From: Jim Procter Date: Tue, 12 Jul 2016 16:14:28 +0000 (+0100) Subject: JAL-2110 javadoc and TODO re shortcomings of implementation X-Git-Tag: Release_2_10_0~140^2~5^2~6 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=856a8f8457237311c570b4abc118aadf436077bc;hp=5dd0323d078fc1f0bab425fcbd4d8bcf1528eb14;p=jalview.git JAL-2110 javadoc and TODO re shortcomings of implementation --- 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