Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d8858a9..0ebd3c3 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -302,7 +302,7 @@ 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();
     }
 
@@ -316,7 +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
-      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()];
@@ -425,7 +425,7 @@ public class DBRefFetcher implements Runnable
                             true);
                   } catch (Exception e)
                   {
-                    System.err.println(
+                    jalview.bin.Console.errPrintln(
                             "Exception with Picr for '" + token + "'\n");
                     e.printStackTrace();
                   }
@@ -438,7 +438,7 @@ 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);
@@ -447,7 +447,7 @@ 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));
@@ -512,7 +512,7 @@ public class DBRefFetcher implements Runnable
           DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
           boolean trimDatasetSeqs, List<String> warningMessages)
   {
-    // System.out.println("trimming ? " + trimDatasetSeqs);
+    // jalview.bin.Console.outPrintln("trimming ? " + trimDatasetSeqs);
     if (retrievedAl == null || retrievedAl.getHeight() == 0)
     {
       return false;
@@ -678,7 +678,7 @@ public class DBRefFetcher implements Runnable
           }
         }
 
-        System.out.println("Adding dbrefs to " + sequence.getName()
+        jalview.bin.Console.outPrintln("Adding dbrefs to " + sequence.getName()
                 + " from " + dbSource + " sequence : "
                 + retrievedSeq.getName());
         sequence.transferAnnotation(retrievedSeq, mp);