X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=7745b74610e8e0e295a62ce948badf111ded6185;hb=d248065f96125e06c038bc0b641558d8a878833f;hp=1677ecae8ec6e5e3a481fe1612877283e979c0f8;hpb=0a849b60d2a0419da55f9a3a05b3fe2ed9a576bf;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 1677eca..7745b74 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -28,15 +28,13 @@ import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; 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.gui.Preferences; 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; @@ -119,7 +117,7 @@ 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]; @@ -137,8 +135,7 @@ 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 = SequenceFetcher.getInstance(); // set default behaviour for transferring excess sequence data to the // dataset trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true); @@ -165,23 +162,7 @@ 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) { @@ -191,7 +172,7 @@ 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); @@ -235,30 +216,6 @@ 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 @@ -311,14 +268,14 @@ 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); } @@ -346,7 +303,7 @@ public class DBRefFetcher implements Runnable } try { - if (Cache.getDefault("DBREFFETCH_USEPICR", false)) + if (Cache.getDefault(Preferences.DBREFFETCH_USEPICR, false)) { picrClient = new AccessionMapperServiceLocator() .getAccessionMapperPort(); @@ -357,9 +314,9 @@ 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<>(); int db = 0; while (sdataset.size() > 0 && db < dbSources.length) @@ -371,8 +328,8 @@ 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; @@ -438,18 +395,19 @@ public class DBRefFetcher implements Runnable && (i < 50); seqIndex++, i++) { SequenceI sequence = dataset[seqIndex]; - DBRefEntry[] uprefs = DBRefUtils + 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()); + DBRefEntry upref = uprefs.get(j); + addSeqId(sequence, upref.getAccessionId()); queries.addElement( - uprefs[j].getAccessionId().toUpperCase()); + upref.getAccessionId().toUpperCase()); } } else @@ -574,9 +532,9 @@ public class DBRefFetcher implements Runnable { // 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 + List entryRefs = DBRefUtils .selectRefs(retrievedSeq.getDBRefs(), new String[] { dbSource }); if (entryRefs == null) @@ -586,9 +544,10 @@ 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())) { @@ -626,7 +585,7 @@ 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 @@ -647,7 +606,7 @@ 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 @@ -713,7 +672,8 @@ public class DBRefFetcher implements Runnable int startShift = absStart - sequenceStart + 1; if (startShift != 0) { - modified |= sequence.getFeatures().shiftFeatures(startShift); + modified |= sequence.getFeatures().shiftFeatures(1, + startShift); } } } @@ -797,8 +757,6 @@ 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; @@ -826,28 +784,35 @@ 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; }