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package jalview.ws; |
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import jalview.analysis.AlignSeq; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.Mapping; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.CutAndPasteTransfer; |
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import jalview.gui.Desktop; |
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import jalview.gui.FeatureSettings; |
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import jalview.gui.IProgressIndicator; |
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import jalview.gui.OOMWarning; |
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import jalview.util.DBRefUtils; |
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import jalview.util.MessageManager; |
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import jalview.ws.seqfetcher.DbSourceProxy; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Enumeration; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.StringTokenizer; |
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import java.util.Vector; |
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import uk.ac.ebi.picr.model.UPEntry; |
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import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator; |
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@author |
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@version |
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| 0% |
Uncovered Elements: 364 (364) |
Complexity: 92 |
Complexity Density: 0.4 |
|
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public class DBRefFetcher implements Runnable |
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{ |
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private static final String NEWLINE = System.lineSeparator(); |
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public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS"; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 0 |
Complexity Density: - |
|
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public interface FetchFinishedListenerI |
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{ |
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void finished(); |
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} |
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SequenceI[] dataset; |
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IProgressIndicator progressWindow; |
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CutAndPasteTransfer output = new CutAndPasteTransfer(); |
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boolean running = false; |
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uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null; |
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Hashtable<String, Vector<SequenceI>> seqRefs; |
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DbSourceProxy[] dbSources; |
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SequenceFetcher sfetcher; |
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private List<FetchFinishedListenerI> listeners; |
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private SequenceI[] alseqs; |
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private boolean trimDsSeqs = true; |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 21 (21) |
Complexity: 4 |
Complexity Density: 0.27 |
|
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public DBRefFetcher(SequenceI[] seqs,... |
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IProgressIndicator progressIndicatorFrame, |
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DbSourceProxy[] sources, FeatureSettings featureSettings, |
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boolean isNucleotide) |
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{ |
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listeners = new ArrayList<>(); |
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this.progressWindow = progressIndicatorFrame; |
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alseqs = new SequenceI[seqs.length]; |
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SequenceI[] ds = new SequenceI[seqs.length]; |
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for (int i = 0; i < seqs.length; i++) |
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{ |
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alseqs[i] = seqs[i]; |
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if (seqs[i].getDatasetSequence() != null) |
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{ |
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ds[i] = seqs[i].getDatasetSequence(); |
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} |
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else |
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{ |
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ds[i] = seqs[i]; |
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} |
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} |
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this.dataset = ds; |
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sfetcher = jalview.gui.SequenceFetcher |
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.getSequenceFetcherSingleton(progressIndicatorFrame); |
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trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true); |
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if (sources == null) |
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{ |
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setDatabaseSources(featureSettings, isNucleotide); |
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} |
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else |
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{ |
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dbSources = sources; |
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} |
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} |
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@param |
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@param |
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| 0% |
Uncovered Elements: 20 (20) |
Complexity: 4 |
Complexity Density: 0.29 |
|
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void setDatabaseSources(FeatureSettings featureSettings,... |
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boolean forNucleotide) |
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{ |
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String[] defdb = null; |
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List<DbSourceProxy> selsources = new ArrayList<>(); |
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if (forNucleotide) |
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{ |
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defdb = DBRefSource.DNACODINGDBS; |
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} |
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else |
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{ |
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defdb = DBRefSource.PROTEINDBS; |
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} |
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List<DbSourceProxy> srces = new ArrayList<>(); |
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for (String ddb : defdb) |
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{ |
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List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb); |
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if (srcesfordb != null) |
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{ |
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for (DbSourceProxy src : srcesfordb) |
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{ |
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if (!srces.contains(src)) |
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{ |
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srces.addAll(srcesfordb); |
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} |
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} |
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} |
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} |
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srces.addAll(selsources); |
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dbSources = srces.toArray(new DbSourceProxy[srces.size()]); |
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} |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public DBRefFetcher(SequenceI[] sequences)... |
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{ |
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this(sequences, null, null, null, false); |
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} |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addListener(FetchFinishedListenerI l)... |
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{ |
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listeners.add(l); |
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} |
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@param |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 4 |
Complexity Density: 0.57 |
|
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public void fetchDBRefs(boolean waitTillFinished)... |
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{ |
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Thread thread = new Thread(this); |
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thread.start(); |
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running = true; |
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if (waitTillFinished) |
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{ |
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while (running) |
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{ |
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try |
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{ |
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Thread.sleep(500); |
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} catch (Exception ex) |
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{ |
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} |
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} |
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} |
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} |
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@param |
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@param |
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| 0% |
Uncovered Elements: 18 (18) |
Complexity: 5 |
Complexity Density: 0.42 |
|
256 |
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void addSeqId(SequenceI seq, String key)... |
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{ |
258 |
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key = key.toUpperCase(); |
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260 |
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Vector<SequenceI> seqs; |
261 |
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if (seqRefs.containsKey(key)) |
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{ |
263 |
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seqs = seqRefs.get(key); |
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265 |
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if (seqs != null && !seqs.contains(seq)) |
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{ |
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seqs.addElement(seq); |
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} |
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else if (seqs == null) |
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{ |
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seqs = new Vector<>(); |
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seqs.addElement(seq); |
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} |
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275 |
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} |
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else |
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{ |
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seqs = new Vector<>(); |
279 |
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seqs.addElement(seq); |
280 |
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} |
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282 |
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seqRefs.put(key, seqs); |
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} |
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286 |
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287 |
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| 0% |
Uncovered Elements: 123 (123) |
Complexity: 32 |
Complexity Density: 0.4 |
|
288 |
0 |
@Override... |
289 |
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public void run() |
290 |
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{ |
291 |
0 |
if (dbSources == null) |
292 |
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{ |
293 |
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throw new Error(MessageManager |
294 |
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.getString("error.implementation_error_must_init_dbsources")); |
295 |
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} |
296 |
0 |
running = true; |
297 |
0 |
long startTime = System.currentTimeMillis(); |
298 |
0 |
if (progressWindow != null) |
299 |
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{ |
300 |
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progressWindow.setProgressBar( |
301 |
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MessageManager.getString("status.fetching_db_refs"), |
302 |
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startTime); |
303 |
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} |
304 |
0 |
try |
305 |
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{ |
306 |
0 |
if (Cache.getDefault("DBREFFETCH_USEPICR", false)) |
307 |
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{ |
308 |
0 |
picrClient = new AccessionMapperServiceLocator() |
309 |
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.getAccessionMapperPort(); |
310 |
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} |
311 |
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} catch (Exception e) |
312 |
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{ |
313 |
0 |
System.err.println("Couldn't locate PICR service instance.\n"); |
314 |
0 |
e.printStackTrace(); |
315 |
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} |
316 |
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|
317 |
0 |
Vector<SequenceI> sdataset = new Vector<>( |
318 |
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Arrays.asList(dataset)); |
319 |
0 |
List<String> warningMessages = new ArrayList<>(); |
320 |
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|
321 |
0 |
int db = 0; |
322 |
0 |
while (sdataset.size() > 0 && db < dbSources.length) |
323 |
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{ |
324 |
0 |
int maxqlen = 1; |
325 |
0 |
System.out.println("Verifying against " + dbSources[db].getDbName()); |
326 |
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327 |
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328 |
0 |
SequenceI[] currSeqs = new SequenceI[sdataset.size()]; |
329 |
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sdataset.copyInto(currSeqs); |
330 |
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331 |
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Vector<String> queries = new Vector<>(); |
332 |
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seqRefs = new Hashtable<>(); |
333 |
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334 |
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int seqIndex = 0; |
335 |
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336 |
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DbSourceProxy dbsource = dbSources[db]; |
337 |
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338 |
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339 |
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340 |
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341 |
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342 |
0 |
maxqlen = dbsource.getMaximumQueryCount(); |
343 |
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344 |
0 |
while (queries.size() > 0 || seqIndex < currSeqs.length) |
345 |
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{ |
346 |
0 |
if (queries.size() > 0) |
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{ |
348 |
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349 |
0 |
StringBuffer queryString = new StringBuffer(""); |
350 |
0 |
int numq = 0; |
351 |
0 |
int nqSize = (maxqlen > queries.size()) ? queries.size() |
352 |
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: maxqlen; |
353 |
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354 |
0 |
while (queries.size() > 0 && numq < nqSize) |
355 |
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{ |
356 |
0 |
String query = queries.elementAt(0); |
357 |
0 |
if (dbsource.isValidReference(query)) |
358 |
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{ |
359 |
0 |
queryString.append( |
360 |
0 |
(numq == 0) ? "" : dbsource.getAccessionSeparator()); |
361 |
0 |
queryString.append(query); |
362 |
0 |
numq++; |
363 |
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} |
364 |
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|
365 |
0 |
queries.removeElementAt(0); |
366 |
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} |
367 |
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|
368 |
0 |
AlignmentI retrieved = null; |
369 |
0 |
try |
370 |
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{ |
371 |
0 |
if (Cache.log.isDebugEnabled()) |
372 |
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{ |
373 |
0 |
Cache.log.debug("Querying " + dbsource.getDbName() |
374 |
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+ " with : '" + queryString.toString() + "'"); |
375 |
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} |
376 |
0 |
retrieved = dbsource.getSequenceRecords(queryString.toString()); |
377 |
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} catch (Exception ex) |
378 |
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{ |
379 |
0 |
ex.printStackTrace(); |
380 |
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} catch (OutOfMemoryError err) |
381 |
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{ |
382 |
0 |
new OOMWarning("retrieving database references (" |
383 |
|
+ queryString.toString() + ")", err); |
384 |
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} |
385 |
0 |
if (retrieved != null) |
386 |
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{ |
387 |
0 |
transferReferences(sdataset, dbsource.getDbSource(), retrieved, |
388 |
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trimDsSeqs, warningMessages); |
389 |
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} |
390 |
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} |
391 |
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else |
392 |
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{ |
393 |
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|
394 |
0 |
for (int i = 0; (seqIndex < dataset.length) |
395 |
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&& (i < 50); seqIndex++, i++) |
396 |
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{ |
397 |
0 |
SequenceI sequence = dataset[seqIndex]; |
398 |
0 |
DBRefEntry[] uprefs = DBRefUtils |
399 |
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.selectRefs(sequence.getDBRefs(), new String[] |
400 |
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{ dbsource.getDbSource() }); |
401 |
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402 |
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|
403 |
0 |
if (uprefs != null && uprefs.length > 0) |
404 |
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{ |
405 |
0 |
for (int j = 0; j < uprefs.length; j++) |
406 |
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{ |
407 |
0 |
addSeqId(sequence, uprefs[j].getAccessionId()); |
408 |
0 |
queries.addElement( |
409 |
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uprefs[j].getAccessionId().toUpperCase()); |
410 |
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} |
411 |
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} |
412 |
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else |
413 |
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{ |
414 |
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|
415 |
0 |
StringTokenizer st = new StringTokenizer(sequence.getName(), |
416 |
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"|"); |
417 |
0 |
while (st.hasMoreTokens()) |
418 |
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{ |
419 |
0 |
String token = st.nextToken(); |
420 |
0 |
UPEntry[] presp = null; |
421 |
0 |
if (picrClient != null) |
422 |
|
{ |
423 |
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|
424 |
0 |
try |
425 |
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{ |
426 |
0 |
presp = picrClient.getUPIForAccession(token, null, |
427 |
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picrClient.getMappedDatabaseNames(), null, |
428 |
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true); |
429 |
|
} catch (Exception e) |
430 |
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{ |
431 |
0 |
System.err.println( |
432 |
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"Exception with Picr for '" + token + "'\n"); |
433 |
0 |
e.printStackTrace(); |
434 |
|
} |
435 |
|
} |
436 |
0 |
if (presp != null && presp.length > 0) |
437 |
|
{ |
438 |
0 |
for (int id = 0; id < presp.length; id++) |
439 |
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{ |
440 |
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|
441 |
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442 |
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|
443 |
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} |
444 |
0 |
System.out.println( |
445 |
|
"Validated ID against PICR... (for what its worth):" |
446 |
|
+ token); |
447 |
0 |
addSeqId(sequence, token); |
448 |
0 |
queries.addElement(token.toUpperCase()); |
449 |
|
} |
450 |
|
else |
451 |
|
{ |
452 |
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|
453 |
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|
454 |
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|
455 |
0 |
addSeqId(sequence, token); |
456 |
0 |
queries.addElement(token.toUpperCase()); |
457 |
|
} |
458 |
|
} |
459 |
|
} |
460 |
|
} |
461 |
|
} |
462 |
|
} |
463 |
|
|
464 |
0 |
db++; |
465 |
|
} |
466 |
0 |
if (!warningMessages.isEmpty()) |
467 |
|
{ |
468 |
0 |
StringBuilder sb = new StringBuilder(warningMessages.size() * 30); |
469 |
0 |
sb.append(MessageManager |
470 |
|
.getString("label.your_sequences_have_been_verified")); |
471 |
0 |
for (String msg : warningMessages) |
472 |
|
{ |
473 |
0 |
sb.append(msg).append(NEWLINE); |
474 |
|
} |
475 |
0 |
output.setText(sb.toString()); |
476 |
|
|
477 |
0 |
Desktop.addInternalFrame(output, |
478 |
|
MessageManager.getString("label.sequences_updated"), 600, |
479 |
|
300); |
480 |
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|
481 |
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|
482 |
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|
483 |
|
} |
484 |
0 |
if (progressWindow != null) |
485 |
|
{ |
486 |
0 |
progressWindow.setProgressBar( |
487 |
|
MessageManager.getString("label.dbref_search_completed"), |
488 |
|
startTime); |
489 |
|
} |
490 |
|
|
491 |
0 |
for (FetchFinishedListenerI listener : listeners) |
492 |
|
{ |
493 |
0 |
listener.finished(); |
494 |
|
} |
495 |
0 |
running = false; |
496 |
|
} |
497 |
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|
498 |
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|
499 |
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|
500 |
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|
501 |
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|
502 |
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|
503 |
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@param |
504 |
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|
505 |
|
@param |
506 |
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|
507 |
|
@param |
508 |
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|
509 |
|
@param |
510 |
|
|
511 |
|
|
512 |
|
@param |
513 |
|
|
514 |
|
|
|
|
| 0% |
Uncovered Elements: 132 (132) |
Complexity: 30 |
Complexity Density: 0.37 |
|
515 |
0 |
boolean transferReferences(Vector<SequenceI> sdataset, String dbSource,... |
516 |
|
AlignmentI retrievedAl, boolean trimDatasetSeqs, |
517 |
|
List<String> warningMessages) |
518 |
|
{ |
519 |
|
|
520 |
0 |
if (retrievedAl == null || retrievedAl.getHeight() == 0) |
521 |
|
{ |
522 |
0 |
return false; |
523 |
|
} |
524 |
|
|
525 |
0 |
boolean modified = false; |
526 |
0 |
SequenceI[] retrieved = recoverDbSequences( |
527 |
|
retrievedAl.getSequencesArray()); |
528 |
0 |
SequenceI sequence = null; |
529 |
|
|
530 |
0 |
for (SequenceI retrievedSeq : retrieved) |
531 |
|
{ |
532 |
|
|
533 |
|
|
534 |
0 |
Vector<SequenceI> sequenceMatches = new Vector<>(); |
535 |
|
|
536 |
0 |
DBRefEntry[] entryRefs = DBRefUtils |
537 |
|
.selectRefs(retrievedSeq.getDBRefs(), new String[] |
538 |
|
{ dbSource }); |
539 |
0 |
if (entryRefs == null) |
540 |
|
{ |
541 |
0 |
System.err |
542 |
|
.println("Dud dbSource string ? no entryrefs selected for " |
543 |
|
+ dbSource + " on " + retrievedSeq.getName()); |
544 |
0 |
continue; |
545 |
|
} |
546 |
0 |
for (int j = 0; j < entryRefs.length; j++) |
547 |
|
{ |
548 |
0 |
String accessionId = entryRefs[j].getAccessionId(); |
549 |
|
|
550 |
0 |
if (seqRefs.containsKey(accessionId.toUpperCase())) |
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 |
|
|
566 |
|
|
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 |
|
|
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
|
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
|
597 |
0 |
final String retrievedSeqString = retrievedSeq.getSequenceAsString(); |
598 |
0 |
String entrySeq = retrievedSeqString.toUpperCase(); |
599 |
0 |
for (int m = 0; m < sequenceMatches.size(); m++) |
600 |
|
{ |
601 |
0 |
sequence = sequenceMatches.elementAt(m); |
602 |
|
|
603 |
|
|
604 |
|
|
605 |
|
|
606 |
0 |
boolean updateRefFrame = sequence.getDBRefs() == null |
607 |
|
|| sequence.getDBRefs().length == 0; |
608 |
|
|
609 |
|
|
610 |
|
|
611 |
0 |
Mapping mp; |
612 |
0 |
final int sequenceStart = sequence.getStart(); |
613 |
|
|
614 |
0 |
boolean remoteEnclosesLocal = false; |
615 |
0 |
String nonGapped = AlignSeq |
616 |
|
.extractGaps("-. ", sequence.getSequenceAsString()) |
617 |
|
.toUpperCase(); |
618 |
0 |
int absStart = entrySeq.indexOf(nonGapped); |
619 |
0 |
if (absStart == -1) |
620 |
|
{ |
621 |
|
|
622 |
|
|
623 |
0 |
absStart = nonGapped.indexOf(entrySeq); |
624 |
0 |
if (absStart == -1) |
625 |
|
{ |
626 |
|
|
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
|
633 |
0 |
continue; |
634 |
|
} |
635 |
|
|
636 |
|
|
637 |
|
|
638 |
0 |
String msg = sequence.getName() + " has " + absStart |
639 |
|
+ " prefixed residues compared to " |
640 |
|
+ retrievedSeq.getName(); |
641 |
0 |
addWarningMessage(warningMessages, msg); |
642 |
|
|
643 |
|
|
644 |
|
|
645 |
|
|
646 |
|
|
647 |
0 |
mp = new Mapping(null, |
648 |
|
new int[] |
649 |
|
{ sequenceStart + absStart, |
650 |
|
sequenceStart + absStart + entrySeq.length() - 1 }, |
651 |
|
new int[] |
652 |
|
{ retrievedSeq.getStart(), |
653 |
|
retrievedSeq.getStart() + entrySeq.length() - 1 }, |
654 |
|
1, 1); |
655 |
0 |
updateRefFrame = false; |
656 |
|
} |
657 |
|
else |
658 |
|
{ |
659 |
|
|
660 |
|
|
661 |
|
|
662 |
0 |
remoteEnclosesLocal = true; |
663 |
0 |
mp = null; |
664 |
|
|
665 |
0 |
if (updateRefFrame) |
666 |
|
{ |
667 |
|
|
668 |
|
|
669 |
|
|
670 |
0 |
int startShift = absStart - sequenceStart + 1; |
671 |
0 |
if (startShift != 0) |
672 |
|
{ |
673 |
0 |
modified |= sequence.getFeatures().shiftFeatures(startShift); |
674 |
|
} |
675 |
|
} |
676 |
|
} |
677 |
|
|
678 |
0 |
System.out.println("Adding dbrefs to " + sequence.getName() |
679 |
|
+ " from " + dbSource + " sequence : " |
680 |
|
+ retrievedSeq.getName()); |
681 |
0 |
sequence.transferAnnotation(retrievedSeq, mp); |
682 |
|
|
683 |
0 |
absStart += retrievedSeq.getStart(); |
684 |
0 |
int absEnd = absStart + nonGapped.length() - 1; |
685 |
0 |
if (!trimDatasetSeqs) |
686 |
|
{ |
687 |
|
|
688 |
|
|
689 |
|
|
690 |
0 |
if (!retrievedSeqString.equals(sequence.getSequenceAsString()) |
691 |
|
&& remoteEnclosesLocal) |
692 |
|
{ |
693 |
0 |
sequence.setSequence(retrievedSeqString); |
694 |
0 |
modified = true; |
695 |
0 |
addWarningMessage(warningMessages, |
696 |
|
"Sequence for " + sequence.getName() + " expanded from " |
697 |
|
+ retrievedSeq.getName()); |
698 |
|
} |
699 |
0 |
if (sequence.getStart() != retrievedSeq.getStart()) |
700 |
|
{ |
701 |
0 |
sequence.setStart(retrievedSeq.getStart()); |
702 |
0 |
modified = true; |
703 |
0 |
if (absStart != sequenceStart) |
704 |
|
{ |
705 |
0 |
addWarningMessage(warningMessages, |
706 |
|
"Start/end position for " + sequence.getName() |
707 |
|
+ " updated from " + retrievedSeq.getName()); |
708 |
|
} |
709 |
|
} |
710 |
|
} |
711 |
0 |
if (updateRefFrame) |
712 |
|
{ |
713 |
|
|
714 |
0 |
if (trimDatasetSeqs) |
715 |
|
{ |
716 |
|
|
717 |
0 |
if (sequence.getStart() != absStart |
718 |
|
|| sequence.getEnd() != absEnd) |
719 |
|
{ |
720 |
0 |
sequence.setStart(absStart); |
721 |
0 |
sequence.setEnd(absEnd); |
722 |
0 |
modified = true; |
723 |
0 |
addWarningMessage(warningMessages, |
724 |
|
"Start/end for " + sequence.getName() |
725 |
|
+ " updated from " + retrievedSeq.getName()); |
726 |
|
} |
727 |
|
} |
728 |
|
|
729 |
0 |
for (int alsq = 0; alsq < alseqs.length; alsq++) |
730 |
|
{ |
731 |
0 |
if (alseqs[alsq].getDatasetSequence() == sequence) |
732 |
|
{ |
733 |
0 |
String ngAlsq = AlignSeq |
734 |
|
.extractGaps("-. ", |
735 |
|
alseqs[alsq].getSequenceAsString()) |
736 |
|
.toUpperCase(); |
737 |
0 |
int oldstrt = alseqs[alsq].getStart(); |
738 |
0 |
alseqs[alsq].setStart(sequence.getSequenceAsString() |
739 |
|
.toUpperCase().indexOf(ngAlsq) + sequence.getStart()); |
740 |
0 |
if (oldstrt != alseqs[alsq].getStart()) |
741 |
|
{ |
742 |
0 |
alseqs[alsq].setEnd( |
743 |
|
ngAlsq.length() + alseqs[alsq].getStart() - 1); |
744 |
0 |
modified = true; |
745 |
|
} |
746 |
|
} |
747 |
|
} |
748 |
|
|
749 |
|
|
750 |
|
|
751 |
|
|
752 |
|
|
753 |
|
} |
754 |
|
|
755 |
|
|
756 |
0 |
sdataset.remove(sequence); |
757 |
|
|
758 |
|
|
759 |
|
} |
760 |
|
} |
761 |
0 |
return modified; |
762 |
|
} |
763 |
|
|
764 |
|
|
765 |
|
|
766 |
|
|
767 |
|
@param |
768 |
|
@param |
769 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
770 |
0 |
void addWarningMessage(List<String> messageList, String msg)... |
771 |
|
{ |
772 |
0 |
if (!messageList.contains(msg)) |
773 |
|
{ |
774 |
0 |
messageList.add(msg); |
775 |
|
} |
776 |
|
} |
777 |
|
|
778 |
|
|
779 |
|
|
780 |
|
|
781 |
|
@param |
782 |
|
@return |
783 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 9 |
Complexity Density: 0.69 |
|
784 |
0 |
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)... |
785 |
|
{ |
786 |
0 |
Vector<SequenceI> nseq = new Vector<>(); |
787 |
0 |
for (int i = 0; sequencesArray != null |
788 |
|
&& i < sequencesArray.length; i++) |
789 |
|
{ |
790 |
0 |
nseq.addElement(sequencesArray[i]); |
791 |
0 |
DBRefEntry[] dbr = sequencesArray[i].getDBRefs(); |
792 |
0 |
Mapping map = null; |
793 |
0 |
for (int r = 0; (dbr != null) && r < dbr.length; r++) |
794 |
|
{ |
795 |
0 |
if ((map = dbr[r].getMap()) != null) |
796 |
|
{ |
797 |
0 |
if (map.getTo() != null && !nseq.contains(map.getTo())) |
798 |
|
{ |
799 |
0 |
nseq.addElement(map.getTo()); |
800 |
|
} |
801 |
|
} |
802 |
|
} |
803 |
|
} |
804 |
0 |
if (nseq.size() > 0) |
805 |
|
{ |
806 |
0 |
sequencesArray = new SequenceI[nseq.size()]; |
807 |
0 |
nseq.toArray(sequencesArray); |
808 |
|
} |
809 |
0 |
return sequencesArray; |
810 |
|
} |
811 |
|
} |