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 (executable)
--- 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