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  1. Project Clover database Thu Nov 7 2024 10:11:34 GMT
  2. Package jalview.ws

File DBRefFetcher.java

 

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60% of files have more coverage

Code metrics

136
240
12
2
850
577
97
0.4
20
6
8.08

Classes

Class Line # Actions
DBRefFetcher 64 240 97
0.00%
DBRefFetcher.FetchFinishedListenerI 70 0 0
-1.0 -
 

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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.ws;
22   
23    import java.util.Locale;
24   
25    import java.util.ArrayList;
26    import java.util.Arrays;
27    import java.util.Enumeration;
28    import java.util.HashMap;
29    import java.util.Hashtable;
30    import java.util.List;
31    import java.util.Map;
32    import java.util.StringTokenizer;
33    import java.util.Vector;
34    import java.util.regex.Matcher;
35    import java.util.regex.Pattern;
36   
37    import jalview.analysis.AlignSeq;
38    import jalview.api.FeatureSettingsModelI;
39    import jalview.bin.Cache;
40    import jalview.bin.Console;
41    import jalview.datamodel.AlignmentI;
42    import jalview.datamodel.DBRefEntry;
43    import jalview.datamodel.DBRefSource;
44    import jalview.datamodel.Mapping;
45    import jalview.datamodel.SequenceI;
46    import jalview.gui.CutAndPasteTransfer;
47    import jalview.gui.Desktop;
48    import jalview.gui.FeatureSettings;
49    import jalview.gui.IProgressIndicator;
50    import jalview.gui.OOMWarning;
51    import jalview.util.DBRefUtils;
52    import jalview.util.MessageManager;
53    import jalview.ws.seqfetcher.DbSourceProxy;
54    import uk.ac.ebi.picr.model.UPEntry;
55    import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
56   
57    /**
58    * Implements a runnable for validating a sequence against external databases
59    * and then propagating references and features onto the sequence(s)
60    *
61    * @author $author$
62    * @version $Revision$
63    */
 
64    public class DBRefFetcher implements Runnable
65    {
66    private static final String NEWLINE = System.lineSeparator();
67   
68    public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
69   
 
70    public interface FetchFinishedListenerI
71    {
72    void finished();
73    }
74   
75    SequenceI[] dataset;
76   
77    IProgressIndicator progressWindow;
78   
79    CutAndPasteTransfer output = new CutAndPasteTransfer();
80   
81    /**
82    * picr client instance
83    */
84    uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
85   
86    // This will be a collection of Vectors of sequenceI refs.
87    // The key will be the seq name or accession id of the seq
88    Hashtable<String, Vector<SequenceI>> seqRefs;
89   
90    DbSourceProxy[] dbSources;
91   
92    SequenceFetcher sfetcher;
93   
94    private List<FetchFinishedListenerI> listeners;
95   
96    private SequenceI[] alseqs;
97   
98    /*
99    * when true - retrieved sequences will be trimmed to cover longest derived
100    * alignment sequence
101    */
102    private boolean trimDsSeqs = true;
103   
104    /**
105    * Creates a new DBRefFetcher object and fetches from the currently selected
106    * set of databases, if this is null then it fetches based on feature settings
107    *
108    * @param seqs
109    * fetch references for these SequenceI array
110    * @param progressIndicatorFrame
111    * the frame for progress bar monitoring
112    * @param sources
113    * array of DbSourceProxy to query references form
114    * @param featureSettings
115    * FeatureSettings to get alternative DbSourceProxy from
116    * @param isNucleotide
117    * indicates if the array of SequenceI are Nucleotides or not
118    */
 
119  0 toggle public DBRefFetcher(SequenceI[] seqs,
120    IProgressIndicator progressIndicatorFrame,
121    DbSourceProxy[] sources, FeatureSettings featureSettings,
122    boolean isNucleotide)
123    {
124  0 listeners = new ArrayList<>();
125  0 this.progressWindow = progressIndicatorFrame;
126  0 alseqs = new SequenceI[seqs.length];
127  0 SequenceI[] ds = new SequenceI[seqs.length];
128  0 for (int i = 0; i < seqs.length; i++)
129    {
130  0 alseqs[i] = seqs[i];
131  0 if (seqs[i].getDatasetSequence() != null)
132    {
133  0 ds[i] = seqs[i].getDatasetSequence();
134    }
135    else
136    {
137  0 ds[i] = seqs[i];
138    }
139    }
140  0 this.dataset = ds;
141    // TODO Jalview 2.5 lots of this code should be in the gui package!
142  0 sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
143    // set default behaviour for transferring excess sequence data to the
144    // dataset
145  0 trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
146  0 if (sources == null)
147    {
148  0 setDatabaseSources(featureSettings, isNucleotide);
149    }
150    else
151    {
152    // we assume the caller knows what they're doing and ensured that all the
153    // db source names are valid
154  0 dbSources = sources;
155    }
156    }
157   
158    /**
159    * Helper method to configure the list of database sources to query
160    *
161    * @param featureSettings
162    * @param forNucleotide
163    */
 
164  0 toggle void setDatabaseSources(FeatureSettings featureSettings,
165    boolean forNucleotide)
166    {
167    // af.featureSettings_actionPerformed(null);
168  0 String[] defdb = null;
169  0 List<DbSourceProxy> selsources = new ArrayList<>();
170    // select appropriate databases based on alignFrame context.
171  0 if (forNucleotide)
172    {
173  0 defdb = DBRefSource.DNACODINGDBS;
174    }
175    else
176    {
177  0 defdb = DBRefSource.PROTEINDBS;
178    }
179  0 List<DbSourceProxy> srces = new ArrayList<>();
180  0 for (String ddb : defdb)
181    {
182  0 List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
183  0 if (srcesfordb != null)
184    {
185  0 for (DbSourceProxy src : srcesfordb)
186    {
187  0 if (!srces.contains(src))
188    {
189  0 srces.addAll(srcesfordb);
190    }
191    }
192    }
193    }
194    // append the PDB data source, since it is 'special', catering for both
195    // nucleotide and protein
196    // srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
197   
198  0 srces.addAll(selsources);
199  0 dbSources = srces.toArray(new DbSourceProxy[srces.size()]);
200    }
201   
202    /**
203    * Constructor with only sequences provided
204    *
205    * @param sequences
206    */
 
207  0 toggle public DBRefFetcher(SequenceI[] sequences)
208    {
209  0 this(sequences, null, null, null, false);
210    }
211   
212    /**
213    * Add a listener to be notified when sequence fetching is complete
214    *
215    * @param l
216    */
 
217  0 toggle public void addListener(FetchFinishedListenerI l)
218    {
219  0 listeners.add(l);
220    }
221   
222    /**
223    * start the fetcher thread
224    *
225    * @param waitTillFinished
226    * true to block until the fetcher has finished
227    */
 
228  0 toggle public void fetchDBRefs(boolean waitTillFinished)
229    {
230  0 if (waitTillFinished)
231    {
232  0 run();
233    }
234    else
235    {
236  0 new Thread(this).start();
237    }
238    }
239   
240    /**
241    * The sequence will be added to a vector of sequences belonging to key which
242    * could be either seq name or dbref id
243    *
244    * @param seq
245    * SequenceI
246    * @param key
247    * String
248    */
 
249  0 toggle void addSeqId(SequenceI seq, String key)
250    {
251  0 key = key.toUpperCase(Locale.ROOT);
252   
253  0 Vector<SequenceI> seqs;
254  0 if (seqRefs.containsKey(key))
255    {
256  0 seqs = seqRefs.get(key);
257   
258  0 if (seqs != null && !seqs.contains(seq))
259    {
260  0 seqs.addElement(seq);
261    }
262  0 else if (seqs == null)
263    {
264  0 seqs = new Vector<>();
265  0 seqs.addElement(seq);
266    }
267   
268    }
269    else
270    {
271  0 seqs = new Vector<>();
272  0 seqs.addElement(seq);
273    }
274   
275  0 seqRefs.put(key, seqs);
276    }
277   
278    /**
279    * DOCUMENT ME!
280    */
 
281  0 toggle @Override
282    public void run()
283    {
284  0 if (dbSources == null)
285    {
286  0 throw new Error(MessageManager
287    .getString("error.implementation_error_must_init_dbsources"));
288    }
289  0 long startTime = System.currentTimeMillis();
290  0 if (progressWindow != null)
291    {
292  0 progressWindow.setProgressBar(
293    MessageManager.getString("status.fetching_db_refs"),
294    startTime);
295    }
296  0 try
297    {
298  0 if (Cache.getDefault("DBREFFETCH_USEPICR", false))
299    {
300  0 picrClient = new AccessionMapperServiceLocator()
301    .getAccessionMapperPort();
302    }
303    } catch (Exception e)
304    {
305  0 jalview.bin.Console
306    .errPrintln("Couldn't locate PICR service instance.\n");
307  0 e.printStackTrace();
308    }
309   
310  0 Vector<SequenceI> sdataset = new Vector<>(Arrays.asList(dataset));
311  0 List<String> warningMessages = new ArrayList<>();
312   
313    // clear any old feature display settings recorded from past sessions
314  0 featureDisplaySettings = null;
315   
316  0 int db = 0;
317  0 while (sdataset.size() > 0 && db < dbSources.length)
318    {
319  0 int maxqlen = 1; // default number of queries made at one time
320  0 jalview.bin.Console
321    .outPrintln("Verifying against " + dbSources[db].getDbName());
322   
323    // iterate through db for each remaining un-verified sequence
324  0 SequenceI[] currSeqs = new SequenceI[sdataset.size()];
325  0 sdataset.copyInto(currSeqs);// seqs that are to be validated against
326    // dbSources[db]
327  0 Vector<String> queries = new Vector<>(); // generated queries curSeq
328  0 seqRefs = new Hashtable<>();
329   
330  0 int seqIndex = 0;
331   
332  0 DbSourceProxy dbsource = dbSources[db];
333    // for moment, we dumbly iterate over all retrieval sources for a
334    // particular database
335    // TODO: introduce multithread multisource queries and logic to remove a
336    // query from other sources if any source for a database returns a
337    // record
338  0 maxqlen = dbsource.getMaximumQueryCount();
339   
340  0 while (queries.size() > 0 || seqIndex < currSeqs.length)
341    {
342  0 if (queries.size() > 0)
343    {
344    // Still queries to make for current seqIndex
345  0 StringBuffer queryString = new StringBuffer("");
346  0 int numq = 0;
347  0 int nqSize = (maxqlen > queries.size()) ? queries.size()
348    : maxqlen;
349   
350  0 while (queries.size() > 0 && numq < nqSize)
351    {
352  0 String query = queries.elementAt(0);
353  0 if (dbsource.isValidReference(query))
354    {
355  0 queryString.append(
356  0 (numq == 0) ? "" : dbsource.getAccessionSeparator());
357  0 queryString.append(query);
358  0 numq++;
359    }
360    // remove the extracted query string
361  0 queries.removeElementAt(0);
362    }
363    // make the queries and process the response
364  0 AlignmentI retrieved = null;
365  0 try
366    {
367  0 if (Console.isDebugEnabled())
368    {
369  0 Console.debug("Querying " + dbsource.getDbName() + " with : '"
370    + queryString.toString() + "'");
371    }
372  0 retrieved = dbsource.getSequenceRecords(queryString.toString());
373    } catch (Exception ex)
374    {
375  0 ex.printStackTrace();
376    } catch (OutOfMemoryError err)
377    {
378  0 new OOMWarning("retrieving database references ("
379    + queryString.toString() + ")", err);
380    }
381  0 if (retrieved != null)
382    {
383  0 transferReferences(sdataset, dbsource, retrieved, trimDsSeqs,
384    warningMessages);
385    }
386    }
387    else
388    {
389    // make some more strings for use as queries
390  0 for (int i = 0; (seqIndex < dataset.length)
391    && (i < 50); seqIndex++, i++)
392    {
393  0 SequenceI sequence = dataset[seqIndex];
394  0 List<DBRefEntry> uprefs = DBRefUtils
395    .selectRefs(sequence.getDBRefs(), new String[]
396    { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
397    // });
398    // check for existing dbrefs to use
399  0 if (uprefs != null && uprefs.size() > 0)
400    {
401  0 for (int j = 0, n = uprefs.size(); j < n; j++)
402    {
403  0 DBRefEntry upref = uprefs.get(j);
404  0 addSeqId(sequence, upref.getAccessionId());
405  0 queries.addElement(
406    upref.getAccessionId().toUpperCase(Locale.ROOT));
407    }
408    }
409    else
410    {
411  0 Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
412    // generate queries from sequence ID string
413  0 Matcher tokens = possibleIds.matcher(sequence.getName());
414  0 int p = 0;
415  0 while (tokens.find(p))
416    {
417  0 String token = tokens.group();
418  0 p = tokens.end();
419  0 UPEntry[] presp = null;
420  0 if (picrClient != null)
421    {
422    // resolve the string against PICR to recover valid IDs
423  0 try
424    {
425  0 presp = picrClient.getUPIForAccession(token, null,
426    picrClient.getMappedDatabaseNames(), null,
427    true);
428    } catch (Exception e)
429    {
430  0 jalview.bin.Console.errPrintln(
431    "Exception with Picr for '" + token + "'\n");
432  0 e.printStackTrace();
433    }
434    }
435  0 if (presp != null && presp.length > 0)
436    {
437  0 for (int id = 0; id < presp.length; id++)
438    {
439    // construct sequences from response if sequences are
440    // present, and do a transferReferences
441    // otherwise transfer non sequence x-references directly.
442    }
443  0 jalview.bin.Console.outPrintln(
444    "Validated ID against PICR... (for what its worth):"
445    + token);
446  0 addSeqId(sequence, token);
447  0 queries.addElement(token.toUpperCase(Locale.ROOT));
448    }
449    else
450    {
451    // if ()
452    // jalview.bin.Console.outPrintln("Not querying source with
453    // token="+token+"\n");
454  0 addSeqId(sequence, token);
455  0 queries.addElement(token.toUpperCase(Locale.ROOT));
456    }
457    }
458    }
459    }
460    }
461    }
462    // advance to next database
463  0 db++;
464    } // all databases have been queried
465  0 if (!warningMessages.isEmpty())
466    {
467  0 StringBuilder sb = new StringBuilder(warningMessages.size() * 30);
468  0 sb.append(MessageManager
469    .getString("label.your_sequences_have_been_verified"));
470  0 for (String msg : warningMessages)
471    {
472  0 sb.append(msg).append(NEWLINE);
473    }
474  0 output.setText(sb.toString());
475   
476  0 Desktop.addInternalFrame(output,
477    MessageManager.getString("label.sequences_updated"), 600,
478    300);
479    // The above is the dataset, we must now find out the index
480    // of the viewed sequence
481   
482    }
483  0 if (progressWindow != null)
484    {
485  0 progressWindow.setProgressBar(
486    MessageManager.getString("label.dbref_search_completed"),
487    startTime);
488    }
489   
490  0 for (FetchFinishedListenerI listener : listeners)
491    {
492  0 listener.finished();
493    }
494    }
495   
496    /**
497    * Verify local sequences in seqRefs against the retrieved sequence database
498    * records. Returns true if any sequence was modified as a result (start/end
499    * changed and/or sequence enlarged), else false.
500    *
501    * @param sdataset
502    * dataset sequences we are retrieving for
503    * @param dbSource
504    * database source we are retrieving from
505    * @param retrievedAl
506    * retrieved sequences as alignment
507    * @param trimDatasetSeqs
508    * if true, sequences will not be enlarged to match longer retrieved
509    * sequences, only their start/end adjusted
510    * @param warningMessages
511    * a list of messages to add to
512    */
 
513  0 toggle boolean transferReferences(Vector<SequenceI> sdataset,
514    DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
515    boolean trimDatasetSeqs, List<String> warningMessages)
516    {
517    // jalview.bin.Console.outPrintln("trimming ? " + trimDatasetSeqs);
518  0 if (retrievedAl == null || retrievedAl.getHeight() == 0)
519    {
520  0 return false;
521    }
522   
523  0 String dbSource = dbSourceProxy.getDbName();
524  0 boolean modified = false;
525  0 SequenceI[] retrieved = recoverDbSequences(
526    retrievedAl.getSequencesArray());
527  0 SequenceI sequence = null;
528   
529  0 for (SequenceI retrievedSeq : retrieved)
530    {
531    // Work out which sequences this sequence matches,
532    // taking into account all accessionIds and names in the file
533  0 Vector<SequenceI> sequenceMatches = new Vector<>();
534    // look for corresponding accession ids
535  0 List<DBRefEntry> entryRefs = DBRefUtils
536    .selectRefs(retrievedSeq.getDBRefs(), new String[]
537    { dbSource });
538  0 if (entryRefs == null)
539    {
540  0 System.err
541    .println("Dud dbSource string ? no entryrefs selected for "
542    + dbSource + " on " + retrievedSeq.getName());
543  0 continue;
544    }
545  0 for (int j = 0, n = entryRefs.size(); j < n; j++)
546    {
547  0 DBRefEntry ref = entryRefs.get(j);
548  0 String accessionId = ref.getAccessionId();
549    // match up on accessionId
550  0 if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
551    {
552  0 Vector<SequenceI> seqs = seqRefs.get(accessionId);
553  0 for (int jj = 0; jj < seqs.size(); jj++)
554    {
555  0 sequence = seqs.elementAt(jj);
556  0 if (!sequenceMatches.contains(sequence))
557    {
558  0 sequenceMatches.addElement(sequence);
559    }
560    }
561    }
562    }
563  0 if (sequenceMatches.isEmpty())
564    {
565    // failed to match directly on accessionId==query so just compare all
566    // sequences to entry
567  0 Enumeration<String> e = seqRefs.keys();
568  0 while (e.hasMoreElements())
569    {
570  0 Vector<SequenceI> sqs = seqRefs.get(e.nextElement());
571  0 if (sqs != null && sqs.size() > 0)
572    {
573  0 Enumeration<SequenceI> sqe = sqs.elements();
574  0 while (sqe.hasMoreElements())
575    {
576  0 sequenceMatches.addElement(sqe.nextElement());
577    }
578    }
579    }
580    }
581    // look for corresponding names
582    // this is uniprot specific ?
583    // could be useful to extend this so we try to find any 'significant'
584    // information in common between two sequence objects.
585    /*
586    * List<DBRefEntry> entryRefs =
587    * jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] {
588    * dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String
589    * name = entry.getName().elementAt(j).toString(); if
590    * (seqRefs.containsKey(name)) { Vector seqs = (Vector) seqRefs.get(name);
591    * for (int jj = 0; jj < seqs.size(); jj++) { sequence = (SequenceI)
592    * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {
593    * sequenceMatches.addElement(sequence); } } } }
594    */
595  0 if (sequenceMatches.size() > 0)
596    {
597  0 addFeatureSettings(dbSourceProxy);
598    }
599    // sequenceMatches now contains the set of all sequences associated with
600    // the returned db record
601  0 final String retrievedSeqString = retrievedSeq.getSequenceAsString();
602  0 String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT);
603  0 for (int m = 0; m < sequenceMatches.size(); m++)
604    {
605  0 sequence = sequenceMatches.elementAt(m);
606    // only update start and end positions and shift features if there are
607    // no existing references
608    // TODO: test for legacy where uniprot or EMBL refs exist but no
609    // mappings are made (but content matches retrieved set)
610  0 boolean updateRefFrame = sequence.getDBRefs() == null
611    || sequence.getDBRefs().size() == 0;
612    // TODO:
613    // verify sequence against the entry sequence
614   
615  0 Mapping mp;
616  0 final int sequenceStart = sequence.getStart();
617   
618  0 boolean remoteEnclosesLocal = false;
619  0 String nonGapped = AlignSeq
620    .extractGaps("-. ", sequence.getSequenceAsString())
621    .toUpperCase(Locale.ROOT);
622  0 int absStart = entrySeq.indexOf(nonGapped);
623  0 if (absStart == -1)
624    {
625    // couldn't find local sequence in sequence from database, so check if
626    // the database sequence is a subsequence of local sequence
627  0 absStart = nonGapped.indexOf(entrySeq);
628  0 if (absStart == -1)
629    {
630    // verification failed. couldn't find any relationship between
631    // entrySeq and local sequence
632    // messages suppressed as many-to-many matches are confusing
633    // String msg = sequence.getName()
634    // + " Sequence not 100% match with "
635    // + retrievedSeq.getName();
636    // addWarningMessage(warningMessages, msg);
637  0 continue;
638    }
639    /*
640    * retrieved sequence is a proper subsequence of local sequence
641    */
642  0 String msg = sequence.getName() + " has " + absStart
643    + " prefixed residues compared to "
644    + retrievedSeq.getName();
645  0 addWarningMessage(warningMessages, msg);
646   
647    /*
648    * So create a mapping to the external entry from the matching region of
649    * the local sequence, and leave local start/end untouched.
650    */
651  0 mp = new Mapping(null,
652    new int[]
653    { sequenceStart + absStart,
654    sequenceStart + absStart + entrySeq.length() - 1 },
655    new int[]
656    { retrievedSeq.getStart(),
657    retrievedSeq.getStart() + entrySeq.length() - 1 },
658    1, 1);
659  0 updateRefFrame = false;
660    }
661    else
662    {
663    /*
664    * local sequence is a subsequence of (or matches) retrieved sequence
665    */
666  0 remoteEnclosesLocal = true;
667  0 mp = null;
668   
669  0 if (updateRefFrame)
670    {
671    /*
672    * relocate existing sequence features by offset
673    */
674  0 int startShift = absStart - sequenceStart + 1;
675  0 if (startShift != 0)
676    {
677  0 modified |= sequence.getFeatures().shiftFeatures(1,
678    startShift);
679    }
680    }
681    }
682   
683  0 jalview.bin.Console.outPrintln("Adding dbrefs to "
684    + sequence.getName() + " from " + dbSource + " sequence : "
685    + retrievedSeq.getName());
686  0 sequence.transferAnnotation(retrievedSeq, mp);
687   
688  0 absStart += retrievedSeq.getStart();
689  0 int absEnd = absStart + nonGapped.length() - 1;
690  0 if (!trimDatasetSeqs)
691    {
692    /*
693    * update start position and/or expand to longer retrieved sequence
694    */
695  0 if (!retrievedSeqString.equals(sequence.getSequenceAsString())
696    && remoteEnclosesLocal)
697    {
698  0 sequence.setSequence(retrievedSeqString);
699  0 modified = true;
700  0 addWarningMessage(warningMessages,
701    "Sequence for " + sequence.getName() + " expanded from "
702    + retrievedSeq.getName());
703    }
704  0 if (sequence.getStart() != retrievedSeq.getStart())
705    {
706  0 sequence.setStart(retrievedSeq.getStart());
707  0 modified = true;
708  0 if (absStart != sequenceStart)
709    {
710  0 addWarningMessage(warningMessages,
711    "Start/end position for " + sequence.getName()
712    + " updated from " + retrievedSeq.getName());
713    }
714    }
715    }
716  0 if (updateRefFrame)
717    {
718    // finally, update local sequence reference frame if we're allowed
719  0 if (trimDatasetSeqs)
720    {
721    // just fix start/end
722  0 if (sequence.getStart() != absStart
723    || sequence.getEnd() != absEnd)
724    {
725  0 sequence.setStart(absStart);
726  0 sequence.setEnd(absEnd);
727  0 modified = true;
728  0 addWarningMessage(warningMessages,
729    "Start/end for " + sequence.getName()
730    + " updated from " + retrievedSeq.getName());
731    }
732    }
733    // search for alignment sequences to update coordinate frame for
734  0 for (int alsq = 0; alsq < alseqs.length; alsq++)
735    {
736  0 if (alseqs[alsq].getDatasetSequence() == sequence)
737    {
738  0 String ngAlsq = AlignSeq
739    .extractGaps("-. ",
740    alseqs[alsq].getSequenceAsString())
741    .toUpperCase(Locale.ROOT);
742  0 int oldstrt = alseqs[alsq].getStart();
743  0 alseqs[alsq].setStart(sequence.getSequenceAsString()
744    .toUpperCase(Locale.ROOT).indexOf(ngAlsq)
745    + sequence.getStart());
746  0 if (oldstrt != alseqs[alsq].getStart())
747    {
748  0 alseqs[alsq].setEnd(
749    ngAlsq.length() + alseqs[alsq].getStart() - 1);
750  0 modified = true;
751    }
752    }
753    }
754    // TODO: search for all other references to this dataset sequence, and
755    // update start/end
756    // TODO: update all AlCodonMappings which involve this alignment
757    // sequence (e.g. Q30167 cdna translation from exon2 product (vamsas
758    // demo)
759    }
760    // and remove it from the rest
761    // TODO: decide if we should remove annotated sequence from set
762  0 sdataset.remove(sequence);
763    }
764    }
765  0 return modified;
766    }
767   
768    Map<String, FeatureSettingsModelI> featureDisplaySettings = null;
769   
 
770  0 toggle private void addFeatureSettings(DbSourceProxy dbSourceProxy)
771    {
772  0 FeatureSettingsModelI fsettings = dbSourceProxy
773    .getFeatureColourScheme();
774  0 if (fsettings != null)
775    {
776  0 if (featureDisplaySettings == null)
777    {
778  0 featureDisplaySettings = new HashMap<>();
779    }
780  0 featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings);
781    }
782    }
783   
784    /**
785    *
786    * @return any feature settings associated with sources that have provided
787    * sequences
788    */
 
789  0 toggle public List<FeatureSettingsModelI> getFeatureSettingsModels()
790    {
791  0 return featureDisplaySettings == null
792    ? Arrays.asList(new FeatureSettingsModelI[0])
793    : Arrays.asList(featureDisplaySettings.values()
794    .toArray(new FeatureSettingsModelI[1]));
795    }
796   
797    /**
798    * Adds the message to the list unless it already contains it
799    *
800    * @param messageList
801    * @param msg
802    */
 
803  0 toggle void addWarningMessage(List<String> messageList, String msg)
804    {
805  0 if (!messageList.contains(msg))
806    {
807  0 messageList.add(msg);
808    }
809    }
810   
811    /**
812    * loop thru and collect additional sequences in Map.
813    *
814    * @param sequencesArray
815    * @return
816    */
 
817  0 toggle private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
818    {
819  0 int n;
820  0 if (sequencesArray == null || (n = sequencesArray.length) == 0)
821  0 return sequencesArray;
822  0 ArrayList<SequenceI> nseq = new ArrayList<>();
823  0 for (int i = 0; i < n; i++)
824    {
825  0 nseq.add(sequencesArray[i]);
826  0 List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
827  0 Mapping map = null;
828  0 if (dbr != null)
829    {
830  0 for (int r = 0, rn = dbr.size(); r < rn; r++)
831    {
832  0 if ((map = dbr.get(r).getMap()) != null)
833    {
834  0 if (map.getTo() != null && !nseq.contains(map.getTo()))
835    {
836  0 nseq.add(map.getTo());
837    }
838    }
839    }
840    }
841    }
842    // BH 2019.01.25 question here if this is the right logic. Return the
843    // original if nothing found?
844  0 if (nseq.size() > 0)
845    {
846  0 return nseq.toArray(new SequenceI[nseq.size()]);
847    }
848  0 return sequencesArray;
849    }
850    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 7 2024 10:19:08 GMT using coverage data from Thu Nov 7 2024 10:18:53 GMT.
  • OpenClover is free and open-source software.