Package de.unirostock.sems.bives.cellml.parser

Class CellMLReactionSubstance

java.lang.Object

de.unirostock.sems.bives.cellml.parser.CellMLEntity

de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

public class CellMLReactionSubstance
extends CellMLEntity

The Class CellMLReactionSubstance representing a substance taking part in a reaction.

Author:

Martin Scharm

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	CellMLReactionSubstance.Role	The Class Role.

Field Summary

Fields

Modifier and Type	Field	Description
static int	DIRECTION_BOTH	The Constant DIRECTION_BOTH representing a reversable reaction.
static int	DIRECTION_FORWARD	The Constant DIRECTION_FORWARD representing a forward reaction.
static int	DIRECTION_REVERSE	The Constant DIRECTION_REVERSE representing a reverse reaction.
static int	ROLE_ACTIVATOR	The Constant ROLE_ACTIVATOR representing an activator.
static int	ROLE_CATALYST	The Constant ROLE_CATALYST representing a catalyst.
static int	ROLE_INHIBITOR	The Constant ROLE_INHIBITOR representing an inhibitor.
static int	ROLE_MODIFIER	The Constant ROLE_MODIFIER representing a modifier.
static int	ROLE_PRODUCT	The Constant ROLE_PRODUCT representing a product.
static int	ROLE_RATE	The Constant ROLE_RATE representing a the rate variable.
static int	ROLE_REACTANT	The Constant ROLE_REACTANT representing a reactant.

Fields inherited from class de.unirostock.sems.bives.cellml.parser.CellMLEntity

model

Constructor Summary

Constructors

Constructor	Description
CellMLReactionSubstance(CellMLModel model, CellMLComponent component, de.unirostock.sems.xmlutils.ds.DocumentNode node)	Instantiates a new CellML reaction substance.

Method Summary

Modifier and Type	Method	Description
List<CellMLReactionSubstance.Role>	getRoles()	Gets the roles of this substance.
CellMLVariable	getVariable()	Gets the corresponding CellML variable.
static String	resolveDirection(int direction)	Resolve direction of this substance.
static int	resolveDirection(String direction)	Resolve direction.
static String	resolveRole(int role)	Resolve the role flag to get a textual representation.
static int	resolveRole(String role)	Resolve role as a string to get the corresponding flag.

Methods inherited from class de.unirostock.sems.bives.cellml.parser.CellMLEntity

associateRdfDescription, flagMetaModifcations, getDocumentNode, getMetaId, getModel, getRdfBlocks, getRdfDescriptions, setMetaId, setModel

Methods inherited from class java.lang.Object

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

Field Detail

ROLE_REACTANT

public static final int ROLE_REACTANT

The Constant ROLE_REACTANT representing a reactant.

See Also:

Constant Field Values

ROLE_PRODUCT

public static final int ROLE_PRODUCT

The Constant ROLE_PRODUCT representing a product.

See Also:

Constant Field Values

ROLE_CATALYST

public static final int ROLE_CATALYST

The Constant ROLE_CATALYST representing a catalyst.

See Also:

Constant Field Values

ROLE_INHIBITOR

public static final int ROLE_INHIBITOR

The Constant ROLE_INHIBITOR representing an inhibitor.

See Also:

Constant Field Values

ROLE_ACTIVATOR

public static final int ROLE_ACTIVATOR

The Constant ROLE_ACTIVATOR representing an activator.

See Also:

Constant Field Values

ROLE_RATE

public static final int ROLE_RATE

The Constant ROLE_RATE representing a the rate variable.

See Also:

Constant Field Values

ROLE_MODIFIER

public static final int ROLE_MODIFIER

The Constant ROLE_MODIFIER representing a modifier.

See Also:

Constant Field Values

DIRECTION_FORWARD

public static final int DIRECTION_FORWARD

The Constant DIRECTION_FORWARD representing a forward reaction.

See Also:

Constant Field Values

DIRECTION_REVERSE

public static final int DIRECTION_REVERSE

The Constant DIRECTION_REVERSE representing a reverse reaction.

See Also:

Constant Field Values

DIRECTION_BOTH

public static final int DIRECTION_BOTH

The Constant DIRECTION_BOTH representing a reversable reaction.

See Also:

Constant Field Values

Constructor Detail

CellMLReactionSubstance

public CellMLReactionSubstance(CellMLModel model,
                               CellMLComponent component,
                               de.unirostock.sems.xmlutils.ds.DocumentNode node)
                        throws de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                               BivesCellMLParseException,
                               de.unirostock.sems.bives.exception.BivesLogicalException

Instantiates a new CellML reaction substance.

Parameters:

model - the model that defines this substance

component - the component that hosts the reaction

node - the corresponding node in the XML tree

Throws:

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

BivesCellMLParseException - the bives cell ml parse exception

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

Method Detail

getVariable

public CellMLVariable getVariable()

Gets the corresponding CellML variable.

Returns:

the variable

getRoles

public List<CellMLReactionSubstance.Role> getRoles()

Gets the roles of this substance.

Returns:

the roles

resolveDirection

public static final String resolveDirection(int direction)
                                     throws BivesCellMLParseException

Resolve direction of this substance.

Parameters:

direction - the direction flag

Returns:

the direction as a string

Throws:

BivesCellMLParseException - the bives cell ml parse exception

resolveDirection

public static final int resolveDirection(String direction)
                                  throws BivesCellMLParseException

Resolve direction.

Parameters:

direction - the direction as a string

Returns:

the direction flag

Throws:

BivesCellMLParseException - the bives cell ml parse exception

resolveRole

public static final String resolveRole(int role)
                                throws BivesCellMLParseException

Resolve the role flag to get a textual representation.

Parameters:

role - the role flag

Returns:

the role as a string

Throws:

BivesCellMLParseException - the bives cell ml parse exception

resolveRole

public static final int resolveRole(String role)
                             throws BivesCellMLParseException

Resolve role as a string to get the corresponding flag.

Parameters:

role - the role as a sting

Returns:

the role flag

Throws:

BivesCellMLParseException - the bives cell ml parse exception