Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
CrossRefAction	57	137	53	214	0.00%	Show methods

Class CrossRefAction

Class CrossRefAction	Line # 57	Total Statements 137	Complexity 53	Uncovered Elements 214	TOTAL Coverage 0.00%
getXrefViews() : List<AlignmentViewPanel>   getXrefViews() : List<AlignmentViewPanel>	6969	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	7474	56.056	18.018	86.086	0.0 0.00%
findGeneLoci(List<SequenceI>) : void   findGeneLoci(List<SequenceI>) : void	247247	3.03	1.01	3.03	0.0 0.00%
findGeneLoci(SequenceI,Map<DBRefEntry, GeneLociI>) : void   findGeneLoci(SequenceI,Map<DBRefEntry, GeneLociI>) : void	267267	18.018	11.011	30.030	0.0 0.00%
fetchGeneLoci(SequenceI,DBRefEntry,Map<DBRefEntry, GeneLociI>) : boolean   fetchGeneLoci(SequenceI,DBRefEntry,Map<DBRefEntry, GeneLociI>) : boolean	335335	22.022	6.06	32.032	0.0 0.00%
copyAlignmentForSplitFrame(AlignmentI,AlignmentI,boolean,AlignmentI,AlignmentI) : AlignmentI   copyAlignmentForSplitFrame(AlignmentI,AlignmentI,boolean,AlignmentI,AlignmentI) : AlignmentI	399399	23.023	10.010	35.035	0.0 0.00%
makeCrossReferencesAlignment(AlignmentI,AlignmentI) : AlignmentI   makeCrossReferencesAlignment(AlignmentI,AlignmentI) : AlignmentI	488488	9.09	4.04	13.013	0.0 0.00%
CrossRefAction(AlignFrame,SequenceI[],boolean,String)   CrossRefAction(AlignFrame,SequenceI[],boolean,String)	515515	4.04	1.01	4.04	0.0 0.00%
getHandlerFor(SequenceI[],boolean,String,AlignFrame) : CrossRefAction   getHandlerFor(SequenceI[],boolean,String,AlignFrame) : CrossRefAction	524524	1.01	1.01	1.01	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.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.ws.SequenceFetcher;
43
44		import java.util.ArrayList;
45		import java.util.HashMap;
46		import java.util.List;
47		import java.util.Map;
48		import java.util.Set;
49
50		/**
51		* Factory constructor and runnable for discovering and displaying
52		* cross-references for a set of aligned sequences
53		*
54		* @author jprocter
55		*
56		*/
		0% Uncovered Elements: 214 (214) Complexity: 53 Complexity Density: 0.39
57		public class CrossRefAction implements Runnable
58		{
59		private AlignFrame alignFrame;
60
61		private SequenceI[] sel;
62
63		private final boolean _odna;
64
65		private String source;
66
67		List<AlignmentViewPanel> xrefViews = new ArrayList<>();
68
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
69	0	List<AlignmentViewPanel> getXrefViews()...
70		{
71	0	return xrefViews;
72		}
73
		0% Uncovered Elements: 86 (86) Complexity: 18 Complexity Density: 0.32
74	0	@Override...
75		public void run()
76		{
77	0	final long sttime = System.currentTimeMillis();
78	0	alignFrame.setProgressBar(MessageManager.formatMessage(
79		"status.searching_for_sequences_from", new Object[]
80		{ source }), sttime);
81	0	try
82		{
83	0	AlignmentI alignment = alignFrame.getViewport().getAlignment();
84	0	AlignmentI dataset = alignment.getDataset() == null ? alignment
85		: alignment.getDataset();
86	0	boolean dna = alignment.isNucleotide();
87	0	if (_odna != dna)
88		{
89	0	System.err
90		.println("Conflict: showProducts for alignment originally "
91	0	+ "thought to be " + (_odna ? "DNA" : "Protein")
92	0	+ " now searching for " + (dna ? "DNA" : "Protein")
93		+ " Context.");
94		}
95	0	AlignmentI xrefs = new CrossRef(sel, dataset)
96		.findXrefSequences(source, dna);
97	0	if (xrefs == null)
98		{
99	0	return;
100		}
101
102		/*
103		* try to look up chromosomal coordinates for nucleotide
104		* sequences (if not already retrieved)
105		*/
106	0	findGeneLoci(xrefs.getSequences());
107
108		/*
109		* get display scheme (if any) to apply to features
110		*/
111	0	FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
112		.getFeatureColourScheme(source);
113
114	0	AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
115		xrefs);
116	0	if (!dna)
117		{
118	0	xrefsAlignment = AlignmentUtils.makeCdsAlignment(
119		xrefsAlignment.getSequencesArray(), dataset, sel);
120	0	xrefsAlignment.alignAs(alignment);
121		}
122
123		/*
124		* If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
125		* sequences). If we are DNA, drop introns and update mappings
126		*/
127	0	AlignmentI copyAlignment = null;
128
129	0	if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
130		{
131	0	copyAlignment = copyAlignmentForSplitFrame(alignment, dataset, dna,
132		xrefs, xrefsAlignment);
133	0	if (copyAlignment == null)
134		{
135	0	return; // failed
136		}
137		}
138
139		/*
140		* build AlignFrame(s) according to available alignment data
141		*/
142	0	AlignFrame newFrame = new AlignFrame(xrefsAlignment,
143		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
144	0	if (Cache.getDefault("HIDE_INTRONS", true))
145		{
146	0	newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
147		}
148	0	String newtitle = String.format("%s %s %s",
149	0	dna ? MessageManager.getString("label.proteins")
150		: MessageManager.getString("label.nucleotides"),
151		MessageManager.getString("label.for"), alignFrame.getTitle());
152	0	newFrame.setTitle(newtitle);
153
154	0	if (copyAlignment == null)
155		{
156		/*
157		* split frame display is turned off in preferences file
158		*/
159	0	Desktop.addInternalFrame(newFrame, newtitle,
160		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
161	0	xrefViews.add(newFrame.alignPanel);
162	0	return; // via finally clause
163		}
164
165	0	AlignFrame copyThis = new AlignFrame(copyAlignment,
166		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
167	0	copyThis.setTitle(alignFrame.getTitle());
168
169	0	boolean showSequenceFeatures = alignFrame.getViewport()
170		.isShowSequenceFeatures();
171	0	newFrame.setShowSeqFeatures(showSequenceFeatures);
172	0	copyThis.setShowSeqFeatures(showSequenceFeatures);
173	0	FeatureRenderer myFeatureStyling = alignFrame.alignPanel
174		.getSeqPanel().seqCanvas.getFeatureRenderer();
175
176		/*
177		* copy feature rendering settings to split frame
178		*/
179	0	FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
180		.getFeatureRenderer();
181	0	fr1.transferSettings(myFeatureStyling);
182	0	fr1.findAllFeatures(true);
183	0	FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
184		.getFeatureRenderer();
185	0	fr2.transferSettings(myFeatureStyling);
186	0	fr2.findAllFeatures(true);
187
188		/*
189		* apply 'database source' feature configuration
190		* if any was found
191		*/
192		// TODO is this the feature colouring for the original
193		// alignment or the fetched xrefs? either could be Ensembl
194	0	newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
195	0	copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
196
197	0	SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
198	0	dna ? newFrame : copyThis);
199	0	newFrame.setVisible(true);
200	0	copyThis.setVisible(true);
201	0	String linkedTitle = MessageManager
202		.getString("label.linked_view_title");
203	0	Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
204	0	sf.adjustInitialLayout();
205
206		// finally add the top, then bottom frame to the view list
207	0	xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
208	0	xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
209
210		} catch (OutOfMemoryError e)
211		{
212	0	new OOMWarning("whilst fetching crossreferences", e);
213		} catch (Throwable e)
214		{
215	0	Cache.log.error("Error when finding crossreferences", e);
216		} finally
217		{
218	0	alignFrame.setProgressBar(MessageManager.formatMessage(
219		"status.finished_searching_for_sequences_from", new Object[]
220		{ source }), sttime);
221		}
222		}
223
224		/**
225		* Tries to add chromosomal coordinates to any nucleotide sequence which does
226		* not already have them. Coordinates are retrieved from Ensembl given an
227		* Ensembl identifier, either on the sequence itself or on a peptide sequence
228		* it has a reference to.
229		*
230		* <pre>
231		* Example (human):
232		* - fetch EMBLCDS cross-references for Uniprot entry P30419
233		* - the EMBL sequences do not have xrefs to Ensembl
234		* - the Uniprot entry has xrefs to
235		* ENSP00000258960, ENSP00000468424, ENST00000258960, ENST00000592782
236		* - either of the transcript ids can be used to retrieve gene loci e.g.
237		* http://rest.ensembl.org/map/cds/ENST00000592782/1..100000
238		* Example (invertebrate):
239		* - fetch EMBLCDS cross-references for Uniprot entry Q43517 (FER1_SOLLC)
240		* - the Uniprot entry has an xref to ENSEMBLPLANTS Solyc10g044520.1.1
241		* - can retrieve gene loci with
242		* http://rest.ensemblgenomes.org/map/cds/Solyc10g044520.1.1/1..100000
243		* </pre>
244		*
245		* @param sequences
246		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
247	0	public static void findGeneLoci(List<SequenceI> sequences)...
248		{
249	0	Map<DBRefEntry, GeneLociI> retrievedLoci = new HashMap<>();
250	0	for (SequenceI seq : sequences)
251		{
252	0	findGeneLoci(seq, retrievedLoci);
253		}
254		}
255
256		/**
257		* Tres to find chromosomal coordinates for the sequence, by searching its
258		* direct and indirect cross-references for Ensembl. If the loci have already
259		* been retrieved, just reads them out of the map of retrievedLoci; this is
260		* the case of an alternative transcript for the same protein. Otherwise calls
261		* a REST service to retrieve the loci, and if successful, adds them to the
262		* sequence and to the retrievedLoci.
263		*
264		* @param seq
265		* @param retrievedLoci
266		*/
		0% Uncovered Elements: 30 (30) Complexity: 11 Complexity Density: 0.61
267	0	static void findGeneLoci(SequenceI seq,...
268		Map<DBRefEntry, GeneLociI> retrievedLoci)
269		{
270		/*
271		* don't replace any existing chromosomal coordinates
272		*/
273	0	if (seq == null || seq.isProtein() || seq.getGeneLoci() != null
274		|| seq.getDBRefs() == null)
275		{
276	0	return;
277		}
278
279	0	Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
280
281		/*
282		* first look for direct dbrefs from sequence to Ensembl
283		*/
284	0	String[] divisionsArray = ensemblDivisions
285		.toArray(new String[ensemblDivisions.size()]);
286	0	DBRefEntry[] seqRefs = seq.getDBRefs();
287	0	DBRefEntry[] directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
288		divisionsArray);
289	0	if (directEnsemblRefs != null)
290		{
291	0	for (DBRefEntry ensemblRef : directEnsemblRefs)
292		{
293	0	if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
294		{
295	0	return;
296		}
297		}
298		}
299
300		/*
301		* else look for indirect dbrefs from sequence to Ensembl
302		*/
303	0	for (DBRefEntry dbref : seq.getDBRefs())
304		{
305	0	if (dbref.getMap() != null && dbref.getMap().getTo() != null)
306		{
307	0	DBRefEntry[] dbrefs = dbref.getMap().getTo().getDBRefs();
308	0	DBRefEntry[] indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
309		divisionsArray);
310	0	if (indirectEnsemblRefs != null)
311		{
312	0	for (DBRefEntry ensemblRef : indirectEnsemblRefs)
313		{
314	0	if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
315		{
316	0	return;
317		}
318		}
319		}
320		}
321		}
322		}
323
324		/**
325		* Retrieves chromosomal coordinates for the Ensembl (or EnsemblGenomes)
326		* identifier in dbref. If successful, and the sequence length matches gene
327		* loci length, then add it to the sequence, and to the retrievedLoci map.
328		* Answers true if successful, else false.
329		*
330		* @param seq
331		* @param dbref
332		* @param retrievedLoci
333		* @return
334		*/
		0% Uncovered Elements: 32 (32) Complexity: 6 Complexity Density: 0.27
335	0	static boolean fetchGeneLoci(SequenceI seq, DBRefEntry dbref,...
336		Map<DBRefEntry, GeneLociI> retrievedLoci)
337		{
338	0	String accession = dbref.getAccessionId();
339	0	String division = dbref.getSource();
340
341		/*
342		* hack: ignore cross-references to Ensembl protein ids
343		* (or use map/translation perhaps?)
344		* todo: is there an equivalent in EnsemblGenomes?
345		*/
346	0	if (accession.startsWith("ENSP"))
347		{
348	0	return false;
349		}
350	0	EnsemblMap mapper = new EnsemblMap();
351
352		/*
353		* try CDS mapping first
354		*/
355	0	GeneLociI geneLoci = mapper.getCdsMapping(division, accession, 1,
356		seq.getLength());
357	0	if (geneLoci != null)
358		{
359	0	MapList map = geneLoci.getMap();
360	0	int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
361	0	if (mappedFromLength == seq.getLength())
362		{
363	0	seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
364		geneLoci.getChromosomeId(), geneLoci.getMap());
365	0	retrievedLoci.put(dbref, geneLoci);
366	0	return true;
367		}
368		}
369
370		/*
371		* else try CDNA mapping
372		*/
373	0	geneLoci = mapper.getCdnaMapping(division, accession, 1,
374		seq.getLength());
375	0	if (geneLoci != null)
376		{
377	0	MapList map = geneLoci.getMap();
378	0	int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
379	0	if (mappedFromLength == seq.getLength())
380		{
381	0	seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
382		geneLoci.getChromosomeId(), geneLoci.getMap());
383	0	retrievedLoci.put(dbref, geneLoci);
384	0	return true;
385		}
386		}
387
388	0	return false;
389		}
390
391		/**
392		* @param alignment
393		* @param dataset
394		* @param dna
395		* @param xrefs
396		* @param xrefsAlignment
397		* @return
398		*/
		0% Uncovered Elements: 35 (35) Complexity: 10 Complexity Density: 0.43
399	0	protected AlignmentI copyAlignmentForSplitFrame(AlignmentI alignment,...
400		AlignmentI dataset, boolean dna, AlignmentI xrefs,
401		AlignmentI xrefsAlignment)
402		{
403	0	AlignmentI copyAlignment;
404	0	boolean copyAlignmentIsAligned = false;
405	0	if (dna)
406		{
407	0	copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
408		xrefsAlignment.getSequencesArray());
409	0	if (copyAlignment.getHeight() == 0)
410		{
411	0	JvOptionPane.showMessageDialog(alignFrame,
412		MessageManager.getString("label.cant_map_cds"),
413		MessageManager.getString("label.operation_failed"),
414		JvOptionPane.OK_OPTION);
415	0	System.err.println("Failed to make CDS alignment");
416	0	return null;
417		}
418
419		/*
420		* pending getting Embl transcripts to 'align',
421		* we are only doing this for Ensembl
422		*/
423		// TODO proper criteria for 'can align as cdna'
424	0	if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
425		|| AlignmentUtils.looksLikeEnsembl(alignment))
426		{
427	0	copyAlignment.alignAs(alignment);
428	0	copyAlignmentIsAligned = true;
429		}
430		}
431		else
432		{
433	0	copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
434		xrefs.getSequencesArray(), dataset);
435		}
436	0	copyAlignment
437		.setGapCharacter(alignFrame.viewport.getGapCharacter());
438
439	0	StructureSelectionManager ssm = StructureSelectionManager
440		.getStructureSelectionManager(Desktop.instance);
441
442		/*
443		* register any new mappings for sequence mouseover etc
444		* (will not duplicate any previously registered mappings)
445		*/
446	0	ssm.registerMappings(dataset.getCodonFrames());
447
448	0	if (copyAlignment.getHeight() <= 0)
449		{
450	0	System.err.println(
451		"No Sequences generated for xRef type " + source);
452	0	return null;
453		}
454
455		/*
456		* align protein to dna
457		*/
458	0	if (dna && copyAlignmentIsAligned)
459		{
460	0	xrefsAlignment.alignAs(copyAlignment);
461		}
462		else
463		{
464		/*
465		* align cdna to protein - currently only if
466		* fetching and aligning Ensembl transcripts!
467		*/
468		// TODO: generalise for other sources of locus/transcript/cds data
469	0	if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
470		{
471	0	copyAlignment.alignAs(xrefsAlignment);
472		}
473		}
474
475	0	return copyAlignment;
476		}
477
478		/**
479		* Makes an alignment containing the given sequences, and adds them to the
480		* given dataset, which is also set as the dataset for the new alignment
481		*
482		* TODO: refactor to DatasetI method
483		*
484		* @param dataset
485		* @param seqs
486		* @return
487		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.44
488	0	protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,...
489		AlignmentI seqs)
490		{
491	0	SequenceI[] sprods = new SequenceI[seqs.getHeight()];
492	0	for (int s = 0; s < sprods.length; s++)
493		{
494	0	sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
495	0	if (dataset.getSequences() == null || !dataset.getSequences()
496		.contains(sprods[s].getDatasetSequence()))
497		{
498	0	dataset.addSequence(sprods[s].getDatasetSequence());
499		}
500	0	sprods[s].updatePDBIds();
501		}
502	0	Alignment al = new Alignment(sprods);
503	0	al.setDataset(dataset);
504	0	return al;
505		}
506
507		/**
508		* Constructor
509		*
510		* @param af
511		* @param seqs
512		* @param fromDna
513		* @param dbSource
514		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
515	0	CrossRefAction(AlignFrame af, SequenceI[] seqs, boolean fromDna,...
516		String dbSource)
517		{
518	0	this.alignFrame = af;
519	0	this.sel = seqs;
520	0	this._odna = fromDna;
521	0	this.source = dbSource;
522		}
523
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
524	0	public static CrossRefAction getHandlerFor(final SequenceI[] sel,...
525		final boolean fromDna, final String source,
526		final AlignFrame alignFrame)
527		{
528	0	return new CrossRefAction(alignFrame, sel, fromDna, source);
529		}
530
531		}