API reference

pd2af does one thing in three steps, and the package follows them: core checks the arguments and runs the transformation, asp asks clingo what the activities and influences are, and building turns the answer into a map.

Top level

• Core: the public transform() entry point and the TransformerResult it returns
• Modes: everything a user chooses from, the input languages, the layout modes, the influence pairings and the transformation modes
• CLI: command-line entry point

asp: the question asked to clingo

• Solver: build the clingo control, solve, and return the answer with the element registry
• Rules: the rule groups and the composition of a mode's ASP program
• Predicates: the clorm predicates the program and the builders share

building: turning the answer into a map

Shared by both output languages:

• Context: the slots the model pass fills and the layout pass reads back
• Model: the model pass steps that are the same for either language
• Layout: the layout helpers that are the same for either language, styling, arcs and dot
• Provenance: where each output element comes from, and the annotations and notes it inherits

CellDesigner output:

• CellDesigner model: build the AF model from the clingo atoms
• CellDesigner layout: build the AF layout, plain, overlay or dot

SBGN-AF output:

• SBGN-AF model: build the SBGN-AF model from the clingo atoms
• SBGN-AF layout: build the SBGN-AF layout, plain or dot
• SBGN-AF labels: build an SBGN-AF activity's label from an SBGN-PD entity pool