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nfevent.schema.json
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nfevent.schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/RuleWorld/nfsim/ASinanSaglam/issue35/nf.schema.json",
"title": "NFsim simulation",
"description": "Output from a NFsim simulation",
"type": "object",
"properties": {
"simulation": {
"type": "object",
"properties": {
"info": {
"description": "Information regarding the simulation",
"type": "object",
"properties": {
"name": {
"description": "Name of our simulation",
"type": "string"
},
"global_molecule_limit": {
"description": "Number of global molecules allowed for the simulation",
"type": "number"
},
"number_of_molecule_types": {
"description": "Number of total molecule types defined",
"type": "number"
},
"number_of_molecules": {
"description": "Number of total starting molecules",
"type": "number"
}
},
"required": [ "name" ]
},
"molecule_types": {
"description": "Molecule types in a simulation",
"type": "array",
"items": { "$ref": "#/$defs/molecule_type" },
"minItems": 1,
"uniqueItems": true
},
"initialState": {
"description": "Initial state of the simulation",
"type": "object",
"properties": {
"molTypes": {
"description": "A run-length encoded array of molecule type IDs for the starting state",
"type": "array",
"items": { "$ref": "#/$defs/molType" },
"minItems": 0,
"uniqueItems": false
},
"ops": {
"description": "A set of operations that need to be performed on the initial molecules to get the inital state",
"type": "array",
"items": { "$ref": "#/$defs/operation" },
"minItems": 0,
"uniqueItems": false
}
},
"required": [ "molTypes", "ops" ]
},
"firings": {
"description": "All firings in the simulation",
"type": "array",
"items": { "$ref": "#/$defs/firing" },
"minItems": 0,
"uniqueItems": false
}
},
"required": [ "info", "molecule_types", "initialState", "firings" ]
}
},
"$defs": {
"molecule_type": {
"description": "Description of each molecule type, their names, IDs and components",
"type": "object",
"properties": {
"name": {
"description": "Name of the molecule type",
"type": "string"
},
"typeID": {
"description": "Internal ID used for the molecule type, every operation refers to this ID",
"type": "number"
},
"components": {
"description": "Names of each component for the molecule type",
"type": "array",
"items": { "type": "string" },
"minItems": 0
},
"componentStates": {
"description": "Names of each component states, by default the first state is used upon initialization",
"type": "array",
"minItems": 0,
"items": {
"type": "array",
"items": { "type": "string" },
"minItems": 0
}
}
},
"required": [ "name", "typeID", "components", "componentStates" ]
},
"molecule_array": {
"description": "This is an item in a run-length encoded array, first item is the molecule type index, second item is how many times it repeats",
"type": "array",
"prefixItems": [
{"type": "number"},
{"type": "number"}
],
"items": false,
"uniqueItems": false
},
"operation": {
"description": "Array fully describing an operation and what it operates on. Each operation has different inputs.",
"type": "array",
"prefixItems": [
{"enum": ["Add", "Delete", "StateChange", "AddBond", "DeleteBond", "IncrementState", "DecrementState", "DecrementPopulation"] },
{"type": "number"}
],
"items": { "type": "number" },
"minItems": 2,
"maxItems": 5,
"uniqueItems": false
},
"firing": {
"description": "Full description of a single event in the simulation.",
"type": "object",
"properties": {
"props": {
"description": "The name of the reaction that fired, the global event number followed by the internal time it happened",
"type": "array",
"prefixItems": [
{"type": "string"},
{"type": "number"},
{"type": "number"}
],
"items": false,
"uniqueItems": false
},
"ops": {
"description": "The set of operations that occured during the event.",
"type": "array",
"items": { "$ref": "#/$defs/operation" }
}
},
"required": [ "props", "ops" ]
}
}
}