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Move transition matrix computation outside of main function - #15

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mfalkiewicz wants to merge 7 commits into
sensein:masterfrom
mfalkiewicz:refactor_dm
Open

Move transition matrix computation outside of main function#15
mfalkiewicz wants to merge 7 commits into
sensein:masterfrom
mfalkiewicz:refactor_dm

Return affinity matrix, but not as part of self

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