X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=b1c987ecd8400a39093002c31c0cfc846a76fa88;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=8c8a717dc2928ed67fee511f5d9f8ea188c15f60;hpb=b44349fe3a5f2d70b74a1b110018a753a1036aca;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 8c8a717..b1c987e 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -28,15 +28,12 @@ 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.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; @@ -61,6 +58,8 @@ 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(); @@ -117,7 +116,7 @@ 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]; @@ -135,11 +134,10 @@ 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); @@ -163,23 +161,7 @@ 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) { @@ -189,7 +171,7 @@ 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); @@ -233,29 +215,6 @@ 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 @@ -308,14 +267,14 @@ 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); } @@ -330,9 +289,8 @@ 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(); @@ -355,9 +313,9 @@ 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) @@ -369,8 +327,8 @@ 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; @@ -397,8 +355,8 @@ 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++; } @@ -432,20 +390,23 @@ public class DBRefFetcher implements Runnable 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()); } } else @@ -462,14 +423,13 @@ public class DBRefFetcher implements Runnable // 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(); } } @@ -481,8 +441,8 @@ 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()); @@ -490,7 +450,8 @@ public class DBRefFetcher implements Runnable 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()); } @@ -514,7 +475,8 @@ 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 @@ -561,18 +523,19 @@ public class DBRefFetcher implements Runnable } 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 @@ -580,9 +543,10 @@ 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())) { @@ -620,7 +584,7 @@ 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 @@ -641,7 +605,7 @@ 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 @@ -649,8 +613,9 @@ 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(); int absStart = entrySeq.indexOf(nonGapped); if (absStart == -1) { @@ -680,10 +645,14 @@ 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 @@ -702,7 +671,8 @@ public class DBRefFetcher implements Runnable int startShift = absStart - sequenceStart + 1; if (startShift != 0) { - modified |= sequence.getFeatures().shiftFeatures(startShift); + modified |= sequence.getFeatures().shiftFeatures(1, + startShift); } } } @@ -725,8 +695,8 @@ 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()) { @@ -734,9 +704,9 @@ 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()); } } } @@ -752,9 +722,9 @@ 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 @@ -762,16 +732,17 @@ 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(); int oldstrt = alseqs[alsq].getStart(); alseqs[alsq].setStart(sequence.getSequenceAsString() - .toUpperCase().indexOf(ngAlsq) - + sequence.getStart()); + .toUpperCase().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; } } @@ -785,8 +756,6 @@ 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; @@ -814,27 +783,33 @@ 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; }