org.sbml.jsbml

Class CVTerm

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AnnotationElement

org.sbml.jsbml.CVTerm

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, TreeNodeWithChangeSupport

public class CVTerm
extends AnnotationElement

Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element of a SBML component.

Since:

0.8

Version:

$Rev: 1639 $

Author:

Andreas Dräger, Marine Dumousseau, Nicolas Rodriguez

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CVTerm.Qualifier This enum list all the possible MIRIAM qualifiers.
static class	CVTerm.Type This enum list all the possible MIRIAM qualifiers type.

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	INVALID_TYPE_AND_QUALIFIER_COMBINATION_MSG Message to indicate an illegal combination of a CVTerm.Type and a CVTerm.Qualifier attribute.
private CVTerm.Qualifier	qualifier Represents the MIRIAM qualifier node in the annotation node of a SBML component.
private java.util.List<java.lang.String>	resourceURIs Contains all the MIRIAM URI associated with the qualifier of this CVTerm instance.
private static long	serialVersionUID Generated serial version identifier.
private CVTerm.Type	type Represents the type of MIRIAM qualifier for this CVTerm.
static java.lang.String	URI_BIOMODELS_NET_BIOLOGY_QUALIFIERS The Uniform Resource Identifier pointing to http://biomodels.net/biology-qualifiers/
static java.lang.String	URI_BIOMODELS_NET_MODEL_QUALIFIERS The Uniform Resource Identifier pointing to http://biomodels.net/model-qualifiers/

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
CVTerm() Creates a CVTerm instance.
CVTerm(CVTerm.Qualifier qualifier, java.lang.String... resources) Guesses the CVTerm.Type argument and sets the CVTerm.Qualifier attribute appropriately.
CVTerm(CVTerm.Type type, CVTerm.Qualifier qualifier, java.lang.String... resources) Creates a new CVTerm with the given CVTerm.Type and CVTerm.Qualifier pointing to all given resources.
CVTerm(CVTerm term) Creates a CVTerm instance from a given CVTerm.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addResource(java.lang.String urn) Adds a resource to the CVTerm.
boolean	addResources(java.lang.String... resources) Adds list of resources to the CVTerm.
boolean	addResourceURI(java.lang.String uri) Adds a resource to the CVTerm.
CVTerm	clone()
boolean	equals(java.lang.Object object)
java.util.List<java.lang.String>	filterResources(java.lang.String pattern) Returns a list of resources that contain the given pattern.
boolean	getAllowsChildren()
CVTerm.Qualifier	getBiologicalQualifierType() Returns the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.BIOLOGICAL_QUALIFIER, null otherwise.
javax.swing.tree.TreeNode	getChildAt(int childIndex)
int	getChildCount()
CVTerm.Qualifier	getModelQualifierType() Returns the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.MODEL_QUALIFIER, null otherwise.
int	getNumResources() Returns the number of resources for this CVTerm.
CVTerm.Qualifier	getQualifier() Returns the CVTerm.Qualifier for this CVTerm.
CVTerm.Type	getQualifierType() Returns the qualifier CVTerm.Type for this CVTerm.
int	getResourceCount() Returns the number of resources for this CVTerm.
java.util.List<java.lang.String>	getResources() Returns the resources for this CVTerm.
java.lang.String	getResourceURI(int i) Returns the value of the nth resource for this CVTerm.
int	hashCode()
boolean	isBiologicalQualifier() Returns true if this qualifier is a biological qualifier.
boolean	isModelQualifier() Returns true if this qualifier is a model qualifier.
boolean	isSetBiologicalQualifierType() Returns true if the CVTerm.Qualifier is set and is of type CVTerm.Type.BIOLOGICAL_QUALIFIER
boolean	isSetModelQualifierType() Returns true if the CVTerm.Qualifier is set and is of type CVTerm.Type.MODEL_QUALIFIER
boolean	isSetQualifier() Returns true if the CVTerm.Qualifier of this CVTerm is set and is different from CVTerm.Qualifier.BQM_UNKNOWN and CVTerm.Qualifier.BQB_UNKNOWN.
boolean	isSetQualifierType() Checks whether or not the CVTerm.Type has been set for this CVTerm.
boolean	isSetType() Returns true if the CVTerm.Type of this CVTerm is set and is different from CVTerm.Type.UNKNOWN_QUALIFIER.
boolean	isSetTypeQualifier() Deprecated. use isSetQualifier()
boolean	readAttribute(java.lang.String elementName, java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	removeResource(int index) Removes the ith resource from the CVTerm.
void	removeResource(java.lang.String resource) Removes a resource from the CVTerm.
void	setBiologicalQualifierType(CVTerm.Qualifier qualifier) Sets the biological qualifier type of this CVTerm.
void	setBiologicalQualifierType(int specificQualifierType) Sets the biological qualifier type, using the CVTerm.Qualifier.values() array.
void	setModelQualifierType(CVTerm.Qualifier qualifier) Sets the model qualifier type of this CVTerm.
void	setModelQualifierType(int specificQualifierType) Sets the model qualifier type of this CVTerm, using the CVTerm.Qualifier.values() array.
void	setQualifier(CVTerm.Qualifier qualifier) Sets the CVTerm.Qualifier of this CVTerm, sets at the same time the CVTerm.Type to the proper value.
void	setQualifierType(CVTerm.Type type) Sets the type of this CVTerm to 'type', the value of the CVTerm.Qualifier is reset to CVTerm.Qualifier.BQB_UNKNOWN or CVTerm.Qualifier.BQM_UNKNOWN.
void	setQualifierType(int qualifierType) Sets the type of this CVTerm to the CVTerm.Type represented by 'qualifierType'.
java.lang.String	toString() Returns a String containing the qualifier and all the resource URIs of this CVTerm.
void	toXML(java.lang.String indent, java.lang.StringBuffer buffer) Writes all the MIRIAM annotations of the CVTerm in 'buffer'
void	unsetBiologicalQualifierType() Unsets the biological qualifier if it is set and of the type CVTerm.Type.BIOLOGICAL_QUALIFIER
void	unsetModelQualifierType() Unsets the CVTerm.Qualifier if it is set and of the type CVTerm.Type.MODEL_QUALIFIER.
void	unsetQualifier() Unsets the qualifier if it is set.
void	unsetQualifierType() Unsets the qualifier type if it is set.

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getParent, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

URI_BIOMODELS_NET_MODEL_QUALIFIERS

public static final java.lang.String URI_BIOMODELS_NET_MODEL_QUALIFIERS

The Uniform Resource Identifier pointing to http://biomodels.net/model-qualifiers/

See Also:

Constant Field Values

URI_BIOMODELS_NET_BIOLOGY_QUALIFIERS

public static final java.lang.String URI_BIOMODELS_NET_BIOLOGY_QUALIFIERS

The Uniform Resource Identifier pointing to http://biomodels.net/biology-qualifiers/

See Also:

Constant Field Values

INVALID_TYPE_AND_QUALIFIER_COMBINATION_MSG

private static final java.lang.String INVALID_TYPE_AND_QUALIFIER_COMBINATION_MSG

Message to indicate an illegal combination of a CVTerm.Type and a CVTerm.Qualifier attribute.

See Also:

Constant Field Values

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

qualifier

private CVTerm.Qualifier qualifier

Represents the MIRIAM qualifier node in the annotation node of a SBML component.

resourceURIs

private java.util.List<java.lang.String> resourceURIs

Contains all the MIRIAM URI associated with the qualifier of this CVTerm instance.

type

private CVTerm.Type type

Represents the type of MIRIAM qualifier for this CVTerm. It depends on the name space in the SBML file, it can be a model qualifier or a biological qualifier.

Constructor Detail

CVTerm

public CVTerm()

Creates a CVTerm instance. By default, the type and qualifier of this CVTerm are null. The list of resourceURIS is empty.

CVTerm

public CVTerm(CVTerm term)

Creates a CVTerm instance from a given CVTerm.

Parameters:

term - the CVTerm to clone

CVTerm

public CVTerm(CVTerm.Qualifier qualifier,
      java.lang.String... resources)

Guesses the CVTerm.Type argument and sets the CVTerm.Qualifier attribute appropriately. Then it adds all the given resources.

Parameters:

qualifier -

resources -

CVTerm

public CVTerm(CVTerm.Type type,
      CVTerm.Qualifier qualifier,
      java.lang.String... resources)

Creates a new CVTerm with the given CVTerm.Type and CVTerm.Qualifier pointing to all given resources.

Parameters:

type -

qualifier -

resources -

Throws:

java.lang.IllegalArgumentException - if the combination of the given type and qualifier is not possible or if the given resources are invalid.

Method Detail

addResource

public boolean addResource(java.lang.String urn)

Adds a resource to the CVTerm.

Same method a addResourceURI(String)

Parameters:

urn - string representing the resource; e.g., 'urn:miriam:kegg.reaction:R00351'

Returns:

true as specified in Collection.add(Object)

addResources

public boolean addResources(java.lang.String... resources)

Adds list of resources to the CVTerm.

Parameters:

resources - a list of strings representing the resources; e.g., 'urn:miriam:kegg.reaction:R00351'

Returns:

true if all the resources have been added properly.

addResourceURI

public boolean addResourceURI(java.lang.String uri)

Adds a resource to the CVTerm.

Same method a addResource(String)

Parameters:

uri - string representing the resource; e.g., 'urn:miriam:kegg.reaction:R00351'

Returns:

true if 'uri' has been added to the list of resourceURI of this CVTerm.

clone

public CVTerm clone()

Specified by:

clone in class AbstractTreeNode

equals

public boolean equals(java.lang.Object object)

Overrides:

equals in class AbstractTreeNode

filterResources

public java.util.List<java.lang.String> filterResources(java.lang.String pattern)

Returns a list of resources that contain the given pattern. This is useful to obtain, e.g., all KEGG resources this term points to.

Parameters:

pattern - e.g., "urn:miriam:kegg.reaction:R" or just "kegg".

Returns:

A list of all resources that contain the given pattern. This list can be empty.

getAllowsChildren

public boolean getAllowsChildren()

getBiologicalQualifierType

public CVTerm.Qualifier getBiologicalQualifierType()

Returns the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.BIOLOGICAL_QUALIFIER, null otherwise.

Returns:

the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.BIOLOGICAL_QUALIFIER, null otherwise.

getChildAt

public javax.swing.tree.TreeNode getChildAt(int childIndex)

getChildCount

public int getChildCount()

getModelQualifierType

public CVTerm.Qualifier getModelQualifierType()

Returns the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.MODEL_QUALIFIER, null otherwise.

Returns:

the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.MODEL_QUALIFIER, null otherwise.

getNumResources

public int getNumResources()

Returns the number of resources for this CVTerm.

Returns:

the number of resources for this CVTerm.

getQualifier

public CVTerm.Qualifier getQualifier()

Returns the CVTerm.Qualifier for this CVTerm.

If you want to know if the Qualifier is a model qualifier or a biological modifier, you can use CVTerm.Qualifier.isModelQualifier() and CVTerm.Qualifier.isBiologicalQualifier().

If you want to display the name of the Qualifier, you can use CVTerm.Qualifier.getElementNameEquivalent().

Returns:

the CVTerm.Qualifier for this CVTerm.

getResourceCount

public int getResourceCount()

Returns the number of resources for this CVTerm.

Returns:

the number of resources for this CVTerm.

getQualifierType

public CVTerm.Type getQualifierType()

Returns the qualifier CVTerm.Type for this CVTerm.

Returns:

the qualifier CVTerm.Type for this CVTerm.

getResources

public java.util.List<java.lang.String> getResources()

Returns the resources for this CVTerm.

Returns:

the list of urns that store the resources of this CVTerm.

getResourceURI

public java.lang.String getResourceURI(int i)

Returns the value of the nth resource for this CVTerm.

Parameters:

i - index of the resourceURI in the list of the resourceURI.

Returns:

the value of the nth resource for this CVTerm.

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractTreeNode

isBiologicalQualifier

public boolean isBiologicalQualifier()

Returns true if this qualifier is a biological qualifier.

Returns:

true if this qualifier is a biological qualifier, false otherwise.

isModelQualifier

public boolean isModelQualifier()

Returns true if this qualifier is a model qualifier.

Returns:

true if this qualifier is a model qualifier, false otherwise.

isSetBiologicalQualifierType

public boolean isSetBiologicalQualifierType()

Returns true if the CVTerm.Qualifier is set and is of type CVTerm.Type.BIOLOGICAL_QUALIFIER

Returns:

true if the CVTerm.Qualifier is set and is of type CVTerm.Type.BIOLOGICAL_QUALIFIER, false otherwise.

isSetModelQualifierType

public boolean isSetModelQualifierType()

Returns true if the CVTerm.Qualifier is set and is of type CVTerm.Type.MODEL_QUALIFIER

Returns:

true if the CVTerm.Qualifier is set and is of type CVTerm.Type.MODEL_QUALIFIER, false otherwise.

isSetQualifierType

public boolean isSetQualifierType()

Checks whether or not the CVTerm.Type has been set for this CVTerm.

Returns:

true if the CVTerm.Type of this CVTerm is set.

isSetType

public boolean isSetType()

Returns true if the CVTerm.Type of this CVTerm is set and is different from CVTerm.Type.UNKNOWN_QUALIFIER.

Returns:

true if the CVTerm.Type of this CVTerm is set and is different from CVTerm.Type.UNKNOWN_QUALIFIER.

isSetTypeQualifier

@Deprecated
public boolean isSetTypeQualifier()

Deprecated. use isSetQualifier()

Returns true if the CVTerm.Qualifier of this CVTerm is set and is different from CVTerm.Qualifier.BQM_UNKNOWN and CVTerm.Qualifier.BQB_UNKNOWN.

Returns:

true if the CVTerm.Qualifier of this CVTerm is set.

isSetQualifier

public boolean isSetQualifier()

Returns true if the CVTerm.Qualifier of this CVTerm is set and is different from CVTerm.Qualifier.BQM_UNKNOWN and CVTerm.Qualifier.BQB_UNKNOWN.

Returns:

true if the CVTerm.Qualifier of this CVTerm is set.

readAttribute

public boolean readAttribute(java.lang.String elementName,
                    java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

removeResource

public void removeResource(java.lang.String resource)

Removes a resource from the CVTerm.

Parameters:

resource -

removeResource

public void removeResource(int index)

Removes the ith resource from the CVTerm.

Parameters:

resource -

setBiologicalQualifierType

public void setBiologicalQualifierType(int specificQualifierType)

Sets the biological qualifier type, using the CVTerm.Qualifier.values() array.

Parameters:

specificQualifierType -

setBiologicalQualifierType

public void setBiologicalQualifierType(CVTerm.Qualifier qualifier)

Sets the biological qualifier type of this CVTerm.

Parameters:

qualifier -

Throws:

java.lang.IllegalArgumentException - if the CVTerm.Qualifier is not a biological one or if the CVTerm.Type was not set to CVTerm.Type.BIOLOGICAL_QUALIFIER.

See Also:

#setQualifier(Qualifier)}

setModelQualifierType

public void setModelQualifierType(int specificQualifierType)

Sets the model qualifier type of this CVTerm, using the CVTerm.Qualifier.values() array.

Parameters:

specificQualifierType -

setModelQualifierType

public void setModelQualifierType(CVTerm.Qualifier qualifier)

Sets the model qualifier type of this CVTerm.

Parameters:

qualifier -

Throws:

java.lang.IllegalArgumentException - if the CVTerm.Qualifier is not a model one or if the CVTerm.Type was not set to CVTerm.Type.MODEL_QUALIFIER.

See Also:

#setQualifier(Qualifier)}

setQualifier

public void setQualifier(CVTerm.Qualifier qualifier)

Sets the CVTerm.Qualifier of this CVTerm, sets at the same time the CVTerm.Type to the proper value.

Parameters:

qualifier -

setQualifierType

public void setQualifierType(int qualifierType)

Sets the type of this CVTerm to the CVTerm.Type represented by 'qualifierType'.

Parameters:

qualifierType - the Type to set as an integer.

setQualifierType

public void setQualifierType(CVTerm.Type type)

Sets the type of this CVTerm to 'type', the value of the CVTerm.Qualifier is reset to CVTerm.Qualifier.BQB_UNKNOWN or CVTerm.Qualifier.BQM_UNKNOWN.

Parameters:

type -

See Also:

#setQualifier(Qualifier)}

toString

public java.lang.String toString()

Returns a String containing the qualifier and all the resource URIs of this CVTerm.

Overrides:

toString in class AbstractTreeNode

Returns:

a String containing the qualifier and all the resource URIs of this CVTerm.

unsetBiologicalQualifierType

public void unsetBiologicalQualifierType()

Unsets the biological qualifier if it is set and of the type CVTerm.Type.BIOLOGICAL_QUALIFIER

See Also:

unsetQualifier()

unsetModelQualifierType

public void unsetModelQualifierType()

Unsets the CVTerm.Qualifier if it is set and of the type CVTerm.Type.MODEL_QUALIFIER.

See Also:

unsetQualifier()

unsetQualifier

public void unsetQualifier()

Unsets the qualifier if it is set.

unsetQualifierType

public void unsetQualifierType()

Unsets the qualifier type if it is set.

toXML

public void toXML(java.lang.String indent,
         java.lang.StringBuffer buffer)

Writes all the MIRIAM annotations of the CVTerm in 'buffer'

Parameters:

indent -

buffer -