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|MAl stands for Multiple Alignment, it is a container class for sequences in such an alignment. |
MAl stands for Multiple Alignment, it is a container class for sequences in such an alignment.
The idea is that this class should have "two" interfaces, one alignment/matrix interface with global indexes, columns etc and one sequence collection interface similar to the old cosmid interface.
First version is a front end to the Berkeley DB. This could be made more flexible in future versions, allowing any storage of data using pImpl idiom.
Problem: BDB has 1-based indexing (recno), while every algo written in the TRAP system uses 0-based indexing. I'll stick to 0-based indexing in this system, to avoid future hassle.
Future plans: make this system plugable along the same lines as the data classes in trapper, as the first implementation of the MAl class will be based on these classes. Also remove the coupling between this class and TrapperDoc...