From: Jim Procter 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 }