From 48f5f04700dcb49463b20303c2075292f9d4d1d3 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 23 Sep 2020 17:34:32 +0100 Subject: [PATCH] =?utf8?q?JAL-3748=20not=20testing=20for=20sequence=E2=80=99?= =?utf8?q?s=20containment=20in=20mapped=20range=20breaks=20CDS=20reconstruct?= =?utf8?q?ion=20but=20allows=20=20testAlignProteinAsDna=5FincompleteStartCod?= =?utf8?q?on=20to=20pass?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/datamodel/AlignedCodonFrame.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index 84a74b6..25f1c27 100644 --- a/src/jalview/datamodel/AlignedCodonFrame.java +++ b/src/jalview/datamodel/AlignedCodonFrame.java @@ -504,7 +504,9 @@ public class AlignedCodonFrame { int mStart=ssm.getMapping().getMap().getFromLowest(),mEnd=ssm.getMapping().map.getFromHighest(); if ((ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence()) - && seq.getStart()>=mStart && seq.getEnd()<=mEnd) + // here AlignmentUtilsTest. testAlignProteinAsDna_incompleteStartCodon fails because mStart/mEnd is contained by seq + // without this filter, we don't get the correct mapping, however + )// && seq.getStart()>=mStart && seq.getEnd()<=mEnd) { for (SequenceI sourceAligned : al.getSequences()) { -- 1.7.10.2