a number of things changed, all up for discussion:
renamed Modification table to SearchModification - i think that's clearer
added protocol_id as part of primary key for SearchModification, alternative would be to move where the mod id is initialised (to outside protocol loop) but i think this is better. (Otherwise files with multiple protocols fail, needs a test but the xifdr example file i have is too large to check in)
crosslinker specificity is stored with other modiifications in SearchModification table - can discuss
the Peptides have arrays of mod positions, accessions and masses - this is my way of dealing with the unknown modifications, probably want to talk about it (i think a lot xifdr output will fail without this change)
theres a change to how the linears are put in the map used for matching up crosslinks in main loop (you had a comment about changing it)
sorry... several changes in one pull request, anyway we can go thru them at some point and see whats good and bad
a number of things changed, all up for discussion:
sorry... several changes in one pull request, anyway we can go thru them at some point and see whats good and bad