I am using this class just as a container for a group of sequences. This is causing me to use the class in ways that are no longer aligned to the biological meaning of the word 'haplotype'. How much confusion will this cause in the future? Is it worth the effort of renaming it now?
If I name if something like sequence_group, how does that fit in with BStringSet? How will I handle the BString / DNAString / AAString duplication? Should I address this more strictly for the haplotype class as it is currently implemented?
The haplotype class currently provides optimized ways of dealing with multiple copies of the same sequences. Once distance matrices gets attached to the data structure, even more functionality will be provided so there is a reason for the class to exist.
I am using this class just as a container for a group of sequences. This is causing me to use the class in ways that are no longer aligned to the biological meaning of the word 'haplotype'. How much confusion will this cause in the future? Is it worth the effort of renaming it now?
If I name if something like sequence_group, how does that fit in with BStringSet? How will I handle the BString / DNAString / AAString duplication? Should I address this more strictly for the haplotype class as it is currently implemented?
The haplotype class currently provides optimized ways of dealing with multiple copies of the same sequences. Once distance matrices gets attached to the data structure, even more functionality will be provided so there is a reason for the class to exist.