JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[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 afb46e9..47e82de 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.
  * 
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.util.MessageManager;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
@@ -114,8 +115,8 @@ public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
         rslt = aaservice.customAnalize(seqs, getJabaArguments());
       } catch (WrongParameterException x)
       {
-        throw new JobSubmissionException(
-                "Invalid parameter set. Check Jalview implementation.", x);
+        throw new JobSubmissionException(MessageManager.getString(
+                "exception.jobsubmission_invalid_params_set"), x);
 
       }
     }
@@ -141,7 +142,7 @@ 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()
+    jalview.bin.Console.outPrintln("Creating annotation on dseq:" + dseq.getStart()
             + " base is " + base + " and length=" + dseq.getLength()
             + " == " + scr.getScores().size());
     // AlignmentAnnotation annotation = new AlignmentAnnotation(
@@ -158,6 +159,30 @@ public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
     return annotation;
   }
 
+  protected void replaceAnnotationOnAlignmentWith(
+          AlignmentAnnotation newAnnot, String typeName, String calcId,
+          SequenceI aSeq)
+  {
+    SequenceI dsseq = aSeq.getDatasetSequence();
+    while (dsseq.getDatasetSequence() != null)
+    {
+      dsseq = dsseq.getDatasetSequence();
+    }
+    // look for same annotation on dataset and lift this one over
+    List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+            typeName);
+    if (dsan != null && dsan.size() > 0)
+    {
+      for (AlignmentAnnotation dssan : dsan)
+      {
+        dsseq.removeAlignmentAnnotation(dssan);
+      }
+    }
+    AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+    dsseq.addAlignmentAnnotation(dssan);
+    dssan.adjustForAlignment();
+  }
+
   private void constructAnnotationFromScore(AlignmentAnnotation annotation,
           int base, int alWidth, Score scr)
   {