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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ws

File DBRefFetcher.java

 

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56% of files have more coverage

Code metrics

136
237
12
2
839
570
97
0.41
19.75
6
8.08

Classes

Class Line # Actions
DBRefFetcher 59 237 97
0.00%
DBRefFetcher.FetchFinishedListenerI 65 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.ArrayList;
24    import java.util.Arrays;
25    import java.util.Enumeration;
26    import java.util.HashMap;
27    import java.util.Hashtable;
28    import java.util.List;
29    import java.util.Map;
30    import java.util.StringTokenizer;
31    import java.util.Vector;
32   
33    import jalview.analysis.AlignSeq;
34    import jalview.api.FeatureSettingsModelI;
35    import jalview.bin.Cache;
36    import jalview.datamodel.AlignmentI;
37    import jalview.datamodel.DBRefEntry;
38    import jalview.datamodel.DBRefSource;
39    import jalview.datamodel.Mapping;
40    import jalview.datamodel.SequenceI;
41    import jalview.gui.CutAndPasteTransfer;
42    import jalview.gui.Desktop;
43    import jalview.gui.FeatureSettings;
44    import jalview.gui.IProgressIndicator;
45    import jalview.gui.OOMWarning;
46    import jalview.util.DBRefUtils;
47    import jalview.util.MessageManager;
48    import jalview.ws.seqfetcher.DbSourceProxy;
49    import uk.ac.ebi.picr.model.UPEntry;
50    import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
51   
52    /**
53    * Implements a runnable for validating a sequence against external databases
54    * and then propagating references and features onto the sequence(s)
55    *
56    * @author $author$
57    * @version $Revision$
58    */
 
59    public class DBRefFetcher implements Runnable
60    {
61    private static final String NEWLINE = System.lineSeparator();
62   
63    public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
64   
 
65    public interface FetchFinishedListenerI
66    {
67    void finished();
68    }
69   
70    SequenceI[] dataset;
71   
72    IProgressIndicator progressWindow;
73   
74    CutAndPasteTransfer output = new CutAndPasteTransfer();
75   
76    /**
77    * picr client instance
78    */
79    uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
80   
81    // This will be a collection of Vectors of sequenceI refs.
82    // The key will be the seq name or accession id of the seq
83    Hashtable<String, Vector<SequenceI>> seqRefs;
84   
85    DbSourceProxy[] dbSources;
86   
87    SequenceFetcher sfetcher;
88   
89    private List<FetchFinishedListenerI> listeners;
90   
91    private SequenceI[] alseqs;
92   
93    /*
94    * when true - retrieved sequences will be trimmed to cover longest derived
95    * alignment sequence
96    */
97    private boolean trimDsSeqs = true;
98   
99    /**
100    * Creates a new DBRefFetcher object and fetches from the currently selected
101    * set of databases, if this is null then it fetches based on feature settings
102    *
103    * @param seqs
104    * fetch references for these SequenceI array
105    * @param progressIndicatorFrame
106    * the frame for progress bar monitoring
107    * @param sources
108    * array of DbSourceProxy to query references form
109    * @param featureSettings
110    * FeatureSettings to get alternative DbSourceProxy from
111    * @param isNucleotide
112    * indicates if the array of SequenceI are Nucleotides or not
113    */
 
114  0 toggle public DBRefFetcher(SequenceI[] seqs,
115    IProgressIndicator progressIndicatorFrame,
116    DbSourceProxy[] sources, FeatureSettings featureSettings,
117    boolean isNucleotide)
118    {
119  0 listeners = new ArrayList<>();
120  0 this.progressWindow = progressIndicatorFrame;
121  0 alseqs = new SequenceI[seqs.length];
122  0 SequenceI[] ds = new SequenceI[seqs.length];
123  0 for (int i = 0; i < seqs.length; i++)
124    {
125  0 alseqs[i] = seqs[i];
126  0 if (seqs[i].getDatasetSequence() != null)
127    {
128  0 ds[i] = seqs[i].getDatasetSequence();
129    }
130    else
131    {
132  0 ds[i] = seqs[i];
133    }
134    }
135  0 this.dataset = ds;
136    // TODO Jalview 2.5 lots of this code should be in the gui package!
137  0 sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
138    // set default behaviour for transferring excess sequence data to the
139    // dataset
140  0 trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
141  0 if (sources == null)
142    {
143  0 setDatabaseSources(featureSettings, isNucleotide);
144    }
145    else
146    {
147    // we assume the caller knows what they're doing and ensured that all the
148    // db source names are valid
149  0 dbSources = sources;
150    }
151    }
152   
153    /**
154    * Helper method to configure the list of database sources to query
155    *
156    * @param featureSettings
157    * @param forNucleotide
158    */
 
159  0 toggle void setDatabaseSources(FeatureSettings featureSettings,
160    boolean forNucleotide)
161    {
162    // af.featureSettings_actionPerformed(null);
163  0 String[] defdb = null;
164  0 List<DbSourceProxy> selsources = new ArrayList<>();
165    // select appropriate databases based on alignFrame context.
166  0 if (forNucleotide)
167    {
168  0 defdb = DBRefSource.DNACODINGDBS;
169    }
170    else
171    {
172  0 defdb = DBRefSource.PROTEINDBS;
173    }
174  0 List<DbSourceProxy> srces = new ArrayList<>();
175  0 for (String ddb : defdb)
176    {
177  0 List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
178  0 if (srcesfordb != null)
179    {
180  0 for (DbSourceProxy src : srcesfordb)
181    {
182  0 if (!srces.contains(src))
183    {
184  0 srces.addAll(srcesfordb);
185    }
186    }
187    }
188    }
189    // append the PDB data source, since it is 'special', catering for both
190    // nucleotide and protein
191    // srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
192   
193  0 srces.addAll(selsources);
194  0 dbSources = srces.toArray(new DbSourceProxy[srces.size()]);
195    }
196   
197    /**
198    * Constructor with only sequences provided
199    *
200    * @param sequences
201    */
 
202  0 toggle public DBRefFetcher(SequenceI[] sequences)
203    {
204  0 this(sequences, null, null, null, false);
205    }
206   
207    /**
208    * Add a listener to be notified when sequence fetching is complete
209    *
210    * @param l
211    */
 
212  0 toggle public void addListener(FetchFinishedListenerI l)
213    {
214  0 listeners.add(l);
215    }
216   
217    /**
218    * start the fetcher thread
219    *
220    * @param waitTillFinished
221    * true to block until the fetcher has finished
222    */
 
223  0 toggle public void fetchDBRefs(boolean waitTillFinished)
224    {
225  0 if (waitTillFinished)
226    {
227  0 run();
228    }
229    else
230    {
231  0 new Thread(this).start();
232    }
233    }
234   
235    /**
236    * The sequence will be added to a vector of sequences belonging to key which
237    * could be either seq name or dbref id
238    *
239    * @param seq
240    * SequenceI
241    * @param key
242    * String
243    */
 
244  0 toggle void addSeqId(SequenceI seq, String key)
245    {
246  0 key = key.toUpperCase();
247   
248  0 Vector<SequenceI> seqs;
249  0 if (seqRefs.containsKey(key))
250    {
251  0 seqs = seqRefs.get(key);
252   
253  0 if (seqs != null && !seqs.contains(seq))
254    {
255  0 seqs.addElement(seq);
256    }
257  0 else if (seqs == null)
258    {
259  0 seqs = new Vector<>();
260  0 seqs.addElement(seq);
261    }
262   
263    }
264    else
265    {
266  0 seqs = new Vector<>();
267  0 seqs.addElement(seq);
268    }
269   
270  0 seqRefs.put(key, seqs);
271    }
272   
273    /**
274    * DOCUMENT ME!
275    */
 
276  0 toggle @Override
277    public void run()
278    {
279  0 if (dbSources == null)
280    {
281  0 throw new Error(MessageManager
282    .getString("error.implementation_error_must_init_dbsources"));
283    }
284  0 long startTime = System.currentTimeMillis();
285  0 if (progressWindow != null)
286    {
287  0 progressWindow.setProgressBar(
288    MessageManager.getString("status.fetching_db_refs"),
289    startTime);
290    }
291  0 try
292    {
293  0 if (Cache.getDefault("DBREFFETCH_USEPICR", false))
294    {
295  0 picrClient = new AccessionMapperServiceLocator()
296    .getAccessionMapperPort();
297    }
298    } catch (Exception e)
299    {
300  0 System.err.println("Couldn't locate PICR service instance.\n");
301  0 e.printStackTrace();
302    }
303   
304  0 Vector<SequenceI> sdataset = new Vector<>(
305    Arrays.asList(dataset));
306  0 List<String> warningMessages = new ArrayList<>();
307   
308    // clear any old feature display settings recorded from past sessions
309  0 featureDisplaySettings = null;
310   
311  0 int db = 0;
312  0 while (sdataset.size() > 0 && db < dbSources.length)
313    {
314  0 int maxqlen = 1; // default number of queries made at one time
315  0 System.out.println("Verifying against " + dbSources[db].getDbName());
316   
317    // iterate through db for each remaining un-verified sequence
318  0 SequenceI[] currSeqs = new SequenceI[sdataset.size()];
319  0 sdataset.copyInto(currSeqs);// seqs that are to be validated against
320    // dbSources[db]
321  0 Vector<String> queries = new Vector<>(); // generated queries curSeq
322  0 seqRefs = new Hashtable<>();
323   
324  0 int seqIndex = 0;
325   
326  0 DbSourceProxy dbsource = dbSources[db];
327    // for moment, we dumbly iterate over all retrieval sources for a
328    // particular database
329    // TODO: introduce multithread multisource queries and logic to remove a
330    // query from other sources if any source for a database returns a
331    // record
332  0 maxqlen = dbsource.getMaximumQueryCount();
333   
334  0 while (queries.size() > 0 || seqIndex < currSeqs.length)
335    {
336  0 if (queries.size() > 0)
337    {
338    // Still queries to make for current seqIndex
339  0 StringBuffer queryString = new StringBuffer("");
340  0 int numq = 0;
341  0 int nqSize = (maxqlen > queries.size()) ? queries.size()
342    : maxqlen;
343   
344  0 while (queries.size() > 0 && numq < nqSize)
345    {
346  0 String query = queries.elementAt(0);
347  0 if (dbsource.isValidReference(query))
348    {
349  0 queryString.append(
350  0 (numq == 0) ? "" : dbsource.getAccessionSeparator());
351  0 queryString.append(query);
352  0 numq++;
353    }
354    // remove the extracted query string
355  0 queries.removeElementAt(0);
356    }
357    // make the queries and process the response
358  0 AlignmentI retrieved = null;
359  0 try
360    {
361  0 if (Cache.log.isDebugEnabled())
362    {
363  0 Cache.log.debug("Querying " + dbsource.getDbName()
364    + " with : '" + queryString.toString() + "'");
365    }
366  0 retrieved = dbsource.getSequenceRecords(queryString.toString());
367    } catch (Exception ex)
368    {
369  0 ex.printStackTrace();
370    } catch (OutOfMemoryError err)
371    {
372  0 new OOMWarning("retrieving database references ("
373    + queryString.toString() + ")", err);
374    }
375  0 if (retrieved != null)
376    {
377  0 transferReferences(sdataset, dbsource, retrieved,
378    trimDsSeqs, warningMessages);
379    }
380    }
381    else
382    {
383    // make some more strings for use as queries
384  0 for (int i = 0; (seqIndex < dataset.length)
385    && (i < 50); seqIndex++, i++)
386    {
387  0 SequenceI sequence = dataset[seqIndex];
388  0 List<DBRefEntry> uprefs = DBRefUtils
389    .selectRefs(sequence.getDBRefs(), new String[]
390    { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
391    // });
392    // check for existing dbrefs to use
393  0 if (uprefs != null && uprefs.size() > 0)
394    {
395  0 for (int j = 0, n = uprefs.size(); j < n; j++)
396    {
397  0 DBRefEntry upref = uprefs.get(j);
398  0 addSeqId(sequence, upref.getAccessionId());
399  0 queries.addElement(
400    upref.getAccessionId().toUpperCase());
401    }
402    }
403    else
404    {
405    // generate queries from sequence ID string
406  0 StringTokenizer st = new StringTokenizer(sequence.getName(),
407    "|");
408  0 while (st.hasMoreTokens())
409    {
410  0 String token = st.nextToken();
411  0 UPEntry[] presp = null;
412  0 if (picrClient != null)
413    {
414    // resolve the string against PICR to recover valid IDs
415  0 try
416    {
417  0 presp = picrClient.getUPIForAccession(token, null,
418    picrClient.getMappedDatabaseNames(), null,
419    true);
420    } catch (Exception e)
421    {
422  0 System.err.println(
423    "Exception with Picr for '" + token + "'\n");
424  0 e.printStackTrace();
425    }
426    }
427  0 if (presp != null && presp.length > 0)
428    {
429  0 for (int id = 0; id < presp.length; id++)
430    {
431    // construct sequences from response if sequences are
432    // present, and do a transferReferences
433    // otherwise transfer non sequence x-references directly.
434    }
435  0 System.out.println(
436    "Validated ID against PICR... (for what its worth):"
437    + token);
438  0 addSeqId(sequence, token);
439  0 queries.addElement(token.toUpperCase());
440    }
441    else
442    {
443    // if ()
444    // System.out.println("Not querying source with
445    // token="+token+"\n");
446  0 addSeqId(sequence, token);
447  0 queries.addElement(token.toUpperCase());
448    }
449    }
450    }
451    }
452    }
453    }
454    // advance to next database
455  0 db++;
456    } // all databases have been queried
457  0 if (!warningMessages.isEmpty())
458    {
459  0 StringBuilder sb = new StringBuilder(warningMessages.size() * 30);
460  0 sb.append(MessageManager
461    .getString("label.your_sequences_have_been_verified"));
462  0 for (String msg : warningMessages)
463    {
464  0 sb.append(msg).append(NEWLINE);
465    }
466  0 output.setText(sb.toString());
467   
468  0 Desktop.addInternalFrame(output,
469    MessageManager.getString("label.sequences_updated"), 600,
470    300);
471    // The above is the dataset, we must now find out the index
472    // of the viewed sequence
473   
474    }
475  0 if (progressWindow != null)
476    {
477  0 progressWindow.setProgressBar(
478    MessageManager.getString("label.dbref_search_completed"),
479    startTime);
480    }
481   
482  0 for (FetchFinishedListenerI listener : listeners)
483    {
484  0 listener.finished();
485    }
486    }
487   
488    /**
489    * Verify local sequences in seqRefs against the retrieved sequence database
490    * records. Returns true if any sequence was modified as a result (start/end
491    * changed and/or sequence enlarged), else false.
492    *
493    * @param sdataset
494    * dataset sequences we are retrieving for
495    * @param dbSource
496    * database source we are retrieving from
497    * @param retrievedAl
498    * retrieved sequences as alignment
499    * @param trimDatasetSeqs
500    * if true, sequences will not be enlarged to match longer retrieved
501    * sequences, only their start/end adjusted
502    * @param warningMessages
503    * a list of messages to add to
504    */
 
505  0 toggle boolean transferReferences(Vector<SequenceI> sdataset,
506    DbSourceProxy dbSourceProxy,
507    AlignmentI retrievedAl, boolean trimDatasetSeqs,
508    List<String> warningMessages)
509    {
510    // System.out.println("trimming ? " + trimDatasetSeqs);
511  0 if (retrievedAl == null || retrievedAl.getHeight() == 0)
512    {
513  0 return false;
514    }
515   
516  0 String dbSource = dbSourceProxy.getDbName();
517  0 boolean modified = false;
518  0 SequenceI[] retrieved = recoverDbSequences(
519    retrievedAl.getSequencesArray());
520  0 SequenceI sequence = null;
521   
522  0 for (SequenceI retrievedSeq : retrieved)
523    {
524    // Work out which sequences this sequence matches,
525    // taking into account all accessionIds and names in the file
526  0 Vector<SequenceI> sequenceMatches = new Vector<>();
527    // look for corresponding accession ids
528  0 List<DBRefEntry> entryRefs = DBRefUtils
529    .selectRefs(retrievedSeq.getDBRefs(), new String[]
530    { dbSource });
531  0 if (entryRefs == null)
532    {
533  0 System.err
534    .println("Dud dbSource string ? no entryrefs selected for "
535    + dbSource + " on " + retrievedSeq.getName());
536  0 continue;
537    }
538  0 for (int j = 0, n = entryRefs.size(); j < n; j++)
539    {
540  0 DBRefEntry ref = entryRefs.get(j);
541  0 String accessionId = ref.getAccessionId();
542    // match up on accessionId
543  0 if (seqRefs.containsKey(accessionId.toUpperCase()))
544    {
545  0 Vector<SequenceI> seqs = seqRefs.get(accessionId);
546  0 for (int jj = 0; jj < seqs.size(); jj++)
547    {
548  0 sequence = seqs.elementAt(jj);
549  0 if (!sequenceMatches.contains(sequence))
550    {
551  0 sequenceMatches.addElement(sequence);
552    }
553    }
554    }
555    }
556  0 if (sequenceMatches.isEmpty())
557    {
558    // failed to match directly on accessionId==query so just compare all
559    // sequences to entry
560  0 Enumeration<String> e = seqRefs.keys();
561  0 while (e.hasMoreElements())
562    {
563  0 Vector<SequenceI> sqs = seqRefs.get(e.nextElement());
564  0 if (sqs != null && sqs.size() > 0)
565    {
566  0 Enumeration<SequenceI> sqe = sqs.elements();
567  0 while (sqe.hasMoreElements())
568    {
569  0 sequenceMatches.addElement(sqe.nextElement());
570    }
571    }
572    }
573    }
574    // look for corresponding names
575    // this is uniprot specific ?
576    // could be useful to extend this so we try to find any 'significant'
577    // information in common between two sequence objects.
578    /*
579    * List<DBRefEntry> entryRefs =
580    * jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] {
581    * dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String
582    * name = entry.getName().elementAt(j).toString(); if
583    * (seqRefs.containsKey(name)) { Vector seqs = (Vector) seqRefs.get(name);
584    * for (int jj = 0; jj < seqs.size(); jj++) { sequence = (SequenceI)
585    * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {
586    * sequenceMatches.addElement(sequence); } } } }
587    */
588  0 if (sequenceMatches.size() > 0)
589    {
590  0 addFeatureSettings(dbSourceProxy);
591    }
592    // sequenceMatches now contains the set of all sequences associated with
593    // the returned db record
594  0 final String retrievedSeqString = retrievedSeq.getSequenceAsString();
595  0 String entrySeq = retrievedSeqString.toUpperCase();
596  0 for (int m = 0; m < sequenceMatches.size(); m++)
597    {
598  0 sequence = sequenceMatches.elementAt(m);
599    // only update start and end positions and shift features if there are
600    // no existing references
601    // TODO: test for legacy where uniprot or EMBL refs exist but no
602    // mappings are made (but content matches retrieved set)
603  0 boolean updateRefFrame = sequence.getDBRefs() == null
604    || sequence.getDBRefs().size() == 0;
605    // TODO:
606    // verify sequence against the entry sequence
607   
608  0 Mapping mp;
609  0 final int sequenceStart = sequence.getStart();
610   
611  0 boolean remoteEnclosesLocal = false;
612  0 String nonGapped = AlignSeq
613    .extractGaps("-. ", sequence.getSequenceAsString())
614    .toUpperCase();
615  0 int absStart = entrySeq.indexOf(nonGapped);
616  0 if (absStart == -1)
617    {
618    // couldn't find local sequence in sequence from database, so check if
619    // the database sequence is a subsequence of local sequence
620  0 absStart = nonGapped.indexOf(entrySeq);
621  0 if (absStart == -1)
622    {
623    // verification failed. couldn't find any relationship between
624    // entrySeq and local sequence
625    // messages suppressed as many-to-many matches are confusing
626    // String msg = sequence.getName()
627    // + " Sequence not 100% match with "
628    // + retrievedSeq.getName();
629    // addWarningMessage(warningMessages, msg);
630  0 continue;
631    }
632    /*
633    * retrieved sequence is a proper subsequence of local sequence
634    */
635  0 String msg = sequence.getName() + " has " + absStart
636    + " prefixed residues compared to "
637    + retrievedSeq.getName();
638  0 addWarningMessage(warningMessages, msg);
639   
640    /*
641    * So create a mapping to the external entry from the matching region of
642    * the local sequence, and leave local start/end untouched.
643    */
644  0 mp = new Mapping(null,
645    new int[]
646    { sequenceStart + absStart,
647    sequenceStart + absStart + entrySeq.length() - 1 },
648    new int[]
649    { retrievedSeq.getStart(),
650    retrievedSeq.getStart() + entrySeq.length() - 1 },
651    1, 1);
652  0 updateRefFrame = false;
653    }
654    else
655    {
656    /*
657    * local sequence is a subsequence of (or matches) retrieved sequence
658    */
659  0 remoteEnclosesLocal = true;
660  0 mp = null;
661   
662  0 if (updateRefFrame)
663    {
664    /*
665    * relocate existing sequence features by offset
666    */
667  0 int startShift = absStart - sequenceStart + 1;
668  0 if (startShift != 0)
669    {
670  0 modified |= sequence.getFeatures().shiftFeatures(1,
671    startShift);
672    }
673    }
674    }
675   
676  0 System.out.println("Adding dbrefs to " + sequence.getName()
677    + " from " + dbSource + " sequence : "
678    + retrievedSeq.getName());
679  0 sequence.transferAnnotation(retrievedSeq, mp);
680   
681  0 absStart += retrievedSeq.getStart();
682  0 int absEnd = absStart + nonGapped.length() - 1;
683  0 if (!trimDatasetSeqs)
684    {
685    /*
686    * update start position and/or expand to longer retrieved sequence
687    */
688  0 if (!retrievedSeqString.equals(sequence.getSequenceAsString())
689    && remoteEnclosesLocal)
690    {
691  0 sequence.setSequence(retrievedSeqString);
692  0 modified = true;
693  0 addWarningMessage(warningMessages,
694    "Sequence for " + sequence.getName() + " expanded from "
695    + retrievedSeq.getName());
696    }
697  0 if (sequence.getStart() != retrievedSeq.getStart())
698    {
699  0 sequence.setStart(retrievedSeq.getStart());
700  0 modified = true;
701  0 if (absStart != sequenceStart)
702    {
703  0 addWarningMessage(warningMessages,
704    "Start/end position for " + sequence.getName()
705    + " updated from " + retrievedSeq.getName());
706    }
707    }
708    }
709  0 if (updateRefFrame)
710    {
711    // finally, update local sequence reference frame if we're allowed
712  0 if (trimDatasetSeqs)
713    {
714    // just fix start/end
715  0 if (sequence.getStart() != absStart
716    || sequence.getEnd() != absEnd)
717    {
718  0 sequence.setStart(absStart);
719  0 sequence.setEnd(absEnd);
720  0 modified = true;
721  0 addWarningMessage(warningMessages,
722    "Start/end for " + sequence.getName()
723    + " updated from " + retrievedSeq.getName());
724    }
725    }
726    // search for alignment sequences to update coordinate frame for
727  0 for (int alsq = 0; alsq < alseqs.length; alsq++)
728    {
729  0 if (alseqs[alsq].getDatasetSequence() == sequence)
730    {
731  0 String ngAlsq = AlignSeq
732    .extractGaps("-. ",
733    alseqs[alsq].getSequenceAsString())
734    .toUpperCase();
735  0 int oldstrt = alseqs[alsq].getStart();
736  0 alseqs[alsq].setStart(sequence.getSequenceAsString()
737    .toUpperCase().indexOf(ngAlsq) + sequence.getStart());
738  0 if (oldstrt != alseqs[alsq].getStart())
739    {
740  0 alseqs[alsq].setEnd(
741    ngAlsq.length() + alseqs[alsq].getStart() - 1);
742  0 modified = true;
743    }
744    }
745    }
746    // TODO: search for all other references to this dataset sequence, and
747    // update start/end
748    // TODO: update all AlCodonMappings which involve this alignment
749    // sequence (e.g. Q30167 cdna translation from exon2 product (vamsas
750    // demo)
751    }
752    // and remove it from the rest
753    // TODO: decide if we should remove annotated sequence from set
754  0 sdataset.remove(sequence);
755    }
756    }
757  0 return modified;
758    }
759   
760    Map<String, FeatureSettingsModelI> featureDisplaySettings = null;
761   
 
762  0 toggle private void addFeatureSettings(DbSourceProxy dbSourceProxy)
763    {
764  0 FeatureSettingsModelI fsettings = dbSourceProxy
765    .getFeatureColourScheme();
766  0 if (fsettings != null)
767    {
768  0 if (featureDisplaySettings == null)
769    {
770  0 featureDisplaySettings = new HashMap<>();
771    }
772  0 featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings);
773    }
774    }
775   
776    /**
777    *
778    * @return any feature settings associated with sources that have provided sequences
779    */
 
780  0 toggle public List<FeatureSettingsModelI>getFeatureSettingsModels()
781    {
782  0 return featureDisplaySettings == null
783    ? Arrays.asList(new FeatureSettingsModelI[0])
784    : Arrays.asList(featureDisplaySettings.values()
785    .toArray(new FeatureSettingsModelI[1]));
786    }
787    /**
788    * Adds the message to the list unless it already contains it
789    *
790    * @param messageList
791    * @param msg
792    */
 
793  0 toggle void addWarningMessage(List<String> messageList, String msg)
794    {
795  0 if (!messageList.contains(msg))
796    {
797  0 messageList.add(msg);
798    }
799    }
800   
801    /**
802    * loop thru and collect additional sequences in Map.
803    *
804    * @param sequencesArray
805    * @return
806    */
 
807  0 toggle private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
808    {
809  0 int n;
810  0 if (sequencesArray == null || (n = sequencesArray.length) == 0)
811  0 return sequencesArray;
812  0 ArrayList<SequenceI> nseq = new ArrayList<>();
813  0 for (int i = 0;i < n; i++)
814    {
815  0 nseq.add(sequencesArray[i]);
816  0 List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
817  0 Mapping map = null;
818  0 if (dbr != null)
819    {
820  0 for (int r = 0, rn = dbr.size(); r < rn; r++)
821    {
822  0 if ((map = dbr.get(r).getMap()) != null)
823    {
824  0 if (map.getTo() != null && !nseq.contains(map.getTo()))
825    {
826  0 nseq.add(map.getTo());
827    }
828    }
829    }
830    }
831    }
832    // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
833  0 if (nseq.size() > 0)
834    {
835  0 return nseq.toArray(new SequenceI[nseq.size()]);
836    }
837  0 return sequencesArray;
838    }
839    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.