import { randomItem, ordinalSuffix } from './utils.mjs' import AminoAcid from './amino-acid.mjs' import AminoAcidSelector from './amino-acid-selector.mjs' import Die from './die.mjs' import Error from './error.mjs' import Genome from './genome.mjs' import GenomeList from './genome-list.mjs' import Nucleotide from './nucleotide.mjs' import NucleotideSelector from './nucleotide-selector.mjs' class RollForNucleotide { constructor(rules) { this.rules = rules this.id = 'roll-for-nucleotide' } enter() { this.rules.die.value = '--' this.rules.die.onChanged = this.handleDieRoll.bind(this) this.rules.die.enable() } exit() { this.rules.die.disable() this.rules.die.onChanged = undefined } handleDieRoll() { this.rules.next(new NucleotideSelect(this.rules)) } } class NucleotideSelect { constructor(rules) { this.rules = rules this.id = 'nucleotide-select' this._boundCloneHandler = this.handleClone.bind(this) this.cloneButtons = document.querySelectorAll(`#${this.id} .clone`) } enter() { this.cloneButtons.forEach(button => { button.addEventListener('click', this._boundCloneHandler) button.disabled = false }) this.want = this.rules.die.value this.rules.currentGenome.onNucleotideSelectionChanged = this.handleSelectionChanged.bind(this) this.rules.currentGenome.unlock() } exit() { this.rules.currentGenome.lock() this.cloneButtons.forEach(button => { button.removeEventListener('click', this._boundCloneHandler) button.disabled = true }) this.rules.currentGenome.onNucleotideSelectionChanged = undefined; } handleClone(evt) { if (this.rules.die.value <= this.rules.currentGenome.length) { this.rules.next(new ShowError(this.rules, this, `Select the ${this.ordinalFor(this.rules.die.value)} nucleotide.`)) return } this.rules.iterations-- if (this.rules.iterations === 0) { this.rules.next(new PrintResults(this.rules, this.rules.currentGenome.clone())) } else { this.rules.genomeList.push(this.rules.currentGenome.clone()) this.rules.next(new RollForNucleotide(this.rules)) } } handleSelectionChanged(nucleotide, i) { i++; if (this.rules.die.value > this.rules.currentGenome.length) { this.rules.currentGenome.selectedNucleotide = undefined this.rules.next(new ShowError(this.rules, this, `You need to clone this genome.`)) return } else if (i != this.rules.die.value) { this.rules.currentGenome.selectedNucleotide = undefined this.rules.next(new ShowError(this.rules, this, `You selected the ${this.ordinalFor(i)} nucleotide. Please select the ${this.ordinalFor(this.want)} one.`)) return } this.rules.next(new RollForMutation(this.rules)) } ordinalFor(i) { return `${i}${ordinalSuffix(i)}` } } class RollForMutation { constructor(rules) { this.rules = rules this.id = 'roll-for-mutation' } enter() { this.rules.die.value = '--' this.rules.die.onChanged = this.handleDieRoll.bind(this) this.rules.die.enable() } exit() { this.rules.die.disable() this.rules.die.onChanged = undefined } handleDieRoll() { this.rules.next(new PerformMutation(this.rules)) } } class PerformMutation { constructor(rules) { this.rules = rules this.id = 'perform-mutation' this.originalGenome = this.rules.currentGenome.clone() } enter() { const selector = this.rules.nucleotideSelector selector.onItemSelected = this.handleItemSelected.bind(this) selector.attach(this.selectedNucleotide) } exit() { this.rules.nucleotideSelector.detach() } validMutation(from, to) { return to == this.expectedMutation[from] } get expectedMutation() { if (this.rules.die.value <= 14) { return Nucleotide.transition } else if (this.rules.die.value <= 17) { return Nucleotide.complementingTransversion } else { return Nucleotide.defaultTransversion } } get selectedNucleotide() { return this.rules.currentGenome.selectedNucleotide } get errorTransitionHTML() { return `Select the base that corresponds to a transition of ${this.selectedNucleotide.value}.` } get errorComplementingTransversionHTML() { return `Select the base that corresponds to a complementing transversion of ${this.selectedNucleotide.value}.` } get errorDefaultTransversionHTML() { return `Select the base that corresponds to the other transversion of ${this.selectedNucleotide.value}.` } get errorHTML() { if (this.expectedMutation == Nucleotide.transition) { return this.errorTransitionHTML } else if (this.expectedMutation == Nucleotide.complementingTransversion) { return this.errorComplementingTransversionHTML } else { return this.errorDefaultTransversionHTML } } handleItemSelected(base) { if (!this.validMutation(this.selectedNucleotide.value, base)) { this.rules.next(new ShowError(this.rules, this, this.errorHTML)) return } this.selectedNucleotide.value = base this.rules.next(new SelectAminoAcid(this.rules, this.originalGenome)) } } class SelectAminoAcid { constructor(rules, originalGenome) { this.rules = rules this.originalGenome = originalGenome this.id ='amino-acid-select' } enter() { const selector = this.rules.aminoAcidSelector this.codon = this.rules.currentGenome.selectedCodon this.expected = AminoAcid.codonMap[this.codon.value] console.debug('expected: ', this.expected) let x = selector.elt.querySelector('#amino-acid-selector .codon').innerHTML = this.codon.value selector.onItemSelected = this.handleItemSelected.bind(this) selector.attach(this.selectedNucleotide) this.rules.aminoAcidSelector.attach() } exit() { this.rules.aminoAcidSelector.detach() } validSelection(aminoAcid) { return aminoAcid == this.expected } handleItemSelected(aminoAcid) { if (!this.validSelection(aminoAcid)) { this.rules.next(new ShowError(this.rules, this, `The codon ${this.codon.value} does not code for ${aminoAcid}`)) return } const newAminoAcid = new AminoAcid(...this.codon.value.split('')) const isLethal = this.codon.aminoAcid.value !== newAminoAcid.value this.codon.aminoAcid = newAminoAcid this.rules.next(new MarkAsLethal(this.rules, this.originalGenome, isLethal)) } } class MarkAsLethal { constructor(rules, originalGenome, isLethal) { this.rules = rules this.originalGenome = originalGenome this.isLethal = isLethal this.id = 'mark-as-lethal' this._boundCloneHandler = this.handleClone.bind(this) this._boundKillHandler = this.handleKill.bind(this) this.cloneButtons = document.querySelectorAll(`#${this.id} .clone`) this.killButtons = document.querySelectorAll(`#${this.id} .kill`) } enter() { this.cloneButtons.forEach(button => { button.addEventListener('click', this._boundCloneHandler) button.disabled = false }) this.killButtons.forEach(button => { button.addEventListener('click', this._boundKillHandler) button.disabled = false }) } exit() { this.cloneButtons.forEach(button => { button.removeEventListener('click', this._boundCloneHandler) button.disabled = true }) this.killButtons.forEach(button => { button.removeEventListener('click', this._boundKillHandler) button.disabled = true }) } get lethalHTML() { return 'A change in amino acid is a lethal change.' } get nonLethalHTML() { return 'If the amino acid doesn\'t change it is non-lethal.' } handleClone(evt) { if (this.isLethal) { this.rules.next(new ShowError(this.rules, this, this.lethalHTML)) return } this.nextGoodState(this.rules.currentGenome) } handleKill(evt) { if (!this.isLethal) { this.rules.next(new ShowError(this.rules, this, this.nonLethalHTML)) return } this.nextGoodState(this.originalGenome) } nextGoodState(genome) { this.rules.iterations-- if (this.rules.iterations === 0) { this.rules.next(new PrintResults(this.rules, genome.clone())) } else { this.rules.genomeList.push(genome.clone()) this.rules.next(new RollForNucleotide(this.rules)) } } } class PrintResults { constructor(rules, finalGenome) { this.rules = rules this.finalGenome = finalGenome this.id = 'print-results' this._boundClickHandler = this.clickHandler.bind(this) } enter() { this.rules.genomeList.finalGenome = this.finalGenome this.rules.printButton.addEventListener('click', this._boundClickHandler) this.rules.printButton.disabled = false } exit() { this.rules.printButton.disabled = true this.rules.printButton.removeEventListener('click', this._boundClickHandler) } clickHandler() { window.print() } } class ShowError { constructor(rules, nextState, message) { this.rules = rules this.nextState = nextState this.rules.error.innerHTML = message this._boundClickHandler = this.clickHandler.bind(this) } enter() { this.rules.error.onClick = this._boundClickHandler this.rules.error.show() } exit() { this.rules.error.hide() this.rules.error.onClick = undefined } clickHandler() { this.rules.next(this.nextState) } } class Rules { constructor(die, instructions, genomeList, aminoAcidSelector, nucleotideSelector, remainingIterations, printButton, errors) { this.die = new Die(die) this.instructions = instructions this.genomeList = new GenomeList(genomeList) this.aminoAcidSelector = new AminoAcidSelector(aminoAcidSelector) this.nucleotideSelector = new NucleotideSelector(nucleotideSelector) this.remainingIterations = remainingIterations this.printButton = printButton this.error = new Error(errors) this.iterations = Rules.maxIterations const initialGenome = new Genome(Rules.initialGenomeBases) this.genomeList.initialGenome = initialGenome this.genomeList.push(initialGenome.clone()) if (false) { this._debugStartAtRollForMutation() } else if (false) { this._debugStartAtPerformMutation(9) } else if (false) { this._debugStartAtSelectAminoAcid() } else if (false) { this._debugStartAtSelectLethality() } else if (false) { this._debugStartWithError() } else { this.currentState = new RollForNucleotide(this) } this.enterState() } get iterations() { return Number(this.remainingIterations.innerText) } set iterations(val) { this.remainingIterations.innerText = val } get isLastIteration() { return this.iterations == 0 } _debugStartAtRollForMutation() { this.currentState = new RollForMutation(this) const nucleotide = this.currentGenome.nucleotides[2] this.currentGenome.selectedNucleotide = nucleotide } _debugStartAtPerformMutation(n) { [...Array(n)].forEach(i => { const n = randomItem(this.currentGenome.nucleotides) n.value = randomItem(Nucleotide.bases) this.currentGenome.selectedNucleotide = n const g = this.currentGenome.clone() this.genomeList.push(g) }) this.iterations -= n this.currentState = new PerformMutation(this) this.die.value = 14 const nucleotide = this.currentGenome.nucleotides[17] this.currentGenome.selectedNucleotide = nucleotide } _debugStartAtSelectAminoAcid() { this.currentState = new SelectAminoAcid(this) this.die.value = 15 const nucleotide = this.currentGenome.nucleotides[15] nucleotide.value = 'A' this.currentGenome.selectedNucleotide = nucleotide } _debugStartAtSelectLethality() { this.currentState = new MarkAsLethal(this, this.currentGenome.clone(), true) this.die.value = 15 const nucleotide = this.currentGenome.nucleotides[15] nucleotide.value = 'A' this.currentGenome.selectedNucleotide = nucleotide this.currentGenome.codons[5].aminoAcid = new AminoAcid('A', 'C', 'T') } _debugStartWithError() { this.currentState = new ShowError(this, new RollForNucleotide(this), 'test an error') } get currentGenome() { return this.genomeList.last } showCurrent() { if (this.currentState.id === undefined) { return } const elt = this.instructions.querySelector(`#${this.currentState.id}`) elt.classList.add('current') elt.scrollIntoView(true) } hideCurrent() { if (this.currentState.id === undefined) { return } const elt = this.instructions.querySelector(`#${this.currentState.id}`) elt.classList.remove('current') } enterState() { this.currentState.enter() this.showCurrent() } exitState() { this.hideCurrent() this.currentState.exit() } next(nextState) { this.exitState() this.currentState = nextState this.enterState() } } Rules.maxIterations = 10 Rules.initialGenomeBases = [ 'G', 'C', 'A', 'C', 'T', 'C', 'G', 'G', 'A', 'T', 'C', 'G', 'A', 'A', 'T', 'T', 'C', 'T' ] export default Rules