From da3b58afa56be8d7177ff824a3490509dbcf984d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 16 Sep 2020 17:37:15 +0100 Subject: [PATCH] JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that matches a CDS sequence --- src/jalview/datamodel/AlignedCodonFrame.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index 9fa11cc..fbc8a61 100644 --- a/src/jalview/datamodel/AlignedCodonFrame.java +++ b/src/jalview/datamodel/AlignedCodonFrame.java @@ -464,8 +464,7 @@ public class AlignedCodonFrame { for (SequenceI sourceAligned : al.getSequences()) { - if (ssm.mapping.to == sourceAligned.getDatasetSequence() - || ssm.mapping.to == sourceAligned) + if (ssm.covers(sourceAligned,true)) { return sourceAligned; } @@ -483,7 +482,7 @@ public class AlignedCodonFrame { for (SequenceI sourceAligned : al.getSequences()) { - if (ssm.fromSeq == sourceAligned.getDatasetSequence()) + if (ssm.covers(sourceAligned,true)) { return sourceAligned; } -- 1.7.10.2