From 50f7ec9ae3c5859e388f45e18ce4bcd75024a5eb Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 20 Dec 2023 20:28:49 +0000
Subject: [PATCH] JAL-4238 Marked where JalviewJS is hanging on 3DBeacons
 search.

---
 src/jalview/ws/DBRefFetcher.java |   20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

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<String> 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);
 
-- 
1.7.10.2