mx.unam.iimas.griffin.grn.code

Class EncoderUtil

java.lang.Object

mx.unam.iimas.griffin.grn.code.EncoderUtil

public class EncoderUtil
extends java.lang.Object

Auxiliary class for encoding regulations

Version:

1.0

Author:

Stalin Muñoz Gutiérrez (stalinmunoz@yahoo.com)

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	REGEXP_REGULATION_VARIABLE Regular expression for parsing elements of regulations
static java.lang.String	REGULATED Regulated gene capture group name
static java.lang.String	REGULATOR Regulator gene capture group name
static java.lang.String	SEPARATOR Name-index separator for encoding variables
static java.lang.String	SIGN Gene regulation sign capture group name

Constructor Summary

Constructors

Constructor and Description
EncoderUtil()

Method Summary

Modifier and Type	Method and Description
static GeneRegulation	extractRegulation(Literal literal) Decodes the regulation from a given literal
static java.util.Set<GeneRegulation>	extractRegulations(PropositionalModel model) Obtains the list of true regulations from a propositional model
static java.util.Map<Gene,java.util.Set<Gene>>	findDependencies(java.util.Set<GeneInteraction> interactions) Finds the dependencies for every gene given a set of interactions
static java.lang.String	getEncodedRowVariableName(Gene regulated, int row) Obtains the variable encoding for the given gene and row
static java.lang.String	getRegulationVariableName(Gene source, Gene target, GeneRegulation.Type type) Obtains the variable encoding the positive regulation for the given genes
static boolean	isRegulationVariable(Literal literal) Verifies that the literal contains a regulation variable (It is considered a regulation variable if its name contains the reserved prefix)

Methods inherited from class java.lang.Object

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

Field Detail

SEPARATOR

public static final java.lang.String SEPARATOR

Name-index separator for encoding variables

See Also:

Constant Field Values

SIGN

public static final java.lang.String SIGN

Gene regulation sign capture group name

See Also:

Constant Field Values

REGULATOR

public static final java.lang.String REGULATOR

Regulator gene capture group name

See Also:

Constant Field Values

REGULATED

public static final java.lang.String REGULATED

Regulated gene capture group name

See Also:

Constant Field Values

REGEXP_REGULATION_VARIABLE

public static final java.lang.String REGEXP_REGULATION_VARIABLE

Regular expression for parsing elements of regulations

See Also:

Constant Field Values

Constructor Detail

EncoderUtil

public EncoderUtil()

Method Detail

getRegulationVariableName

public static java.lang.String getRegulationVariableName(Gene source,
                                                         Gene target,
                                                         GeneRegulation.Type type)

Obtains the variable encoding the positive regulation for the given genes

Parameters:

source - the regulator

target - the regulated gene

type - the type of the regulation

Returns:

the name of the encoding variable

isRegulationVariable

public static boolean isRegulationVariable(Literal literal)

Verifies that the literal contains a regulation variable (It is considered a regulation variable if its name contains the reserved prefix)

Parameters:

literal - the literal to check

Returns:

true if the prefix of the variable associated with the literal is for a regulation variable

extractRegulation

public static GeneRegulation extractRegulation(Literal literal)

Decodes the regulation from a given literal

Parameters:

literal - the literal representing the regulation

Returns:

the decoded regulation

extractRegulations

public static java.util.Set<GeneRegulation> extractRegulations(PropositionalModel model)

Obtains the list of true regulations from a propositional model

Parameters:

model - the propositional model

Returns:

the list of regulations present in the model

getEncodedRowVariableName

public static java.lang.String getEncodedRowVariableName(Gene regulated,
                                                         int row)

Obtains the variable encoding for the given gene and row

Parameters:

regulated - the regulated gene

row - the row of the truth table (lexicographic order)

Returns:

the name of the encoding variable

findDependencies

public static java.util.Map<Gene,java.util.Set<Gene>> findDependencies(java.util.Set<GeneInteraction> interactions)

Finds the dependencies for every gene given a set of interactions

Parameters:

interactions - the interactions

Returns:

dependencies for every gene