Q: please explain the layout of the model shown in .model

[IanCodes]

How does the explanation of how decide whether the model (in .model) is correct relates to the statement in the readme.

"The open state should have the highest emission parameters for all 4 signal components, the nucleosome state should have the second highest emission parameters for all 4 signal components and the background state should have the lowest emission parameters for all 4 signal components."

State 0
  Pi: 0.3333333333333333
  Aij: 0.962 0.031 0.007
  Opdf: Multi-variate Gaussian distribution --- Mean: [ 0 0 0 0 ]

State 1
  Pi: 0.3333333333333333
  Aij: 0.045 0.939 0.015
  Opdf: Multi-variate Gaussian distribution --- Mean: [ 0.075 0.125 0.009 0 ]

State 2
  Pi: 0.3333333333333333
  Aij: 0.005 0.007 0.988
  Opdf: Multi-variate Gaussian distribution --- Mean: [ 0.134 0.217 0.188 0.097 ]

How does 'open', 'nuclear' and 'background' states relate to the above model? Should the 'aij' values or 'mean' values be used?
Thank you.

[EvanTarbell]

State 0 is the background State, State 1 is the nucleosome state and state 2 is the open state (assuming default -k value)
Pi is the starting probability, ie the chance that the sequence starts with State i
Aij is the transition probability of moving from state i to state j
And the Opdf means are the mean values for the separated signal components. So for this model, the signal values for the open state are:
Mean: [ 0.134 0.217 0.188 0.097 ]
which satisfies the recommendation