[Biojava-dev] ScoringMatrix interface/implementations

[Rahul Karnik]

As a first step in the building of a framework for sequence alignment, I
have attached:

- a ScoringMatrix interface
- two simple implementations
- a matrix reader
- a junit test case and a test file

Please let me know if and how I should integrate this ScoringMatrix
design with the existing WeightMatrix used with the HMM code. Of course,
any other comments and suggestions are welcome too.

Thanks,
Rahul
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#  Matrix made by matblas from blosum50.iij
#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 50
#  Entropy =   0.4808, Expected =  -0.3573
   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X
A  5 -2 -1 -2 -1 -1 -1  0 -2 -1 -2 -1 -1 -3 -1  1  0 -3 -2  0 -2 -1 -1
R -2  7 -1 -2 -4  1  0 -3  0 -4 -3  3 -2 -3 -3 -1 -1 -3 -1 -3 -1  0 -1
N -1 -1  7  2 -2  0  0  0  1 -3 -4  0 -2 -4 -2  1  0 -4 -2 -3  4  0 -1
D -2 -2  2  8 -4  0  2 -1 -1 -4 -4 -1 -4 -5 -1  0 -1 -5 -3 -4  5  1 -1
C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2
Q -1  1  0  0 -3  7  2 -2  1 -3 -2  2  0 -4 -1  0 -1 -1 -1 -3  0  4 -1
E -1  0  0  2 -3  2  6 -3  0 -4 -3  1 -2 -3 -1 -1 -1 -3 -2 -3  1  5 -1
G  0 -3  0 -1 -3 -2 -3  8 -2 -4 -4 -2 -3 -4 -2  0 -2 -3 -3 -4 -1 -2 -2
H -2  0  1 -1 -3  1  0 -2 10 -4 -3  0 -1 -1 -2 -1 -2 -3  2 -4  0  0 -1
I -1 -4 -3 -4 -2 -3 -4 -4 -4  5  2 -3  2  0 -3 -3 -1 -3 -1  4 -4 -3 -1
L -2 -3 -4 -4 -2 -2 -3 -4 -3  2  5 -3  3  1 -4 -3 -1 -2 -1  1 -4 -3 -1
K -1  3  0 -1 -3  2  1 -2  0 -3 -3  6 -2 -4 -1  0 -1 -3 -2 -3  0  1 -1
M -1 -2 -2 -4 -2  0 -2 -3 -1  2  3 -2  7  0 -3 -2 -1 -1  0  1 -3 -1 -1
F -3 -3 -4 -5 -2 -4 -3 -4 -1  0  1 -4  0  8 -4 -3 -2  1  4 -1 -4 -4 -2
P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2
S  1 -1  1  0 -1  0 -1  0 -1 -3 -3  0 -2 -3 -1  5  2 -4 -2 -2  0  0 -1
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  2  5 -3 -2  0  0 -1  0
W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1  1 -4 -4 -3 15  2 -3 -5 -2 -3
Y -2 -1 -2 -3 -3 -1 -2 -3  2 -1 -1 -2  0  4 -3 -2 -2  2  8 -1 -3 -2 -1
V  0 -3 -3 -4 -1 -3 -3 -4 -4  4  1 -3  1 -1 -3 -2  0 -3 -1  5 -4 -3 -1
B -2 -1  4  5 -3  0  1 -1  0 -4 -4  0 -3 -4 -2  0  0 -5 -3 -4  5  2 -1
Z -1  0  0  1 -3  4  5 -2  0 -3 -3  1 -1 -4 -1  0 -1 -2 -2 -3  2  5 -1
X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1  0 -3 -1 -1 -1 -1 -1