- Direct Known Subclasses:
- RnaFileIO.NucIndexConverter.DoubleStrand, RnaFileIO.NucIndexConverter.MultiStrand
- Enclosing class:
- RnaFileIO
abstract static class RnaFileIO.NucIndexConverter
extends java.lang.Object
The backend uses "III" (or some other character in extended nucleobase alphabets) to
indicate an inter-molecular linker. I.e. a single sequence actually encodes two (or potentially more)
RNA molecules. In this Java interface, each molecule is stored in a separate "Strand" in an RnaScene.
This class builds an index that helps convert between the two representations by storing the position
at which an "I" is encountered (which ends the first strand) as well as the position when the next valid
base is encountered (which starts the second strand).
Usually, there are three consecutive "I" characters, but this function assumes that that number is subject
to change, which is why both the start and end positions of each linker are stored.