X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=d8858a928da000aee0c8ceeaccd31d02a581bf04;hb=320583fd2ac3ea714e6afdac050961978bd34c81;hp=6b8843da91fd92fb117becbb1ca2b5d242069c9b;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 6b8843d..d8858a9 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -20,9 +20,24 @@ */ 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.bin.Console; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; @@ -36,17 +51,6 @@ import jalview.gui.OOMWarning; import jalview.util.DBRefUtils; import jalview.util.MessageManager; import jalview.ws.seqfetcher.DbSourceProxy; - -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 uk.ac.ebi.picr.model.UPEntry; import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator; @@ -74,8 +78,6 @@ public class DBRefFetcher implements Runnable CutAndPasteTransfer output = new CutAndPasteTransfer(); - boolean running = false; - /** * picr client instance */ @@ -225,24 +227,13 @@ 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(); } } @@ -257,7 +248,7 @@ 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)) @@ -295,7 +286,6 @@ public class DBRefFetcher implements Runnable throw new Error(MessageManager .getString("error.implementation_error_must_init_dbsources")); } - running = true; long startTime = System.currentTimeMillis(); if (progressWindow != null) { @@ -316,8 +306,7 @@ public class DBRefFetcher implements Runnable e.printStackTrace(); } - Vector sdataset = new Vector<>( - Arrays.asList(dataset)); + Vector sdataset = new Vector<>(Arrays.asList(dataset)); List warningMessages = new ArrayList<>(); // clear any old feature display settings recorded from past sessions @@ -373,10 +362,10 @@ public class DBRefFetcher implements Runnable AlignmentI retrieved = null; try { - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.debug("Querying " + dbsource.getDbName() - + " with : '" + queryString.toString() + "'"); + Console.debug("Querying " + dbsource.getDbName() + " with : '" + + queryString.toString() + "'"); } retrieved = dbsource.getSequenceRecords(queryString.toString()); } catch (Exception ex) @@ -389,8 +378,8 @@ public class DBRefFetcher implements Runnable } if (retrieved != null) { - transferReferences(sdataset, dbsource, retrieved, - trimDsSeqs, warningMessages); + transferReferences(sdataset, dbsource, retrieved, trimDsSeqs, + warningMessages); } } else @@ -409,20 +398,22 @@ public class DBRefFetcher implements Runnable { for (int j = 0, n = uprefs.size(); j < n; j++) { - DBRefEntry upref = uprefs.get(j); + DBRefEntry upref = uprefs.get(j); addSeqId(sequence, upref.getAccessionId()); queries.addElement( - upref.getAccessionId().toUpperCase()); + 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) { @@ -451,7 +442,7 @@ public class DBRefFetcher implements Runnable "Validated ID against PICR... (for what its worth):" + token); addSeqId(sequence, token); - queries.addElement(token.toUpperCase()); + queries.addElement(token.toUpperCase(Locale.ROOT)); } else { @@ -459,7 +450,7 @@ public class DBRefFetcher implements Runnable // System.out.println("Not querying source with // token="+token+"\n"); addSeqId(sequence, token); - queries.addElement(token.toUpperCase()); + queries.addElement(token.toUpperCase(Locale.ROOT)); } } } @@ -498,7 +489,6 @@ public class DBRefFetcher implements Runnable { listener.finished(); } - running = false; } /** @@ -519,9 +509,8 @@ public class DBRefFetcher implements Runnable * a list of messages to add to */ boolean transferReferences(Vector sdataset, - DbSourceProxy dbSourceProxy, - AlignmentI retrievedAl, boolean trimDatasetSeqs, - List warningMessages) + DbSourceProxy dbSourceProxy, AlignmentI retrievedAl, + boolean trimDatasetSeqs, List warningMessages) { // System.out.println("trimming ? " + trimDatasetSeqs); if (retrievedAl == null || retrievedAl.getHeight() == 0) @@ -553,10 +542,10 @@ public class DBRefFetcher implements Runnable } for (int j = 0, n = entryRefs.size(); j < n; j++) { - DBRefEntry ref = entryRefs.get(j); + 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++) @@ -608,7 +597,7 @@ public class DBRefFetcher implements Runnable // 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); @@ -627,7 +616,7 @@ public class DBRefFetcher implements Runnable boolean remoteEnclosesLocal = false; String nonGapped = AlignSeq .extractGaps("-. ", sequence.getSequenceAsString()) - .toUpperCase(); + .toUpperCase(Locale.ROOT); int absStart = entrySeq.indexOf(nonGapped); if (absStart == -1) { @@ -747,10 +736,11 @@ public class DBRefFetcher implements Runnable String ngAlsq = AlignSeq .extractGaps("-. ", alseqs[alsq].getSequenceAsString()) - .toUpperCase(); + .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( @@ -791,15 +781,17 @@ public class DBRefFetcher implements Runnable /** * - * @return any feature settings associated with sources that have provided sequences + * @return any feature settings associated with sources that have provided + * sequences */ - public ListgetFeatureSettingsModels() + public List getFeatureSettingsModels() { 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 * @@ -822,11 +814,11 @@ public class DBRefFetcher implements Runnable */ private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray) { - int n; - if (sequencesArray == null || (n = sequencesArray.length) == 0) - return sequencesArray; + int n; + if (sequencesArray == null || (n = sequencesArray.length) == 0) + return sequencesArray; ArrayList nseq = new ArrayList<>(); - for (int i = 0;i < n; i++) + for (int i = 0; i < n; i++) { nseq.add(sequencesArray[i]); List dbr = sequencesArray[i].getDBRefs(); @@ -841,11 +833,12 @@ public class DBRefFetcher implements Runnable { nseq.add(map.getTo()); } - } + } } } } - // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found? + // BH 2019.01.25 question here if this is the right logic. Return the + // original if nothing found? if (nseq.size() > 0) { return nseq.toArray(new SequenceI[nseq.size()]);