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

[jalview.git] / src / jalview / ws / seqfetcher / ASequenceFetcher.java

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 0d0a314..374147a 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -191,9 +191,9 @@ public class ASequenceFetcher
               seqset = fetcher.getSequenceRecords(qsb.toString());
             } catch (Exception ex)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Failed to retrieve the following from " + db);
-              System.err.println(qsb);
+              jalview.bin.Console.errPrintln(qsb);
               ex.printStackTrace(System.err);
             }
             // TODO: Merge alignment together - perhaps
@@ -222,7 +222,7 @@ public class ASequenceFetcher
               {
                 if (fetcher.getRawRecords() != null)
                 {
-                  System.out.println(
+                  jalview.bin.Console.outPrintln(
                           "# Retrieved from " + db + ":" + qsb.toString());
                   StringBuffer rrb = fetcher.getRawRecords();
                   /*
@@ -235,12 +235,12 @@ public class ASequenceFetcher
                   /*
                    * } else { hdr = "# part "+rr; }
                    */
-                  System.out.println(hdr);
+                  jalview.bin.Console.outPrintln(hdr);
                   if (rrb != null)
                   {
-                    System.out.println(rrb);
+                    jalview.bin.Console.outPrintln(rrb);
                   }
-                  System.out.println("# end of " + hdr);
+                  jalview.bin.Console.outPrintln("# end of " + hdr);
                 }
 
               }
@@ -253,7 +253,7 @@ public class ASequenceFetcher
         }
         if (queriesMade.size() > 0)
         {
-          System.out.println("# Adding " + queriesMade.size()
+          jalview.bin.Console.outPrintln("# Adding " + queriesMade.size()
                   + " ids back to queries list for searching again (" + db
                   + ")");
           queriesLeft.addAll(queriesMade);
@@ -279,7 +279,7 @@ public class ASequenceFetcher
           Exception ex)
   {
 
-    System.err.println(
+    jalview.bin.Console.errPrintln(
             "Failed to retrieve the following references from " + db);
     int n = 0;
     for (String qv : queriesMade)
@@ -287,11 +287,11 @@ public class ASequenceFetcher
       System.err.print(" " + qv + ";");
       if (n++ > 10)
       {
-        System.err.println();
+        jalview.bin.Console.errPrintln();
         n = 0;
       }
     }
-    System.err.println();
+    jalview.bin.Console.errPrintln();
     ex.printStackTrace();
   }