From f23b980dfbe309bdeb10514dad28c357b06768a4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 23 Sep 2019 11:30:06 +0100
Subject: [PATCH] =?utf8?q?JAL-3070=20configure=20annotation=20service=20mana?=
 =?utf8?q?ger=20from=20service=E2=80=99s=20input=20validation=20flags?=
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---
 .../ws/jws2/SeqAnnotationServiceCalcWorker.java    |   30 +++++--------------
 src/jalview/ws/jws2/jabaws2/Jws2Instance.java      |   31 ++++++++++++++++++++
 2 files changed, 39 insertions(+), 22 deletions(-)

diff --git a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index 6793f1e..e92a338 100644
--- 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;
-    }
   }
 
   /**
diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 29f1ed1..194b315 100644
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -305,4 +305,35 @@ public class Jws2Instance extends ServiceWithParameters
   {
     return aaui != null && aaui.isAA();
   }
+  // config flags for SeqAnnotationServiceCalcWorker
+
+  public boolean isProteinService()
+  {
+    return aaui == null ? true : aaui.isPr();
+  }
+
+  public boolean isNucleotideService()
+  {
+    return aaui == null ? false : aaui.isNa();
+  }
+
+  public boolean isNeedsAlignedSequences()
+  {
+    return aaui == null ? false : aaui.isNeedsAlignedSeqs();
+  }
+
+  public boolean isAlignmentAnalysis()
+  {
+    return aaui == null ? false : aaui.isAA();
+  }
+
+  public boolean isFilterSymbols()
+  {
+    return aaui != null ? aaui.isFilterSymbols() : true;
+  }
+
+  public int getMinimumInputSequences()
+  {
+    return aaui != null ? aaui.getMinimumSequences() : 1;
+  }
 }
-- 
1.7.10.2