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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.appletgui

File AlignFrame.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
56% of files have more coverage

Code metrics

682
1,709
131
2
4,363
3,483
568
0.33
13.05
65.5
4.34

Classes

Class Line # Actions
AlignFrame 123 1,687 566
0.00%
AlignFrame.AboutPanel 3000 22 2
0.00%
 

Contributing tests

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.appletgui;
22   
23    import jalview.analysis.AlignmentSorter;
24    import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25    import jalview.analysis.TreeBuilder;
26    import jalview.analysis.scoremodels.PIDModel;
27    import jalview.analysis.scoremodels.ScoreModels;
28    import jalview.api.AlignViewControllerGuiI;
29    import jalview.api.AlignViewControllerI;
30    import jalview.api.AlignViewportI;
31    import jalview.api.FeatureColourI;
32    import jalview.api.FeatureRenderer;
33    import jalview.api.FeatureSettingsControllerI;
34    import jalview.api.SequenceStructureBinding;
35    import jalview.bin.JalviewLite;
36    import jalview.commands.CommandI;
37    import jalview.commands.EditCommand;
38    import jalview.commands.EditCommand.Action;
39    import jalview.commands.OrderCommand;
40    import jalview.commands.RemoveGapColCommand;
41    import jalview.commands.RemoveGapsCommand;
42    import jalview.commands.SlideSequencesCommand;
43    import jalview.commands.TrimRegionCommand;
44    import jalview.datamodel.Alignment;
45    import jalview.datamodel.AlignmentAnnotation;
46    import jalview.datamodel.AlignmentI;
47    import jalview.datamodel.AlignmentOrder;
48    import jalview.datamodel.ColumnSelection;
49    import jalview.datamodel.HiddenColumns;
50    import jalview.datamodel.PDBEntry;
51    import jalview.datamodel.Sequence;
52    import jalview.datamodel.SequenceGroup;
53    import jalview.datamodel.SequenceI;
54    import jalview.io.AnnotationFile;
55    import jalview.io.AppletFormatAdapter;
56    import jalview.io.DataSourceType;
57    import jalview.io.FeaturesFile;
58    import jalview.io.FileFormat;
59    import jalview.io.FileFormatI;
60    import jalview.io.FileFormats;
61    import jalview.io.TCoffeeScoreFile;
62    import jalview.schemes.Blosum62ColourScheme;
63    import jalview.schemes.BuriedColourScheme;
64    import jalview.schemes.ClustalxColourScheme;
65    import jalview.schemes.ColourSchemeI;
66    import jalview.schemes.HelixColourScheme;
67    import jalview.schemes.HydrophobicColourScheme;
68    import jalview.schemes.NucleotideColourScheme;
69    import jalview.schemes.PIDColourScheme;
70    import jalview.schemes.PurinePyrimidineColourScheme;
71    import jalview.schemes.RNAHelicesColour;
72    import jalview.schemes.StrandColourScheme;
73    import jalview.schemes.TCoffeeColourScheme;
74    import jalview.schemes.TaylorColourScheme;
75    import jalview.schemes.TurnColourScheme;
76    import jalview.schemes.ZappoColourScheme;
77    import jalview.structure.StructureSelectionManager;
78    import jalview.structures.models.AAStructureBindingModel;
79    import jalview.util.MappingUtils;
80    import jalview.util.MessageManager;
81    import jalview.viewmodel.AlignmentViewport;
82    import jalview.viewmodel.ViewportRanges;
83   
84    import java.awt.BorderLayout;
85    import java.awt.Canvas;
86    import java.awt.CheckboxMenuItem;
87    import java.awt.Color;
88    import java.awt.FlowLayout;
89    import java.awt.Font;
90    import java.awt.FontMetrics;
91    import java.awt.Frame;
92    import java.awt.Graphics;
93    import java.awt.Label;
94    import java.awt.Menu;
95    import java.awt.MenuBar;
96    import java.awt.MenuItem;
97    import java.awt.Panel;
98    import java.awt.Rectangle;
99    import java.awt.event.ActionEvent;
100    import java.awt.event.ActionListener;
101    import java.awt.event.FocusEvent;
102    import java.awt.event.FocusListener;
103    import java.awt.event.ItemEvent;
104    import java.awt.event.ItemListener;
105    import java.awt.event.KeyEvent;
106    import java.awt.event.KeyListener;
107    import java.awt.event.WindowAdapter;
108    import java.awt.event.WindowEvent;
109    import java.io.IOException;
110    import java.io.UnsupportedEncodingException;
111    import java.net.URL;
112    import java.net.URLEncoder;
113    import java.util.Arrays;
114    import java.util.Deque;
115    import java.util.HashMap;
116    import java.util.List;
117    import java.util.Map;
118    import java.util.StringTokenizer;
119    import java.util.Vector;
120   
121    import org.jmol.viewer.Viewer;
122   
 
123    public class AlignFrame extends EmbmenuFrame implements ActionListener,
124    ItemListener, KeyListener, AlignViewControllerGuiI
125    {
126    public AlignViewControllerI avc;
127   
128    public AlignmentPanel alignPanel;
129   
130    public AlignViewport viewport;
131   
132    // width and height may be overridden by applet parameters
133    int frameWidth = 700;
134   
135    int frameHeight = 500;
136   
137    String jalviewServletURL;
138   
139    /*
140    * Flag for showing autocalculated consensus above or below other consensus
141    * rows
142    */
143    private boolean showAutoCalculatedAbove;
144   
145    private SequenceAnnotationOrder annotationSortOrder;
146   
147    /**
148    * Constructor that creates the frame and adds it to the display.
149    *
150    * @param al
151    * @param applet
152    * @param title
153    * @param embedded
154    */
 
155  0 toggle public AlignFrame(AlignmentI al, JalviewLite applet, String title,
156    boolean embedded)
157    {
158  0 this(al, applet, title, embedded, true);
159    }
160   
161    /**
162    * Constructor that optionally allows the frame to be displayed or only
163    * created.
164    *
165    * @param al
166    * @param applet
167    * @param title
168    * @param embedded
169    * @param addToDisplay
170    */
 
171  0 toggle public AlignFrame(AlignmentI al, JalviewLite applet, String title,
172    boolean embedded, boolean addToDisplay)
173    {
174  0 this(al, null, null, applet, title, embedded, addToDisplay);
175    }
176   
 
177  0 toggle public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
178    HiddenColumns hidden, JalviewLite applet, String title,
179    boolean embedded)
180    {
181  0 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182    }
183   
 
184  0 toggle public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
185    HiddenColumns hidden, JalviewLite applet, String title,
186    boolean embedded, boolean addToDisplay)
187    {
188  0 if (applet != null)
189    {
190  0 jalviewServletURL = applet.getParameter("APPLICATION_URL");
191    }
192   
193  0 try
194    {
195  0 jbInit();
196    } catch (Exception ex)
197    {
198  0 ex.printStackTrace();
199    }
200    // need to get window geometry before we calculate alignment layout
201  0 if (applet != null)
202    {
203  0 String param;
204  0 try
205    {
206  0 param = applet.getParameter("windowWidth");
207  0 if (param != null)
208    {
209  0 int width = Integer.parseInt(param);
210  0 frameWidth = width;
211    }
212  0 param = applet.getParameter("windowHeight");
213  0 if (param != null)
214    {
215  0 int height = Integer.parseInt(param);
216  0 frameHeight = height;
217    }
218    } catch (Exception ex)
219    {
220    }
221    }
222  0 viewport = new AlignViewport(al, applet);
223   
224  0 if (hiddenSeqs != null && hiddenSeqs.length > 0)
225    {
226  0 viewport.hideSequence(hiddenSeqs);
227    }
228  0 if (hidden != null)
229    {
230  0 viewport.getAlignment().setHiddenColumns(hidden);
231    }
232  0 viewport.setScaleAboveWrapped(scaleAbove.getState());
233   
234  0 alignPanel = new AlignmentPanel(this, viewport);
235  0 avc = new jalview.controller.AlignViewController(this, viewport,
236    alignPanel);
237  0 viewport.updateConservation(alignPanel);
238  0 viewport.updateConsensus(alignPanel);
239   
240  0 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
241  0 followMouseOverFlag.setState(viewport.isFollowHighlight());
242  0 showGroupConsensus.setState(viewport.isShowGroupConsensus());
243  0 showGroupConservation.setState(viewport.isShowGroupConservation());
244  0 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
245  0 showSequenceLogo.setState(viewport.isShowSequenceLogo());
246  0 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
247  0 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
248  0 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
249  0 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
250  0 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
251  0 showAlignmentAnnotations.setState(true);
252  0 showSequenceAnnotations.setState(false);
253   
254  0 seqLimits.setState(viewport.getShowJVSuffix());
255   
256  0 if (applet != null)
257    {
258  0 String param = applet.getParameter("sortBy");
259  0 if (param != null)
260    {
261  0 if (param.equalsIgnoreCase("Id"))
262    {
263  0 sortIDMenuItem_actionPerformed();
264    }
265  0 else if (param.equalsIgnoreCase("Pairwise Identity"))
266    {
267  0 sortPairwiseMenuItem_actionPerformed();
268    }
269  0 else if (param.equalsIgnoreCase("Length"))
270    {
271  0 sortLengthMenuItem_actionPerformed();
272    }
273    }
274   
275  0 param = applet.getParameter("wrap");
276  0 if (param != null)
277    {
278  0 if (param.equalsIgnoreCase("true"))
279    {
280  0 wrapMenuItem.setState(true);
281  0 wrapMenuItem_actionPerformed();
282    }
283    }
284  0 param = applet.getParameter("centrecolumnlabels");
285  0 if (param != null)
286    {
287  0 centreColumnLabelFlag.setState(true);
288  0 centreColumnLabelFlag_stateChanged();
289    }
290   
291    }
292  0 if (viewport.getAlignment().isNucleotide())
293    {
294  0 conservationMenuItem.setEnabled(false);
295  0 clustalColour.setEnabled(false);
296  0 BLOSUM62Colour.setEnabled(false);
297  0 zappoColour.setEnabled(false);
298  0 taylorColour.setEnabled(false);
299  0 hydrophobicityColour.setEnabled(false);
300  0 helixColour.setEnabled(false);
301  0 strandColour.setEnabled(false);
302  0 turnColour.setEnabled(false);
303  0 buriedColour.setEnabled(false);
304  0 viewport.updateStrucConsensus(alignPanel);
305  0 if (viewport.getAlignment().hasRNAStructure())
306    {
307  0 RNAHelixColour.setEnabled(true);
308    }
309    else
310    {
311  0 RNAHelixColour.setEnabled(false);
312    }
313    }
314    else
315    {
316  0 RNAHelixColour.setEnabled(false);
317  0 purinePyrimidineColour.setEnabled(false);
318  0 nucleotideColour.setEnabled(false);
319    }
320    // Some JVMS send keyevents to Top frame or lowest panel,
321    // Havent worked out why yet. So add to both this frame and seqCanvas for
322    // now
323  0 this.addKeyListener(this);
324  0 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
325  0 alignPanel.idPanel.idCanvas.addKeyListener(this);
326  0 alignPanel.scalePanel.addKeyListener(this);
327  0 alignPanel.annotationPanel.addKeyListener(this);
328  0 alignPanel.annotationPanelHolder.addKeyListener(this);
329  0 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
330  0 alignPanel.alabels.addKeyListener(this);
331   
332  0 setAnnotationsVisibility();
333   
334  0 if (addToDisplay)
335    {
336  0 addToDisplay(embedded);
337    }
338    }
339   
340    /**
341    * @param embedded
342    */
 
343  0 toggle public void addToDisplay(boolean embedded)
344    {
345  0 createAlignFrameWindow(embedded);
346  0 validate();
347  0 alignPanel.adjustAnnotationHeight();
348  0 alignPanel.paintAlignment(true, true);
349    }
350   
 
351  0 toggle public AlignViewport getAlignViewport()
352    {
353  0 return viewport;
354    }
355   
 
356  0 toggle public SeqCanvas getSeqcanvas()
357    {
358  0 return alignPanel.seqPanel.seqCanvas;
359    }
360   
361    /**
362    * Load a features file onto the alignment
363    *
364    * @param file
365    * file URL, content, or other resolvable path
366    * @param type
367    * is protocol for accessing data referred to by file
368    */
369   
 
370  0 toggle public boolean parseFeaturesFile(String file, DataSourceType type)
371    {
372  0 return parseFeaturesFile(file, type, true);
373    }
374   
375    /**
376    * Load a features file onto the alignment
377    *
378    * @param file
379    * file URL, content, or other resolvable path
380    * @param sourceType
381    * is protocol for accessing data referred to by file
382    * @param autoenabledisplay
383    * when true, display features flag will be automatically enabled if
384    * features are loaded
385    * @return true if data parsed as a features file
386    */
 
387  0 toggle public boolean parseFeaturesFile(String file, DataSourceType sourceType,
388    boolean autoenabledisplay)
389    {
390  0 boolean featuresFile = false;
391  0 try
392    {
393  0 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
394    .getFeatureRenderer().getFeatureColours();
395  0 boolean relaxedIdMatching = viewport.applet
396    .getDefaultParameter("relaxedidmatch", false);
397  0 featuresFile = new FeaturesFile(file, sourceType).parse(
398    viewport.getAlignment(), colours, true, relaxedIdMatching);
399    } catch (Exception ex)
400    {
401  0 ex.printStackTrace();
402    }
403   
404  0 if (featuresFile)
405    {
406  0 if (autoenabledisplay)
407    {
408  0 viewport.setShowSequenceFeatures(true);
409  0 sequenceFeatures.setState(true);
410    }
411  0 if (alignPanel.seqPanel.seqCanvas.fr != null)
412    {
413    // update the min/max ranges where necessary
414  0 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
415    }
416  0 if (viewport.featureSettings != null)
417    {
418  0 viewport.featureSettings.refreshTable();
419    }
420  0 alignPanel.paintAlignment(true, true);
421  0 setStatus(MessageManager
422    .getString("label.successfully_added_features_alignment"));
423    }
424  0 return featuresFile;
425    }
426   
 
427  0 toggle @Override
428    public void keyPressed(KeyEvent evt)
429    {
430  0 ViewportRanges ranges = viewport.getRanges();
431   
432  0 if (viewport.cursorMode
433    && ((evt.getKeyCode() >= KeyEvent.VK_0
434    && evt.getKeyCode() <= KeyEvent.VK_9)
435    || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
436    && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
437    && Character.isDigit(evt.getKeyChar()))
438    {
439  0 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
440    }
441   
442  0 switch (evt.getKeyCode())
443    {
444  0 case 27: // escape key
445  0 deselectAllSequenceMenuItem_actionPerformed();
446   
447  0 alignPanel.alabels.cancelDrag();
448  0 break;
449  0 case KeyEvent.VK_X:
450  0 if (evt.isControlDown() || evt.isMetaDown())
451    {
452  0 cut_actionPerformed();
453    }
454  0 break;
455  0 case KeyEvent.VK_C:
456  0 if (viewport.cursorMode && !evt.isControlDown())
457    {
458  0 alignPanel.seqPanel.setCursorColumn();
459    }
460  0 if (evt.isControlDown() || evt.isMetaDown())
461    {
462  0 copy_actionPerformed();
463    }
464  0 break;
465  0 case KeyEvent.VK_V:
466  0 if (evt.isControlDown())
467    {
468  0 paste(evt.isShiftDown());
469    }
470  0 break;
471  0 case KeyEvent.VK_A:
472  0 if (evt.isControlDown() || evt.isMetaDown())
473    {
474  0 selectAllSequenceMenuItem_actionPerformed();
475    }
476  0 break;
477  0 case KeyEvent.VK_DOWN:
478  0 if (viewport.cursorMode)
479    {
480  0 alignPanel.seqPanel.moveCursor(0, 1);
481    }
482    else
483    {
484  0 moveSelectedSequences(false);
485    }
486  0 break;
487   
488  0 case KeyEvent.VK_UP:
489  0 if (viewport.cursorMode)
490    {
491  0 alignPanel.seqPanel.moveCursor(0, -1);
492    }
493    else
494    {
495  0 moveSelectedSequences(true);
496    }
497  0 break;
498   
499  0 case KeyEvent.VK_LEFT:
500  0 if (evt.isAltDown() || !viewport.cursorMode)
501    {
502  0 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
503    }
504    else
505    {
506  0 alignPanel.seqPanel.moveCursor(-1, 0);
507    }
508  0 break;
509   
510  0 case KeyEvent.VK_RIGHT:
511  0 if (evt.isAltDown() || !viewport.cursorMode)
512    {
513  0 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
514    }
515    else
516    {
517  0 alignPanel.seqPanel.moveCursor(1, 0);
518    }
519  0 break;
520   
521  0 case KeyEvent.VK_SPACE:
522  0 if (viewport.cursorMode)
523    {
524  0 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
525    || evt.isShiftDown() || evt.isAltDown());
526    }
527  0 break;
528   
529  0 case KeyEvent.VK_DELETE:
530  0 case KeyEvent.VK_BACK_SPACE:
531  0 if (viewport.cursorMode)
532    {
533  0 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
534    || evt.isShiftDown() || evt.isAltDown());
535    }
536    else
537    {
538  0 cut_actionPerformed();
539  0 alignPanel.seqPanel.seqCanvas.repaint();
540    }
541  0 break;
542   
543  0 case KeyEvent.VK_S:
544  0 if (viewport.cursorMode)
545    {
546  0 alignPanel.seqPanel.setCursorRow();
547    }
548  0 break;
549  0 case KeyEvent.VK_P:
550  0 if (viewport.cursorMode)
551    {
552  0 alignPanel.seqPanel.setCursorPosition();
553    }
554  0 break;
555   
556  0 case KeyEvent.VK_ENTER:
557  0 case KeyEvent.VK_COMMA:
558  0 if (viewport.cursorMode)
559    {
560  0 alignPanel.seqPanel.setCursorRowAndColumn();
561    }
562  0 break;
563   
564  0 case KeyEvent.VK_Q:
565  0 if (viewport.cursorMode)
566    {
567  0 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
568    }
569  0 break;
570  0 case KeyEvent.VK_M:
571  0 if (viewport.cursorMode)
572    {
573  0 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
574    }
575  0 break;
576   
577  0 case KeyEvent.VK_F2:
578  0 viewport.cursorMode = !viewport.cursorMode;
579  0 setStatus(MessageManager
580    .formatMessage("label.keyboard_editing_mode", new String[]
581  0 { (viewport.cursorMode ? "on" : "off") }));
582  0 if (viewport.cursorMode)
583    {
584  0 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
585  0 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
586    }
587  0 break;
588   
589  0 case KeyEvent.VK_F:
590  0 if (evt.isControlDown())
591    {
592  0 findMenuItem_actionPerformed();
593    }
594  0 break;
595   
596  0 case KeyEvent.VK_H:
597    {
598  0 boolean toggleSeqs = !evt.isControlDown();
599  0 boolean toggleCols = !evt.isShiftDown();
600  0 toggleHiddenRegions(toggleSeqs, toggleCols);
601  0 break;
602    }
603   
604  0 case KeyEvent.VK_PAGE_UP:
605  0 ranges.pageUp();
606  0 break;
607   
608  0 case KeyEvent.VK_PAGE_DOWN:
609  0 ranges.pageDown();
610  0 break;
611   
612  0 case KeyEvent.VK_Z:
613  0 if (evt.isControlDown())
614    {
615  0 undoMenuItem_actionPerformed();
616    }
617  0 break;
618   
619  0 case KeyEvent.VK_Y:
620  0 if (evt.isControlDown())
621    {
622  0 redoMenuItem_actionPerformed();
623    }
624  0 break;
625   
626  0 case KeyEvent.VK_L:
627  0 if (evt.isControlDown())
628    {
629  0 trimAlignment(true);
630    }
631  0 break;
632   
633  0 case KeyEvent.VK_R:
634  0 if (evt.isControlDown())
635    {
636  0 trimAlignment(false);
637    }
638  0 break;
639   
640  0 case KeyEvent.VK_E:
641  0 if (evt.isControlDown())
642    {
643  0 if (evt.isShiftDown())
644    {
645  0 this.removeAllGapsMenuItem_actionPerformed();
646    }
647    else
648    {
649  0 removeGappedColumnMenuItem_actionPerformed();
650    }
651    }
652  0 break;
653  0 case KeyEvent.VK_I:
654  0 if (evt.isControlDown())
655    {
656  0 if (evt.isAltDown())
657    {
658  0 invertColSel_actionPerformed();
659    }
660    else
661    {
662  0 invertSequenceMenuItem_actionPerformed();
663    }
664    }
665  0 break;
666   
667  0 case KeyEvent.VK_G:
668  0 if (evt.isControlDown())
669    {
670  0 if (evt.isShiftDown())
671    {
672  0 this.unGroup_actionPerformed();
673    }
674    else
675    {
676  0 this.createGroup_actionPerformed();
677    }
678    }
679  0 break;
680   
681  0 case KeyEvent.VK_U:
682  0 if (evt.isControlDown())
683    {
684  0 this.deleteGroups_actionPerformed();
685    }
686  0 break;
687   
688  0 case KeyEvent.VK_T:
689  0 if (evt.isControlDown())
690    {
691  0 newView(null);
692    }
693  0 break;
694   
695    }
696    // TODO: repaint flags set only if the keystroke warrants it
697  0 alignPanel.paintAlignment(true, true);
698    }
699   
700    /**
701    * called by key handler and the hide all/show all menu items
702    *
703    * @param toggleSeqs
704    * @param toggleCols
705    */
 
706  0 toggle private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
707    {
708  0 boolean hide = false;
709  0 SequenceGroup sg = viewport.getSelectionGroup();
710  0 if (!toggleSeqs && !toggleCols)
711    {
712    // Hide everything by the current selection - this is a hack - we do the
713    // invert and then hide
714    // first check that there will be visible columns after the invert.
715  0 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
716    && sg.getStartRes() <= sg.getEndRes()))
717    {
718    // now invert the sequence set, if required - empty selection implies
719    // that no hiding is required.
720  0 if (sg != null)
721    {
722  0 invertSequenceMenuItem_actionPerformed();
723  0 sg = viewport.getSelectionGroup();
724  0 toggleSeqs = true;
725   
726    }
727  0 viewport.expandColSelection(sg, true);
728    // finally invert the column selection and get the new sequence
729    // selection and indicate it should be hidden.
730  0 invertColSel_actionPerformed();
731  0 toggleCols = true;
732    }
733    }
734   
735  0 if (toggleSeqs)
736    {
737  0 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
738    {
739  0 hide = true;
740  0 viewport.hideAllSelectedSeqs();
741    }
742  0 else if (!(toggleCols && viewport.hasSelectedColumns()))
743    {
744  0 viewport.showAllHiddenSeqs();
745    }
746    }
747   
748  0 if (toggleCols)
749    {
750  0 if (viewport.hasSelectedColumns())
751    {
752  0 viewport.hideSelectedColumns();
753  0 if (!toggleSeqs)
754    {
755  0 viewport.setSelectionGroup(sg);
756    }
757    }
758  0 else if (!hide)
759    {
760  0 viewport.showAllHiddenColumns();
761    }
762  0 viewport.sendSelection();
763    }
764    }
765   
 
766  0 toggle @Override
767    public void keyReleased(KeyEvent evt)
768    {
769    }
770   
 
771  0 toggle @Override
772    public void keyTyped(KeyEvent evt)
773    {
774    }
775   
 
776  0 toggle @Override
777    public void itemStateChanged(ItemEvent evt)
778    {
779  0 final Object source = evt.getSource();
780  0 if (source == displayNonconservedMenuItem)
781    {
782  0 displayNonconservedMenuItem_actionPerformed();
783    }
784  0 else if (source == colourTextMenuItem)
785    {
786  0 colourTextMenuItem_actionPerformed();
787    }
788  0 else if (source == wrapMenuItem)
789    {
790  0 wrapMenuItem_actionPerformed();
791    }
792  0 else if (source == scaleAbove)
793    {
794  0 viewport.setScaleAboveWrapped(scaleAbove.getState());
795    }
796  0 else if (source == scaleLeft)
797    {
798  0 viewport.setScaleLeftWrapped(scaleLeft.getState());
799    }
800  0 else if (source == scaleRight)
801    {
802  0 viewport.setScaleRightWrapped(scaleRight.getState());
803    }
804  0 else if (source == seqLimits)
805    {
806  0 seqLimits_itemStateChanged();
807    }
808  0 else if (source == viewBoxesMenuItem)
809    {
810  0 viewport.setShowBoxes(viewBoxesMenuItem.getState());
811    }
812  0 else if (source == viewTextMenuItem)
813    {
814  0 viewport.setShowText(viewTextMenuItem.getState());
815    }
816  0 else if (source == renderGapsMenuItem)
817    {
818  0 viewport.setRenderGaps(renderGapsMenuItem.getState());
819    }
820  0 else if (source == annotationPanelMenuItem)
821    {
822  0 boolean showAnnotations = annotationPanelMenuItem.getState();
823  0 showAlignmentAnnotations.setEnabled(showAnnotations);
824  0 showSequenceAnnotations.setEnabled(showAnnotations);
825  0 viewport.setShowAnnotation(showAnnotations);
826  0 alignPanel.setAnnotationVisible(showAnnotations);
827    }
828  0 else if (source == sequenceFeatures)
829    {
830  0 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
831  0 alignPanel.seqPanel.seqCanvas.repaint();
832    }
833  0 else if (source == showAlignmentAnnotations)
834    {
835  0 setAnnotationsVisibility();
836    }
837  0 else if (source == showSequenceAnnotations)
838    {
839  0 setAnnotationsVisibility();
840    }
841  0 else if (source == sortAnnBySequence)
842    {
843  0 boolean newState = sortAnnBySequence.getState();
844  0 sortAnnByLabel.setState(false);
845  0 setAnnotationSortOrder(
846  0 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
847    : SequenceAnnotationOrder.NONE);
848  0 setViewportAnnotationOrder();
849    }
850  0 else if (source == sortAnnByLabel)
851    {
852  0 boolean newState = sortAnnByLabel.getState();
853  0 sortAnnBySequence.setState(false);
854  0 setAnnotationSortOrder(
855  0 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
856    : SequenceAnnotationOrder.NONE);
857  0 setViewportAnnotationOrder();
858    }
859  0 else if (source == showAutoFirst)
860    {
861  0 showAutoLast.setState(!showAutoFirst.getState());
862  0 setShowAutoCalculatedAbove(showAutoFirst.getState());
863  0 setViewportAnnotationOrder();
864    }
865  0 else if (source == showAutoLast)
866    {
867  0 showAutoFirst.setState(!showAutoLast.getState());
868  0 setShowAutoCalculatedAbove(showAutoFirst.getState());
869  0 setViewportAnnotationOrder();
870    }
871  0 else if (source == conservationMenuItem)
872    {
873  0 conservationMenuItem_actionPerformed();
874    }
875  0 else if (source == abovePIDThreshold)
876    {
877  0 abovePIDThreshold_actionPerformed();
878    }
879  0 else if (source == applyToAllGroups)
880    {
881  0 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
882    }
883  0 else if (source == autoCalculate)
884    {
885  0 viewport.autoCalculateConsensus = autoCalculate.getState();
886    }
887  0 else if (source == sortByTree)
888    {
889  0 viewport.sortByTree = sortByTree.getState();
890    }
891  0 else if (source == this.centreColumnLabelFlag)
892    {
893  0 centreColumnLabelFlag_stateChanged();
894    }
895  0 else if (source == this.followMouseOverFlag)
896    {
897  0 mouseOverFlag_stateChanged();
898    }
899  0 else if (source == showGroupConsensus)
900    {
901  0 showGroupConsensus_actionPerformed();
902    }
903  0 else if (source == showGroupConservation)
904    {
905  0 showGroupConservation_actionPerformed();
906    }
907  0 else if (source == showSequenceLogo)
908    {
909  0 showSequenceLogo_actionPerformed();
910    }
911  0 else if (source == normSequenceLogo)
912    {
913  0 normSequenceLogo_actionPerformed();
914    }
915  0 else if (source == showConsensusHistogram)
916    {
917  0 showConsensusHistogram_actionPerformed();
918    }
919  0 else if (source == applyAutoAnnotationSettings)
920    {
921  0 applyAutoAnnotationSettings_actionPerformed();
922    }
923    // TODO: repaint flags set only if warranted
924  0 alignPanel.paintAlignment(true, true);
925    }
926   
927    /**
928    * Set the visibility state of sequence-related and/or alignment-related
929    * annotations depending on checkbox selections, and repaint.
930    *
931    * @param visible
932    */
 
933  0 toggle private void setAnnotationsVisibility()
934    {
935  0 boolean showForAlignment = showAlignmentAnnotations.getState();
936  0 boolean showForSequences = showSequenceAnnotations.getState();
937  0 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
938    {
939  0 for (AlignmentAnnotation aa : alignPanel.getAlignment()
940    .getAlignmentAnnotation())
941    {
942  0 boolean visible = (aa.sequenceRef == null ? showForAlignment
943    : showForSequences);
944  0 aa.visible = visible;
945    }
946    }
947  0 alignPanel.validateAnnotationDimensions(true);
948  0 validate();
949  0 repaint();
950    }
951   
 
952  0 toggle private void setAnnotationSortOrder(SequenceAnnotationOrder order)
953    {
954  0 this.annotationSortOrder = order;
955    }
956   
957    /**
958    * Set flags on the viewport that control annotation ordering
959    */
 
960  0 toggle private void setViewportAnnotationOrder()
961    {
962  0 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
963  0 this.alignPanel.av
964    .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
965    }
966   
 
967  0 toggle private void setShowAutoCalculatedAbove(boolean showAbove)
968    {
969  0 this.showAutoCalculatedAbove = showAbove;
970    }
971   
 
972  0 toggle private void mouseOverFlag_stateChanged()
973    {
974  0 viewport.setFollowHighlight(followMouseOverFlag.getState());
975    // TODO: could kick the scrollTo mechanism to reset view for current
976    // searchresults.
977    }
978   
 
979  0 toggle private void centreColumnLabelFlag_stateChanged()
980    {
981  0 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
982  0 this.alignPanel.annotationPanel.repaint();
983    }
984   
 
985  0 toggle @Override
986    public void actionPerformed(ActionEvent evt)
987    {
988  0 viewport.applet.currentAlignFrame = this;
989   
990  0 Object source = evt.getSource();
991   
992  0 if (source == inputText)
993    {
994  0 inputText_actionPerformed();
995    }
996  0 else if (source == loadTree)
997    {
998  0 loadTree_actionPerformed();
999    }
1000  0 else if (source == loadApplication)
1001    {
1002  0 launchFullApplication();
1003    }
1004  0 else if (source == loadAnnotations)
1005    {
1006  0 loadAnnotations();
1007    }
1008  0 else if (source == outputAnnotations)
1009    {
1010  0 outputAnnotations(true);
1011    }
1012  0 else if (source == outputFeatures)
1013    {
1014  0 outputFeatures(true, "Jalview");
1015    }
1016  0 else if (source == closeMenuItem)
1017    {
1018  0 closeMenuItem_actionPerformed();
1019    }
1020  0 else if (source == copy)
1021    {
1022  0 copy_actionPerformed();
1023    }
1024  0 else if (source == undoMenuItem)
1025    {
1026  0 undoMenuItem_actionPerformed();
1027    }
1028  0 else if (source == redoMenuItem)
1029    {
1030  0 redoMenuItem_actionPerformed();
1031    }
1032  0 else if (source == inputText)
1033    {
1034  0 inputText_actionPerformed();
1035    }
1036  0 else if (source == closeMenuItem)
1037    {
1038  0 closeMenuItem_actionPerformed();
1039    }
1040  0 else if (source == undoMenuItem)
1041    {
1042  0 undoMenuItem_actionPerformed();
1043    }
1044  0 else if (source == redoMenuItem)
1045    {
1046  0 redoMenuItem_actionPerformed();
1047    }
1048  0 else if (source == copy)
1049    {
1050  0 copy_actionPerformed();
1051    }
1052  0 else if (source == pasteNew)
1053    {
1054  0 pasteNew_actionPerformed();
1055    }
1056  0 else if (source == pasteThis)
1057    {
1058  0 pasteThis_actionPerformed();
1059    }
1060  0 else if (source == cut)
1061    {
1062  0 cut_actionPerformed();
1063    }
1064  0 else if (source == delete)
1065    {
1066  0 delete_actionPerformed();
1067    }
1068  0 else if (source == createGroup)
1069    {
1070  0 createGroup_actionPerformed();
1071    }
1072  0 else if (source == unGroup)
1073    {
1074  0 unGroup_actionPerformed();
1075    }
1076  0 else if (source == grpsFromSelection)
1077    {
1078  0 makeGrpsFromSelection_actionPerformed();
1079    }
1080  0 else if (source == deleteGroups)
1081    {
1082  0 deleteGroups_actionPerformed();
1083    }
1084  0 else if (source == selectAllSequenceMenuItem)
1085    {
1086  0 selectAllSequenceMenuItem_actionPerformed();
1087    }
1088  0 else if (source == deselectAllSequenceMenuItem)
1089    {
1090  0 deselectAllSequenceMenuItem_actionPerformed();
1091    }
1092  0 else if (source == invertSequenceMenuItem)
1093    {
1094  0 invertSequenceMenuItem_actionPerformed();
1095    // uncomment to slave sequence selections in split frame
1096    // viewport.sendSelection();
1097    }
1098  0 else if (source == invertColSel)
1099    {
1100  0 viewport.invertColumnSelection();
1101  0 alignPanel.paintAlignment(false, false);
1102  0 viewport.sendSelection();
1103    }
1104  0 else if (source == remove2LeftMenuItem)
1105    {
1106  0 trimAlignment(true);
1107    }
1108  0 else if (source == remove2RightMenuItem)
1109    {
1110  0 trimAlignment(false);
1111    }
1112  0 else if (source == removeGappedColumnMenuItem)
1113    {
1114  0 removeGappedColumnMenuItem_actionPerformed();
1115    }
1116  0 else if (source == removeAllGapsMenuItem)
1117    {
1118  0 removeAllGapsMenuItem_actionPerformed();
1119    }
1120  0 else if (source == findMenuItem)
1121    {
1122  0 findMenuItem_actionPerformed();
1123    }
1124  0 else if (source == font)
1125    {
1126  0 new FontChooser(alignPanel);
1127    }
1128  0 else if (source == newView)
1129    {
1130  0 newView(null);
1131    }
1132  0 else if (source == showColumns)
1133    {
1134  0 viewport.showAllHiddenColumns();
1135  0 alignPanel.paintAlignment(true, true);
1136  0 viewport.sendSelection();
1137    }
1138  0 else if (source == showSeqs)
1139    {
1140  0 viewport.showAllHiddenSeqs();
1141  0 alignPanel.paintAlignment(true, true);
1142    // uncomment if we want to slave sequence selections in split frame
1143    // viewport.sendSelection();
1144    }
1145  0 else if (source == hideColumns)
1146    {
1147  0 viewport.hideSelectedColumns();
1148  0 alignPanel.paintAlignment(true, true);
1149  0 viewport.sendSelection();
1150    }
1151  0 else if (source == hideSequences
1152    && viewport.getSelectionGroup() != null)
1153    {
1154  0 viewport.hideAllSelectedSeqs();
1155  0 alignPanel.paintAlignment(true, true);
1156    // uncomment if we want to slave sequence selections in split frame
1157    // viewport.sendSelection();
1158    }
1159  0 else if (source == hideAllButSelection)
1160    {
1161  0 toggleHiddenRegions(false, false);
1162  0 alignPanel.paintAlignment(true, true);
1163  0 viewport.sendSelection();
1164    }
1165  0 else if (source == hideAllSelection)
1166    {
1167  0 SequenceGroup sg = viewport.getSelectionGroup();
1168  0 viewport.expandColSelection(sg, false);
1169  0 viewport.hideAllSelectedSeqs();
1170  0 viewport.hideSelectedColumns();
1171  0 alignPanel.paintAlignment(true, true);
1172  0 viewport.sendSelection();
1173    }
1174  0 else if (source == showAllHidden)
1175    {
1176  0 viewport.showAllHiddenColumns();
1177  0 viewport.showAllHiddenSeqs();
1178  0 alignPanel.paintAlignment(true, true);
1179  0 viewport.sendSelection();
1180    }
1181  0 else if (source == showGroupConsensus)
1182    {
1183  0 showGroupConsensus_actionPerformed();
1184    }
1185  0 else if (source == showGroupConservation)
1186    {
1187  0 showGroupConservation_actionPerformed();
1188    }
1189  0 else if (source == showSequenceLogo)
1190    {
1191  0 showSequenceLogo_actionPerformed();
1192    }
1193  0 else if (source == normSequenceLogo)
1194    {
1195  0 normSequenceLogo_actionPerformed();
1196    }
1197  0 else if (source == showConsensusHistogram)
1198    {
1199  0 showConsensusHistogram_actionPerformed();
1200    }
1201  0 else if (source == applyAutoAnnotationSettings)
1202    {
1203  0 applyAutoAnnotationSettings_actionPerformed();
1204    }
1205  0 else if (source == featureSettings)
1206    {
1207  0 showFeatureSettingsUI();
1208    }
1209  0 else if (source == alProperties)
1210    {
1211  0 StringBuffer contents = new jalview.io.AlignmentProperties(
1212    viewport.getAlignment()).formatAsString();
1213  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214  0 cap.setText(contents.toString());
1215  0 Frame frame = new Frame();
1216  0 frame.add(cap);
1217  0 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1218    .formatMessage("label.alignment_properties", new String[]
1219    { getTitle() }), 400, 250);
1220    }
1221  0 else if (source == overviewMenuItem)
1222    {
1223  0 overviewMenuItem_actionPerformed();
1224    }
1225  0 else if (source == noColourmenuItem)
1226    {
1227  0 changeColour(null);
1228    }
1229  0 else if (source == clustalColour)
1230    {
1231  0 abovePIDThreshold.setState(false);
1232  0 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1233    }
1234  0 else if (source == zappoColour)
1235    {
1236  0 changeColour(new ZappoColourScheme());
1237    }
1238  0 else if (source == taylorColour)
1239    {
1240  0 changeColour(new TaylorColourScheme());
1241    }
1242  0 else if (source == hydrophobicityColour)
1243    {
1244  0 changeColour(new HydrophobicColourScheme());
1245    }
1246  0 else if (source == helixColour)
1247    {
1248  0 changeColour(new HelixColourScheme());
1249    }
1250  0 else if (source == strandColour)
1251    {
1252  0 changeColour(new StrandColourScheme());
1253    }
1254  0 else if (source == turnColour)
1255    {
1256  0 changeColour(new TurnColourScheme());
1257    }
1258  0 else if (source == buriedColour)
1259    {
1260  0 changeColour(new BuriedColourScheme());
1261    }
1262  0 else if (source == nucleotideColour)
1263    {
1264  0 changeColour(new NucleotideColourScheme());
1265    }
1266  0 else if (source == purinePyrimidineColour)
1267    {
1268  0 changeColour(new PurinePyrimidineColourScheme());
1269    }
1270    // else if (source == RNAInteractionColour)
1271    // {
1272    // changeColour(new RNAInteractionColourScheme());
1273    // }
1274  0 else if (source == RNAHelixColour)
1275    {
1276  0 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1277    // new RNAHelicesColourChooser(viewport, alignPanel);
1278    }
1279  0 else if (source == modifyPID)
1280    {
1281  0 modifyPID_actionPerformed();
1282    }
1283  0 else if (source == modifyConservation)
1284    {
1285  0 modifyConservation_actionPerformed();
1286    }
1287  0 else if (source == userDefinedColour)
1288    {
1289  0 new UserDefinedColours(alignPanel, null);
1290    }
1291  0 else if (source == PIDColour)
1292    {
1293  0 changeColour(new PIDColourScheme());
1294    }
1295  0 else if (source == BLOSUM62Colour)
1296    {
1297  0 changeColour(new Blosum62ColourScheme());
1298    }
1299  0 else if (source == tcoffeeColour)
1300    {
1301  0 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1302    }
1303  0 else if (source == annotationColour)
1304    {
1305  0 new AnnotationColourChooser(viewport, alignPanel);
1306    }
1307  0 else if (source == annotationColumnSelection)
1308    {
1309  0 new AnnotationColumnChooser(viewport, alignPanel);
1310    }
1311  0 else if (source == sortPairwiseMenuItem)
1312    {
1313  0 sortPairwiseMenuItem_actionPerformed();
1314    }
1315  0 else if (source == sortIDMenuItem)
1316    {
1317  0 sortIDMenuItem_actionPerformed();
1318    }
1319  0 else if (source == sortLengthMenuItem)
1320    {
1321  0 sortLengthMenuItem_actionPerformed();
1322    }
1323  0 else if (source == sortGroupMenuItem)
1324    {
1325  0 sortGroupMenuItem_actionPerformed();
1326    }
1327  0 else if (source == removeRedundancyMenuItem)
1328    {
1329  0 removeRedundancyMenuItem_actionPerformed();
1330    }
1331  0 else if (source == pairwiseAlignmentMenuItem)
1332    {
1333  0 pairwiseAlignmentMenuItem_actionPerformed();
1334    }
1335  0 else if (source == PCAMenuItem)
1336    {
1337  0 PCAMenuItem_actionPerformed();
1338    }
1339  0 else if (source == averageDistanceTreeMenuItem)
1340    {
1341  0 averageDistanceTreeMenuItem_actionPerformed();
1342    }
1343  0 else if (source == neighbourTreeMenuItem)
1344    {
1345  0 neighbourTreeMenuItem_actionPerformed();
1346    }
1347  0 else if (source == njTreeBlosumMenuItem)
1348    {
1349  0 njTreeBlosumMenuItem_actionPerformed();
1350    }
1351  0 else if (source == avDistanceTreeBlosumMenuItem)
1352    {
1353  0 avTreeBlosumMenuItem_actionPerformed();
1354    }
1355  0 else if (source == documentation)
1356    {
1357  0 documentation_actionPerformed();
1358    }
1359  0 else if (source == about)
1360    {
1361  0 about_actionPerformed();
1362    }
1363   
1364    }
1365   
 
1366  0 toggle public void inputText_actionPerformed()
1367    {
1368  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1369  0 Frame frame = new Frame();
1370  0 frame.add(cap);
1371  0 jalview.bin.JalviewLite.addFrame(frame,
1372    MessageManager.getString("label.input_cut_paste"), 500, 500);
1373    }
1374   
 
1375  0 toggle protected void outputText_actionPerformed(ActionEvent e)
1376    {
1377  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378  0 Frame frame = new Frame();
1379  0 frame.add(cap);
1380  0 JalviewLite.addFrame(frame, MessageManager
1381    .formatMessage("label.alignment_output_command", new Object[]
1382    { e.getActionCommand() }), 600, 500);
1383   
1384  0 FileFormatI fileFormat = FileFormats.getInstance()
1385    .forName(e.getActionCommand());
1386  0 cap.setText(
1387    new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1388    viewport.getAlignment(), viewport.getShowJVSuffix()));
1389    }
1390   
 
1391  0 toggle public void loadAnnotations()
1392    {
1393  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1394  0 cap.setText(MessageManager
1395    .getString("label.paste_features_annotations_Tcoffee_here"));
1396  0 cap.setAnnotationImport();
1397  0 Frame frame = new Frame();
1398  0 frame.add(cap);
1399  0 jalview.bin.JalviewLite.addFrame(frame,
1400    MessageManager.getString("action.paste_annotations"), 400, 300);
1401   
1402    }
1403   
 
1404  0 toggle public String outputAnnotations(boolean displayTextbox)
1405    {
1406  0 String annotation = new AnnotationFile()
1407    .printAnnotationsForView(viewport);
1408   
1409  0 if (displayTextbox)
1410    {
1411  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1412  0 Frame frame = new Frame();
1413  0 frame.add(cap);
1414  0 jalview.bin.JalviewLite.addFrame(frame,
1415    MessageManager.getString("label.annotations"), 600, 500);
1416  0 cap.setText(annotation);
1417    }
1418   
1419  0 return annotation;
1420    }
1421   
 
1422  0 toggle private Map<String, FeatureColourI> getDisplayedFeatureCols()
1423    {
1424  0 if (alignPanel.getFeatureRenderer() != null
1425    && viewport.getFeaturesDisplayed() != null)
1426    {
1427  0 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1428   
1429    }
1430  0 return null;
1431    }
1432   
 
1433  0 toggle private List<String> getDisplayedFeatureGroups()
1434    {
1435  0 if (alignPanel.getFeatureRenderer() != null
1436    && viewport.getFeaturesDisplayed() != null)
1437    {
1438  0 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1439   
1440    }
1441  0 return null;
1442    }
1443   
 
1444  0 toggle public String outputFeatures(boolean displayTextbox, String format)
1445    {
1446  0 String features;
1447  0 FeaturesFile formatter = new FeaturesFile();
1448  0 if (format.equalsIgnoreCase("Jalview"))
1449    {
1450  0 features = formatter.printJalviewFormat(
1451    viewport.getAlignment().getSequencesArray(),
1452    alignPanel.getFeatureRenderer(), true, false);
1453    }
1454    else
1455    {
1456  0 features = formatter.printGffFormat(viewport.getAlignment()
1457    .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1458    false);
1459    }
1460   
1461  0 if (displayTextbox)
1462    {
1463  0 boolean frimport = false;
1464  0 if (features == null || features.equals("No Features Visible"))
1465    {
1466  0 features = "# No features visible - paste some and import them here.";
1467  0 frimport = true;
1468    }
1469   
1470  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1471  0 if (frimport)
1472    {
1473  0 cap.setAnnotationImport();
1474    }
1475  0 Frame frame = new Frame();
1476  0 frame.add(cap);
1477  0 jalview.bin.JalviewLite.addFrame(frame,
1478    MessageManager.getString("label.features"), 600, 500);
1479  0 cap.setText(features);
1480    }
1481    else
1482    {
1483  0 if (features == null)
1484    {
1485  0 features = "";
1486    }
1487    }
1488   
1489  0 return features;
1490    }
1491   
 
1492  0 toggle void launchFullApplication()
1493    {
1494  0 StringBuffer url = new StringBuffer(jalviewServletURL);
1495   
1496    // allow servlet parameters to be passed in applet parameter
1497  0 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1498    : "?";
1499  0 url.append(firstSep);
1500   
1501  0 url.append(
1502    "open=" + appendProtocol(viewport.applet.getParameter("file")));
1503   
1504  0 if (viewport.applet.getParameter("features") != null)
1505    {
1506  0 url.append("&features=");
1507  0 url.append(appendProtocol(viewport.applet.getParameter("features")));
1508    }
1509   
1510  0 if (viewport.applet.getParameter("annotations") != null)
1511    {
1512  0 url.append("&annotations=");
1513  0 url.append(
1514    appendProtocol(viewport.applet.getParameter("annotations")));
1515    }
1516   
1517  0 if (viewport.applet.getParameter("jnetfile") != null
1518    || viewport.applet.getParameter("jpredfile") != null)
1519    {
1520  0 url.append("&annotations=");
1521  0 url.append(appendProtocol(
1522  0 viewport.applet.getParameter("jnetfile") != null
1523    ? viewport.applet.getParameter("jnetfile")
1524    : viewport.applet.getParameter("jpredfile")));
1525    }
1526   
1527  0 if (viewport.applet.getParameter("defaultColour") != null)
1528    {
1529  0 url.append("&colour=" + removeWhiteSpace(
1530    viewport.applet.getParameter("defaultColour")));
1531    }
1532   
1533  0 if (viewport.applet.getParameter("userDefinedColour") != null)
1534    {
1535  0 url.append("&colour=" + removeWhiteSpace(
1536    viewport.applet.getParameter("userDefinedColour")));
1537    }
1538  0 if (viewport.applet.getParameter("tree") != null)
1539    {
1540  0 url.append("&tree="
1541    + appendProtocol(viewport.applet.getParameter("tree")));
1542    }
1543  0 if (viewport.applet.getParameter("treeFile") != null)
1544    {
1545  0 url.append("&tree="
1546    + appendProtocol(viewport.applet.getParameter("treeFile")));
1547    }
1548   
1549  0 showURL(url.toString(), "FULL_APP");
1550    }
1551   
 
1552  0 toggle String removeWhiteSpace(String colour)
1553    {
1554  0 StringBuffer sb = new StringBuffer();
1555  0 for (int i = 0; i < colour.length(); i++)
1556    {
1557  0 if (Character.isWhitespace(colour.charAt(i)))
1558    {
1559  0 sb.append("%20");
1560    }
1561    else
1562    {
1563  0 sb.append(colour.charAt(i));
1564    }
1565    }
1566   
1567  0 return sb.toString();
1568    }
1569   
 
1570  0 toggle String appendProtocol(String url)
1571    {
1572  0 try
1573    {
1574  0 new URL(url);
1575  0 url = URLEncoder.encode(url, "UTF-8");
1576    }
1577    /*
1578    * When we finally deprecate 1.1 compatibility, we can start to use
1579    * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1580    * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1581    * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1582    * ex.printStackTrace(); }
1583    */
1584    catch (java.net.MalformedURLException ex)
1585    {
1586  0 url = viewport.applet.getCodeBase() + url;
1587    }
1588    catch (UnsupportedEncodingException ex)
1589    {
1590  0 System.err.println(
1591    "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1592    + url);
1593  0 ex.printStackTrace();
1594    }
1595  0 return url;
1596    }
1597   
 
1598  0 toggle public void closeMenuItem_actionPerformed()
1599    {
1600  0 PaintRefresher.RemoveComponent(alignPanel);
1601  0 if (alignPanel.seqPanel != null
1602    && alignPanel.seqPanel.seqCanvas != null)
1603    {
1604  0 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1605    }
1606  0 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1607    {
1608  0 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1609    }
1610   
1611  0 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1612    {
1613  0 System.exit(0);
1614    }
1615   
1616  0 viewport = null;
1617  0 if (alignPanel != null && alignPanel.overviewPanel != null)
1618    {
1619  0 alignPanel.overviewPanel.dispose();
1620    }
1621  0 alignPanel = null;
1622  0 this.dispose();
1623    }
1624   
1625    /**
1626    * TODO: JAL-1104
1627    */
 
1628  0 toggle void updateEditMenuBar()
1629    {
1630   
1631  0 if (viewport.getHistoryList().size() > 0)
1632    {
1633  0 undoMenuItem.setEnabled(true);
1634  0 CommandI command = viewport.getHistoryList().peek();
1635  0 undoMenuItem.setLabel(MessageManager
1636    .formatMessage("label.undo_command", new Object[]
1637    { command.getDescription() }));
1638    }
1639    else
1640    {
1641  0 undoMenuItem.setEnabled(false);
1642  0 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1643    }
1644   
1645  0 if (viewport.getRedoList().size() > 0)
1646    {
1647  0 redoMenuItem.setEnabled(true);
1648   
1649  0 CommandI command = viewport.getRedoList().peek();
1650  0 redoMenuItem.setLabel(MessageManager
1651    .formatMessage("label.redo_command", new Object[]
1652    { command.getDescription() }));
1653    }
1654    else
1655    {
1656  0 redoMenuItem.setEnabled(false);
1657  0 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1658    }
1659    }
1660   
1661    /**
1662    * TODO: JAL-1104
1663    */
 
1664  0 toggle @Override
1665    public void addHistoryItem(CommandI command)
1666    {
1667  0 if (command.getSize() > 0)
1668    {
1669  0 viewport.addToHistoryList(command);
1670  0 viewport.clearRedoList();
1671  0 updateEditMenuBar();
1672  0 viewport.updateHiddenColumns();
1673    }
1674    }
1675   
1676    /**
1677    * TODO: JAL-1104 DOCUMENT ME!
1678    *
1679    * @param e
1680    * DOCUMENT ME!
1681    */
 
1682  0 toggle protected void undoMenuItem_actionPerformed()
1683    {
1684  0 if (viewport.getHistoryList().isEmpty())
1685    {
1686  0 return;
1687    }
1688   
1689  0 CommandI command = viewport.getHistoryList().pop();
1690  0 viewport.addToRedoList(command);
1691  0 command.undoCommand(null);
1692   
1693  0 AlignmentViewport originalSource = getOriginatingSource(command);
1694    // JBPNote Test
1695  0 if (originalSource != viewport)
1696    {
1697  0 System.err
1698    .println("Warning: Viewport object mismatch whilst undoing");
1699    }
1700  0 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1701    // viewport.getColumnSelection().getHiddenColumns()
1702    // != null;
1703  0 updateEditMenuBar();
1704  0 originalSource.firePropertyChange("alignment", null,
1705    originalSource.getAlignment().getSequences());
1706    }
1707   
1708    /**
1709    * TODO: JAL-1104 DOCUMENT ME!
1710    *
1711    * @param e
1712    * DOCUMENT ME!
1713    */
 
1714  0 toggle protected void redoMenuItem_actionPerformed()
1715    {
1716  0 if (viewport.getRedoList().isEmpty())
1717    {
1718  0 return;
1719    }
1720   
1721  0 CommandI command = viewport.getRedoList().pop();
1722  0 viewport.addToHistoryList(command);
1723  0 command.doCommand(null);
1724   
1725  0 AlignmentViewport originalSource = getOriginatingSource(command);
1726    // JBPNote Test
1727  0 if (originalSource != viewport)
1728    {
1729  0 System.err
1730    .println("Warning: Viewport object mismatch whilst re-doing");
1731    }
1732  0 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1733    // viewport.getColumnSelection().getHiddenColumns()
1734    // != null;
1735   
1736  0 updateEditMenuBar();
1737  0 originalSource.firePropertyChange("alignment", null,
1738    originalSource.getAlignment().getSequences());
1739    }
1740   
 
1741  0 toggle AlignmentViewport getOriginatingSource(CommandI command)
1742    {
1743  0 AlignmentViewport originalSource = null;
1744    // For sequence removal and addition, we need to fire
1745    // the property change event FROM the viewport where the
1746    // original alignment was altered
1747  0 AlignmentI al = null;
1748  0 if (command instanceof EditCommand)
1749    {
1750  0 EditCommand editCommand = (EditCommand) command;
1751  0 al = editCommand.getAlignment();
1752  0 Vector comps = PaintRefresher.components
1753    .get(viewport.getSequenceSetId());
1754  0 for (int i = 0; i < comps.size(); i++)
1755    {
1756  0 if (comps.elementAt(i) instanceof AlignmentPanel)
1757    {
1758  0 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1759    {
1760  0 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1761  0 break;
1762    }
1763    }
1764    }
1765    }
1766   
1767  0 if (originalSource == null)
1768    {
1769    // The original view is closed, we must validate
1770    // the current view against the closed view first
1771  0 if (al != null)
1772    {
1773  0 PaintRefresher.validateSequences(al, viewport.getAlignment());
1774    }
1775   
1776  0 originalSource = viewport;
1777    }
1778   
1779  0 return originalSource;
1780    }
1781   
1782    /**
1783    * Move the currently selected sequences up or down one position in the
1784    * alignment
1785    *
1786    * @param up
1787    */
 
1788  0 toggle public void moveSelectedSequences(boolean up)
1789    {
1790  0 SequenceGroup sg = viewport.getSelectionGroup();
1791  0 if (sg == null)
1792    {
1793  0 return;
1794    }
1795  0 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1796  0 up ? null : viewport.getHiddenRepSequences(), up);
1797  0 alignPanel.paintAlignment(true, false);
1798   
1799    /*
1800    * Also move cDNA/protein complement sequences
1801    */
1802  0 AlignViewportI complement = viewport.getCodingComplement();
1803  0 if (complement != null)
1804    {
1805  0 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1806    viewport, complement);
1807  0 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1808  0 up ? null : complement.getHiddenRepSequences(), up);
1809  0 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1810    false);
1811    }
1812    }
1813   
 
1814  0 toggle synchronized void slideSequences(boolean right, int size)
1815    {
1816  0 List<SequenceI> sg = new Vector<>();
1817  0 if (viewport.cursorMode)
1818    {
1819  0 sg.add(viewport.getAlignment()
1820    .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1821    }
1822  0 else if (viewport.getSelectionGroup() != null
1823    && viewport.getSelectionGroup().getSize() != viewport
1824    .getAlignment().getHeight())
1825    {
1826  0 sg = viewport.getSelectionGroup()
1827    .getSequences(viewport.getHiddenRepSequences());
1828    }
1829   
1830  0 if (sg.size() < 1)
1831    {
1832  0 return;
1833    }
1834   
1835  0 Vector<SequenceI> invertGroup = new Vector();
1836   
1837  0 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1838    {
1839  0 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1840    {
1841  0 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1842    }
1843    }
1844   
1845  0 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1846   
1847  0 SequenceI[] seqs2 = invertGroup
1848    .toArray(new SequenceI[invertGroup.size()]);
1849  0 for (int i = 0; i < invertGroup.size(); i++)
1850    {
1851  0 seqs2[i] = invertGroup.elementAt(i);
1852    }
1853   
1854  0 SlideSequencesCommand ssc;
1855  0 if (right)
1856    {
1857  0 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1858    viewport.getGapCharacter());
1859    }
1860    else
1861    {
1862  0 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1863    viewport.getGapCharacter());
1864    }
1865   
1866  0 int groupAdjustment = 0;
1867  0 if (ssc.getGapsInsertedBegin() && right)
1868    {
1869  0 if (viewport.cursorMode)
1870    {
1871  0 alignPanel.seqPanel.moveCursor(size, 0);
1872    }
1873    else
1874    {
1875  0 groupAdjustment = size;
1876    }
1877    }
1878  0 else if (!ssc.getGapsInsertedBegin() && !right)
1879    {
1880  0 if (viewport.cursorMode)
1881    {
1882  0 alignPanel.seqPanel.moveCursor(-size, 0);
1883    }
1884    else
1885    {
1886  0 groupAdjustment = -size;
1887    }
1888    }
1889   
1890  0 if (groupAdjustment != 0)
1891    {
1892  0 viewport.getSelectionGroup().setStartRes(
1893    viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1894  0 viewport.getSelectionGroup().setEndRes(
1895    viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1896    }
1897   
1898  0 boolean appendHistoryItem = false;
1899  0 Deque<CommandI> historyList = viewport.getHistoryList();
1900  0 if (historyList != null && historyList.size() > 0
1901    && historyList.peek() instanceof SlideSequencesCommand)
1902    {
1903  0 appendHistoryItem = ssc.appendSlideCommand(
1904    (SlideSequencesCommand) historyList.peek());
1905    }
1906   
1907  0 if (!appendHistoryItem)
1908    {
1909  0 addHistoryItem(ssc);
1910    }
1911   
1912  0 repaint();
1913    }
1914   
1915    static StringBuffer copiedSequences;
1916   
1917    static HiddenColumns copiedHiddenColumns;
1918   
 
1919  0 toggle protected void copy_actionPerformed()
1920    {
1921  0 if (viewport.getSelectionGroup() == null)
1922    {
1923  0 return;
1924    }
1925   
1926  0 SequenceGroup sg = viewport.getSelectionGroup();
1927  0 copiedSequences = new StringBuffer();
1928  0 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1929  0 for (int i = 0; i < sg.getSize(); i++)
1930    {
1931  0 SequenceI seq = sg.getSequenceAt(i);
1932  0 int index = viewport.getAlignment().findIndex(seq);
1933  0 orderedSeqs.put(index, seq);
1934    }
1935   
1936  0 int index = 0, startRes, endRes;
1937  0 char ch;
1938   
1939  0 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1940    {
1941  0 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1942  0 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1943   
1944    // create new HiddenColumns object with copy of hidden regions
1945    // between startRes and endRes, offset by startRes
1946  0 copiedHiddenColumns = new HiddenColumns(
1947    viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1948    hiddenCutoff, hiddenOffset);
1949    }
1950    else
1951    {
1952  0 copiedHiddenColumns = null;
1953    }
1954   
1955  0 for (int i = 0; i < sg.getSize(); i++)
1956    {
1957  0 SequenceI seq = null;
1958   
1959  0 while (seq == null)
1960    {
1961  0 if (orderedSeqs.containsKey(index))
1962    {
1963  0 seq = orderedSeqs.get(index);
1964  0 index++;
1965  0 break;
1966    }
1967    else
1968    {
1969  0 index++;
1970    }
1971    }
1972   
1973    // FIND START RES
1974    // Returns residue following index if gap
1975  0 startRes = seq.findPosition(sg.getStartRes());
1976   
1977    // FIND END RES
1978    // Need to find the residue preceeding index if gap
1979  0 endRes = 0;
1980   
1981  0 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1982    {
1983  0 ch = seq.getCharAt(j);
1984  0 if (!jalview.util.Comparison.isGap((ch)))
1985    {
1986  0 endRes++;
1987    }
1988    }
1989   
1990  0 if (endRes > 0)
1991    {
1992  0 endRes += seq.getStart() - 1;
1993    }
1994   
1995  0 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1996    + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1997    sg.getEndRes() + 1)
1998    + "\n");
1999    }
2000   
2001    }
2002   
 
2003  0 toggle protected void pasteNew_actionPerformed()
2004    {
2005  0 paste(true);
2006    }
2007   
 
2008  0 toggle protected void pasteThis_actionPerformed()
2009    {
2010  0 paste(false);
2011    }
2012   
 
2013  0 toggle void paste(boolean newAlignment)
2014    {
2015  0 try
2016    {
2017  0 if (copiedSequences == null)
2018    {
2019  0 return;
2020    }
2021   
2022  0 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2023    "\t");
2024  0 Vector seqs = new Vector();
2025  0 while (st.hasMoreElements())
2026    {
2027  0 String name = st.nextToken();
2028  0 int start = Integer.parseInt(st.nextToken());
2029  0 int end = Integer.parseInt(st.nextToken());
2030  0 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2031    }
2032  0 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2033  0 for (int i = 0; i < seqs.size(); i++)
2034    {
2035  0 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2036    }
2037   
2038  0 if (newAlignment)
2039    {
2040  0 String newtitle = MessageManager
2041    .getString("label.copied_sequences");
2042  0 if (getTitle().startsWith(
2043    MessageManager.getString("label.copied_sequences")))
2044    {
2045  0 newtitle = getTitle();
2046    }
2047    else
2048    {
2049  0 newtitle = newtitle.concat(MessageManager
2050    .formatMessage("label.from_msname", new String[]
2051    { getTitle() }));
2052    }
2053  0 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2054    viewport.applet, newtitle, false);
2055  0 af.viewport.setHiddenColumns(copiedHiddenColumns);
2056   
2057  0 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2058    frameHeight);
2059    }
2060    else
2061    {
2062  0 addSequences(newSeqs);
2063    }
2064   
2065    } catch (Exception ex)
2066    {
2067    } // could be anything being pasted in here
2068   
2069    }
2070   
 
2071  0 toggle void addSequences(SequenceI[] seqs)
2072    {
2073  0 for (int i = 0; i < seqs.length; i++)
2074    {
2075  0 viewport.getAlignment().addSequence(seqs[i]);
2076    }
2077   
2078    // !newAlignment
2079  0 addHistoryItem(new EditCommand(
2080    MessageManager.getString("label.add_sequences"), Action.PASTE,
2081    seqs, 0, viewport.getAlignment().getWidth(),
2082    viewport.getAlignment()));
2083   
2084  0 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2085    // 2019.04.18
2086  0 viewport.getAlignment().getWidth();
2087  0 viewport.firePropertyChange("alignment", null,
2088    viewport.getAlignment().getSequences());
2089   
2090    }
2091   
 
2092  0 toggle protected void cut_actionPerformed()
2093    {
2094  0 copy_actionPerformed();
2095  0 delete_actionPerformed();
2096    }
2097   
 
2098  0 toggle protected void delete_actionPerformed()
2099    {
2100   
2101  0 SequenceGroup sg = viewport.getSelectionGroup();
2102  0 if (sg == null)
2103    {
2104  0 return;
2105    }
2106   
2107  0 Vector seqs = new Vector();
2108  0 SequenceI seq;
2109  0 for (int i = 0; i < sg.getSize(); i++)
2110    {
2111  0 seq = sg.getSequenceAt(i);
2112  0 seqs.addElement(seq);
2113    }
2114   
2115    /*
2116    * If the cut affects all sequences, warn, remove highlighted columns
2117    */
2118  0 if (sg.getSize() == viewport.getAlignment().getHeight())
2119    {
2120  0 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2121    + 1) == viewport.getAlignment().getWidth()) ? true : false;
2122  0 if (isEntireAlignWidth)
2123    {
2124  0 String title = MessageManager.getString("label.delete_all");
2125  0 Panel infoPanel = new Panel();
2126  0 infoPanel.setLayout(new FlowLayout());
2127  0 infoPanel.add(
2128    new Label(MessageManager.getString("warn.delete_all")));
2129   
2130  0 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2131  0 dialog.setMainPanel(infoPanel);
2132  0 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2133  0 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2134  0 dialog.setVisible(true);
2135   
2136  0 if (!dialog.accept)
2137    {
2138  0 return;
2139    }
2140    }
2141  0 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2142    sg.getEndRes() + 1);
2143    }
2144   
2145  0 SequenceI[] cut = new SequenceI[seqs.size()];
2146  0 for (int i = 0; i < seqs.size(); i++)
2147    {
2148  0 cut[i] = (SequenceI) seqs.elementAt(i);
2149    }
2150   
2151    /*
2152    * //ADD HISTORY ITEM
2153    */
2154  0 addHistoryItem(new EditCommand(
2155    MessageManager.getString("label.cut_sequences"), Action.CUT,
2156    cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2157    viewport.getAlignment()));
2158   
2159  0 viewport.setSelectionGroup(null);
2160  0 viewport.getAlignment().deleteGroup(sg);
2161   
2162  0 viewport.firePropertyChange("alignment", null,
2163    viewport.getAlignment().getSequences());
2164   
2165  0 if (viewport.getAlignment().getHeight() < 1)
2166    {
2167  0 this.setVisible(false);
2168    }
2169  0 viewport.sendSelection();
2170    }
2171   
2172    /**
2173    * group consensus toggled
2174    *
2175    */
 
2176  0 toggle protected void showGroupConsensus_actionPerformed()
2177    {
2178  0 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2179  0 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180   
2181    }
2182   
2183    /**
2184    * group conservation toggled.
2185    */
 
2186  0 toggle protected void showGroupConservation_actionPerformed()
2187    {
2188  0 viewport.setShowGroupConservation(showGroupConservation.getState());
2189  0 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190    }
2191   
2192    /*
2193    * (non-Javadoc)
2194    *
2195    * @see
2196    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2197    * .event.ActionEvent)
2198    */
 
2199  0 toggle protected void showConsensusHistogram_actionPerformed()
2200    {
2201  0 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2202  0 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2203    }
2204   
2205    /*
2206    * (non-Javadoc)
2207    *
2208    * @see
2209    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2210    * .event.ActionEvent)
2211    */
 
2212  0 toggle protected void showSequenceLogo_actionPerformed()
2213    {
2214  0 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2215  0 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2216    }
2217   
 
2218  0 toggle protected void normSequenceLogo_actionPerformed()
2219    {
2220  0 showSequenceLogo.setState(true);
2221  0 viewport.setShowSequenceLogo(true);
2222  0 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2223  0 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2224    }
2225   
 
2226  0 toggle protected void applyAutoAnnotationSettings_actionPerformed()
2227    {
2228  0 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2229    }
2230   
 
2231  0 toggle protected void makeGrpsFromSelection_actionPerformed()
2232    {
2233  0 if (avc.makeGroupsFromSelection())
2234    {
2235  0 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2236  0 alignPanel.updateAnnotation();
2237  0 alignPanel.paintAlignment(true, true);
2238    }
2239    }
2240   
 
2241  0 toggle protected void createGroup_actionPerformed()
2242    {
2243  0 avc.createGroup();
2244    }
2245   
 
2246  0 toggle protected void unGroup_actionPerformed()
2247    {
2248  0 if (avc.unGroup())
2249    {
2250  0 alignPanel.alignmentChanged();
2251    }
2252    }
2253   
 
2254  0 toggle protected void deleteGroups_actionPerformed()
2255    {
2256  0 if (avc.deleteGroups())
2257    {
2258  0 alignPanel.alignmentChanged();
2259    }
2260    }
2261   
 
2262  0 toggle public void selectAllSequenceMenuItem_actionPerformed()
2263    {
2264  0 SequenceGroup sg = new SequenceGroup();
2265  0 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2266    {
2267  0 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2268    }
2269  0 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2270  0 viewport.setSelectionGroup(sg);
2271    // JAL-2034 - should delegate to
2272    // alignPanel to decide if overview needs
2273    // updating.
2274  0 alignPanel.paintAlignment(false, false);
2275  0 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2276  0 viewport.sendSelection();
2277    }
2278   
 
2279  0 toggle public void deselectAllSequenceMenuItem_actionPerformed()
2280    {
2281  0 if (viewport.cursorMode)
2282    {
2283  0 alignPanel.seqPanel.keyboardNo1 = null;
2284  0 alignPanel.seqPanel.keyboardNo2 = null;
2285    }
2286  0 viewport.setSelectionGroup(null);
2287  0 viewport.getColumnSelection().clear();
2288  0 viewport.setSelectionGroup(null);
2289  0 alignPanel.idPanel.idCanvas.searchResults = null;
2290  0 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2291    // JAL-2034 - should delegate to
2292    // alignPanel to decide if overview needs
2293    // updating.
2294  0 alignPanel.paintAlignment(false, false);
2295  0 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2296  0 viewport.sendSelection();
2297    }
2298   
 
2299  0 toggle public void invertSequenceMenuItem_actionPerformed()
2300    {
2301  0 SequenceGroup sg = viewport.getSelectionGroup();
2302  0 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2303    {
2304  0 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2305    }
2306   
2307  0 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2308  0 viewport.sendSelection();
2309    }
2310   
 
2311  0 toggle public void invertColSel_actionPerformed()
2312    {
2313  0 viewport.invertColumnSelection();
2314  0 alignPanel.paintAlignment(true, false);
2315  0 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2316  0 viewport.sendSelection();
2317    }
2318   
 
2319  0 toggle void trimAlignment(boolean trimLeft)
2320    {
2321  0 AlignmentI al = viewport.getAlignment();
2322  0 ViewportRanges ranges = viewport.getRanges();
2323  0 ColumnSelection colSel = viewport.getColumnSelection();
2324  0 int column;
2325   
2326  0 if (!colSel.isEmpty())
2327    {
2328  0 if (trimLeft)
2329    {
2330  0 column = colSel.getMin();
2331    }
2332    else
2333    {
2334  0 column = colSel.getMax();
2335    }
2336   
2337  0 SequenceI[] seqs;
2338  0 if (viewport.getSelectionGroup() != null)
2339    {
2340  0 seqs = viewport.getSelectionGroup()
2341    .getSequencesAsArray(viewport.getHiddenRepSequences());
2342    }
2343    else
2344    {
2345  0 seqs = al.getSequencesArray();
2346    }
2347   
2348  0 TrimRegionCommand trimRegion;
2349  0 if (trimLeft)
2350    {
2351  0 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2352    column, al);
2353  0 ranges.setStartRes(0);
2354    }
2355    else
2356    {
2357  0 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2358    column, al);
2359    }
2360   
2361  0 setStatus(MessageManager
2362    .formatMessage("label.removed_columns", new String[]
2363    { Integer.valueOf(trimRegion.getSize()).toString() }));
2364  0 addHistoryItem(trimRegion);
2365   
2366  0 for (SequenceGroup sg : al.getGroups())
2367    {
2368  0 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2369    || (!trimLeft && !sg.adjustForRemoveRight(column)))
2370    {
2371  0 al.deleteGroup(sg);
2372    }
2373    }
2374   
2375  0 viewport.firePropertyChange("alignment", null, al.getSequences());
2376    }
2377    }
2378   
 
2379  0 toggle public void removeGappedColumnMenuItem_actionPerformed()
2380    {
2381  0 AlignmentI al = viewport.getAlignment();
2382  0 ViewportRanges ranges = viewport.getRanges();
2383  0 int start = 0;
2384  0 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2385   
2386  0 SequenceI[] seqs;
2387  0 if (viewport.getSelectionGroup() != null)
2388    {
2389  0 seqs = viewport.getSelectionGroup()
2390    .getSequencesAsArray(viewport.getHiddenRepSequences());
2391  0 start = viewport.getSelectionGroup().getStartRes();
2392  0 end = viewport.getSelectionGroup().getEndRes();
2393    }
2394    else
2395    {
2396  0 seqs = viewport.getAlignment().getSequencesArray();
2397    }
2398   
2399  0 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2400    "Remove Gapped Columns", seqs, start, end,
2401    viewport.getAlignment());
2402   
2403  0 addHistoryItem(removeGapCols);
2404   
2405  0 setStatus(MessageManager
2406    .formatMessage("label.removed_empty_columns", new String[]
2407    { Integer.valueOf(removeGapCols.getSize()).toString() }));
2408   
2409    // This is to maintain viewport position on first residue
2410    // of first sequence
2411  0 SequenceI seq = al.getSequenceAt(0);
2412  0 int startRes = seq.findPosition(ranges.getStartRes());
2413    // ShiftList shifts;
2414    // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2415    // edit.alColumnChanges=shifts.getInverse();
2416    // if (viewport.hasHiddenColumns)
2417    // viewport.getColumnSelection().compensateForEdits(shifts);
2418  0 ranges.setStartRes(seq.findIndex(startRes) - 1);
2419  0 viewport.firePropertyChange("alignment", null, al.getSequences());
2420   
2421    }
2422   
 
2423  0 toggle public void removeAllGapsMenuItem_actionPerformed()
2424    {
2425  0 AlignmentI al = viewport.getAlignment();
2426  0 ViewportRanges ranges = viewport.getRanges();
2427  0 int start = 0;
2428  0 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2429   
2430  0 SequenceI[] seqs;
2431  0 if (viewport.getSelectionGroup() != null)
2432    {
2433  0 seqs = viewport.getSelectionGroup()
2434    .getSequencesAsArray(viewport.getHiddenRepSequences());
2435  0 start = viewport.getSelectionGroup().getStartRes();
2436  0 end = viewport.getSelectionGroup().getEndRes();
2437    }
2438    else
2439    {
2440  0 seqs = viewport.getAlignment().getSequencesArray();
2441    }
2442   
2443    // This is to maintain viewport position on first residue
2444    // of first sequence
2445  0 SequenceI seq = al.getSequenceAt(0);
2446  0 int startRes = seq.findPosition(ranges.getStartRes());
2447   
2448  0 addHistoryItem(
2449    new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2450   
2451  0 ranges.setStartRes(seq.findIndex(startRes) - 1);
2452   
2453  0 viewport.firePropertyChange("alignment", null, al.getSequences());
2454   
2455    }
2456   
 
2457  0 toggle public void findMenuItem_actionPerformed()
2458    {
2459  0 new Finder(alignPanel);
2460    }
2461   
2462    /**
2463    * create a new view derived from the current view
2464    *
2465    * @param viewtitle
2466    * @return frame for the new view
2467    */
 
2468  0 toggle public AlignFrame newView(String viewtitle)
2469    {
2470  0 AlignmentI newal;
2471  0 if (viewport.hasHiddenRows())
2472    {
2473  0 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2474    .getFullAlignment().getSequencesArray());
2475    }
2476    else
2477    {
2478  0 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2479    }
2480   
2481  0 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2482    {
2483  0 for (int i = 0; i < viewport.getAlignment()
2484    .getAlignmentAnnotation().length; i++)
2485    {
2486  0 if (!viewport.getAlignment()
2487    .getAlignmentAnnotation()[i].autoCalculated)
2488    {
2489  0 newal.addAnnotation(
2490    viewport.getAlignment().getAlignmentAnnotation()[i]);
2491    }
2492    }
2493    }
2494   
2495  0 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2496   
2497  0 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2498  0 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2499  0 PaintRefresher.Register(newaf.alignPanel,
2500    newaf.alignPanel.av.getSequenceSetId());
2501   
2502  0 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2503    newaf.alignPanel.av.getSequenceSetId());
2504  0 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2505    newaf.alignPanel.av.getSequenceSetId());
2506   
2507  0 Vector comps = PaintRefresher.components
2508    .get(viewport.getSequenceSetId());
2509  0 int viewSize = -1;
2510  0 for (int i = 0; i < comps.size(); i++)
2511    {
2512  0 if (comps.elementAt(i) instanceof AlignmentPanel)
2513    {
2514  0 viewSize++;
2515    }
2516    }
2517   
2518  0 String title = new String(this.getTitle());
2519  0 if (viewtitle != null)
2520    {
2521  0 title = viewtitle + " ( " + title + ")";
2522    }
2523    else
2524    {
2525  0 if (title.indexOf("(View") > -1)
2526    {
2527  0 title = title.substring(0, title.indexOf("(View"));
2528    }
2529  0 title += "(View " + viewSize + ")";
2530    }
2531   
2532  0 newaf.setTitle(title.toString());
2533   
2534  0 newaf.viewport.setHistoryList(viewport.getHistoryList());
2535  0 newaf.viewport.setRedoList(viewport.getRedoList());
2536  0 return newaf;
2537    }
2538   
2539    /**
2540    *
2541    * @return list of feature groups on the view
2542    */
 
2543  0 toggle public String[] getFeatureGroups()
2544    {
2545  0 FeatureRenderer fr = null;
2546  0 if (alignPanel != null
2547    && (fr = alignPanel.getFeatureRenderer()) != null)
2548    {
2549  0 List<String> gps = fr.getFeatureGroups();
2550  0 String[] _gps = gps.toArray(new String[gps.size()]);
2551  0 return _gps;
2552    }
2553  0 return null;
2554    }
2555   
2556    /**
2557    * get sequence feature groups that are hidden or shown
2558    *
2559    * @param visible
2560    * true is visible
2561    * @return list
2562    */
 
2563  0 toggle public String[] getFeatureGroupsOfState(boolean visible)
2564    {
2565  0 FeatureRenderer fr = null;
2566  0 if (alignPanel != null
2567    && (fr = alignPanel.getFeatureRenderer()) != null)
2568    {
2569  0 List<String> gps = fr.getGroups(visible);
2570  0 String[] _gps = gps.toArray(new String[gps.size()]);
2571  0 return _gps;
2572    }
2573  0 return null;
2574    }
2575   
2576    /**
2577    * Change the display state for the given feature groups
2578    *
2579    * @param groups
2580    * list of group strings
2581    * @param state
2582    * visible or invisible
2583    */
 
2584  0 toggle public void setFeatureGroupState(String[] groups, boolean state)
2585    {
2586  0 FeatureRenderer fr = null;
2587  0 this.sequenceFeatures.setState(true);
2588  0 viewport.setShowSequenceFeatures(true);
2589  0 if (alignPanel != null
2590    && (fr = alignPanel.getFeatureRenderer()) != null)
2591    {
2592   
2593  0 fr.setGroupVisibility(Arrays.asList(groups), state);
2594  0 alignPanel.seqPanel.seqCanvas.repaint();
2595  0 if (alignPanel.overviewPanel != null)
2596    {
2597  0 alignPanel.overviewPanel.updateOverviewImage();
2598    }
2599    }
2600    }
2601   
 
2602  0 toggle public void seqLimits_itemStateChanged()
2603    {
2604  0 viewport.setShowJVSuffix(seqLimits.getState());
2605  0 alignPanel.fontChanged();
2606  0 alignPanel.paintAlignment(true, false);
2607    }
2608   
 
2609  0 toggle protected void colourTextMenuItem_actionPerformed()
2610    {
2611  0 viewport.setColourText(colourTextMenuItem.getState());
2612  0 alignPanel.paintAlignment(false, false);
2613    }
2614   
 
2615  0 toggle protected void displayNonconservedMenuItem_actionPerformed()
2616    {
2617  0 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2618  0 alignPanel.paintAlignment(false, false);
2619    }
2620   
 
2621  0 toggle protected void wrapMenuItem_actionPerformed()
2622    {
2623  0 viewport.setWrapAlignment(wrapMenuItem.getState());
2624  0 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2625  0 scaleAbove.setEnabled(wrapMenuItem.getState());
2626  0 scaleLeft.setEnabled(wrapMenuItem.getState());
2627  0 scaleRight.setEnabled(wrapMenuItem.getState());
2628  0 alignPanel.paintAlignment(true, false);
2629    }
2630   
 
2631  0 toggle public void overviewMenuItem_actionPerformed()
2632    {
2633  0 if (alignPanel.overviewPanel != null)
2634    {
2635  0 return;
2636    }
2637   
2638  0 Frame frame = new Frame();
2639  0 final OverviewPanel overview = new OverviewPanel(alignPanel);
2640  0 frame.add(overview);
2641    // +50 must allow for applet frame window
2642  0 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2643    .formatMessage("label.overview_params", new String[]
2644    { this.getTitle() }), overview.getPreferredSize().width,
2645    overview.getPreferredSize().height + 50);
2646   
2647  0 frame.pack();
2648  0 final AlignmentPanel ap = alignPanel;
2649  0 frame.addWindowListener(new WindowAdapter()
2650    {
 
2651  0 toggle @Override
2652    public void windowClosing(WindowEvent e)
2653    {
2654  0 overview.dispose();
2655  0 if (ap != null)
2656    {
2657  0 ap.setOverviewPanel(null);
2658    }
2659    };
2660    });
2661   
2662  0 alignPanel.setOverviewPanel(overview);
2663   
2664    }
2665   
 
2666  0 toggle @Override
2667    public void changeColour(ColourSchemeI cs)
2668    {
2669  0 viewport.setGlobalColourScheme(cs);
2670   
2671  0 alignPanel.paintAlignment(true, true);
2672    }
2673   
 
2674  0 toggle protected void modifyPID_actionPerformed()
2675    {
2676  0 if (viewport.getAbovePIDThreshold()
2677    && viewport.getGlobalColourScheme() != null)
2678    {
2679  0 SliderPanel.setPIDSliderSource(alignPanel,
2680    viewport.getResidueShading(), alignPanel.getViewName());
2681  0 SliderPanel.showPIDSlider();
2682    }
2683    }
2684   
 
2685  0 toggle protected void modifyConservation_actionPerformed()
2686    {
2687  0 if (viewport.getConservationSelected()
2688    && viewport.getGlobalColourScheme() != null)
2689    {
2690  0 SliderPanel.setConservationSlider(alignPanel,
2691    viewport.getResidueShading(), alignPanel.getViewName());
2692  0 SliderPanel.showConservationSlider();
2693    }
2694    }
2695   
 
2696  0 toggle protected void conservationMenuItem_actionPerformed()
2697    {
2698  0 boolean selected = conservationMenuItem.getState();
2699  0 modifyConservation.setEnabled(selected);
2700  0 viewport.setConservationSelected(selected);
2701  0 viewport.getResidueShading().setConservationApplied(selected);
2702   
2703  0 changeColour(viewport.getGlobalColourScheme());
2704   
2705  0 if (selected)
2706    {
2707  0 modifyConservation_actionPerformed();
2708    }
2709    else
2710    {
2711  0 SliderPanel.hideConservationSlider();
2712    }
2713    }
2714   
 
2715  0 toggle public void abovePIDThreshold_actionPerformed()
2716    {
2717  0 boolean selected = abovePIDThreshold.getState();
2718  0 modifyPID.setEnabled(selected);
2719  0 viewport.setAbovePIDThreshold(selected);
2720  0 if (!selected)
2721    {
2722  0 viewport.getResidueShading().setThreshold(0,
2723    viewport.isIgnoreGapsConsensus());
2724    }
2725   
2726  0 changeColour(viewport.getGlobalColourScheme());
2727   
2728  0 if (selected)
2729    {
2730  0 modifyPID_actionPerformed();
2731    }
2732    else
2733    {
2734  0 SliderPanel.hidePIDSlider();
2735    }
2736    }
2737   
 
2738  0 toggle public void sortPairwiseMenuItem_actionPerformed()
2739    {
2740  0 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741  0 AlignmentSorter.sortByPID(viewport.getAlignment(),
2742    viewport.getAlignment().getSequenceAt(0));
2743   
2744  0 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2745    viewport.getAlignment()));
2746  0 alignPanel.paintAlignment(true, false);
2747    }
2748   
 
2749  0 toggle public void sortIDMenuItem_actionPerformed()
2750    {
2751  0 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752  0 AlignmentSorter.sortByID(viewport.getAlignment());
2753  0 addHistoryItem(
2754    new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2755  0 alignPanel.paintAlignment(true, false);
2756    }
2757   
 
2758  0 toggle public void sortLengthMenuItem_actionPerformed()
2759    {
2760  0 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2761  0 AlignmentSorter.sortByLength(viewport.getAlignment());
2762  0 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2763    viewport.getAlignment()));
2764  0 alignPanel.paintAlignment(true, false);
2765    }
2766   
 
2767  0 toggle public void sortGroupMenuItem_actionPerformed()
2768    {
2769  0 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2770  0 AlignmentSorter.sortByGroup(viewport.getAlignment());
2771  0 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2772    viewport.getAlignment()));
2773  0 alignPanel.paintAlignment(true, false);
2774   
2775    }
2776   
 
2777  0 toggle public void removeRedundancyMenuItem_actionPerformed()
2778    {
2779  0 new RedundancyPanel(alignPanel);
2780    }
2781   
 
2782  0 toggle public void pairwiseAlignmentMenuItem_actionPerformed()
2783    {
2784  0 if (viewport.getSelectionGroup() != null
2785    && viewport.getSelectionGroup().getSize() > 1)
2786    {
2787  0 Frame frame = new Frame();
2788  0 frame.add(new PairwiseAlignPanel(alignPanel));
2789  0 jalview.bin.JalviewLite.addFrame(frame,
2790    MessageManager.getString("action.pairwise_alignment"), 600,
2791    500);
2792    }
2793    }
2794   
 
2795  0 toggle public void PCAMenuItem_actionPerformed()
2796    {
2797    // are the sequences aligned?
2798  0 if (!viewport.getAlignment().isAligned(false))
2799    {
2800  0 SequenceI current;
2801  0 int Width = viewport.getAlignment().getWidth();
2802   
2803  0 for (int i = 0; i < viewport.getAlignment().getSequences()
2804    .size(); i++)
2805    {
2806  0 current = viewport.getAlignment().getSequenceAt(i);
2807   
2808  0 if (current.getLength() < Width)
2809    {
2810  0 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2811    }
2812    }
2813  0 alignPanel.paintAlignment(false, false);
2814    }
2815   
2816  0 if ((viewport.getSelectionGroup() != null
2817    && viewport.getSelectionGroup().getSize() < 4
2818    && viewport.getSelectionGroup().getSize() > 0)
2819    || viewport.getAlignment().getHeight() < 4)
2820    {
2821  0 return;
2822    }
2823   
2824  0 try
2825    {
2826  0 new PCAPanel(viewport);
2827    } catch (java.lang.OutOfMemoryError ex)
2828    {
2829    }
2830   
2831    }
2832   
 
2833  0 toggle public void averageDistanceTreeMenuItem_actionPerformed()
2834    {
2835  0 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2836    "Average distance tree using PID");
2837    }
2838   
 
2839  0 toggle public void neighbourTreeMenuItem_actionPerformed()
2840    {
2841  0 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2842    "Neighbour joining tree using PID");
2843    }
2844   
 
2845  0 toggle protected void njTreeBlosumMenuItem_actionPerformed()
2846    {
2847  0 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2848    ScoreModels.getInstance().getBlosum62().getName(),
2849    "Neighbour joining tree using BLOSUM62");
2850    }
2851   
 
2852  0 toggle protected void avTreeBlosumMenuItem_actionPerformed()
2853    {
2854  0 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2855    ScoreModels.getInstance().getBlosum62().getName(),
2856    "Average distance tree using BLOSUM62");
2857    }
2858   
 
2859  0 toggle void newTreePanel(String type, String pwType, String title)
2860    {
2861    // are the sequences aligned?
2862  0 if (!viewport.getAlignment().isAligned(false))
2863    {
2864  0 SequenceI current;
2865  0 int Width = viewport.getAlignment().getWidth();
2866   
2867  0 for (int i = 0; i < viewport.getAlignment().getSequences()
2868    .size(); i++)
2869    {
2870  0 current = viewport.getAlignment().getSequenceAt(i);
2871   
2872  0 if (current.getLength() < Width)
2873    {
2874  0 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2875    }
2876    }
2877  0 alignPanel.paintAlignment(false, false);
2878   
2879    }
2880   
2881  0 if ((viewport.getSelectionGroup() != null
2882    && viewport.getSelectionGroup().getSize() > 1)
2883    || (viewport.getAlignment().getHeight() > 1))
2884    {
2885  0 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2886   
2887  0 addTreeMenuItem(tp, title);
2888   
2889  0 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2890    }
2891    }
2892   
 
2893  0 toggle void loadTree_actionPerformed()
2894    {
2895  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2896  0 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2897  0 cap.setTreeImport();
2898  0 Frame frame = new Frame();
2899  0 frame.add(cap);
2900  0 jalview.bin.JalviewLite.addFrame(frame,
2901    MessageManager.getString("label.paste_newick_file"), 400, 300);
2902    }
2903   
 
2904  0 toggle public void loadTree(jalview.io.NewickFile tree, String treeFile)
2905    {
2906  0 TreePanel tp = new TreePanel(alignPanel, treeFile,
2907    MessageManager.getString("label.load_tree_from_file"), tree);
2908  0 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2909  0 addTreeMenuItem(tp, treeFile);
2910    }
2911   
2912    /**
2913    * sort the alignment using the given treePanel
2914    *
2915    * @param treePanel
2916    * tree used to sort view
2917    * @param title
2918    * string used for undo event name
2919    */
 
2920  0 toggle public void sortByTree(TreePanel treePanel, String title)
2921    {
2922  0 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2923  0 AlignmentSorter.sortByTree(viewport.getAlignment(),
2924    treePanel.getTree());
2925    // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2926    // HistoryItem.SORT));
2927  0 addHistoryItem(new OrderCommand(MessageManager
2928    .formatMessage("label.order_by_params", new String[]
2929    { title }), oldOrder, viewport.getAlignment()));
2930  0 alignPanel.paintAlignment(true, false);
2931    }
2932   
2933    /**
2934    * Do any automatic reordering of the alignment and add the necessary bits to
2935    * the menu structure for the new tree
2936    *
2937    * @param treePanel
2938    * @param title
2939    */
 
2940  0 toggle protected void addTreeMenuItem(final TreePanel treePanel,
2941    final String title)
2942    {
2943  0 final MenuItem item = new MenuItem(title);
2944  0 sortByTreeMenu.add(item);
2945  0 item.addActionListener(new java.awt.event.ActionListener()
2946    {
 
2947  0 toggle @Override
2948    public void actionPerformed(ActionEvent evt)
2949    {
2950  0 sortByTree(treePanel, title); // treePanel.getTitle());
2951    }
2952    });
2953   
2954  0 treePanel.addWindowListener(new WindowAdapter()
2955    {
 
2956  0 toggle @Override
2957    public void windowOpened(WindowEvent e)
2958    {
2959  0 if (viewport.sortByTree)
2960    {
2961  0 sortByTree(treePanel, title);
2962    }
2963  0 super.windowOpened(e);
2964    }
2965   
 
2966  0 toggle @Override
2967    public void windowClosing(WindowEvent e)
2968    {
2969  0 sortByTreeMenu.remove(item);
2970    };
2971    });
2972    }
2973   
 
2974  0 toggle public boolean sortBy(AlignmentOrder alorder, String undoname)
2975    {
2976  0 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2977  0 if (viewport.applet.debug)
2978    {
2979  0 System.err.println("Sorting " + alorder.getOrder().size()
2980    + " in alignment '" + getTitle() + "'");
2981    }
2982  0 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2983  0 if (undoname != null)
2984    {
2985  0 addHistoryItem(new OrderCommand(undoname, oldOrder,
2986    viewport.getAlignment()));
2987    }
2988  0 alignPanel.paintAlignment(true, false);
2989  0 return true;
2990    }
2991   
 
2992  0 toggle protected void documentation_actionPerformed()
2993    {
2994  0 alignPanel.av.applet.openJalviewHelpUrl();
2995    }
2996   
 
2997  0 toggle protected void about_actionPerformed()
2998    {
2999   
 
3000    class AboutPanel extends Canvas
3001    {
3002    String version;
3003   
3004    String builddate;
3005   
 
3006  0 toggle public AboutPanel(String version, String builddate)
3007    {
3008  0 this.version = version;
3009  0 this.builddate = builddate;
3010    }
3011   
 
3012  0 toggle @Override
3013    public void paint(Graphics g)
3014    {
3015  0 g.setColor(Color.white);
3016  0 g.fillRect(0, 0, getSize().width, getSize().height);
3017  0 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3018  0 FontMetrics fm = g.getFontMetrics();
3019  0 int fh = fm.getHeight();
3020  0 int y = 5, x = 7;
3021  0 g.setColor(Color.black);
3022    // TODO: update this text for each release or centrally store it for
3023    // lite and application
3024  0 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3025  0 g.drawString(MessageManager
3026    .formatMessage("label.jalviewLite_release", new String[]
3027    { version }), x, y += fh);
3028  0 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3029  0 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3030    new String[]
3031    { builddate }), x, y += fh);
3032  0 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3033  0 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3034    y += fh * 1.5);
3035  0 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3036    x + 50, y += fh + 8);
3037  0 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3038    x, y += fh);
3039  0 g.drawString(MessageManager
3040    .getString("label.jalview_distribution_lists"), x, y += fh);
3041  0 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3042    x, y += fh + 8);
3043  0 g.drawString(
3044    MessageManager.getString("label.jalview_cite_1_authors"), x,
3045    y += fh);
3046  0 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3047    x, y += fh);
3048  0 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3049    x, y += fh);
3050    }
3051    }
3052   
3053  0 Frame frame = new Frame();
3054  0 frame.add(new AboutPanel(JalviewLite.getVersion(),
3055    JalviewLite.getBuildDate()));
3056  0 jalview.bin.JalviewLite.addFrame(frame,
3057    MessageManager.getString("label.jalview"), 580, 220);
3058   
3059    }
3060   
 
3061  0 toggle public void showURL(String url, String target)
3062    {
3063  0 if (viewport.applet == null)
3064    {
3065  0 System.out.println("Not running as applet - no browser available.");
3066    }
3067    else
3068    {
3069  0 viewport.applet.showURL(url, target);
3070    }
3071    }
3072   
3073    // ////////////////////////////////////////////////////////////////////////////////
3074    // JBuilder Graphics here
3075   
3076    MenuBar alignFrameMenuBar = new MenuBar();
3077   
3078    Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3079   
3080    MenuItem loadApplication = new MenuItem(
3081    MessageManager.getString("label.view_full_application"));
3082   
3083    MenuItem loadTree = new MenuItem(
3084    MessageManager.getString("label.load_associated_tree"));
3085   
3086    MenuItem loadAnnotations = new MenuItem(
3087    MessageManager.getString("label.load_features_annotations"));
3088   
3089    MenuItem outputFeatures = new MenuItem(
3090    MessageManager.getString("label.export_features"));
3091   
3092    MenuItem outputAnnotations = new MenuItem(
3093    MessageManager.getString("label.export_annotations"));
3094   
3095    MenuItem closeMenuItem = new MenuItem(
3096    MessageManager.getString("action.close"));
3097   
3098    MenuItem selectAllSequenceMenuItem = new MenuItem(
3099    MessageManager.getString("action.select_all"));
3100   
3101    MenuItem deselectAllSequenceMenuItem = new MenuItem(
3102    MessageManager.getString("action.deselect_all"));
3103   
3104    MenuItem invertSequenceMenuItem = new MenuItem(
3105    MessageManager.getString("action.invert_selection"));
3106   
3107    MenuItem remove2LeftMenuItem = new MenuItem();
3108   
3109    MenuItem remove2RightMenuItem = new MenuItem();
3110   
3111    MenuItem removeGappedColumnMenuItem = new MenuItem();
3112   
3113    MenuItem removeAllGapsMenuItem = new MenuItem();
3114   
3115    CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3116   
3117    CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3118   
3119    MenuItem sortPairwiseMenuItem = new MenuItem();
3120   
3121    MenuItem sortIDMenuItem = new MenuItem();
3122   
3123    MenuItem sortLengthMenuItem = new MenuItem();
3124   
3125    MenuItem sortGroupMenuItem = new MenuItem();
3126   
3127    MenuItem removeRedundancyMenuItem = new MenuItem();
3128   
3129    MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3130   
3131    MenuItem PCAMenuItem = new MenuItem();
3132   
3133    MenuItem averageDistanceTreeMenuItem = new MenuItem();
3134   
3135    MenuItem neighbourTreeMenuItem = new MenuItem();
3136   
3137    BorderLayout borderLayout1 = new BorderLayout();
3138   
3139    public Label statusBar = new Label();
3140   
3141    MenuItem clustalColour = new MenuItem();
3142   
3143    MenuItem zappoColour = new MenuItem();
3144   
3145    MenuItem taylorColour = new MenuItem();
3146   
3147    MenuItem hydrophobicityColour = new MenuItem();
3148   
3149    MenuItem helixColour = new MenuItem();
3150   
3151    MenuItem strandColour = new MenuItem();
3152   
3153    MenuItem turnColour = new MenuItem();
3154   
3155    MenuItem buriedColour = new MenuItem();
3156   
3157    MenuItem purinePyrimidineColour = new MenuItem();
3158   
3159    // MenuItem RNAInteractionColour = new MenuItem();
3160   
3161    MenuItem RNAHelixColour = new MenuItem();
3162   
3163    MenuItem userDefinedColour = new MenuItem();
3164   
3165    MenuItem PIDColour = new MenuItem();
3166   
3167    MenuItem BLOSUM62Colour = new MenuItem();
3168   
3169    MenuItem tcoffeeColour = new MenuItem();
3170   
3171    MenuItem njTreeBlosumMenuItem = new MenuItem();
3172   
3173    MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3174   
3175    CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3176   
3177    CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3178   
3179    CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3180   
3181    MenuItem alProperties = new MenuItem(
3182    MessageManager.getString("label.alignment_props"));
3183   
3184    MenuItem overviewMenuItem = new MenuItem();
3185   
3186    MenuItem undoMenuItem = new MenuItem();
3187   
3188    MenuItem redoMenuItem = new MenuItem();
3189   
3190    CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3191   
3192    MenuItem noColourmenuItem = new MenuItem();
3193   
3194    CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3195   
3196    CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3197   
3198    MenuItem findMenuItem = new MenuItem();
3199   
3200    CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3201   
3202    MenuItem nucleotideColour = new MenuItem();
3203   
3204    MenuItem deleteGroups = new MenuItem();
3205   
3206    MenuItem grpsFromSelection = new MenuItem();
3207   
3208    MenuItem createGroup = new MenuItem();
3209   
3210    MenuItem unGroup = new MenuItem();
3211   
3212    MenuItem delete = new MenuItem();
3213   
3214    MenuItem copy = new MenuItem();
3215   
3216    MenuItem cut = new MenuItem();
3217   
3218    Menu pasteMenu = new Menu();
3219   
3220    MenuItem pasteNew = new MenuItem();
3221   
3222    MenuItem pasteThis = new MenuItem();
3223   
3224    CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3225   
3226    MenuItem font = new MenuItem();
3227   
3228    CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3229   
3230    CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3231   
3232    CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3233   
3234    MenuItem modifyPID = new MenuItem();
3235   
3236    MenuItem modifyConservation = new MenuItem();
3237   
3238    CheckboxMenuItem autoCalculate = null;
3239   
3240    CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3241    "Sort Alignment With New Tree", true);
3242   
3243    Menu sortByTreeMenu = new Menu();
3244   
3245    MenuItem inputText = new MenuItem();
3246   
3247    MenuItem documentation = new MenuItem();
3248   
3249    MenuItem about = new MenuItem();
3250   
3251    CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3252   
3253    CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3254   
3255    CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3256   
3257    CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3258   
3259    CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3260   
3261    CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3262   
3263    CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3264   
3265    CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3266   
3267    CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3268   
3269    /**
3270    * Initialise menus and other items
3271    *
3272    * @throws Exception
3273    */
 
3274  0 toggle private void jbInit() throws Exception
3275    {
3276  0 setMenuBar(alignFrameMenuBar);
3277   
3278    /*
3279    * Configure File menu items and actions
3280    */
3281  0 inputText
3282    .setLabel(MessageManager.getString("label.input_from_textbox"));
3283  0 inputText.addActionListener(this);
3284  0 Menu outputTextboxMenu = new Menu(
3285    MessageManager.getString("label.out_to_textbox"));
3286  0 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3287    {
3288  0 MenuItem item = new MenuItem(ff);
3289   
3290  0 item.addActionListener(new java.awt.event.ActionListener()
3291    {
 
3292  0 toggle @Override
3293    public void actionPerformed(ActionEvent e)
3294    {
3295  0 outputText_actionPerformed(e);
3296    }
3297    });
3298   
3299  0 outputTextboxMenu.add(item);
3300    }
3301  0 closeMenuItem.addActionListener(this);
3302  0 loadApplication.addActionListener(this);
3303  0 loadTree.addActionListener(this);
3304  0 loadAnnotations.addActionListener(this);
3305  0 outputFeatures.addActionListener(this);
3306  0 outputAnnotations.addActionListener(this);
3307   
3308    /*
3309    * Configure Edit menu items and actions
3310    */
3311  0 undoMenuItem.setEnabled(false);
3312  0 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3313  0 undoMenuItem.addActionListener(this);
3314  0 redoMenuItem.setEnabled(false);
3315  0 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3316  0 redoMenuItem.addActionListener(this);
3317  0 copy.setLabel(MessageManager.getString("action.copy"));
3318  0 copy.addActionListener(this);
3319  0 cut.setLabel(MessageManager.getString("action.cut"));
3320  0 cut.addActionListener(this);
3321  0 delete.setLabel(MessageManager.getString("action.delete"));
3322  0 delete.addActionListener(this);
3323  0 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3324  0 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3325  0 pasteNew.addActionListener(this);
3326  0 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3327  0 pasteThis.addActionListener(this);
3328  0 remove2LeftMenuItem
3329    .setLabel(MessageManager.getString("action.remove_left"));
3330  0 remove2LeftMenuItem.addActionListener(this);
3331  0 remove2RightMenuItem
3332    .setLabel(MessageManager.getString("action.remove_right"));
3333  0 remove2RightMenuItem.addActionListener(this);
3334  0 removeGappedColumnMenuItem.setLabel(
3335    MessageManager.getString("action.remove_empty_columns"));
3336  0 removeGappedColumnMenuItem.addActionListener(this);
3337  0 removeAllGapsMenuItem
3338    .setLabel(MessageManager.getString("action.remove_all_gaps"));
3339  0 removeAllGapsMenuItem.addActionListener(this);
3340  0 removeRedundancyMenuItem
3341    .setLabel(MessageManager.getString("action.remove_redundancy"));
3342  0 removeRedundancyMenuItem.addActionListener(this);
3343   
3344    /*
3345    * Configure Select menu items and actions
3346    */
3347  0 findMenuItem.setLabel(MessageManager.getString("action.find"));
3348  0 findMenuItem.addActionListener(this);
3349  0 selectAllSequenceMenuItem.addActionListener(this);
3350  0 deselectAllSequenceMenuItem.addActionListener(this);
3351  0 invertSequenceMenuItem.setLabel(
3352    MessageManager.getString("action.invert_sequence_selection"));
3353  0 invertSequenceMenuItem.addActionListener(this);
3354  0 invertColSel.setLabel(
3355    MessageManager.getString("action.invert_column_selection"));
3356  0 invertColSel.addActionListener(this);
3357  0 deleteGroups
3358    .setLabel(MessageManager.getString("action.undefine_groups"));
3359  0 deleteGroups.addActionListener(this);
3360  0 grpsFromSelection.setLabel(
3361    MessageManager.getString("action.make_groups_selection"));
3362  0 grpsFromSelection.addActionListener(this);
3363  0 createGroup.setLabel(MessageManager.getString("action.create_group"));
3364  0 createGroup.addActionListener(this);
3365  0 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3366  0 unGroup.addActionListener(this);
3367   
3368  0 annotationColumnSelection.setLabel(
3369    MessageManager.getString("action.select_by_annotation"));
3370  0 annotationColumnSelection.addActionListener(this);
3371   
3372    /*
3373    * Configure View menu items and actions
3374    */
3375  0 newView.setLabel(MessageManager.getString("action.new_view"));
3376  0 newView.addActionListener(this);
3377  0 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3378  0 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3379  0 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3380  0 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3381  0 hideColumns
3382    .setLabel(MessageManager.getString("label.selected_columns"));
3383  0 hideSequences
3384    .setLabel(MessageManager.getString("label.selected_sequences"));
3385  0 hideAllButSelection.setLabel(
3386    MessageManager.getString("label.all_but_selected_region"));
3387  0 hideAllSelection
3388    .setLabel(MessageManager.getString("label.selected_region"));
3389  0 showAllHidden.setLabel(
3390    MessageManager.getString("label.all_sequences_columns"));
3391  0 showColumns.addActionListener(this);
3392  0 showSeqs.addActionListener(this);
3393  0 hideColumns.addActionListener(this);
3394  0 hideSequences.addActionListener(this);
3395  0 hideAllButSelection.addActionListener(this);
3396  0 hideAllSelection.addActionListener(this);
3397  0 showAllHidden.addActionListener(this);
3398  0 featureSettings
3399    .setLabel(MessageManager.getString("action.feature_settings"));
3400  0 featureSettings.addActionListener(this);
3401  0 sequenceFeatures.setLabel(
3402    MessageManager.getString("label.show_sequence_features"));
3403  0 sequenceFeatures.addItemListener(this);
3404  0 sequenceFeatures.setState(false);
3405  0 followMouseOverFlag.setLabel(
3406    MessageManager.getString("label.automatic_scrolling"));
3407  0 followMouseOverFlag.addItemListener(this);
3408  0 alProperties.addActionListener(this);
3409  0 overviewMenuItem
3410    .setLabel(MessageManager.getString("label.overview_window"));
3411  0 overviewMenuItem.addActionListener(this);
3412   
3413    /*
3414    * Configure Annotations menu items and actions
3415    */
3416  0 annotationPanelMenuItem
3417    .setLabel(MessageManager.getString("label.show_annotations"));
3418  0 annotationPanelMenuItem.addItemListener(this);
3419  0 showGroupConsensus
3420    .setLabel(MessageManager.getString("label.group_consensus"));
3421  0 showGroupConservation
3422    .setLabel(MessageManager.getString("label.group_conservation"));
3423  0 showConsensusHistogram.setLabel(
3424    MessageManager.getString("label.show_consensus_histogram"));
3425  0 showSequenceLogo.setLabel(
3426    MessageManager.getString("label.show_consensus_logo"));
3427  0 normSequenceLogo.setLabel(
3428    MessageManager.getString("label.norm_consensus_logo"));
3429  0 applyAutoAnnotationSettings
3430    .setLabel(MessageManager.getString("label.apply_all_groups"));
3431  0 applyAutoAnnotationSettings.setState(true);
3432  0 Menu autoAnnMenu = new Menu(
3433    MessageManager.getString("label.autocalculated_annotation"));
3434  0 showGroupConsensus.addItemListener(this);
3435  0 showGroupConservation.addItemListener(this);
3436  0 showConsensusHistogram.addItemListener(this);
3437  0 showSequenceLogo.addItemListener(this);
3438  0 normSequenceLogo.addItemListener(this);
3439  0 applyAutoAnnotationSettings.addItemListener(this);
3440  0 showAlignmentAnnotations = new CheckboxMenuItem(
3441    MessageManager.getString("label.show_all_al_annotations"));
3442  0 showSequenceAnnotations = new CheckboxMenuItem(
3443    MessageManager.getString("label.show_all_seq_annotations"));
3444  0 sortAnnBySequence = new CheckboxMenuItem(
3445    MessageManager.getString("label.sort_annotations_by_sequence"));
3446  0 sortAnnByLabel = new CheckboxMenuItem(
3447    MessageManager.getString("label.sort_annotations_by_label"));
3448  0 showAutoFirst = new CheckboxMenuItem(
3449    MessageManager.getString("label.show_first"));
3450  0 showAutoFirst.setState(false); // pending applet parameter
3451  0 setShowAutoCalculatedAbove(showAutoFirst.getState());
3452  0 showAutoLast = new CheckboxMenuItem(
3453    MessageManager.getString("label.show_last"));
3454  0 showAutoLast.setState(!showAutoFirst.getState());
3455  0 showAlignmentAnnotations.addItemListener(this);
3456  0 showSequenceAnnotations.addItemListener(this);
3457  0 sortAnnBySequence.addItemListener(this);
3458  0 sortAnnByLabel.addItemListener(this);
3459  0 showAutoFirst.addItemListener(this);
3460  0 showAutoLast.addItemListener(this);
3461   
3462    /*
3463    * Configure Format menu items and actions
3464    */
3465  0 font.setLabel(MessageManager.getString("action.font"));
3466  0 font.addActionListener(this);
3467  0 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3468  0 scaleAbove.setState(true);
3469  0 scaleAbove.setEnabled(false);
3470  0 scaleAbove.addItemListener(this);
3471  0 scaleLeft.setEnabled(false);
3472  0 scaleLeft.setState(true);
3473  0 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3474  0 scaleLeft.addItemListener(this);
3475  0 scaleRight.setEnabled(false);
3476  0 scaleRight.setState(true);
3477  0 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3478  0 scaleRight.addItemListener(this);
3479  0 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3480  0 viewBoxesMenuItem.setState(true);
3481  0 viewBoxesMenuItem.addItemListener(this);
3482  0 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3483  0 viewTextMenuItem.setState(true);
3484  0 viewTextMenuItem.addItemListener(this);
3485  0 colourTextMenuItem
3486    .setLabel(MessageManager.getString("label.colour_text"));
3487  0 colourTextMenuItem.addItemListener(this);
3488  0 displayNonconservedMenuItem
3489    .setLabel(MessageManager.getString("label.show_non_conserved"));
3490  0 displayNonconservedMenuItem.addItemListener(this);
3491  0 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3492  0 wrapMenuItem.addItemListener(this);
3493  0 renderGapsMenuItem
3494    .setLabel(MessageManager.getString("action.show_gaps"));
3495  0 renderGapsMenuItem.setState(true);
3496  0 renderGapsMenuItem.addItemListener(this);
3497  0 centreColumnLabelFlag.setLabel(
3498    MessageManager.getString("label.centre_column_labels"));
3499  0 centreColumnLabelFlag.addItemListener(this);
3500  0 seqLimits.setState(true);
3501  0 seqLimits.setLabel(
3502    MessageManager.getString("label.show_sequence_limits"));
3503  0 seqLimits.addItemListener(this);
3504   
3505    /*
3506    * Configure Colour menu items and actions
3507    */
3508  0 applyToAllGroups.setLabel(
3509    MessageManager.getString("label.apply_colour_to_all_groups"));
3510  0 applyToAllGroups.setState(true);
3511  0 applyToAllGroups.addItemListener(this);
3512  0 clustalColour.setLabel(
3513    MessageManager.getString("label.colourScheme_clustal"));
3514  0 clustalColour.addActionListener(this);
3515  0 zappoColour
3516    .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3517  0 zappoColour.addActionListener(this);
3518  0 taylorColour.setLabel(
3519    MessageManager.getString("label.colourScheme_taylor"));
3520  0 taylorColour.addActionListener(this);
3521  0 hydrophobicityColour.setLabel(
3522    MessageManager.getString("label.colourScheme_hydrophobic"));
3523  0 hydrophobicityColour.addActionListener(this);
3524  0 helixColour.setLabel(MessageManager
3525    .getString("label.colourScheme_helixpropensity"));
3526  0 helixColour.addActionListener(this);
3527  0 strandColour.setLabel(MessageManager
3528    .getString("label.colourScheme_strandpropensity"));
3529  0 strandColour.addActionListener(this);
3530  0 turnColour.setLabel(
3531    MessageManager.getString("label.colourScheme_turnpropensity"));
3532  0 turnColour.addActionListener(this);
3533  0 buriedColour.setLabel(
3534    MessageManager.getString("label.colourScheme_buriedindex"));
3535  0 buriedColour.addActionListener(this);
3536  0 purinePyrimidineColour.setLabel(MessageManager
3537    .getString("label.colourScheme_purine/pyrimidine"));
3538  0 purinePyrimidineColour.addActionListener(this);
3539    // RNAInteractionColour.setLabel(MessageManager
3540    // .getString("label.rna_interaction"));
3541    // RNAInteractionColour.addActionListener(this);
3542  0 RNAHelixColour.setLabel(
3543    MessageManager.getString("label.colourScheme_rnahelices"));
3544  0 RNAHelixColour.addActionListener(this);
3545  0 userDefinedColour
3546    .setLabel(MessageManager.getString("action.user_defined"));
3547  0 userDefinedColour.addActionListener(this);
3548  0 PIDColour.setLabel(
3549    MessageManager.getString("label.colourScheme_%identity"));
3550  0 PIDColour.addActionListener(this);
3551  0 BLOSUM62Colour.setLabel(
3552    MessageManager.getString("label.colourScheme_blosum62"));
3553  0 BLOSUM62Colour.addActionListener(this);
3554  0 tcoffeeColour.setLabel(
3555    MessageManager.getString("label.colourScheme_t-coffeescores"));
3556    // it will be enabled only if a score file is provided
3557  0 tcoffeeColour.setEnabled(false);
3558  0 tcoffeeColour.addActionListener(this);
3559  0 conservationMenuItem
3560    .setLabel(MessageManager.getString("action.by_conservation"));
3561  0 conservationMenuItem.addItemListener(this);
3562  0 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3563  0 noColourmenuItem.addActionListener(this);
3564  0 abovePIDThreshold.setLabel(
3565    MessageManager.getString("label.above_identity_threshold"));
3566  0 abovePIDThreshold.addItemListener(this);
3567  0 nucleotideColour.setLabel(
3568    MessageManager.getString("label.colourScheme_nucleotide"));
3569  0 nucleotideColour.addActionListener(this);
3570  0 modifyPID.setLabel(
3571    MessageManager.getString("label.modify_identity_threshold"));
3572  0 modifyPID.setEnabled(abovePIDThreshold.getState());
3573  0 modifyPID.addActionListener(this);
3574  0 modifyConservation.setLabel(MessageManager
3575    .getString("label.modify_conservation_threshold"));
3576  0 modifyConservation.setEnabled(conservationMenuItem.getState());
3577  0 modifyConservation.addActionListener(this);
3578  0 annotationColour
3579    .setLabel(MessageManager.getString("action.by_annotation"));
3580  0 annotationColour.addActionListener(this);
3581   
3582    /*
3583    * Configure Calculate menu items and actions
3584    */
3585  0 sortPairwiseMenuItem
3586    .setLabel(MessageManager.getString("action.by_pairwise_id"));
3587  0 sortPairwiseMenuItem.addActionListener(this);
3588  0 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3589  0 sortIDMenuItem.addActionListener(this);
3590  0 sortLengthMenuItem
3591    .setLabel(MessageManager.getString("action.by_length"));
3592  0 sortLengthMenuItem.addActionListener(this);
3593  0 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3594  0 sortGroupMenuItem.addActionListener(this);
3595  0 pairwiseAlignmentMenuItem.setLabel(
3596    MessageManager.getString("action.pairwise_alignment"));
3597  0 pairwiseAlignmentMenuItem.addActionListener(this);
3598  0 PCAMenuItem.setLabel(
3599    MessageManager.getString("label.principal_component_analysis"));
3600  0 PCAMenuItem.addActionListener(this);
3601  0 autoCalculate = new CheckboxMenuItem(
3602    MessageManager.getString("label.autocalculate_consensus"),
3603    true);
3604  0 averageDistanceTreeMenuItem.setLabel(
3605    MessageManager.getString("label.average_distance_identity"));
3606  0 averageDistanceTreeMenuItem.addActionListener(this);
3607  0 neighbourTreeMenuItem.setLabel(
3608    MessageManager.getString("label.neighbour_joining_identity"));
3609  0 neighbourTreeMenuItem.addActionListener(this);
3610  0 avDistanceTreeBlosumMenuItem.setLabel(
3611    MessageManager.getString("label.average_distance_blosum62"));
3612  0 avDistanceTreeBlosumMenuItem.addActionListener(this);
3613  0 njTreeBlosumMenuItem
3614    .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3615  0 njTreeBlosumMenuItem.addActionListener(this);
3616  0 sortByTreeMenu
3617    .setLabel(MessageManager.getString("action.by_tree_order"));
3618  0 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3619  0 Menu calculateTreeMenu = new Menu(
3620    MessageManager.getString("action.calculate_tree"));
3621  0 autoCalculate.addItemListener(this);
3622  0 sortByTree.addItemListener(this);
3623   
3624    /*
3625    * Configure Help menu items and actions
3626    */
3627  0 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3628  0 documentation.setLabel(MessageManager.getString("label.documentation"));
3629  0 documentation.addActionListener(this);
3630  0 about.setLabel(MessageManager.getString("label.about"));
3631  0 about.addActionListener(this);
3632   
3633    /*
3634    * Add top level menus to frame
3635    */
3636  0 alignFrameMenuBar.add(fileMenu);
3637  0 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3638  0 alignFrameMenuBar.add(editMenu);
3639  0 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3640  0 alignFrameMenuBar.add(selectMenu);
3641  0 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3642  0 alignFrameMenuBar.add(viewMenu);
3643  0 Menu annotationsMenu = new Menu(
3644    MessageManager.getString("action.annotations"));
3645  0 alignFrameMenuBar.add(annotationsMenu);
3646  0 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3647  0 alignFrameMenuBar.add(formatMenu);
3648  0 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3649  0 alignFrameMenuBar.add(colourMenu);
3650  0 Menu calculateMenu = new Menu(
3651    MessageManager.getString("action.calculate"));
3652  0 alignFrameMenuBar.add(calculateMenu);
3653  0 alignFrameMenuBar.add(helpMenu);
3654   
3655    /*
3656    * File menu
3657    */
3658  0 fileMenu.add(inputText);
3659  0 fileMenu.add(loadTree);
3660  0 fileMenu.add(loadAnnotations);
3661  0 fileMenu.addSeparator();
3662  0 fileMenu.add(outputTextboxMenu);
3663  0 fileMenu.add(outputFeatures);
3664  0 fileMenu.add(outputAnnotations);
3665  0 if (jalviewServletURL != null)
3666    {
3667  0 fileMenu.add(loadApplication);
3668    }
3669  0 fileMenu.addSeparator();
3670  0 fileMenu.add(closeMenuItem);
3671   
3672    /*
3673    * Edit menu
3674    */
3675  0 editMenu.add(undoMenuItem);
3676  0 editMenu.add(redoMenuItem);
3677  0 editMenu.add(cut);
3678  0 editMenu.add(copy);
3679  0 pasteMenu.add(pasteNew);
3680  0 pasteMenu.add(pasteThis);
3681  0 editMenu.add(pasteMenu);
3682  0 editMenu.add(delete);
3683  0 editMenu.addSeparator();
3684  0 editMenu.add(remove2LeftMenuItem);
3685  0 editMenu.add(remove2RightMenuItem);
3686  0 editMenu.add(removeGappedColumnMenuItem);
3687  0 editMenu.add(removeAllGapsMenuItem);
3688  0 editMenu.add(removeRedundancyMenuItem);
3689   
3690    /*
3691    * Select menu
3692    */
3693  0 selectMenu.add(findMenuItem);
3694  0 selectMenu.addSeparator();
3695  0 selectMenu.add(selectAllSequenceMenuItem);
3696  0 selectMenu.add(deselectAllSequenceMenuItem);
3697  0 selectMenu.add(invertSequenceMenuItem);
3698  0 selectMenu.add(invertColSel);
3699  0 selectMenu.add(createGroup);
3700  0 selectMenu.add(unGroup);
3701  0 selectMenu.add(grpsFromSelection);
3702  0 selectMenu.add(deleteGroups);
3703  0 selectMenu.add(annotationColumnSelection);
3704   
3705    /*
3706    * View menu
3707    */
3708  0 viewMenu.add(newView);
3709  0 viewMenu.addSeparator();
3710  0 showMenu.add(showColumns);
3711  0 showMenu.add(showSeqs);
3712  0 showMenu.add(showAllHidden);
3713  0 viewMenu.add(showMenu);
3714  0 hideMenu.add(hideColumns);
3715  0 hideMenu.add(hideSequences);
3716  0 hideMenu.add(hideAllSelection);
3717  0 hideMenu.add(hideAllButSelection);
3718  0 viewMenu.add(hideMenu);
3719  0 viewMenu.addSeparator();
3720  0 viewMenu.add(followMouseOverFlag);
3721  0 viewMenu.addSeparator();
3722  0 viewMenu.add(sequenceFeatures);
3723  0 viewMenu.add(featureSettings);
3724  0 viewMenu.addSeparator();
3725  0 viewMenu.add(alProperties);
3726  0 viewMenu.addSeparator();
3727  0 viewMenu.add(overviewMenuItem);
3728   
3729    /*
3730    * Annotations menu
3731    */
3732  0 annotationsMenu.add(annotationPanelMenuItem);
3733  0 annotationsMenu.addSeparator();
3734  0 annotationsMenu.add(showAlignmentAnnotations);
3735  0 annotationsMenu.add(showSequenceAnnotations);
3736  0 annotationsMenu.add(sortAnnBySequence);
3737  0 annotationsMenu.add(sortAnnByLabel);
3738  0 annotationsMenu.addSeparator();
3739  0 autoAnnMenu.add(showAutoFirst);
3740  0 autoAnnMenu.add(showAutoLast);
3741  0 autoAnnMenu.addSeparator();
3742  0 autoAnnMenu.add(applyAutoAnnotationSettings);
3743  0 autoAnnMenu.add(showConsensusHistogram);
3744  0 autoAnnMenu.add(showSequenceLogo);
3745  0 autoAnnMenu.add(normSequenceLogo);
3746  0 autoAnnMenu.addSeparator();
3747  0 autoAnnMenu.add(showGroupConservation);
3748  0 autoAnnMenu.add(showGroupConsensus);
3749  0 annotationsMenu.add(autoAnnMenu);
3750   
3751    /*
3752    * Format menu
3753    */
3754  0 formatMenu.add(font);
3755  0 formatMenu.add(seqLimits);
3756  0 formatMenu.add(wrapMenuItem);
3757  0 formatMenu.add(scaleAbove);
3758  0 formatMenu.add(scaleLeft);
3759  0 formatMenu.add(scaleRight);
3760  0 formatMenu.add(viewBoxesMenuItem);
3761  0 formatMenu.add(viewTextMenuItem);
3762  0 formatMenu.add(colourTextMenuItem);
3763  0 formatMenu.add(displayNonconservedMenuItem);
3764  0 formatMenu.add(renderGapsMenuItem);
3765  0 formatMenu.add(centreColumnLabelFlag);
3766   
3767    /*
3768    * Colour menu
3769    */
3770  0 colourMenu.add(applyToAllGroups);
3771  0 colourMenu.addSeparator();
3772  0 colourMenu.add(noColourmenuItem);
3773  0 colourMenu.add(clustalColour);
3774  0 colourMenu.add(BLOSUM62Colour);
3775  0 colourMenu.add(PIDColour);
3776  0 colourMenu.add(zappoColour);
3777  0 colourMenu.add(taylorColour);
3778  0 colourMenu.add(hydrophobicityColour);
3779  0 colourMenu.add(helixColour);
3780  0 colourMenu.add(strandColour);
3781  0 colourMenu.add(turnColour);
3782  0 colourMenu.add(buriedColour);
3783  0 colourMenu.add(nucleotideColour);
3784  0 colourMenu.add(purinePyrimidineColour);
3785    // colourMenu.add(RNAInteractionColour);
3786  0 colourMenu.add(tcoffeeColour);
3787  0 colourMenu.add(userDefinedColour);
3788  0 colourMenu.addSeparator();
3789  0 colourMenu.add(conservationMenuItem);
3790  0 colourMenu.add(modifyConservation);
3791  0 colourMenu.add(abovePIDThreshold);
3792  0 colourMenu.add(modifyPID);
3793  0 colourMenu.add(annotationColour);
3794  0 colourMenu.add(RNAHelixColour);
3795   
3796    /*
3797    * Calculate menu
3798    */
3799  0 sortMenu.add(sortIDMenuItem);
3800  0 sortMenu.add(sortLengthMenuItem);
3801  0 sortMenu.add(sortByTreeMenu);
3802  0 sortMenu.add(sortGroupMenuItem);
3803  0 sortMenu.add(sortPairwiseMenuItem);
3804  0 calculateMenu.add(sortMenu);
3805  0 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3806  0 calculateTreeMenu.add(neighbourTreeMenuItem);
3807  0 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3808  0 calculateTreeMenu.add(njTreeBlosumMenuItem);
3809  0 calculateMenu.add(calculateTreeMenu);
3810  0 calculateMenu.addSeparator();
3811  0 calculateMenu.add(pairwiseAlignmentMenuItem);
3812  0 calculateMenu.add(PCAMenuItem);
3813  0 calculateMenu.add(autoCalculate);
3814  0 calculateMenu.add(sortByTree);
3815   
3816    /*
3817    * Help menu
3818    */
3819  0 helpMenu.add(documentation);
3820  0 helpMenu.add(about);
3821   
3822    /*
3823    * Status bar
3824    */
3825  0 statusBar.setBackground(Color.white);
3826  0 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3827  0 setStatus(MessageManager.getString("label.status_bar"));
3828  0 this.add(statusBar, BorderLayout.SOUTH);
3829    }
3830   
 
3831  0 toggle @Override
3832    public void setStatus(String string)
3833    {
3834  0 statusBar.setText(string);
3835    };
3836   
3837    MenuItem featureSettings = new MenuItem();
3838   
3839    CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3840   
3841    MenuItem annotationColour = new MenuItem();
3842   
3843    MenuItem annotationColumnSelection = new MenuItem();
3844   
3845    MenuItem invertColSel = new MenuItem();
3846   
3847    MenuItem showColumns = new MenuItem();
3848   
3849    MenuItem showSeqs = new MenuItem();
3850   
3851    MenuItem hideColumns = new MenuItem();
3852   
3853    MenuItem hideSequences = new MenuItem();
3854   
3855    MenuItem hideAllButSelection = new MenuItem();
3856   
3857    MenuItem hideAllSelection = new MenuItem();
3858   
3859    MenuItem showAllHidden = new MenuItem();
3860   
3861    MenuItem newView = new MenuItem();
3862   
3863    private CheckboxMenuItem showAlignmentAnnotations;
3864   
3865    private CheckboxMenuItem showSequenceAnnotations;
3866   
3867    private CheckboxMenuItem sortAnnBySequence;
3868   
3869    private CheckboxMenuItem sortAnnByLabel;
3870   
3871    private CheckboxMenuItem showAutoFirst;
3872   
3873    private CheckboxMenuItem showAutoLast;
3874   
3875    private SplitFrame splitFrame;
3876   
3877    /**
3878    * Attach the alignFrame panels after embedding menus, if necessary. This used
3879    * to be called setEmbedded, but is now creates the dropdown menus in a
3880    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3881    *
3882    * @param reallyEmbedded
3883    * true to attach the view to the applet area on the page rather than
3884    * in a new window
3885    */
 
3886  0 toggle public void createAlignFrameWindow(boolean reallyEmbedded)
3887    {
3888  0 if (reallyEmbedded)
3889    {
3890  0 embedAlignFrameInApplet(viewport.applet);
3891    }
3892    else
3893    {
3894    // //////
3895    // test and embed menu bar if necessary.
3896    //
3897  0 if (embedMenuIfNeeded(alignPanel))
3898    {
3899    /*
3900    * adjust for status bar height too. ? pointless as overridden by layout
3901    * manager
3902    */
3903  0 alignPanel.setSize(getSize().width,
3904    getSize().height - statusBar.getHeight());
3905    }
3906  0 add(statusBar, BorderLayout.SOUTH);
3907  0 add(alignPanel, BorderLayout.CENTER);
3908    // and register with the applet so it can pass external API calls to us
3909  0 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3910    frameHeight);
3911    }
3912    }
3913   
3914    /**
3915    * Add the components of this AlignFrame to the applet container.
3916    *
3917    * @param theApplet
3918    */
 
3919  0 toggle public void embedAlignFrameInApplet(final JalviewLite theApplet)
3920    {
3921    // ////
3922    // Explicitly build the embedded menu panel for the on-page applet
3923    //
3924    // view cannot be closed if its actually on the page
3925  0 fileMenu.remove(closeMenuItem);
3926  0 fileMenu.remove(3); // Remove Separator
3927    // construct embedded menu, using default font
3928  0 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3929    // and actually add the components to the applet area
3930  0 theApplet.setLayout(new BorderLayout());
3931  0 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3932  0 theApplet.add(statusBar, BorderLayout.SOUTH);
3933    // TODO should size be left to the layout manager?
3934  0 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3935    - embeddedMenu.getHeight() - statusBar.getHeight());
3936  0 theApplet.add(alignPanel, BorderLayout.CENTER);
3937  0 final AlignFrame me = this;
3938  0 theApplet.addFocusListener(new FocusListener()
3939    {
3940   
 
3941  0 toggle @Override
3942    public void focusLost(FocusEvent e)
3943    {
3944  0 if (theApplet.currentAlignFrame == me)
3945    {
3946  0 theApplet.currentAlignFrame = null;
3947    }
3948    }
3949   
 
3950  0 toggle @Override
3951    public void focusGained(FocusEvent e)
3952    {
3953  0 theApplet.currentAlignFrame = me;
3954    }
3955    });
3956  0 theApplet.validate();
3957    }
3958   
3959    /**
3960    * create a new binding between structures in an existing jmol viewer instance
3961    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3962    * this does not open a new Jmol window, or modify the display of the
3963    * structures in the original jmol window. Note This method doesn't work
3964    * without an additional javascript library to exchange messages between the
3965    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3966    *
3967    * @param jmolViewer
3968    * JmolViewer instance
3969    * @param sequenceIds
3970    * - sequence Ids to search for associations
3971    */
 
3972  0 toggle public SequenceStructureBinding addStructureViewInstance(
3973    Object jmolviewer, String[] sequenceIds)
3974    {
3975  0 Viewer viewer = null;
3976  0 try
3977    {
3978  0 viewer = (Viewer) jmolviewer;
3979    } catch (ClassCastException ex)
3980    {
3981  0 System.err.println(
3982    "Unsupported viewer object :" + jmolviewer.getClass());
3983    }
3984  0 if (viewer == null)
3985    {
3986  0 System.err.println("Can't use this object as a structure viewer:"
3987    + jmolviewer.getClass());
3988  0 return null;
3989    }
3990  0 SequenceI[] seqs = null;
3991  0 if (sequenceIds == null || sequenceIds.length == 0)
3992    {
3993  0 seqs = viewport.getAlignment().getSequencesArray();
3994    }
3995    else
3996    {
3997  0 Vector sqi = new Vector();
3998  0 AlignmentI al = viewport.getAlignment();
3999  0 for (int sid = 0; sid < sequenceIds.length; sid++)
4000    {
4001  0 SequenceI sq = al.findName(sequenceIds[sid]);
4002  0 if (sq != null)
4003    {
4004  0 sqi.addElement(sq);
4005    }
4006    }
4007  0 if (sqi.size() > 0)
4008    {
4009  0 seqs = new SequenceI[sqi.size()];
4010  0 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4011    {
4012  0 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4013    }
4014    }
4015    else
4016    {
4017  0 return null;
4018    }
4019    }
4020  0 AAStructureBindingModel jmv = null;
4021    // TODO: search for a jmv that involves viewer
4022  0 if (jmv == null)
4023    { // create a new viewer/jalview binding.
4024  0 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4025    }
4026  0 return jmv;
4027   
4028    }
4029   
4030    /**
4031    * bind a pdb file to a sequence in the current view
4032    *
4033    * @param sequenceId
4034    * - sequenceId within the dataset.
4035    * @param pdbEntryString
4036    * - the short name for the PDB file
4037    * @param pdbFile
4038    * - pdb file - either a URL or a valid PDB file.
4039    * @return true if binding was as success TODO: consider making an exception
4040    * structure for indicating when PDB parsing or sequenceId location
4041    * fails.
4042    */
 
4043  0 toggle public boolean addPdbFile(String sequenceId, String pdbEntryString,
4044    String pdbFile)
4045    {
4046  0 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4047  0 boolean needtoadd = false;
4048  0 if (toaddpdb != null)
4049    {
4050  0 Vector pdbe = toaddpdb.getAllPDBEntries();
4051  0 PDBEntry pdbentry = null;
4052  0 if (pdbe != null && pdbe.size() > 0)
4053    {
4054  0 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4055    {
4056  0 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4057  0 if (!pdbentry.getId().equals(pdbEntryString)
4058    && !pdbentry.getFile().equals(pdbFile))
4059    {
4060  0 pdbentry = null;
4061    }
4062    else
4063    {
4064  0 continue;
4065    }
4066    }
4067    }
4068  0 if (pdbentry == null)
4069    {
4070  0 pdbentry = new PDBEntry();
4071  0 pdbentry.setId(pdbEntryString);
4072  0 pdbentry.setFile(pdbFile);
4073  0 needtoadd = true; // add this new entry to sequence.
4074    }
4075    // resolve data source
4076    // TODO: this code should be a refactored to an io package
4077  0 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4078    FileFormat.PDB);
4079  0 if (protocol == null)
4080    {
4081  0 return false;
4082    }
4083  0 if (needtoadd)
4084    {
4085  0 pdbentry.setProperty("protocol", protocol);
4086  0 toaddpdb.addPDBId(pdbentry);
4087  0 alignPanel.getStructureSelectionManager()
4088    .registerPDBEntry(pdbentry);
4089    }
4090    }
4091  0 return true;
4092    }
4093   
 
4094  0 toggle private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4095    {
4096  0 if (seqs != null)
4097    {
4098  0 Vector sequences = new Vector();
4099  0 for (int i = 0; i < seqs.length; i++)
4100    {
4101  0 if (seqs[i] != null)
4102    {
4103  0 sequences
4104    .addElement(new Object[]
4105  0 { seqs[i], (chains != null) ? chains[i] : null });
4106    }
4107    }
4108  0 seqs = new SequenceI[sequences.size()];
4109  0 chains = new String[sequences.size()];
4110  0 for (int i = 0, isize = sequences.size(); i < isize; i++)
4111    {
4112  0 Object[] oj = (Object[]) sequences.elementAt(i);
4113   
4114  0 seqs[i] = (SequenceI) oj[0];
4115  0 chains[i] = (String) oj[1];
4116    }
4117    }
4118  0 return new Object[] { seqs, chains };
4119   
4120    }
4121   
 
4122  0 toggle public void newStructureView(JalviewLite applet, PDBEntry pdb,
4123    SequenceI[] seqs, String[] chains, DataSourceType protocol)
4124    {
4125    // Scrub any null sequences from the array
4126  0 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4127  0 seqs = (SequenceI[]) sqch[0];
4128  0 chains = (String[]) sqch[1];
4129  0 if (seqs == null || seqs.length == 0)
4130    {
4131  0 System.err.println(
4132    "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4133    }
4134  0 if (protocol == null)
4135    {
4136  0 String sourceType = (String) pdb.getProperty("protocol");
4137  0 try
4138    {
4139  0 protocol = DataSourceType.valueOf(sourceType);
4140    } catch (IllegalArgumentException e)
4141    {
4142    // ignore
4143    }
4144  0 if (protocol == null)
4145    {
4146  0 System.err.println("Couldn't work out protocol to open structure: "
4147    + pdb.getId());
4148  0 return;
4149    }
4150    }
4151  0 if (applet.useXtrnalSviewer)
4152    {
4153    // register the association(s) and quit, don't create any windows.
4154  0 if (StructureSelectionManager.getStructureSelectionManager(applet)
4155    .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4156    {
4157  0 System.err.println("Failed to map " + pdb.getFile() + " ("
4158    + protocol + ") to any sequences");
4159    }
4160  0 return;
4161    }
4162  0 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4163    {
4164    // can only do alignments with Jmol
4165    // find the last jmol window assigned to this alignment
4166  0 AppletJmol ajm = null, tajm;
4167  0 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4168  0 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4169    {
4170  0 tajm = (AppletJmol) jmols.elementAt(i);
4171  0 if (tajm.ap.alignFrame == this)
4172    {
4173  0 ajm = tajm;
4174  0 break;
4175    }
4176    }
4177  0 if (ajm != null)
4178    {
4179  0 System.err.println(
4180    "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4181    // try and add the pdb structure
4182    // ajm.addS
4183  0 ajm = null;
4184    }
4185    }
4186    // otherwise, create a new window
4187  0 if (applet.jmolAvailable)
4188    {
4189  0 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4190  0 applet.lastFrameX += 40;
4191  0 applet.lastFrameY += 40;
4192    }
4193    else
4194    {
4195  0 new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4196    }
4197   
4198    }
4199   
 
4200  0 toggle public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4201    SequenceI[][] seqs, String[][] chains, String[] protocols)
4202    {
4203    // TODO Auto-generated method stub
4204  0 System.err.println("Aligned Structure View: Not yet implemented.");
4205    }
4206   
4207    /**
4208    * modify the current selection, providing the user has not made a selection
4209    * already.
4210    *
4211    * @param sel
4212    * - sequences from this alignment
4213    * @param csel
4214    * - columns to be selected on the alignment
4215    */
 
4216  0 toggle public void select(SequenceGroup sel, ColumnSelection csel,
4217    HiddenColumns hidden)
4218    {
4219  0 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4220    }
4221   
 
4222  0 toggle public void scrollTo(int row, int column)
4223    {
4224  0 alignPanel.seqPanel.scrollTo(row, column);
4225    }
4226   
 
4227  0 toggle public void scrollToRow(int row)
4228    {
4229  0 alignPanel.seqPanel.scrollToRow(row);
4230    }
4231   
 
4232  0 toggle public void scrollToColumn(int column)
4233    {
4234  0 alignPanel.seqPanel.scrollToColumn(column);
4235    }
4236   
4237    /**
4238    * @return the alignments unique ID.
4239    */
 
4240  0 toggle public String getSequenceSetId()
4241    {
4242  0 return viewport.getSequenceSetId();
4243    }
4244   
4245    /**
4246    * Load the (T-Coffee) score file from the specified url
4247    *
4248    * @param source
4249    * File/URL/T-COFFEE score file contents
4250    * @throws IOException
4251    * @return true if alignment was annotated with data from source
4252    */
 
4253  0 toggle public boolean loadScoreFile(String source) throws IOException
4254    {
4255   
4256  0 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4257    AppletFormatAdapter.checkProtocol(source));
4258  0 if (!file.isValid())
4259    {
4260    // TODO: raise dialog for gui
4261  0 System.err.println("Problems parsing T-Coffee scores: "
4262    + file.getWarningMessage());
4263  0 System.err.println("Origin was:\n" + source);
4264  0 return false;
4265    }
4266   
4267    /*
4268    * check that the score matrix matches the alignment dimensions
4269    */
4270  0 AlignmentI aln;
4271  0 if ((aln = viewport.getAlignment()) != null
4272    && (aln.getHeight() != file.getHeight()
4273    || aln.getWidth() != file.getWidth()))
4274    {
4275    // TODO: raise a dialog box here rather than bomb out.
4276  0 System.err.println(
4277    "The scores matrix does not match the alignment dimensions");
4278   
4279    }
4280   
4281    // TODO add parameter to indicate if matching should be done
4282  0 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4283    {
4284  0 alignPanel.fontChanged();
4285  0 tcoffeeColour.setEnabled(true);
4286    // switch to this color
4287  0 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4288  0 return true;
4289    }
4290    else
4291    {
4292  0 System.err.println("Problems resolving T-Coffee scores:");
4293  0 if (file.getWarningMessage() != null)
4294    {
4295  0 System.err.println(file.getWarningMessage());
4296    }
4297    }
4298  0 return false;
4299    }
4300   
 
4301  0 toggle public SplitFrame getSplitFrame()
4302    {
4303  0 return this.splitFrame;
4304    }
4305   
 
4306  0 toggle public void setSplitFrame(SplitFrame sf)
4307    {
4308  0 this.splitFrame = sf;
4309    }
4310   
4311    // may not need this
 
4312  0 toggle @Override
4313    public void setShowSeqFeatures(boolean b)
4314    {
4315    // showSeqFeatures.setSelected(b);
4316  0 viewport.setShowSequenceFeatures(b);
4317   
4318    }
4319   
 
4320  0 toggle @Override
4321    public void setMenusForViewport()
4322    {
4323    // setMenusFromViewport(viewport);
4324   
4325    }
4326   
 
4327  0 toggle @Override
4328    public void refreshFeatureUI(boolean enableIfNecessary)
4329    {
4330  0 if (enableIfNecessary)
4331    {
4332  0 sequenceFeatures.setState(true);
4333  0 alignPanel.av.setShowSequenceFeatures(true);
4334    }
4335    }
4336   
 
4337  0 toggle @Override
4338    public FeatureSettingsControllerI getFeatureSettingsUI()
4339    {
4340  0 return alignPanel.av.featureSettings;
4341    }
4342   
 
4343  0 toggle @Override
4344    public FeatureSettingsControllerI showFeatureSettingsUI()
4345    {
4346  0 return new FeatureSettings(alignPanel);
4347    }
4348   
4349    private Rectangle fs_bounds = null;
4350   
 
4351  0 toggle @Override
4352    public void setFeatureSettingsGeometry(Rectangle bounds)
4353    {
4354  0 fs_bounds = bounds;
4355    }
4356   
 
4357  0 toggle @Override
4358    public Rectangle getFeatureSettingsGeometry()
4359    {
4360  0 return fs_bounds;
4361    }
4362   
4363    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.