From: Ben Soares Date: Wed, 20 Dec 2023 20:28:49 +0000 (+0000) Subject: JAL-4238 Marked where JalviewJS is hanging on 3DBeacons search. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=50f7ec9ae3c5859e388f45e18ce4bcd75024a5eb;p=jalview.git JAL-4238 Marked where JalviewJS is hanging on 3DBeacons search. --- diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index d4e34e7..b48c02c 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -302,8 +302,7 @@ public class DBRefFetcher implements Runnable } } catch (Exception e) { - jalview.bin.Console - .errPrintln("Couldn't locate PICR service instance.\n"); + Console.errPrintln("Couldn't locate PICR service instance.\n"); e.printStackTrace(); } @@ -317,8 +316,7 @@ public class DBRefFetcher implements Runnable while (sdataset.size() > 0 && db < dbSources.length) { int maxqlen = 1; // default number of queries made at one time - jalview.bin.Console - .outPrintln("Verifying against " + dbSources[db].getDbName()); + Console.info("Verifying against " + dbSources[db].getDbName()); // iterate through db for each remaining un-verified sequence SequenceI[] currSeqs = new SequenceI[sdataset.size()]; @@ -414,7 +412,7 @@ public class DBRefFetcher implements Runnable int p = 0; while (tokens.find(p)) { - String token = tokens.group(); + String token = tokens.group(); // JALVIEWJS is hanging here p = tokens.end(); UPEntry[] presp = null; if (picrClient != null) @@ -427,7 +425,7 @@ public class DBRefFetcher implements Runnable true); } catch (Exception e) { - jalview.bin.Console.errPrintln( + Console.errPrintln( "Exception with Picr for '" + token + "'\n"); e.printStackTrace(); } @@ -440,7 +438,7 @@ public class DBRefFetcher implements Runnable // present, and do a transferReferences // otherwise transfer non sequence x-references directly. } - jalview.bin.Console.outPrintln( + Console.outPrintln( "Validated ID against PICR... (for what its worth):" + token); addSeqId(sequence, token); @@ -449,7 +447,7 @@ public class DBRefFetcher implements Runnable else { // if () - // jalview.bin.Console.outPrintln("Not querying source with + // Console.outPrintln("Not querying source with // token="+token+"\n"); addSeqId(sequence, token); queries.addElement(token.toUpperCase(Locale.ROOT)); @@ -514,7 +512,7 @@ public class DBRefFetcher implements Runnable DbSourceProxy dbSourceProxy, AlignmentI retrievedAl, boolean trimDatasetSeqs, List warningMessages) { - // jalview.bin.Console.outPrintln("trimming ? " + trimDatasetSeqs); + // Console.outPrintln("trimming ? " + trimDatasetSeqs); if (retrievedAl == null || retrievedAl.getHeight() == 0) { return false; @@ -680,8 +678,8 @@ public class DBRefFetcher implements Runnable } } - jalview.bin.Console.outPrintln("Adding dbrefs to " - + sequence.getName() + " from " + dbSource + " sequence : " + Console.outPrintln("Adding dbrefs to " + sequence.getName() + + " from " + dbSource + " sequence : " + retrievedSeq.getName()); sequence.transferAnnotation(retrievedSeq, mp);