X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAbstractJabaCalcWorker.java;h=26fe0a20ce215c830d6559ce064abc5036202fba;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=f2795d2b8d1e550f4e79c205146a86656ae9070b;hpb=7c70cb09e9de68ab567e38520d6d09f0c17a3939;p=jalview.git

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index f2795d2..26fe0a2 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -78,8 +78,10 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
               getCalcId(),
               new AAConSettings(true, service, this.preset,
-                      (arguments != null) ? JabaParamStore
-                              .getJwsArgsfromJaba(arguments) : null), true);
+                      (arguments != null)
+                              ? JabaParamStore.getJwsArgsfromJaba(arguments)
+                              : null),
+              true);
     }
   }
 
@@ -164,8 +166,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     super(alignViewport, alignPanel);
   }
 
-  public AbstractJabaCalcWorker(Jws2Instance service,
-          AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+  public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+          WsParamSetI preset, List<Argument> paramset)
   {
     this(alignFrame.getCurrentView(), alignFrame.alignPanel);
     this.guiProgress = alignFrame;
@@ -322,9 +324,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
         }
         if (collectAnnotationResultsFor(rslt))
         {
-          jalview.bin.Cache.log
-                  .debug("Updating result annotation from Job " + rslt
-                          + " at " + service.getUri());
+          jalview.bin.Cache.log.debug("Updating result annotation from Job "
+                  + rslt + " at " + service.getUri());
           updateResultAnnotation(true);
           ap.adjustAnnotationHeight();
         }
@@ -334,8 +335,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     catch (JobSubmissionException x)
     {
 
-      System.err.println("submission error with " + getServiceActionText()
-              + " :");
+      System.err.println(
+              "submission error with " + getServiceActionText() + " :");
       x.printStackTrace();
       calcMan.disableWorker(this);
     } catch (ResultNotAvailableException x)
@@ -444,8 +445,9 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
           AnnotatedCollectionI inputSeqs)
   {
     if (alignment == null || alignment.getWidth() <= 0
-            || alignment.getSequences() == null || alignment.isNucleotide() ? !nucleotidesAllowed
-            : !proteinAllowed)
+            || alignment.getSequences() == null || alignment.isNucleotide()
+                    ? !nucleotidesAllowed
+                    : !proteinAllowed)
     {
       return null;
     }
@@ -470,9 +472,10 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
 
     for (SequenceI sq : (inputSeqs.getSequences()))
     {
-      if (bySequence ? sq.findPosition(end + 1)
-              - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
-              - sq.getStart() > minlen - 1)
+      if (bySequence
+              ? sq.findPosition(end + 1)
+                      - sq.findPosition(start + 1) > minlen - 1
+              : sq.getEnd() - sq.getStart() > minlen - 1)
       {
         String newname = SeqsetUtils.unique_name(seqs.size() + 1);
         // make new input sequence with or without gaps
@@ -537,8 +540,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
         FastaSequence sq = seqs.get(p);
         int l = sq.getSequence().length();
         // strip gapped columns
-        char[] padded = new char[realw], orig = sq.getSequence()
-                .toCharArray();
+        char[] padded = new char[realw],
+                orig = sq.getSequence().toCharArray();
         for (int i = 0, pp = 0; i < realw; pp++)
         {
           if (gapMap[pp])