Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CrossRefAction	59	141	55	0.5136363551.4%	Show methods

Class CrossRefAction

Class CrossRefAction	Line # 59	Total Statements 141	Complexity 55	TOTAL Coverage 0.5136363551.4%
getXrefViews() : List<AlignmentViewPanel>   getXrefViews() : List<AlignmentViewPanel>	7171	1.01	1.01	0.0 0.00%
run() : void   run() : void	7676	60.060	20.020	0.6956522 0.695652269.6%
findGeneLoci(List<SequenceI>) : void   findGeneLoci(List<SequenceI>) : void	267267	3.03	1.01	1.0 1.0100%
findGeneLoci(SequenceI,Map<DBRefEntry, GeneLociI>) : void   findGeneLoci(SequenceI,Map<DBRefEntry, GeneLociI>) : void	287287	18.018	11.011	0.1 0.110%
fetchGeneLoci(SequenceI,DBRefEntry,Map<DBRefEntry, GeneLociI>) : boolean   fetchGeneLoci(SequenceI,DBRefEntry,Map<DBRefEntry, GeneLociI>) : boolean	355355	22.022	6.06	0.0 0.00%
copyAlignmentForSplitFrame(AlignmentI,AlignmentI,boolean,AlignmentI,AlignmentI) : AlignmentI   copyAlignmentForSplitFrame(AlignmentI,AlignmentI,boolean,AlignmentI,AlignmentI) : AlignmentI	419419	23.023	10.010	0.5714286 0.571428657.1%
makeCrossReferencesAlignment(AlignmentI,AlignmentI) : AlignmentI   makeCrossReferencesAlignment(AlignmentI,AlignmentI) : AlignmentI	507507	9.09	4.04	0.84615386 0.8461538684.6%
CrossRefAction(AlignFrame,SequenceI[],boolean,String)   CrossRefAction(AlignFrame,SequenceI[],boolean,String)	534534	4.04	1.01	1.0 1.0100%
getHandlerFor(SequenceI[],boolean,String,AlignFrame) : CrossRefAction   getHandlerFor(SequenceI[],boolean,String,AlignFrame) : CrossRefAction	543543	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.bin.Console;
29		import jalview.datamodel.Alignment;
30		import jalview.datamodel.AlignmentI;
31		import jalview.datamodel.DBRefEntry;
32		import jalview.datamodel.DBRefSource;
33		import jalview.datamodel.GeneLociI;
34		import jalview.datamodel.SequenceI;
35		import jalview.ext.ensembl.EnsemblInfo;
36		import jalview.ext.ensembl.EnsemblMap;
37		import jalview.io.gff.SequenceOntologyI;
38		import jalview.structure.StructureSelectionManager;
39		import jalview.util.DBRefUtils;
40		import jalview.util.MapList;
41		import jalview.util.MappingUtils;
42		import jalview.util.MessageManager;
43		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
44		import jalview.ws.SequenceFetcher;
45
46		import java.util.ArrayList;
47		import java.util.HashMap;
48		import java.util.List;
49		import java.util.Map;
50		import java.util.Set;
51
52		/**
53		* Factory constructor and runnable for discovering and displaying
54		* cross-references for a set of aligned sequences
55		*
56		* @author jprocter
57		*
58		*/
		51.4% Uncovered Elements: 107 (220) Complexity: 55 Complexity Density: 0.39
59		public class CrossRefAction implements Runnable
60		{
61		private AlignFrame alignFrame;
62
63		private SequenceI[] sel;
64
65		private final boolean _odna;
66
67		private String source;
68
69		List<AlignmentViewPanel> xrefViews = new ArrayList<>();
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	List<AlignmentViewPanel> getXrefViews()...
72		{
73	0	return xrefViews;
74		}
75
		69.6% Uncovered Elements: 28 (92) Complexity: 20 Complexity Density: 0.33
76	2	@Override...
77		public void run()
78		{
79	2	final long sttime = System.currentTimeMillis();
80	2	alignFrame.setProgressBar(MessageManager.formatMessage(
81		"status.searching_for_sequences_from", new Object[]
82		{ source }), sttime);
83	2	try
84		{
85	2	AlignmentI alignment = alignFrame.getViewport().getAlignment();
86	2	AlignmentI dataset = alignment.getDataset() == null ? alignment
87		: alignment.getDataset();
88	2	boolean dna = alignment.isNucleotide();
89	2	if (_odna != dna)
90		{
91	0	System.err
92		.println("Conflict: showProducts for alignment originally "
93	0	+ "thought to be " + (_odna ? "DNA" : "Protein")
94	0	+ " now searching for " + (dna ? "DNA" : "Protein")
95		+ " Context.");
96		}
97	2	AlignmentI xrefs = new CrossRef(sel, dataset)
98		.findXrefSequences(source, dna);
99	2	if (xrefs == null)
100		{
101	0	return;
102		}
103
104		/*
105		* try to look up chromosomal coordinates for nucleotide
106		* sequences (if not already retrieved)
107		*/
108	2	findGeneLoci(xrefs.getSequences());
109
110		/*
111		* get display scheme (if any) to apply to features
112		*/
113	2	FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
114		.getFeatureColourScheme(source);
115
116	2	if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
117		{
118		// override default featureColourScheme so products have Ensembl variant
119		// colours
120	2	featureColourScheme = new SequenceFetcher()
121		.getFeatureColourScheme(DBRefSource.ENSEMBL);
122		}
123
124	2	AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
125		xrefs);
126	2	if (!dna)
127		{
128	0	xrefsAlignment = AlignmentUtils.makeCdsAlignment(
129		xrefsAlignment.getSequencesArray(), dataset, sel);
130	0	xrefsAlignment.alignAs(alignment);
131		}
132
133		/*
134		* If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
135		* sequences). If we are DNA, drop introns and update mappings
136		*/
137	2	AlignmentI copyAlignment = null;
138
139	2	if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
140		{
141	2	copyAlignment = copyAlignmentForSplitFrame(alignment, dataset, dna,
142		xrefs, xrefsAlignment);
143	2	if (copyAlignment == null)
144		{
145	0	return; // failed
146		}
147		}
148
149		/*
150		* build AlignFrame(s) according to available alignment data
151		*/
152	2	AlignFrame newFrame = new AlignFrame(xrefsAlignment,
153		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
154	2	if (Cache.getDefault("HIDE_INTRONS", true))
155		{
156	2	newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
157		}
158	2	String newtitle = String.format("%s %s %s",
159	2	dna ? MessageManager.getString("label.proteins")
160		: MessageManager.getString("label.nucleotides"),
161		MessageManager.getString("label.for"), alignFrame.getTitle());
162	2	newFrame.setTitle(newtitle);
163
164	2	if (copyAlignment == null)
165		{
166		/*
167		* split frame display is turned off in preferences file
168		*/
169	0	Desktop.addInternalFrame(newFrame, newtitle,
170		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
171	0	xrefViews.add(newFrame.alignPanel);
172	0	return; // via finally clause
173		}
174
175	2	AlignFrame copyThis = new AlignFrame(copyAlignment,
176		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
177	2	copyThis.setTitle(alignFrame.getTitle());
178
179	2	boolean showSequenceFeatures = alignFrame.getViewport()
180		.isShowSequenceFeatures();
181	2	newFrame.setShowSeqFeatures(showSequenceFeatures);
182	2	copyThis.setShowSeqFeatures(showSequenceFeatures);
183	2	FeatureRendererModel myFeatureStyling = alignFrame.alignPanel
184		.getSeqPanel().seqCanvas.getFeatureRenderer();
185
186		/*
187		* copy feature rendering settings to split frame
188		*/
189	2	FeatureRendererModel fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
190		.getFeatureRenderer();
191	2	fr1.transferSettings(myFeatureStyling);
192	2	fr1.findAllFeatures(true);
193	2	FeatureRendererModel fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
194		.getFeatureRenderer();
195	2	fr2.transferSettings(myFeatureStyling);
196	2	fr2.findAllFeatures(true);
197
198		/*
199		* apply 'database source' feature configuration
200		* if any - first to the new splitframe view about to be displayed
201		*/
202
203	2	newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
204	2	copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
205
206		/*
207		* and for JAL-3330 also to original alignFrame view(s)
208		* this currently trashes any original settings.
209		*/
210	2	for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
211		{
212	2	origpanel.getAlignViewport()
213		.mergeFeaturesStyle(featureColourScheme);
214		}
215
216	2	SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
217	2	dna ? newFrame : copyThis);
218
219	2	newFrame.setVisible(true);
220	2	copyThis.setVisible(true);
221	2	String linkedTitle = MessageManager
222		.getString("label.linked_view_title");
223	2	Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
224	2	sf.adjustInitialLayout();
225
226		// finally add the top, then bottom frame to the view list
227	2	xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
228	2	xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
229
230		} catch (OutOfMemoryError e)
231		{
232	0	new OOMWarning("whilst fetching crossreferences", e);
233		} catch (Throwable e)
234		{
235	0	Console.error("Error when finding crossreferences", e);
236		} finally
237		{
238	2	alignFrame.setProgressBar(MessageManager.formatMessage(
239		"status.finished_searching_for_sequences_from", new Object[]
240		{ source }), sttime);
241		}
242		}
243
244		/**
245		* Tries to add chromosomal coordinates to any nucleotide sequence which does
246		* not already have them. Coordinates are retrieved from Ensembl given an
247		* Ensembl identifier, either on the sequence itself or on a peptide sequence
248		* it has a reference to.
249		*
250		* <pre>
251		* Example (human):
252		* - fetch EMBLCDS cross-references for Uniprot entry P30419
253		* - the EMBL sequences do not have xrefs to Ensembl
254		* - the Uniprot entry has xrefs to
255		* ENSP00000258960, ENSP00000468424, ENST00000258960, ENST00000592782
256		* - either of the transcript ids can be used to retrieve gene loci e.g.
257		* http://rest.ensembl.org/map/cds/ENST00000592782/1..100000
258		* Example (invertebrate):
259		* - fetch EMBLCDS cross-references for Uniprot entry Q43517 (FER1_SOLLC)
260		* - the Uniprot entry has an xref to ENSEMBLPLANTS Solyc10g044520.1.1
261		* - can retrieve gene loci with
262		* http://rest.ensemblgenomes.org/map/cds/Solyc10g044520.1.1/1..100000
263		* </pre>
264		*
265		* @param sequences
266		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
267	2	public static void findGeneLoci(List<SequenceI> sequences)...
268		{
269	2	Map<DBRefEntry, GeneLociI> retrievedLoci = new HashMap<>();
270	2	for (SequenceI seq : sequences)
271		{
272	22	findGeneLoci(seq, retrievedLoci);
273		}
274		}
275
276		/**
277		* Tres to find chromosomal coordinates for the sequence, by searching its
278		* direct and indirect cross-references for Ensembl. If the loci have already
279		* been retrieved, just reads them out of the map of retrievedLoci; this is
280		* the case of an alternative transcript for the same protein. Otherwise calls
281		* a REST service to retrieve the loci, and if successful, adds them to the
282		* sequence and to the retrievedLoci.
283		*
284		* @param seq
285		* @param retrievedLoci
286		*/
		10% Uncovered Elements: 27 (30) Complexity: 11 Complexity Density: 0.61
287	22	static void findGeneLoci(SequenceI seq,...
288		Map<DBRefEntry, GeneLociI> retrievedLoci)
289		{
290		/*
291		* don't replace any existing chromosomal coordinates
292		*/
293	22	if (seq == null || seq.isProtein() || seq.getGeneLoci() != null
294		|| seq.getDBRefs() == null)
295		{
296	22	return;
297		}
298
299	0	Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
300
301		/*
302		* first look for direct dbrefs from sequence to Ensembl
303		*/
304	0	String[] divisionsArray = ensemblDivisions
305		.toArray(new String[ensemblDivisions.size()]);
306	0	List<DBRefEntry> seqRefs = seq.getDBRefs();
307	0	List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
308		divisionsArray);
309	0	if (directEnsemblRefs != null)
310		{
311	0	for (DBRefEntry ensemblRef : directEnsemblRefs)
312		{
313	0	if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
314		{
315	0	return;
316		}
317		}
318		}
319
320		/*
321		* else look for indirect dbrefs from sequence to Ensembl
322		*/
323	0	for (DBRefEntry dbref : seq.getDBRefs())
324		{
325	0	if (dbref.getMap() != null && dbref.getMap().getTo() != null)
326		{
327	0	List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
328	0	List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
329		divisionsArray);
330	0	if (indirectEnsemblRefs != null)
331		{
332	0	for (DBRefEntry ensemblRef : indirectEnsemblRefs)
333		{
334	0	if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
335		{
336	0	return;
337		}
338		}
339		}
340		}
341		}
342		}
343
344		/**
345		* Retrieves chromosomal coordinates for the Ensembl (or EnsemblGenomes)
346		* identifier in dbref. If successful, and the sequence length matches gene
347		* loci length, then add it to the sequence, and to the retrievedLoci map.
348		* Answers true if successful, else false.
349		*
350		* @param seq
351		* @param dbref
352		* @param retrievedLoci
353		* @return
354		*/
		0% Uncovered Elements: 32 (32) Complexity: 6 Complexity Density: 0.27
355	0	static boolean fetchGeneLoci(SequenceI seq, DBRefEntry dbref,...
356		Map<DBRefEntry, GeneLociI> retrievedLoci)
357		{
358	0	String accession = dbref.getAccessionId();
359	0	String division = dbref.getSource();
360
361		/*
362		* hack: ignore cross-references to Ensembl protein ids
363		* (or use map/translation perhaps?)
364		* todo: is there an equivalent in EnsemblGenomes?
365		*/
366	0	if (accession.startsWith("ENSP"))
367		{
368	0	return false;
369		}
370	0	EnsemblMap mapper = new EnsemblMap();
371
372		/*
373		* try CDS mapping first
374		*/
375	0	GeneLociI geneLoci = mapper.getCdsMapping(division, accession, 1,
376		seq.getLength());
377	0	if (geneLoci != null)
378		{
379	0	MapList map = geneLoci.getMapping();
380	0	int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
381	0	if (mappedFromLength == seq.getLength())
382		{
383	0	seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
384		geneLoci.getChromosomeId(), map);
385	0	retrievedLoci.put(dbref, geneLoci);
386	0	return true;
387		}
388		}
389
390		/*
391		* else try CDNA mapping
392		*/
393	0	geneLoci = mapper.getCdnaMapping(division, accession, 1,
394		seq.getLength());
395	0	if (geneLoci != null)
396		{
397	0	MapList map = geneLoci.getMapping();
398	0	int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
399	0	if (mappedFromLength == seq.getLength())
400		{
401	0	seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
402		geneLoci.getChromosomeId(), map);
403	0	retrievedLoci.put(dbref, geneLoci);
404	0	return true;
405		}
406		}
407
408	0	return false;
409		}
410
411		/**
412		* @param alignment
413		* @param dataset
414		* @param dna
415		* @param xrefs
416		* @param xrefsAlignment
417		* @return
418		*/
		57.1% Uncovered Elements: 15 (35) Complexity: 10 Complexity Density: 0.43
419	2	protected AlignmentI copyAlignmentForSplitFrame(AlignmentI alignment,...
420		AlignmentI dataset, boolean dna, AlignmentI xrefs,
421		AlignmentI xrefsAlignment)
422		{
423	2	AlignmentI copyAlignment;
424	2	boolean copyAlignmentIsAligned = false;
425	2	if (dna)
426		{
427	2	copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
428		xrefsAlignment.getSequencesArray());
429	2	if (copyAlignment.getHeight() == 0)
430		{
431	0	JvOptionPane.showMessageDialog(alignFrame,
432		MessageManager.getString("label.cant_map_cds"),
433		MessageManager.getString("label.operation_failed"),
434		JvOptionPane.OK_OPTION);
435	0	jalview.bin.Console.errPrintln("Failed to make CDS alignment");
436	0	return null;
437		}
438
439		/*
440		* pending getting Embl transcripts to 'align',
441		* we are only doing this for Ensembl
442		*/
443		// TODO proper criteria for 'can align as cdna'
444	2	if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
445		|| AlignmentUtils.looksLikeEnsembl(alignment))
446		{
447	2	copyAlignment.alignAs(alignment);
448	2	copyAlignmentIsAligned = true;
449		}
450		}
451		else
452		{
453	0	copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
454		xrefs.getSequencesArray(), dataset);
455		}
456	2	copyAlignment.setGapCharacter(alignFrame.viewport.getGapCharacter());
457
458	2	StructureSelectionManager ssm = StructureSelectionManager
459		.getStructureSelectionManager(Desktop.instance);
460
461		/*
462		* register any new mappings for sequence mouseover etc
463		* (will not duplicate any previously registered mappings)
464		*/
465	2	ssm.registerMappings(dataset.getCodonFrames());
466
467	2	if (copyAlignment.getHeight() <= 0)
468		{
469	0	jalview.bin.Console
470		.errPrintln("No Sequences generated for xRef type " + source);
471	0	return null;
472		}
473
474		/*
475		* align protein to dna
476		*/
477	2	if (dna && copyAlignmentIsAligned)
478		{
479	2	xrefsAlignment.alignAs(copyAlignment);
480		}
481		else
482		{
483		/*
484		* align cdna to protein - currently only if
485		* fetching and aligning Ensembl transcripts!
486		*/
487		// TODO: generalise for other sources of locus/transcript/cds data
488	0	if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
489		{
490	0	copyAlignment.alignAs(xrefsAlignment);
491		}
492		}
493
494	2	return copyAlignment;
495		}
496
497		/**
498		* Makes an alignment containing the given sequences, and adds them to the
499		* given dataset, which is also set as the dataset for the new alignment
500		*
501		* TODO: refactor to DatasetI method
502		*
503		* @param dataset
504		* @param seqs
505		* @return
506		*/
		84.6% Uncovered Elements: 2 (13) Complexity: 4 Complexity Density: 0.44
507	2	protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,...
508		AlignmentI seqs)
509		{
510	2	SequenceI[] sprods = new SequenceI[seqs.getHeight()];
511	24	for (int s = 0; s < sprods.length; s++)
512		{
513	22	sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
514	22	if (dataset.getSequences() == null || !dataset.getSequences()
515		.contains(sprods[s].getDatasetSequence()))
516		{
517	0	dataset.addSequence(sprods[s].getDatasetSequence());
518		}
519	22	sprods[s].updatePDBIds();
520		}
521	2	Alignment al = new Alignment(sprods);
522	2	al.setDataset(dataset);
523	2	return al;
524		}
525
526		/**
527		* Constructor
528		*
529		* @param af
530		* @param seqs
531		* @param fromDna
532		* @param dbSource
533		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
534	2	CrossRefAction(AlignFrame af, SequenceI[] seqs, boolean fromDna,...
535		String dbSource)
536		{
537	2	this.alignFrame = af;
538	2	this.sel = seqs;
539	2	this._odna = fromDna;
540	2	this.source = dbSource;
541		}
542
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
543	2	public static CrossRefAction getHandlerFor(final SequenceI[] sel,...
544		final boolean fromDna, final String source,
545		final AlignFrame alignFrame)
546		{
547	2	return new CrossRefAction(alignFrame, sel, fromDna, source);
548		}
549
550		}