From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 14 Aug 2017 13:17:35 +0000 (+0100)
Subject: JAL-2335 choose appropriate alphabet for filtering nonstandard symbols
X-Git-Tag: Release_2_10_2~3^2~4^2~1^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e2c4a2f38549ca11856aa94c6f75c2babfa78013;p=jalview.git

JAL-2335 choose appropriate alphabet for filtering nonstandard symbols
---

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index 3c5ce63..f2795d2 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -497,8 +497,10 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
           }
           for (int apos : sq.gapMap())
           {
+            char sqc = sq.getCharAt(apos);
             if (!filterNonStandardResidues
-                    || ResidueProperties.aaIndex[sq.getCharAt(apos)] < 20)
+                    || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
+                            : ResidueProperties.nucleotideIndex[sqc] < 5))
             {
               gapMap[apos] = true; // aligned and real amino acid residue
             }