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libSBML C# API
5.18.0
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libSBML C# API
5.18.0
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This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. It is a class used in the implementation of extra functionality provided by libSBML.
This converter takes a model in “fbc” Version 2 format and converts it to COBRA format.
FbcToCobraConverter is enabled by creating a ConversionProperties object with the option 'convert fbc to cobra' (literally that full string, including the spaces), and passing this properties object to SBMLDocument::convert(). The converter offers one option:
'overwriteReactionNotes': should gene associations be written into the 'notes' subelement attached to Reaction objects, even if a Reaction already has 'notes' content?The use of all the converters follows a similar approach. First, one creates a ConversionProperties object and calls ConversionProperties::addOption() on this object with one argument: a text string that identifies the desired converter. (The text string is specific to each converter; consult the documentation for a given converter to find out how it should be enabled.)
Next, for some converters, the caller can optionally set some converter-specific properties using additional calls to ConversionProperties::addOption(). Many converters provide the ability to configure their behavior to some extent; this is realized through the use of properties that offer different options. The default property values for each converter can be interrogated using the method SBMLConverter::getDefaultProperties() on the converter class in question .
Finally, the caller should invoke the method SBMLDocument::convert() with the ConversionProperties object as an argument.
The following code fragment illustrates an example using SBMLReactionConverter, which is invoked using the option string 'replaceReactions':
In the case of SBMLReactionConverter, there are no options to affect its behavior, so the next step is simply to invoke the converter on an SBMLDocument object. Continuing the example code:
Here is an example of using a converter that offers an option. The following code invokes SBMLStripPackageConverter to remove the SBML Level 3 Layout package from a model. It sets the name of the package to be removed by adding a value for the option named 'package' defined by that converter:
LibSBML provides a number of built-in converters; by convention, their names end in Converter. The following are the built-in converters provided by libSBML 5.18.0:
Public Member Functions | |
| new SBMLConverter | clone () |
| Creates and returns a deep copy of this FbcToCobraConverter object. More... | |
| new int | convert () |
| Perform the conversion. More... | |
| override void | Dispose () |
| FbcToCobraConverter () | |
| Creates a new FbcToCobraConverter object. More... | |
| FbcToCobraConverter (FbcToCobraConverter orig) | |
| Copy constructor; creates a copy of an FbcToCobraConverter object. More... | |
| new ConversionProperties | getDefaultProperties () |
| Returns the default properties of this converter. More... | |
| new SBMLDocument | getDocument () |
| Returns the SBML document that is the subject of the conversions. More... | |
| string | getName () |
| Returns the name of this converter. More... | |
| virtual ConversionProperties | getProperties () |
| Returns the current properties in effect for this converter. More... | |
| virtual SBMLNamespaces | getTargetNamespaces () |
| Returns the target SBML namespaces of the currently set properties. More... | |
| new bool | matchesProperties (ConversionProperties props) |
Returns true if this converter object's properties match the given properties. More... | |
| virtual int | setDocument (SBMLDocument doc) |
| Sets the SBML document to be converted. More... | |
| virtual int | setProperties (ConversionProperties props) |
| Sets the configuration properties to be used by this converter. More... | |
| delegate global::System.IntPtr | SwigDelegateSBMLConverter_0 () |
| delegate global::System.IntPtr | SwigDelegateSBMLConverter_1 () |
| delegate global::System.IntPtr | SwigDelegateSBMLConverter_2 () |
| delegate global::System.IntPtr | SwigDelegateSBMLConverter_3 () |
| delegate global::System.IntPtr | SwigDelegateSBMLConverter_4 () |
| delegate bool | SwigDelegateSBMLConverter_5 (global::System.IntPtr props) |
| delegate int | SwigDelegateSBMLConverter_6 (global::System.IntPtr doc) |
| delegate int | SwigDelegateSBMLConverter_7 (global::System.IntPtr props) |
| delegate global::System.IntPtr | SwigDelegateSBMLConverter_8 () |
| delegate int | SwigDelegateSBMLConverter_9 () |
Static Public Member Functions | |
| static void | init () |
Protected Attributes | |
| bool | swigCMemOwn |
| libsbmlcs.FbcToCobraConverter.FbcToCobraConverter | ( | ) |
Creates a new FbcToCobraConverter object.
| libsbmlcs.FbcToCobraConverter.FbcToCobraConverter | ( | FbcToCobraConverter | orig | ) |
Copy constructor; creates a copy of an FbcToCobraConverter object.
| orig | the FbcToCobraConverter object to copy. |
| new SBMLConverter libsbmlcs.FbcToCobraConverter.clone | ( | ) |
Creates and returns a deep copy of this FbcToCobraConverter object.
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Perform the conversion.
This method causes the converter to do the actual conversion work, that is, to convert the SBMLDocument object set by SBMLConverter::setDocument() and with the configuration options set by SBMLConverter::setProperties().
Reimplemented from libsbmlcs.SBMLConverter.
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Reimplemented from libsbmlcs.SBMLConverter.
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Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the default property settings for this converter. It is meant to be called in order to discover all the settings for the converter object.
Reimplemented from libsbmlcs.SBMLConverter.
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inherited |
Returns the SBML document that is the subject of the conversions.
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Returns the name of this converter.
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Returns the current properties in effect for this converter.
A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the current properties for this converter; in other words, the settings in effect at this moment. To change the property values, you can use SBMLConverter::setProperties(ConversionProperties props).
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Returns the target SBML namespaces of the currently set properties.
SBML namespaces are used by libSBML to express the Level+Version of the SBML document (and, possibly, any SBML Level 3 packages in use). Some converters' behavior is affected by the SBML namespace configured in the converter. For example, in SBMLLevelVersionConverter (the converter for converting SBML documents from one Level+Version combination to another), the actions are fundamentally dependent on the SBML namespaces targeted.
null if none are set.
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Returns true if this converter object's properties match the given properties.
A typical use of this method involves creating a ConversionProperties object, setting the options desired, and then calling this method on an FbcToCobraConverter object to find out if the object's property values match the given ones. This method is also used by SBMLConverterRegistry::getConverterFor() to search across all registered converters for one matching particular properties.
| props | the properties to match. |
true if this converter's properties match, false otherwise. Reimplemented from libsbmlcs.SBMLConverter.
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Sets the SBML document to be converted.
| doc | the document to use for this conversion. |
Reimplemented in libsbmlcs.SBMLReactionConverter.
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Sets the configuration properties to be used by this converter.
| props | the ConversionProperties object defining the properties to set. |
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