Hello! I have a problem with aligning the sequences with the help of NiedlemanWunsch class. The problem is following: I found the sequences, where method "getSimilarity" got negative numbers, but the description said: "It returns score as a similarity between 0.0 and 1.0" I looked at the output of methods "getMaxScore", "getMinScore" and "getScore", which are involved in calculations of method "getSimilarity", and I have noticed, that "getMinScore" and "getMaxScore" got strange numbers (maxScore was less than minScore or both were negative), but output of "getScore" seemed adequate. I used SimpleGapPenalty and SubstitutionMatrixHelper.getNuc4_4() as a parameters of constructor of NiedlemanWunsch class. According to rules, i can't attach file with sequences to my letter. But in case it is possible, I would kindly ask you to explain me, how to do it correctly,and then i'll send you the sequences. They are too long to be send like a text in a letter.
Thanks for your attention! -- Regards, Alexander Beskrovnyy
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