I'm returning to a project i started having a look at a few months ago and i still can't figure out how to do the following since i'm new to Java and Biojava. It seems to me that this should be easy to do since it is essentially why alignments are generated in the first instance - to infer homology of residues (symbols) at the same position (column) in the alignment.
I want to be able to iterate over all positions in an alignment and then do something with the symbols at a given position, in my case calculate the proportion of each symbol at that position. I understand that i could loop over the length of the alignment, use an index to represent the position of the column in the alignment and generate a subalignment of length 1 for all labels. However, is this efficient and how would i access the symbols so i can calculate the proportions for each symbol at the position. I would really appreciate some hand holding on this, as i'm strugling to climb the steep learning curve of OOP, Java and Biojava :o( Thanks Nathan _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
