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

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index ee0fbc5..611aa79 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -703,7 +703,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       {
         j.setSubmitted(true);
         j.setSubjobComplete(false);
-        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+        // jalview.bin.Console.outPrintln(WsURL + " Job Id '" + jobId + "'");
         return;
       }
       else
@@ -749,7 +749,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     } catch (Error e)
     {
       // For unexpected errors
-      System.err.println(WebServiceName
+      jalview.bin.Console.errPrintln(WebServiceName
               + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
               + "When contacting Server:" + WsUrl + "\n");
       e.printStackTrace(System.err);
@@ -759,7 +759,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     } catch (Exception e)
     {
       // For unexpected errors
-      System.err.println(WebServiceName
+      jalview.bin.Console.errPrintln(WebServiceName
               + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
               + "When contacting Server:" + WsUrl + "\n");
       e.printStackTrace(System.err);
@@ -837,10 +837,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
           if (Console.isDebugEnabled())
           {
-            System.out.println("Job Execution file for job: "
+            jalview.bin.Console.outPrintln("Job Execution file for job: "
                     + msjob.getJobId() + " on server " + WsUrl);
-            System.out.println(msjob.getStatus());
-            System.out.println("*** End of status");
+            jalview.bin.Console.outPrintln(msjob.getStatus());
+            jalview.bin.Console.outPrintln("*** End of status");
 
           }
           try
@@ -986,7 +986,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     else
     {
       // TODO 2.9.x feature
-      System.out.println("MERGE WITH OLD FRAME");
+      jalview.bin.Console.outPrintln("MERGE WITH OLD FRAME");
       // TODO: modify alignment in original frame, replacing old for new
       // alignment using the commands.EditCommand model to ensure the update can
       // be undone