X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FMsaWSThread.java;fp=src%2Fjalview%2Fws%2Fjws1%2FMsaWSThread.java;h=727f5bee7d53cf055c49392a4ff429e2d94424e1;hb=e83ce5d8ef826fc0b509a51f154abdf734501077;hp=e0270389b9a07bc8307ad04369626ed20362db0b;hpb=786475501a15799d7c4058dbf74e4bf896d03736;p=jalview.git

diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index e027038..727f5be 100644
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -479,7 +479,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
         j.setJobId(jobsubmit.getJobId());
         j.setSubmitted(true);
         j.setSubjobComplete(false);
-        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+        // jalview.bin.Console.outPrintln(WsURL + " Job Id '" + jobId + "'");
       }
       else
       {
@@ -497,7 +497,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     {
       // TODO: JBPNote catch timeout or other fault types explicitly
       // 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.toString()
               + "\n");
@@ -544,9 +544,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
           results++;
           // if (Cache.isDebugEnabled())
           // {
-          // System.out.println("Job lob for job
+          // jalview.bin.Console.outPrintln("Job lob for job
           // "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
-          // System.out.println(jobs[j].getStatus());
+          // jalview.bin.Console.outPrintln(jobs[j].getStatus());
           // }
 
           vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result)
@@ -709,7 +709,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
     else
     {
-      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