X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=d108d4d63f08d5695e107e1ab62fd4c9c6ac240f;hb=0ebbad305e982eeda562a1842362dc415c36cc8d;hp=942046596ce3bdbc8c9d8986910de170a035ab08;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 9420465..d108d4d 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -31,10 +31,13 @@ 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; @@ -299,12 +302,12 @@ public class DBRefFetcher implements Runnable } } catch (Exception e) { - System.err.println("Couldn't locate PICR service instance.\n"); + jalview.bin.Console + .errPrintln("Couldn't locate PICR service instance.\n"); 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 @@ -314,7 +317,8 @@ public class DBRefFetcher implements Runnable while (sdataset.size() > 0 && db < dbSources.length) { int maxqlen = 1; // default number of queries made at one time - System.out.println("Verifying against " + dbSources[db].getDbName()); + jalview.bin.Console + .outPrintln("Verifying against " + dbSources[db].getDbName()); // iterate through db for each remaining un-verified sequence SequenceI[] currSeqs = new SequenceI[sdataset.size()]; @@ -360,10 +364,10 @@ 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) @@ -376,8 +380,8 @@ public class DBRefFetcher implements Runnable } if (retrieved != null) { - transferReferences(sdataset, dbsource, retrieved, - trimDsSeqs, warningMessages); + transferReferences(sdataset, dbsource, retrieved, trimDsSeqs, + warningMessages); } } else @@ -396,7 +400,7 @@ 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(Locale.ROOT)); @@ -404,12 +408,14 @@ public class DBRefFetcher implements Runnable } 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) { @@ -421,7 +427,7 @@ public class DBRefFetcher implements Runnable true); } catch (Exception e) { - System.err.println( + jalview.bin.Console.errPrintln( "Exception with Picr for '" + token + "'\n"); e.printStackTrace(); } @@ -434,7 +440,7 @@ public class DBRefFetcher implements Runnable // present, and do a transferReferences // otherwise transfer non sequence x-references directly. } - System.out.println( + jalview.bin.Console.outPrintln( "Validated ID against PICR... (for what its worth):" + token); addSeqId(sequence, token); @@ -443,7 +449,7 @@ public class DBRefFetcher implements Runnable else { // if () - // System.out.println("Not querying source with + // jalview.bin.Console.outPrintln("Not querying source with // token="+token+"\n"); addSeqId(sequence, token); queries.addElement(token.toUpperCase(Locale.ROOT)); @@ -505,11 +511,10 @@ 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); + // jalview.bin.Console.outPrintln("trimming ? " + trimDatasetSeqs); if (retrievedAl == null || retrievedAl.getHeight() == 0) { return false; @@ -539,7 +544,7 @@ 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(Locale.ROOT))) @@ -675,8 +680,8 @@ public class DBRefFetcher implements Runnable } } - System.out.println("Adding dbrefs to " + sequence.getName() - + " from " + dbSource + " sequence : " + jalview.bin.Console.outPrintln("Adding dbrefs to " + + sequence.getName() + " from " + dbSource + " sequence : " + retrievedSeq.getName()); sequence.transferAnnotation(retrievedSeq, mp); @@ -736,7 +741,8 @@ public class DBRefFetcher implements Runnable .toUpperCase(Locale.ROOT); int oldstrt = alseqs[alsq].getStart(); alseqs[alsq].setStart(sequence.getSequenceAsString() - .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart()); + .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + + sequence.getStart()); if (oldstrt != alseqs[alsq].getStart()) { alseqs[alsq].setEnd( @@ -777,15 +783,17 @@ 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 * @@ -808,11 +816,11 @@ 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(); @@ -827,11 +835,12 @@ 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()]);