X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=899fffc99d0557d76fbaf594f864098b7890c171;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=fd511dcd4de0f101f4d8d6e4db9353539bd73849;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index fd511dc..899fffc 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -20,34 +20,36 @@ */ package jalview.ws; +import java.util.Locale; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + import jalview.analysis.AlignSeq; +import jalview.api.FeatureSettingsModelI; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; -import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.CutAndPasteTransfer; -import jalview.gui.DasSourceBrowser; import jalview.gui.Desktop; import jalview.gui.FeatureSettings; import jalview.gui.IProgressIndicator; import jalview.gui.OOMWarning; import jalview.util.DBRefUtils; import jalview.util.MessageManager; -import jalview.ws.dbsources.das.api.jalviewSourceI; -import jalview.ws.dbsources.das.datamodel.DasSequenceSource; import jalview.ws.seqfetcher.DbSourceProxy; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.StringTokenizer; -import java.util.Vector; - import uk.ac.ebi.picr.model.UPEntry; import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator; @@ -62,6 +64,8 @@ public class DBRefFetcher implements Runnable { private static final String NEWLINE = System.lineSeparator(); + public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS"; + public interface FetchFinishedListenerI { void finished(); @@ -73,8 +77,6 @@ public class DBRefFetcher implements Runnable CutAndPasteTransfer output = new CutAndPasteTransfer(); - boolean running = false; - /** * picr client instance */ @@ -118,7 +120,7 @@ public class DBRefFetcher implements Runnable DbSourceProxy[] sources, FeatureSettings featureSettings, boolean isNucleotide) { - listeners = new ArrayList(); + listeners = new ArrayList<>(); this.progressWindow = progressIndicatorFrame; alseqs = new SequenceI[seqs.length]; SequenceI[] ds = new SequenceI[seqs.length]; @@ -136,11 +138,10 @@ public class DBRefFetcher implements Runnable } this.dataset = ds; // TODO Jalview 2.5 lots of this code should be in the gui package! - sfetcher = jalview.gui.SequenceFetcher - .getSequenceFetcherSingleton(progressIndicatorFrame); + sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(); // set default behaviour for transferring excess sequence data to the // dataset - trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true); + trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true); if (sources == null) { setDatabaseSources(featureSettings, isNucleotide); @@ -164,23 +165,7 @@ public class DBRefFetcher implements Runnable { // af.featureSettings_actionPerformed(null); String[] defdb = null; - List selsources = new ArrayList(); - Vector dasselsrc = (featureSettings != null) ? featureSettings - .getSelectedSources() : new DasSourceBrowser() - .getSelectedSources(); - - for (jalviewSourceI src : dasselsrc) - { - List sp = src.getSequenceSourceProxies(); - if (sp != null) - { - selsources.addAll(sp); - if (sp.size() > 1) - { - Cache.log.debug("Added many Db Sources for :" + src.getTitle()); - } - } - } + List selsources = new ArrayList<>(); // select appropriate databases based on alignFrame context. if (forNucleotide) { @@ -190,7 +175,7 @@ public class DBRefFetcher implements Runnable { defdb = DBRefSource.PROTEINDBS; } - List srces = new ArrayList(); + List srces = new ArrayList<>(); for (String ddb : defdb) { List srcesfordb = sfetcher.getSourceProxy(ddb); @@ -234,29 +219,6 @@ public class DBRefFetcher implements Runnable } /** - * retrieve all the das sequence sources and add them to the list of db - * sources to retrieve from - */ - public void appendAllDasSources() - { - if (dbSources == null) - { - dbSources = new DbSourceProxy[0]; - } - // append additional sources - DbSourceProxy[] otherdb = sfetcher - .getDbSourceProxyInstances(DasSequenceSource.class); - if (otherdb != null && otherdb.length > 0) - { - DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length - + otherdb.length]; - System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length); - System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length); - dbSources = newsrc; - } - } - - /** * start the fetcher thread * * @param waitTillFinished @@ -264,24 +226,13 @@ public class DBRefFetcher implements Runnable */ public void fetchDBRefs(boolean waitTillFinished) { - // TODO can we not simply write - // if (waitTillFinished) { run(); } else { new Thread(this).start(); } - - Thread thread = new Thread(this); - thread.start(); - running = true; - if (waitTillFinished) { - while (running) - { - try - { - Thread.sleep(500); - } catch (Exception ex) - { - } - } + run(); + } + else + { + new Thread(this).start(); } } @@ -296,7 +247,7 @@ public class DBRefFetcher implements Runnable */ void addSeqId(SequenceI seq, String key) { - key = key.toUpperCase(); + key = key.toUpperCase(Locale.ROOT); Vector seqs; if (seqRefs.containsKey(key)) @@ -309,14 +260,14 @@ public class DBRefFetcher implements Runnable } else if (seqs == null) { - seqs = new Vector(); + seqs = new Vector<>(); seqs.addElement(seq); } } else { - seqs = new Vector(); + seqs = new Vector<>(); seqs.addElement(seq); } @@ -331,11 +282,9 @@ public class DBRefFetcher implements Runnable { if (dbSources == null) { - throw new Error( - MessageManager - .getString("error.implementation_error_must_init_dbsources")); + throw new Error(MessageManager + .getString("error.implementation_error_must_init_dbsources")); } - running = true; long startTime = System.currentTimeMillis(); if (progressWindow != null) { @@ -356,9 +305,12 @@ public class DBRefFetcher implements Runnable e.printStackTrace(); } - Vector sdataset = new Vector( + Vector sdataset = new Vector<>( Arrays.asList(dataset)); - List warningMessages = new ArrayList(); + List warningMessages = new ArrayList<>(); + + // clear any old feature display settings recorded from past sessions + featureDisplaySettings = null; int db = 0; while (sdataset.size() > 0 && db < dbSources.length) @@ -370,8 +322,8 @@ public class DBRefFetcher implements Runnable SequenceI[] currSeqs = new SequenceI[sdataset.size()]; sdataset.copyInto(currSeqs);// seqs that are to be validated against // dbSources[db] - Vector queries = new Vector(); // generated queries curSeq - seqRefs = new Hashtable>(); + Vector queries = new Vector<>(); // generated queries curSeq + seqRefs = new Hashtable<>(); int seqIndex = 0; @@ -398,8 +350,8 @@ public class DBRefFetcher implements Runnable String query = queries.elementAt(0); if (dbsource.isValidReference(query)) { - queryString.append((numq == 0) ? "" : dbsource - .getAccessionSeparator()); + queryString.append( + (numq == 0) ? "" : dbsource.getAccessionSeparator()); queryString.append(query); numq++; } @@ -410,9 +362,9 @@ public class DBRefFetcher implements Runnable AlignmentI retrieved = null; try { - if (Cache.log.isDebugEnabled()) + if (Cache.isDebugEnabled()) { - Cache.log.debug("Querying " + dbsource.getDbName() + Cache.debug("Querying " + dbsource.getDbName() + " with : '" + queryString.toString() + "'"); } retrieved = dbsource.getSequenceRecords(queryString.toString()); @@ -426,51 +378,55 @@ public class DBRefFetcher implements Runnable } if (retrieved != null) { - transferReferences(sdataset, dbsource.getDbSource(), retrieved, + transferReferences(sdataset, dbsource, retrieved, trimDsSeqs, warningMessages); } } else { // make some more strings for use as queries - for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++) + for (int i = 0; (seqIndex < dataset.length) + && (i < 50); seqIndex++, i++) { SequenceI sequence = dataset[seqIndex]; - DBRefEntry[] uprefs = DBRefUtils.selectRefs( - sequence.getDBRefs(), - new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT + List uprefs = DBRefUtils + .selectRefs(sequence.getDBRefs(), new String[] + { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT // }); // check for existing dbrefs to use - if (uprefs != null && uprefs.length > 0) + if (uprefs != null && uprefs.size() > 0) { - for (int j = 0; j < uprefs.length; j++) + for (int j = 0, n = uprefs.size(); j < n; j++) { - addSeqId(sequence, uprefs[j].getAccessionId()); - queries.addElement(uprefs[j].getAccessionId().toUpperCase()); + DBRefEntry upref = uprefs.get(j); + addSeqId(sequence, upref.getAccessionId()); + queries.addElement( + upref.getAccessionId().toUpperCase(Locale.ROOT)); } } else { + Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+"); // generate queries from sequence ID string - StringTokenizer st = new StringTokenizer(sequence.getName(), - "|"); - while (st.hasMoreTokens()) + Matcher tokens = possibleIds.matcher(sequence.getName()); + int p=0; + while (tokens.find(p)) { - String token = st.nextToken(); + String token = tokens.group(); + p = tokens.end(); UPEntry[] presp = null; if (picrClient != null) { // resolve the string against PICR to recover valid IDs try { - presp = picrClient - .getUPIForAccession(token, null, - picrClient.getMappedDatabaseNames(), - null, true); + presp = picrClient.getUPIForAccession(token, null, + picrClient.getMappedDatabaseNames(), null, + true); } catch (Exception e) { - System.err.println("Exception with Picr for '" + token - + "'\n"); + System.err.println( + "Exception with Picr for '" + token + "'\n"); e.printStackTrace(); } } @@ -482,18 +438,19 @@ public class DBRefFetcher implements Runnable // present, and do a transferReferences // otherwise transfer non sequence x-references directly. } - System.out - .println("Validated ID against PICR... (for what its worth):" + System.out.println( + "Validated ID against PICR... (for what its worth):" + token); addSeqId(sequence, token); - queries.addElement(token.toUpperCase()); + queries.addElement(token.toUpperCase(Locale.ROOT)); } else { // if () - // System.out.println("Not querying source with token="+token+"\n"); + // System.out.println("Not querying source with + // token="+token+"\n"); addSeqId(sequence, token); - queries.addElement(token.toUpperCase()); + queries.addElement(token.toUpperCase(Locale.ROOT)); } } } @@ -515,7 +472,8 @@ public class DBRefFetcher implements Runnable output.setText(sb.toString()); Desktop.addInternalFrame(output, - MessageManager.getString("label.sequences_updated"), 600, 300); + MessageManager.getString("label.sequences_updated"), 600, + 300); // The above is the dataset, we must now find out the index // of the viewed sequence @@ -531,7 +489,6 @@ public class DBRefFetcher implements Runnable { listener.finished(); } - running = false; } /** @@ -551,7 +508,8 @@ public class DBRefFetcher implements Runnable * @param warningMessages * a list of messages to add to */ - boolean transferReferences(Vector sdataset, String dbSource, + boolean transferReferences(Vector sdataset, + DbSourceProxy dbSourceProxy, AlignmentI retrievedAl, boolean trimDatasetSeqs, List warningMessages) { @@ -561,19 +519,21 @@ public class DBRefFetcher implements Runnable return false; } + String dbSource = dbSourceProxy.getDbName(); boolean modified = false; - SequenceI[] retrieved = recoverDbSequences(retrievedAl - .getSequencesArray()); + SequenceI[] retrieved = recoverDbSequences( + retrievedAl.getSequencesArray()); SequenceI sequence = null; for (SequenceI retrievedSeq : retrieved) { // Work out which sequences this sequence matches, // taking into account all accessionIds and names in the file - Vector sequenceMatches = new Vector(); + Vector sequenceMatches = new Vector<>(); // look for corresponding accession ids - DBRefEntry[] entryRefs = DBRefUtils.selectRefs( - retrievedSeq.getDBRefs(), new String[] { dbSource }); + List entryRefs = DBRefUtils + .selectRefs(retrievedSeq.getDBRefs(), new String[] + { dbSource }); if (entryRefs == null) { System.err @@ -581,11 +541,12 @@ public class DBRefFetcher implements Runnable + dbSource + " on " + retrievedSeq.getName()); continue; } - for (int j = 0; j < entryRefs.length; j++) + for (int j = 0, n = entryRefs.size(); j < n; j++) { - String accessionId = entryRefs[j].getAccessionId(); + DBRefEntry ref = entryRefs.get(j); + String accessionId = ref.getAccessionId(); // match up on accessionId - if (seqRefs.containsKey(accessionId.toUpperCase())) + if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT))) { Vector seqs = seqRefs.get(accessionId); for (int jj = 0; jj < seqs.size(); jj++) @@ -621,7 +582,7 @@ public class DBRefFetcher implements Runnable // could be useful to extend this so we try to find any 'significant' // information in common between two sequence objects. /* - * DBRefEntry[] entryRefs = + * List entryRefs = * jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] { * dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String * name = entry.getName().elementAt(j).toString(); if @@ -630,10 +591,14 @@ public class DBRefFetcher implements Runnable * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) { * sequenceMatches.addElement(sequence); } } } } */ + if (sequenceMatches.size() > 0) + { + addFeatureSettings(dbSourceProxy); + } // sequenceMatches now contains the set of all sequences associated with // the returned db record final String retrievedSeqString = retrievedSeq.getSequenceAsString(); - String entrySeq = retrievedSeqString.toUpperCase(); + String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT); for (int m = 0; m < sequenceMatches.size(); m++) { sequence = sequenceMatches.elementAt(m); @@ -642,7 +607,7 @@ public class DBRefFetcher implements Runnable // TODO: test for legacy where uniprot or EMBL refs exist but no // mappings are made (but content matches retrieved set) boolean updateRefFrame = sequence.getDBRefs() == null - || sequence.getDBRefs().length == 0; + || sequence.getDBRefs().size() == 0; // TODO: // verify sequence against the entry sequence @@ -650,8 +615,9 @@ public class DBRefFetcher implements Runnable final int sequenceStart = sequence.getStart(); boolean remoteEnclosesLocal = false; - String nonGapped = AlignSeq.extractGaps("-. ", - sequence.getSequenceAsString()).toUpperCase(); + String nonGapped = AlignSeq + .extractGaps("-. ", sequence.getSequenceAsString()) + .toUpperCase(Locale.ROOT); int absStart = entrySeq.indexOf(nonGapped); if (absStart == -1) { @@ -681,10 +647,14 @@ public class DBRefFetcher implements Runnable * So create a mapping to the external entry from the matching region of * the local sequence, and leave local start/end untouched. */ - mp = new Mapping(null, new int[] { sequenceStart + absStart, - sequenceStart + absStart + entrySeq.length() - 1 }, new int[] - { retrievedSeq.getStart(), - retrievedSeq.getStart() + entrySeq.length() - 1 }, 1, 1); + mp = new Mapping(null, + new int[] + { sequenceStart + absStart, + sequenceStart + absStart + entrySeq.length() - 1 }, + new int[] + { retrievedSeq.getStart(), + retrievedSeq.getStart() + entrySeq.length() - 1 }, + 1, 1); updateRefFrame = false; } else @@ -697,28 +667,14 @@ public class DBRefFetcher implements Runnable if (updateRefFrame) { - SequenceFeature[] sfs = sequence.getSequenceFeatures(); - if (sfs != null) + /* + * relocate existing sequence features by offset + */ + int startShift = absStart - sequenceStart + 1; + if (startShift != 0) { - /* - * relocate existing sequence features by offset - */ - int start = sequenceStart; - int end = sequence.getEnd(); - int startShift = 1 - absStart - start; - - if (startShift != 0) - { - for (SequenceFeature sf : sfs) - { - if (sf.getBegin() >= start && sf.getEnd() <= end) - { - sf.setBegin(sf.getBegin() + startShift); - sf.setEnd(sf.getEnd() + startShift); - modified = true; - } - } - } + modified |= sequence.getFeatures().shiftFeatures(1, + startShift); } } } @@ -741,8 +697,8 @@ public class DBRefFetcher implements Runnable sequence.setSequence(retrievedSeqString); modified = true; addWarningMessage(warningMessages, - "Sequence for " + sequence.getName() - + " expanded from " + retrievedSeq.getName()); + "Sequence for " + sequence.getName() + " expanded from " + + retrievedSeq.getName()); } if (sequence.getStart() != retrievedSeq.getStart()) { @@ -750,9 +706,9 @@ public class DBRefFetcher implements Runnable modified = true; if (absStart != sequenceStart) { - addWarningMessage(warningMessages, "Start/end position for " - + sequence.getName() + " updated from " - + retrievedSeq.getName()); + addWarningMessage(warningMessages, + "Start/end position for " + sequence.getName() + + " updated from " + retrievedSeq.getName()); } } } @@ -768,9 +724,9 @@ public class DBRefFetcher implements Runnable sequence.setStart(absStart); sequence.setEnd(absEnd); modified = true; - addWarningMessage(warningMessages, "Start/end for " - + sequence.getName() + " updated from " - + retrievedSeq.getName()); + addWarningMessage(warningMessages, + "Start/end for " + sequence.getName() + + " updated from " + retrievedSeq.getName()); } } // search for alignment sequences to update coordinate frame for @@ -778,16 +734,17 @@ public class DBRefFetcher implements Runnable { if (alseqs[alsq].getDatasetSequence() == sequence) { - String ngAlsq = AlignSeq.extractGaps("-. ", - alseqs[alsq].getSequenceAsString()).toUpperCase(); + String ngAlsq = AlignSeq + .extractGaps("-. ", + alseqs[alsq].getSequenceAsString()) + .toUpperCase(Locale.ROOT); int oldstrt = alseqs[alsq].getStart(); alseqs[alsq].setStart(sequence.getSequenceAsString() - .toUpperCase().indexOf(ngAlsq) - + sequence.getStart()); + .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart()); if (oldstrt != alseqs[alsq].getStart()) { - alseqs[alsq].setEnd(ngAlsq.length() - + alseqs[alsq].getStart() - 1); + alseqs[alsq].setEnd( + ngAlsq.length() + alseqs[alsq].getStart() - 1); modified = true; } } @@ -801,13 +758,38 @@ public class DBRefFetcher implements Runnable // and remove it from the rest // TODO: decide if we should remove annotated sequence from set sdataset.remove(sequence); - // TODO: should we make a note of sequences that have received new DB - // ids, so we can query all enabled DAS servers for them ? } } return modified; } + Map featureDisplaySettings = null; + + private void addFeatureSettings(DbSourceProxy dbSourceProxy) + { + FeatureSettingsModelI fsettings = dbSourceProxy + .getFeatureColourScheme(); + if (fsettings != null) + { + if (featureDisplaySettings == null) + { + featureDisplaySettings = new HashMap<>(); + } + featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings); + } + } + + /** + * + * @return any feature settings associated with sources that have provided sequences + */ + public ListgetFeatureSettingsModels() + { + return featureDisplaySettings == null + ? Arrays.asList(new FeatureSettingsModelI[0]) + : Arrays.asList(featureDisplaySettings.values() + .toArray(new FeatureSettingsModelI[1])); + } /** * Adds the message to the list unless it already contains it * @@ -830,27 +812,33 @@ public class DBRefFetcher implements Runnable */ private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray) { - Vector nseq = new Vector(); - for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++) + int n; + if (sequencesArray == null || (n = sequencesArray.length) == 0) + return sequencesArray; + ArrayList nseq = new ArrayList<>(); + for (int i = 0;i < n; i++) { - nseq.addElement(sequencesArray[i]); - DBRefEntry[] dbr = sequencesArray[i].getDBRefs(); + nseq.add(sequencesArray[i]); + List dbr = sequencesArray[i].getDBRefs(); Mapping map = null; - for (int r = 0; (dbr != null) && r < dbr.length; r++) + if (dbr != null) { - if ((map = dbr[r].getMap()) != null) + for (int r = 0, rn = dbr.size(); r < rn; r++) { - if (map.getTo() != null && !nseq.contains(map.getTo())) + if ((map = dbr.get(r).getMap()) != null) { - nseq.addElement(map.getTo()); - } + if (map.getTo() != null && !nseq.contains(map.getTo())) + { + nseq.add(map.getTo()); + } + } } } } + // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found? if (nseq.size() > 0) { - sequencesArray = new SequenceI[nseq.size()]; - nseq.toArray(sequencesArray); + return nseq.toArray(new SequenceI[nseq.size()]); } return sequencesArray; }