0.1.3The API contains two other submodules: libsbgn.render and libsbgn.annot
Represents the <arc> element.
Represents the <arcgroup> element.
Extends SBGNBase
Represents the <bbox> element.
Extends SBGNBase
Represents the <callout> element.
Represents the <clone> element.
Represents the <end> element.
Represents the <entity> element.
Represents the <extension> element.
Represents the <glyph> element.
Extends SBGNBase
(Object)
| Name | Description |
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params.id string?
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params.class_ string?
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params.compartmentRef string?
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params.compartmentOrder (string | number)?
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params.mapRef string?
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params.tagRef string?
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params.orientation string?
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params.label Label?
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params.bbox Bbox?
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params.state State?
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params.clone Clone?
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params.callout Callout?
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params.entity Entity?
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params.glyphMembers Array<Glyph>?
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params.ports Array<Port>?
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Represents the <label> element.
Extends SBGNBase
Represents the <map> element.
Extends SBGNBase
Represents the <next> element.
Represents the <notes> element.
Its single content attribute stores xhtml elements as string.
Represents the <point> element.
Represents the <port> element.
Represents the <sbgn> element.
Extends SBGNBase
Parent class for several sbgn elements. Used to provide extension and notes element. End users don't need to interact with it. It can be safely ignored.
Represents the <start> element.
Represents the <state> element.
This submodule contains the classes to manage the render extension's xml and some utility functions. It adds the ability to save the styles and colors used in an SBGN map, as features like background-color, border thickness or font properties are not part of the SBGN standard.
It is loosely based on the render extension of the SBML format. A subset of this specification has been adapted for SBGN-ML integration.
See Extension for more general information on extensions in the SBGN-ML format.
You can access the following classes like this: libsbgn.render.ColorDefinition
Represents the <colorDefinition> element.
(String)
ColorDefinition:
(Object)
xml2js formatted object
ColorDefinition:
Represents the <listOfColorDefinitions> element.
(String)
ListOfColorDefinitions:
(Object)
xml2js formatted object
ListOfColorDefinitions:
(ColorDefinition)
Represents the <listOfStyles> element.
(String)
ListOfStyles:
(Object)
xml2js formatted object
ListOfStyles:
Convenience function returning a map of ids to their respective RenderGroup object, for all the styles. The style properties can then be directly accessed. Example: map[id].stroke
Object<string, RenderGroup>:
Represents the <g> element.
(Object)
| Name | Description |
|---|---|
params.id string?
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params.fontSize string?
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params.fontFamily string?
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params.fontWeight string?
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params.fontStyle string?
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params.textAnchor string?
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params.vtextAnchor string?
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params.fill string?
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The element's background color |
params.stroke string?
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Border color for glyphs, line color for arcs. |
params.strokeWidth string?
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(String)
RenderGroup:
(Object)
xml2js formatted object
RenderGroup:
Represents the <renderInformation> element.
(Object)
| Name | Description |
|---|---|
params.id string?
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params.name string?
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params.programName string?
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params.programVersion string?
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params.backgroundColor string?
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params.listOfColorDefinitions ListOfColorDefinitions?
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params.listOfStyles ListOfStyles?
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(String)
RenderInformation:
(Object)
xml2js formatted object
RenderInformation:
(ListOfColorDefinitions)
(ListOfStyles)
Represents the <style> element.
(Object)
| Name | Description |
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params.id string?
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params.name string?
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params.idList string?
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params.renderGroup RenderGroup?
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(RenderGroup)
Convenience function returning a map of ids to their respective RenderGroup object. The style properties can then be directly accessed. Example: map[id].stroke
Object<string, RenderGroup>:
This submodule manages the annotations extension. It adds the ability to save semantic data into SBGN-ML in the form of RDF elements. Any SBGN element that can host an extension tag can also get RDF annotations. This means that almost every element can get annotated.
The annotations here are intended to be used in two ways:
The formal way of using annotations is to use specific vocabulary with specific identifiers to provide additional information that can not be conveyed otherwise through the SBGN format. See --link to combine qualifiers-- and --link to identifiers.org and MIRIAM--- This was also based on the annotation extension of SBML --link to annotation proposal for SBML--
See Extension for more general information on extensions in the SBGN-ML format.
You can access the following classes like this: libsbgn.annot.Annotation
Represents the <annotation> element.
(Object)
| Name | Description |
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params.rdfElement RdfElement?
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(RdfElement)
Represents the <rd:RDFf> element.
(any)
(any)
(Element)
RdfElement:
will add triples to represent key/value properties attached to the id kvObject can have one or multiple properties
(any)
(any)
(any)
returns the id of a newly created blank node representing the HasProperty predicate if one already exists, returns its id returns array, potentially several SIO223 present
(any)
(any)
(any)
kvobject contains biology qualifier as key and miriam resource as value
(any)
(any)
(any)