From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 14 Aug 2017 13:16:17 +0000 (+0100)
Subject: JAL-2335 filterNonStandardResidues configurable for jabaws clients
X-Git-Tag: Release_2_10_2~3^2~4^2~1^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4decc3e365ce990f54773d24bb9583df48d2797a;p=jalview.git

JAL-2335 filterNonStandardResidues configurable for jabaws clients
---

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index b9abb84..3594aa4 100644
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -48,6 +48,7 @@ public class AAConClient extends JabawsCalcWorker
     alignedSeqs = true;
     nucleotidesAllowed = false;
     proteinAllowed = true;
+    filterNonStandardResidues = true;
     gapMap = new boolean[0];
     initViewportParams();
   }
diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index c691fee..3c5ce63 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -66,7 +66,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
   /**
    * by default, we filter out non-standard residues before submission
    */
-  private boolean filterNonStandardResidues = true;
+  protected boolean filterNonStandardResidues = true;
 
   /**
    * Recover any existing parameters for this service