"Long" bonds for uneven double stranded sequences in snake and flex modes

[ljubica-milovic]

Background

In the scope of this ticket layout logic for uneven double stranded sequences in snake and flex modes should be changed from the current one described in ticket #5712.

An uneven double stranded sequence for the purpose of this ticket is a double stranded sequence where not every monomer that participates in a H-bond has the same y coordinate as the other monomer in that H-bond (if a monomer has multiple H-bonds one one must have the same y coordinate with its partner, but the others do not).
This is an uneven double stranded sequence (current layout):

This is not:

Also this is not:

Monomers baA and U have the same y coordinate, and that is why the different y coordinates of tCo and U are acceptable.

Requirements

1. Every monomer that has only one hydrogen bond should be placed on the same y position as the other participant in the hydrogen bond (and that bond should not behave as a side chain connection in snake mode).

This is incorrect (current behavior):

Every monomer that has an H-bond has only one H-bond, but the monomer pairs are not placed on a vertical line.
This is correct:

2. If a monomer has multiple H-bonds, it should be placed bellow/above the monomer that has the fewest number of H-bonds (or to the left one if the number of H-bonds is the same).

Again, "straight" H-bonds (same y coordinates) should not behave as side-chain connections in snake mode. But the "not-straight" ones should.

This is incorrect (current behavior):

Monomer A has two H-bonds: with o8G and tfU. Both o8G and tfU have one H-bond. That means that monomer A should be aligned bellow o8G (it is to the left of tfU).
This is correct:

3. For every region between two hydrogen bonds, one chain must have backbone bonds with the length of one bond. For the other chain, all the other monomers should be aligned to the left so that the "long" bond is to the right for sense chains, and aligned to the right so that the "long" bond is to the left for antisense chains.

Region between two H-bonds is defined as a part of the backbone (that contains at least one monomer) between monomers who participate in an H-bond, or between sugars whose R1-R3 connected base participates in an H-bond.

This is incorrect (current behavior):

There are three regions between H-bonds in the example:

First and third contain the same number of monomers on both chains, but the second region contains two on the upper chain (Hhs and oxy) and one on the lower chain (Hhs).
That means after the H-bond connected bases are arranged vertically, Hhs of the lower chain should be placed to the right because it is in the antisense chain (if it was in sense, alignment would happen to the left):

Examples

Incorrect (current):

Correct:

Incorrect (current):

Correct: