Package edu.cmu.tetrad.data

Class Knowledge

java.lang.Object

edu.cmu.tetrad.data.Knowledge

All Implemented Interfaces:

TetradSerializable, Serializable

public final class Knowledge
extends Object
implements TetradSerializable

Stores information about required and forbidden edges and common causes for use in algorithm. This information can be set edge by edge or else globally via temporal tiers. When setting temporal tiers, all edges from later tiers to earlier tiers are forbidden.

For this class, all variable names are referenced by name only. This is because the same Knowledge object is intended to plug into different graphs with MyNodes that possibly have the same names. Thus, if the Knowledge object forbids the edge X --> Y, then it forbids any edge which connects a MyNode named "X" to a MyNode named "Y", even if the underlying MyNodes themselves named "X" and "Y", respectively, are not the same.

In place of variable names, wildcard expressions containing the wildcard '*' may be substituted. These will be matched to as many myNodes as possible. The '*' wildcard matches any string of consecutive characters up until the following character is encountered. Thus, "X*a" will match "X123a" and "X45a".

Version:

$Id: $Id

Author:

josephramsey, Kevin V. Bui (kvb2@pitt.edu)

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
Knowledge()	Constructor for Knowledge.
Knowledge(Knowledge knowledge)	Constructor for Knowledge.
Knowledge(Collection<String> nodes)	Constructor for Knowledge.

Method Summary

Modifier and Type	Method	Description
void	addKnowledgeGroup(KnowledgeGroup group)	Adds a knowledge group.
void	addToTier(int tier, String spec)	Adds the given variable or wildcard cpdag to the given tier.
void	addToTiersByVarNames(List<String> varNames)	Puts a variable into tier i if its name is xxx:ti for some xxx and some i.
void	addVariable(String varName)	addVariable.
void	clear()	Removes explicit knowledge and tier information.
Knowledge	copy()	Makes a shallow copy.
boolean	equals(Object o)	Compares this Knowledge object with the specified object for equality.
Iterator<KnowledgeEdge>	forbiddenEdgesIterator()	Iterator over the KnowledgeEdge's representing forbidden edges.
List<KnowledgeGroup>	getKnowledgeGroups()	Getter for the field knowledgeGroups.
List<KnowledgeEdge>	getListOfExplicitlyForbiddenEdges()	getListOfExplicitlyForbiddenEdges.
List<KnowledgeEdge>	getListOfExplicitlyRequiredEdges()	getListOfExplicitlyRequiredEdges.
List<KnowledgeEdge>	getListOfForbiddenEdges()	getListOfForbiddenEdges.
List<KnowledgeEdge>	getListOfRequiredEdges()	getListOfRequiredEdges.
int	getMaxTierForbiddenWithin()	getMaxTierForbiddenWithin.
int	getNumTiers()	getNumTiers.
List<String>	getTier(int tier)	getTier.
List<String>	getVariables()	Get a list of variables.
List<String>	getVariablesNotInTiers()	getVariablesNotInTiers.
int	hashCode()	Computes a hashcode.
boolean	isDefaultToKnowledgeLayout()	isDefaultToKnowledgeLayout.
boolean	isEmpty()	true if there is no background knowledge recorded.
boolean	isForbidden(String var1, String var2)	Determines whether the edge var1 --> var2 is forbidden.
boolean	isForbiddenByGroups(String var1, String var2)	Legacy.
boolean	isForbiddenByTiers(String var1, String var2)	Determines whether the edge var1 --> var2 is forbidden by the temporal tiers.
int	isInWhichTier(Node node)	Returns the index of the tier of node if it's in a tier, otherwise -1.
boolean	isOnlyCanCauseNextTier(int tier)	isOnlyCanCauseNextTier.
boolean	isRequired(String var1, String var2)	Determines whether the edge var1 --> var2 is required.
boolean	isRequiredByGroups(String var1, String var2)	Legacy.
boolean	isTierForbiddenWithin(int tier)	Checks whether it is the case that any variable is forbidden by any other variable within a given tier.
boolean	isViolatedBy(Graph graph)	isViolatedBy.
boolean	noEdgeRequired(String x, String y)	noEdgeRequired.
void	removeForbidden(String var1, String var2)	Marks the edge var1 --> var2 as not forbid.
void	removeFromTiers(String spec)	Removes the given variable by name or search string from all tiers.
void	removeKnowledgeGroup(int index)	Removes the knowledge group at the given index.
void	removeRequired(String var1, String var2)	Marks the edge var1 --> var2 as not required.
Iterator<KnowledgeEdge>	requiredEdgesIterator()	Iterator over the KnowledgeEdge's representing required edges.
static Knowledge	serializableInstance()	Generates a simple exemplar of this class to test serialization.
void	setDefaultToKnowledgeLayout(boolean defaultToKnowledgeLayout)	Setter for the field defaultToKnowledgeLayout.
void	setForbidden(String var1, String var2)	Marks the edge var1 --> var2 as forbid.
void	setKnowledgeGroup(int index, KnowledgeGroup group)	Legacy, do not use.
void	setOnlyCanCauseNextTier(int tier, boolean onlyCausesNext)	setOnlyCanCauseNextTier.
void	setRequired(String var1, String var2)	Marks the edge var1 --> var2 as required.
void	setTier(int tier, List<String> vars)	Sets the variable in a given tier to the specified list.
void	setTierForbiddenWithin(int tier, boolean forbidden)	Forbids any variable from being parent of any other variable within the given tier, or cancels this forbidding.
String	toString()	toString.

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Details

Knowledge

public Knowledge()

Constructor for Knowledge.

Knowledge

public Knowledge(Collection<String> nodes)

Constructor for Knowledge.

Parameters:

nodes - a Collection object

Knowledge

public Knowledge(Knowledge knowledge)

Constructor for Knowledge.

Parameters:

knowledge - a Knowledge object

Method Details

serializableInstance

public static Knowledge serializableInstance()

Generates a simple exemplar of this class to test serialization.

Returns:

a Knowledge object

addToTier

public void addToTier(int tier,
 String spec)

Adds the given variable or wildcard cpdag to the given tier. The tier is a non-negative integer.

Parameters:

tier - a int

spec - a String object

addToTiersByVarNames

public void addToTiersByVarNames(List<String> varNames)

Puts a variable into tier i if its name is xxx:ti for some xxx and some i.

Parameters:

varNames - a List object

addKnowledgeGroup

public void addKnowledgeGroup(KnowledgeGroup group)

Adds a knowledge group. Legacy method, replaced by setForbidden, setRequired with cpdags. Needed for the interface.

Parameters:

group - a KnowledgeGroup object

addVariable

public void addVariable(String varName)

addVariable.

Parameters:

varName - a String object

clear

public void clear()

Removes explicit knowledge and tier information.

forbiddenEdgesIterator

public Iterator<KnowledgeEdge> forbiddenEdgesIterator()

Iterator over the KnowledgeEdge's representing forbidden edges.

Returns:

a Iterator object

getKnowledgeGroups

public List<KnowledgeGroup> getKnowledgeGroups()

Getter for the field knowledgeGroups.

Returns:

a shallow copy of the list of group rules.

getVariables

public List<String> getVariables()

Get a list of variables.

Returns:

a copy of the list of variable, in alphabetical order.

getVariablesNotInTiers

public List<String> getVariablesNotInTiers()

getVariablesNotInTiers.

Returns:

the list of edges not in any tier.

getTier

public List<String> getTier(int tier)

getTier.

Parameters:

tier - the index of the desired tier

Returns:

a copy of this tier

getNumTiers

public int getNumTiers()

getNumTiers.

Returns:

the number of temporal tiers

isDefaultToKnowledgeLayout

public boolean isDefaultToKnowledgeLayout()

isDefaultToKnowledgeLayout.

Returns:

a boolean

setDefaultToKnowledgeLayout

public void setDefaultToKnowledgeLayout(boolean defaultToKnowledgeLayout)

Setter for the field defaultToKnowledgeLayout.

Parameters:

defaultToKnowledgeLayout - a boolean

isForbidden

public boolean isForbidden(String var1,
 String var2)

Determines whether the edge var1 --> var2 is forbidden.

Parameters:

var1 - a String object

var2 - a String object

Returns:

a boolean

isForbiddenByGroups

public boolean isForbiddenByGroups(String var1,
 String var2)

Legacy.

Parameters:

var1 - a String object

var2 - a String object

Returns:

a boolean

isForbiddenByTiers

public boolean isForbiddenByTiers(String var1,
 String var2)

Determines whether the edge var1 --> var2 is forbidden by the temporal tiers.

Parameters:

var1 - a String object

var2 - a String object

Returns:

a boolean

isRequired

public boolean isRequired(String var1,
 String var2)

Determines whether the edge var1 --> var2 is required.

Parameters:

var1 - a String object

var2 - a String object

Returns:

a boolean

isRequiredByGroups

public boolean isRequiredByGroups(String var1,
 String var2)

Legacy.

Parameters:

var1 - a String object

var2 - a String object

Returns:

a boolean

isEmpty

public boolean isEmpty()

true if there is no background knowledge recorded.

Returns:

a boolean

isTierForbiddenWithin

public boolean isTierForbiddenWithin(int tier)

Checks whether it is the case that any variable is forbidden by any other variable within a given tier.

Parameters:

tier - a int

Returns:

a boolean

isViolatedBy

public boolean isViolatedBy(Graph graph)

isViolatedBy.

Parameters:

graph - a Graph object

Returns:

a boolean

noEdgeRequired

public boolean noEdgeRequired(String x,
 String y)

noEdgeRequired.

Parameters:

x - a String object

y - a String object

Returns:

a boolean

removeFromTiers

public void removeFromTiers(String spec)

Removes the given variable by name or search string from all tiers.

Parameters:

spec - a String object

removeKnowledgeGroup

public void removeKnowledgeGroup(int index)

Removes the knowledge group at the given index.

Parameters:

index - a int

requiredEdgesIterator

public Iterator<KnowledgeEdge> requiredEdgesIterator()

Iterator over the KnowledgeEdge's representing required edges.

Returns:

a Iterator object

setForbidden

public void setForbidden(String var1,
 String var2)

Marks the edge var1 --> var2 as forbid.

Parameters:

var1 - a String object

var2 - a String object

removeForbidden

public void removeForbidden(String var1,
 String var2)

Marks the edge var1 --> var2 as not forbid.

Parameters:

var1 - a String object

var2 - a String object

setRequired

public void setRequired(String var1,
 String var2)

Marks the edge var1 --> var2 as required.

Parameters:

var1 - a String object

var2 - a String object

removeRequired

public void removeRequired(String var1,
 String var2)

Marks the edge var1 --> var2 as not required.

Parameters:

var1 - a String object

var2 - a String object

setKnowledgeGroup

public void setKnowledgeGroup(int index,
 KnowledgeGroup group)

Legacy, do not use.

Parameters:

index - a int

group - a KnowledgeGroup object

setTier

public void setTier(int tier,
 List<String> vars)

Sets the variable in a given tier to the specified list.

Parameters:

tier - a int

vars - a List object

setTierForbiddenWithin

public void setTierForbiddenWithin(int tier,
 boolean forbidden)

Forbids any variable from being parent of any other variable within the given tier, or cancels this forbidding.

Parameters:

tier - a int

forbidden - a boolean

getMaxTierForbiddenWithin

public int getMaxTierForbiddenWithin()

getMaxTierForbiddenWithin.

Returns:

the largest indes of a tier in which every variable is forbidden by every other variable, or -1 if there is not such tier.

copy

public Knowledge copy()

Makes a shallow copy.

Returns:

a Knowledge object

isInWhichTier

public int isInWhichTier(Node node)

Returns the index of the tier of node if it's in a tier, otherwise -1.

Parameters:

node - a Node object

Returns:

a int

getListOfRequiredEdges

public List<KnowledgeEdge> getListOfRequiredEdges()

getListOfRequiredEdges.

Returns:

a List object

getListOfExplicitlyRequiredEdges

public List<KnowledgeEdge> getListOfExplicitlyRequiredEdges()

getListOfExplicitlyRequiredEdges.

Returns:

a List object

getListOfForbiddenEdges

public List<KnowledgeEdge> getListOfForbiddenEdges()

getListOfForbiddenEdges.

Returns:

a List object

getListOfExplicitlyForbiddenEdges

public List<KnowledgeEdge> getListOfExplicitlyForbiddenEdges()

getListOfExplicitlyForbiddenEdges.

Returns:

a List object

isOnlyCanCauseNextTier

public boolean isOnlyCanCauseNextTier(int tier)

isOnlyCanCauseNextTier.

Parameters:

tier - a int

Returns:

a boolean

setOnlyCanCauseNextTier

public void setOnlyCanCauseNextTier(int tier,
 boolean onlyCausesNext)

setOnlyCanCauseNextTier.

Parameters:

tier - a int

onlyCausesNext - a boolean

hashCode

public int hashCode()

Computes a hashcode.

Overrides:

hashCode in class Object

Returns:

a int

equals

public boolean equals(Object o)

Compares this Knowledge object with the specified object for equality.

Overrides:

equals in class Object

Parameters:

o - the object to compare this Knowledge with

Returns:

true if the specified object is equal to this Knowledge, false otherwise

toString

public String toString()

toString.

Overrides:

toString in class Object

Returns:

the contents of this Knowledge object in String form.