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Class Summary |
| AlignmentCreator |
This class is responsible for creating an output alignment by populating the input alignment
with gaps at positions given by the discretization of the particles positions. |
| AlignmentVisualizer |
This class serves as a measurement, its puspose is to display the output alignment. |
| BestMatch |
A scoring function based on the highest number of matches per column. |
| BinaryAlignmentCreator |
This class is responsible for creating an output alignment by populating the input alignment
with gaps at positions given by the discretization of the particles positions. |
| BinaryMSAProblem |
This class represents the Optimization Problem to be solved for the MSA (Binary representation). |
| BLOSUM62SoP |
This class implements the Sum Of Pairs scoring function that uses the BLOSUM62 substitutions matrices
that give scores for proteins in a biologically meaningful manner. |
| DesiredMaximizationFitness |
This class serves as a crude implementation of a stopping condition that forces the optimizer to
stop whenever a arbitrary fitness has been reached. |
| DynamicProgramming |
This class implements a technique for pairwise sequence alignment known as Dynamic Programming. |
| FASTADataSetBuilder |
Builds the input data set that gets fed as sequences to be aligned. |
| GapFogel |
Method that calculates a gap score by linearly or not scale the number of gaps over all columns. |
| GapFourFour |
Method that penalises gaps. |
| GapOpeningAndExtensionPenalty |
Method that penalises indels as gap groups. |
| MatchFogel |
A scoring function based on the overall score for the number of matched symbols
over all columns. |
| MSAProblem |
This class represents the Optimization Problem to be solved for the MSA (Real representation). |
| PAM250SoP |
This class implements the Sum Of Pairs scoring function that uses PAM250 substitutions matrices
that give scores for proteins in a biologically meaningful manner. |
| Similarity |
SIMILARITY SCORING FUNCTION
Score all possible pairwise combinations in column
Requires (N * (N-1))/2 comparisons for N sequences
Total score = sum of score for each column
SoP routine has been optimized for speed. |