general

Class Bind

java.lang.Object

general.Bind

Direct Known Subclasses:

CplexBind, GLPKBind

public abstract class Bind
extends java.lang.Object

Bind handles the problem. It is the central class of FlexFlux, it is used to create variables, constraints, interactions, and translate them to the solver.

Author:

lmarmiesse 6 mars 2013

Field Summary

Fields

Modifier and Type	Field and Description
protected parsebionet.biodata.BioNetwork	bioNet The metabolic network of the problem.
protected java.util.List<Objective>	constraintObjectives List used when several objectives are given in the condition file.
protected java.util.List<Constraint>	constraints All problem's constraints.
protected java.util.Collection<parsebionet.biodata.BioChemicalReaction>	deadReactions List of dead reactions.
protected java.util.Map<parsebionet.biodata.BioChemicalReaction,java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double>>	exchangeInteractions Map used for rFBA to link exchange reactions to external metabolites.
protected boolean	interactionInSolver Decides if the interactions will be treated in ther solver or before.
protected java.util.Map<parsebionet.biodata.BioEntity,Relation>	interactionsEntitiesCause
protected java.util.Map<parsebionet.biodata.BioEntity,java.util.Map<Relation,double[]>>	interactionsEntitiesConsequence To handle time dependent interactions. the Relation is true if the bioEntity is > 0 . double[0] corresponds to how long it takes for the interactions to become active and double[1] corresponds to how long it stays active.
protected InteractionNetwork	intNet The interaction network of the problem.
protected java.util.Map<Interaction,java.util.List<Constraint>>	intToConstraint Links an interactions to a list of constraints to check if the interaction is true.
protected java.util.Map<java.lang.String,java.lang.Double>	lastSolve Contains the results of the last FBA performed.
private boolean	loadObjective Used for pareto analysis, if set to false, the objective in the condition file is ignored.
protected Objective	obj Objective of the problem.
protected OperationFactory	operationFactory Will permit to create the right operations.
protected java.util.Map<parsebionet.biodata.BioEntity,Relation>	reactionToActiveGPR Link a reaction to it's GPR interaction.
protected RelationFactory	relationFactory To create the right relations.
protected java.util.Map<parsebionet.biodata.BioEntity,Constraint>	simpleConstraints Contains the constraints of just one entity and with coeff = 1, it make it easier to get and change them.
private boolean	solverPrepared If false the fba cannot strat.
protected java.util.Map<parsebionet.biodata.BioEntity,java.lang.Object>	solverSimpleConstraints The solver constraint objcet corresponding to an entity.
protected java.util.Map<parsebionet.biodata.BioEntity,java.util.List<Constraint>>	steadyStateConstraints Contains all the constraints caused by the steady state assumption.
protected ThreadFactory	threadFactory To create the right type of thread.

Constructor Summary

Constructors

Constructor and Description
Bind(boolean interactionInSolver)
Bind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver) Constructor used to copy the bind.

Method Summary

Methods

Modifier and Type	Method and Description
private void	addNetworkEntities() Adds entities to the problem from the metaboblic network.
private void	addRightEntityType(parsebionet.biodata.BioEntity b, boolean integer, boolean binary) Adds an entity to the problem.
abstract void	changeObjVarValue(parsebionet.biodata.BioEntity e, double d) Changes the coefficient of an entity in the objective.
protected abstract void	changeVarBounds(java.lang.String entity, double[] bounds) Changes the bounds of an entity.
java.util.Map<Constraint,Interaction>	checkInteractions() Checks all interactions.
java.util.List<Constraint>	checkInteractionsForEntities(java.util.Map<parsebionet.biodata.BioEntity,double[]> entititesMap) Returns list of true interactions when setting the given entities to the given values. double[0]=lb, double[1]=ub.
protected abstract void	clear() Clears the solver's model.
protected void	clearSolver() Clears the solver.
protected void	constraintsToSolverConstraints() Transforms all problem's constraints into solver constraints.
parsebionet.biodata.BioEntity	createFluxesSummation()
protected abstract void	deleteConstraints(java.util.List<java.lang.Object> solverConstraints) Deletes solver constraints.
void	displayConstraints() Prints the constraints
abstract void	end()
abstract void	entitiesToSolverVars() Transforms problem entities into the right solver variables.
DoubleResult	FBA(boolean saveResults, boolean chechInt) Checks the interactions if it has to, and performs the FBA.
DoubleResult	FBAWithConstraints(java.util.List<Constraint> constraintsToAdd, boolean saveResults, boolean chechInt) Takes constraints, checks interactions for those constraints, and performs FBA.
parsebionet.biodata.BioNetwork	getBioNetwork()
java.util.List<Constraint>	getConstraints()
java.util.Collection<parsebionet.biodata.BioChemicalReaction>	getDeadReactions()
java.util.Map<parsebionet.biodata.BioChemicalReaction,java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double>>	getExchangeInteractions()
InteractionNetwork	getInteractionNetwork()
java.util.Map<parsebionet.biodata.BioEntity,java.util.Map<Relation,double[]>>	getInteractionsEntities()
java.util.Map<parsebionet.biodata.BioEntity,Relation>	getInteractionsEntitiesCause()
java.util.Map<Interaction,java.util.List<Constraint>>	getIntToConstraint()
Objective	getObjective()
java.util.Map<parsebionet.biodata.BioEntity,Constraint>	getSimpleConstraints()
double	getSolvedValue(parsebionet.biodata.BioEntity ent) Return the value of the last solve for a given entity.
ThreadFactory	getThreadFactory()
protected abstract DoubleResult	go(boolean saveResults) Make the solver perform the solves.
private DoubleResult	goWithConstraints(java.util.List<Constraint> constraints, boolean saveResults) Performs the solver solve with constraints.
private void	gprInteractions(boolean ext) Adds GPR interactions to the problem.
protected abstract void	interactionsToSolverConstraints(java.util.List<Interaction> interactions) Transforms problem interactions into solver constraints.
boolean	isInteractionInSolver()
boolean	isLastSolveEmpty()
abstract boolean	isMIP()
void	loadConditionsFile(java.lang.String path) Loads the objective, creates variables and constraints from the condition file
void	loadInteractionsFile(java.lang.String path) Creates interactions from the interaction file.
void	loadSbmlNetwork(java.lang.String path, boolean ext) Loads an SBML file.
private java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double>	makeFormulaFromString(java.lang.String s) Creates an equation from a string.
Objective	makeObjectiveFromString(java.lang.String expr, boolean maximize, java.lang.String name) * creates an objective from a string.
private Relation	makeRelationFromString(java.lang.String line, int nbLine) Creates a Relation from a string.
protected abstract void	makeSolverConstraint(Constraint c, java.util.List<java.lang.Object> toRemoveFromModel, java.util.Map<java.lang.String,double[]> oldBounds) Creates a constraint for the solver.
abstract void	makeSolverObjective() Transforms the porblem's objective into a solver objective.
private void	makeSteadyStateConstraints() Adds steady-state constraints to the problem from the metabolic network.
private Unique	makeUniqueFromCondition(java.lang.String condition, int nbLine) Creates a Unique from a string.
void	prepareSolver() Transforms all problem entities, constraints an interaction into solver entities, constraints an interactions.
void	setLoadObjective(boolean load)
void	setNetwork(parsebionet.biodata.BioNetwork network, boolean ext) Sets the problem's network and adds constraints and interactions included in it.
void	setObjective(Objective obj) Sets the objective.
abstract void	setObjSense(boolean maximize) Sets the sense of the objective function.
private void	setReactionsBounds() Sets the bounds of reaction entities from the bioNetwork values.
private void	setRightEntityType(parsebionet.biodata.BioEntity entity, boolean integer, boolean binary) Changes the type of an entity to a new one.

Methods inherited from class java.lang.Object

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

Field Detail

loadObjective

private boolean loadObjective

Used for pareto analysis, if set to false, the objective in the condition file is ignored.

obj

protected Objective obj

Objective of the problem.

constraintObjectives

protected java.util.List<Objective> constraintObjectives

List used when several objectives are given in the condition file.

operationFactory

protected OperationFactory operationFactory

Will permit to create the right operations.

relationFactory

protected RelationFactory relationFactory

To create the right relations.

threadFactory

protected ThreadFactory threadFactory

To create the right type of thread.

intNet

protected InteractionNetwork intNet

The interaction network of the problem.

bioNet

protected parsebionet.biodata.BioNetwork bioNet

The metabolic network of the problem.

constraints

protected java.util.List<Constraint> constraints

All problem's constraints.

intToConstraint

protected java.util.Map<Interaction,java.util.List<Constraint>> intToConstraint

Links an interactions to a list of constraints to check if the interaction is true.

deadReactions

protected java.util.Collection<parsebionet.biodata.BioChemicalReaction> deadReactions

List of dead reactions.

lastSolve

protected java.util.Map<java.lang.String,java.lang.Double> lastSolve

Contains the results of the last FBA performed.

simpleConstraints

protected java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints

Contains the constraints of just one entity and with coeff = 1, it make it easier to get and change them.

steadyStateConstraints

protected java.util.Map<parsebionet.biodata.BioEntity,java.util.List<Constraint>> steadyStateConstraints

Contains all the constraints caused by the steady state assumption.

solverSimpleConstraints

protected java.util.Map<parsebionet.biodata.BioEntity,java.lang.Object> solverSimpleConstraints

The solver constraint objcet corresponding to an entity.

interactionInSolver

protected boolean interactionInSolver

Decides if the interactions will be treated in ther solver or before.

solverPrepared

private boolean solverPrepared

If false the fba cannot strat.

exchangeInteractions

protected java.util.Map<parsebionet.biodata.BioChemicalReaction,java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double>> exchangeInteractions

Map used for rFBA to link exchange reactions to external metabolites.

interactionsEntitiesConsequence

protected java.util.Map<parsebionet.biodata.BioEntity,java.util.Map<Relation,double[]>> interactionsEntitiesConsequence

To handle time dependent interactions. the Relation is true if the bioEntity is > 0 . double[0] corresponds to how long it takes for the interactions to become active and double[1] corresponds to how long it stays active.

interactionsEntitiesCause

protected java.util.Map<parsebionet.biodata.BioEntity,Relation> interactionsEntitiesCause

reactionToActiveGPR

protected java.util.Map<parsebionet.biodata.BioEntity,Relation> reactionToActiveGPR

Link a reaction to it's GPR interaction.

Constructor Detail

Bind

public Bind(java.util.List<Constraint> constraints,
    java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints,
    InteractionNetwork intNet,
    parsebionet.biodata.BioNetwork bioNet,
    boolean interactionInSolver)

Constructor used to copy the bind.

Parameters:

constraints - Constraints to copy.

simpleConstraints - Simple constraints to copy.

intNet - Interaction network to copy.

bioNet - BioNetwork to copy.

interactionInSolver - Determines if interactions will be treated by the solver of before.

Bind

public Bind(boolean interactionInSolver)

Method Detail

entitiesToSolverVars

public abstract void entitiesToSolverVars()

Transforms problem entities into the right solver variables.

interactionsToSolverConstraints

protected abstract void interactionsToSolverConstraints(java.util.List<Interaction> interactions)

Transforms problem interactions into solver constraints.

makeSolverConstraint

protected abstract void makeSolverConstraint(Constraint c,
                        java.util.List<java.lang.Object> toRemoveFromModel,
                        java.util.Map<java.lang.String,double[]> oldBounds)

Creates a constraint for the solver.

Parameters:

c - Constraint to create

toRemoveFromModel - is used to come back to how it was before.

oldBounds - is used to come back to how it was before.

deleteConstraints

protected abstract void deleteConstraints(java.util.List<java.lang.Object> solverConstraints)

Deletes solver constraints.

Parameters:

solverConstraints -

changeVarBounds

protected abstract void changeVarBounds(java.lang.String entity,
                   double[] bounds)

Changes the bounds of an entity.

Parameters:

entity - The entity to change

bounds - New bounds

makeSolverObjective

public abstract void makeSolverObjective()

Transforms the porblem's objective into a solver objective.

changeObjVarValue

public abstract void changeObjVarValue(parsebionet.biodata.BioEntity e,
                     double d)

Changes the coefficient of an entity in the objective.

Parameters:

e - The entity

d - The coefficient

setObjSense

public abstract void setObjSense(boolean maximize)

Sets the sense of the objective function.

Parameters:

maximize - if true : maximize, if false : minimize

clear

protected abstract void clear()

Clears the solver's model.

clearSolver

protected void clearSolver()

Clears the solver.

isMIP

public abstract boolean isMIP()

Returns:

true : the problem is a MIP, false : it is not

go

protected abstract DoubleResult go(boolean saveResults)

Make the solver perform the solves.

Parameters:

saveResults -

Returns:

An object containing the objective value and a flag that says if the problem was feasible or not.

FBA

public DoubleResult FBA(boolean saveResults,
               boolean chechInt)

Checks the interactions if it has to, and performs the FBA.

FBAWithConstraints

public DoubleResult FBAWithConstraints(java.util.List<Constraint> constraintsToAdd,
                              boolean saveResults,
                              boolean chechInt)

Takes constraints, checks interactions for those constraints, and performs FBA.

Parameters:

constraintsToAdd - List of constraints to add before the FBA.

saveResults - Determines if the results will be saved.

chechInt - Determines if all interactions will be checked.

Returns:

A doubleResult object containing the result and a flag saying if the problem was feasible

goWithConstraints

private DoubleResult goWithConstraints(java.util.List<Constraint> constraints,
                             boolean saveResults)

Performs the solver solve with constraints.

Parameters:

constraints - Constraints to add before the FBA is done.

saveResults - Determines if the results will be saved.

Returns:

A doubleResult object containing the result and a flag saying if the problem was feasible

loadSbmlNetwork

public void loadSbmlNetwork(java.lang.String path,
                   boolean ext)

Loads an SBML file.

Parameters:

path - Path to the SBML file.

ext - If true : uses extended SBML format.

setNetwork

public void setNetwork(parsebionet.biodata.BioNetwork network,
              boolean ext)

Sets the problem's network and adds constraints and interactions included in it.

Parameters:

network - Network to give the problem.

ext - If true : uses extended SBML format.

loadInteractionsFile

public void loadInteractionsFile(java.lang.String path)

Creates interactions from the interaction file.

Parameters:

path - Path to the interaction file.

addRightEntityType

private void addRightEntityType(parsebionet.biodata.BioEntity b,
                      boolean integer,
                      boolean binary)

Adds an entity to the problem.

Parameters:

b - Entity to add.

integer - If it is an integer entity.

binary - If it is a binary entity.

loadConditionsFile

public void loadConditionsFile(java.lang.String path)

Loads the objective, creates variables and constraints from the condition file

Parameters:

path - Path to the condition file.

setRightEntityType

private void setRightEntityType(parsebionet.biodata.BioEntity entity,
                      boolean integer,
                      boolean binary)

Changes the type of an entity to a new one.

Parameters:

entity - Entity to change.

integer - If it is an integer entity.

binary - If it is a binary entity.

createFluxesSummation

public parsebionet.biodata.BioEntity createFluxesSummation()

Returns:

The entity corresponding to the sum of the absolute value of all the reaction fluxes.

makeObjectiveFromString

public Objective makeObjectiveFromString(java.lang.String expr,
                                boolean maximize,
                                java.lang.String name)

* creates an objective from a string.

Parameters:

expr - string used to create the objective.

maximize - Boolean that determines if the objectives maximizes of minimizes the function.

name - The name of the objective.

Returns:

The created objective.

makeFormulaFromString

private java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> makeFormulaFromString(java.lang.String s)

Creates an equation from a string.

Parameters:

s - String to create the equation from.

Returns:

A map of entities and their coefficients.

prepareSolver

public void prepareSolver()

Transforms all problem entities, constraints an interaction into solver entities, constraints an interactions. Without this step, the solver cannot solve the problem.

addNetworkEntities

private void addNetworkEntities()

Adds entities to the problem from the metaboblic network.

makeSteadyStateConstraints

private void makeSteadyStateConstraints()

Adds steady-state constraints to the problem from the metabolic network.

setReactionsBounds

private void setReactionsBounds()

Sets the bounds of reaction entities from the bioNetwork values.

gprInteractions

private void gprInteractions(boolean ext)

Adds GPR interactions to the problem.

Parameters:

ext - true : uses extended SBML format.

constraintsToSolverConstraints

protected void constraintsToSolverConstraints()

Transforms all problem's constraints into solver constraints.

getBioNetwork

public parsebionet.biodata.BioNetwork getBioNetwork()

getInteractionNetwork

public InteractionNetwork getInteractionNetwork()

getConstraints

public java.util.List<Constraint> getConstraints()

displayConstraints

public void displayConstraints()

Prints the constraints

makeRelationFromString

private Relation makeRelationFromString(java.lang.String line,
                              int nbLine)

Creates a Relation from a string. This is used when parsing the interaction file.

Parameters:

line - String to create the Relation from.

nbLine - Line number of the interaction file.

Returns:

The created Relation.

makeUniqueFromCondition

private Unique makeUniqueFromCondition(java.lang.String condition,
                             int nbLine)

Creates a Unique from a string. Used when parsing the interaction file.

Parameters:

condition - The string to create the Unique from.

nbLine - Line number of the interaction file.

Returns:

The created Unique.

setObjective

public void setObjective(Objective obj)

Sets the objective.

Parameters:

obj - Objective to set.

end

public abstract void end()

getObjective

public Objective getObjective()

checkInteractions

public java.util.Map<Constraint,Interaction> checkInteractions()

Checks all interactions.

Returns:

Returns a list of true constraints with the interaction they belong to.

checkInteractionsForEntities

public java.util.List<Constraint> checkInteractionsForEntities(java.util.Map<parsebionet.biodata.BioEntity,double[]> entititesMap)

Returns list of true interactions when setting the given entities to the given values. double[0]=lb, double[1]=ub.

Parameters:

entititesMap - Entities and the values they will be set to.

Returns:

List of true interactions.

isInteractionInSolver

public boolean isInteractionInSolver()

getIntToConstraint

public java.util.Map<Interaction,java.util.List<Constraint>> getIntToConstraint()

getThreadFactory

public ThreadFactory getThreadFactory()

getExchangeInteractions

public java.util.Map<parsebionet.biodata.BioChemicalReaction,java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double>> getExchangeInteractions()

getSimpleConstraints

public java.util.Map<parsebionet.biodata.BioEntity,Constraint> getSimpleConstraints()

isLastSolveEmpty

public boolean isLastSolveEmpty()

getSolvedValue

public double getSolvedValue(parsebionet.biodata.BioEntity ent)

Return the value of the last solve for a given entity.

Parameters:

ent - The entity to get the value.

Returns:

Returns the calculated value for an entity for the last solve.

getInteractionsEntities

public java.util.Map<parsebionet.biodata.BioEntity,java.util.Map<Relation,double[]>> getInteractionsEntities()

getInteractionsEntitiesCause

public java.util.Map<parsebionet.biodata.BioEntity,Relation> getInteractionsEntitiesCause()

setLoadObjective

public void setLoadObjective(boolean load)

getDeadReactions

public java.util.Collection<parsebionet.biodata.BioChemicalReaction> getDeadReactions()