Added astar module, containing AStar and AStarNode class. It graph is
virtual, in the sense that nodes are created on demand instead of
beforehand.
First steps towards an edit graph based aligner. It is just here to show
how the scoring is going to work.
Implemented simple scoring algoritm for the edit graph based aligner.
Alternative edit graph implementation and scoring algorithm.
More prototyping: astar python stuff.
Fix scoring of additions/omissions: it does not matter whether x, y is a
match or not.
Refitted the EditGraphAligner in such a way that it can function as a
replacement of the DekkerSuffixAlgorithm class. Made EditGraphAligner
the default for testing purposes.
Fix backwards travel through table. First two witnesses of the Darwin
example work now with the new aligner (without suffix optimization).
Added the creation of a new superbase based on the alignment of previous
superbase with a witness.
EditGraphAligner: align 3 witnesses.
Added ability to EditGraphAligner to align n witnesses.
Added WordPunctuationTokenizer; made it the default.
Moved DekkerSuffixAlgorithm class to its own module, since code from
this class will be integrated in the EditGraphAligner class.
Updated TODO's, Moved suffix specific classes from collatex dekker
algorithm module to collatex_suffix module.
Combining the EditGraphAligner and the DekkerSuffixAlgorithm into one
algorithm. The DekkerSuffixEditGraph aligner works now for two
witnesses.
DekkerSuffixEditGraphAligner: now works with n witnesses.
Disabled debug statements. Switched to Whitespace tokenizer for the
moment. Tokenization is duplicated in external library. That needs to be
fixed before punctuation can be treated as significant.
Removed old DekkerSuffixAlgorithm class. DekkerSuffixEditAligner class
replaces it. Removed TODO. Switched to WordPunctuation tokenizer by
default.
Updated History, updated TODOs, updated version number.
Reverted back to EditGraphAligner based on Tokens instead of
Occurrences. Extracted Scorer class to customize scoring function.