JAL-3070 configure annotation service manager from service’s input validation flags

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

diff --git a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index 6793f1e..e92a338 100644 (file)
--- a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
+++ b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
@@ -183,31 +183,17 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
 
     }
     // configure submission flags
-    if (service.getAlignAnalysisUI() != null)
+    proteinAllowed = service.isProteinService();
+    nucleotidesAllowed = service.isNucleotideService();
+    alignedSeqs = service.isNeedsAlignedSequences();
+    bySequence = !service.isAlignmentAnalysis();
+    filterNonStandardResidues = service.isFilterSymbols();
+    min_valid_seqs = service.getMinimumInputSequences();
+
+    if (service.isInteractiveUpdate())
     {
-      // instantaneous calculation. Right now that's either AACons or RNAAliFold
-      proteinAllowed = service.getAlignAnalysisUI().isPr();
-      nucleotidesAllowed = service.getAlignAnalysisUI().isNa();
-      alignedSeqs = service.getAlignAnalysisUI().isNeedsAlignedSeqs();
-      bySequence = !service.getAlignAnalysisUI().isAA();
-      filterNonStandardResidues = service.getAlignAnalysisUI()
-              .isFilterSymbols();
-      min_valid_seqs = service.getAlignAnalysisUI().getMinimumSequences();
       initViewportParams();
     }
-    else
-    {
-      // assume disorder prediction : per-sequence protein only no gaps
-      // analysis.
-      // TODO - move configuration to UIInfo base class for all these flags !
-      alignedSeqs = false;
-      bySequence = true;
-      filterNonStandardResidues = true;
-      nucleotidesAllowed = false;
-      proteinAllowed = true;
-      submitGaps = false;
-      min_valid_seqs = 1;
-    }
   }
 
   /**