{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://abdenlab.github.io/lefsim/schemas/model.v2.json",
  "title": "lefsim model",
  "description": "A lefsim model, version 2: a lattice with CTCFs, the LEFs on it, their rates and a spawn rule. Loading also runs the checks a schema can't express, such as CTCF sites and leg positions lying inside the lattice.",
  "type": "object",
  "properties": {
    "format": { "const": "lefsim.model" },
    "version": { "const": 2 },
    "lattice": { "$ref": "#/$defs/lattice" },
    "lefs": {
      "description": "One entry per LEF; LEF i is entry i.",
      "type": "array",
      "items": { "$ref": "#/$defs/lef" }
    },
    "rates": { "$ref": "#/$defs/rates" },
    "spawn": { "$ref": "#/$defs/spawn" }
  },
  "required": ["format", "version", "lattice", "lefs", "rates", "spawn"],
  "additionalProperties": false,
  "$defs": {
    "position": {
      "description": "A site index, from 0 to n_sites - 1.",
      "type": "integer",
      "minimum": 0,
      "maximum": 4294967295
    },
    "mobility": {
      "description": "A leg's intrinsic mobility. Whether it's blocked is derived, not stored.",
      "enum": ["moving", "captured"]
    },
    "lattice": {
      "type": "object",
      "properties": {
        "n_sites": { "type": "integer", "minimum": 1, "maximum": 4294967295 },
        "ctcfs": {
          "description": "At most one CTCF per site. Defaults to none.",
          "type": "array",
          "items": { "$ref": "#/$defs/ctcf" }
        }
      },
      "required": ["n_sites"],
      "additionalProperties": false
    },
    "ctcf": {
      "type": "object",
      "properties": {
        "site": { "$ref": "#/$defs/position" },
        "captures_from": {
          "description": "The CTCF's capture side. Legs arriving from the other side may be evicted.",
          "enum": ["left", "right"]
        },
        "strength": {
          "description": "The probability p of capture from the capture side, or eviction from the other side.",
          "type": "number",
          "minimum": 0,
          "maximum": 1
        }
      },
      "required": ["site", "captures_from", "strength"],
      "additionalProperties": false
    },
    "lef": {
      "description": "left_pos <= right_pos. A LEF's two legs may share a site; two LEFs may not. A captured leg sits on a CTCF that captures from the side it arrived from: right for a left leg, left for a right leg.",
      "type": "object",
      "properties": {
        "left_pos": { "$ref": "#/$defs/position" },
        "right_pos": { "$ref": "#/$defs/position" },
        "left_mobility": { "$ref": "#/$defs/mobility", "default": "moving" },
        "right_mobility": { "$ref": "#/$defs/mobility", "default": "moving" }
      },
      "required": ["left_pos", "right_pos"],
      "additionalProperties": false
    },
    "rate": {
      "description": "Events per unit time, positive and finite.",
      "type": "number",
      "exclusiveMinimum": 0
    },
    "rates": {
      "type": "object",
      "properties": {
        "step": { "$ref": "#/$defs/rate", "description": "A leg's step rate." },
        "respawn": { "$ref": "#/$defs/rate", "description": "The basal unloading rate." },
        "respawn_blocked": { "$ref": "#/$defs/rate", "description": "The unloading rate while either leg is blocked." },
        "respawn_captured": { "$ref": "#/$defs/rate", "description": "The unloading rate while either leg is captured; it takes precedence over respawn_blocked." }
      },
      "required": ["step", "respawn", "respawn_blocked", "respawn_captured"],
      "additionalProperties": false
    },
    "spawn": {
      "description": "Where an unloaded LEF binds again.",
      "type": "object",
      "properties": {
        "rule": {
          "description": "uniform_non_ctcf: a uniformly random site that isn't a CTCF and isn't occupied, with both legs on it. It needs at least 2n - 1 non-CTCF sites for n LEFs.",
          "enum": ["uniform_non_ctcf"]
        }
      },
      "required": ["rule"]
    }
  }
}