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

[jalview.git] / src / jalview / ws / jws1 / SeqSearchWSThread.java

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 0f28230..805f64c 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -212,9 +212,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           }
         } catch (Exception e)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Failed to parse the annotation file associated with the alignment.");
-          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          jalview.bin.Console.errPrintln(">>>EOF" + inFile + "\n<<<EOF\n");
           e.printStackTrace(System.err);
         }
 
@@ -229,9 +229,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           }
         } catch (Exception e)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Failed to parse the Features file associated with the alignment.");
-          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          jalview.bin.Console.errPrintln(">>>EOF" + inFile + "\n<<<EOF\n");
           e.printStackTrace(System.err);
         }
         jalview.io.NewickFile nf = null;
@@ -250,9 +250,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           }
         } catch (Exception e)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Failed to parse the treeFile associated with the alignment.");
-          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          jalview.bin.Console.errPrintln(">>>EOF" + inFile + "\n<<<EOF\n");
           e.printStackTrace(System.err);
         }
 
@@ -496,7 +496,7 @@ class SeqSearchWSThread 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
       {
@@ -514,7 +514,7 @@ class SeqSearchWSThread 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");
@@ -616,7 +616,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
   {
     if (!newFrame)
     {
-      System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+      jalview.bin.Console.errPrintln("MERGE WITH OLD FRAME NOT IMPLEMENTED");
       return;
     }
     // each subjob is an independent alignment for the moment