Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/ws/jws2/JabawsCalcWorker.java b/src/jalview/ws/jws2/JabawsCalcWorker.java
index e01c648..3d3e6cb 100644 (file)
--- a/src/jalview/ws/jws2/JabawsCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsCalcWorker.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -115,7 +115,8 @@ public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
         rslt = aaservice.customAnalize(seqs, getJabaArguments());
       } catch (WrongParameterException x)
       {
-        throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
+        throw new JobSubmissionException(MessageManager.getString(
+                "exception.jobsubmission_invalid_params_set"), x);
 
       }
     }
@@ -141,9 +142,9 @@ public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
           List<AlignmentAnnotation> ourAnnot, String typeName,
           String calcId, SequenceI dseq, int base, Score scr)
   {
-    System.out.println("Creating annotation on dseq:" + dseq.getStart()
-            + " base is " + base + " and length=" + dseq.getLength()
-            + " == " + scr.getScores().size());
+    jalview.bin.Console.outPrintln("Creating annotation on dseq:"
+            + dseq.getStart() + " base is " + base + " and length="
+            + dseq.getLength() + " == " + scr.getScores().size());
     // AlignmentAnnotation annotation = new AlignmentAnnotation(
     // scr.getMethod(), typeName, new Annotation[]
     // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);