java -cp ./:./jstacs-1.2.2.jar:./numericalMethods.jar MotifAdjuster <file> <ignoreChar> <length> <fgOrder> <fgEss> <bothStrands> <output> <sigma> <p(no motif)>
| name | comment | type |
| file | the location of the data set | String |
| ignoreChar | char for comment lines (e.g. for a FastA-file '>') | char |
| length | the motif length | int |
| fgOrder | the order of the inhomogeneous Markov model that is uses for the motif; 0 yields in a PWM | byte |
| ess | the equivalent sample size that is used for the mixture model | double >= 0 |
| bothStrands | use both strands | boolean |
| output | output of the EM | boolean |
| sigma | the sigma of the truncated discrete Gaussian distribution | double>0 |
| p(no motif) | the probability for finding no motif | 0<=double<1 |