| Classes |
BIObject |
All object in the BioInfer hierarchy inherit from
BIObject. |
BioInfer |
The top-level class in the hierarchy of objects which represents the
corpus. |
BIXMLWriteable |
Definition of methods and variables for XML output. |
Entity |
The representation of Entity as a list of subtokens. |
EntityNesting |
This class is only used during the XML parsing and it corresponds to
the entitynesting tag and mediates the inclusion of entities into
other entities to represent entity nesting. |
EntityNode |
A formula node which represents an entity argument. |
Formula |
The representation of a single relationship formula. |
FormulaNode |
The base class from which formula nodes are inherited. |
Formulas |
This class is only used during the XML parsing and it corresponds to
the formulas tag and mediates the inclusion of formulas into
sentences. |
Link |
The representation of a link in a linkage. |
Linkage |
A representation of a single linkage as a collection of links between
tokens. |
Linkages |
This class is only used during the XML parsing and it corresponds to
the linkages tag and mediates the inclusion of linkages into the
sentence instances. |
NestedSubtoken |
This class is only used during the XML parsing and it corresponds to
the nestedsubtoken tag and mediates the inclusion of subtokens
into entities. |
RelNode |
A formula node which represents a relationship among its
arguments. |
Sentence |
Sentence holds all annotation for a single sentence:
entities, formulas, and linkages. |
Sentences |
Sentences holds the sentences of the corpus. |
SubToken |
The representation of a subToken. |
Token |
The representation of a single token as collection of subtokens. |