X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAbstractJabaCalcWorker.java;fp=src%2Fjalview%2Fws%2Fjws2%2FAbstractJabaCalcWorker.java;h=9a1e2d30e5258c35891255c4bf0eebdf0a2e90b8;hp=a7cc5b630ec120aab32c6277824de962a2b61109;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hpb=eee8dfa05eeea5b7cc295ba020647842502efe63

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index a7cc5b6..9a1e2d3 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -4,12 +4,15 @@ import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
 import jalview.gui.IProgressIndicator;
+import jalview.util.Comparison;
 import jalview.workers.AlignCalcWorker;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.dm.JabaWsParamSet;
@@ -49,7 +52,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
   {
     if (getCalcId() != null)
     {
-      ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+      ((AlignViewport) alignViewport).setCalcIdSettingsFor(
               getCalcId(),
               new AAConSettings(true, service, this.preset,
                       (arguments != null) ? JabaParamStore
@@ -296,7 +299,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
         }
         if (collectAnnotationResultsFor(rslt))
         {
-          jalview.bin.Cache.log
+          Cache.log
                   .debug("Updating result annotation from Job " + rslt
                           + " at " + service.getUri());
           updateResultAnnotation(true);
@@ -440,7 +443,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     start = inputSeqs.getStartRes();
     end = inputSeqs.getEndRes();
 
-    for (SequenceI sq : ((List<SequenceI>) inputSeqs.getSequences()))
+    for (SequenceI sq : (inputSeqs.getSequences()))
     {
       if (bySequence ? sq.findPosition(end + 1)
               - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
@@ -475,7 +478,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
         else
         {
           seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
-                  AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                  AlignSeq.extractGaps(Comparison.GapChars,
                           sq.getSequenceAsString(start, end + 1))));
         }
         if (seq.getSequence().length() > ln)