Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail...

[jalview.git] / src / jalview / util / UrlLink.java

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 18ee9b6..78d0b4c 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -322,7 +322,7 @@ public class UrlLink
             // debug
             for (int s = 0; s <= rg.numSubs(); s++)
             {
-              System.err.println("Sub " + s + " : " + rg.matchedFrom(s)
+              jalview.bin.Console.errPrintln("Sub " + s + " : " + rg.matchedFrom(s)
                       + " : " + rg.matchedTo(s) + " : '"
                       + rg.stringMatched(s) + "'");
             }
@@ -612,17 +612,17 @@ public class UrlLink
     if (usesDBAccession()) // link is ID
     {
       // collect matching db-refs
-      DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
+      List<DBRefEntry> dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
               new String[]
               { target });
 
       // if there are any dbrefs which match up with the link
       if (dbr != null)
       {
-        for (int r = 0; r < dbr.length; r++)
+        for (int r = 0, nd = dbr.size(); r < nd; r++)
         {
           // create Bare ID link for this URL
-          createBareURLLink(dbr[r].getAccessionId(), true, linkset);
+          createBareURLLink(dbr.get(r).getAccessionId(), true, linkset);
         }
       }
     }