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  1. Project Clover database Wed Nov 6 2024 00:56:24 GMT
  2. Package jalview.util

File DBRefUtils.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
36% of files have more coverage

Code metrics

132
179
22
2
826
506
155
0.87
8.14
11
7.05

Classes

Class Line # Actions
DBRefUtils 43 178 154
0.6072507560.7%
DBRefUtils.DbRefComp 292 1 1
0.00%
 

Contributing tests

This file is covered by 275 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.util;
22   
23    import java.util.ArrayList;
24    import java.util.BitSet;
25    import java.util.HashMap;
26    import java.util.HashSet;
27    import java.util.List;
28    import java.util.Locale;
29    import java.util.Map;
30   
31    import com.stevesoft.pat.Regex;
32   
33    import jalview.bin.Console;
34    import jalview.datamodel.DBRefEntry;
35    import jalview.datamodel.DBRefSource;
36    import jalview.datamodel.Mapping;
37    import jalview.datamodel.PDBEntry;
38    import jalview.datamodel.SequenceI;
39   
40    /**
41    * Utilities for handling DBRef objects and their collections.
42    */
 
43    public class DBRefUtils
44    {
45    /*
46    * lookup from lower-case form of a name to its canonical (standardised) form
47    */
48    private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
49   
50    public final static int DB_SOURCE = 1;
51   
52    public final static int DB_VERSION = 2;
53   
54    public final static int DB_ID = 4;
55   
56    public final static int DB_MAP = 8;
57   
58    public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID;
59   
60    public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID
61    | DB_MAP;
62   
 
63  50 toggle static
64    {
65    // TODO load these from a resource file?
66  50 canonicalSourceNameLookup.put("uniprotkb/swiss-prot",
67    DBRefSource.UNIPROT);
68  50 canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
69   
70    // Ensembl values for dbname in xref REST service:
71  50 canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT);
72  50 canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT);
73   
74  50 canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
75  50 canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
76    // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
77    // from ENA.
78  50 canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
79  50 canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
80   
81    // guarantee we always have lowercase entries for canonical string lookups
82  50 for (String k : canonicalSourceNameLookup.keySet())
83    {
84  400 canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
85    canonicalSourceNameLookup.get(k));
86    }
87    }
88   
89    /**
90    * Returns those DBRefEntry objects whose source identifier (once converted to
91    * Jalview's canonical form) is in the list of sources to search for. Returns
92    * null if no matches found.
93    *
94    * @param dbrefs
95    * DBRefEntry objects to search
96    * @param sources
97    * array of sources to select
98    * @return
99    */
 
100  13849 toggle public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs,
101    String[] sources)
102    {
103  13849 if (dbrefs == null || sources == null)
104    {
105  9938 return dbrefs;
106    }
107   
108    // BH TODO (what?)
109  3911 HashSet<String> srcs = new HashSet<String>();
110  3911 for (String src : sources)
111    {
112  17413 srcs.add(src.toUpperCase(Locale.ROOT));
113    }
114   
115  3911 int nrefs = dbrefs.size();
116  3911 List<DBRefEntry> res = new ArrayList<DBRefEntry>();
117  24754 for (int ib = 0; ib < nrefs; ib++)
118    {
119  20843 DBRefEntry dbr = dbrefs.get(ib);
120  20843 String source = getCanonicalName(dbr.getSource());
121  20843 if (srcs.contains(source.toUpperCase(Locale.ROOT)))
122    {
123  3493 res.add(dbr);
124    }
125    }
126  3911 if (res.size() > 0)
127    {
128    // List<DBRefEntry> reply = new DBRefEntry[res.size()];
129  2178 return res;// .toArray(reply);
130    }
131  1733 return null;
132    }
133   
 
134  23 toggle private static boolean selectRefsBS(List<DBRefEntry> dbrefs,
135    int sourceKeys, BitSet bsSelect)
136    {
137  23 if (dbrefs == null || sourceKeys == 0)
138    {
139  0 return false;
140    }
141  348 for (int i = 0, n = dbrefs.size(); i < n; i++)
142    {
143  325 DBRefEntry dbr = dbrefs.get(i);
144  325 if ((dbr.getSourceKey() & sourceKeys) != 0)
145    {
146  90 bsSelect.clear(i);
147    }
148    }
149  23 return !bsSelect.isEmpty();
150    }
151   
152    /**
153    * Returns a (possibly empty) list of those references that match the given
154    * entry, according to the given comparator.
155    *
156    * @param refs
157    * an array of database references to search
158    * @param entry
159    * an entry to compare against
160    * @param comparator
161    * @return
162    */
 
163  0 toggle static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
164    DbRefComp comparator)
165    {
166  0 List<DBRefEntry> rfs = new ArrayList<>();
167  0 if (refs == null || entry == null)
168    {
169  0 return rfs;
170    }
171  0 for (int i = 0; i < refs.length; i++)
172    {
173  0 if (comparator.matches(entry, refs[i]))
174    {
175  0 rfs.add(refs[i]);
176    }
177    }
178  0 return rfs;
179    }
180   
181    /**
182    * look up source in an internal list of database reference sources and return
183    * the canonical jalview name for the source, or the original string if it has
184    * no canonical form.
185    *
186    * @param source
187    * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*)
188    * or original source
189    */
 
190  271806 toggle public static String getCanonicalName(String source)
191    {
192  271806 if (source == null)
193    {
194  1 return null;
195    }
196  271805 String canonical = canonicalSourceNameLookup
197    .get(source.toLowerCase(Locale.ROOT));
198  271804 return canonical == null ? source : canonical;
199    }
200   
201    /**
202    * Returns a (possibly empty) list of those references that match the given
203    * entry. Currently uses a comparator which matches if
204    * <ul>
205    * <li>database sources are the same</li>
206    * <li>accession ids are the same</li>
207    * <li>both have no mapping, or the mappings are the same</li>
208    * </ul>
209    *
210    * @param ref
211    * Set of references to search
212    * @param entry
213    * pattern to match
214    * @param mode
215    * SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
216    * @return
217    */
 
218  5048 toggle public static List<DBRefEntry> searchRefs(List<DBRefEntry> ref,
219    DBRefEntry entry, int mode)
220    {
221  5048 return searchRefs(ref, entry,
222    matchDbAndIdAndEitherMapOrEquivalentMapList, mode);
223    }
224   
225    /**
226    * Returns a list of those references that match the given accession id
227    * <ul>
228    * <li>database sources are the same</li>
229    * <li>accession ids are the same</li>
230    * <li>both have no mapping, or the mappings are the same</li>
231    * </ul>
232    *
233    * @param refs
234    * Set of references to search
235    * @param accId
236    * accession id to match
237    * @return
238    */
 
239  6 toggle public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs,
240    String accId)
241    {
242  6 List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
243  6 if (refs == null || accId == null)
244    {
245  0 return rfs;
246    }
247  22 for (int i = 0, n = refs.size(); i < n; i++)
248    {
249  16 DBRefEntry e = refs.get(i);
250  16 if (accId.equals(e.getAccessionId()))
251    {
252  8 rfs.add(e);
253    }
254    }
255  6 return rfs;
256    // return searchRefs(refs, new DBRefEntry("", "", accId), matchId,
257    // SEARCH_MODE_FULL);
258    }
259   
260    /**
261    * Returns a (possibly empty) list of those references that match the given
262    * entry, according to the given comparator.
263    *
264    * @param refs
265    * an array of database references to search
266    * @param entry
267    * an entry to compare against
268    * @param comparator
269    * @param mode
270    * SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
271    * @return
272    */
 
273  5048 toggle static List<DBRefEntry> searchRefs(List<DBRefEntry> refs,
274    DBRefEntry entry, DbRefComp comparator, int mode)
275    {
276  5048 List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
277  5048 if (refs == null || entry == null)
278    {
279  1 return rfs;
280    }
281  106882 for (int i = 0, n = refs.size(); i < n; i++)
282    {
283  101835 DBRefEntry e = refs.get(i);
284  101835 if (comparator.matches(entry, e, SEARCH_MODE_FULL))
285    {
286  889 rfs.add(e);
287    }
288    }
289  5047 return rfs;
290    }
291   
 
292    interface DbRefComp
293    {
 
294  0 toggle default public boolean matches(DBRefEntry refa, DBRefEntry refb)
295    {
296  0 return matches(refa, refb, SEARCH_MODE_FULL);
297    };
298   
299    public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode);
300    }
301   
302    /**
303    * match on all non-null fields in refa
304    */
305    // TODO unused - remove? would be broken by equating "" with null
306    public static DbRefComp matchNonNullonA = new DbRefComp()
307    {
 
308  0 toggle @Override
309    public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
310    {
311  0 if ((mode & DB_SOURCE) != 0 && (refa.getSource() == null
312    || DBRefUtils.getCanonicalName(refb.getSource()).equals(
313    DBRefUtils.getCanonicalName(refa.getSource()))))
314    {
315  0 if ((mode & DB_VERSION) != 0 && (refa.getVersion() == null
316    || refb.getVersion().equals(refa.getVersion())))
317    {
318  0 if ((mode & DB_ID) != 0 && (refa.getAccessionId() == null
319    || refb.getAccessionId().equals(refa.getAccessionId())))
320    {
321  0 if ((mode & DB_MAP) != 0
322    && (refa.getMap() == null || (refb.getMap() != null
323    && refb.getMap().equals(refa.getMap()))))
324    {
325  0 return true;
326    }
327    }
328    }
329    }
330  0 return false;
331    }
332    };
333   
334    /**
335    * either field is null or field matches for all of source, version, accession
336    * id and map.
337    */
338    // TODO unused - remove?
339    public static DbRefComp matchEitherNonNull = new DbRefComp()
340    {
 
341  0 toggle @Override
342    public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
343    {
344  0 if (nullOrEqualSource(refa.getSource(), refb.getSource())
345    && nullOrEqual(refa.getVersion(), refb.getVersion())
346    && nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
347    && nullOrEqual(refa.getMap(), refb.getMap()))
348    {
349  0 return true;
350    }
351  0 return false;
352    }
353   
354    };
355   
356    /**
357    * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
358    * database is PDB.
359    * <p>
360    * Used by file parsers to generate DBRefs from annotation within file (eg
361    * Stockholm)
362    *
363    * @param dbname
364    * @param version
365    * @param acn
366    * @param seq
367    * where to annotate with reference
368    * @return parsed version of entry that was added to seq (if any)
369    */
 
370  1551 toggle public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
371    String version, String acn)
372    {
373  1551 DBRefEntry ref = null;
374  1551 if (dbname != null)
375    {
376  1551 String locsrc = DBRefUtils.getCanonicalName(dbname);
377  1551 if (locsrc.equals(DBRefSource.PDB))
378    {
379    /*
380    * Check for PFAM style stockhom PDB accession id citation e.g.
381    * "1WRI A; 7-80;"
382    */
383  27 Regex r = new com.stevesoft.pat.Regex(
384    "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
385  27 if (r.search(acn.trim()))
386    {
387  27 String pdbid = r.stringMatched(1);
388  27 String chaincode = r.stringMatched(2);
389  27 if (chaincode == null)
390    {
391  0 chaincode = " ";
392    }
393    // String mapstart = r.stringMatched(3);
394    // String mapend = r.stringMatched(4);
395  27 if (chaincode.equals(" "))
396    {
397  0 chaincode = "_";
398    }
399    // construct pdb ref.
400  27 ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
401  27 PDBEntry pdbr = new PDBEntry();
402  27 pdbr.setId(pdbid);
403  27 pdbr.setType(PDBEntry.Type.PDB);
404  27 pdbr.setChainCode(chaincode);
405  27 seq.addPDBId(pdbr);
406    }
407    else
408    {
409  0 jalview.bin.Console.errPrintln("Malformed PDB DR line:" + acn);
410    }
411    }
412    else
413    {
414    // default:
415  1524 ref = new DBRefEntry(locsrc, version, acn.trim());
416    }
417    }
418  1551 if (ref != null)
419    {
420  1551 seq.addDBRef(ref);
421    }
422  1551 return ref;
423    }
424   
425    /**
426    * accession ID and DB must be identical. Version is ignored. Map is either
427    * not defined or is a match (or is compatible?)
428    */
429    // TODO unused - remove?
430    public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
431    {
 
432  0 toggle @Override
433    public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
434    {
435  0 if (refa.getSource() != null && refb.getSource() != null
436    && DBRefUtils.getCanonicalName(refb.getSource()).equals(
437    DBRefUtils.getCanonicalName(refa.getSource())))
438    {
439    // We dont care about version
440  0 if (refa.getAccessionId() != null && refb.getAccessionId() != null
441    // FIXME should be && not || here?
442    || refb.getAccessionId().equals(refa.getAccessionId()))
443    {
444  0 if ((refa.getMap() == null || refb.getMap() == null)
445    || (refa.getMap() != null && refb.getMap() != null
446    && refb.getMap().equals(refa.getMap())))
447    {
448  0 return true;
449    }
450    }
451    }
452  0 return false;
453    }
454    };
455   
456    /**
457    * accession ID and DB must be identical. Version is ignored. No map on either
458    * or map but no maplist on either or maplist of map on a is the complement of
459    * maplist of map on b.
460    */
461    // TODO unused - remove?
462    public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
463    {
 
464  0 toggle @Override
465    public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
466    {
467  0 if (refa.getSource() != null && refb.getSource() != null
468    && DBRefUtils.getCanonicalName(refb.getSource()).equals(
469    DBRefUtils.getCanonicalName(refa.getSource())))
470    {
471    // We dont care about version
472  0 if (refa.getAccessionId() != null && refb.getAccessionId() != null
473    || refb.getAccessionId().equals(refa.getAccessionId()))
474    {
475  0 if ((refa.getMap() == null && refb.getMap() == null)
476    || (refa.getMap() != null && refb.getMap() != null))
477    {
478  0 if ((refb.getMap().getMap() == null
479    && refa.getMap().getMap() == null)
480    || (refb.getMap().getMap() != null
481    && refa.getMap().getMap() != null
482    && refb.getMap().getMap().getInverse()
483    .equals(refa.getMap().getMap())))
484    {
485  0 return true;
486    }
487    }
488    }
489    }
490  0 return false;
491    }
492    };
493   
494    /**
495    * accession ID and DB must be identical. Version is ignored. No map on both
496    * or or map but no maplist on either or maplist of map on a is equivalent to
497    * the maplist of map on b.
498    */
499    // TODO unused - remove?
500    public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
501    {
 
502  0 toggle @Override
503    public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
504    {
505  0 if (refa.getSource() != null && refb.getSource() != null
506    && DBRefUtils.getCanonicalName(refb.getSource()).equals(
507    DBRefUtils.getCanonicalName(refa.getSource())))
508    {
509    // We dont care about version
510    // if ((refa.getVersion()==null || refb.getVersion()==null)
511    // || refb.getVersion().equals(refa.getVersion()))
512    // {
513  0 if (refa.getAccessionId() != null && refb.getAccessionId() != null
514    || refb.getAccessionId().equals(refa.getAccessionId()))
515    {
516  0 if (refa.getMap() == null && refb.getMap() == null)
517    {
518  0 return true;
519    }
520  0 if (refa.getMap() != null && refb.getMap() != null
521    && ((refb.getMap().getMap() == null
522    && refa.getMap().getMap() == null)
523    || (refb.getMap().getMap() != null
524    && refa.getMap().getMap() != null
525    && refb.getMap().getMap()
526    .equals(refa.getMap().getMap()))))
527    {
528  0 return true;
529    }
530    }
531    }
532  0 return false;
533    }
534    };
535   
536    /**
537    * accession ID and DB must be identical, or null on a. Version is ignored. No
538    * map on either or map but no maplist on either or maplist of map on a is
539    * equivalent to the maplist of map on b.
540    */
541    public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
542    {
 
543  101835 toggle @Override
544    public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
545    {
546  101835 if (refa.getSource() != null && refb.getSource() != null
547    && DBRefUtils.getCanonicalName(refb.getSource()).equals(
548    DBRefUtils.getCanonicalName(refa.getSource())))
549    {
550    // We dont care about version
551  11597 if (refa.getAccessionId() == null
552    || refa.getAccessionId().equals(refb.getAccessionId()))
553    {
554  912 if (refa.getMap() == null || refb.getMap() == null)
555    {
556  888 return true;
557    }
558  24 if ((refa.getMap() != null && refb.getMap() != null)
559    && (refb.getMap().getMap() == null
560    && refa.getMap().getMap() == null)
561    || (refb.getMap().getMap() != null
562    && refa.getMap().getMap() != null
563    && (refb.getMap().getMap()
564    .equals(refa.getMap().getMap()))))
565    {
566  1 return true;
567    }
568    }
569    }
570  100946 return false;
571    }
572    };
573   
574    /**
575    * Returns the (possibly empty) list of those supplied dbrefs which have the
576    * specified source database, with a case-insensitive match of source name
577    *
578    * @param dbRefs
579    * @param source
580    * @return
581    */
 
582  0 toggle public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
583    String source)
584    {
585  0 List<DBRefEntry> matches = new ArrayList<>();
586  0 if (dbRefs != null && source != null)
587    {
588  0 for (DBRefEntry dbref : dbRefs)
589    {
590  0 if (source.equalsIgnoreCase(dbref.getSource()))
591    {
592  0 matches.add(dbref);
593    }
594    }
595    }
596  0 return matches;
597    }
598   
599    /**
600    * Returns true if either object is null, or they are equal
601    *
602    * @param o1
603    * @param o2
604    * @return
605    */
 
606  0 toggle public static boolean nullOrEqual(Object o1, Object o2)
607    {
608  0 if (o1 == null || o2 == null)
609    {
610  0 return true;
611    }
612  0 return o1.equals(o2);
613    }
614   
615    /**
616    * canonicalise source string before comparing. null is always wildcard
617    *
618    * @param o1
619    * - null or source string to compare
620    * @param o2
621    * - null or source string to compare
622    * @return true if either o1 or o2 are null, or o1 equals o2 under
623    * DBRefUtils.getCanonicalName
624    * (o1).equals(DBRefUtils.getCanonicalName(o2))
625    */
 
626  0 toggle public static boolean nullOrEqualSource(String o1, String o2)
627    {
628  0 if (o1 == null || o2 == null)
629    {
630  0 return true;
631    }
632  0 return DBRefUtils.getCanonicalName(o1)
633    .equals(DBRefUtils.getCanonicalName(o2));
634    }
635   
636    /**
637    * Selects just the DNA or protein references from a set of references
638    *
639    * @param selectDna
640    * if true, select references to 'standard' DNA databases, else to
641    * 'standard' peptide databases
642    * @param refs
643    * a set of references to select from
644    * @return
645    */
 
646  13752 toggle public static List<DBRefEntry> selectDbRefs(boolean selectDna,
647    List<DBRefEntry> refs)
648    {
649  13752 return selectRefs(refs,
650  13752 selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
651    // could attempt to find other cross
652    // refs here - ie PDB xrefs
653    // (not dna, not protein seq)
654    }
655   
656    /**
657    * Returns the (possibly empty) list of those supplied dbrefs which have the
658    * specified source database, with a case-insensitive match of source name
659    *
660    * @param dbRefs
661    * @param source
662    * @return
663    */
 
664  48 toggle public static List<DBRefEntry> searchRefsForSource(
665    List<DBRefEntry> dbRefs, String source)
666    {
667  48 List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
668  48 if (dbRefs != null && source != null)
669    {
670  46 for (DBRefEntry dbref : dbRefs)
671    {
672  129 if (source.equalsIgnoreCase(dbref.getSource()))
673    {
674  48 matches.add(dbref);
675    }
676    }
677    }
678  48 return matches;
679    }
680   
681    /**
682    * promote direct database references to primary for nucleotide or protein
683    * sequences if they have an appropriate primary ref
684    * <table>
685    * <tr>
686    * <th>Seq Type</th>
687    * <th>Primary DB</th>
688    * <th>Direct which will be promoted</th>
689    * </tr>
690    * <tr align=center>
691    * <td>peptides</td>
692    * <td>Ensembl</td>
693    * <td>Uniprot</td>
694    * </tr>
695    * <tr align=center>
696    * <td>peptides</td>
697    * <td>Ensembl</td>
698    * <td>Uniprot</td>
699    * </tr>
700    * <tr align=center>
701    * <td>dna</td>
702    * <td>Ensembl</td>
703    * <td>ENA</td>
704    * </tr>
705    * </table>
706    *
707    * @param sequence
708    */
 
709  288 toggle public static void ensurePrimaries(SequenceI sequence,
710    List<DBRefEntry> pr)
711    {
712  288 if (pr.size() == 0)
713    {
714    // nothing to do
715  268 return;
716    }
717  20 int sstart = sequence.getStart();
718  20 int send = sequence.getEnd();
719  20 boolean isProtein = sequence.isProtein();
720  20 BitSet bsSelect = new BitSet();
721   
722    // List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
723    // {
724   
725    // List<DBRefEntry> selddfs = selectDbRefs(!isprot, sequence.getDBRefs());
726    // if (selfs == null || selfs.size() == 0)
727    // {
728    // // nothing to do
729    // return;
730    // }
731   
732  20 List<DBRefEntry> dbrefs = sequence.getDBRefs();
733  20 bsSelect.set(0, dbrefs.size());
734   
735  20 if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK
736    : DBRefSource.DNA_CODING_MASK, bsSelect))
737  2 return;
738   
739    // selfs.addAll(selfArray);
740    // }
741   
742    // filter non-primary refs
743  42 for (int ip = pr.size(); --ip >= 0;)
744    {
745  24 DBRefEntry p = pr.get(ip);
746  268 for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect
747    .nextSetBit(i + 1))
748    {
749  244 if (dbrefs.get(i) == p)
750  3 bsSelect.clear(i);
751    }
752    // while (selfs.contains(p))
753    // {
754    // selfs.remove(p);
755    // }
756    }
757    // List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
758   
759  20 for (int ip = pr.size(), keys = 0; --ip >= 0
760    && keys != DBRefSource.PRIMARY_MASK;)
761    {
762  19 DBRefEntry p = pr.get(ip);
763  19 if (isProtein)
764    {
765  5 switch (getCanonicalName(p.getSource()))
766    {
767  3 case DBRefSource.UNIPROT:
768  3 keys |= DBRefSource.UNIPROT_MASK;
769  3 break;
770  0 case DBRefSource.ENSEMBL:
771  0 keys |= DBRefSource.ENSEMBL_MASK;
772  0 break;
773    }
774    }
775    else
776    {
777    // TODO: promote transcript refs ??
778    }
779  19 if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
780  17 return;
781    // if (candidates != null)
782    {
783  8 for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect
784    .nextSetBit(ic + 1))
785    // for (int ic = 0, n = candidates.size(); ic < n; ic++)
786    {
787  6 DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic);
788  6 if (cand.hasMap())
789    {
790  0 Mapping map = cand.getMap();
791  0 SequenceI cto = map.getTo();
792  0 if (cto != null && cto != sequence)
793    {
794    // can't promote refs with mappings to other sequences
795  0 continue;
796    }
797  0 MapList mlist = map.getMap();
798  0 if (mlist.getFromLowest() != sstart
799    && mlist.getFromHighest() != send)
800    {
801    // can't promote refs with mappings from a region of this sequence
802    // - eg CDS
803  0 continue;
804    }
805    }
806    // and promote - not that version must be non-null here,
807    // as p must have passed isPrimaryCandidate()
808  6 cand.setVersion(cand.getVersion() + " (promoted)");
809  6 bsSelect.clear(ic);
810    // selfs.remove(cand);
811    // toPromote.add(cand);
812  6 if (!cand.isPrimaryCandidate())
813    {
814  3 if (Console.isDebugEnabled())
815    {
816  0 Console.debug(
817    "Warning: Couldn't promote dbref " + cand.toString()
818    + " for sequence " + sequence.toString());
819    }
820    }
821    }
822    }
823    }
824    }
825   
826    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 6 2024 01:03:43 GMT using coverage data from Wed Nov 6 2024 01:03:32 GMT.
  • OpenClover is free and open-source software.