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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,260 @@ | ||
| // const multipipe = require('multipipe') | ||
| // | ||
| // const Reader = require('./reader') | ||
| // const Builder = require('./builder') | ||
| // | ||
| // const {isObj, entries} = require('./util') | ||
| // | ||
| // const cons = ({}).constructor | ||
| // | ||
| // const clonable = ['ATP', 'ADP', 'NAD', 'NADH', 'NADP', 'NADPH', 'P', 'O2', 'H2O'] | ||
| // | ||
| // function revive (o) { | ||
| // const m = new WeakMap() | ||
| // const set = (k, v) => { m.set(k, v); return v } | ||
| // function rev (o) { | ||
| // const x = m.get(o) | ||
| // if (x) return x | ||
| // if (isArr(o)) return set(o, o.map(rev)) | ||
| // if (isObj(o)) { | ||
| // if (o.$constructor && o.constructor === cons) { | ||
| // const v = Object.create(module.exports[o.$constructor].prototype) | ||
| // set(o, v) | ||
| // for (let [k, v] of entries(o)) o[k] = rev(v) | ||
| // assign(v, o) | ||
| // return v | ||
| // } else { | ||
| // for (let [k, v] of entries(o)) o[k] = rev(v) | ||
| // set(o, o) | ||
| // return o | ||
| // } | ||
| // } | ||
| // return o | ||
| // } | ||
| // return rev(o) | ||
| // } | ||
| // | ||
| // function create (attributes) { | ||
| // switch (attributes.$name) { | ||
| // case 'model': return new Model(attributes) | ||
| // case 'unitDefinition': return new Unit(attributes) | ||
| // case 'compartment': return new Compartment(attributes) | ||
| // case 'species': return new Species(attributes) | ||
| // case 'reaction': return new Reaction(attributes) | ||
| // case 'speciesReference': return new SpeciesReference(attributes) | ||
| // case 'modifierSpeciesReference': return new ModifierSpeciesReference(attributes) | ||
| // default: return attributes | ||
| // } | ||
| // } | ||
| // | ||
| // class Clazz { | ||
| // constructor (attr) { | ||
| // assign(this, attr, { $constructor: this.constructor.name }) | ||
| // } | ||
| // } | ||
| // | ||
| // class Entity extends Clazz { | ||
| // get label () { return this.id } | ||
| // } | ||
| // | ||
| // class Shape extends Clazz { | ||
| // constructor (attr) { | ||
| // super(assign({x: 0, y: 0, X: 0, Y: 0}, attr)) | ||
| // } | ||
| // } | ||
| // | ||
| // class Rect extends Shape { | ||
| // constructor (attr) { | ||
| // super(assign({shape: 'rect'}, attr)) | ||
| // } | ||
| // get rx () { return 0 } | ||
| // get ry () { return 0 } | ||
| // } | ||
| // | ||
| // class Group extends Rect { | ||
| // constructor (compartment) { | ||
| // super({ compartment, leaves: [], groups: [] }) | ||
| // } | ||
| // get id () { return this.compartment.id } | ||
| // get label () { return this.compartment.id } | ||
| // get className () { return `group compartment ${this.id}` } | ||
| // get rx () { return 8 } | ||
| // get ry () { return 8 } | ||
| // } | ||
| // | ||
| // class Transform extends Rect { | ||
| // constructor (reaction) { super({ reaction, leaves: [], groups: [] }) } | ||
| // get id () { return this.reaction.id } | ||
| // get label () { return this.reaction.id } | ||
| // get className () { return `node reaction ${this.id}` } | ||
| // get rx () { return 2 } | ||
| // get ry () { return 2 } | ||
| // } | ||
| // | ||
| // class Pool extends Entity { | ||
| // constructor (species) { super({species, refs: [], clones: []}) } | ||
| // get id () { return this.species.id } | ||
| // addClone () { let c = new PoolClone(this); this.clones.push(c); return c } | ||
| // getClone () { | ||
| // if (clonable.indexOf(this.id) !== -1) return this.addClone() | ||
| // if (this.clones.length < 1) return this.addClone() | ||
| // return this.clones[0] | ||
| // } | ||
| // } | ||
| // | ||
| // class PoolClone extends Rect { | ||
| // constructor (pool) { super({pool}) } | ||
| // get id () { return this.pool.species.id } | ||
| // get label () { return this.pool.species.id } | ||
| // get className () { return `node pool ${this.id} ${this.pool.clones.length > 1 ? 'clone' : ''}` } | ||
| // get rx () { return this.innerBounds.height() / 2 } | ||
| // get ry () { return this.innerBounds.height() / 2 } | ||
| // } | ||
| // | ||
| // class Graph extends Entity { | ||
| // constructor (attr) { | ||
| // super(assign({nodes: [], links: [], groups: [], constraints: []}, attr)) | ||
| // } | ||
| // } | ||
| // | ||
| // class Model extends Entity { | ||
| // constructor (attr) { | ||
| // super(assign({ | ||
| // graph: new Graph(), | ||
| // species: new Map(), | ||
| // reactions: new Map(), | ||
| // compartments: new Map() | ||
| // }, attr)) | ||
| // } | ||
| // | ||
| // addCompartment (x) { | ||
| // let c = new Compartment(x) | ||
| // let g = new Group(c) | ||
| // c.group = g | ||
| // c.model = this | ||
| // | ||
| // this.compartments.set(c.id, c) | ||
| // let i = g.nodeIndex = this.graph.groups.push(g) - 1 | ||
| // if (c.outside) { | ||
| // c.outside = this.compartments.get(c.outside) | ||
| // c.outside.group.groups.push(i) | ||
| // } | ||
| // return c | ||
| // } | ||
| // | ||
| // addSpecies (x) { | ||
| // let s = new Species(x) | ||
| // let p = new Pool(s) | ||
| // s.pool = p | ||
| // s.model = this | ||
| // | ||
| // this.species.set(s.id, s) | ||
| // s.compartment = this.compartments.get(s.compartment) | ||
| let i = p.nodeIndex = this.graph.nodes.push(p) - 1 | ||
| s.compartment.group.leaves.push(i) | ||
| // return s | ||
| // } | ||
| // | ||
| // addReaction (x) { | ||
| // let r = new Reaction(x) | ||
| // let t = new Transform(r) | ||
| // r.transform = t | ||
| // r.model = this | ||
| // | ||
| // this.reactions.set(r.id, r) | ||
| // t.nodeIndex = this.graph.nodes.push(t) - 1 | ||
| // return r | ||
| // } | ||
| // } | ||
| // | ||
| // class Link extends Entity { | ||
| // constructor (source, target, reversible = true) { super({source, target, reversible}) } | ||
| // get className () { return 'link' + (this.reversible ? ' reversible' : '') } | ||
| // } | ||
| // | ||
| // class ModifierLink extends Link { | ||
| // get className () { return 'link modifier' } | ||
| // } | ||
| // | ||
| // class Reaction extends Entity { | ||
| // constructor (attr) { super(assign({reversible: true, modifiers: [], reactants: [], products: []}, attr)) } | ||
| // get label () { return this.name } | ||
| // get compartment () { return this._compartment } | ||
| // set compartment (c) { | ||
| // if (this._compartment) { | ||
| todo remove from old compartment | ||
| // } | ||
| // this._compartment = c | ||
| // c.group.leaves.push(this.transform.nodeIndex) | ||
| // } | ||
| // | ||
| // _mkSpeciesRef (x) { | ||
| // let s = new SpeciesReference(x) | ||
| // s.species = this.model.species.get(s.species) | ||
| // s.species.pool.refs.push(s) | ||
| // if (!this.compartment) this.compartment = s.species.compartment | ||
| // return s | ||
| // } | ||
| // | ||
| // _getClone (s) { | ||
| // let c = s.species.pool.getClone() | ||
| // if (this.model.graph.nodes.indexOf(c) === -1) { | ||
| // c.nodeIndex = this.model.graph.nodes.push(c) - 1 | ||
| // this.compartment.group.leaves.push(c.nodeIndex) | ||
| // } | ||
| // return c | ||
| // } | ||
| // | ||
| // _addMod (x, arr, Cls) { | ||
| // const s = this._mkSpeciesRef(x) | ||
| // const c = this._getClone(s) | ||
| // arr.push(s) | ||
| // this.model.graph.links.push(new Cls(c, this.transform, this.reversible)) | ||
| // return s | ||
| // } | ||
| // | ||
| // addModifier (x) { | ||
| // return this._addMod(x, this.modifiers, ModifierLink) | ||
| // } | ||
| // | ||
| // addReactant (x) { | ||
| // return this._addMod(x, this.reactants, Link) | ||
| // } | ||
| // | ||
| // addProduct (x) { | ||
| // return this._addMod(x, this.products, Link) | ||
| // } | ||
| // } | ||
| // | ||
| // class SpeciesReference extends Entity { | ||
| // constructor (attr) { super(assign({stoichiometry: 1}, attr)) } | ||
| // } | ||
| // | ||
| // class Unit extends Entity { } | ||
| // class Species extends Entity { } | ||
| // class Compartment extends Entity { } | ||
| // class ModifierSpeciesReference extends SpeciesReference {} | ||
| // | ||
| // module.exports = { | ||
| // Pool, | ||
| // PoolClone, | ||
| // Link, | ||
| // ModifierLink, | ||
| // Transform, | ||
| // Model, | ||
| // Species, | ||
| // Compartment, | ||
| // Unit, | ||
| // Reaction, | ||
| // SpeciesReference, | ||
| // ModifierSpeciesReference, | ||
| // Group, | ||
| // Graph, | ||
| // create, | ||
| // revive, | ||
| // Reader, | ||
| // createXmlReader (opt) { return new Reader(opt) }, | ||
| // createModelBuilder (opt) { return new Builder(opt) }, | ||
| // createParser (opt) { return multipipe(new Reader(opt), new Builder(opt))} | ||
| // } | ||
| // |