Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
index 3f0e47d..53f447e 100644 (file)
--- a/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.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.
  * 
@@ -20,32 +20,31 @@
  */
 package jalview.ws.jws2;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+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;
+
 import java.util.Iterator;
 import java.util.List;
 
 import compbio.data.msa.MsaWS;
-import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.Score;
-import compbio.data.sequence.ScoreManager;
 import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.metadata.WrongParameterException;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.util.MessageManager;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
 
-public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalcWorker
+public abstract class JabawsMsaInterfaceAlignCalcWorker
+        extends AbstractJabaCalcWorker
 {
 
   @SuppressWarnings("unchecked")
@@ -59,8 +58,9 @@ public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalc
     super(alignViewport, alignPanel);
   }
 
-  public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
-          WsParamSetI preset, List<Argument> paramset)
+  public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
+          AlignFrame alignFrame, WsParamSetI preset,
+          List<Argument> paramset)
   {
     this(alignFrame.getCurrentView(), alignFrame.alignPanel);
     this.guiProgress = alignFrame;
@@ -130,7 +130,8 @@ public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalc
         rslt = msaservice.customAlign(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);
       }
     }
     return rslt;
@@ -155,9 +156,9 @@ public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalc
           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);