gff-nostream 1.3.9 → 2.0.0

package/dist/api.d.ts

@@ -1,4 +1,8 @@
-import { GFF3Feature } from './util';
+import type { GFF3Feature } from './util.ts';
+export interface LineRecord {
+    fields: string[];
+    lineHash?: string | number;
+}
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
  * parsed items.
@@ -8,4 +12,21 @@ import { GFF3Feature } from './util';
  * @returns array of parsed features, directives, comments and/or sequences
  */
 export declare function parseStringSync(str: string): GFF3Feature[];
-export { type GFF3FeatureLine, type GFF3Comment, type GFF3FeatureLineWithRefs, type GFF3Directive, type GFF3Sequence, type GFF3Feature, type GFF3Item, } from './util';
+/**
+ * Synchronously parse an array of strings containing GFF3 and return an array of the
+ * parsed items.
+ *
+ * @param arr - GFF3 array of strings
+ * @param inputOptions - Parsing options
+ * @returns array of parsed features, directives, comments and/or sequences
+ */
+export declare function parseArraySync(arr: string[]): GFF3Feature[];
+/**
+ * Synchronously parse an array of LineRecord objects containing pre-split GFF3
+ * fields and return an array of the parsed items.
+ *
+ * @param records - Array of LineRecord objects with fields array and optional lineHash
+ * @returns array of parsed features
+ */
+export declare function parseRecordsSync(records: LineRecord[]): GFF3Feature[];
+export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, } from './util.ts';

package/dist/api.js

@@ -4,7 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseStringSync = parseStringSync;
-const parse_1 = __importDefault(require("./parse"));
+exports.parseArraySync = parseArraySync;
+exports.parseRecordsSync = parseRecordsSync;
+const parse_ts_1 = __importDefault(require("./parse.js"));
+const util_ts_1 = require("./util.js");
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
  * parsed items.
@@ -15,11 +18,11 @@ const parse_1 = __importDefault(require("./parse"));
  */
 function parseStringSync(str) {
     const items = [];
-    const parser = new parse_1.default({
+    const parser = new parse_ts_1.default({
         featureCallback: arg => items.push(arg),
         disableDerivesFromReferences: true,
         errorCallback: err => {
-            throw err;
+            throw new Error(err);
         },
     });
     for (const line of str.split(/\r?\n/)) {
@@ -28,4 +31,56 @@ function parseStringSync(str) {
     parser.finish();
     return items;
 }
+/**
+ * Synchronously parse an array of strings containing GFF3 and return an array of the
+ * parsed items.
+ *
+ * @param arr - GFF3 array of strings
+ * @param inputOptions - Parsing options
+ * @returns array of parsed features, directives, comments and/or sequences
+ */
+function parseArraySync(arr) {
+    const items = [];
+    const parser = new parse_ts_1.default({
+        featureCallback: arg => items.push(arg),
+        disableDerivesFromReferences: true,
+        errorCallback: err => {
+            throw new Error(err);
+        },
+    });
+    for (const line of arr) {
+        parser.addLine(line);
+    }
+    parser.finish();
+    return items;
+}
+/**
+ * Synchronously parse an array of LineRecord objects containing pre-split GFF3
+ * fields and return an array of the parsed items.
+ *
+ * @param records - Array of LineRecord objects with fields array and optional lineHash
+ * @returns array of parsed features
+ */
+function parseRecordsSync(records) {
+    const items = [];
+    const parser = new parse_ts_1.default({
+        featureCallback: arg => items.push(arg),
+        disableDerivesFromReferences: true,
+        errorCallback: err => {
+            throw new Error(err);
+        },
+    });
+    for (const record of records) {
+        const featureLine = (0, util_ts_1.parseFieldsArray)(record.fields);
+        if (record.lineHash !== undefined) {
+            if (!featureLine.attributes) {
+                featureLine.attributes = {};
+            }
+            featureLine.attributes._lineHash = [String(record.lineHash)];
+        }
+        parser.addParsedFeatureLine(featureLine);
+    }
+    parser.finish();
+    return items;
+}
 //# sourceMappingURL=api.js.map

package/dist/api.js.map

@@ -1 +1 @@
-{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":";;;;;AAWA,0CAgBC;AA3BD,oDAA4B;AAG5B;;;;;;;GAOG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,eAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,GAAG,CAAA;QACX,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,MAAM,IAAI,IAAI,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;QACtC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IACtB,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC"}
+{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":";;;;;AAkBA,0CAgBC;AAUD,wCAgBC;AASD,4CAuBC;AA5FD,0DAA+B;AAC/B,uCAA4C;AAS5C;;;;;;;GAOG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,kBAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACtB,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,MAAM,IAAI,IAAI,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;QACtC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IACtB,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;;GAOG;AACH,SAAgB,cAAc,CAAC,GAAa;IAC1C,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,kBAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACtB,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;QACvB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IACtB,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,gBAAgB,CAAC,OAAqB;IACpD,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,kBAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACtB,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,WAAW,GAAoB,IAAA,0BAAgB,EAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,IAAI,CAAC,WAAW,CAAC,UAAU,EAAE,CAAC;gBAC5B,WAAW,CAAC,UAAU,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,WAAW,CAAC,UAAU,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,CAAC;QACD,MAAM,CAAC,oBAAoB,CAAC,WAAW,CAAC,CAAA;IAC1C,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC"}

package/dist/index.d.ts

@@ -1,3 +1,3 @@
-import { parseStringSync } from './api';
-export { parseStringSync };
-export type { GFF3Comment, GFF3Feature, GFF3Directive, GFF3FeatureLineWithRefs, GFF3FeatureLine, GFF3Item, GFF3Sequence, } from './api';
+import { parseArraySync, parseRecordsSync, parseStringSync } from './api.ts';
+export { parseArraySync, parseRecordsSync, parseStringSync };
+export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, LineRecord, } from './api.ts';

package/dist/index.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseStringSync = void 0;
-const api_1 = require("./api");
-Object.defineProperty(exports, "parseStringSync", { enumerable: true, get: function () { return api_1.parseStringSync; } });
+exports.parseStringSync = exports.parseRecordsSync = exports.parseArraySync = void 0;
+const api_ts_1 = require("./api.js");
+Object.defineProperty(exports, "parseArraySync", { enumerable: true, get: function () { return api_ts_1.parseArraySync; } });
+Object.defineProperty(exports, "parseRecordsSync", { enumerable: true, get: function () { return api_ts_1.parseRecordsSync; } });
+Object.defineProperty(exports, "parseStringSync", { enumerable: true, get: function () { return api_ts_1.parseStringSync; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,+BAAuC;AAC9B,gGADA,qBAAe,OACA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,qCAA4E;AACnE,+FADA,uBAAc,OACA;AAAE,iGADA,yBAAgB,OACA;AAAE,gGADA,wBAAe,OACA"}

package/dist/parse.d.ts

@@ -1,23 +1,10 @@
-import * as GFF3 from './util';
-export declare class FASTAParser {
-    seqCallback: (sequence: GFF3.GFF3Sequence) => void;
-    currentSequence: {
-        id: string;
-        sequence: string;
-        description?: string;
-    } | undefined;
-    constructor(seqCallback: (sequence: GFF3.GFF3Sequence) => void);
-    addLine(line: string): void;
-    private _flush;
-    finish(): void;
-}
+import * as GFF3 from './util.ts';
 interface ParserArgs {
     featureCallback?(feature: GFF3.GFF3Feature): void;
     endCallback?(): void;
     commentCallback?(comment: GFF3.GFF3Comment): void;
     errorCallback?(error: string): void;
     directiveCallback?(directive: GFF3.GFF3Directive): void;
-    sequenceCallback?(sequence: GFF3.GFF3Sequence): void;
     bufferSize?: number;
     disableDerivesFromReferences?: boolean;
 }
@@ -28,9 +15,7 @@ export default class Parser {
     errorCallback: (error: string) => void;
     disableDerivesFromReferences: boolean;
     directiveCallback: (directive: GFF3.GFF3Directive) => void;
-    sequenceCallback: (sequence: GFF3.GFF3Sequence) => void;
     bufferSize: number;
-    fastaParser: FASTAParser | undefined;
     eof: boolean;
     lineNumber: number;
     private _underConstructionTopLevel;
@@ -39,6 +24,7 @@ export default class Parser {
     private _underConstructionOrphans;
     constructor(args: ParserArgs);
     addLine(line: string): void;
+    addParsedFeatureLine(featureLine: GFF3.GFF3FeatureLine): void;
     finish(): void;
     private _emitItem;
     private _enforceBufferSizeLimit;
@@ -48,6 +34,7 @@ export default class Parser {
      */
     private _emitAllUnderConstructionFeatures;
     private _bufferLine;
+    private _bufferParsedLine;
     private _resolveReferencesTo;
     private _parseError;
     private _resolveReferencesFrom;

package/dist/parse.js

@@ -33,46 +33,18 @@ var __importStar = (this && this.__importStar) || (function () {
     };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FASTAParser = void 0;
-const GFF3 = __importStar(require("./util"));
+const GFF3 = __importStar(require("./util.js"));
 const containerAttributes = {
     Parent: 'child_features',
     Derives_from: 'derived_features',
 };
-class FASTAParser {
-    constructor(seqCallback) {
-        this.seqCallback = seqCallback;
-        this.currentSequence = undefined;
-    }
-    addLine(line) {
-        const defMatch = /^>\s*(\S+)\s*(.*)/.exec(line);
-        if (defMatch) {
-            this._flush();
-            this.currentSequence = { id: defMatch[1], sequence: '' };
-            if (defMatch[2]) {
-                this.currentSequence.description = defMatch[2].trim();
-            }
-        }
-        else if (this.currentSequence && /\S/.test(line)) {
-            this.currentSequence.sequence += line.replaceAll(/\s/g, '');
-        }
-    }
-    _flush() {
-        if (this.currentSequence) {
-            this.seqCallback(this.currentSequence);
-        }
-    }
-    finish() {
-        this._flush();
-    }
-}
-exports.FASTAParser = FASTAParser;
+const featureLineRegex = /^\s*[^#\s>]/;
+const commentOrDirectiveRegex = /^\s*(#+)(.*)/;
+const blankLineRegex = /^\s*$/;
+const fastaStartRegex = /^\s*>/;
+const lineEndingRegex = /\r?\n?$/g;
 class Parser {
     constructor(args) {
-        this.fastaParser = undefined;
-        // if this is true, the parser ignores the
-        // rest of the lines in the file.  currently
-        // set when the file switches over to FASTA
         this.eof = false;
         this.lineNumber = 0;
         // features that we have to keep on hand for now because they
@@ -96,29 +68,22 @@ class Parser {
         this.commentCallback = args.commentCallback || nullFunc;
         this.errorCallback = args.errorCallback || nullFunc;
         this.directiveCallback = args.directiveCallback || nullFunc;
-        this.sequenceCallback = args.sequenceCallback || nullFunc;
         this.disableDerivesFromReferences =
             args.disableDerivesFromReferences || false;
         // number of lines to buffer
         this.bufferSize = args.bufferSize === undefined ? Infinity : args.bufferSize;
     }
     addLine(line) {
-        // if we have transitioned to a fasta section, just delegate to that parser
-        if (this.fastaParser) {
-            this.fastaParser.addLine(line);
-            return;
-        }
         if (this.eof) {
-            // otherwise, if we are done, ignore this line
             return;
         }
         this.lineNumber += 1;
-        if (/^\s*[^#\s>]/.test(line)) {
+        if (featureLineRegex.test(line)) {
             // feature line, most common case
             this._bufferLine(line);
             return;
         }
-        const match = /^\s*(#+)(.*)/.exec(line);
+        const match = commentOrDirectiveRegex.exec(line);
         if (match) {
             // directive or comment
             const [, hashsigns] = match;
@@ -133,7 +98,6 @@ class Parser {
                     if (directive.directive === 'FASTA') {
                         this._emitAllUnderConstructionFeatures();
                         this.eof = true;
-                        this.fastaParser = new FASTAParser(this.sequenceCallback);
                     }
                     else {
                         this._emitItem(directive);
@@ -141,31 +105,32 @@ class Parser {
                 }
             }
             else {
-                contents = contents.replace(/\s*/, '');
-                this._emitItem({ comment: contents });
+                this._emitItem({ comment: contents.trimStart() });
             }
         }
-        else if (/^\s*$/.test(line)) {
+        else if (blankLineRegex.test(line)) {
             // blank line, do nothing
         }
-        else if (/^\s*>/.test(line)) {
-            // implicit beginning of a FASTA section
+        else if (fastaStartRegex.test(line)) {
+            // implicit beginning of a FASTA section, stop parsing
             this._emitAllUnderConstructionFeatures();
             this.eof = true;
-            this.fastaParser = new FASTAParser(this.sequenceCallback);
-            this.fastaParser.addLine(line);
         }
         else {
             // it's a parse error
-            const errLine = line.replaceAll(/\r?\n?$/g, '');
+            const errLine = line.replaceAll(lineEndingRegex, '');
             throw new Error(`GFF3 parse error.  Cannot parse '${errLine}'.`);
         }
     }
+    addParsedFeatureLine(featureLine) {
+        if (this.eof) {
+            return;
+        }
+        this.lineNumber += 1;
+        this._bufferParsedLine(featureLine);
+    }
     finish() {
         this._emitAllUnderConstructionFeatures();
-        if (this.fastaParser) {
-            this.fastaParser.finish();
-        }
         this.endCallback();
     }
     _emitItem(i) {
@@ -181,19 +146,24 @@ class Parser {
     }
     _enforceBufferSizeLimit(additionalItemCount = 0) {
         const _unbufferItem = (item) => {
-            var _a, _b;
-            if (item && Array.isArray(item) && ((_b = (_a = item[0].attributes) === null || _a === void 0 ? void 0 : _a.ID) === null || _b === void 0 ? void 0 : _b[0])) {
+            if (item && Array.isArray(item) && item[0].attributes?.ID?.[0]) {
                 const ids = item[0].attributes.ID;
                 ids.forEach(id => {
                     delete this._underConstructionById[id];
                     delete this._completedReferences[id];
                 });
                 item.forEach(i => {
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                     if (i.child_features) {
-                        i.child_features.forEach(c => _unbufferItem(c));
+                        i.child_features.forEach(c => {
+                            _unbufferItem(c);
+                        });
                     }
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                     if (i.derived_features) {
-                        i.derived_features.forEach(d => _unbufferItem(d));
+                        i.derived_features.forEach(d => {
+                            _unbufferItem(d);
+                        });
                     }
                 });
             }
@@ -218,25 +188,24 @@ class Parser {
         this._completedReferences = {};
         // if we have any orphans hanging around still, this is a
         // problem. die with a parse error
-        if (Array.from(Object.values(this._underConstructionOrphans)).length) {
-            throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${Object.keys(this._underConstructionOrphans).join(',')}`);
+        const orphanKeys = Object.keys(this._underConstructionOrphans);
+        if (orphanKeys.length) {
+            throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${orphanKeys.join(',')}`);
         }
     }
-    // do the right thing with a newly-parsed feature line
     _bufferLine(line) {
-        var _a, _b, _c;
-        const rawFeatureLine = GFF3.parseFeature(line);
-        const featureLine = Object.assign(Object.assign({}, rawFeatureLine), { child_features: [], derived_features: [] });
-        // featureLine._lineNumber = this.lineNumber //< debugging aid
-        // NOTE: a feature is an arrayref of one or more feature lines.
-        const ids = ((_a = featureLine.attributes) === null || _a === void 0 ? void 0 : _a.ID) || [];
-        const parents = ((_b = featureLine.attributes) === null || _b === void 0 ? void 0 : _b.Parent) || [];
+        this._bufferParsedLine(GFF3.parseFeature(line));
+    }
+    _bufferParsedLine(rawFeatureLine) {
+        const featureLine = rawFeatureLine;
+        featureLine.child_features = [];
+        featureLine.derived_features = [];
+        const ids = featureLine.attributes?.ID || [];
+        const parents = featureLine.attributes?.Parent || [];
         const derives = this.disableDerivesFromReferences
             ? []
-            : ((_c = featureLine.attributes) === null || _c === void 0 ? void 0 : _c.Derives_from) || [];
+            : featureLine.attributes?.Derives_from || [];
         if (!ids.length && !parents.length && !derives.length) {
-            // if it has no IDs and does not refer to anything, we can just
-            // output it
             this._emitItem([featureLine]);
             return;
         }
@@ -244,7 +213,6 @@ class Parser {
         ids.forEach(id => {
             const existing = this._underConstructionById[id];
             if (existing) {
-                // another location of the same feature
                 if (existing[existing.length - 1].type !== featureLine.type) {
                     this._parseError(`multi-line feature "${id}" has inconsistent types: "${featureLine.type}", "${existing[existing.length - 1].type}"`);
                 }
@@ -252,37 +220,28 @@ class Parser {
                 feature = existing;
             }
             else {
-                // haven't seen it yet, so buffer it so we can attach
-                // child features to it
                 feature = [featureLine];
                 this._enforceBufferSizeLimit(1);
                 if (!parents.length && !derives.length) {
                     this._underConstructionTopLevel.push(feature);
                 }
                 this._underConstructionById[id] = feature;
-                // see if we have anything buffered that refers to it
                 this._resolveReferencesTo(feature, id);
             }
         });
-        // try to resolve all its references
-        this._resolveReferencesFrom(feature || [featureLine], { Parent: parents, Derives_from: derives }, ids);
+        this._resolveReferencesFrom(
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        feature || [featureLine], { Parent: parents, Derives_from: derives }, ids);
     }
     _resolveReferencesTo(feature, id) {
         const references = this._underConstructionOrphans[id];
-        //   references is of the form
-        //   {
-        //     'Parent' : [ orphans that have a Parent attr referencing this feature ],
-        //     'Derives_from' : [ orphans that have a Derives_from attr referencing this feature ],
-        //    }
         if (!references) {
             return;
         }
-        feature.forEach(loc => {
+        for (const loc of feature) {
             loc.child_features.push(...references.Parent);
-        });
-        feature.forEach(loc => {
             loc.derived_features.push(...references.Derives_from);
-        });
+        }
         delete this._underConstructionOrphans[id];
     }
     _parseError(message) {
@@ -290,61 +249,60 @@ class Parser {
         this.errorCallback(`${this.lineNumber}: ${message}`);
     }
     _resolveReferencesFrom(feature, references, ids) {
-        // this is all a bit more awkward in javascript than it was in perl
-        function postSet(obj, slot1, slot2) {
-            let subObj = obj[slot1];
-            if (!subObj) {
-                subObj = {};
-                obj[slot1] = subObj;
-            }
-            const returnVal = subObj[slot2] || false;
-            subObj[slot2] = true;
-            return returnVal;
-        }
-        references.Parent.forEach(toId => {
+        for (const toId of references.Parent) {
             const otherFeature = this._underConstructionById[toId];
             if (otherFeature) {
-                const pname = containerAttributes.Parent;
-                if (!ids.filter(id => postSet(this._completedReferences, id, `Parent,${toId}`)).length) {
-                    otherFeature.forEach(location => {
-                        location[pname].push(feature);
-                    });
+                let dominated = false;
+                for (const id of ids) {
+                    const domKey = `Parent,${toId}`;
+                    const rec = this._completedReferences[id] || (this._completedReferences[id] = {});
+                    if (rec[domKey]) {
+                        dominated = true;
+                    }
+                    rec[domKey] = true;
+                }
+                if (!dominated) {
+                    for (const location of otherFeature) {
+                        location.child_features.push(feature);
+                    }
                 }
             }
             else {
                 let ref = this._underConstructionOrphans[toId];
                 if (!ref) {
-                    ref = {
-                        Parent: [],
-                        Derives_from: [],
-                    };
+                    ref = { Parent: [], Derives_from: [] };
                     this._underConstructionOrphans[toId] = ref;
                 }
                 ref.Parent.push(feature);
             }
-        });
-        references.Derives_from.forEach(toId => {
+        }
+        for (const toId of references.Derives_from) {
             const otherFeature = this._underConstructionById[toId];
             if (otherFeature) {
-                const pname = containerAttributes.Derives_from;
-                if (!ids.filter(id => postSet(this._completedReferences, id, `Derives_from,${toId}`)).length) {
-                    otherFeature.forEach(location => {
-                        location[pname].push(feature);
-                    });
+                let dominated = false;
+                for (const id of ids) {
+                    const domKey = `Derives_from,${toId}`;
+                    const rec = this._completedReferences[id] || (this._completedReferences[id] = {});
+                    if (rec[domKey]) {
+                        dominated = true;
+                    }
+                    rec[domKey] = true;
+                }
+                if (!dominated) {
+                    for (const location of otherFeature) {
+                        location.derived_features.push(feature);
+                    }
                 }
             }
             else {
                 let ref = this._underConstructionOrphans[toId];
                 if (!ref) {
-                    ref = {
-                        Parent: [],
-                        Derives_from: [],
-                    };
+                    ref = { Parent: [], Derives_from: [] };
                     this._underConstructionOrphans[toId] = ref;
                 }
                 ref.Derives_from.push(feature);
             }
-        });
+        }
     }
 }
 exports.default = Parser;

package/dist/parse.js.map

@@ -1 +1 @@
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package/dist/util.d.ts

@@ -33,6 +33,7 @@ export declare function parseAttributes(attrString: string): GFF3Attributes;
  * @returns The parsed feature
  */
 export declare function parseFeature(line: string): GFF3FeatureLine;
+export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
 /**
  * Parse a GFF3 directive line.
  *