 // allow servlet parameters to be passed in applet parameter
1411 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1413 url.append(firstSep);
1416 + appendProtocol(viewport.applet.getParameter("file")));
1418 if (viewport.applet.getParameter("features") != null)
1420 url.append("&features=");
1421 url.append(appendProtocol(viewport.applet.getParameter("features")));
1424 if (viewport.applet.getParameter("annotations") != null)
1426 url.append("&annotations=");
1427 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1430 if (viewport.applet.getParameter("jnetfile") != null)
1432 url.append("&annotations=");
1433 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1436 if (viewport.applet.getParameter("defaultColour") != null)
1438 url.append("&colour="
1439 + removeWhiteSpace(viewport.applet
1440 .getParameter("defaultColour")));
1443 if (viewport.applet.getParameter("userDefinedColour") != null)
1445 url.append("&colour="
1446 + removeWhiteSpace(viewport.applet
1447 .getParameter("userDefinedColour")));
1449 if (viewport.applet.getParameter("tree") != null)
1452 + appendProtocol(viewport.applet.getParameter("tree")));
1454 if (viewport.applet.getParameter("treeFile") != null)
1457 + appendProtocol(viewport.applet.getParameter("treeFile")));
1460 showURL(url.toString(), "FULL_APP");
1463 String removeWhiteSpace(String colour)
1465 StringBuffer sb = new StringBuffer();
1466 for (int i = 0; i < colour.length(); i++)
1468 if (Character.isWhitespace(colour.charAt(i)))
1474 sb.append(colour.charAt(i));
1478 return sb.toString();
1481 String appendProtocol(String url)
1486 url = URLEncoder.encode(url);
1489 * When we finally deprecate 1.1 compatibility, we can start to use
1490 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1491 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1492 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1493 * ex.printStackTrace(); }
1495 catch (java.net.MalformedURLException ex)
1497 url = viewport.applet.getCodeBase() + url;
1502 public void closeMenuItem_actionPerformed()
1504 PaintRefresher.RemoveComponent(alignPanel);
1505 if (alignPanel.seqPanel != null
1506 && alignPanel.seqPanel.seqCanvas != null)
1508 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1510 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1512 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1515 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1530 void updateEditMenuBar()
1533 if (viewport.getHistoryList().size() > 0)
1535 undoMenuItem.setEnabled(true);
1536 CommandI command = viewport.getHistoryList().peek();
1537 undoMenuItem.setLabel(MessageManager.formatMessage(
1538 "label.undo_command", new Object[]
1539 { command.getDescription() }));
1543 undoMenuItem.setEnabled(false);
1544 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1547 if (viewport.getRedoList().size() > 0)
1549 redoMenuItem.setEnabled(true);
1551 CommandI command = viewport.getRedoList().peek();
1552 redoMenuItem.setLabel(MessageManager.formatMessage(
1553 "label.redo_command", new Object[]
1554 { command.getDescription() }));
1558 redoMenuItem.setEnabled(false);
1559 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1567 public void addHistoryItem(CommandI command)
1569 if (command.getSize() > 0)
1571 viewport.addToHistoryList(command);
1572 viewport.clearRedoList();
1573 updateEditMenuBar();
1574 viewport.updateHiddenColumns();
1579 * TODO: JAL-1104 DOCUMENT ME!
1584 protected void undoMenuItem_actionPerformed()
1586 if (viewport.getHistoryList().isEmpty())
1591 CommandI command = viewport.getHistoryList().pop();
1592 viewport.addToRedoList(command);
1593 command.undoCommand(null);
1595 AlignViewport originalSource = getOriginatingSource(command);
1597 if (originalSource != viewport)
1600 .println("Warning: Viewport object mismatch whilst undoing");
1602 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1603 // viewport.getColumnSelection().getHiddenColumns()
1605 updateEditMenuBar();
1606 originalSource.firePropertyChange("alignment", null, originalSource
1607 .getAlignment().getSequences());
1611 * TODO: JAL-1104 DOCUMENT ME!
1616 protected void redoMenuItem_actionPerformed()
1618 if (viewport.getRedoList().isEmpty())
1623 CommandI command = viewport.getRedoList().pop();
1624 viewport.addToHistoryList(command);
1625 command.doCommand(null);
1627 AlignViewport originalSource = getOriginatingSource(command);
1629 if (originalSource != viewport)
1632 .println("Warning: Viewport object mismatch whilst re-doing");
1634 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1635 // viewport.getColumnSelection().getHiddenColumns()
1638 updateEditMenuBar();
1639 originalSource.firePropertyChange("alignment", null, originalSource
1640 .getAlignment().getSequences());
1643 AlignViewport getOriginatingSource(CommandI command)
1645 AlignViewport originalSource = null;
1646 // For sequence removal and addition, we need to fire
1647 // the property change event FROM the viewport where the
1648 // original alignment was altered
1649 AlignmentI al = null;
1650 if (command instanceof EditCommand)
1652 EditCommand editCommand = (EditCommand) command;
1653 al = editCommand.getAlignment();
1654 Vector comps = (Vector) PaintRefresher.components.get(viewport
1655 .getSequenceSetId());
1656 for (int i = 0; i < comps.size(); i++)
1658 if (comps.elementAt(i) instanceof AlignmentPanel)
1660 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1662 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1669 if (originalSource == null)
1671 // The original view is closed, we must validate
1672 // the current view against the closed view first
1675 PaintRefresher.validateSequences(al, viewport.getAlignment());
1678 originalSource = viewport;
1681 return originalSource;
1685 * Move the currently selected sequences up or down one position in the
1690 public void moveSelectedSequences(boolean up)
1692 SequenceGroup sg = viewport.getSelectionGroup();
1697 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1698 up ? null : viewport.getHiddenRepSequences(), up);
1699 alignPanel.paintAlignment(true);
1702 * Also move cDNA/protein complement sequences
1704 AlignViewportI complement = viewport.getCodingComplement();
1705 if (complement != null)
1707 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1708 viewport, complement);
1709 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1710 up ? null : complement.getHiddenRepSequences(), up);
1711 // TODO need to trigger a repaint of the complementary panel - how?
1712 // would prefer to handle in SplitFrame but it is not overriding key
1717 synchronized void slideSequences(boolean right, int size)
1719 List<SequenceI> sg = new Vector<SequenceI>();
1720 if (viewport.cursorMode)
1722 sg.add(viewport.getAlignment().getSequenceAt(
1723 alignPanel.seqPanel.seqCanvas.cursorY));
1725 else if (viewport.getSelectionGroup() != null
1726 && viewport.getSelectionGroup().getSize() != viewport
1727 .getAlignment().getHeight())
1729 sg = viewport.getSelectionGroup().getSequences(
1730 viewport.getHiddenRepSequences());
1738 Vector<SequenceI> invertGroup = new Vector();
1740 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1742 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1744 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1748 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1750 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1752 for (int i = 0; i < invertGroup.size(); i++)
1754 seqs2[i] = invertGroup.elementAt(i);
1757 SlideSequencesCommand ssc;
1760 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1761 size, viewport.getGapCharacter());
1765 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1766 size, viewport.getGapCharacter());
1769 int groupAdjustment = 0;
1770 if (ssc.getGapsInsertedBegin() && right)
1772 if (viewport.cursorMode)
1774 alignPanel.seqPanel.moveCursor(size, 0);
1778 groupAdjustment = size;
1781 else if (!ssc.getGapsInsertedBegin() && !right)
1783 if (viewport.cursorMode)
1785 alignPanel.seqPanel.moveCursor(-size, 0);
1789 groupAdjustment = -size;
1793 if (groupAdjustment != 0)
1795 viewport.getSelectionGroup().setStartRes(
1796 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1797 viewport.getSelectionGroup().setEndRes(
1798 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1801 boolean appendHistoryItem = false;
1802 Deque<CommandI> historyList = viewport.getHistoryList();
1803 if (historyList != null && historyList.size() > 0
1804 && historyList.peek() instanceof SlideSequencesCommand)
1806 appendHistoryItem = ssc
1807 .appendSlideCommand((SlideSequencesCommand) historyList
1811 if (!appendHistoryItem)
1813 addHistoryItem(ssc);
1819 static StringBuffer copiedSequences;
1821 static Vector copiedHiddenColumns;
1823 protected void copy_actionPerformed()
1825 if (viewport.getSelectionGroup() == null)
1830 SequenceGroup sg = viewport.getSelectionGroup();
1831 copiedSequences = new StringBuffer();
1832 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1833 for (int i = 0; i < sg.getSize(); i++)
1835 SequenceI seq = sg.getSequenceAt(i);
1836 int index = viewport.getAlignment().findIndex(seq);
1837 orderedSeqs.put(index, seq);
1840 int index = 0, startRes, endRes;
1843 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1845 copiedHiddenColumns = new Vector();
1846 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1847 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1849 copiedHiddenColumns.addElement(new int[]
1850 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1855 copiedHiddenColumns = null;
1858 for (int i = 0; i < sg.getSize(); i++)
1860 SequenceI seq = null;
1864 if (orderedSeqs.containsKey(index))
1866 seq = orderedSeqs.get(index);
1877 // Returns residue following index if gap
1878 startRes = seq.findPosition(sg.getStartRes());
1881 // Need to find the residue preceeding index if gap
1884 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1886 ch = seq.getCharAt(j);
1887 if (!jalview.util.Comparison.isGap((ch)))
1895 endRes += seq.getStart() - 1;
1898 copiedSequences.append(seq.getName()
1904 + seq.getSequenceAsString(sg.getStartRes(),
1905 sg.getEndRes() + 1) + "\n");
1910 protected void pasteNew_actionPerformed()
1915 protected void pasteThis_actionPerformed()
1920 void paste(boolean newAlignment)
1925 if (copiedSequences == null)
1930 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1931 Vector seqs = new Vector();
1932 while (st.hasMoreElements())
1934 String name = st.nextToken();
1935 int start = Integer.parseInt(st.nextToken());
1936 int end = Integer.parseInt(st.nextToken());
1937 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1939 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1940 for (int i = 0; i < seqs.size(); i++)
1942 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1947 String newtitle = MessageManager.getString("label.copied_sequences");
1948 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1950 newtitle = getTitle();
1954 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1956 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1957 viewport.applet, newtitle, false);
1958 if (copiedHiddenColumns != null)
1960 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1962 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1963 af.viewport.hideColumns(region[0], region[1]);
1967 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1972 addSequences(newSeqs);
1975 } catch (Exception ex)
1977 } // could be anything being pasted in here
1981 void addSequences(SequenceI[] seqs)
1983 for (int i = 0; i < seqs.length; i++)
1985 viewport.getAlignment().addSequence(seqs[i]);
1989 addHistoryItem(new EditCommand(
1990 MessageManager.getString("label.add_sequences"), Action.PASTE,
1991 seqs, 0, viewport.getAlignment().getWidth(),
1992 viewport.getAlignment()));
1994 viewport.setEndSeq(viewport.getAlignment().getHeight());
1995 viewport.getAlignment().getWidth();
1996 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2001 protected void cut_actionPerformed()
2003 copy_actionPerformed();
2004 delete_actionPerformed();
2007 protected void delete_actionPerformed()
2010 SequenceGroup sg = viewport.getSelectionGroup();
2016 Vector seqs = new Vector();
2018 for (int i = 0; i < sg.getSize(); i++)
2020 seq = sg.getSequenceAt(i);
2021 seqs.addElement(seq);
2024 // If the cut affects all sequences, remove highlighted columns
2025 if (sg.getSize() == viewport.getAlignment().getHeight())
2027 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2028 sg.getEndRes() + 1);
2031 SequenceI[] cut = new SequenceI[seqs.size()];
2032 for (int i = 0; i < seqs.size(); i++)
2034 cut[i] = (SequenceI) seqs.elementAt(i);
2038 * //ADD HISTORY ITEM
2040 addHistoryItem(new EditCommand(
2041 MessageManager.getString("label.cut_sequences"), Action.CUT,
2042 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2043 viewport.getAlignment()));
2045 viewport.setSelectionGroup(null);
2046 viewport.getAlignment().deleteGroup(sg);
2048 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2051 if (viewport.getAlignment().getHeight() < 1)
2053 this.setVisible(false);
2055 viewport.sendSelection();
2059 * group consensus toggled
2062 protected void showGroupConsensus_actionPerformed()
2064 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2065 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2070 * group conservation toggled.
2072 protected void showGroupConservation_actionPerformed()
2074 viewport.setShowGroupConservation(showGroupConservation.getState());
2075 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2082 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2083 * .event.ActionEvent)
2085 protected void showConsensusHistogram_actionPerformed()
2087 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2088 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2095 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2096 * .event.ActionEvent)
2098 protected void showSequenceLogo_actionPerformed()
2100 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2101 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2104 protected void normSequenceLogo_actionPerformed()
2106 showSequenceLogo.setState(true);
2107 viewport.setShowSequenceLogo(true);
2108 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2109 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2112 protected void applyAutoAnnotationSettings_actionPerformed()
2114 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2117 protected void makeGrpsFromSelection_actionPerformed()
2119 if (avc.makeGroupsFromSelection())
2121 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2122 alignPanel.updateAnnotation();
2123 alignPanel.paintAlignment(true);
2127 protected void createGroup_actionPerformed()
2132 protected void unGroup_actionPerformed()
2136 alignPanel.alignmentChanged();
2140 protected void deleteGroups_actionPerformed()
2142 if (avc.deleteGroups())
2144 alignPanel.alignmentChanged();
2148 public void selectAllSequenceMenuItem_actionPerformed()
2150 SequenceGroup sg = new SequenceGroup();
2151 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2153 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2155 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2156 viewport.setSelectionGroup(sg);
2157 alignPanel.paintAlignment(true);
2158 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2159 viewport.sendSelection();
2162 public void deselectAllSequenceMenuItem_actionPerformed()
2164 if (viewport.cursorMode)
2166 alignPanel.seqPanel.keyboardNo1 = null;
2167 alignPanel.seqPanel.keyboardNo2 = null;
2169 viewport.setSelectionGroup(null);
2170 viewport.getColumnSelection().clear();
2171 viewport.setSelectionGroup(null);
2172 alignPanel.idPanel.idCanvas.searchResults = null;
2173 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2174 alignPanel.paintAlignment(true);
2175 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2176 viewport.sendSelection();
2179 public void invertSequenceMenuItem_actionPerformed()
2181 SequenceGroup sg = viewport.getSelectionGroup();
2182 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2184 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2187 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2188 viewport.sendSelection();
2191 public void invertColSel_actionPerformed()
2193 viewport.invertColumnSelection();
2194 alignPanel.paintAlignment(true);
2195 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2196 viewport.sendSelection();
2199 void trimAlignment(boolean trimLeft)
2201 ColumnSelection colSel = viewport.getColumnSelection();
2204 if (colSel.size() > 0)
2208 column = colSel.getMin();
2212 column = colSel.getMax();
2216 if (viewport.getSelectionGroup() != null)
2218 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2219 viewport.getHiddenRepSequences());
2223 seqs = viewport.getAlignment().getSequencesArray();
2226 TrimRegionCommand trimRegion;
2229 trimRegion = new TrimRegionCommand("Remove Left",
2230 TrimRegionCommand.TRIM_LEFT, seqs, column,
2231 viewport.getAlignment(), viewport.getColumnSelection(),
2232 viewport.getSelectionGroup());
2233 viewport.setStartRes(0);
2237 trimRegion = new TrimRegionCommand("Remove Right",
2238 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2239 viewport.getAlignment(), viewport.getColumnSelection(),
2240 viewport.getSelectionGroup());
2243 statusBar.setText(MessageManager.formatMessage(
2244 "label.removed_columns", new String[]
2245 { Integer.valueOf(trimRegion.getSize()).toString() }));
2246 addHistoryItem(trimRegion);
2248 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2250 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2251 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2253 viewport.getAlignment().deleteGroup(sg);
2257 viewport.firePropertyChange("alignment", null, viewport
2258 .getAlignment().getSequences());
2262 public void removeGappedColumnMenuItem_actionPerformed()
2264 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2267 if (viewport.getSelectionGroup() != null)
2269 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2270 viewport.getHiddenRepSequences());
2271 start = viewport.getSelectionGroup().getStartRes();
2272 end = viewport.getSelectionGroup().getEndRes();
2276 seqs = viewport.getAlignment().getSequencesArray();
2279 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2280 "Remove Gapped Columns", seqs, start, end,
2281 viewport.getAlignment());
2283 addHistoryItem(removeGapCols);
2285 statusBar.setText(MessageManager.formatMessage(
2286 "label.removed_empty_columns", new String[]
2287 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2289 // This is to maintain viewport position on first residue
2290 // of first sequence
2291 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2292 int startRes = seq.findPosition(viewport.startRes);
2293 // ShiftList shifts;
2294 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2295 // edit.alColumnChanges=shifts.getInverse();
2296 // if (viewport.hasHiddenColumns)
2297 // viewport.getColumnSelection().compensateForEdits(shifts);
2298 viewport.setStartRes(seq.findIndex(startRes) - 1);
2299 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2304 public void removeAllGapsMenuItem_actionPerformed()
2306 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2309 if (viewport.getSelectionGroup() != null)
2311 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2312 viewport.getHiddenRepSequences());
2313 start = viewport.getSelectionGroup().getStartRes();
2314 end = viewport.getSelectionGroup().getEndRes();
2318 seqs = viewport.getAlignment().getSequencesArray();
2321 // This is to maintain viewport position on first residue
2322 // of first sequence
2323 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2324 int startRes = seq.findPosition(viewport.startRes);
2326 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2327 viewport.getAlignment()));
2329 viewport.setStartRes(seq.findIndex(startRes) - 1);
2331 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2336 public void findMenuItem_actionPerformed()
2338 new Finder(alignPanel);
2342 * create a new view derived from the current view
2345 * @return frame for the new view
2347 public AlignFrame newView(String viewtitle)
2350 if (viewport.hasHiddenRows())
2352 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2353 .getFullAlignment().getSequencesArray());
2357 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2360 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2362 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2364 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2366 newal.addAnnotation(viewport.getAlignment()
2367 .getAlignmentAnnotation()[i]);
2372 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2374 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2375 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2376 PaintRefresher.Register(newaf.alignPanel,
2377 newaf.alignPanel.av.getSequenceSetId());
2379 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2380 newaf.alignPanel.av.getSequenceSetId());
2381 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2382 newaf.alignPanel.av.getSequenceSetId());
2384 Vector comps = (Vector) PaintRefresher.components.get(viewport
2385 .getSequenceSetId());
2387 for (int i = 0; i < comps.size(); i++)
2389 if (comps.elementAt(i) instanceof AlignmentPanel)
2395 String title = new String(this.getTitle());
2396 if (viewtitle != null)
2398 title = viewtitle + " ( " + title + ")";
2402 if (title.indexOf("(View") > -1)
2404 title = title.substring(0, title.indexOf("(View"));
2406 title += "(View " + viewSize + ")";
2409 newaf.setTitle(title.toString());
2411 newaf.viewport.setHistoryList(viewport.getHistoryList());
2412 newaf.viewport.setRedoList(viewport.getRedoList());
2418 * @return list of feature groups on the view
2420 public String[] getFeatureGroups()
2422 FeatureRenderer fr = null;
2423 if (alignPanel != null
2424 && (fr = alignPanel.getFeatureRenderer()) != null)
2426 List<String> gps = fr.getFeatureGroups();
2427 String[] _gps = gps.toArray(new String[gps.size()]);
2434 * get sequence feature groups that are hidden or shown
2440 public String[] getFeatureGroupsOfState(boolean visible)
2442 FeatureRenderer fr = null;
2443 if (alignPanel != null
2444 && (fr = alignPanel.getFeatureRenderer()) != null)
2446 List<String> gps = fr.getGroups(visible);
2447 String[] _gps = gps.toArray(new String[gps.size()]);
2454 * Change the display state for the given feature groups
2457 * list of group strings
2459 * visible or invisible
2461 public void setFeatureGroupState(String[] groups, boolean state)
2463 FeatureRenderer fr = null;
2464 this.sequenceFeatures.setState(true);
2465 viewport.setShowSequenceFeatures(true);
2466 if (alignPanel != null
2467 && (fr = alignPanel.getFeatureRenderer()) != null)
2470 fr.setGroupVisibility(Arrays.asList(groups), state);
2471 alignPanel.seqPanel.seqCanvas.repaint();
2472 if (alignPanel.overviewPanel != null)
2474 alignPanel.overviewPanel.updateOverviewImage();
2479 public void seqLimits_itemStateChanged()
2481 viewport.setShowJVSuffix(seqLimits.getState());
2482 alignPanel.fontChanged();
2483 alignPanel.paintAlignment(true);
2486 protected void colourTextMenuItem_actionPerformed()
2488 viewport.setColourText(colourTextMenuItem.getState());
2489 alignPanel.paintAlignment(true);
2492 protected void displayNonconservedMenuItem_actionPerformed()
2494 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2495 alignPanel.paintAlignment(true);
2498 protected void wrapMenuItem_actionPerformed()
2500 viewport.setWrapAlignment(wrapMenuItem.getState());
2501 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2502 scaleAbove.setEnabled(wrapMenuItem.getState());
2503 scaleLeft.setEnabled(wrapMenuItem.getState());
2504 scaleRight.setEnabled(wrapMenuItem.getState());
2505 alignPanel.paintAlignment(true);
2508 public void overviewMenuItem_actionPerformed()
2510 if (alignPanel.overviewPanel != null)
2515 Frame frame = new Frame();
2516 OverviewPanel overview = new OverviewPanel(alignPanel);
2517 frame.add(overview);
2518 // +50 must allow for applet frame window
2519 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2520 "label.overview_params", new String[]
2521 { this.getTitle() }), overview.getPreferredSize().width,
2522 overview.getPreferredSize().height + 50);
2525 final AlignmentPanel ap = alignPanel;
2526 frame.addWindowListener(new WindowAdapter()
2529 public void windowClosing(WindowEvent e)
2533 ap.setOverviewPanel(null);
2538 alignPanel.setOverviewPanel(overview);
2542 void changeColour(ColourSchemeI cs)
2548 if (viewport.getAbovePIDThreshold())
2550 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2554 if (viewport.getConservationSelected())
2556 cs.setConservationApplied(true);
2557 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2562 cs.setConservationApplied(false);
2565 viewport.setGlobalColourScheme(cs);
2567 if (alignPanel.getOverviewPanel() != null)
2569 alignPanel.getOverviewPanel().updateOverviewImage();
2572 jalview.structure.StructureSelectionManager
2573 .getStructureSelectionManager(viewport.applet)
2574 .sequenceColoursChanged(alignPanel);
2576 alignPanel.paintAlignment(true);
2579 protected void modifyPID_actionPerformed()
2581 if (viewport.getAbovePIDThreshold()
2582 && viewport.getGlobalColourScheme() != null)
2584 SliderPanel.setPIDSliderSource(alignPanel,
2585 viewport.getGlobalColourScheme(), "Background");
2586 SliderPanel.showPIDSlider();
2590 protected void modifyConservation_actionPerformed()
2592 if (viewport.getConservationSelected()
2593 && viewport.getGlobalColourScheme() != null)
2595 SliderPanel.setConservationSlider(alignPanel,
2596 viewport.getGlobalColourScheme(), "Background");
2597 SliderPanel.showConservationSlider();
2601 protected void conservationMenuItem_actionPerformed()
2603 viewport.setConservationSelected(conservationMenuItem.getState());
2605 viewport.setAbovePIDThreshold(false);
2606 abovePIDThreshold.setState(false);
2608 changeColour(viewport.getGlobalColourScheme());
2610 modifyConservation_actionPerformed();
2613 public void abovePIDThreshold_actionPerformed()
2615 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2617 conservationMenuItem.setState(false);
2618 viewport.setConservationSelected(false);
2620 changeColour(viewport.getGlobalColourScheme());
2622 modifyPID_actionPerformed();
2625 public void sortPairwiseMenuItem_actionPerformed()
2627 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2628 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2629 .getAlignment().getSequenceAt(0), null);
2631 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2632 viewport.getAlignment()));
2633 alignPanel.paintAlignment(true);
2636 public void sortIDMenuItem_actionPerformed()
2638 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2639 AlignmentSorter.sortByID(viewport.getAlignment());
2640 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2641 viewport.getAlignment()));
2642 alignPanel.paintAlignment(true);
2645 public void sortLengthMenuItem_actionPerformed()
2647 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2648 AlignmentSorter.sortByLength(viewport.getAlignment());
2649 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2650 viewport.getAlignment()));
2651 alignPanel.paintAlignment(true);
2654 public void sortGroupMenuItem_actionPerformed()
2656 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2657 AlignmentSorter.sortByGroup(viewport.getAlignment());
2658 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2659 viewport.getAlignment()));
2660 alignPanel.paintAlignment(true);
2664 public void removeRedundancyMenuItem_actionPerformed()
2666 new RedundancyPanel(alignPanel);
2669 public void pairwiseAlignmentMenuItem_actionPerformed()
2671 if (viewport.getSelectionGroup() != null
2672 && viewport.getSelectionGroup().getSize() > 1)
2674 Frame frame = new Frame();
2675 frame.add(new PairwiseAlignPanel(alignPanel));
2676 jalview.bin.JalviewLite.addFrame(frame,
2677 MessageManager.getString("action.pairwise_alignment"), 600,
2682 public void PCAMenuItem_actionPerformed()
2684 // are the sequences aligned?
2685 if (!viewport.getAlignment().isAligned(false))
2688 int Width = viewport.getAlignment().getWidth();
2690 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2692 current = viewport.getAlignment().getSequenceAt(i);
2694 if (current.getLength() < Width)
2696 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2699 alignPanel.paintAlignment(true);
2702 if ((viewport.getSelectionGroup() != null
2703 && viewport.getSelectionGroup().getSize() < 4 && viewport
2704 .getSelectionGroup().getSize() > 0)
2705 || viewport.getAlignment().getHeight() < 4)
2712 new PCAPanel(viewport);
2713 } catch (java.lang.OutOfMemoryError ex)
2719 public void averageDistanceTreeMenuItem_actionPerformed()
2721 NewTreePanel("AV", "PID", "Average distance tree using PID");
2724 public void neighbourTreeMenuItem_actionPerformed()
2726 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2729 protected void njTreeBlosumMenuItem_actionPerformed()
2731 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2734 protected void avTreeBlosumMenuItem_actionPerformed()
2736 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2739 void NewTreePanel(String type, String pwType, String title)
2741 // are the sequences aligned?
2742 if (!viewport.getAlignment().isAligned(false))
2745 int Width = viewport.getAlignment().getWidth();
2747 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2749 current = viewport.getAlignment().getSequenceAt(i);
2751 if (current.getLength() < Width)
2753 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2756 alignPanel.paintAlignment(true);
2760 if ((viewport.getSelectionGroup() != null && viewport
2761 .getSelectionGroup().getSize() > 1)
2762 || (viewport.getAlignment().getHeight() > 1))
2764 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2766 addTreeMenuItem(tp, title);
2768 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2772 void loadTree_actionPerformed()
2774 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2775 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2776 cap.setTreeImport();
2777 Frame frame = new Frame();
2779 jalview.bin.JalviewLite.addFrame(frame,
2780 MessageManager.getString("label.paste_newick_file"), 400, 300);
2783 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2785 TreePanel tp = new TreePanel(alignPanel, treeFile,
2786 MessageManager.getString("label.load_tree_from_file"), tree);
2787 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2788 addTreeMenuItem(tp, treeFile);
2792 * sort the alignment using the given treePanel
2795 * tree used to sort view
2797 * string used for undo event name
2799 public void sortByTree(TreePanel treePanel, String title)
2801 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2803 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2804 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2805 // HistoryItem.SORT));
2806 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2807 "label.order_by_params", new String[]
2808 { title }), oldOrder, viewport.getAlignment()));
2809 alignPanel.paintAlignment(true);
2813 * Do any automatic reordering of the alignment and add the necessary bits to
2814 * the menu structure for the new tree
2819 protected void addTreeMenuItem(final TreePanel treePanel,
2822 final MenuItem item = new MenuItem(title);
2823 sortByTreeMenu.add(item);
2824 item.addActionListener(new java.awt.event.ActionListener()
2827 public void actionPerformed(ActionEvent evt)
2829 sortByTree(treePanel, title); // treePanel.getTitle());
2833 treePanel.addWindowListener(new WindowAdapter()
2836 public void windowOpened(WindowEvent e)
2838 if (viewport.sortByTree)
2840 sortByTree(treePanel, title);
2842 super.windowOpened(e);
2846 public void windowClosing(WindowEvent e)
2848 sortByTreeMenu.remove(item);
2853 public boolean sortBy(AlignmentOrder alorder, String undoname)
2855 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2856 if (viewport.applet.debug)
2858 System.err.println("Sorting " + alorder.getOrder().size()
2859 + " in alignment '" + getTitle() + "'");
2861 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2862 if (undoname != null)
2864 addHistoryItem(new OrderCommand(undoname, oldOrder,
2865 viewport.getAlignment()));
2867 alignPanel.paintAlignment(true);
2871 protected void documentation_actionPerformed()
2873 alignPanel.av.applet.openJalviewHelpUrl();
2876 protected void about_actionPerformed()
2879 class AboutPanel extends Canvas
2885 public AboutPanel(String version, String builddate)
2887 this.version = version;
2888 this.builddate = builddate;
2892 public void paint(Graphics g)
2894 g.setColor(Color.white);
2895 g.fillRect(0, 0, getSize().width, getSize().height);
2896 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2897 FontMetrics fm = g.getFontMetrics();
2898 int fh = fm.getHeight();
2900 g.setColor(Color.black);
2901 // TODO: update this text for each release or centrally store it for
2902 // lite and application
2903 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2904 g.drawString(MessageManager.formatMessage(
2905 "label.jalviewLite_release", new String[]
2906 { version }), x, y += fh);
2907 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2908 g.drawString(MessageManager.formatMessage(
2909 "label.jaview_build_date", new String[]
2910 { builddate }), x, y += fh);
2911 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2912 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2914 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2915 x + 50, y += fh + 8);
2917 MessageManager.getString("label.jalview_dev_managers"), x,
2919 g.drawString(MessageManager
2920 .getString("label.jalview_distribution_lists"), x, y += fh);
2921 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2924 MessageManager.getString("label.jalview_cite_1_authors"),
2927 MessageManager.getString("label.jalview_cite_1_title"), x,
2929 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2934 Frame frame = new Frame();
2935 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2937 jalview.bin.JalviewLite.addFrame(frame,
2938 MessageManager.getString("label.jalview"), 580, 220);
2942 public void showURL(String url, String target)
2944 if (viewport.applet == null)
2946 System.out.println("Not running as applet - no browser available.");
2950 viewport.applet.showURL(url, target);
2954 // ////////////////////////////////////////////////////////////////////////////////
2955 // JBuilder Graphics here
2957 MenuBar alignFrameMenuBar = new MenuBar();
2959 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2961 MenuItem loadApplication = new MenuItem(
2962 MessageManager.getString("label.view_full_application"));
2964 MenuItem loadTree = new MenuItem(
2965 MessageManager.getString("label.load_associated_tree"));
2967 MenuItem loadAnnotations = new MenuItem(
2968 MessageManager.getString("label.load_features_annotations"));
2970 MenuItem outputFeatures = new MenuItem(
2971 MessageManager.getString("label.export_features").concat("..."));
2973 MenuItem outputAnnotations = new MenuItem(
2974 MessageManager.getString("label.export_annotations").concat("..."));
2976 MenuItem closeMenuItem = new MenuItem(
2977 MessageManager.getString("action.close"));
2979 MenuItem selectAllSequenceMenuItem = new MenuItem(
2980 MessageManager.getString("action.select_all"));
2982 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2983 MessageManager.getString("action.deselect_all"));
2985 MenuItem invertSequenceMenuItem = new MenuItem(
2986 MessageManager.getString("action.invert_selection"));
2988 MenuItem remove2LeftMenuItem = new MenuItem();
2990 MenuItem remove2RightMenuItem = new MenuItem();
2992 MenuItem removeGappedColumnMenuItem = new MenuItem();
2994 MenuItem removeAllGapsMenuItem = new MenuItem();
2996 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2998 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3000 MenuItem sortPairwiseMenuItem = new MenuItem();
3002 MenuItem sortIDMenuItem = new MenuItem();
3004 MenuItem sortLengthMenuItem = new MenuItem();
3006 MenuItem sortGroupMenuItem = new MenuItem();
3008 MenuItem removeRedundancyMenuItem = new MenuItem();
3010 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3012 MenuItem PCAMenuItem = new MenuItem();
3014 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3016 MenuItem neighbourTreeMenuItem = new MenuItem();
3018 BorderLayout borderLayout1 = new BorderLayout();
3020 public Label statusBar = new Label();
3022 MenuItem clustalColour = new MenuItem();
3024 MenuItem zappoColour = new MenuItem();
3026 MenuItem taylorColour = new MenuItem();
3028 MenuItem hydrophobicityColour = new MenuItem();
3030 MenuItem helixColour = new MenuItem();
3032 MenuItem strandColour = new MenuItem();
3034 MenuItem turnColour = new MenuItem();
3036 MenuItem buriedColour = new MenuItem();
3038 MenuItem purinePyrimidineColour = new MenuItem();
3040 MenuItem RNAInteractionColour = new MenuItem();
3042 MenuItem RNAHelixColour = new MenuItem();
3044 MenuItem userDefinedColour = new MenuItem();
3046 MenuItem PIDColour = new MenuItem();
3048 MenuItem BLOSUM62Colour = new MenuItem();
3050 MenuItem tcoffeeColour = new MenuItem();
3052 MenuItem njTreeBlosumMenuItem = new MenuItem();
3054 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3056 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3058 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3060 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3062 MenuItem alProperties = new MenuItem(
3063 MessageManager.getString("label.alignment_props"));
3065 MenuItem overviewMenuItem = new MenuItem();
3067 MenuItem undoMenuItem = new MenuItem();
3069 MenuItem redoMenuItem = new MenuItem();
3071 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3073 MenuItem noColourmenuItem = new MenuItem();
3075 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3077 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3079 MenuItem findMenuItem = new MenuItem();
3081 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3083 MenuItem nucleotideColour = new MenuItem();
3085 MenuItem deleteGroups = new MenuItem();
3087 MenuItem grpsFromSelection = new MenuItem();
3089 MenuItem createGroup = new MenuItem();
3091 MenuItem unGroup = new MenuItem();
3093 MenuItem delete = new MenuItem();
3095 MenuItem copy = new MenuItem();
3097 MenuItem cut = new MenuItem();
3099 Menu pasteMenu = new Menu();
3101 MenuItem pasteNew = new MenuItem();
3103 MenuItem pasteThis = new MenuItem();
3105 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3107 MenuItem font = new MenuItem();
3109 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3111 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3113 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3115 MenuItem modifyPID = new MenuItem();
3117 MenuItem modifyConservation = new MenuItem();
3119 CheckboxMenuItem autoCalculate = null;
3121 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3122 "Sort Alignment With New Tree", true);
3124 Menu sortByTreeMenu = new Menu();
3126 MenuItem inputText = new MenuItem();
3128 MenuItem documentation = new MenuItem();
3130 MenuItem about = new MenuItem();
3132 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3134 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3136 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3138 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3140 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3142 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3144 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3146 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3148 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3151 * Initialise menus and other items
3155 private void jbInit() throws Exception
3157 setMenuBar(alignFrameMenuBar);
3160 * Configure File menu items and actions
3163 .setLabel(MessageManager.getString("label.input_from_textbox"));
3164 inputText.addActionListener(this);
3165 Menu outputTextboxMenu = new Menu(
3166 MessageManager.getString("label.out_to_textbox"));
3167 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3170 MenuItem item = new MenuItem(
3171 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3173 item.addActionListener(new java.awt.event.ActionListener()
3176 public void actionPerformed(ActionEvent e)
3178 outputText_actionPerformed(e);
3182 outputTextboxMenu.add(item);
3184 closeMenuItem.addActionListener(this);
3185 loadApplication.addActionListener(this);
3186 loadTree.addActionListener(this);
3187 loadAnnotations.addActionListener(this);
3188 outputFeatures.addActionListener(this);
3189 outputAnnotations.addActionListener(this);
3192 * Configure Edit menu items and actions
3194 undoMenuItem.setEnabled(false);
3195 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3196 undoMenuItem.addActionListener(this);
3197 redoMenuItem.setEnabled(false);
3198 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3199 redoMenuItem.addActionListener(this);
3200 copy.setLabel(MessageManager.getString("action.copy"));
3201 copy.addActionListener(this);
3202 cut.setLabel(MessageManager.getString("action.cut"));
3203 cut.addActionListener(this);
3204 delete.setLabel(MessageManager.getString("action.delete"));
3205 delete.addActionListener(this);
3206 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3207 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3208 pasteNew.addActionListener(this);
3209 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3210 pasteThis.addActionListener(this);
3211 remove2LeftMenuItem.setLabel(MessageManager
3212 .getString("action.remove_left"));
3213 remove2LeftMenuItem.addActionListener(this);
3214 remove2RightMenuItem.setLabel(MessageManager
3215 .getString("action.remove_right"));
3216 remove2RightMenuItem.addActionListener(this);
3217 removeGappedColumnMenuItem.setLabel(MessageManager
3218 .getString("action.remove_empty_columns"));
3219 removeGappedColumnMenuItem.addActionListener(this);
3220 removeAllGapsMenuItem.setLabel(MessageManager
3221 .getString("action.remove_all_gaps"));
3222 removeAllGapsMenuItem.addActionListener(this);
3223 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3224 "action.remove_redundancy").concat("..."));
3225 removeRedundancyMenuItem.addActionListener(this);
3228 * Configure Select menu items and actions
3230 findMenuItem.setLabel(MessageManager.getString("action.find"));
3231 findMenuItem.addActionListener(this);
3232 selectAllSequenceMenuItem.addActionListener(this);
3233 deselectAllSequenceMenuItem.addActionListener(this);
3234 invertSequenceMenuItem.setLabel(MessageManager
3235 .getString("action.invert_sequence_selection"));
3236 invertSequenceMenuItem.addActionListener(this);
3237 invertColSel.setLabel(MessageManager
3238 .getString("action.invert_column_selection"));
3239 invertColSel.addActionListener(this);
3240 deleteGroups.setLabel(MessageManager
3241 .getString("action.undefine_groups"));
3242 deleteGroups.addActionListener(this);
3243 grpsFromSelection.setLabel(MessageManager
3244 .getString("action.make_groups_selection"));
3245 grpsFromSelection.addActionListener(this);
3246 createGroup.setLabel(MessageManager.getString("action.create_group"));
3247 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3248 annotationColumnSelection.setLabel("Select by Annotation");
3249 annotationColumnSelection.addActionListener(this);
3252 * Configure View menu items and actions
3254 newView.setLabel(MessageManager.getString("action.new_view"));
3255 newView.addActionListener(this);
3256 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3257 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3258 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3259 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3261 .setLabel(MessageManager.getString("label.selected_columns"));
3262 hideSequences.setLabel(MessageManager
3263 .getString("label.selected_sequences"));
3264 hideAllButSelection.setLabel(MessageManager
3265 .getString("label.all_but_selected_region"));
3266 hideAllSelection.setLabel(MessageManager
3267 .getString("label.selected_region"));
3268 showAllHidden.setLabel(MessageManager
3269 .getString("label.all_sequences_columns"));
3270 showColumns.addActionListener(this);
3271 showSeqs.addActionListener(this);
3272 hideColumns.addActionListener(this);
3273 hideSequences.addActionListener(this);
3274 hideAllButSelection.addActionListener(this);
3275 hideAllSelection.addActionListener(this);
3276 showAllHidden.addActionListener(this);
3277 featureSettings.setLabel(MessageManager
3278 .getString("label.feature_settings"));
3279 featureSettings.addActionListener(this);
3280 sequenceFeatures.setLabel(MessageManager
3281 .getString("label.show_sequence_features"));
3282 sequenceFeatures.addItemListener(this);
3283 sequenceFeatures.setState(false);
3284 followMouseOverFlag.setLabel(MessageManager
3285 .getString("label.automatic_scrolling"));
3286 followMouseOverFlag.addItemListener(this);
3287 alProperties.addActionListener(this);
3288 overviewMenuItem.setLabel(MessageManager
3289 .getString("label.overview_window"));
3290 overviewMenuItem.addActionListener(this);
3293 * Configure Annotations menu items and actions
3295 annotationPanelMenuItem.setLabel(MessageManager
3296 .getString("label.show_annotations"));
3297 annotationPanelMenuItem.addItemListener(this);
3298 showGroupConsensus.setLabel(MessageManager
3299 .getString("label.group_consensus"));
3300 showGroupConservation.setLabel(MessageManager
3301 .getString("label.group_conservation"));
3302 showConsensusHistogram.setLabel(MessageManager
3303 .getString("label.show_consensus_histogram"));
3304 showSequenceLogo.setLabel(MessageManager
3305 .getString("label.show_consensus_logo"));
3306 normSequenceLogo.setLabel(MessageManager
3307 .getString("label.norm_consensus_logo"));
3308 applyAutoAnnotationSettings.setLabel(MessageManager
3309 .getString("label.apply_all_groups"));
3310 applyAutoAnnotationSettings.setState(true);
3311 Menu autoAnnMenu = new Menu(
3312 MessageManager.getString("label.autocalculated_annotation"));
3313 showGroupConsensus.addItemListener(this);
3314 showGroupConservation.addItemListener(this);
3315 showConsensusHistogram.addItemListener(this);
3316 showSequenceLogo.addItemListener(this);
3317 normSequenceLogo.addItemListener(this);
3318 applyAutoAnnotationSettings.addItemListener(this);
3319 showAlignmentAnnotations = new CheckboxMenuItem(
3320 MessageManager.getString("label.show_all_al_annotations"));
3321 showSequenceAnnotations = new CheckboxMenuItem(
3322 MessageManager.getString("label.show_all_seq_annotations"));
3323 sortAnnBySequence = new CheckboxMenuItem(
3324 MessageManager.getString("label.sort_annotations_by_sequence"));
3325 sortAnnByLabel = new CheckboxMenuItem(
3326 MessageManager.getString("label.sort_annotations_by_label"));
3327 showAutoFirst = new CheckboxMenuItem(
3328 MessageManager.getString("label.show_first"));
3329 showAutoLast = new CheckboxMenuItem(
3330 MessageManager.getString("label.show_last"));
3331 showAlignmentAnnotations.addItemListener(this);
3332 showSequenceAnnotations.addItemListener(this);
3333 sortAnnBySequence.addItemListener(this);
3334 sortAnnByLabel.addItemListener(this);
3335 showAutoFirst.addItemListener(this);
3336 showAutoLast.addItemListener(this);
3339 * Configure Format menu items and actions
3341 font.setLabel(MessageManager.getString("action.font"));
3342 font.addActionListener(this);
3343 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3344 scaleAbove.setState(true);
3345 scaleAbove.setEnabled(false);
3346 scaleAbove.addItemListener(this);
3347 scaleLeft.setEnabled(false);
3348 scaleLeft.setState(true);
3349 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3350 scaleLeft.addItemListener(this);
3351 scaleRight.setEnabled(false);
3352 scaleRight.setState(true);
3353 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3354 scaleRight.addItemListener(this);
3355 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3356 viewBoxesMenuItem.setState(true);
3357 viewBoxesMenuItem.addItemListener(this);
3358 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3359 viewTextMenuItem.setState(true);
3360 viewTextMenuItem.addItemListener(this);
3361 colourTextMenuItem.setLabel(MessageManager
3362 .getString("label.colour_text"));
3363 colourTextMenuItem.addItemListener(this);
3364 displayNonconservedMenuItem.setLabel(MessageManager
3365 .getString("label.show_non_conversed"));
3366 displayNonconservedMenuItem.addItemListener(this);
3367 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3368 wrapMenuItem.addItemListener(this);
3369 renderGapsMenuItem.setLabel(MessageManager
3370 .getString("action.show_gaps"));
3371 renderGapsMenuItem.setState(true);
3372 renderGapsMenuItem.addItemListener(this);
3373 centreColumnLabelFlag.setLabel(MessageManager
3374 .getString("label.centre_column_labels"));
3375 centreColumnLabelFlag.addItemListener(this);
3376 seqLimits.setState(true);
3377 seqLimits.setLabel(MessageManager
3378 .getString("label.show_sequence_limits"));
3379 seqLimits.addItemListener(this);
3382 * Configure Colour menu items and actions
3384 applyToAllGroups.setLabel(MessageManager
3385 .getString("label.apply_colour_to_all_groups"));
3386 applyToAllGroups.setState(true);
3387 applyToAllGroups.addItemListener(this);
3388 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3389 clustalColour.addActionListener(this);
3390 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3391 zappoColour.addActionListener(this);
3392 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3393 taylorColour.addActionListener(this);
3394 hydrophobicityColour.setLabel(MessageManager
3395 .getString("label.hydrophobicity"));
3396 hydrophobicityColour.addActionListener(this);
3398 .setLabel(MessageManager.getString("label.helix_propensity"));
3399 helixColour.addActionListener(this);
3400 strandColour.setLabel(MessageManager
3401 .getString("label.strand_propensity"));
3402 strandColour.addActionListener(this);
3403 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3404 turnColour.addActionListener(this);
3405 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3406 buriedColour.addActionListener(this);
3407 purinePyrimidineColour.setLabel(MessageManager
3408 .getString("label.purine_pyrimidine"));
3409 purinePyrimidineColour.addActionListener(this);
3410 RNAInteractionColour.setLabel(MessageManager
3411 .getString("label.rna_interaction"));
3412 RNAInteractionColour.addActionListener(this);
3413 RNAHelixColour.setLabel(MessageManager
3414 .getString("action.by_rna_helixes"));
3415 RNAHelixColour.addActionListener(this);
3416 userDefinedColour.setLabel(MessageManager
3417 .getString("action.user_defined"));
3418 userDefinedColour.addActionListener(this);
3419 PIDColour.setLabel(MessageManager
3420 .getString("label.percentage_identity"));
3421 PIDColour.addActionListener(this);
3422 BLOSUM62Colour.setLabel(MessageManager
3423 .getString("label.blosum62_score"));
3424 BLOSUM62Colour.addActionListener(this);
3426 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3427 // it will be enabled only if a score file is provided
3428 tcoffeeColour.setEnabled(false);
3429 tcoffeeColour.addActionListener(this);
3430 conservationMenuItem.setLabel(MessageManager
3431 .getString("action.by_conservation"));
3432 conservationMenuItem.addItemListener(this);
3433 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3434 noColourmenuItem.addActionListener(this);
3435 abovePIDThreshold.setLabel(MessageManager
3436 .getString("label.above_identity_threshold"));
3437 abovePIDThreshold.addItemListener(this);
3438 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3439 nucleotideColour.addActionListener(this);
3440 modifyPID.setLabel(MessageManager
3441 .getString("label.modify_identity_thereshold"));
3442 modifyPID.addActionListener(this);
3443 modifyConservation.setLabel(MessageManager
3444 .getString("label.modify_conservation_thereshold"));
3445 modifyConservation.addActionListener(this);
3446 annotationColour.setLabel(MessageManager
3447 .getString("action.by_annotation"));
3448 annotationColour.addActionListener(this);
3451 * Configure Calculate menu items and actions
3453 sortPairwiseMenuItem.setLabel(MessageManager
3454 .getString("action.by_pairwise_id"));
3455 sortPairwiseMenuItem.addActionListener(this);
3456 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3457 sortIDMenuItem.addActionListener(this);
3458 sortLengthMenuItem.setLabel(MessageManager
3459 .getString("action.by_length"));
3460 sortLengthMenuItem.addActionListener(this);
3461 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3462 sortGroupMenuItem.addActionListener(this);
3463 pairwiseAlignmentMenuItem.setLabel(MessageManager
3464 .getString("action.pairwise_alignment"));
3465 pairwiseAlignmentMenuItem.addActionListener(this);
3466 PCAMenuItem.setLabel(MessageManager
3467 .getString("label.principal_component_analysis"));
3468 PCAMenuItem.addActionListener(this);
3469 autoCalculate = new CheckboxMenuItem(
3470 MessageManager.getString("label.autocalculate_consensus"), true);
3471 averageDistanceTreeMenuItem.setLabel(MessageManager
3472 .getString("label.average_distance_identity"));
3473 averageDistanceTreeMenuItem.addActionListener(this);
3474 neighbourTreeMenuItem.setLabel(MessageManager
3475 .getString("label.neighbour_joining_identity"));
3476 neighbourTreeMenuItem.addActionListener(this);
3477 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3478 .getString("label.average_distance_bloslum62"));
3479 avDistanceTreeBlosumMenuItem.addActionListener(this);
3480 njTreeBlosumMenuItem.setLabel(MessageManager
3481 .getString("label.neighbour_blosum62"));
3482 njTreeBlosumMenuItem.addActionListener(this);
3483 sortByTreeMenu.setLabel(MessageManager
3484 .getString("action.by_tree_order"));
3485 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3486 Menu calculateTreeMenu = new Menu(
3487 MessageManager.getString("action.calculate_tree"));
3488 autoCalculate.addItemListener(this);
3489 sortByTree.addItemListener(this);
3492 * Configure Help menu items and actions
3494 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3495 documentation.setLabel(MessageManager.getString("label.documentation"));
3496 documentation.addActionListener(this);
3497 about.setLabel(MessageManager.getString("label.about"));
3498 about.addActionListener(this);
3501 * Add top level menus to frame
3503 alignFrameMenuBar.add(fileMenu);
3504 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3505 alignFrameMenuBar.add(editMenu);
3506 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3507 alignFrameMenuBar.add(selectMenu);
3508 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3509 alignFrameMenuBar.add(viewMenu);
3510 Menu annotationsMenu = new Menu(
3511 MessageManager.getString("action.annotations"));
3512 alignFrameMenuBar.add(annotationsMenu);
3513 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3514 alignFrameMenuBar.add(formatMenu);
3515 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3516 alignFrameMenuBar.add(colourMenu);
3517 Menu calculateMenu = new Menu(
3518 MessageManager.getString("action.calculate"));
3519 alignFrameMenuBar.add(calculateMenu);
3520 alignFrameMenuBar.add(helpMenu);
3525 fileMenu.add(inputText);
3526 fileMenu.add(loadTree);
3527 fileMenu.add(loadAnnotations);
3528 fileMenu.addSeparator();
3529 fileMenu.add(outputTextboxMenu);
3530 fileMenu.add(outputFeatures);
3531 fileMenu.add(outputAnnotations);
3532 if (jalviewServletURL != null)
3534 fileMenu.add(loadApplication);
3536 fileMenu.addSeparator();
3537 fileMenu.add(closeMenuItem);
3542 editMenu.add(undoMenuItem);
3543 editMenu.add(redoMenuItem);
3546 pasteMenu.add(pasteNew);
3547 pasteMenu.add(pasteThis);
3548 editMenu.add(pasteMenu);
3549 editMenu.add(delete);
3550 editMenu.addSeparator();
3551 editMenu.add(remove2LeftMenuItem);
3552 editMenu.add(remove2RightMenuItem);
3553 editMenu.add(removeGappedColumnMenuItem);
3554 editMenu.add(removeAllGapsMenuItem);
3555 editMenu.add(removeRedundancyMenuItem);
3560 selectMenu.add(findMenuItem);
3561 selectMenu.addSeparator();
3562 selectMenu.add(selectAllSequenceMenuItem);
3563 selectMenu.add(deselectAllSequenceMenuItem);
3564 selectMenu.add(invertSequenceMenuItem);
3565 selectMenu.add(invertColSel);
3566 selectMenu.add(createGroup);
3567 selectMenu.add(unGroup);
3568 selectMenu.add(grpsFromSelection);
3569 selectMenu.add(deleteGroups);
3570 selectMenu.add(annotationColumnSelection);
3575 viewMenu.add(newView);
3576 viewMenu.addSeparator();
3577 showMenu.add(showColumns);
3578 showMenu.add(showSeqs);
3579 showMenu.add(showAllHidden);
3580 viewMenu.add(showMenu);
3581 hideMenu.add(hideColumns);
3582 hideMenu.add(hideSequences);
3583 hideMenu.add(hideAllSelection);
3584 hideMenu.add(hideAllButSelection);
3585 viewMenu.add(hideMenu);
3586 viewMenu.addSeparator();
3587 viewMenu.add(followMouseOverFlag);
3588 viewMenu.addSeparator();
3589 viewMenu.add(sequenceFeatures);
3590 viewMenu.add(featureSettings);
3591 viewMenu.addSeparator();
3592 viewMenu.add(alProperties);
3593 viewMenu.addSeparator();
3594 viewMenu.add(overviewMenuItem);
3599 // annotationsMenu.add(annotationPanelMenuItem);
3600 // annotationsMenu.addSeparator();
3601 annotationsMenu.add(showAlignmentAnnotations);
3602 annotationsMenu.add(showSequenceAnnotations);
3603 annotationsMenu.add(sortAnnBySequence);
3604 annotationsMenu.add(sortAnnByLabel);
3605 annotationsMenu.addSeparator();
3606 autoAnnMenu.add(showAutoFirst);
3607 autoAnnMenu.add(showAutoLast);
3608 autoAnnMenu.addSeparator();
3609 autoAnnMenu.add(applyAutoAnnotationSettings);
3610 autoAnnMenu.add(showConsensusHistogram);
3611 autoAnnMenu.add(showSequenceLogo);
3612 autoAnnMenu.add(normSequenceLogo);
3613 autoAnnMenu.addSeparator();
3614 autoAnnMenu.add(showGroupConservation);
3615 autoAnnMenu.add(showGroupConsensus);
3616 annotationsMenu.add(autoAnnMenu);
3621 formatMenu.add(font);
3622 formatMenu.add(seqLimits);
3623 formatMenu.add(wrapMenuItem);
3624 formatMenu.add(scaleAbove);
3625 formatMenu.add(scaleLeft);
3626 formatMenu.add(scaleRight);
3627 formatMenu.add(viewBoxesMenuItem);
3628 formatMenu.add(viewTextMenuItem);
3629 formatMenu.add(colourTextMenuItem);
3630 formatMenu.add(displayNonconservedMenuItem);
3631 formatMenu.add(renderGapsMenuItem);
3632 formatMenu.add(centreColumnLabelFlag);
3637 colourMenu.add(applyToAllGroups);
3638 colourMenu.addSeparator();
3639 colourMenu.add(noColourmenuItem);
3640 colourMenu.add(clustalColour);
3641 colourMenu.add(BLOSUM62Colour);
3642 colourMenu.add(PIDColour);
3643 colourMenu.add(zappoColour);
3644 colourMenu.add(taylorColour);
3645 colourMenu.add(hydrophobicityColour);
3646 colourMenu.add(helixColour);
3647 colourMenu.add(strandColour);
3648 colourMenu.add(turnColour);
3649 colourMenu.add(buriedColour);
3650 colourMenu.add(nucleotideColour);
3651 colourMenu.add(purinePyrimidineColour);
3652 // colourMenu.add(RNAInteractionColour);
3653 colourMenu.add(tcoffeeColour);
3654 colourMenu.add(userDefinedColour);
3655 colourMenu.addSeparator();
3656 colourMenu.add(conservationMenuItem);
3657 colourMenu.add(modifyConservation);
3658 colourMenu.add(abovePIDThreshold);
3659 colourMenu.add(modifyPID);
3660 colourMenu.add(annotationColour);
3661 colourMenu.add(RNAHelixColour);
3666 sortMenu.add(sortIDMenuItem);
3667 sortMenu.add(sortLengthMenuItem);
3668 sortMenu.add(sortByTreeMenu);
3669 sortMenu.add(sortGroupMenuItem);
3670 sortMenu.add(sortPairwiseMenuItem);
3671 calculateMenu.add(sortMenu);
3672 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3673 calculateTreeMenu.add(neighbourTreeMenuItem);
3674 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3675 calculateTreeMenu.add(njTreeBlosumMenuItem);
3676 calculateMenu.add(calculateTreeMenu);
3677 calculateMenu.addSeparator();
3678 calculateMenu.add(pairwiseAlignmentMenuItem);
3679 calculateMenu.add(PCAMenuItem);
3680 calculateMenu.add(autoCalculate);
3681 calculateMenu.add(sortByTree);
3686 helpMenu.add(documentation);
3687 helpMenu.add(about);
3692 statusBar.setBackground(Color.white);
3693 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3694 statusBar.setText(MessageManager.getString("label.status_bar"));
3695 this.add(statusBar, BorderLayout.SOUTH);
3698 public void setStatus(String string)
3700 statusBar.setText(string);
3703 MenuItem featureSettings = new MenuItem();
3705 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3707 MenuItem annotationColour = new MenuItem();
3709 MenuItem annotationColumnSelection = new MenuItem();
3711 MenuItem invertColSel = new MenuItem();
3713 MenuItem showColumns = new MenuItem();
3715 MenuItem showSeqs = new MenuItem();
3717 MenuItem hideColumns = new MenuItem();
3719 MenuItem hideSequences = new MenuItem();
3721 MenuItem hideAllButSelection = new MenuItem();
3723 MenuItem hideAllSelection = new MenuItem();
3725 MenuItem showAllHidden = new MenuItem();
3727 MenuItem newView = new MenuItem();
3729 private CheckboxMenuItem showAlignmentAnnotations;
3731 private CheckboxMenuItem showSequenceAnnotations;
3733 private CheckboxMenuItem sortAnnBySequence;
3735 private CheckboxMenuItem sortAnnByLabel;
3737 private CheckboxMenuItem showAutoFirst;
3739 private CheckboxMenuItem showAutoLast;
3742 * Attach the alignFrame panels after embedding menus, if necessary. This used
3743 * to be called setEmbedded, but is now creates the dropdown menus in a
3744 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3746 * @param reallyEmbedded
3747 * true to attach the view to the applet area on the page rather than
3750 public void createAlignFrameWindow(boolean reallyEmbedded)
3754 embedAlignFrameInApplet(viewport.applet);
3759 // test and embed menu bar if necessary.
3761 if (embedMenuIfNeeded(alignPanel))
3764 * adjust for status bar height too. ? pointless as overridden by layout
3767 alignPanel.setSize(getSize().width,
3768 getSize().height - statusBar.getHeight());
3770 add(statusBar, BorderLayout.SOUTH);
3771 add(alignPanel, BorderLayout.CENTER);
3772 // and register with the applet so it can pass external API calls to us
3773 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3780 * Add the components of this AlignFrame to the applet container.
3784 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3787 // Explicitly build the embedded menu panel for the on-page applet
3789 // view cannot be closed if its actually on the page
3790 fileMenu.remove(closeMenuItem);
3791 fileMenu.remove(3); // Remove Separator
3792 // construct embedded menu, using default font
3793 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3794 // and actually add the components to the applet area
3795 theApplet.setLayout(new BorderLayout());
3796 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3797 theApplet.add(statusBar, BorderLayout.SOUTH);
3798 // TODO should size be left to the layout manager?
3799 alignPanel.setSize(theApplet.getSize().width,
3800 theApplet.getSize().height - embeddedMenu.getHeight()
3801 - statusBar.getHeight());
3802 theApplet.add(alignPanel, BorderLayout.CENTER);
3803 final AlignFrame me = this;
3804 theApplet.addFocusListener(new FocusListener()
3808 public void focusLost(FocusEvent e)
3810 if (theApplet.currentAlignFrame == me)
3812 theApplet.currentAlignFrame = null;
3817 public void focusGained(FocusEvent e)
3819 theApplet.currentAlignFrame = me;
3822 theApplet.validate();
3826 * create a new binding between structures in an existing jmol viewer instance
3827 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3828 * this does not open a new Jmol window, or modify the display of the
3829 * structures in the original jmol window. Note This method doesn't work
3830 * without an additional javascript library to exchange messages between the
3831 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3834 * JmolViewer instance
3835 * @param sequenceIds
3836 * - sequence Ids to search for associations
3838 public SequenceStructureBinding addStructureViewInstance(
3839 Object jmolviewer, String[] sequenceIds)
3841 org.jmol.api.JmolViewer viewer = null;
3844 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3845 } catch (ClassCastException ex)
3847 System.err.println("Unsupported viewer object :"
3848 + jmolviewer.getClass());
3852 System.err.println("Can't use this object as a structure viewer:"
3853 + jmolviewer.getClass());
3856 SequenceI[] seqs = null;
3857 if (sequenceIds == null || sequenceIds.length == 0)
3859 seqs = viewport.getAlignment().getSequencesArray();
3863 Vector sqi = new Vector();
3864 AlignmentI al = viewport.getAlignment();
3865 for (int sid = 0; sid < sequenceIds.length; sid++)
3867 SequenceI sq = al.findName(sequenceIds[sid]);
3875 seqs = new SequenceI[sqi.size()];
3876 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3878 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3886 AAStructureBindingModel jmv = null;
3887 // TODO: search for a jmv that involves viewer
3889 { // create a new viewer/jalview binding.
3890 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3898 * bind a pdb file to a sequence in the current view
3901 * - sequenceId within the dataset.
3902 * @param pdbEntryString
3903 * - the short name for the PDB file
3905 * - pdb file - either a URL or a valid PDB file.
3906 * @return true if binding was as success TODO: consider making an exception
3907 * structure for indicating when PDB parsing or sequenceId location
3910 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3913 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3914 boolean needtoadd = false;
3915 if (toaddpdb != null)
3917 Vector pdbe = toaddpdb.getPDBId();
3918 PDBEntry pdbentry = null;
3919 if (pdbe != null && pdbe.size() > 0)
3921 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3923 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3924 if (!pdbentry.getId().equals(pdbEntryString)
3925 && !pdbentry.getFile().equals(pdbFile))
3935 if (pdbentry == null)
3937 pdbentry = new PDBEntry();
3938 pdbentry.setId(pdbEntryString);
3939 pdbentry.setFile(pdbFile);
3940 needtoadd = true; // add this new entry to sequence.
3942 // resolve data source
3943 // TODO: this code should be a refactored to an io package
3944 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3945 if (protocol == null)
3951 // make a note of the access mode and add
3952 if (pdbentry.getProperty() == null)
3954 pdbentry.setProperty(new Hashtable());
3956 pdbentry.getProperty().put("protocol", protocol);
3957 toaddpdb.addPDBId(pdbentry);
3958 alignPanel.getStructureSelectionManager()
3959 .registerPDBEntry(pdbentry);
3965 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3969 Vector sequences = new Vector();
3970 for (int i = 0; i < seqs.length; i++)
3972 if (seqs[i] != null)
3974 sequences.addElement(new Object[]
3975 { seqs[i], (chains != null) ? chains[i] : null });
3978 seqs = new SequenceI[sequences.size()];
3979 chains = new String[sequences.size()];
3980 for (int i = 0, isize = sequences.size(); i < isize; i++)
3982 Object[] oj = (Object[]) sequences.elementAt(i);
3984 seqs[i] = (SequenceI) oj[0];
3985 chains[i] = (String) oj[1];
3993 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3994 SequenceI[] seqs, String[] chains, String protocol)
3996 // Scrub any null sequences from the array
3997 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3998 seqs = (SequenceI[]) sqch[0];
3999 chains = (String[]) sqch[1];
4000 if (seqs == null || seqs.length == 0)
4003 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4005 if (protocol == null || protocol.trim().length() == 0
4006 || protocol.equals("null"))
4008 protocol = (String) pdb.getProperty().get("protocol");
4009 if (protocol == null)
4011 System.err.println("Couldn't work out protocol to open structure: "
4016 if (applet.useXtrnalSviewer)
4018 // register the association(s) and quit, don't create any windows.
4019 if (StructureSelectionManager.getStructureSelectionManager(applet)
4020 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4022 System.err.println("Failed to map " + pdb.getFile() + " ("
4023 + protocol + ") to any sequences");
4027 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4029 // can only do alignments with Jmol
4030 // find the last jmol window assigned to this alignment
4031 jalview.appletgui.AppletJmol ajm = null, tajm;
4032 Vector jmols = applet
4033 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4034 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4036 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4037 if (tajm.ap.alignFrame == this)
4046 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4047 // try and add the pdb structure
4052 // otherwise, create a new window
4053 if (applet.jmolAvailable)
4055 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4057 applet.lastFrameX += 40;
4058 applet.lastFrameY += 40;
4062 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4067 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4068 SequenceI[][] seqs, String[][] chains, String[] protocols)
4070 // TODO Auto-generated method stub
4071 System.err.println("Aligned Structure View: Not yet implemented.");
4075 * modify the current selection, providing the user has not made a selection
4079 * - sequences from this alignment
4081 * - columns to be selected on the alignment
4083 public void select(SequenceGroup sel, ColumnSelection csel)
4085 alignPanel.seqPanel.selection(sel, csel, null);
4088 public void scrollTo(int row, int column)
4090 alignPanel.seqPanel.scrollTo(row, column);
4093 public void scrollToRow(int row)
4095 alignPanel.seqPanel.scrollToRow(row);
4098 public void scrollToColumn(int column)
4100 alignPanel.seqPanel.scrollToColumn(column);
4104 * @return the alignments unique ID.
4106 public String getSequenceSetId()
4108 return viewport.getSequenceSetId();
4112 * Load the (T-Coffee) score file from the specified url
4115 * File/URL/T-COFFEE score file contents
4116 * @throws IOException
4117 * @return true if alignment was annotated with data from source
4119 public boolean loadScoreFile(String source) throws IOException
4122 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4123 AppletFormatAdapter.checkProtocol(source));
4124 if (!file.isValid())
4126 // TODO: raise dialog for gui
4127 System.err.println("Problems parsing T-Coffee scores: "
4128 + file.getWarningMessage());
4129 System.err.println("Origin was:\n" + source);
4134 * check that the score matrix matches the alignment dimensions
4137 if ((aln = viewport.getAlignment()) != null
4138 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4141 // TODO: raise a dialog box here rather than bomb out.
4143 .println("The scores matrix does not match the alignment dimensions");
4147 // TODO add parameter to indicate if matching should be done
4148 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4150 alignPanel.fontChanged();
4151 tcoffeeColour.setEnabled(true);
4152 // switch to this color
4153 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4158 System.err.println("Problems resolving T-Coffee scores:");
4159 if (file.getWarningMessage() != null)
4161 System.err.println(file.getWarningMessage());