libSBML C# API
5.18.0
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Public Member Functions | |
int | addLayout (Layout layout) |
Adds a copy of the layout object to the list of layouts. More... | |
int | appendFrom (Model model) |
new SBasePlugin | clone () |
Creates and returns a deep copy of this LayoutModelPlugin object. More... | |
Layout | createLayout () |
Creates a new layout object and adds it to the list of layout objects and returns it. More... | |
override void | Dispose () |
long | getColumn () |
new SBase | getElementByMetaId (string metaid) |
Return the first child object found with a given meta identifier. More... | |
new SBase | getElementBySId (string id) |
Return the first child object found with a given identifier. More... | |
string | getElementNamespace () |
Returns the namespace URI of the package to which this plugin object belongs. More... | |
Layout | getLayout (long index) |
Returns the layout object that belongs to the given index. More... | |
Layout | getLayout (string sid) |
Returns the layout object with the given sid attribute. More... | |
long | getLevel () |
Returns the SBML Level of the package extension of this plugin object. More... | |
long | getLine () |
SBaseList | getListOfAllElements (ElementFilter filter) |
SBaseList | getListOfAllElements () |
ListOfLayouts | getListOfLayouts () |
Returns the ListOfLayouts object for this Model. More... | |
int | getNumLayouts () |
Returns the number of layout objects. More... | |
string | getPackageName () |
Returns the short-form name of the package to which this plugin object belongs. More... | |
long | getPackageVersion () |
Returns the package version of the package extension of this plugin object. More... | |
SBase | getParentSBMLObject () |
Returns the parent object to which this plugin object is connected. More... | |
string | getPrefix () |
Returns the XML namespace prefix of the package to which this plugin object belongs. More... | |
SBMLDocument | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLExtension | getSBMLExtension () |
string | getURI () |
Returns the XML namespace URI for the package to which this object belongs. More... | |
long | getVersion () |
Returns the Version within the SBML Level of the package extension of this plugin object. More... | |
new bool | isValidTypeForList (SBase item) |
LayoutModelPlugin (string uri, string prefix, LayoutPkgNamespaces layoutns) | |
Creates a new LayoutModelPlugin object using the given parameters. More... | |
LayoutModelPlugin (LayoutModelPlugin orig) | |
Copy constructor. More... | |
Layout | removeLayout (long n) |
Removes the nth Layout object from this Model object and returns a pointer to it. More... | |
new void | renameMetaIdRefs (string oldid, string newid) |
Replaces all uses of a given meta identifier attribute value with another value. More... | |
new void | renameSIdRefs (string oldid, string newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
new void | renameUnitSIdRefs (string oldid, string newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
int | setElementNamespace (string uri) |
Sets the XML namespace to which this object belongs. More... | |
Protected Attributes | |
bool | swigCMemOwn |
libsbmlcs.LayoutModelPlugin.LayoutModelPlugin | ( | string | uri, |
string | prefix, | ||
LayoutPkgNamespaces | layoutns | ||
) |
Creates a new LayoutModelPlugin object using the given parameters.
In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
uri | the URI of the SBML Level 3 package implemented by this libSBML package extension. |
prefix | the XML namespace prefix being used for the package. |
layoutns | the namespaces object for the package. |
libsbmlcs.LayoutModelPlugin.LayoutModelPlugin | ( | LayoutModelPlugin | orig | ) |
int libsbmlcs.LayoutModelPlugin.addLayout | ( | Layout | layout | ) |
Adds a copy of the layout object to the list of layouts.
layout | the layout object to be added. |
int libsbmlcs.LayoutModelPlugin.appendFrom | ( | Model | model | ) |
new SBasePlugin libsbmlcs.LayoutModelPlugin.clone | ( | ) |
Creates and returns a deep copy of this LayoutModelPlugin object.
Layout libsbmlcs.LayoutModelPlugin.createLayout | ( | ) |
Creates a new layout object and adds it to the list of layout objects and returns it.
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virtual |
Reimplemented from libsbmlcs.SBasePlugin.
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inherited |
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inherited |
Return the first child object found with a given meta identifier.
This method searches all the subobjects under this one, compares their meta identifiers to metaid
, and returns the first one that machines.
metaid | string, the metaid of the object to find. |
metaid
.
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inherited |
Return the first child object found with a given identifier.
This method searches all the subobjects under this one, compares their identifiers to id
, and returns the first one that machines.
Normally, SId
type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.
id | string representing the identifier of the object to find. |
id
.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
Layout libsbmlcs.LayoutModelPlugin.getLayout | ( | long | index | ) |
Returns the layout object that belongs to the given index.
If the index is invalid, null
is returned.
index | the index of list of layout objects. |
Layout libsbmlcs.LayoutModelPlugin.getLayout | ( | string | sid | ) |
Returns the layout object with the given sid
attribute.
If the id is invalid, null
is returned.
sid | the id attribute of the layout object. |
sid
attribute. null is returned if the given sid
is invalid.
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inherited |
Returns the SBML Level of the package extension of this plugin object.
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inherited |
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inherited |
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inherited |
ListOfLayouts libsbmlcs.LayoutModelPlugin.getListOfLayouts | ( | ) |
Returns the ListOfLayouts object for this Model.
int libsbmlcs.LayoutModelPlugin.getNumLayouts | ( | ) |
Returns the number of layout objects.
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inherited |
Returns the short-form name of the package to which this plugin object belongs.
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inherited |
Returns the package version of the package extension of this plugin object.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
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inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
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inherited |
Returns the XML namespace URI for the package to which this object belongs.
In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
.
This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().
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inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
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inherited |
Layout libsbmlcs.LayoutModelPlugin.removeLayout | ( | long | n | ) |
Removes the nth Layout object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Layout object to remove. |
null
is returned if the given index is out of range.
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inherited |
Replaces all uses of a given meta identifier attribute value with another value.
In SBML, object 'meta' identifiers are of the XML data type ID
; the SBML object attribute itself is typically named metaid
. All attributes that hold values referring to values of type ID
are of the XML data type IDREF
. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef
.
This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier. |
newid | the new identifier. |
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inherited |
Replaces all uses of a given SIdRef
type attribute value with another value.
In SBML, object identifiers are of a data type called SId
. In SBML Level 3, an explicit data type called SIdRef
was introduced for attribute values that refer to SId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRef
in Level 3. These and other methods of libSBML refer to the type SIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid
. If any matches are found, the matching values are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier. |
newid | the new identifier. |
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inherited |
Replaces all uses of a given UnitSIdRef
type attribute value with another value.
In SBML, unit definitions have identifiers of type UnitSId
. In SBML Level 3, an explicit data type called UnitSIdRef
was introduced for attribute values that refer to UnitSId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef
in Level 3. These and other methods of libSBML refer to the type UnitSIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid
. If any matches are found, the matching values are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier. |
newid | the new identifier. |
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inherited |
Sets the XML namespace to which this object belongs.
In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'
. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
.
uri | the URI to assign to this object. |
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protectedinherited |