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Coverage Report

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

File AlignViewport.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
27% of files have more coverage

Code metrics

108
261
53
1
1,134
682
129
0.49
4.92
53
2.43

Classes

Class Line # Actions
AlignViewport 73 261 129
0.701421870.1%
 

Contributing tests

This file is covered by 149 tests. .

Source view

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.gui;
22   
23    import jalview.analysis.AlignmentUtils;
24    import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25    import jalview.api.AlignViewportI;
26    import jalview.api.AlignmentViewPanel;
27    import jalview.api.FeatureColourI;
28    import jalview.api.FeatureSettingsModelI;
29    import jalview.api.FeaturesDisplayedI;
30    import jalview.api.ViewStyleI;
31    import jalview.bin.Cache;
32    import jalview.commands.CommandI;
33    import jalview.datamodel.AlignedCodonFrame;
34    import jalview.datamodel.Alignment;
35    import jalview.datamodel.AlignmentI;
36    import jalview.datamodel.ColumnSelection;
37    import jalview.datamodel.HiddenColumns;
38    import jalview.datamodel.SearchResults;
39    import jalview.datamodel.SearchResultsI;
40    import jalview.datamodel.SequenceGroup;
41    import jalview.datamodel.SequenceI;
42    import jalview.renderer.ResidueShader;
43    import jalview.schemes.ColourSchemeI;
44    import jalview.schemes.ColourSchemeProperty;
45    import jalview.schemes.ResidueColourScheme;
46    import jalview.schemes.UserColourScheme;
47    import jalview.structure.SelectionSource;
48    import jalview.structure.StructureSelectionManager;
49    import jalview.structure.VamsasSource;
50    import jalview.util.ColorUtils;
51    import jalview.util.MessageManager;
52    import jalview.viewmodel.AlignmentViewport;
53    import jalview.ws.params.AutoCalcSetting;
54   
55    import java.awt.Container;
56    import java.awt.Dimension;
57    import java.awt.Font;
58    import java.awt.FontMetrics;
59    import java.awt.Rectangle;
60    import java.util.ArrayList;
61    import java.util.Hashtable;
62    import java.util.Iterator;
63    import java.util.List;
64   
65    import javax.swing.JInternalFrame;
66   
67    /**
68    * DOCUMENT ME!
69    *
70    * @author $author$
71    * @version $Revision: 1.141 $
72    */
 
73    public class AlignViewport extends AlignmentViewport
74    implements SelectionSource
75    {
76    Font font;
77   
78    boolean cursorMode = false;
79   
80    boolean antiAlias = false;
81   
82    private Rectangle explodedGeometry = null;
83   
84    private String viewName = null;
85   
86    /*
87    * Flag set true on the view that should 'gather' multiple views of the same
88    * sequence set id when a project is reloaded. Set false on all views when
89    * they are 'exploded' into separate windows. Set true on the current view
90    * when 'Gather' is performed, and also on the first tab when the first new
91    * view is created.
92    */
93    private boolean gatherViewsHere = false;
94   
95    private AnnotationColumnChooser annotationColumnSelectionState;
96   
97    /**
98    * Creates a new AlignViewport object.
99    *
100    * @param al
101    * alignment to view
102    */
 
103  35 toggle public AlignViewport(AlignmentI al)
104    {
105  35 super(al);
106  35 init();
107    }
108   
109    /**
110    * Create a new AlignViewport object with a specific sequence set ID
111    *
112    * @param al
113    * @param seqsetid
114    * (may be null - but potential for ambiguous constructor exception)
115    */
 
116  0 toggle public AlignViewport(AlignmentI al, String seqsetid)
117    {
118  0 this(al, seqsetid, null);
119    }
120   
 
121  0 toggle public AlignViewport(AlignmentI al, String seqsetid, String viewid)
122    {
123  0 super(al);
124  0 sequenceSetID = seqsetid;
125  0 viewId = viewid;
126    // TODO remove these once 2.4.VAMSAS release finished
127  0 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
128    {
129  0 Cache.log.debug(
130    "Setting viewport's sequence set id : " + sequenceSetID);
131    }
132  0 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
133    {
134  0 Cache.log.debug("Setting viewport's view id : " + viewId);
135    }
136  0 init();
137   
138    }
139   
140    /**
141    * Create a new AlignViewport with hidden regions
142    *
143    * @param al
144    * AlignmentI
145    * @param hiddenColumns
146    * ColumnSelection
147    */
 
148  25 toggle public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
149    {
150  25 super(al);
151  25 if (hiddenColumns != null)
152    {
153  25 al.setHiddenColumns(hiddenColumns);
154    }
155  25 init();
156    }
157   
158    /**
159    * New viewport with hidden columns and an existing sequence set id
160    *
161    * @param al
162    * @param hiddenColumns
163    * @param seqsetid
164    * (may be null)
165    */
 
166  0 toggle public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
167    String seqsetid)
168    {
169  0 this(al, hiddenColumns, seqsetid, null);
170    }
171   
172    /**
173    * New viewport with hidden columns and an existing sequence set id and viewid
174    *
175    * @param al
176    * @param hiddenColumns
177    * @param seqsetid
178    * (may be null)
179    * @param viewid
180    * (may be null)
181    */
 
182  234 toggle public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
183    String seqsetid, String viewid)
184    {
185  234 super(al);
186  234 sequenceSetID = seqsetid;
187  234 viewId = viewid;
188    // TODO remove these once 2.4.VAMSAS release finished
189  234 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
190    {
191  70 Cache.log.debug(
192    "Setting viewport's sequence set id : " + sequenceSetID);
193    }
194  234 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
195    {
196  64 Cache.log.debug("Setting viewport's view id : " + viewId);
197    }
198   
199  234 if (hiddenColumns != null)
200    {
201  0 al.setHiddenColumns(hiddenColumns);
202    }
203  234 init();
204    }
205   
206    /**
207    * Apply any settings saved in user preferences
208    */
 
209  294 toggle private void applyViewProperties()
210    {
211  294 antiAlias = Cache.getDefault("ANTI_ALIAS", true);
212   
213  294 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
214  294 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
215   
216  294 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
217  294 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
218  294 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
219   
220  294 setPadGaps(Cache.getDefault("PAD_GAPS", true));
221  294 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
222  294 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
223  294 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
224  294 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
225  294 viewStyle.setShowUnconserved(
226    Cache.getDefault("SHOW_UNCONSERVED", false));
227  294 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
228  294 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
229  294 sortAnnotationsBy = SequenceAnnotationOrder
230    .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
231    SequenceAnnotationOrder.NONE.name()));
232  294 showAutocalculatedAbove = Cache
233    .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
234  294 viewStyle.setScaleProteinAsCdna(
235    Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
236    }
237   
 
238  294 toggle void init()
239    {
240  294 applyViewProperties();
241   
242  294 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
243  294 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
244  294 String fontSize = Cache.getDefault("FONT_SIZE", "10");
245   
246  294 int style = 0;
247   
248  294 if (fontStyle.equals("bold"))
249    {
250  0 style = 1;
251    }
252  294 else if (fontStyle.equals("italic"))
253    {
254  0 style = 2;
255    }
256   
257  294 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
258   
259  294 alignment
260    .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
261   
262    // We must set conservation and consensus before setting colour,
263    // as Blosum and Clustal require this to be done
264  294 if (hconsensus == null && !isDataset)
265    {
266  294 if (!alignment.isNucleotide())
267    {
268  248 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
269  248 showQuality = Cache.getDefault("SHOW_QUALITY", true);
270  248 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
271    false);
272    }
273  294 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
274    true);
275  294 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
276  294 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
277    false);
278  294 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
279  294 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
280   
281  294 showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
282    }
283  294 initAutoAnnotation();
284  294 String colourProperty = alignment.isNucleotide()
285    ? Preferences.DEFAULT_COLOUR_NUC
286    : Preferences.DEFAULT_COLOUR_PROT;
287  294 String schemeName = Cache.getProperty(colourProperty);
288  294 if (schemeName == null)
289    {
290    // only DEFAULT_COLOUR available in Jalview before 2.9
291  286 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
292    ResidueColourScheme.NONE);
293    }
294  294 ColourSchemeI colourScheme = ColourSchemeProperty
295    .getColourScheme(this, alignment, schemeName);
296  294 residueShading = new ResidueShader(colourScheme);
297   
298  294 if (colourScheme instanceof UserColourScheme)
299    {
300  0 residueShading = new ResidueShader(
301    UserDefinedColours.loadDefaultColours());
302  0 residueShading.setThreshold(0, isIgnoreGapsConsensus());
303    }
304   
305  294 if (residueShading != null)
306    {
307  294 residueShading.setConsensus(hconsensus);
308    }
309  294 setColourAppliesToAllGroups(true);
310    }
311   
312    boolean validCharWidth;
313   
314    /**
315    * {@inheritDoc}
316    */
 
317  439 toggle @Override
318    public void setFont(Font f, boolean setGrid)
319    {
320  439 font = f;
321   
322  439 Container c = new Container();
323   
324  439 if (setGrid)
325    {
326  368 FontMetrics fm = c.getFontMetrics(font);
327  368 int ww = fm.charWidth('M');
328  368 setCharHeight(fm.getHeight());
329  368 setCharWidth(ww);
330    }
331  439 viewStyle.setFontName(font.getName());
332  439 viewStyle.setFontStyle(font.getStyle());
333  439 viewStyle.setFontSize(font.getSize());
334   
335  439 validCharWidth = true;
336    }
337   
 
338  71 toggle @Override
339    public void setViewStyle(ViewStyleI settingsForView)
340    {
341  71 super.setViewStyle(settingsForView);
342  71 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
343    viewStyle.getFontSize()), false);
344    }
345   
346    /**
347    * DOCUMENT ME!
348    *
349    * @return DOCUMENT ME!
350    */
 
351  8015 toggle public Font getFont()
352    {
353  8015 return font;
354    }
355   
356    /**
357    * DOCUMENT ME!
358    *
359    * @param align
360    * DOCUMENT ME!
361    */
 
362  396 toggle @Override
363    public void setAlignment(AlignmentI align)
364    {
365  396 replaceMappings(align);
366  396 super.setAlignment(align);
367    }
368   
369    /**
370    * Replace any codon mappings for this viewport with those for the given
371    * viewport
372    *
373    * @param align
374    */
 
375  402 toggle public void replaceMappings(AlignmentI align)
376    {
377   
378    /*
379    * Deregister current mappings (if any)
380    */
381  402 deregisterMappings();
382   
383    /*
384    * Register new mappings (if any)
385    */
386  402 if (align != null)
387    {
388  300 StructureSelectionManager ssm = StructureSelectionManager
389    .getStructureSelectionManager(Desktop.instance);
390  300 ssm.registerMappings(align.getCodonFrames());
391    }
392   
393    /*
394    * replace mappings on our alignment
395    */
396  402 if (alignment != null && align != null)
397    {
398  6 alignment.setCodonFrames(align.getCodonFrames());
399    }
400    }
401   
 
402  402 toggle protected void deregisterMappings()
403    {
404  402 AlignmentI al = getAlignment();
405  402 if (al != null)
406    {
407  108 List<AlignedCodonFrame> mappings = al.getCodonFrames();
408  108 if (mappings != null)
409    {
410  108 StructureSelectionManager ssm = StructureSelectionManager
411    .getStructureSelectionManager(Desktop.instance);
412  108 for (AlignedCodonFrame acf : mappings)
413    {
414  69 if (noReferencesTo(acf))
415    {
416  15 ssm.deregisterMapping(acf);
417    }
418    }
419    }
420    }
421    }
422   
423    /**
424    * DOCUMENT ME!
425    *
426    * @return DOCUMENT ME!
427    */
 
428  32 toggle @Override
429    public char getGapCharacter()
430    {
431  32 return getAlignment().getGapCharacter();
432    }
433   
434    /**
435    * DOCUMENT ME!
436    *
437    * @param gap
438    * DOCUMENT ME!
439    */
 
440  0 toggle public void setGapCharacter(char gap)
441    {
442  0 if (getAlignment() != null)
443    {
444  0 getAlignment().setGapCharacter(gap);
445    }
446    }
447   
448    /**
449    * returns the visible column regions of the alignment
450    *
451    * @param selectedRegionOnly
452    * true to just return the contigs intersecting with the selected
453    * area
454    * @return
455    */
 
456  1 toggle public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
457    {
458  1 int start = 0;
459  1 int end = 0;
460  1 if (selectedRegionOnly && selectionGroup != null)
461    {
462  0 start = selectionGroup.getStartRes();
463  0 end = selectionGroup.getEndRes() + 1;
464    }
465    else
466    {
467  1 end = alignment.getWidth();
468    }
469  1 return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
470    false));
471    }
472   
473    /**
474    * get hash of undo and redo list for the alignment
475    *
476    * @return long[] { historyList.hashCode, redoList.hashCode };
477    */
 
478  1 toggle public long[] getUndoRedoHash()
479    {
480    // TODO: JAL-1126
481  1 if (historyList == null || redoList == null)
482    {
483  0 return new long[] { -1, -1 };
484    }
485  1 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
486    }
487   
488    /**
489    * test if a particular set of hashcodes are different to the hashcodes for
490    * the undo and redo list.
491    *
492    * @param undoredo
493    * the stored set of hashcodes as returned by getUndoRedoHash
494    * @return true if the hashcodes differ (ie the alignment has been edited) or
495    * the stored hashcode array differs in size
496    */
 
497  0 toggle public boolean isUndoRedoHashModified(long[] undoredo)
498    {
499  0 if (undoredo == null)
500    {
501  0 return true;
502    }
503  0 long[] cstate = getUndoRedoHash();
504  0 if (cstate.length != undoredo.length)
505    {
506  0 return true;
507    }
508   
509  0 for (int i = 0; i < cstate.length; i++)
510    {
511  0 if (cstate[i] != undoredo[i])
512    {
513  0 return true;
514    }
515    }
516  0 return false;
517    }
518   
519    public boolean followSelection = true;
520   
521    /**
522    * @return true if view selection should always follow the selections
523    * broadcast by other selection sources
524    */
 
525  0 toggle public boolean getFollowSelection()
526    {
527  0 return followSelection;
528    }
529   
530    /**
531    * Send the current selection to be broadcast to any selection listeners.
532    */
 
533  21 toggle @Override
534    public void sendSelection()
535    {
536  21 jalview.structure.StructureSelectionManager
537    .getStructureSelectionManager(Desktop.instance)
538    .sendSelection(new SequenceGroup(getSelectionGroup()),
539    new ColumnSelection(getColumnSelection()),
540    new HiddenColumns(getAlignment().getHiddenColumns()),
541    this);
542    }
543   
544    /**
545    * return the alignPanel containing the given viewport. Use this to get the
546    * components currently handling the given viewport.
547    *
548    * @param av
549    * @return null or an alignPanel guaranteed to have non-null alignFrame
550    * reference
551    */
 
552  431 toggle public AlignmentPanel getAlignPanel()
553    {
554  431 AlignmentPanel[] aps = PaintRefresher
555    .getAssociatedPanels(this.getSequenceSetId());
556  687 for (int p = 0; aps != null && p < aps.length; p++)
557    {
558  451 if (aps[p].av == this)
559    {
560  195 return aps[p];
561    }
562    }
563  236 return null;
564    }
565   
 
566  11 toggle public boolean getSortByTree()
567    {
568  11 return sortByTree;
569    }
570   
 
571  2 toggle public void setSortByTree(boolean sort)
572    {
573  2 sortByTree = sort;
574    }
575   
576    /**
577    * Returns the (Desktop) instance of the StructureSelectionManager
578    */
 
579  1672 toggle @Override
580    public StructureSelectionManager getStructureSelectionManager()
581    {
582  1672 return StructureSelectionManager
583    .getStructureSelectionManager(Desktop.instance);
584    }
585   
 
586  1246 toggle @Override
587    public boolean isNormaliseSequenceLogo()
588    {
589  1246 return normaliseSequenceLogo;
590    }
591   
 
592  70 toggle public void setNormaliseSequenceLogo(boolean state)
593    {
594  70 normaliseSequenceLogo = state;
595    }
596   
597    /**
598    *
599    * @return true if alignment characters should be displayed
600    */
 
601  28735 toggle @Override
602    public boolean isValidCharWidth()
603    {
604  28735 return validCharWidth;
605    }
606   
607    private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
608   
 
609  3 toggle public AutoCalcSetting getCalcIdSettingsFor(String calcId)
610    {
611  3 return calcIdParams.get(calcId);
612    }
613   
 
614  0 toggle public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
615    boolean needsUpdate)
616    {
617  0 calcIdParams.put(calcId, settings);
618    // TODO: create a restart list to trigger any calculations that need to be
619    // restarted after load
620    // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
621  0 if (needsUpdate)
622    {
623  0 Cache.log.debug("trigger update for " + calcId);
624    }
625    }
626   
627    /**
628    * Method called when another alignment's edit (or possibly other) command is
629    * broadcast to here.
630    *
631    * To allow for sequence mappings (e.g. protein to cDNA), we have to first
632    * 'unwind' the command on the source sequences (in simulation, not in fact),
633    * and then for each edit in turn:
634    * <ul>
635    * <li>compute the equivalent edit on the mapped sequences</li>
636    * <li>apply the mapped edit</li>
637    * <li>'apply' the source edit to the working copy of the source
638    * sequences</li>
639    * </ul>
640    *
641    * @param command
642    * @param undo
643    * @param ssm
644    */
 
645  0 toggle @Override
646    public void mirrorCommand(CommandI command, boolean undo,
647    StructureSelectionManager ssm, VamsasSource source)
648    {
649    /*
650    * Do nothing unless we are a 'complement' of the source. May replace this
651    * with direct calls not via SSM.
652    */
653  0 if (source instanceof AlignViewportI
654    && ((AlignViewportI) source).getCodingComplement() == this)
655    {
656    // ok to continue;
657    }
658    else
659    {
660  0 return;
661    }
662   
663  0 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
664    getGapCharacter());
665  0 if (mappedCommand != null)
666    {
667  0 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
668  0 mappedCommand.doCommand(views);
669  0 getAlignPanel().alignmentChanged();
670    }
671    }
672   
673    /**
674    * Add the sequences from the given alignment to this viewport. Optionally,
675    * may give the user the option to open a new frame, or split panel, with cDNA
676    * and protein linked.
677    *
678    * @param toAdd
679    * @param title
680    */
 
681  1 toggle public void addAlignment(AlignmentI toAdd, String title)
682    {
683    // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
684   
685    // JBPComment: title is a largely redundant parameter at the moment
686    // JBPComment: this really should be an 'insert/pre/append' controller
687    // JBPComment: but the DNA/Protein check makes it a bit more complex
688   
689    // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
690    // this comment:
691    // TODO: create undo object for this JAL-1101
692   
693    /*
694    * Ensure datasets are created for the new alignment as
695    * mappings operate on dataset sequences
696    */
697  1 toAdd.setDataset(null);
698   
699    /*
700    * Check if any added sequence could be the object of a mapping or
701    * cross-reference; if so, make the mapping explicit
702    */
703  1 getAlignment().realiseMappings(toAdd.getSequences());
704   
705    /*
706    * If any cDNA/protein mappings exist or can be made between the alignments,
707    * offer to open a split frame with linked alignments
708    */
709  1 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
710    {
711  1 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
712    {
713  0 openLinkedAlignment(toAdd, title);
714  0 return;
715    }
716    }
717  1 addDataToAlignment(toAdd);
718    }
719   
720    /**
721    * adds sequences to this alignment
722    *
723    * @param toAdd
724    */
 
725  1 toggle void addDataToAlignment(AlignmentI toAdd)
726    {
727    // TODO: JAL-407 regardless of above - identical sequences (based on ID and
728    // provenance) should share the same dataset sequence
729   
730  1 AlignmentI al = getAlignment();
731  1 String gap = String.valueOf(al.getGapCharacter());
732  5 for (int i = 0; i < toAdd.getHeight(); i++)
733    {
734  4 SequenceI seq = toAdd.getSequenceAt(i);
735    /*
736    * experimental!
737    * - 'align' any mapped sequences as per existing
738    * e.g. cdna to genome, domain hit to protein sequence
739    * very experimental! (need a separate menu option for this)
740    * - only add mapped sequences ('select targets from a dataset')
741    */
742  4 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
743    {
744  4 al.addSequence(seq);
745    }
746    }
747   
748  1 ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
749  1 firePropertyChange("alignment", null, getAlignment().getSequences());
750    }
751   
752    /**
753    * Show a dialog with the option to open and link (cDNA <-> protein) as a new
754    * alignment, either as a standalone alignment or in a split frame. Returns
755    * true if the new alignment was opened, false if not, because the user
756    * declined the offer.
757    *
758    * @param al
759    * @param title
760    */
 
761  0 toggle protected void openLinkedAlignment(AlignmentI al, String title)
762    {
763  0 String[] options = new String[] { MessageManager.getString("action.no"),
764    MessageManager.getString("label.split_window"),
765    MessageManager.getString("label.new_window"), };
766  0 final String question = JvSwingUtils.wrapTooltip(true,
767    MessageManager.getString("label.open_split_window?"));
768  0 final AlignViewport us = this;
769   
770    /*
771    * options No, Split Window, New Window correspond to
772    * dialog responses 0, 1, 2 (even though JOptionPane shows them
773    * in reverse order)
774    */
775  0 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
776    .setResponseHandler(0, new Runnable()
777    {
 
778  0 toggle @Override
779    public void run()
780    {
781  0 addDataToAlignment(al);
782    }
783    }).setResponseHandler(1, new Runnable()
784    {
 
785  0 toggle @Override
786    public void run()
787    {
788  0 us.openLinkedAlignmentAs(al, title, true);
789    }
790    }).setResponseHandler(2, new Runnable()
791    {
 
792  0 toggle @Override
793    public void run()
794    {
795  0 us.openLinkedAlignmentAs(al, title, false);
796    }
797    });
798  0 dialog.showDialog(question,
799    MessageManager.getString("label.open_split_window"),
800    JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
801    options, options[0]);
802    }
803   
 
804  0 toggle protected void openLinkedAlignmentAs(AlignmentI al, String title,
805    boolean newWindowOrSplitPane)
806    {
807    /*
808    * Identify protein and dna alignments. Make a copy of this one if opening
809    * in a new split pane.
810    */
811  0 AlignmentI thisAlignment = newWindowOrSplitPane
812    ? new Alignment(getAlignment())
813    : getAlignment();
814  0 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
815  0 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
816   
817    /*
818    * Map sequences. At least one should get mapped as we have already passed
819    * the test for 'mappability'. Any mappings made will be added to the
820    * protein alignment. Note creating dataset sequences on the new alignment
821    * is a pre-requisite for building mappings.
822    */
823  0 al.setDataset(null);
824  0 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
825   
826    /*
827    * Create the AlignFrame for the added alignment. If it is protein, mappings
828    * are registered with StructureSelectionManager as a side-effect.
829    */
830  0 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
831    AlignFrame.DEFAULT_HEIGHT);
832  0 newAlignFrame.setTitle(title);
833  0 newAlignFrame.setStatus(MessageManager
834    .formatMessage("label.successfully_loaded_file", new Object[]
835    { title }));
836   
837    // TODO if we want this (e.g. to enable reload of the alignment from file),
838    // we will need to add parameters to the stack.
839    // if (!protocol.equals(DataSourceType.PASTE))
840    // {
841    // alignFrame.setFileName(file, format);
842    // }
843   
844  0 if (!newWindowOrSplitPane)
845    {
846  0 Desktop.addInternalFrame(newAlignFrame, title,
847    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
848    }
849   
850  0 try
851    {
852  0 newAlignFrame.setMaximum(
853    jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
854    } catch (java.beans.PropertyVetoException ex)
855    {
856    }
857   
858  0 if (newWindowOrSplitPane)
859    {
860  0 al.alignAs(thisAlignment);
861  0 protein = openSplitFrame(newAlignFrame, thisAlignment);
862    }
863    }
864   
865    /**
866    * Helper method to open a new SplitFrame holding linked dna and protein
867    * alignments.
868    *
869    * @param newAlignFrame
870    * containing a new alignment to be shown
871    * @param complement
872    * cdna/protein complement alignment to show in the other split half
873    * @return the protein alignment in the split frame
874    */
 
875  1 toggle protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
876    AlignmentI complement)
877    {
878    /*
879    * Make a new frame with a copy of the alignment we are adding to. If this
880    * is protein, the mappings to cDNA will be registered with
881    * StructureSelectionManager as a side-effect.
882    */
883  1 AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
884    AlignFrame.DEFAULT_HEIGHT);
885  1 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
886   
887  1 AlignmentI al = newAlignFrame.viewport.getAlignment();
888  1 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
889    : newAlignFrame;
890  1 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
891  1 cdnaFrame.setVisible(true);
892  1 proteinFrame.setVisible(true);
893  1 String linkedTitle = MessageManager
894    .getString("label.linked_view_title");
895   
896    /*
897    * Open in split pane. DNA sequence above, protein below.
898    */
899  1 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
900  1 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
901   
902  1 return proteinFrame.viewport.getAlignment();
903    }
904   
 
905  7 toggle public AnnotationColumnChooser getAnnotationColumnSelectionState()
906    {
907  7 return annotationColumnSelectionState;
908    }
909   
 
910  1 toggle public void setAnnotationColumnSelectionState(
911    AnnotationColumnChooser currentAnnotationColumnSelectionState)
912    {
913  1 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
914    }
915   
 
916  247 toggle @Override
917    public void setIdWidth(int i)
918    {
919  247 super.setIdWidth(i);
920  247 AlignmentPanel ap = getAlignPanel();
921  247 if (ap != null)
922    {
923    // modify GUI elements to reflect geometry change
924  11 Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
925  11 idw.width = i;
926  11 ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
927    }
928    }
929   
 
930  34 toggle public Rectangle getExplodedGeometry()
931    {
932  34 return explodedGeometry;
933    }
934   
 
935  49 toggle public void setExplodedGeometry(Rectangle explodedPosition)
936    {
937  49 this.explodedGeometry = explodedPosition;
938    }
939   
 
940  93 toggle public boolean isGatherViewsHere()
941    {
942  93 return gatherViewsHere;
943    }
944   
 
945  135 toggle public void setGatherViewsHere(boolean gatherViewsHere)
946    {
947  135 this.gatherViewsHere = gatherViewsHere;
948    }
949   
950    /**
951    * If this viewport has a (Protein/cDNA) complement, then scroll the
952    * complementary alignment to match this one.
953    */
 
954  402 toggle public void scrollComplementaryAlignment()
955    {
956    /*
957    * Populate a SearchResults object with the mapped location to scroll to. If
958    * there is no complement, or it is not following highlights, or no mapping
959    * is found, the result will be empty.
960    */
961  402 SearchResultsI sr = new SearchResults();
962  402 int verticalOffset = findComplementScrollTarget(sr);
963  402 if (!sr.isEmpty())
964    {
965    // TODO would like next line without cast but needs more refactoring...
966  4 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
967    .getAlignPanel();
968  4 complementPanel.setToScrollComplementPanel(false);
969  4 complementPanel.scrollToCentre(sr, verticalOffset);
970  4 complementPanel.setToScrollComplementPanel(true);
971    }
972    }
973   
974    /**
975    * Answers true if no alignment holds a reference to the given mapping
976    *
977    * @param acf
978    * @return
979    */
 
980  69 toggle protected boolean noReferencesTo(AlignedCodonFrame acf)
981    {
982  69 AlignFrame[] frames = Desktop.getAlignFrames();
983  69 if (frames == null)
984    {
985  12 return true;
986    }
987  57 for (AlignFrame af : frames)
988    {
989  64 if (!af.isClosed())
990    {
991  64 for (AlignmentViewPanel ap : af.getAlignPanels())
992    {
993  64 AlignmentI al = ap.getAlignment();
994  64 if (al != null && al.getCodonFrames().contains(acf))
995    {
996  54 return false;
997    }
998    }
999    }
1000    }
1001  3 return true;
1002    }
1003   
1004    /**
1005    * Applies the supplied feature settings descriptor to currently known
1006    * features. This supports an 'initial configuration' of feature colouring
1007    * based on a preset or user favourite. This may then be modified in the usual
1008    * way using the Feature Settings dialogue.
1009    *
1010    * @param featureSettings
1011    */
 
1012  17 toggle @Override
1013    public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1014    {
1015  17 transferFeaturesStyles(featureSettings, false);
1016    }
1017   
1018    /**
1019    * Applies the supplied feature settings descriptor to currently known features.
1020    * This supports an 'initial configuration' of feature colouring based on a
1021    * preset or user favourite. This may then be modified in the usual way using
1022    * the Feature Settings dialogue.
1023    *
1024    * @param featureSettings
1025    */
 
1026  2 toggle @Override
1027    public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
1028    {
1029  2 transferFeaturesStyles(featureSettings, true);
1030    }
1031   
1032    /**
1033    * when mergeOnly is set, then group and feature visibility or feature colours
1034    * are not modified for features and groups already known to the feature
1035    * renderer. Feature ordering is always adjusted, and transparency is always set
1036    * regardless.
1037    *
1038    * @param featureSettings
1039    * @param mergeOnly
1040    */
 
1041  19 toggle private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
1042    boolean mergeOnly)
1043    {
1044  19 if (featureSettings == null)
1045    {
1046  0 return;
1047    }
1048   
1049  19 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1050    .getFeatureRenderer();
1051  19 List<String> origRenderOrder = new ArrayList(),
1052    origGroups = new ArrayList();
1053    // preserve original render order - allows differentiation between user configured colours and autogenerated ones
1054  19 origRenderOrder.addAll(fr.getRenderOrder());
1055  19 origGroups.addAll(fr.getFeatureGroups());
1056   
1057  19 fr.findAllFeatures(true);
1058  19 List<String> renderOrder = fr.getRenderOrder();
1059  19 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1060  19 if (!mergeOnly)
1061    {
1062    // only clear displayed features if we are mergeing
1063  17 displayed.clear();
1064    }
1065    // TODO this clears displayed.featuresRegistered - do we care?
1066    //
1067    // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
1068    // feature visibility has already been configured is not very friendly
1069    /*
1070    * set feature colour if specified by feature settings
1071    * set visibility of all features
1072    */
1073  19 for (String type : renderOrder)
1074    {
1075  33 FeatureColourI preferredColour = featureSettings
1076    .getFeatureColour(type);
1077  33 FeatureColourI origColour = fr.getFeatureStyle(type);
1078  33 if (!mergeOnly || (!origRenderOrder.contains(type)
1079    || origColour == null
1080    || (!origColour.isGraduatedColour()
1081    && origColour.getColour() != null
1082    && origColour.getColour().equals(
1083    ColorUtils.createColourFromName(type)))))
1084    {
1085    // if we are merging, only update if there wasn't already a colour defined for
1086    // this type
1087  29 if (preferredColour != null)
1088    {
1089  12 fr.setColour(type, preferredColour);
1090    }
1091  29 if (featureSettings.isFeatureDisplayed(type))
1092    {
1093  25 displayed.setVisible(type);
1094    }
1095    }
1096    }
1097   
1098    /*
1099    * set visibility of feature groups
1100    */
1101  19 for (String group : fr.getFeatureGroups())
1102    {
1103  37 if (!mergeOnly || !origGroups.contains(group))
1104    {
1105    // when merging, display groups only if the aren't already marked as not visible
1106  29 fr.setGroupVisibility(group,
1107    featureSettings.isGroupDisplayed(group));
1108    }
1109    }
1110   
1111    /*
1112    * order the features
1113    */
1114  19 if (featureSettings.optimiseOrder())
1115    {
1116    // TODO not supported (yet?)
1117    }
1118    else
1119    {
1120  19 fr.orderFeatures(featureSettings);
1121    }
1122  19 fr.setTransparency(featureSettings.getTransparency());
1123    }
1124   
 
1125  1521 toggle public String getViewName()
1126    {
1127  1521 return viewName;
1128    }
1129   
 
1130  66 toggle public void setViewName(String viewName)
1131    {
1132  66 this.viewName = viewName;
1133    }
1134    }
  • 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.