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

[jalview.git] / src / jalview / ext / ensembl / EnsemblRestClient.java

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 4a5544e..540fc98 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -211,7 +211,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       return pingString != null;
     } catch (Throwable t)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error connecting to " + pingUrl + ": " + t.getMessage());
     } finally
     {
@@ -313,7 +313,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
        * note: a GET request for an invalid id returns an error code e.g. 415
        * but POST request returns 200 and an empty Fasta response 
        */
-      System.err.println("Response code " + responseCode);// + " for " + url);
+      jalview.bin.Console.errPrintln("Response code " + responseCode);// + " for " + url);
       return null;
     }
 
@@ -338,7 +338,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected HttpURLConnection tryConnection(URL url, List<String> ids,
           int readTimeout) throws IOException, ProtocolException
   {
-    // System.out.println(System.currentTimeMillis() + " " + url);
+    // jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
 
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
 
@@ -387,14 +387,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
         int retrySecs = Integer.valueOf(retryDelay);
         if (retrySecs > 0 && retrySecs < 10)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Ensembl REST service rate limit exceeded, waiting "
                           + retryDelay + " seconds before retrying");
           Thread.sleep(1000 * retrySecs);
         }
       } catch (NumberFormatException | InterruptedException e)
       {
-        System.err.println("Error handling Retry-After: " + e.getMessage());
+        jalview.bin.Console.errPrintln("Error handling Retry-After: " + e.getMessage());
       }
     }
   }
@@ -566,7 +566,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
         }
       } catch (NumberFormatException e)
       {
-        System.err.println("Error in REST version: " + e.toString());
+        jalview.bin.Console.errPrintln("Error in REST version: " + e.toString());
       }
 
       /*
@@ -578,14 +578,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
               expected) == 1;
       if (laterVersion)
       {
-        System.err.println(String.format(
+        jalview.bin.Console.errPrintln(String.format(
                 "EnsemblRestClient expected %s REST version %s but found %s, see %s",
                 getDbSource(), expected, version, REST_CHANGE_LOG));
       }
       info.restVersion = version;
     } catch (Throwable t)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error checking Ensembl REST version: " + t.getMessage());
     }
   }
@@ -617,7 +617,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       domainData.get(getDomain()).dataVersion = versions.get(0).toString();
     } catch (Throwable e)
     {// could be IOException | ParseException e) {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error checking Ensembl data version: " + e.getMessage());
     }
   }