The distanceMatrix is renamed to distanceTables to match with the
AFPChain nomenclature. The description of replaceOptAln has also been
changed to be more general.

The pose contains the translation and the rotationMatrix as information
of the 3D transformation of the proteins. A Demo for the display of the
multiple alignment has been created.

In order to generalize the 3D GUI features of the Structure Alignment
and implement a Multiple Alignment GUI for the new MultipleAlignment
object.

The multiple alignments can be visualized through the
MultipleAlignmentJmol class, adapted from the StructureAlignmentJmol.
The coloring of the different blocks and the alignment menus are still
not implemented.

Gaps are described by null values in the Blocks of the
MultipleAlignment. Now the Jmol class accounts for these gaps and does
not color them.

from the Pose class, because it is a static variable that does not
depend on the specific BlockSet. It only stores the intra-residue
distances of every protein.

The wrong line was commented out, so the molecule was not colored.

Adapted the display method in StructureAlignmentDisplay to rotate and
display in Jmol the atoms of a MultipleAlignment.

Minor changes to respond to TODOs

Interfaces for the classes Block, Pose and BlockSet have been created to
generalize and document all the methods needed for a MultipleAlignment
object.

The interfaces have been implemented again and the Jmol display also
works for the new MultipleAlignment DS composition.

Add some methods to calculate internal variables (update), and moved the
cache variables (RMSD, TM-score, similarity, coverage) from the
MultipleAlignment to these two classes.

Another layer in the OO data structure has been added to allow returning
alternative alignments. An ensemble of MSTA is a collection of
MultipleAlignment objects. Another change has been the addition of two
different implementations of Pose, one to determine global
superimpositions and another to determine flexible part
superimpositions.

When an object is created with the constructor and its parent is set,
the parent also gets a link to the object automatically.

The Ensemble can calculate the distance Matrices for every structure in
the updateDistanceMatrix() method. Automatic cross-references added to
the setParent() methods, for consistency.

All pairwise structural comparisons are evaluated to build the
background distance Matrices. Atoms can be rotated from Pose as well.

A new Pose abstract implementation has been created that calculates the
TMscore and RMSD of the alignment. The name of AlignmentJmol has been
changed to AbstractAlignmentJmol to be clear that is an abstract class.

A constructor for a new MultipleAlignment can be used from an AFPChain.
It creats an equivalent alignment object, for backwards compatibility.

The clone methods now entirely change the links between the cloned and
the original objects so that no cross-links occur.

An initial implementation of the CEMC algorithm for multiple structure
alignment has been created. Now a seed MultipleAlignment can be created
with a parallel pairwise all-to-all alignment. The MC optimization is
still not implemented. A demo is available under the structure-gui
package.

In the transition to replace AFPChain with the MultipleAlignment class.
A core structure for the CEMC algorithm has also been created.

Packing by columns is needed instead of by rows.

The transformation calculated in AFPChain was not copied. Now the
information is converted into a Matrix4D and copied.

Bug fixes, Class renames and Code organization

The sequence alignment method has been improved to introduce a gap
between blocks. Many more output conversions need to be implemented
(Web, Aligned Pairs, etc.)

The alignment panel is fully functional, and the sequence alignment to
Jmol connection is now possible for MultipleAlignments.

It was only used for problems loading the Atom arrays and to check
consistency in some parts of the calculations, but the usage was not
clearly defined. 
The exceptions have been replaced by NullPointerException and
IllegalStateException, respectively, and since they are Java runtime
exceptions they do not need to be thrown. 
Because there was no need to catch these exceptions, so they needed to
be thrown always, the change does not affect the behavior of the code,
but simplifies it.

FatCat result, Alignment Residues (as Pairs) and FASTA format.

Two tests to check the correctness of the MultipleAlignment DS have been
implemented. Some bugs have been detected and fixed in the code while
writting the tests.

Implementations for MultipleAlignment DS