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r824
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Reconstructer.java 824 (10 years ago) by duarte: Fixed bug: was reusing the same bounds after every metrization in reconstruct(), now restarting from the initial bounds for each metrization. In metrize() final sampled matrix is now always reinitialising seed.
Embedder.java 821 (10 years ago) by duarte: New classes Reconstructer and ModelPdb. Reconstructer is a one-stop solution for reconstructing from contact maps (RIGraph) using BoundsSmoother and Embedder. At the moment doesn't support reconstruction of contact maps with non-observed residues.
BoundsSmoother.java 824 (10 years ago) by duarte: Fixed bug: was reusing the same bounds after every metrization in reconstruct(), now restarting from the initial bounds for each metrization. In metrize() final sampled matrix is now always reinitialising seed.
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
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