JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging www.jalvie...

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 9420465..4705fe5 100644 (file)
--- 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;
@@ -360,9 +363,9 @@ public class DBRefFetcher implements Runnable
           AlignmentI retrieved = null;
           try
           {
-            if (Cache.log.isDebugEnabled())
+            if (Console.isDebugEnabled())
             {
-              Cache.log.debug("Querying " + dbsource.getDbName()
+              Console.debug("Querying " + dbsource.getDbName()
                       + " with : '" + queryString.toString() + "'");
             }
             retrieved = dbsource.getSequenceRecords(queryString.toString());
@@ -404,12 +407,14 @@ 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)
                 {