From 4decc3e365ce990f54773d24bb9583df48d2797a Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 14 Aug 2017 14:16:17 +0100 Subject: [PATCH] JAL-2335 filterNonStandardResidues configurable for jabaws clients --- src/jalview/ws/jws2/AAConClient.java | 1 + src/jalview/ws/jws2/AbstractJabaCalcWorker.java | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) 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 -- 1.7.10.2