From 34cd990de2acbfc60802d2ab0c869481749a2406 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 15 Oct 2020 11:02:37 +0100 Subject: [PATCH] JAL-3763 unused method removed --- src/jalview/datamodel/AlignedCodonFrame.java | 34 -------------------------- 1 file changed, 34 deletions(-) diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index 5240f0c..0f6a5f3 100644 --- a/src/jalview/datamodel/AlignedCodonFrame.java +++ b/src/jalview/datamodel/AlignedCodonFrame.java @@ -402,40 +402,6 @@ public class AlignedCodonFrame } /** - * Returns the DNA codon positions (base 1) for the given position (base 1) in - * a mapped protein sequence, or null if no mapping is found. - * - * Intended for use in aligning cDNA to match aligned protein. Only the first - * mapping found is returned, so not suitable for use if multiple protein - * sequences are mapped to the same cDNA (but aligning cDNA as protein is - * ill-defined for this case anyway). - * - * @param seq - * the DNA dataset sequence - * @param aaPos - * residue position (base 1) in a protein sequence - * @return - */ - public int[] getDnaPosition(SequenceI seq, int aaPos) - { - /* - * Adapted from markMappedRegion(). - */ - MapList ml = null; - int i = 0; - for (SequenceToSequenceMapping ssm : mappings) - { - if (ssm.fromSeq == seq) - { - ml = getdnaToProt()[i]; - break; - } - i++; - } - return ml == null ? null : ml.locateInFrom(aaPos, aaPos); - } - - /** * Convenience method to return the first aligned sequence in the given * alignment whose dataset has a mapping with the given (aligned or dataset) * sequence. -- 1.7.10.2