C# Class libsbml.SBase

Inheritance: IDisposable

Show file Open project: sys-bio/libroadrunner-deps Class Usage Examples

Protected Properties

Property	Type	Description
swigCMemOwn	bool

Public Methods

Method	Description
Dispose ( ) : void
Equals ( Object sb ) : bool
GetHashCode ( ) : int
addCVTerm ( CVTerm term ) : int
addCVTerm ( CVTerm term, bool newBag ) : int
appendAnnotation ( XMLNode annotation ) : int
appendAnnotation ( string annotation ) : int
appendNotes ( XMLNode notes ) : int
appendNotes ( string notes ) : int
checkCompatibility ( SBase arg0 ) : int
checkMathMLNamespace ( XMLToken elem ) : string
clone ( ) : SBase
connectToChild ( ) : void
connectToParent ( SBase parent ) : void
containsUndeclaredUnits ( ) : bool
deleteDisabledPlugins ( ) : void
deleteDisabledPlugins ( bool recursive ) : void
disablePackage ( string pkgURI, string pkgPrefix ) : int
divideAssignmentsToSIdByFunction ( string id, ASTNode function ) : void
enablePackage ( string pkgURI, string pkgPrefix, bool flag ) : int
enablePackageInternal ( string pkgURI, string pkgPrefix, bool flag ) : void
getAncestorOfType ( int type ) : SBase
getAncestorOfType ( int type, string pkgName ) : SBase
getAnnotation ( ) : XMLNode
getAnnotationString ( ) : string
getCVTerm ( long n ) : CVTerm
getCVTerms ( ) : CVTermList
getColumn ( ) : long
getDerivedUnitDefinition ( ) : UnitDefinition
getDisabledPlugin ( long n ) : SBasePlugin
getElementByMetaId ( string metaid ) : SBase
getElementBySId ( string id ) : SBase
getElementFromPluginsByMetaId ( string metaid ) : SBase
getElementFromPluginsBySId ( string id ) : SBase
getElementName ( ) : string
getId ( ) : string
getLevel ( ) : long
getLine ( ) : long
getListOfAllElements ( ) : SBaseList
getListOfAllElements ( ElementFilter filter ) : SBaseList
getListOfAllElementsFromPlugins ( ) : SBaseList
getListOfAllElementsFromPlugins ( ElementFilter filter ) : SBaseList
getMetaId ( ) : string
getModel ( ) : Model
getModelHistory ( ) : ModelHistory
getName ( ) : string
getNamespaces ( ) : XMLNamespaces
getNotes ( ) : XMLNode
getNotesString ( ) : string
getNumCVTerms ( ) : long
getNumDisabledPlugins ( ) : long
getNumPlugins ( ) : long
getPackageName ( ) : string
getPackageVersion ( ) : long
getParentSBMLObject ( ) : SBase
getPlugin ( long n ) : SBasePlugin
getPlugin ( string package ) : SBasePlugin
getPrefix ( ) : string
getResourceBiologicalQualifier ( string resource ) : int
getResourceModelQualifier ( string resource ) : int
getSBMLDocument ( ) : SBMLDocument
getSBMLNamespaces ( ) : SBMLNamespaces
getSBOTerm ( ) : int
getSBOTermAsURL ( ) : string
getSBOTermID ( ) : string
getTypeCode ( ) : int
getURI ( ) : string
getVersion ( ) : long
hasNonstandardIdentifierBeginningWith ( string prefix ) : bool
hasRequiredAttributes ( ) : bool
hasRequiredElements ( ) : bool
hasValidLevelVersionNamespaceCombination ( ) : bool
isPackageEnabled ( string pkgName ) : bool
isPackageURIEnabled ( string pkgURI ) : bool
isPkgEnabled ( string pkgName ) : bool
isPkgURIEnabled ( string pkgURI ) : bool
isSetAnnotation ( ) : bool
isSetId ( ) : bool
isSetMetaId ( ) : bool
isSetModelHistory ( ) : bool
isSetName ( ) : bool
isSetNotes ( ) : bool
isSetSBOTerm ( ) : bool
isSetUserData ( ) : bool
matchesRequiredSBMLNamespacesForAddition ( SBase sb ) : bool
matchesSBMLNamespaces ( SBase sb ) : bool
multiplyAssignmentsToSIdByFunction ( string id, ASTNode function ) : void
operator ( ) : bool
prependStringToAllIdentifiers ( string prefix ) : int
removeFromParentAndDelete ( ) : int
removeTopLevelAnnotationElement ( string elementName ) : int
removeTopLevelAnnotationElement ( string elementName, string elementURI ) : int
removeTopLevelAnnotationElement ( string elementName, string elementURI, bool removeEmpty ) : int
renameMetaIdRefs ( string oldid, string newid ) : void
renameSIdRefs ( string oldid, string newid ) : void
renameUnitSIdRefs ( string oldid, string newid ) : void
replaceSIDWithFunction ( string id, ASTNode function ) : void
replaceTopLevelAnnotationElement ( XMLNode annotation ) : int
replaceTopLevelAnnotationElement ( string annotation ) : int
setAnnotation ( XMLNode annotation ) : int
setAnnotation ( string annotation ) : int
setId ( string sid ) : int
setMetaId ( string metaid ) : int
setModelHistory ( ModelHistory history ) : int
setName ( string name ) : int
setNamespaces ( XMLNamespaces xmlns ) : int
setNotes ( XMLNode notes ) : int
setNotes ( string notes ) : int
setNotes ( string notes, bool addXHTMLMarkup ) : int
setSBMLNamespacesAndOwn ( SBMLNamespaces disownedNs ) : void
setSBOTerm ( int value ) : int
setSBOTerm ( string sboid ) : int
toSBML ( ) : string
toXMLNode ( ) : XMLNode
transformIdentifiers ( IdentifierTransformer idTransformer ) : int
unsetAnnotation ( ) : int
unsetCVTerms ( ) : int
unsetId ( ) : int
unsetMetaId ( ) : int
unsetModelHistory ( ) : int
unsetName ( ) : int
unsetNotes ( ) : int
unsetSBOTerm ( ) : int
unsetUserData ( ) : int
writeExtensionElements ( XMLOutputStream stream ) : void

Private Methods

Method	Description
SBase ( IntPtr cPtr, bool cMemoryOwn ) : System
getCPtr ( SBase obj ) : HandleRef
getCPtrAndDisown ( SBase obj ) : HandleRef

Method Details

Dispose() public method

public Dispose ( ) : void
return	void

Equals() public method

public Equals ( Object sb ) : bool
sb	Object
return	bool

GetHashCode() public method

public GetHashCode ( ) : int
return	int

addCVTerm() public method

public addCVTerm ( CVTerm term ) : int
term	CVTerm
return	int

addCVTerm() public method

public addCVTerm ( CVTerm term, bool newBag ) : int
term	CVTerm
newBag	bool
return	int

appendAnnotation() public method

public appendAnnotation ( XMLNode annotation ) : int
annotation	XMLNode
return	int

appendAnnotation() public method

public appendAnnotation ( string annotation ) : int
annotation	string
return	int

appendNotes() public method

public appendNotes ( XMLNode notes ) : int
notes	XMLNode
return	int

appendNotes() public method

public appendNotes ( string notes ) : int
notes	string
return	int

checkCompatibility() public method

public checkCompatibility ( SBase arg0 ) : int
arg0	SBase
return	int

checkMathMLNamespace() public method

public checkMathMLNamespace ( XMLToken elem ) : string
elem	XMLToken
return	string

clone() public method

public clone ( ) : SBase
return	SBase

connectToChild() public method

public connectToChild ( ) : void
return	void

connectToParent() public method

public connectToParent ( SBase parent ) : void
parent	SBase
return	void

containsUndeclaredUnits() public method

public containsUndeclaredUnits ( ) : bool
return	bool

deleteDisabledPlugins() public method

public deleteDisabledPlugins ( ) : void
return	void

deleteDisabledPlugins() public method

public deleteDisabledPlugins ( bool recursive ) : void
recursive	bool
return	void

disablePackage() public method

public disablePackage ( string pkgURI, string pkgPrefix ) : int
pkgURI	string
pkgPrefix	string
return	int

divideAssignmentsToSIdByFunction() public method

public divideAssignmentsToSIdByFunction ( string id, ASTNode function ) : void
id	string
function	ASTNode
return	void

enablePackage() public method

public enablePackage ( string pkgURI, string pkgPrefix, bool flag ) : int
pkgURI	string
pkgPrefix	string
flag	bool
return	int

enablePackageInternal() public method

public enablePackageInternal ( string pkgURI, string pkgPrefix, bool flag ) : void
pkgURI	string
pkgPrefix	string
flag	bool
return	void

getAncestorOfType() public method

public getAncestorOfType ( int type ) : SBase
type	int
return	SBase

getAncestorOfType() public method

public getAncestorOfType ( int type, string pkgName ) : SBase
type	int
pkgName	string
return	SBase

getAnnotation() public method

public getAnnotation ( ) : XMLNode
return	XMLNode

getAnnotationString() public method

public getAnnotationString ( ) : string
return	string

getCVTerm() public method

public getCVTerm ( long n ) : CVTerm
n	long
return	CVTerm

getCVTerms() public method

public getCVTerms ( ) : CVTermList
return	CVTermList

getColumn() public method

public getColumn ( ) : long
return	long

getDerivedUnitDefinition() public method

public getDerivedUnitDefinition ( ) : UnitDefinition
return	UnitDefinition

getDisabledPlugin() public method

public getDisabledPlugin ( long n ) : SBasePlugin
n	long
return	SBasePlugin

getElementByMetaId() public method

public getElementByMetaId ( string metaid ) : SBase
metaid	string
return	SBase

getElementBySId() public method

public getElementBySId ( string id ) : SBase
id	string
return	SBase

getElementFromPluginsByMetaId() public method

public getElementFromPluginsByMetaId ( string metaid ) : SBase
metaid	string
return	SBase

getElementFromPluginsBySId() public method

public getElementFromPluginsBySId ( string id ) : SBase
id	string
return	SBase

getElementName() public method

public getElementName ( ) : string
return	string

getId() public method

public getId ( ) : string
return	string

getLevel() public method

public getLevel ( ) : long
return	long

getLine() public method

public getLine ( ) : long
return	long

getListOfAllElements() public method

public getListOfAllElements ( ) : SBaseList
return	SBaseList

getListOfAllElements() public method

public getListOfAllElements ( ElementFilter filter ) : SBaseList
filter	ElementFilter
return	SBaseList

getListOfAllElementsFromPlugins() public method

public getListOfAllElementsFromPlugins ( ) : SBaseList
return	SBaseList

getListOfAllElementsFromPlugins() public method

public getListOfAllElementsFromPlugins ( ElementFilter filter ) : SBaseList
filter	ElementFilter
return	SBaseList

getMetaId() public method

public getMetaId ( ) : string
return	string

getModel() public method

public getModel ( ) : Model
return	Model

getModelHistory() public method

public getModelHistory ( ) : ModelHistory
return	ModelHistory

getName() public method

public getName ( ) : string
return	string

getNamespaces() public method

public getNamespaces ( ) : XMLNamespaces
return	XMLNamespaces

getNotes() public method

public getNotes ( ) : XMLNode
return	XMLNode

getNotesString() public method

public getNotesString ( ) : string
return	string

getNumCVTerms() public method

public getNumCVTerms ( ) : long
return	long

getNumDisabledPlugins() public method

public getNumDisabledPlugins ( ) : long
return	long

getNumPlugins() public method

public getNumPlugins ( ) : long
return	long

getPackageName() public method

public getPackageName ( ) : string
return	string

getPackageVersion() public method

public getPackageVersion ( ) : long
return	long

getParentSBMLObject() public method

public getParentSBMLObject ( ) : SBase
return	SBase

getPlugin() public method

public getPlugin ( long n ) : SBasePlugin
n	long
return	SBasePlugin

getPlugin() public method

public getPlugin ( string package ) : SBasePlugin
package	string
return	SBasePlugin

getPrefix() public method

public getPrefix ( ) : string
return	string

getResourceBiologicalQualifier() public method

public getResourceBiologicalQualifier ( string resource ) : int
resource	string
return	int

getResourceModelQualifier() public method

public getResourceModelQualifier ( string resource ) : int
resource	string
return	int

getSBMLDocument() public method

public getSBMLDocument ( ) : SBMLDocument
return	SBMLDocument

getSBMLNamespaces() public method

public getSBMLNamespaces ( ) : SBMLNamespaces
return	SBMLNamespaces

getSBOTerm() public method

public getSBOTerm ( ) : int
return	int

getSBOTermAsURL() public method

public getSBOTermAsURL ( ) : string
return	string

getSBOTermID() public method

public getSBOTermID ( ) : string
return	string

getTypeCode() public method

public getTypeCode ( ) : int
return	int

getURI() public method

public getURI ( ) : string
return	string

getVersion() public method

public getVersion ( ) : long
return	long

hasNonstandardIdentifierBeginningWith() public method

public hasNonstandardIdentifierBeginningWith ( string prefix ) : bool
prefix	string
return	bool

hasRequiredAttributes() public method

public hasRequiredAttributes ( ) : bool
return	bool

hasRequiredElements() public method

public hasRequiredElements ( ) : bool
return	bool

hasValidLevelVersionNamespaceCombination() public method

public hasValidLevelVersionNamespaceCombination ( ) : bool
return	bool

isPackageEnabled() public method

public isPackageEnabled ( string pkgName ) : bool
pkgName	string
return	bool

isPackageURIEnabled() public method

public isPackageURIEnabled ( string pkgURI ) : bool
pkgURI	string
return	bool

isPkgEnabled() public method

public isPkgEnabled ( string pkgName ) : bool
pkgName	string
return	bool

isPkgURIEnabled() public method

public isPkgURIEnabled ( string pkgURI ) : bool
pkgURI	string
return	bool

isSetAnnotation() public method

public isSetAnnotation ( ) : bool
return	bool

isSetId() public method

public isSetId ( ) : bool
return	bool

isSetMetaId() public method

public isSetMetaId ( ) : bool
return	bool

isSetModelHistory() public method

public isSetModelHistory ( ) : bool
return	bool

isSetName() public method

public isSetName ( ) : bool
return	bool

isSetNotes() public method

public isSetNotes ( ) : bool
return	bool

isSetSBOTerm() public method

public isSetSBOTerm ( ) : bool
return	bool

isSetUserData() public method

public isSetUserData ( ) : bool
return	bool

matchesRequiredSBMLNamespacesForAddition() public method

public matchesRequiredSBMLNamespacesForAddition ( SBase sb ) : bool
sb	SBase
return	bool

matchesSBMLNamespaces() public method

public matchesSBMLNamespaces ( SBase sb ) : bool
sb	SBase
return	bool

multiplyAssignmentsToSIdByFunction() public method

public multiplyAssignmentsToSIdByFunction ( string id, ASTNode function ) : void
id	string
function	ASTNode
return	void

operator() public static method

public static operator ( ) : bool
return	bool

prependStringToAllIdentifiers() public method

public prependStringToAllIdentifiers ( string prefix ) : int
prefix	string
return	int

removeFromParentAndDelete() public method

public removeFromParentAndDelete ( ) : int
return	int

removeTopLevelAnnotationElement() public method

public removeTopLevelAnnotationElement ( string elementName ) : int
elementName	string
return	int

removeTopLevelAnnotationElement() public method

public removeTopLevelAnnotationElement ( string elementName, string elementURI ) : int
elementName	string
elementURI	string
return	int

removeTopLevelAnnotationElement() public method

public removeTopLevelAnnotationElement ( string elementName, string elementURI, bool removeEmpty ) : int
elementName	string
elementURI	string
removeEmpty	bool
return	int

renameMetaIdRefs() public method

public renameMetaIdRefs ( string oldid, string newid ) : void
oldid	string
newid	string
return	void

renameSIdRefs() public method

public renameSIdRefs ( string oldid, string newid ) : void
oldid	string
newid	string
return	void

renameUnitSIdRefs() public method

public renameUnitSIdRefs ( string oldid, string newid ) : void
oldid	string
newid	string
return	void

replaceSIDWithFunction() public method

public replaceSIDWithFunction ( string id, ASTNode function ) : void
id	string
function	ASTNode
return	void

replaceTopLevelAnnotationElement() public method

public replaceTopLevelAnnotationElement ( XMLNode annotation ) : int
annotation	XMLNode
return	int

replaceTopLevelAnnotationElement() public method

public replaceTopLevelAnnotationElement ( string annotation ) : int
annotation	string
return	int

setAnnotation() public method

public setAnnotation ( XMLNode annotation ) : int
annotation	XMLNode
return	int

setAnnotation() public method

public setAnnotation ( string annotation ) : int
annotation	string
return	int

setId() public method

public setId ( string sid ) : int
sid	string
return	int

setMetaId() public method

public setMetaId ( string metaid ) : int
metaid	string
return	int

setModelHistory() public method

public setModelHistory ( ModelHistory history ) : int
history	ModelHistory
return	int

setName() public method

public setName ( string name ) : int
name	string
return	int

setNamespaces() public method

public setNamespaces ( XMLNamespaces xmlns ) : int
xmlns	XMLNamespaces
return	int

setNotes() public method

public setNotes ( XMLNode notes ) : int
notes	XMLNode
return	int

setNotes() public method

public setNotes ( string notes ) : int
notes	string
return	int

setNotes() public method

public setNotes ( string notes, bool addXHTMLMarkup ) : int
notes	string
addXHTMLMarkup	bool
return	int

setSBMLNamespacesAndOwn() public method

public setSBMLNamespacesAndOwn ( SBMLNamespaces disownedNs ) : void
disownedNs	SBMLNamespaces
return	void

setSBOTerm() public method

public setSBOTerm ( int value ) : int
value	int
return	int

setSBOTerm() public method

public setSBOTerm ( string sboid ) : int
sboid	string
return	int

toSBML() public method

public toSBML ( ) : string
return	string

toXMLNode() public method

public toXMLNode ( ) : XMLNode
return	XMLNode

transformIdentifiers() public method

public transformIdentifiers ( IdentifierTransformer idTransformer ) : int
idTransformer	IdentifierTransformer
return	int

unsetAnnotation() public method

public unsetAnnotation ( ) : int
return	int

unsetCVTerms() public method

public unsetCVTerms ( ) : int
return	int

unsetId() public method

public unsetId ( ) : int
return	int

unsetMetaId() public method

public unsetMetaId ( ) : int
return	int

unsetModelHistory() public method

public unsetModelHistory ( ) : int
return	int

unsetName() public method

public unsetName ( ) : int
return	int

unsetNotes() public method

public unsetNotes ( ) : int
return	int

unsetSBOTerm() public method

public unsetSBOTerm ( ) : int
return	int

unsetUserData() public method

public unsetUserData ( ) : int
return	int

writeExtensionElements() public method

public writeExtensionElements ( XMLOutputStream stream ) : void
stream	XMLOutputStream
return	void

Property Details

swigCMemOwn protected property

protected bool swigCMemOwn
return	bool