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  1. Project Clover database Tue Nov 4 2025 11:21:43 GMT
  2. Package jalview.gui

File AlignViewport.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
30% of files have more coverage

Code metrics

112
274
52
1
1,167
706
123
0.45
5.27
52
2.37

Classes

Class Line # Actions
AlignViewport 82 274 123
0.680365368%
 

Contributing tests

This file is covered by 255 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 java.awt.Container;
24    import java.awt.Dimension;
25    import java.awt.Font;
26    import java.awt.FontMetrics;
27    import java.awt.Rectangle;
28    import java.io.File;
29    import java.util.ArrayList;
30    import java.util.Hashtable;
31    import java.util.List;
32   
33    import javax.swing.JInternalFrame;
34   
35    import jalview.analysis.AlignmentUtils;
36    import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
37    import jalview.api.AlignViewportI;
38    import jalview.api.AlignmentViewPanel;
39    import jalview.api.FeatureColourI;
40    import jalview.api.FeatureSettingsModelI;
41    import jalview.api.FeaturesDisplayedI;
42    import jalview.api.ViewStyleI;
43    import jalview.bin.Cache;
44    import jalview.bin.Console;
45    import jalview.commands.CommandI;
46    import jalview.datamodel.AlignedCodonFrame;
47    import jalview.datamodel.Alignment;
48    import jalview.datamodel.AlignmentI;
49    import jalview.datamodel.ColumnSelection;
50    import jalview.datamodel.ContactMatrixI;
51    import jalview.datamodel.HiddenColumns;
52    import jalview.datamodel.SearchResults;
53    import jalview.datamodel.SearchResultsI;
54    import jalview.datamodel.SequenceGroup;
55    import jalview.datamodel.SequenceI;
56    import jalview.io.AppletFormatAdapter;
57    import jalview.io.DataSourceType;
58    import jalview.io.FileFormatException;
59    import jalview.io.FileFormatI;
60    import jalview.io.FileFormats;
61    import jalview.io.FileLoader;
62    import jalview.io.IdentifyFile;
63    import jalview.renderer.ResidueShader;
64    import jalview.schemes.ColourSchemeI;
65    import jalview.schemes.ColourSchemeProperty;
66    import jalview.schemes.ResidueColourScheme;
67    import jalview.schemes.UserColourScheme;
68    import jalview.structure.SelectionSource;
69    import jalview.structure.StructureSelectionManager;
70    import jalview.structure.VamsasSource;
71    import jalview.util.ColorUtils;
72    import jalview.util.MessageManager;
73    import jalview.viewmodel.AlignmentViewport;
74    import jalview.ws.params.AutoCalcSetting;
75   
76    /**
77    * DOCUMENT ME!
78    *
79    * @author $author$
80    * @version $Revision: 1.141 $
81    */
 
82    public class AlignViewport extends AlignmentViewport
83    implements SelectionSource
84    {
85    Font font;
86   
87    boolean cursorMode = false;
88   
89    boolean antiAlias = false;
90   
91    private Rectangle explodedGeometry = null;
92   
93    private String viewName = null;
94   
95    /*
96    * Flag set true on the view that should 'gather' multiple views of the same
97    * sequence set id when a project is reloaded. Set false on all views when
98    * they are 'exploded' into separate windows. Set true on the current view
99    * when 'Gather' is performed, and also on the first tab when the first new
100    * view is created.
101    */
102    private boolean gatherViewsHere = false;
103   
104    private AnnotationColumnChooser annotationColumnSelectionState;
105   
106    /**
107    * Creates a new AlignViewport object.
108    *
109    * @param al
110    * alignment to view
111    */
 
112  38 toggle public AlignViewport(AlignmentI al)
113    {
114  38 super(al);
115  38 init();
116    }
117   
118    /**
119    * Create a new AlignViewport object with a specific sequence set ID
120    *
121    * @param al
122    * @param seqsetid
123    * (may be null - but potential for ambiguous constructor exception)
124    */
 
125  0 toggle public AlignViewport(AlignmentI al, String seqsetid)
126    {
127  0 this(al, seqsetid, null);
128    }
129   
 
130  0 toggle public AlignViewport(AlignmentI al, String seqsetid, String viewid)
131    {
132  0 super(al);
133  0 sequenceSetID = seqsetid;
134  0 viewId = viewid;
135    // TODO remove these once 2.4.VAMSAS release finished
136  0 if (seqsetid != null)
137    {
138  0 Console.debug(
139    "Setting viewport's sequence set id : " + sequenceSetID);
140    }
141  0 if (viewId != null)
142    {
143  0 Console.debug("Setting viewport's view id : " + viewId);
144    }
145  0 init();
146   
147    }
148   
149    /**
150    * Create a new AlignViewport with hidden regions
151    *
152    * @param al
153    * AlignmentI
154    * @param hiddenColumns
155    * ColumnSelection
156    */
 
157  28 toggle public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
158    {
159  28 super(al);
160  28 if (hiddenColumns != null)
161    {
162  28 al.setHiddenColumns(hiddenColumns);
163    }
164  28 init();
165    }
166   
167    /**
168    * New viewport with hidden columns and an existing sequence set id
169    *
170    * @param al
171    * @param hiddenColumns
172    * @param seqsetid
173    * (may be null)
174    */
 
175  0 toggle public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
176    String seqsetid)
177    {
178  0 this(al, hiddenColumns, seqsetid, null);
179    }
180   
181    /**
182    * New viewport with hidden columns and an existing sequence set id and viewid
183    *
184    * @param al
185    * @param hiddenColumns
186    * @param seqsetid
187    * (may be null)
188    * @param viewid
189    * (may be null)
190    */
 
191  469 toggle public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
192    String seqsetid, String viewid)
193    {
194  469 super(al);
195  469 sequenceSetID = seqsetid;
196  469 viewId = viewid;
197    // TODO remove these once 2.4.VAMSAS release finished
198  469 if (seqsetid != null)
199    {
200  89 Console.debug(
201    "Setting viewport's sequence set id : " + sequenceSetID);
202    }
203  469 if (viewId != null)
204    {
205  79 Console.debug("Setting viewport's view id : " + viewId);
206    }
207   
208  469 if (hiddenColumns != null)
209    {
210  0 al.setHiddenColumns(hiddenColumns);
211    }
212  469 init();
213    }
214   
215    /**
216    * Apply any settings saved in user preferences
217    */
 
218  535 toggle private void applyViewProperties()
219    {
220  535 antiAlias = Cache.getDefault("ANTI_ALIAS", true);
221   
222  535 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
223  535 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
224   
225  535 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
226  535 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
227  535 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
228   
229  535 setPadGaps(Cache.getDefault("PAD_GAPS", true));
230  535 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
231  535 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
232  535 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
233  535 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
234  535 viewStyle.setShowUnconserved(
235    Cache.getDefault("SHOW_UNCONSERVED", false));
236  535 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
237  535 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
238  535 sortAnnotationsBy = SequenceAnnotationOrder
239    .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
240    SequenceAnnotationOrder.NONE.name()));
241  535 showAutocalculatedAbove = Cache
242    .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
243  535 viewStyle.setScaleProteinAsCdna(
244    Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
245  535 viewStyle.setShowStructureProvider(
246    Cache.getDefault(Preferences.SHOW_STRUC_PROVIDER, false));
247    }
248   
 
249  535 toggle void init()
250    {
251  535 applyViewProperties();
252   
253  535 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
254  535 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
255  535 String fontSize = Cache.getDefault("FONT_SIZE", "10");
256   
257  535 int style = 0;
258   
259  535 if (fontStyle.equals("bold"))
260    {
261  0 style = 1;
262    }
263  535 else if (fontStyle.equals("italic"))
264    {
265  0 style = 2;
266    }
267   
268  535 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
269   
270  535 alignment
271    .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
272   
273    // We must set conservation and consensus before setting colour,
274    // as Blosum and Clustal require this to be done
275  535 if (hconsensus == null && !isDataset)
276    {
277  535 if (!alignment.isNucleotide())
278    {
279  424 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
280  424 showQuality = Cache.getDefault("SHOW_QUALITY", true);
281  424 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
282    false);
283    }
284  535 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
285    true);
286  535 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", true);
287  535 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
288    false);
289  535 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
290  535 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
291   
292  535 showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false);
293   
294  535 showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
295    }
296  535 initAutoAnnotation();
297  535 String colourProperty = alignment.isNucleotide()
298    ? Preferences.DEFAULT_COLOUR_NUC
299    : Preferences.DEFAULT_COLOUR_PROT;
300  535 String schemeName = Cache.getProperty(colourProperty);
301  535 if (schemeName == null)
302    {
303    // only DEFAULT_COLOUR available in Jalview before 2.9
304  524 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
305    ResidueColourScheme.NONE);
306    }
307  535 ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
308    alignment, schemeName);
309  535 residueShading = new ResidueShader(colourScheme);
310   
311  535 if (colourScheme instanceof UserColourScheme)
312    {
313  0 residueShading = new ResidueShader(
314    UserDefinedColours.loadDefaultColours());
315  0 residueShading.setThreshold(0, isIgnoreGapsConsensus());
316    }
317   
318  535 if (residueShading != null)
319    {
320  535 residueShading.setConsensus(hconsensus);
321  535 residueShading.setSSConsensusProfileMap(hSSConsensusProfileMap);
322    }
323  535 setColourAppliesToAllGroups(true);
324    }
325   
326    boolean validCharWidth;
327   
328    /**
329    * {@inheritDoc}
330    */
 
331  717 toggle @Override
332    public void setFont(Font f, boolean setGrid)
333    {
334  717 font = f;
335   
336  717 Container c = new Container();
337   
338  717 if (setGrid)
339    {
340  581 FontMetrics fm = c.getFontMetrics(font);
341  581 int ww = fm.charWidth('M');
342  581 setCharHeight(fm.getHeight());
343  581 setCharWidth(ww);
344    }
345  717 viewStyle.setFontName(font.getName());
346  717 viewStyle.setFontStyle(font.getStyle());
347  717 viewStyle.setFontSize(font.getSize());
348   
349  717 validCharWidth = true;
350    }
351   
 
352  90 toggle @Override
353    public void setViewStyle(ViewStyleI settingsForView)
354    {
355  90 super.setViewStyle(settingsForView);
356  90 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
357    viewStyle.getFontSize()), false);
358    }
359   
360    /**
361    * DOCUMENT ME!
362    *
363    * @return DOCUMENT ME!
364    */
 
365  29372 toggle public Font getFont()
366    {
367  29372 return font;
368    }
369   
370    /**
371    * DOCUMENT ME!
372    *
373    * @param align
374    * DOCUMENT ME!
375    */
 
376  804 toggle @Override
377    public void setAlignment(AlignmentI align)
378    {
379  804 replaceMappings(align);
380  804 super.setAlignment(align);
381    }
382   
383    /**
384    * Replace any codon mappings for this viewport with those for the given
385    * viewport
386    *
387    * @param align
388    */
 
389  814 toggle public void replaceMappings(AlignmentI align)
390    {
391   
392    /*
393    * Deregister current mappings (if any)
394    */
395  814 deregisterMappings();
396   
397    /*
398    * Register new mappings (if any)
399    */
400  814 if (align != null)
401    {
402  545 StructureSelectionManager ssm = StructureSelectionManager
403    .getStructureSelectionManager(Desktop.instance);
404  545 ssm.registerMappings(align.getCodonFrames());
405    }
406   
407    /*
408    * replace mappings on our alignment
409    */
410  814 if (alignment != null && align != null)
411    {
412  10 alignment.setCodonFrames(align.getCodonFrames());
413    }
414    }
415   
 
416  814 toggle protected void deregisterMappings()
417    {
418  814 AlignmentI al = getAlignment();
419  814 if (al != null)
420    {
421  279 List<AlignedCodonFrame> mappings = al.getCodonFrames();
422  279 if (mappings != null)
423    {
424  279 StructureSelectionManager ssm = StructureSelectionManager
425    .getStructureSelectionManager(Desktop.instance);
426  279 for (AlignedCodonFrame acf : mappings)
427    {
428  125 if (noReferencesTo(acf))
429    {
430  27 ssm.deregisterMapping(acf);
431    }
432    }
433    }
434    }
435    }
436   
437    /**
438    * DOCUMENT ME!
439    *
440    * @return DOCUMENT ME!
441    */
 
442  32 toggle @Override
443    public char getGapCharacter()
444    {
445  32 return getAlignment().getGapCharacter();
446    }
447   
448    /**
449    * DOCUMENT ME!
450    *
451    * @param gap
452    * DOCUMENT ME!
453    */
 
454  0 toggle public void setGapCharacter(char gap)
455    {
456  0 if (getAlignment() != null)
457    {
458  0 getAlignment().setGapCharacter(gap);
459    }
460    }
461   
462    /**
463    * get hash of undo and redo list for the alignment
464    *
465    * @return long[] { historyList.hashCode, redoList.hashCode };
466    */
 
467  1 toggle public long[] getUndoRedoHash()
468    {
469    // TODO: JAL-1126
470  1 if (historyList == null || redoList == null)
471    {
472  0 return new long[] { -1, -1 };
473    }
474  1 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
475    }
476   
477    /**
478    * test if a particular set of hashcodes are different to the hashcodes for
479    * the undo and redo list.
480    *
481    * @param undoredo
482    * the stored set of hashcodes as returned by getUndoRedoHash
483    * @return true if the hashcodes differ (ie the alignment has been edited) or
484    * the stored hashcode array differs in size
485    */
 
486  0 toggle public boolean isUndoRedoHashModified(long[] undoredo)
487    {
488  0 if (undoredo == null)
489    {
490  0 return true;
491    }
492  0 long[] cstate = getUndoRedoHash();
493  0 if (cstate.length != undoredo.length)
494    {
495  0 return true;
496    }
497   
498  0 for (int i = 0; i < cstate.length; i++)
499    {
500  0 if (cstate[i] != undoredo[i])
501    {
502  0 return true;
503    }
504    }
505  0 return false;
506    }
507   
508    public boolean followSelection = true;
509   
510    /**
511    * @return true if view selection should always follow the selections
512    * broadcast by other selection sources
513    */
 
514  0 toggle public boolean getFollowSelection()
515    {
516  0 return followSelection;
517    }
518   
519    /**
520    * Send the current selection to be broadcast to any selection listeners.
521    */
 
522  23 toggle @Override
523    public void sendSelection()
524    {
525  23 jalview.structure.StructureSelectionManager
526    .getStructureSelectionManager(Desktop.instance)
527    .sendSelection(new SequenceGroup(getSelectionGroup()),
528    new ColumnSelection(getColumnSelection()),
529    new HiddenColumns(getAlignment().getHiddenColumns()),
530    this);
531    }
532   
533    /**
534    * return the alignPanel containing the given viewport. Use this to get the
535    * components currently handling the given viewport.
536    *
537    * @param av
538    * @return null or an alignPanel guaranteed to have non-null alignFrame
539    * reference
540    */
 
541  1119 toggle public AlignmentPanel getAlignPanel()
542    {
543  1119 AlignmentPanel[] aps = PaintRefresher
544    .getAssociatedPanels(this.getSequenceSetId());
545  1584 for (int p = 0; aps != null && p < aps.length; p++)
546    {
547  1110 if (aps[p].av == this)
548    {
549  645 return aps[p];
550    }
551    }
552  474 return null;
553    }
554   
 
555  20 toggle public boolean getSortByTree()
556    {
557  20 return sortByTree;
558    }
559   
 
560  3 toggle public void setSortByTree(boolean sort)
561    {
562  3 sortByTree = sort;
563    }
564   
565    /**
566    * Returns the (Desktop) instance of the StructureSelectionManager
567    */
 
568  6316 toggle @Override
569    public StructureSelectionManager getStructureSelectionManager()
570    {
571  6316 return StructureSelectionManager
572    .getStructureSelectionManager(Desktop.instance);
573    }
574   
 
575  3308 toggle @Override
576    public boolean isNormaliseSequenceLogo()
577    {
578  3308 return normaliseSequenceLogo;
579    }
580   
 
581  89 toggle public void setNormaliseSequenceLogo(boolean state)
582    {
583  89 normaliseSequenceLogo = state;
584    }
585   
586    /**
587    *
588    * @return true if alignment characters should be displayed
589    */
 
590  29912 toggle @Override
591    public boolean isValidCharWidth()
592    {
593  29912 return validCharWidth;
594    }
595   
596    private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
597   
 
598  15 toggle public AutoCalcSetting getCalcIdSettingsFor(String calcId)
599    {
600  15 return calcIdParams.get(calcId);
601    }
602   
 
603  0 toggle public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
604    boolean needsUpdate)
605    {
606  0 calcIdParams.put(calcId, settings);
607    // TODO: create a restart list to trigger any calculations that need to be
608    // restarted after load
609    // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
610  0 if (needsUpdate)
611    {
612  0 Console.debug("trigger update for " + calcId);
613    }
614    }
615   
616    /**
617    * Method called when another alignment's edit (or possibly other) command is
618    * broadcast to here.
619    *
620    * To allow for sequence mappings (e.g. protein to cDNA), we have to first
621    * 'unwind' the command on the source sequences (in simulation, not in fact),
622    * and then for each edit in turn:
623    * <ul>
624    * <li>compute the equivalent edit on the mapped sequences</li>
625    * <li>apply the mapped edit</li>
626    * <li>'apply' the source edit to the working copy of the source
627    * sequences</li>
628    * </ul>
629    *
630    * @param command
631    * @param undo
632    * @param ssm
633    */
 
634  0 toggle @Override
635    public void mirrorCommand(CommandI command, boolean undo,
636    StructureSelectionManager ssm, VamsasSource source)
637    {
638    /*
639    * Do nothing unless we are a 'complement' of the source. May replace this
640    * with direct calls not via SSM.
641    */
642  0 if (source instanceof AlignViewportI
643    && ((AlignViewportI) source).getCodingComplement() == this)
644    {
645    // ok to continue;
646    }
647    else
648    {
649  0 return;
650    }
651   
652  0 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
653    getGapCharacter());
654  0 if (mappedCommand != null)
655    {
656  0 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
657  0 mappedCommand.doCommand(views);
658  0 getAlignPanel().alignmentChanged();
659    }
660    }
661   
662    /**
663    * Add the sequences from the given alignment to this viewport. Optionally,
664    * may give the user the option to open a new frame, or split panel, with cDNA
665    * and protein linked.
666    *
667    * @param toAdd
668    * @param title
669    */
 
670  21 toggle public void addAlignment(AlignmentI toAdd, String title)
671    {
672    // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
673   
674    // JBPComment: title is a largely redundant parameter at the moment
675    // JBPComment: this really should be an 'insert/pre/append' controller
676    // JBPComment: but the DNA/Protein check makes it a bit more complex
677   
678    // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
679    // this comment:
680    // TODO: create undo object for this JAL-1101
681   
682    /*
683    * Ensure datasets are created for the new alignment as
684    * mappings operate on dataset sequences
685    */
686  21 toAdd.setDataset(null);
687   
688    /*
689    * Check if any added sequence could be the object of a mapping or
690    * cross-reference; if so, make the mapping explicit
691    */
692  21 getAlignment().realiseMappings(toAdd.getSequences());
693   
694    /*
695    * If any cDNA/protein mappings exist or can be made between the alignments,
696    * offer to open a split frame with linked alignments
697    */
698  21 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
699    {
700  21 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
701    {
702  0 openLinkedAlignment(toAdd, title);
703  0 return;
704    }
705    }
706  21 addDataToAlignment(toAdd);
707    }
708   
709    /**
710    * adds sequences to this alignment
711    *
712    * @param toAdd
713    */
 
714  21 toggle void addDataToAlignment(AlignmentI toAdd)
715    {
716    // TODO: JAL-407 regardless of above - identical sequences (based on ID and
717    // provenance) should share the same dataset sequence
718   
719  21 AlignmentI al = getAlignment();
720  21 String gap = String.valueOf(al.getGapCharacter());
721  79 for (int i = 0; i < toAdd.getHeight(); i++)
722    {
723  58 SequenceI seq = toAdd.getSequenceAt(i);
724    /*
725    * experimental!
726    * - 'align' any mapped sequences as per existing
727    * e.g. cdna to genome, domain hit to protein sequence
728    * very experimental! (need a separate menu option for this)
729    * - only add mapped sequences ('select targets from a dataset')
730    */
731  58 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
732    {
733  58 al.addSequence(seq);
734    }
735    }
736  21 for (ContactMatrixI cm : toAdd.getContactMaps())
737    {
738  0 al.addContactList(cm);
739    }
740  21 ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
741  21 firePropertyChange("alignment", null, getAlignment().getSequences());
742    }
743   
744    /**
745    * Load a File into this AlignViewport attempting to detect format if not
746    * given or given as null.
747    *
748    * @param file
749    * @param format
750    */
 
751  0 toggle public void addFile(File file, FileFormatI format)
752    {
753  0 addFile(file, format, true);
754    }
755   
 
756  0 toggle public void addFile(File file, FileFormatI format, boolean async)
757    {
758  0 DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
759   
760  0 if (format == null)
761    {
762  0 try
763    {
764  0 format = new IdentifyFile().identify(file, protocol);
765    } catch (FileFormatException e1)
766    {
767  0 jalview.bin.Console.error("Unknown file format for '" + file + "'");
768    }
769    }
770  0 else if (FileFormats.getInstance().isIdentifiable(format))
771    {
772  0 try
773    {
774  0 format = new IdentifyFile().identify(file, protocol);
775    } catch (FileFormatException e)
776    {
777  0 jalview.bin.Console.error("Unknown file format for '" + file + "'",
778    e);
779    }
780    }
781   
782  0 new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
783    async);
784    }
785   
 
786  0 toggle public void addFile(File file)
787    {
788  0 addFile(file, null);
789    }
790   
791    /**
792    * Show a dialog with the option to open and link (cDNA <-> protein) as a new
793    * alignment, either as a standalone alignment or in a split frame. Returns
794    * true if the new alignment was opened, false if not, because the user
795    * declined the offer.
796    *
797    * @param al
798    * @param title
799    */
 
800  0 toggle protected void openLinkedAlignment(AlignmentI al, String title)
801    {
802  0 String[] options = new String[] { MessageManager.getString("action.no"),
803    MessageManager.getString("label.split_window"),
804    MessageManager.getString("label.new_window"), };
805  0 final String question = JvSwingUtils.wrapTooltip(true,
806    MessageManager.getString("label.open_split_window?"));
807  0 final AlignViewport us = this;
808   
809    /*
810    * options No, Split Window, New Window correspond to
811    * dialog responses 0, 1, 2 (even though JOptionPane shows them
812    * in reverse order)
813    */
814  0 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
815    .setResponseHandler(0, () -> {
816  0 addDataToAlignment(al);
817    }).setResponseHandler(1, () -> {
818  0 us.openLinkedAlignmentAs(al, title, true);
819    }).setResponseHandler(2, () -> {
820  0 us.openLinkedAlignmentAs(al, title, false);
821    });
822  0 dialog.showDialog(question,
823    MessageManager.getString("label.open_split_window"),
824    JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
825    options, options[0]);
826    }
827   
 
828  0 toggle protected void openLinkedAlignmentAs(AlignmentI al, String title,
829    boolean newWindowOrSplitPane)
830    {
831    /*
832    * Identify protein and dna alignments. Make a copy of this one if opening
833    * in a new split pane.
834    */
835  0 AlignmentI thisAlignment = newWindowOrSplitPane
836    ? new Alignment(getAlignment())
837    : getAlignment();
838  0 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
839  0 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
840   
841    /*
842    * Map sequences. At least one should get mapped as we have already passed
843    * the test for 'mappability'. Any mappings made will be added to the
844    * protein alignment. Note creating dataset sequences on the new alignment
845    * is a pre-requisite for building mappings.
846    */
847  0 al.setDataset(null);
848  0 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
849   
850    /*
851    * Create the AlignFrame for the added alignment. If it is protein, mappings
852    * are registered with StructureSelectionManager as a side-effect.
853    */
854  0 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
855    AlignFrame.DEFAULT_HEIGHT);
856  0 newAlignFrame.setTitle(title);
857  0 newAlignFrame.setStatus(MessageManager
858    .formatMessage("label.successfully_loaded_file", new Object[]
859    { title }));
860   
861    // TODO if we want this (e.g. to enable reload of the alignment from file),
862    // we will need to add parameters to the stack.
863    // if (!protocol.equals(DataSourceType.PASTE))
864    // {
865    // alignFrame.setFileName(file, format);
866    // }
867   
868  0 if (!newWindowOrSplitPane)
869    {
870  0 Desktop.addInternalFrame(newAlignFrame, title,
871    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
872    }
873   
874  0 try
875    {
876  0 newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
877    } catch (java.beans.PropertyVetoException ex)
878    {
879    }
880   
881  0 if (newWindowOrSplitPane)
882    {
883  0 al.alignAs(thisAlignment);
884  0 protein = openSplitFrame(newAlignFrame, thisAlignment);
885    }
886    }
887   
888    /**
889    * Helper method to open a new SplitFrame holding linked dna and protein
890    * alignments.
891    *
892    * @param newAlignFrame
893    * containing a new alignment to be shown
894    * @param complement
895    * cdna/protein complement alignment to show in the other split half
896    * @return the protein alignment in the split frame
897    */
 
898  1 toggle protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
899    AlignmentI complement)
900    {
901    /*
902    * Make a new frame with a copy of the alignment we are adding to. If this
903    * is protein, the mappings to cDNA will be registered with
904    * StructureSelectionManager as a side-effect.
905    */
906  1 AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
907    AlignFrame.DEFAULT_HEIGHT);
908  1 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
909   
910  1 AlignmentI al = newAlignFrame.viewport.getAlignment();
911  1 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
912    : newAlignFrame;
913  1 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
914  1 cdnaFrame.setVisible(true);
915  1 proteinFrame.setVisible(true);
916  1 String linkedTitle = MessageManager
917    .getString("label.linked_view_title");
918   
919    /*
920    * Open in split pane. DNA sequence above, protein below.
921    */
922  1 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
923  1 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
924   
925  1 return proteinFrame.viewport.getAlignment();
926    }
927   
 
928  7 toggle public AnnotationColumnChooser getAnnotationColumnSelectionState()
929    {
930  7 return annotationColumnSelectionState;
931    }
932   
 
933  1 toggle public void setAnnotationColumnSelectionState(
934    AnnotationColumnChooser currentAnnotationColumnSelectionState)
935    {
936  1 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
937    }
938   
 
939  697 toggle @Override
940    public void setIdWidth(int i)
941    {
942  697 super.setIdWidth(i);
943  697 AlignmentPanel ap = getAlignPanel();
944  697 if (ap != null)
945    {
946    // modify GUI elements to reflect geometry change
947  223 Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
948  223 idw.width = i;
949  223 ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
950    }
951    }
952   
 
953  53 toggle public Rectangle getExplodedGeometry()
954    {
955  53 return explodedGeometry;
956    }
957   
 
958  53 toggle public void setExplodedGeometry(Rectangle explodedPosition)
959    {
960  53 this.explodedGeometry = explodedPosition;
961    }
962   
 
963  127 toggle public boolean isGatherViewsHere()
964    {
965  127 return gatherViewsHere;
966    }
967   
 
968  166 toggle public void setGatherViewsHere(boolean gatherViewsHere)
969    {
970  166 this.gatherViewsHere = gatherViewsHere;
971    }
972   
973    /**
974    * If this viewport has a (Protein/cDNA) complement, then scroll the
975    * complementary alignment to match this one.
976    */
 
977  763 toggle public void scrollComplementaryAlignment()
978    {
979    /*
980    * Populate a SearchResults object with the mapped location to scroll to. If
981    * there is no complement, or it is not following highlights, or no mapping
982    * is found, the result will be empty.
983    */
984  763 SearchResultsI sr = new SearchResults();
985  763 int verticalOffset = findComplementScrollTarget(sr);
986  763 if (!sr.isEmpty())
987    {
988    // TODO would like next line without cast but needs more refactoring...
989  2 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
990    .getAlignPanel();
991  2 complementPanel.setToScrollComplementPanel(false);
992  2 complementPanel.scrollToCentre(sr, verticalOffset);
993  2 complementPanel.setToScrollComplementPanel(true);
994    }
995    }
996   
997    /**
998    * Answers true if no alignment holds a reference to the given mapping
999    *
1000    * @param acf
1001    * @return
1002    */
 
1003  125 toggle protected boolean noReferencesTo(AlignedCodonFrame acf)
1004    {
1005  125 AlignFrame[] frames = Desktop.getDesktopAlignFrames();
1006  125 if (frames == null)
1007    {
1008  24 return true;
1009    }
1010  101 for (AlignFrame af : frames)
1011    {
1012  108 if (!af.isClosed())
1013    {
1014  108 for (AlignmentViewPanel ap : af.getAlignPanels())
1015    {
1016  108 AlignmentI al = ap.getAlignment();
1017  108 if (al != null && al.getCodonFrames().contains(acf))
1018    {
1019  98 return false;
1020    }
1021    }
1022    }
1023    }
1024  3 return true;
1025    }
1026   
1027    /**
1028    * Applies the supplied feature settings descriptor to currently known
1029    * features. This supports an 'initial configuration' of feature colouring
1030    * based on a preset or user favourite. This may then be modified in the usual
1031    * way using the Feature Settings dialogue.
1032    *
1033    * @param featureSettings
1034    */
 
1035  102 toggle @Override
1036    public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1037    {
1038  102 transferFeaturesStyles(featureSettings, false);
1039    }
1040   
1041    /**
1042    * Applies the supplied feature settings descriptor to currently known
1043    * features. This supports an 'initial configuration' of feature colouring
1044    * based on a preset or user favourite. This may then be modified in the usual
1045    * way using the Feature Settings dialogue.
1046    *
1047    * @param featureSettings
1048    */
 
1049  2 toggle @Override
1050    public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
1051    {
1052  2 transferFeaturesStyles(featureSettings, true);
1053    }
1054   
1055    /**
1056    * when mergeOnly is set, then group and feature visibility or feature colours
1057    * are not modified for features and groups already known to the feature
1058    * renderer. Feature ordering is always adjusted, and transparency is always
1059    * set regardless.
1060    *
1061    * @param featureSettings
1062    * @param mergeOnly
1063    */
 
1064  104 toggle private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
1065    boolean mergeOnly)
1066    {
1067  104 if (featureSettings == null)
1068    {
1069  18 return;
1070    }
1071   
1072  86 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1073    .getFeatureRenderer();
1074  86 List<String> origRenderOrder = new ArrayList<>();
1075  86 List<String> origGroups = new ArrayList<>();
1076    // preserve original render order - allows differentiation between user
1077    // configured colours and autogenerated ones
1078  86 origRenderOrder.addAll(fr.getRenderOrder());
1079  86 origGroups.addAll(fr.getFeatureGroups());
1080   
1081  86 fr.findAllFeatures(true);
1082  86 List<String> renderOrder = fr.getRenderOrder();
1083  86 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1084  86 if (!mergeOnly)
1085    {
1086    // only clear displayed features if we are mergeing
1087    // displayed.clear();
1088    }
1089    // TODO this clears displayed.featuresRegistered - do we care?
1090    //
1091    // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
1092    // feature visibility has already been configured is not very friendly
1093    /*
1094    * set feature colour if specified by feature settings
1095    * set visibility of all features
1096    */
1097  86 for (String type : renderOrder)
1098    {
1099  250 FeatureColourI preferredColour = featureSettings
1100    .getFeatureColour(type);
1101  250 FeatureColourI origColour = fr.getFeatureStyle(type);
1102  250 if (!mergeOnly || (!origRenderOrder.contains(type)
1103    || origColour == null
1104    || (!origColour.isGraduatedColour()
1105    && origColour.getColour() != null
1106    && origColour.getColour().equals(
1107    ColorUtils.createColourFromName(type)))))
1108    {
1109    // if we are merging, only update if there wasn't already a colour
1110    // defined for
1111    // this type
1112  246 if (preferredColour != null)
1113    {
1114  12 fr.setColour(type, preferredColour);
1115    }
1116  246 if (featureSettings.isFeatureDisplayed(type))
1117    {
1118  0 displayed.setVisible(type);
1119    }
1120  246 else if (featureSettings.isFeatureHidden(type))
1121    {
1122  82 displayed.setHidden(type);
1123    }
1124    }
1125    }
1126   
1127    /*
1128    * set visibility of feature groups
1129    */
1130  86 for (String group : fr.getFeatureGroups())
1131    {
1132  161 if (!mergeOnly || !origGroups.contains(group))
1133    {
1134    // when merging, display groups only if the aren't already marked as not
1135    // visible
1136  153 fr.setGroupVisibility(group,
1137    featureSettings.isGroupDisplayed(group));
1138    }
1139    }
1140   
1141    /*
1142    * order the features
1143    */
1144  86 if (featureSettings.optimiseOrder())
1145    {
1146    // TODO not supported (yet?)
1147    }
1148    else
1149    {
1150  86 fr.orderFeatures(featureSettings);
1151    }
1152  86 fr.setTransparency(featureSettings.getTransparency());
1153   
1154  86 fr.notifyFeaturesChanged();
1155    }
1156   
 
1157  4506 toggle public String getViewName()
1158    {
1159  4506 return viewName;
1160    }
1161   
 
1162  78 toggle public void setViewName(String viewName)
1163    {
1164  78 this.viewName = viewName;
1165    }
1166   
1167    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 4 2025 11:32:25 GMT using coverage data from Tue Nov 4 2025 11:32:11 GMT.
  • OpenClover is free and open-source software.