Refactor/extract scripting api #749
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,170 @@ | ||
| import EPars from 'eterna/EPars'; | ||
| import Folder, {SuboptEnsembleResult} from 'eterna/folding/Folder'; | ||
| import DotPlot from 'eterna/rnatypes/DotPlot'; | ||
| import SecStruct from 'eterna/rnatypes/SecStruct'; | ||
| import Sequence from 'eterna/rnatypes/Sequence'; | ||
| import {ExternalInterfaceCtx} from 'eterna/util/ExternalInterface'; | ||
| import {Assert} from 'flashbang'; | ||
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||
| /** | ||
| * An EternaScript API exposing all functions that handle folding an arbitrary | ||
| * RNA sequence, and aren't dependent on what's the RNA in the puzzle. | ||
| * | ||
| * It adds itself to an existing script API (`ExternalInterfaceCtx`) from | ||
| * `this.registerToScriptInterface`. | ||
| * | ||
| * Note: The API in this class is still affected by the selected folder | ||
| * and the pseudoknot mode of the puzzle - just not the sequence. | ||
| */ | ||
| export default class FoldingAPI { | ||
| private readonly _getFolder: () => Folder | null; | ||
| private readonly _getIsPseudoknot: () => boolean; | ||
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| private get _folder(): Folder | null { | ||
| return this._getFolder(); | ||
| } | ||
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| private get _isPseudoknot(): boolean { | ||
| return this._getIsPseudoknot(); | ||
| } | ||
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| constructor(params: { getFolder: () => Folder, getIsPseudoknot: () => boolean }) { | ||
| this._getIsPseudoknot = params.getIsPseudoknot; | ||
| this._getFolder = params.getFolder; | ||
| } | ||
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| public registerToScriptInterface(scriptInterface: ExternalInterfaceCtx) { | ||
| scriptInterface.addCallback('current_folder', (): string | null => ( | ||
| this._folder ? this._folder.name : null | ||
| )); | ||
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| scriptInterface.addCallback('fold', | ||
| (seq: string, constraint: string | null = null): string | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| const seqArr: Sequence = Sequence.fromSequenceString(seq); | ||
| const folded: SecStruct | null = this._folder.foldSequence( | ||
| seqArr, null, constraint, this._isPseudoknot | ||
| ); | ||
| Assert.assertIsDefined(folded); | ||
| return folded.getParenthesis(null, this._isPseudoknot); | ||
| }); | ||
|
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| scriptInterface.addCallback('fold_with_binding_site', | ||
| (seq: string, site: number[], bonus: number): string | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| const seqArr: Sequence = Sequence.fromSequenceString(seq); | ||
| const folded: SecStruct | null = this._folder.foldSequenceWithBindingSite( | ||
| seqArr, null, site, Math.floor(bonus * 100), 2.5 | ||
| ); | ||
| if (folded === null) { | ||
| return null; | ||
| } | ||
| return folded.getParenthesis(); | ||
| }); | ||
|
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||
| scriptInterface.addCallback('energy_of_structure', (seq: string, secstruct: string): number | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| const seqArr: Sequence = Sequence.fromSequenceString(seq); | ||
| const structArr: SecStruct = SecStruct.fromParens(secstruct); | ||
| const freeEnergy = this._isPseudoknot ? this._folder.scoreStructures(seqArr, structArr, true) | ||
| : this._folder.scoreStructures(seqArr, structArr); | ||
| return 0.01 * freeEnergy; | ||
| }); | ||
|
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||
| // AMW: still give number[] back because external scripts may rely on it | ||
| scriptInterface.addCallback('pairing_probabilities', | ||
| (seq: string, secstruct: string | null = null): number[] | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| const seqArr: Sequence = Sequence.fromSequenceString(seq); | ||
| let folded: SecStruct | null; | ||
| if (secstruct) { | ||
| folded = SecStruct.fromParens(secstruct); | ||
| } else { | ||
| folded = this._folder.foldSequence(seqArr, null, null); | ||
| if (folded === null) { | ||
| return null; | ||
| } | ||
| } | ||
| const pp: DotPlot | null = this._folder.getDotPlot(seqArr, folded); | ||
| Assert.assertIsDefined(pp); | ||
| return pp.data; | ||
| }); | ||
|
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| scriptInterface.addCallback('subopt_single_sequence', | ||
| ( | ||
| seq: string, kcalDelta: number, | ||
| pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE | ||
| ): SuboptEnsembleResult | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| // now get subopt stuff | ||
| const seqArr: Sequence = Sequence.fromSequenceString(seq); | ||
| return this._folder.getSuboptEnsembleNoBindingSite(seqArr, | ||
| kcalDelta, pseudoknotted, temp); | ||
| }); | ||
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| scriptInterface.addCallback('subopt_oligos', | ||
| ( | ||
| seq: string, oligoStrings: string[], kcalDelta: number, | ||
| pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE | ||
| ): SuboptEnsembleResult | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| // make the sequence string from the oligos | ||
| let newSequence: string = seq; | ||
| for (let oligoIndex = 0; oligoIndex < oligoStrings.length; oligoIndex++) { | ||
| const oligoSequence: string = oligoStrings[oligoIndex]; | ||
| newSequence = `${newSequence}&${oligoSequence}`; | ||
| } | ||
|
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||
| // now get subopt stuff | ||
| const seqArr: Sequence = Sequence.fromSequenceString(newSequence); | ||
| return this._folder.getSuboptEnsembleWithOligos(seqArr, | ||
| oligoStrings, kcalDelta, pseudoknotted, temp); | ||
| }); | ||
|
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| scriptInterface.addCallback('cofold', | ||
| ( | ||
| seq: string, oligo: string, malus: number = 0.0, constraint: string | null = null | ||
| ): string | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| const len: number = seq.length; | ||
| const cseq = `${seq}&${oligo}`; | ||
| const seqArr: Sequence = Sequence.fromSequenceString(cseq); | ||
| const folded: SecStruct | null = this._folder.cofoldSequence( | ||
| seqArr, null, Math.floor(malus * 100), constraint | ||
| ); | ||
| if (folded === null) { | ||
| return null; | ||
| } | ||
| return `${folded.slice(0, len).getParenthesis() | ||
| }&${folded.slice(len).getParenthesis()}`; | ||
| }); | ||
|
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| scriptInterface.addCallback('get_defect', | ||
| ( | ||
| seq: string, secstruct: string, pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE | ||
| ): number | null => { | ||
| if (this._folder === null) { | ||
| return null; | ||
| } | ||
| return this._folder.getDefect( | ||
| Sequence.fromSequenceString(seq), | ||
| SecStruct.fromParens(secstruct), | ||
| temp, pseudoknotted | ||
| ); | ||
| }); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| import {ExternalInterfaceCtx} from 'eterna/util/ExternalInterface'; | ||
|
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| /** | ||
| * Adds the ability to modify the folder (via its name) to the EternaScript API. | ||
| */ | ||
| export default function addSelectFolderAPIToInterface({selectFolder, scriptInterface}: { | ||
| selectFolder: (folderName: string) => boolean, | ||
| scriptInterface: ExternalInterfaceCtx, | ||
| }) { | ||
| scriptInterface.addCallback( | ||
| 'select_folder', (folderName: string): boolean => selectFolder(folderName) | ||
| ); | ||
| } |
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You should go commit by commit, since the first commit doesn't modify this code, only moves it (and adds code around it)