June 13

Enduring the toil for 3 weeks, it's like a long night without end. Today I feel a shed of twilight falling onto my pupil. I can no longer stand the obscure faults prompted by the Jahmm library when I read .hmm files, so I decided to implement my own thought. Things worked out neatly and smoothly. After I had built the interface for comparing files, everything got working and I can check the validity of my thought. After all it's 3 weeks! I really have to curse myself for the sluggishness. Anyway, sometimes the results are kinda reasonable and sometimes not. I really want to blame the Jahmm package for this. Well, the truth is, I can't expect anything rigorous from this kind of try-out.

Still there are problems yet to be solved
1) The problem of "matrix is not positive defined" still persist. This is gruesome to debug, because I have to drill into the true implementation of the Jahmm package. (How dare the creator of Jahmm let this happen)
2) (All of a sudden I forgot what to write!)