Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CrossRefAction	58	141	55	0.5136363551.4%	Show methods

Class CrossRefAction

Class CrossRefAction	Line # 58	Total Statements 141	Complexity 55	TOTAL Coverage 0.5136363551.4%
getXrefViews() : List<AlignmentViewPanel>   getXrefViews() : List<AlignmentViewPanel>	7070	1.01	1.01	0.0 0.00%
run() : void   run() : void	7575	60.060	20.020	0.6956522 0.695652269.6%
findGeneLoci(List<SequenceI>) : void   findGeneLoci(List<SequenceI>) : void	264264	3.03	1.01	1.0 1.0100%
findGeneLoci(SequenceI,Map<DBRefEntry, GeneLociI>) : void   findGeneLoci(SequenceI,Map<DBRefEntry, GeneLociI>) : void	284284	18.018	11.011	0.1 0.110%
fetchGeneLoci(SequenceI,DBRefEntry,Map<DBRefEntry, GeneLociI>) : boolean   fetchGeneLoci(SequenceI,DBRefEntry,Map<DBRefEntry, GeneLociI>) : boolean	352352	22.022	6.06	0.0 0.00%
copyAlignmentForSplitFrame(AlignmentI,AlignmentI,boolean,AlignmentI,AlignmentI) : AlignmentI   copyAlignmentForSplitFrame(AlignmentI,AlignmentI,boolean,AlignmentI,AlignmentI) : AlignmentI	416416	23.023	10.010	0.5714286 0.571428657.1%
makeCrossReferencesAlignment(AlignmentI,AlignmentI) : AlignmentI   makeCrossReferencesAlignment(AlignmentI,AlignmentI) : AlignmentI	505505	9.09	4.04	0.84615386 0.8461538684.6%
CrossRefAction(AlignFrame,SequenceI[],boolean,String)   CrossRefAction(AlignFrame,SequenceI[],boolean,String)	532532	4.04	1.01	1.0 1.0100%
getHandlerFor(SequenceI[],boolean,String,AlignFrame) : CrossRefAction   getHandlerFor(SequenceI[],boolean,String,AlignFrame) : CrossRefAction	541541	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.51363635	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS

 

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.CrossRef;
25		import jalview.api.AlignmentViewPanel;
26		import jalview.api.FeatureSettingsModelI;
27		import jalview.bin.Cache;
28		import jalview.datamodel.Alignment;
29		import jalview.datamodel.AlignmentI;
30		import jalview.datamodel.DBRefEntry;
31		import jalview.datamodel.DBRefSource;
32		import jalview.datamodel.GeneLociI;
33		import jalview.datamodel.SequenceI;
34		import jalview.ext.ensembl.EnsemblInfo;
35		import jalview.ext.ensembl.EnsemblMap;
36		import jalview.io.gff.SequenceOntologyI;
37		import jalview.structure.StructureSelectionManager;
38		import jalview.util.DBRefUtils;
39		import jalview.util.MapList;
40		import jalview.util.MappingUtils;
41		import jalview.util.MessageManager;
42		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
43		import jalview.ws.SequenceFetcher;
44
45		import java.util.ArrayList;
46		import java.util.HashMap;
47		import java.util.List;
48		import java.util.Map;
49		import java.util.Set;
50
51		/**
52		* Factory constructor and runnable for discovering and displaying
53		* cross-references for a set of aligned sequences
54		*
55		* @author jprocter
56		*
57		*/
		51.4% Uncovered Elements: 107 (220) Complexity: 55 Complexity Density: 0.39
58		public class CrossRefAction implements Runnable
59		{
60		private AlignFrame alignFrame;
61
62		private SequenceI[] sel;
63
64		private final boolean _odna;
65
66		private String source;
67
68		List<AlignmentViewPanel> xrefViews = new ArrayList<>();
69
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	List<AlignmentViewPanel> getXrefViews()...
71		{
72	0	return xrefViews;
73		}
74
		69.6% Uncovered Elements: 28 (92) Complexity: 20 Complexity Density: 0.33
75	2	@Override...
76		public void run()
77		{
78	2	final long sttime = System.currentTimeMillis();
79	2	alignFrame.setProgressBar(MessageManager.formatMessage(
80		"status.searching_for_sequences_from", new Object[]
81		{ source }), sttime);
82	2	try
83		{
84	2	AlignmentI alignment = alignFrame.getViewport().getAlignment();
85	2	AlignmentI dataset = alignment.getDataset() == null ? alignment
86		: alignment.getDataset();
87	2	boolean dna = alignment.isNucleotide();
88	2	if (_odna != dna)
89		{
90	0	System.err
91		.println("Conflict: showProducts for alignment originally "
92	0	+ "thought to be " + (_odna ? "DNA" : "Protein")
93	0	+ " now searching for " + (dna ? "DNA" : "Protein")
94		+ " Context.");
95		}
96	2	AlignmentI xrefs = new CrossRef(sel, dataset)
97		.findXrefSequences(source, dna);
98	2	if (xrefs == null)
99		{
100	0	return;
101		}
102
103		/*
104		* try to look up chromosomal coordinates for nucleotide
105		* sequences (if not already retrieved)
106		*/
107	2	findGeneLoci(xrefs.getSequences());
108
109		/*
110		* get display scheme (if any) to apply to features
111		*/
112	2	FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
113		.getFeatureColourScheme(source);
114
115	2	if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
116		{
117		// override default featureColourScheme so products have Ensembl variant colours
118	2	featureColourScheme = new SequenceFetcher()
119		.getFeatureColourScheme(DBRefSource.ENSEMBL);
120		}
121
122	2	AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
123		xrefs);
124	2	if (!dna)
125		{
126	0	xrefsAlignment = AlignmentUtils.makeCdsAlignment(
127		xrefsAlignment.getSequencesArray(), dataset, sel);
128	0	xrefsAlignment.alignAs(alignment);
129		}
130
131		/*
132		* If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
133		* sequences). If we are DNA, drop introns and update mappings
134		*/
135	2	AlignmentI copyAlignment = null;
136
137	2	if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
138		{
139	2	copyAlignment = copyAlignmentForSplitFrame(alignment, dataset, dna,
140		xrefs, xrefsAlignment);
141	2	if (copyAlignment == null)
142		{
143	0	return; // failed
144		}
145		}
146
147		/*
148		* build AlignFrame(s) according to available alignment data
149		*/
150	2	AlignFrame newFrame = new AlignFrame(xrefsAlignment,
151		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
152	2	if (Cache.getDefault("HIDE_INTRONS", true))
153		{
154	2	newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
155		}
156	2	String newtitle = String.format("%s %s %s",
157	2	dna ? MessageManager.getString("label.proteins")
158		: MessageManager.getString("label.nucleotides"),
159		MessageManager.getString("label.for"), alignFrame.getTitle());
160	2	newFrame.setTitle(newtitle);
161
162	2	if (copyAlignment == null)
163		{
164		/*
165		* split frame display is turned off in preferences file
166		*/
167	0	Desktop.addInternalFrame(newFrame, newtitle,
168		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
169	0	xrefViews.add(newFrame.alignPanel);
170	0	return; // via finally clause
171		}
172
173	2	AlignFrame copyThis = new AlignFrame(copyAlignment,
174		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
175	2	copyThis.setTitle(alignFrame.getTitle());
176
177	2	boolean showSequenceFeatures = alignFrame.getViewport()
178		.isShowSequenceFeatures();
179	2	newFrame.setShowSeqFeatures(showSequenceFeatures);
180	2	copyThis.setShowSeqFeatures(showSequenceFeatures);
181	2	FeatureRendererModel myFeatureStyling = alignFrame.alignPanel
182		.getSeqPanel().seqCanvas.getFeatureRenderer();
183
184		/*
185		* copy feature rendering settings to split frame
186		*/
187	2	FeatureRendererModel fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
188		.getFeatureRenderer();
189	2	fr1.transferSettings(myFeatureStyling);
190	2	fr1.findAllFeatures(true);
191	2	FeatureRendererModel fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
192		.getFeatureRenderer();
193	2	fr2.transferSettings(myFeatureStyling);
194	2	fr2.findAllFeatures(true);
195
196		/*
197		* apply 'database source' feature configuration
198		* if any - first to the new splitframe view about to be displayed
199		*/
200
201	2	newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
202	2	copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
203
204		/*
205		* and for JAL-3330 also to original alignFrame view(s)
206		* this currently trashes any original settings.
207		*/
208	2	for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
209	2	origpanel.getAlignViewport()
210		.mergeFeaturesStyle(featureColourScheme);
211		}
212
213	2	SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
214	2	dna ? newFrame : copyThis);
215
216	2	newFrame.setVisible(true);
217	2	copyThis.setVisible(true);
218	2	String linkedTitle = MessageManager
219		.getString("label.linked_view_title");
220	2	Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
221	2	sf.adjustInitialLayout();
222
223		// finally add the top, then bottom frame to the view list
224	2	xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
225	2	xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
226
227		} catch (OutOfMemoryError e)
228		{
229	0	new OOMWarning("whilst fetching crossreferences", e);
230		} catch (Throwable e)
231		{
232	0	Cache.log.error("Error when finding crossreferences", e);
233		} finally
234		{
235	2	alignFrame.setProgressBar(MessageManager.formatMessage(
236		"status.finished_searching_for_sequences_from", new Object[]
237		{ source }), sttime);
238		}
239		}
240
241		/**
242		* Tries to add chromosomal coordinates to any nucleotide sequence which does
243		* not already have them. Coordinates are retrieved from Ensembl given an
244		* Ensembl identifier, either on the sequence itself or on a peptide sequence
245		* it has a reference to.
246		*
247		* <pre>
248		* Example (human):
249		* - fetch EMBLCDS cross-references for Uniprot entry P30419
250		* - the EMBL sequences do not have xrefs to Ensembl
251		* - the Uniprot entry has xrefs to
252		* ENSP00000258960, ENSP00000468424, ENST00000258960, ENST00000592782
253		* - either of the transcript ids can be used to retrieve gene loci e.g.
254		* http://rest.ensembl.org/map/cds/ENST00000592782/1..100000
255		* Example (invertebrate):
256		* - fetch EMBLCDS cross-references for Uniprot entry Q43517 (FER1_SOLLC)
257		* - the Uniprot entry has an xref to ENSEMBLPLANTS Solyc10g044520.1.1
258		* - can retrieve gene loci with
259		* http://rest.ensemblgenomes.org/map/cds/Solyc10g044520.1.1/1..100000
260		* </pre>
261		*
262		* @param sequences
263		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
264	2	public static void findGeneLoci(List<SequenceI> sequences)...
265		{
266	2	Map<DBRefEntry, GeneLociI> retrievedLoci = new HashMap<>();
267	2	for (SequenceI seq : sequences)
268		{
269	22	findGeneLoci(seq, retrievedLoci);
270		}
271		}
272
273		/**
274		* Tres to find chromosomal coordinates for the sequence, by searching its
275		* direct and indirect cross-references for Ensembl. If the loci have already
276		* been retrieved, just reads them out of the map of retrievedLoci; this is
277		* the case of an alternative transcript for the same protein. Otherwise calls
278		* a REST service to retrieve the loci, and if successful, adds them to the
279		* sequence and to the retrievedLoci.
280		*
281		* @param seq
282		* @param retrievedLoci
283		*/
		10% Uncovered Elements: 27 (30) Complexity: 11 Complexity Density: 0.61
284	22	static void findGeneLoci(SequenceI seq,...
285		Map<DBRefEntry, GeneLociI> retrievedLoci)
286		{
287		/*
288		* don't replace any existing chromosomal coordinates
289		*/
290	22	if (seq == null || seq.isProtein() || seq.getGeneLoci() != null
291		|| seq.getDBRefs() == null)
292		{
293	22	return;
294		}
295
296	0	Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
297
298		/*
299		* first look for direct dbrefs from sequence to Ensembl
300		*/
301	0	String[] divisionsArray = ensemblDivisions
302		.toArray(new String[ensemblDivisions.size()]);
303	0	List<DBRefEntry> seqRefs = seq.getDBRefs();
304	0	List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
305		divisionsArray);
306	0	if (directEnsemblRefs != null)
307		{
308	0	for (DBRefEntry ensemblRef : directEnsemblRefs)
309		{
310	0	if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
311		{
312	0	return;
313		}
314		}
315		}
316
317		/*
318		* else look for indirect dbrefs from sequence to Ensembl
319		*/
320	0	for (DBRefEntry dbref : seq.getDBRefs())
321		{
322	0	if (dbref.getMap() != null && dbref.getMap().getTo() != null)
323		{
324	0	List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
325	0	List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
326		divisionsArray);
327	0	if (indirectEnsemblRefs != null)
328		{
329	0	for (DBRefEntry ensemblRef : indirectEnsemblRefs)
330		{
331	0	if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
332		{
333	0	return;
334		}
335		}
336		}
337		}
338		}
339		}
340
341		/**
342		* Retrieves chromosomal coordinates for the Ensembl (or EnsemblGenomes)
343		* identifier in dbref. If successful, and the sequence length matches gene
344		* loci length, then add it to the sequence, and to the retrievedLoci map.
345		* Answers true if successful, else false.
346		*
347		* @param seq
348		* @param dbref
349		* @param retrievedLoci
350		* @return
351		*/
		0% Uncovered Elements: 32 (32) Complexity: 6 Complexity Density: 0.27
352	0	static boolean fetchGeneLoci(SequenceI seq, DBRefEntry dbref,...
353		Map<DBRefEntry, GeneLociI> retrievedLoci)
354		{
355	0	String accession = dbref.getAccessionId();
356	0	String division = dbref.getSource();
357
358		/*
359		* hack: ignore cross-references to Ensembl protein ids
360		* (or use map/translation perhaps?)
361		* todo: is there an equivalent in EnsemblGenomes?
362		*/
363	0	if (accession.startsWith("ENSP"))
364		{
365	0	return false;
366		}
367	0	EnsemblMap mapper = new EnsemblMap();
368
369		/*
370		* try CDS mapping first
371		*/
372	0	GeneLociI geneLoci = mapper.getCdsMapping(division, accession, 1,
373		seq.getLength());
374	0	if (geneLoci != null)
375		{
376	0	MapList map = geneLoci.getMapping();
377	0	int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
378	0	if (mappedFromLength == seq.getLength())
379		{
380	0	seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
381		geneLoci.getChromosomeId(), map);
382	0	retrievedLoci.put(dbref, geneLoci);
383	0	return true;
384		}
385		}
386
387		/*
388		* else try CDNA mapping
389		*/
390	0	geneLoci = mapper.getCdnaMapping(division, accession, 1,
391		seq.getLength());
392	0	if (geneLoci != null)
393		{
394	0	MapList map = geneLoci.getMapping();
395	0	int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
396	0	if (mappedFromLength == seq.getLength())
397		{
398	0	seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
399		geneLoci.getChromosomeId(), map);
400	0	retrievedLoci.put(dbref, geneLoci);
401	0	return true;
402		}
403		}
404
405	0	return false;
406		}
407
408		/**
409		* @param alignment
410		* @param dataset
411		* @param dna
412		* @param xrefs
413		* @param xrefsAlignment
414		* @return
415		*/
		57.1% Uncovered Elements: 15 (35) Complexity: 10 Complexity Density: 0.43
416	2	protected AlignmentI copyAlignmentForSplitFrame(AlignmentI alignment,...
417		AlignmentI dataset, boolean dna, AlignmentI xrefs,
418		AlignmentI xrefsAlignment)
419		{
420	2	AlignmentI copyAlignment;
421	2	boolean copyAlignmentIsAligned = false;
422	2	if (dna)
423		{
424	2	copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
425		xrefsAlignment.getSequencesArray());
426	2	if (copyAlignment.getHeight() == 0)
427		{
428	0	JvOptionPane.showMessageDialog(alignFrame,
429		MessageManager.getString("label.cant_map_cds"),
430		MessageManager.getString("label.operation_failed"),
431		JvOptionPane.OK_OPTION);
432	0	System.err.println("Failed to make CDS alignment");
433	0	return null;
434		}
435
436		/*
437		* pending getting Embl transcripts to 'align',
438		* we are only doing this for Ensembl
439		*/
440		// TODO proper criteria for 'can align as cdna'
441	2	if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
442		|| AlignmentUtils.looksLikeEnsembl(alignment))
443		{
444	2	copyAlignment.alignAs(alignment);
445	2	copyAlignmentIsAligned = true;
446		}
447		}
448		else
449		{
450	0	copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
451		xrefs.getSequencesArray(), dataset);
452		}
453	2	copyAlignment
454		.setGapCharacter(alignFrame.viewport.getGapCharacter());
455
456	2	StructureSelectionManager ssm = StructureSelectionManager
457		.getStructureSelectionManager(Desktop.instance);
458
459		/*
460		* register any new mappings for sequence mouseover etc
461		* (will not duplicate any previously registered mappings)
462		*/
463	2	ssm.registerMappings(dataset.getCodonFrames());
464
465	2	if (copyAlignment.getHeight() <= 0)
466		{
467	0	System.err.println(
468		"No Sequences generated for xRef type " + source);
469	0	return null;
470		}
471
472		/*
473		* align protein to dna
474		*/
475	2	if (dna && copyAlignmentIsAligned)
476		{
477	2	xrefsAlignment.alignAs(copyAlignment);
478		}
479		else
480		{
481		/*
482		* align cdna to protein - currently only if
483		* fetching and aligning Ensembl transcripts!
484		*/
485		// TODO: generalise for other sources of locus/transcript/cds data
486	0	if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
487		{
488	0	copyAlignment.alignAs(xrefsAlignment);
489		}
490		}
491
492	2	return copyAlignment;
493		}
494
495		/**
496		* Makes an alignment containing the given sequences, and adds them to the
497		* given dataset, which is also set as the dataset for the new alignment
498		*
499		* TODO: refactor to DatasetI method
500		*
501		* @param dataset
502		* @param seqs
503		* @return
504		*/
		84.6% Uncovered Elements: 2 (13) Complexity: 4 Complexity Density: 0.44
505	2	protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,...
506		AlignmentI seqs)
507		{
508	2	SequenceI[] sprods = new SequenceI[seqs.getHeight()];
509	24	for (int s = 0; s < sprods.length; s++)
510		{
511	22	sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
512	22	if (dataset.getSequences() == null || !dataset.getSequences()
513		.contains(sprods[s].getDatasetSequence()))
514		{
515	0	dataset.addSequence(sprods[s].getDatasetSequence());
516		}
517	22	sprods[s].updatePDBIds();
518		}
519	2	Alignment al = new Alignment(sprods);
520	2	al.setDataset(dataset);
521	2	return al;
522		}
523
524		/**
525		* Constructor
526		*
527		* @param af
528		* @param seqs
529		* @param fromDna
530		* @param dbSource
531		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
532	2	CrossRefAction(AlignFrame af, SequenceI[] seqs, boolean fromDna,...
533		String dbSource)
534		{
535	2	this.alignFrame = af;
536	2	this.sel = seqs;
537	2	this._odna = fromDna;
538	2	this.source = dbSource;
539		}
540
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
541	2	public static CrossRefAction getHandlerFor(final SequenceI[] sel,...
542		final boolean fromDna, final String source,
543		final AlignFrame alignFrame)
544		{
545	2	return new CrossRefAction(alignFrame, sel, fromDna, source);
546		}
547
548		}