From 856a8f8457237311c570b4abc118aadf436077bc Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 12 Jul 2016 17:14:28 +0100 Subject: [PATCH 1/1] JAL-2110 javadoc and TODO re shortcomings of implementation --- src/jalview/datamodel/Alignment.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index f5665db..0ec3780 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1704,9 +1704,11 @@ public class Alignment implements AlignmentI * Parameters control whether gaps in exon (mapped) and intron (unmapped) * regions are preserved. Gaps that connect introns to exons are treated * conservatively, i.e. only preserved if both intron and exon gaps are - * preserved. + * preserved. TODO: check caveats below where the implementation fails * * @param al + * - must have same dataset, and sequences in al must have equivalent + * dataset sequence and start/end bounds under given mapping * @param preserveMappedGaps * if true, gaps within and between mapped codons are preserved * @param preserveUnmappedGaps -- 1.7.10.2