jbil.sequence
Class GibbsMotifSiteSampler

java.lang.Object
  jbil.common.AbstractAlgorithm
      jbil.sequence.GibbsMotifSiteSampler

All Implemented Interfaces:

Algorithm

public class GibbsMotifSiteSampler
extends AbstractAlgorithm

Implementation of the simple Gibbs motif site sampler using motif trie-based K-order Markov models. The inputs for this algorithm are:

INPUT NAME	INPUT TYPE	DESCRIPTION
INPUT_ALPHABET	Alphabet	Alphabet of the input sequences and motifs
INPUT_SEQUENCES	List<Sequence>	Input sequences
MOTIF_LENGTH	Integer	Motif length
MOTIF_ORDER	Integer	Motif model order
BACKGROUND_ORDER	Integer	Background model order
BURN_IN	Integer	Number of burn-in iterations
SAMPLE_SIZE	Integer	Number of sampling iterations
MAX_RESTARTS	Integer	Max number of restarts

The ouputs are:

OUTPUT NAME	OUTPUT TYPE	DESCRIPTION
MOTIF_MODEL	SequenceModel	The learned motif described by the sampled sites.
JOINT_LOG_LKL	double[]	The joint log likelihood of the sampled sites during all iterations.

Author:

Paulo G. S. da Fonseca

Field Summary

static java.lang.String	BACKGROUND_ORDER
static java.lang.String	BURN_IN
static java.lang.String	CONVERGED
static java.lang.String	INPUT_ALPHABET
static java.lang.String	INPUT_SEQUENCES
static java.lang.String	JOINT_LOG_LKL
static java.lang.String	MAX_RESTARTS
static java.lang.String	MOTIF_LENGTH
static java.lang.String	MOTIF_MODEL
static java.lang.String	MOTIF_ORDER
static java.lang.String	SAMPLE_SIZE

Constructor Summary

GibbsMotifSiteSampler()

Method Summary

void	run() Executes the algorithm once.

Methods inherited from class jbil.common.AbstractAlgorithm

getInput, getOutput, setInput, setInputs

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT_ALPHABET

public static final java.lang.String INPUT_ALPHABET

See Also:

Constant Field Values

INPUT_SEQUENCES

public static final java.lang.String INPUT_SEQUENCES

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Constant Field Values

MOTIF_LENGTH

public static final java.lang.String MOTIF_LENGTH

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Constant Field Values

MOTIF_ORDER

public static final java.lang.String MOTIF_ORDER

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Constant Field Values

BACKGROUND_ORDER

public static final java.lang.String BACKGROUND_ORDER

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Constant Field Values

BURN_IN

public static final java.lang.String BURN_IN

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Constant Field Values

SAMPLE_SIZE

public static final java.lang.String SAMPLE_SIZE

See Also:

Constant Field Values

MAX_RESTARTS

public static final java.lang.String MAX_RESTARTS

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Constant Field Values

MOTIF_MODEL

public static final java.lang.String MOTIF_MODEL

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Constant Field Values

CONVERGED

public static final java.lang.String CONVERGED

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Constant Field Values

JOINT_LOG_LKL

public static final java.lang.String JOINT_LOG_LKL

See Also:

Constant Field Values

Constructor Detail

GibbsMotifSiteSampler

public GibbsMotifSiteSampler()

Method Detail

run

public void run()
         throws BadInputException

Description copied from interface: Algorithm

Executes the algorithm once.

Specified by:

run in interface Algorithm

Specified by:

run in class AbstractAlgorithm

Throws:

BadInputException