Constant Field Values

Contents

• jbil.sequence.*

jbil.sequence.*

jbil.sequence.DNAAlphabet

public static final java.lang.String

DNA_ALPHABET

"DNA_ALPHABET"

jbil.sequence.ExtendedDNAAlphabet

public static final java.lang.String

EXTENDED_DNA_ALPHABET

"EXTENDED_DNA_ALPHABET"

jbil.sequence.GibbsMotifSiteSampler

public static final java.lang.String	BACKGROUND_ORDER	"Background model order"
public static final java.lang.String	BURN_IN	"Burn-in size"
public static final java.lang.String	CONVERGED	"Converged"
public static final java.lang.String	INPUT_ALPHABET	"Input alphabet"
public static final java.lang.String	INPUT_SEQUENCES	"Input sequences"
public static final java.lang.String	JOINT_LOG_LKL	"Joint log-likelihoods"
public static final java.lang.String	MAX_RESTARTS	"Max number of restarts"
public static final java.lang.String	MOTIF_LENGTH	"Motif size"
public static final java.lang.String	MOTIF_MODEL	"Motif model"
public static final java.lang.String	MOTIF_ORDER	"Motif model order"
public static final java.lang.String	SAMPLE_SIZE	"Sample size"

jbil.sequence.MarkovFixedLengthSequenceModel

public static final int	PVALUE_BRANCH_AND_BOUND	1
public static final int	PVALUE_BRUTE_FORCE	0
public static final int	PVALUE_ITERATIVE_REFINEMENT	2