Standardize imports

GMOD · Apr 11, 2023 · 226a50a · 226a50a
1 parent 549bd9f
commit 226a50a
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Showing 2 changed files with 33 additions and 25 deletions.
diff --git a/src/api.ts b/src/api.ts
@@ -1,4 +1,4 @@
-import Parser, { ParseCallbacks } from './parse'
+import { GFF3Parser, ParseCallbacks } from './parse'
 import {
   formatItem,
   formatSequence,
@@ -48,7 +48,7 @@ function _processParseOptions(options: ParseOptions): ParseOptionsProcessed {
  */
 export class GFFTransformer implements Transformer<Uint8Array, GFF3Item> {
   private decoder: TextDecoder
-  private parser: Parser
+  private parser: GFF3Parser
   private lastString = ''
   private parseFeatures: boolean
   private parseDirectives: boolean
@@ -63,7 +63,7 @@ export class GFFTransformer implements Transformer<Uint8Array, GFF3Item> {
     this.decoder = new TextDecoder()
     const processedOptions = _processParseOptions(options)
     const { bufferSize, disableDerivesFromReferences } = processedOptions
-    this.parser = new Parser({ bufferSize, disableDerivesFromReferences })
+    this.parser = new GFF3Parser({ bufferSize, disableDerivesFromReferences })
     this.parseFeatures = processedOptions.parseFeatures
     this.parseDirectives = processedOptions.parseDirectives
     this.parseComments = processedOptions.parseComments
@@ -462,7 +462,7 @@ export function parseStringSync(
     callbacks.sequenceCallback = push
   }
 
-  const parser = new Parser({
+  const parser = new GFF3Parser({
     disableDerivesFromReferences: options.disableDerivesFromReferences || false,
     bufferSize: Infinity,
   })
@@ -532,7 +532,8 @@ export class GFFFormattingTransformer implements Transformer<GFF3Item, string> {
    */
   constructor(options: FormatOptions = {}) {
     this.minLinesBetweenSyncMarks = options.minSyncLines || 100
-    this.insertVersionDirective = options.insertVersionDirective || true
+    this.insertVersionDirective =
+      options.insertVersionDirective === false ? false : true
   }
 
   transform(

diff --git a/src/parse.ts b/src/parse.ts
@@ -1,16 +1,24 @@
-import * as GFF3 from './util'
+import {
+  parseDirective,
+  parseFeature,
+  GFF3Feature,
+  GFF3FeatureLineWithRefs,
+  GFF3Comment,
+  GFF3Directive,
+  GFF3Sequence,
+} from './util'
 
 const containerAttributes = {
   Parent: 'child_features' as const,
   Derives_from: 'derived_features' as const,
 }
 
 export interface ParseCallbacks {
-  featureCallback?(feature: GFF3.GFF3Feature): void
-  commentCallback?(comment: GFF3.GFF3Comment): void
+  featureCallback?(feature: GFF3Feature): void
+  commentCallback?(comment: GFF3Comment): void
   errorCallback?(error: string): void
-  directiveCallback?(directive: GFF3.GFF3Directive): void
-  sequenceCallback?(sequence: GFF3.GFF3Sequence): void
+  directiveCallback?(directive: GFF3Directive): void
+  sequenceCallback?(sequence: GFF3Sequence): void
 }
 
 export class FASTAParser {
@@ -20,7 +28,7 @@ export class FASTAParser {
 
   constructor(
     // eslint-disable-next-line @typescript-eslint/no-empty-function
-    private seqCallback: (sequence: GFF3.GFF3Sequence) => void = () => {},
+    private seqCallback: (sequence: GFF3Sequence) => void = () => {},
   ) {
     this.currentSequence = undefined
   }
@@ -52,11 +60,11 @@ interface ParserArgs {
 }
 
 interface References {
-  Parent: GFF3.GFF3Feature[]
-  Derives_from: GFF3.GFF3Feature[]
+  Parent: GFF3Feature[]
+  Derives_from: GFF3Feature[]
 }
 
-export default class Parser {
+export class GFF3Parser {
   endCallback: () => void
   disableDerivesFromReferences: boolean
   bufferSize: number
@@ -67,10 +75,9 @@ export default class Parser {
   lineNumber = 0
   // features that we have to keep on hand for now because they might be
   // referenced by something else
-  private underConstructionTopLevel: GFF3.GFF3Feature[] = []
+  private underConstructionTopLevel: GFF3Feature[] = []
   // index of the above by ID
-  private underConstructionById: Record<string, GFF3.GFF3Feature | undefined> =
-    {}
+  private underConstructionById: Record<string, GFF3Feature | undefined> = {}
   private completedReferences: Record<
     string,
     Record<string, boolean | undefined> | undefined
@@ -125,7 +132,7 @@ export default class Parser {
         // sync directive, all forward-references are resolved.
         this.emitAllUnderConstructionFeatures(callbacks)
       } else if (hashsigns.length === 2) {
-        const directive = GFF3.parseDirective(line)
+        const directive = parseDirective(line)
         if (directive) {
           if (directive.directive === 'FASTA') {
             this.emitAllUnderConstructionFeatures(callbacks)
@@ -161,7 +168,7 @@ export default class Parser {
   }
 
   private emitItem(
-    i: GFF3.GFF3Feature | GFF3.GFF3Directive | GFF3.GFF3Comment,
+    i: GFF3Feature | GFF3Directive | GFF3Comment,
     callbacks: ParseCallbacks,
   ) {
     if (Array.isArray(i) && callbacks.featureCallback)
@@ -176,7 +183,7 @@ export default class Parser {
     additionalItemCount = 0,
     callbacks: ParseCallbacks,
   ) {
-    const _unbufferItem = (item?: GFF3.GFF3Feature) => {
+    const _unbufferItem = (item?: GFF3Feature) => {
       if (
         item &&
         Array.isArray(item) &&
@@ -236,8 +243,8 @@ export default class Parser {
 
   // do the right thing with a newly-parsed feature line
   private bufferLine(line: string, callbacks: ParseCallbacks) {
-    const rawFeatureLine = GFF3.parseFeature(line)
-    const featureLine: GFF3.GFF3FeatureLineWithRefs = {
+    const rawFeatureLine = parseFeature(line)
+    const featureLine: GFF3FeatureLineWithRefs = {
       ...rawFeatureLine,
       child_features: [],
       derived_features: [],
@@ -257,7 +264,7 @@ export default class Parser {
       return
     }
 
-    let feature: GFF3.GFF3Feature | undefined = undefined
+    let feature: GFF3Feature | undefined = undefined
     ids.forEach((id) => {
       const existing = this.underConstructionById[id]
       if (existing) {
@@ -296,7 +303,7 @@ export default class Parser {
     )
   }
 
-  private resolveReferencesTo(feature: GFF3.GFF3Feature, id: string) {
+  private resolveReferencesTo(feature: GFF3Feature, id: string) {
     const references = this.underConstructionOrphans.get(id)
     //   references is of the form
     //   {
@@ -335,7 +342,7 @@ export default class Parser {
   }
 
   private resolveReferencesFrom(
-    feature: GFF3.GFF3Feature,
+    feature: GFF3Feature,
     references: { Parent: string[]; Derives_from: string[] },
     ids: string[],
   ) {