This update migrates the existing plex source code from the mercurial repository (as of Dec 13, 2009) to this repository. The only changes are 1) a folder structure reorganization to make the project more amenable to eclipse and 2) the addition of missing package declarations to a few java source files.
Cleaned unused imports. Removed final modifier in front of class and method definitions (if we subsequently find a good reason for a method or class to be final then we will add the modifer back; otherwise final just breaks extensibility). Removed unused fields in BCPlot and reformatted the code to change indentation to tabs. Finally, removed the notice at the beginning of every class (we can make an ant task to put it back when the code is published).
Minor. Changed eclipse project settings.
Added new base code. Did not overwrite previous plex files.
Small change - added comments to tests.
Updated .classpath file.
Updated many of the data structures. Added basic classes.
Added some initial algorithms.
Added initial version of persistent homology algorithm.
Added implementation of simplicial complex expansion as in the paper by Zomorodian. Added comments. Updated javadoc.
Added initial version of hom complex class. Lots of other changes.
Added deprecated keyword to a few classes.
Updated hom complex computation. Refactored.
Lots of changes. Started duality-based computation. Added cellular homology.
Refactored.
Added comments and updated witness complex
Updated pHcol algorithm
Added augmented barcode collection for storing generators.
Implemented tensor product of chain complexes. Added draft of graph embeddings.
Added hom complex computation.