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r899
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Bound.java 802 (10 years ago) by duarte: Some big changes: now internally we use the data structure Bound[][] for all steps. We only use graphs for when we need to calculate shortest paths. Define some static functions for printing info. Made the scaling method an option passed as an argument to embed() Extracted to separate file the Bound class. Drafted an implementation of metrize
BoundsSmoother.java 855 (10 years ago) by gmueller: new class for some evolution
CorrelationFunction.java 860 (10 years ago) by gmueller: class to estimate the correlation function to a given error function, deals onlz with Population arrays
Distiller.java 853 (10 years ago) by gmueller: distance map and contact map error function
Embedder.java 884 (10 years ago) by duarte: Major commit: - change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors - added many tests and test files for Pdb (and merged some already existing tests from the default package) - removed obsolete classes related to msd - bug fix: PdbfilePdb now properly reads files with alt codes - all tests passed
Individuals.java 861 (10 years ago) by duarte: Fixed +1 issues
Population.java 858 (10 years ago) by gmueller: new class to deal with arrays of Individuals class, provides methods to generate new arrays of Individuals
Reconstructer.java 884 (10 years ago) by duarte: Major commit: - change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors - added many tests and test files for Pdb (and merged some already existing tests from the default package) - removed obsolete classes related to msd - bug fix: PdbfilePdb now properly reads files with alt codes - all tests passed
Scorer.java 855 (10 years ago) by gmueller: new class for some evolution
SetScore.java 835 (10 years ago) by duarte: Changed scoring: from sum(upi-ui)2 to sum of max(0,upi-ui). New methods to write subsets to files in table (tab delimited) format. Now main() writes out all scores/subsets to two files instead of only outputting best, worse and ensemble of bests. Moved ScoreSet to its own file, new static methods to read subsets from db.
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