Module: IO RNA Structure

Project goals

This project aims to implement I/O routines for

• fixed interactions with pseudoknot support
• base pair probability matrix (only read)
• alignments with consensus structure

User scenario 1:

StructureFile sf ("file.db", STRSEQ | ENERGY);
for (auto rec : sf)
{
    structured_rna<rna4, dot_bracket3> structured_sequence;
    structured_sequence = get<STRSEQ>(rec);
    cout << get<ENERGY>(rec) << endl;
}

User scenario 2:

StructureFile sf ("bpp.ps", BPP);
for (auto rec : sf)
    vector<vector<double>> matrix = get<BPP>(rec);

Design ideas

There is a config enum that allows the user to specify data fields to be obtained. A tuple of all required data is returned and can be accessed also through the enum variables.