|
Class Summary |
| Classifier |
This is the abstract class to be subclassed by arbitrary data classifiers. |
| DarwinsCrucible |
This is a framework for running simulations of successive mutation and natural selection. |
| DynamicDuo |
This is the framework for doing pairwise alignments. |
| EuclideanMeanClassifier |
This classifier just figures out the mean of all the features in the training
data, and then classifies data by calculating the Euclidean distance between
the data to be classified and the means for the categories. |
| IdentityComparator |
This trivial comparison function returns "1" if the elements are
completely identical, and "0" if they are not. |
| MonomerComparator |
This is the base implementation for comparing two monomers. |
| Needleman |
This implements the Needleman/Wunsch algorithm, with gap penalties,
including end gap penalties. |
| PSSMFitnessFunction |
This class implements a fitness function based on a PSSM. |
| SequenceAligner |
This interface describes any algorithm for doing pair-wise alignment
of sequences. |
| SequenceFetcher |
Give this class the name of a sequence, and it will fetch it via the web. |
| SimilarityMatrixComparator |
This is a simple implementation of a similarity matrix for
comparing monomers. |