alignments. The class functions as a bean, and contains many variables

used internally by the alignment algorithms implemented in biojava.

The residue equivalencies of the alignment are described in the optimal

alignment variable, a triple array of integers, where the indices stand for:

int[][][] optAln = new int[block][chain][eqr];

* **block**: the blocks divide the alignment into different parts. The division

can be due to non-topological rearrangements (e.g. circular permutations) or

due to flexible parts (e.g. domain switch). There can be any number of blocks

in a structural alignment, defined by the structure alignment algorithm.

* **chain**: in a pairwise alignment there are only two chains, or structures.

* **eqr**: EQR stands for equivalent residue position, i.e. the alignment position.

There are as many positions (EQRs) in a block as the length of the alignment block,

and their number is equal for any of the two chains in the same block.

In each entry (combination of the three indices described above) an integer is

stored, which corresponds to the residue index in the specified chain, i.e. the

Atom index in the chain atom array. In between the same block, the stored integers

(residues) are always in increasing order.

As an overview, the AFPChain data model:

* Only supports **pairwise alignments**, i.e. two chains or structures aligned.

* Can support **flexible alignments** and **non-topological alignments**.

However, their combinatation (a flexible alignment with topological rearrangements)

can not be represented, because the blocks mean either one or the other.

* Can not support **non-sequential alignments**, or they would require a new block for

each EQR, because sequentiality of the residues is assumed inside each block.

alignments. It is a general model that supports any of the following properties,

or their combination:

* Multiple structures: the model is no longer restricted to pairwise alignments.

* Non-topological alignments: such as circular permutations or domain rearrangements.

* Flexible alignments: