org.ginsim.service.export.cadp

Class CADPWriter

java.lang.Object

org.ginsim.service.export.cadp.CADPWriter

Direct Known Subclasses:

CADPCommonWriter, CADPExpWriter, CADPIntegrationWriter, CADPMclWriter, CADPModuleWriter, CADPReadMeWriter, CADPSvlWriter

public abstract class CADPWriter
extends Object

Class providing methods supporting all writers of CADP specifications

Author:

Nuno D. Mendes

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CADPWriter.GateWriter
class	CADPWriter.InitialStateWriter
static class	CADPWriter.StateVarWriter

Constructor Summary

Constructors

Constructor and Description
CADPWriter(CADPExportConfig config)

Method Summary

Modifier and Type	Method and Description
boolean	areNeighbours(int i, int j) Method determines whether modules Mi and Mj are neighbours (this relation is not necessarily symmetrical
String	concreteIntegrationProcessName(RegulatoryNode input, int inputModuleIndex)
String	concreteProcessName(int moduleId)
String	formalIntegrationFunctionName(RegulatoryNode input, int numberArguments, IntegrationFunction integrationFunction)
String	formalIntegrationProcessName(RegulatoryNode input, int numberArguments, IntegrationFunction integrationFunction)
String	formalProcessName(String index)
List<RegulatoryNode>	getAllComponents()
String	getBCGIntegrationFileName(RegulatoryNode input, int moduleIndex)
String	getBCGModelFileName(int moduleId)
static String	getCommonModuleName()
String	getExpFileName()
CADPWriter.GateWriter	getGateWriter()
Collection<RegulatoryNode>	getInfluencedInputs(RegulatoryNode proper)
protected List<byte[]>	getInitialState()
CADPWriter.InitialStateWriter	getInitialStateWriter()
IntegrationFunction	getIntegrationFunctionForInput(RegulatoryNode input)
CADPWriter.InitialStateWriter	getIntegrationInitialStateWriter(List<Map.Entry<RegulatoryNode,Integer>> externalComponents)
List<RegulatoryNode>	getListVisible()
String	getLNTIntegrationFileName()
String	getLNTModelFileName()
Collection<RegulatoryNode>	getMappedInputs()
String	getMCLPropertyFileName(List<byte[]> globalStableState)
org.colomoto.biolqm.LogicalModel	getModel()
String	getModelName()
int	getNumberInstances()
Collection<RegulatoryNode>	getProperComponentsForInput(RegulatoryNode input)
static String	getStableActionName()
CADPWriter.StateVarWriter	getStateVarWriter()
boolean	hasNeighbours(int i)
protected static String	makeCommaList(List<String> list)
protected static String	makeCommaList(List<String> list, String connective)
protected static String	makeUpdatedCommaList(List<String> original, List<String> updated, String toUpdate)
static String	node2Gate(RegulatoryNode node)
static String	node2Gate(RegulatoryNode node, int moduleId)
static String	node2StateVar(RegulatoryNode node)
static String	node2SyncAction(RegulatoryNode input, int inputModuleIndex, RegulatoryNode proper, int properModuleIndex)

Methods inherited from class java.lang.Object

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

Constructor Detail

CADPWriter

public CADPWriter(CADPExportConfig config)

Method Detail

getAllComponents

public List<RegulatoryNode> getAllComponents()

Returns:

ordered list of components of the original LRM

getStableActionName

public static String getStableActionName()

Returns:

name of stable action tau

getCommonModuleName

public static String getCommonModuleName()

node2Gate

public static String node2Gate(RegulatoryNode node,
                               int moduleId)

Parameters:

node - the regulatory node

moduleId - the identification of the instance

Returns:

the name of the corresponding gate

node2Gate

public static String node2Gate(RegulatoryNode node)

Parameters:

node - the regulatory node

Returns:

the name of the corresponding gate

node2StateVar

public static String node2StateVar(RegulatoryNode node)

Parameters:

node - the regulatory node

Returns:

the name of the corresponding state variable

node2SyncAction

public static String node2SyncAction(RegulatoryNode input,
                                     int inputModuleIndex,
                                     RegulatoryNode proper,
                                     int properModuleIndex)

Parameters:

input - the regulatory input node

inputModuleIndex - the identification of the instance where the input node is

proper - the regulatory proper node

properModuleIndex - the identification of the instance where the proper node is

Returns:

the name of the action updating the value of the proper component and the mapped input node influenced by the proper componentn

getNumberInstances

public int getNumberInstances()

Returns:

the number of instances of the composition

getModelName

public String getModelName()

Returns:

the name of the original LRM

getMappedInputs

public Collection<RegulatoryNode> getMappedInputs()

Returns:

a collection of mapped input nodes in the original LRM

getProperComponentsForInput

public Collection<RegulatoryNode> getProperComponentsForInput(RegulatoryNode input)

Parameters:

input - a regulatory input node

Returns:

a collection of proper components influencing the value of the input

getInfluencedInputs

public Collection<RegulatoryNode> getInfluencedInputs(RegulatoryNode proper)

getIntegrationFunctionForInput

public IntegrationFunction getIntegrationFunctionForInput(RegulatoryNode input)

Parameters:

input - a regulatory input node

Returns:

the integration function associated to the input node

getListVisible

public List<RegulatoryNode> getListVisible()

Returns:

the collection of visible components

areNeighbours

public boolean areNeighbours(int i,
                             int j)

Method determines whether modules Mi and Mj are neighbours (this relation is not necessarily symmetrical

Parameters:

i - the index of Module i (starting in 1)

j - the index of Module j (starting in 1)

Returns:

TRUE if they are neighbours, FALSE otherwise

hasNeighbours

public boolean hasNeighbours(int i)

getInitialStateWriter

public CADPWriter.InitialStateWriter getInitialStateWriter()

getIntegrationInitialStateWriter

public CADPWriter.InitialStateWriter getIntegrationInitialStateWriter(List<Map.Entry<RegulatoryNode,Integer>> externalComponents)

getGateWriter

public CADPWriter.GateWriter getGateWriter()

getStateVarWriter

public CADPWriter.StateVarWriter getStateVarWriter()

concreteProcessName

public String concreteProcessName(int moduleId)

formalProcessName

public String formalProcessName(String index)

concreteIntegrationProcessName

public String concreteIntegrationProcessName(RegulatoryNode input,
                                             int inputModuleIndex)

formalIntegrationProcessName

public String formalIntegrationProcessName(RegulatoryNode input,
                                           int numberArguments,
                                           IntegrationFunction integrationFunction)

formalIntegrationFunctionName

public String formalIntegrationFunctionName(RegulatoryNode input,
                                            int numberArguments,
                                            IntegrationFunction integrationFunction)

getModel

public org.colomoto.biolqm.LogicalModel getModel()

getBCGModelFileName

public String getBCGModelFileName(int moduleId)

getLNTModelFileName

public String getLNTModelFileName()

getBCGIntegrationFileName

public String getBCGIntegrationFileName(RegulatoryNode input,
                                        int moduleIndex)

getLNTIntegrationFileName

public String getLNTIntegrationFileName()

getExpFileName

public String getExpFileName()

getMCLPropertyFileName

public String getMCLPropertyFileName(List<byte[]> globalStableState)

getInitialState

protected List<byte[]> getInitialState()

makeCommaList

protected static String makeCommaList(List<String> list)

makeCommaList

protected static String makeCommaList(List<String> list,
                                      String connective)

makeUpdatedCommaList

protected static String makeUpdatedCommaList(List<String> original,
                                             List<String> updated,
                                             String toUpdate)