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Coverage Report

  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.ext.ensembl

File EnsemblSeqProxy.java

 

Coverage histogram

../../../img/srcFileCovDistChart2.png
54% of files have more coverage

Code metrics

100
221
25
2
980
525
87
0.39
8.84
12.5
3.48

Classes

Class Line # Actions
EnsemblSeqProxy 61 219 85
0.1900584819%
EnsemblSeqProxy.EnsemblSeqType 68 2 2
0.00%
 

Contributing tests

This file is covered by 29 tests. .

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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.ext.ensembl;
22   
23    import java.io.IOException;
24    import java.net.MalformedURLException;
25    import java.net.URL;
26    import java.util.ArrayList;
27    import java.util.Arrays;
28    import java.util.Collections;
29    import java.util.List;
30    import java.util.Map;
31   
32    import org.json.simple.parser.ParseException;
33   
34    import jalview.analysis.AlignmentUtils;
35    import jalview.analysis.Dna;
36    import jalview.bin.Console;
37    import jalview.datamodel.Alignment;
38    import jalview.datamodel.AlignmentI;
39    import jalview.datamodel.DBRefEntry;
40    import jalview.datamodel.DBRefSource;
41    import jalview.datamodel.Mapping;
42    import jalview.datamodel.Sequence;
43    import jalview.datamodel.SequenceFeature;
44    import jalview.datamodel.SequenceI;
45    import jalview.datamodel.features.SequenceFeatures;
46    import jalview.exceptions.JalviewException;
47    import jalview.io.gff.Gff3Helper;
48    import jalview.io.gff.SequenceOntologyFactory;
49    import jalview.io.gff.SequenceOntologyI;
50    import jalview.util.Comparison;
51    import jalview.util.DBRefUtils;
52    import jalview.util.IntRangeComparator;
53    import jalview.util.MapList;
54   
55    /**
56    * Base class for Ensembl sequence fetchers
57    *
58    * @see http://rest.ensembl.org/documentation/info/sequence_id
59    * @author gmcarstairs
60    */
 
61    public abstract class EnsemblSeqProxy extends EnsemblRestClient
62    {
63    protected static final String DESCRIPTION = "description";
64   
65    /*
66    * enum for 'type' parameter to the /sequence REST service
67    */
 
68    public enum EnsemblSeqType
69    {
70    /**
71    * type=genomic to fetch full dna including introns
72    */
73    GENOMIC("genomic"),
74   
75    /**
76    * type=cdna to fetch coding dna including UTRs
77    */
78    CDNA("cdna"),
79   
80    /**
81    * type=cds to fetch coding dna excluding UTRs
82    */
83    CDS("cds"),
84   
85    /**
86    * type=protein to fetch peptide product sequence
87    */
88    PROTEIN("protein");
89   
90    /*
91    * the value of the 'type' parameter to fetch this version of
92    * an Ensembl sequence
93    */
94    private String type;
95   
 
96  0 toggle EnsemblSeqType(String t)
97    {
98  0 type = t;
99    }
100   
 
101  0 toggle public String getType()
102    {
103  0 return type;
104    }
105   
106    }
107   
108    /**
109    * Default constructor (to use rest.ensembl.org)
110    */
 
111  49 toggle public EnsemblSeqProxy()
112    {
113  49 super();
114    }
115   
116    /**
117    * Constructor given the target domain to fetch data from
118    */
 
119  0 toggle public EnsemblSeqProxy(String d)
120    {
121  0 super(d);
122    }
123   
124    /**
125    * Makes the sequence queries to Ensembl's REST service and returns an
126    * alignment consisting of the returned sequences.
127    */
 
128  0 toggle @Override
129    public AlignmentI getSequenceRecords(String query) throws Exception
130    {
131    // TODO use a String... query vararg instead?
132   
133    // danger: accession separator used as a regex here, a string elsewhere
134    // in this case it is ok (it is just a space), but (e.g.) '\' would not be
135  0 List<String> allIds = Arrays
136    .asList(query.split(getAccessionSeparator()));
137  0 AlignmentI alignment = null;
138  0 inProgress = true;
139   
140    /*
141    * execute queries, if necessary in batches of the
142    * maximum allowed number of ids
143    */
144  0 int maxQueryCount = getMaximumQueryCount();
145  0 for (int v = 0, vSize = allIds.size(); v < vSize; v += maxQueryCount)
146    {
147  0 int p = Math.min(vSize, v + maxQueryCount);
148  0 List<String> ids = allIds.subList(v, p);
149  0 try
150    {
151  0 alignment = fetchSequences(ids, alignment);
152    } catch (Throwable r)
153    {
154  0 inProgress = false;
155  0 String msg = "Aborting ID retrieval after " + v
156    + " chunks. Unexpected problem (" + r.getLocalizedMessage()
157    + ")";
158  0 jalview.bin.Console.errPrintln(msg);
159  0 r.printStackTrace();
160  0 break;
161    }
162    }
163   
164  0 if (alignment == null)
165    {
166  0 return null;
167    }
168   
169    /*
170    * fetch and transfer genomic sequence features,
171    * fetch protein product and add as cross-reference
172    */
173  0 for (int i = 0, n = allIds.size(); i < n; i++)
174    {
175  0 addFeaturesAndProduct(allIds.get(i), alignment);
176    }
177   
178  0 List<SequenceI> seqs = alignment.getSequences();
179  0 for (int i = 0, n = seqs.size(); i < n; i++)
180    {
181  0 getCrossReferences(seqs.get(i));
182    }
183   
184  0 return alignment;
185    }
186   
187    /**
188    * Fetches Ensembl features using the /overlap REST endpoint, and adds them to
189    * the sequence in the alignment. Also fetches the protein product, maps it
190    * from the CDS features of the sequence, and saves it as a cross-reference of
191    * the dna sequence.
192    *
193    * @param accId
194    * @param alignment
195    */
 
196  0 toggle protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
197    {
198  0 if (alignment == null)
199    {
200  0 return;
201    }
202   
203  0 try
204    {
205    /*
206    * get 'dummy' genomic sequence with gene, transcript,
207    * exon, cds and variation features
208    */
209  0 SequenceI genomicSequence = null;
210  0 EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
211  0 EnsemblFeatureType[] features = getFeaturesToFetch();
212   
213    // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);
214   
215  0 AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
216    features);
217  0 if (geneFeatures != null && geneFeatures.getHeight() > 0)
218    {
219  0 genomicSequence = geneFeatures.getSequenceAt(0);
220    }
221   
222    // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);
223   
224  0 if (genomicSequence != null)
225    {
226    /*
227    * transfer features to the query sequence
228    */
229  0 SequenceI querySeq = alignment.findName(accId, true);
230  0 if (transferFeatures(accId, genomicSequence, querySeq))
231    {
232   
233    /*
234    * fetch and map protein product, and add it as a cross-reference
235    * of the retrieved sequence
236    */
237    // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);
238  0 addProteinProduct(querySeq);
239    }
240    }
241    } catch (IOException e)
242    {
243  0 jalview.bin.Console.errPrintln(
244    "Error transferring Ensembl features: " + e.getMessage());
245    }
246    // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
247    }
248   
249    /**
250    * Returns those sequence feature types to fetch from Ensembl. We may want
251    * features either because they are of interest to the user, or as means to
252    * identify the locations of the sequence on the genomic sequence (CDS
253    * features identify CDS, exon features identify cDNA etc).
254    *
255    * @return
256    */
257    protected abstract EnsemblFeatureType[] getFeaturesToFetch();
258   
259    /**
260    * Fetches and maps the protein product, and adds it as a cross-reference of
261    * the retrieved sequence
262    */
 
263  0 toggle protected void addProteinProduct(SequenceI querySeq)
264    {
265  0 String accId = querySeq.getName();
266  0 try
267    {
268  0 jalview.bin.Console.outPrintln("Adding protein product for " + accId);
269  0 AlignmentI protein = new EnsemblProtein(getDomain())
270    .getSequenceRecords(accId);
271  0 if (protein == null || protein.getHeight() == 0)
272    {
273  0 jalview.bin.Console
274    .outPrintln("No protein product found for " + accId);
275  0 return;
276    }
277  0 SequenceI proteinSeq = protein.getSequenceAt(0);
278   
279    /*
280    * need dataset sequences (to be the subject of mappings)
281    */
282  0 proteinSeq.createDatasetSequence();
283  0 querySeq.createDatasetSequence();
284   
285  0 MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq,
286    proteinSeq);
287  0 if (mapList != null)
288    {
289    // clunky: ensure Uniprot xref if we have one is on mapped sequence
290  0 SequenceI ds = proteinSeq.getDatasetSequence();
291    // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence()
292  0 Mapping map = new Mapping(ds, mapList);
293  0 DBRefEntry dbr = new DBRefEntry(getDbSource(),
294    getEnsemblDataVersion(), proteinSeq.getName(), map);
295  0 querySeq.getDatasetSequence().addDBRef(dbr);
296  0 List<DBRefEntry> uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
297    new String[]
298    { DBRefSource.UNIPROT });
299  0 List<DBRefEntry> upxrefs = DBRefUtils
300    .selectRefs(querySeq.getDBRefs(), new String[]
301    { DBRefSource.UNIPROT });
302  0 if (uprots != null)
303    {
304  0 for (DBRefEntry up : uprots)
305    {
306    // locate local uniprot ref and map
307  0 List<DBRefEntry> upx = DBRefUtils.searchRefs(upxrefs,
308    up.getAccessionId());
309  0 DBRefEntry upxref;
310  0 if (upx.size() != 0)
311    {
312  0 upxref = upx.get(0);
313   
314  0 if (upx.size() > 1)
315    {
316  0 Console.warn(
317    "Implementation issue - multiple uniprot acc on product sequence.");
318    }
319    }
320    else
321    {
322  0 upxref = new DBRefEntry(DBRefSource.UNIPROT,
323    getEnsemblDataVersion(), up.getAccessionId());
324    }
325   
326  0 Mapping newMap = new Mapping(ds, mapList);
327  0 upxref.setVersion(getEnsemblDataVersion());
328  0 upxref.setMap(newMap);
329  0 if (upx.size() == 0)
330    {
331    // add the new uniprot ref
332  0 querySeq.getDatasetSequence().addDBRef(upxref);
333    }
334   
335    }
336    }
337   
338    /*
339    * copy exon features to protein, compute peptide variants from dna
340    * variants and add as features on the protein sequence ta-da
341    */
342    // JAL-3187 render on the fly instead
343    // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList);
344    }
345    } catch (Exception e)
346    {
347  0 System.err
348    .println(String.format("Error retrieving protein for %s: %s",
349    accId, e.getMessage()));
350    }
351    }
352   
353    /**
354    * Get database xrefs from Ensembl, and attach them to the sequence
355    *
356    * @param seq
357    */
 
358  0 toggle protected void getCrossReferences(SequenceI seq)
359    {
360   
361    // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);
362   
363  0 while (seq.getDatasetSequence() != null)
364    {
365  0 seq = seq.getDatasetSequence();
366    }
367   
368    // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);
369   
370  0 EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
371    getEnsemblDataVersion());
372  0 List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
373   
374  0 for (int i = 0, n = xrefs.size(); i < n; i++)
375    {
376    // Platform.timeCheck("ESP. getxref + " + (i) + "/" + n,
377    // Platform.TIME_MARK);
378    // BH 2019.01.25 this next method was taking 174 ms PER addition for a
379    // 266-reference example.
380    // DBRefUtils.ensurePrimaries(seq)
381    // was at the end of seq.addDBRef, so executed after ever addition!
382    // This method was moved to seq.getPrimaryDBRefs()
383  0 seq.addDBRef(xrefs.get(i));
384    }
385   
386    // jalview.bin.Console.outPrintln("primaries are " +
387    // seq.getPrimaryDBRefs().toString());
388    /*
389    * and add a reference to itself
390    */
391   
392    // Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);
393   
394  0 DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
395    seq.getName());
396   
397    // Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);
398   
399  0 seq.addDBRef(self);
400   
401    // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);
402    }
403   
404    /**
405    * Fetches sequences for the list of accession ids and adds them to the
406    * alignment. Returns the extended (or created) alignment.
407    *
408    * @param ids
409    * @param alignment
410    * @return
411    * @throws JalviewException
412    * @throws IOException
413    */
 
414  0 toggle protected AlignmentI fetchSequences(List<String> ids,
415    AlignmentI alignment) throws JalviewException, IOException
416    {
417  0 if (!isEnsemblAvailable())
418    {
419  0 inProgress = false;
420  0 throw new JalviewException("ENSEMBL Rest API not available.");
421    }
422    // Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
423   
424  0 List<SequenceI> seqs = parseSequenceJson(ids);
425  0 if (seqs == null)
426  0 return alignment;
427   
428  0 if (seqs.isEmpty())
429    {
430  0 throw new IOException("No data returned for " + ids);
431    }
432   
433  0 if (seqs.size() != ids.size())
434    {
435  0 jalview.bin.Console.outPrintln(String.format(
436    "Only retrieved %d sequences for %d query strings",
437    seqs.size(), ids.size()));
438    }
439   
440  0 if (!seqs.isEmpty())
441    {
442  0 AlignmentI seqal = new Alignment(
443    seqs.toArray(new SequenceI[seqs.size()]));
444  0 for (SequenceI seq : seqs)
445    {
446  0 if (seq.getDescription() == null)
447    {
448  0 seq.setDescription(getDbName());
449    }
450  0 String name = seq.getName();
451  0 if (ids.contains(name)
452    || ids.contains(name.replace("ENSP", "ENST")))
453    {
454    // TODO JAL-3077 use true accession version in dbref
455  0 DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(),
456    getEnsemblDataVersion(), name);
457  0 seq.addDBRef(dbref);
458    }
459    }
460  0 if (alignment == null)
461    {
462  0 alignment = seqal;
463    }
464    else
465    {
466  0 alignment.append(seqal);
467    }
468    }
469  0 return alignment;
470    }
471   
472    /**
473    * Parses a JSON response for a single sequence ID query
474    *
475    * @param br
476    * @return a single jalview.datamodel.Sequence
477    * @see http://rest.ensembl.org/documentation/info/sequence_id
478    */
 
479  0 toggle @SuppressWarnings("unchecked")
480    protected List<SequenceI> parseSequenceJson(List<String> ids)
481    {
482  0 List<SequenceI> result = new ArrayList<>();
483  0 try
484    {
485    /*
486    * for now, assumes only one sequence returned; refactor if needed
487    * in future to handle a JSONArray with more than one
488    */
489    // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
490  0 Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1,
491    MODE_MAP, null);
492  0 if (val == null)
493  0 return null;
494  0 Object s = val.get("desc");
495  0 String desc = s == null ? null : s.toString();
496  0 s = val.get("id");
497  0 String id = s == null ? null : s.toString();
498  0 s = val.get("seq");
499  0 String seq = s == null ? null : s.toString();
500  0 Sequence sequence = new Sequence(id, seq);
501  0 if (desc != null)
502    {
503  0 sequence.setDescription(desc);
504    }
505    // todo JAL-3077 make a DBRefEntry with true accession version
506    // s = val.get("version");
507    // String version = s == null ? "0" : s.toString();
508    // DBRefEntry dbref = new DBRefEntry(getDbSource(), version, id);
509    // sequence.addDBRef(dbref);
510  0 result.add(sequence);
511    } catch (ParseException | IOException e)
512    {
513  0 jalview.bin.Console.errPrintln(
514    "Error processing JSON response: " + e.toString());
515    // ignore
516    }
517    // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
518  0 return result;
519    }
520   
521    /**
522    * Returns the URL for the REST call
523    *
524    * @return
525    * @throws MalformedURLException
526    */
 
527  0 toggle @Override
528    protected URL getUrl(List<String> ids) throws MalformedURLException
529    {
530    /*
531    * a single id is included in the URL path
532    * multiple ids go in the POST body instead
533    */
534  0 StringBuffer urlstring = new StringBuffer(128);
535  0 urlstring.append(getDomain() + "/sequence/id");
536  0 if (ids.size() == 1)
537    {
538  0 urlstring.append("/").append(ids.get(0));
539    }
540    // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
541  0 urlstring.append("?type=").append(getSourceEnsemblType().getType());
542  0 urlstring.append(("&Accept=application/json"));
543  0 urlstring.append(("&content-type=application/json"));
544   
545  0 String objectType = getObjectType();
546  0 if (objectType != null)
547    {
548  0 urlstring.append("&").append(OBJECT_TYPE).append("=")
549    .append(objectType);
550    }
551   
552  0 URL url = new URL(urlstring.toString());
553  0 return url;
554    }
555   
556    /**
557    * Override this method to specify object_type request parameter
558    *
559    * @return
560    */
 
561  0 toggle protected String getObjectType()
562    {
563  0 return null;
564    }
565   
566    /**
567    * A sequence/id POST request currently allows up to 50 queries
568    *
569    * @see http://rest.ensembl.org/documentation/info/sequence_id_post
570    */
 
571  0 toggle @Override
572    public int getMaximumQueryCount()
573    {
574  0 return 50;
575    }
576   
 
577  0 toggle @Override
578    protected boolean useGetRequest()
579    {
580  0 return false;
581    }
582   
583    /**
584    *
585    * @return the configured sequence return type for this source
586    */
587    protected abstract EnsemblSeqType getSourceEnsemblType();
588   
589    /**
590    * Returns a list of [start, end] genomic ranges corresponding to the sequence
591    * being retrieved.
592    *
593    * The correspondence between the frames of reference is made by locating
594    * those features on the genomic sequence which identify the retrieved
595    * sequence. Specifically
596    * <ul>
597    * <li>genomic sequence is identified by "transcript" features with
598    * ID=transcript:transcriptId</li>
599    * <li>cdna sequence is identified by "exon" features with
600    * Parent=transcript:transcriptId</li>
601    * <li>cds sequence is identified by "CDS" features with
602    * Parent=transcript:transcriptId</li>
603    * </ul>
604    *
605    * The returned ranges are sorted to run forwards (for positive strand) or
606    * backwards (for negative strand). Aborts and returns null if both positive
607    * and negative strand are found (this should not normally happen).
608    *
609    * @param sourceSequence
610    * @param accId
611    * @param start
612    * the start position of the sequence we are mapping to
613    * @return
614    */
 
615  7 toggle protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
616    String accId, int start)
617    {
618  7 List<SequenceFeature> sfs = getIdentifyingFeatures(sourceSequence,
619    accId);
620  7 if (sfs.isEmpty())
621    {
622  1 return null;
623    }
624   
625    /*
626    * generously initial size for number of cds regions
627    * (worst case titin Q8WZ42 has c. 313 exons)
628    */
629  6 List<int[]> regions = new ArrayList<>(100);
630  6 int mappedLength = 0;
631  6 int direction = 1; // forward
632  6 boolean directionSet = false;
633   
634  6 for (SequenceFeature sf : sfs)
635    {
636  11 int strand = sf.getStrand();
637  11 strand = strand == 0 ? 1 : strand; // treat unknown as forward
638   
639  11 if (directionSet && strand != direction)
640    {
641    // abort - mix of forward and backward
642  0 System.err
643    .println("Error: forward and backward strand for " + accId);
644  0 return null;
645    }
646  11 direction = strand;
647  11 directionSet = true;
648   
649    /*
650    * add to CDS ranges, semi-sorted forwards/backwards
651    */
652  11 if (strand < 0)
653    {
654  2 regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
655    }
656    else
657    {
658  9 regions.add(new int[] { sf.getBegin(), sf.getEnd() });
659    }
660  11 mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
661    }
662   
663  6 if (regions.isEmpty())
664    {
665  0 jalview.bin.Console
666    .outPrintln("Failed to identify target sequence for " + accId
667    + " from genomic features");
668  0 return null;
669    }
670   
671    /*
672    * a final sort is needed since Ensembl returns CDS sorted within source
673    * (havana / ensembl_havana)
674    */
675  6 Collections.sort(regions, direction == 1 ? IntRangeComparator.ASCENDING
676    : IntRangeComparator.DESCENDING);
677   
678  6 List<int[]> to = Arrays
679    .asList(new int[]
680    { start, start + mappedLength - 1 });
681   
682  6 return new MapList(regions, to, 1, 1);
683    }
684   
685    /**
686    * Answers a list of sequence features that mark positions of the genomic
687    * sequence feature which are within the sequence being retrieved. For
688    * example, an 'exon' feature whose parent is the target transcript marks the
689    * cdna positions of the transcript. For a gene sequence, this is trivially
690    * just the 'gene' feature with matching gene id.
691    *
692    * @param seq
693    * @param accId
694    * @return
695    */
696    protected abstract List<SequenceFeature> getIdentifyingFeatures(
697    SequenceI seq, String accId);
698   
699    int bhtest = 0;
700   
701    /**
702    * Transfers the sequence feature to the target sequence, locating its start
703    * and end range based on the mapping. Features which do not overlap the
704    * target sequence are ignored.
705    *
706    * @param sf
707    * @param targetSequence
708    * @param mapping
709    * mapping from the sequence feature's coordinates to the target
710    * sequence
711    * @param forwardStrand
712    */
 
713  0 toggle protected void transferFeature(SequenceFeature sf,
714    SequenceI targetSequence, MapList mapping, boolean forwardStrand)
715    {
716  0 int start = sf.getBegin();
717  0 int end = sf.getEnd();
718  0 int[] mappedRange = mapping.locateInTo(start, end);
719   
720  0 if (mappedRange != null)
721    {
722    // Platform.timeCheck(null, Platform.TIME_SET);
723  0 String group = sf.getFeatureGroup();
724  0 if (".".equals(group))
725    {
726  0 group = getDbSource();
727    }
728  0 int newBegin = Math.min(mappedRange[0], mappedRange[1]);
729  0 int newEnd = Math.max(mappedRange[0], mappedRange[1]);
730    // Platform.timeCheck(null, Platform.TIME_MARK);
731  0 bhtest++;
732    // 280 ms/1000 here:
733  0 SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
734    group, sf.getScore());
735    // 0.175 ms here:
736  0 targetSequence.addSequenceFeature(copy);
737   
738    /*
739    * for sequence_variant on reverse strand, have to convert the allele
740    * values to their complements
741    */
742  0 if (!forwardStrand && SequenceOntologyFactory.getInstance()
743    .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
744    {
745  0 reverseComplementAlleles(copy);
746    }
747    }
748    }
749   
750    /**
751    * Change the 'alleles' value of a feature by converting to complementary
752    * bases, and also update the feature description to match
753    *
754    * @param sf
755    */
 
756  1 toggle static void reverseComplementAlleles(SequenceFeature sf)
757    {
758  1 final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
759  1 if (alleles == null)
760    {
761  0 return;
762    }
763  1 StringBuilder complement = new StringBuilder(alleles.length());
764  1 for (String allele : alleles.split(","))
765    {
766  5 reverseComplementAllele(complement, allele);
767    }
768  1 String comp = complement.toString();
769  1 sf.setValue(Gff3Helper.ALLELES, comp);
770  1 sf.setDescription(comp);
771    }
772   
773    /**
774    * Makes the 'reverse complement' of the given allele and appends it to the
775    * buffer, after a comma separator if not the first
776    *
777    * @param complement
778    * @param allele
779    */
 
780  13 toggle static void reverseComplementAllele(StringBuilder complement,
781    String allele)
782    {
783  13 if (complement.length() > 0)
784    {
785  10 complement.append(",");
786    }
787   
788    /*
789    * some 'alleles' are actually descriptive terms
790    * e.g. HGMD_MUTATION, PhenCode_variation
791    * - we don't want to 'reverse complement' these
792    */
793  13 if (!Comparison.isNucleotideSequence(allele, true))
794    {
795  3 complement.append(allele);
796    }
797    else
798    {
799  29 for (int i = allele.length() - 1; i >= 0; i--)
800    {
801  19 complement.append(Dna.getComplement(allele.charAt(i)));
802    }
803    }
804    }
805   
806    /**
807    * Transfers features from sourceSequence to targetSequence
808    *
809    * @param accessionId
810    * @param sourceSequence
811    * @param targetSequence
812    * @return true if any features were transferred, else false
813    */
 
814  0 toggle protected boolean transferFeatures(String accessionId,
815    SequenceI sourceSequence, SequenceI targetSequence)
816    {
817  0 if (sourceSequence == null || targetSequence == null)
818    {
819  0 return false;
820    }
821   
822    // long start = System.currentTimeMillis();
823  0 List<SequenceFeature> sfs = sourceSequence.getFeatures()
824    .getPositionalFeatures();
825  0 MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
826    accessionId, targetSequence.getStart());
827  0 if (mapping == null)
828    {
829  0 return false;
830    }
831   
832    // Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);
833   
834  0 boolean result = transferFeatures(sfs, targetSequence, mapping,
835    accessionId);
836    // jalview.bin.Console.outPrintln("transferFeatures (" + (sfs.size()) + "
837    // --> "
838    // + targetSequence.getFeatures().getFeatureCount(true) + ") to "
839    // + targetSequence.getName() + " took "
840    // + (System.currentTimeMillis() - start) + "ms");
841  0 return result;
842    }
843   
844    /**
845    * Transfer features to the target sequence. The start/end positions are
846    * converted using the mapping. Features which do not overlap are ignored.
847    * Features whose parent is not the specified identifier are also ignored.
848    *
849    * @param sfs
850    * @param targetSequence
851    * @param mapping
852    * @param parentId
853    * @return
854    */
 
855  0 toggle protected boolean transferFeatures(List<SequenceFeature> sfs,
856    SequenceI targetSequence, MapList mapping, String parentId)
857    {
858  0 final boolean forwardStrand = mapping.isFromForwardStrand();
859   
860    /*
861    * sort features by start position (which corresponds to end
862    * position descending if reverse strand) so as to add them in
863    * 'forwards' order to the target sequence
864    */
865  0 SequenceFeatures.sortFeatures(sfs, forwardStrand);
866   
867  0 boolean transferred = false;
868   
869  0 for (int i = 0, n = sfs.size(); i < n; i++)
870    {
871   
872    // if ((i%1000) == 0) {
873    //// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
874    // Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n,
875    // Platform.TIME_MARK);
876    // }
877   
878  0 SequenceFeature sf = sfs.get(i);
879  0 if (retainFeature(sf, parentId))
880    {
881  0 transferFeature(sf, targetSequence, mapping, forwardStrand);
882  0 transferred = true;
883    }
884    }
885   
886  0 return transferred;
887    }
888   
889    /**
890    * Answers true if the feature type is one we want to keep for the sequence.
891    * Some features are only retrieved in order to identify the sequence range,
892    * and may then be discarded as redundant information (e.g. "CDS" feature for
893    * a CDS sequence).
894    */
 
895  0 toggle @SuppressWarnings("unused")
896    protected boolean retainFeature(SequenceFeature sf, String accessionId)
897    {
898  0 return true; // override as required
899    }
900   
901    /**
902    * Answers true if the feature has a Parent which refers to the given
903    * accession id, or if the feature has no parent. Answers false if the
904    * feature's Parent is for a different accession id.
905    *
906    * @param sf
907    * @param identifier
908    * @return
909    */
 
910  10 toggle protected boolean featureMayBelong(SequenceFeature sf, String identifier)
911    {
912  10 String parent = (String) sf.getValue(PARENT);
913  10 if (parent != null && !parent.equalsIgnoreCase(identifier))
914    {
915    // this genomic feature belongs to a different transcript
916  3 return false;
917    }
918  7 return true;
919    }
920   
921    /**
922    * Answers a short description of the sequence fetcher
923    */
 
924  0 toggle @Override
925    public String getDescription()
926    {
927  0 return "Ensembl " + getSourceEnsemblType().getType()
928    + " sequence with variant features";
929    }
930   
931    /**
932    * Returns a (possibly empty) list of features on the sequence which have the
933    * specified sequence ontology term (or a sub-type of it), and the given
934    * identifier as parent
935    *
936    * @param sequence
937    * @param term
938    * @param parentId
939    * @return
940    */
 
941  0 toggle protected List<SequenceFeature> findFeatures(SequenceI sequence,
942    String term, String parentId)
943    {
944  0 List<SequenceFeature> result = new ArrayList<>();
945   
946  0 List<SequenceFeature> sfs = sequence.getFeatures()
947    .getFeaturesByOntology(term);
948  0 for (SequenceFeature sf : sfs)
949    {
950  0 String parent = (String) sf.getValue(PARENT);
951  0 if (parent != null && parent.equalsIgnoreCase(parentId))
952    {
953  0 result.add(sf);
954    }
955    }
956   
957  0 return result;
958    }
959   
960    /**
961    * Answers true if the feature type is either 'NMD_transcript_variant' or
962    * 'transcript' (or one of its sub-types in the Sequence Ontology). This is
963    * because NMD_transcript_variant behaves like 'transcript' in Ensembl
964    * although strictly speaking it is not (it is a sub-type of
965    * sequence_variant).
966    * <p>
967    * (This test was needed when fetching transcript features as GFF. As we are
968    * now fetching as JSON, all features have type 'transcript' so the check for
969    * NMD_transcript_variant is redundant. Left in for any future case arising.)
970    *
971    * @param featureType
972    * @return
973    */
 
974  18 toggle public static boolean isTranscript(String featureType)
975    {
976  18 return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
977    || SequenceOntologyFactory.getInstance().isA(featureType,
978    SequenceOntologyI.TRANSCRIPT);
979    }
980    }
  • Report generated by OpenClover v 4.4.1 on Mon Sep 2 2024 18:05:00 BST using coverage data from Mon Sep 2 2024 18:04:45 BST.
  • OpenClover is free and open-source software.