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Updated project files and tests #19

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@enury enury commented Feb 11, 2015

Prevented re-tokenization occuring in Collation.tokens
Added detection of pretokenized json
Merged collate_pretokenized_json with collate function

Update create_from_json method.
Update tokens property of Collation.
Added pretokenized keyword argument in function collate, and created new function get_tokenized_at.
Deleted function collate_pretokenized_json.
Added option of vertical layout also for json output.
Replaced Collation.tokens property with an attribute combined_tokens.
Replaced Collation.tokens property with combined_tokens attribute.
Added auto-detection of pretokenized json.
Added exception handling in Witness class.
Added layout for tokenized alignment table
Attempt at creating the tokenized alignment table when tokens are joined into segments.
@enury enury changed the title Updated project files Updated project files and tests Apr 14, 2015
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