gff-nostream 2.0.0 → 2.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/api.d.ts +10 -0
- package/dist/api.js +33 -0
- package/dist/api.js.map +1 -1
- package/dist/index.d.ts +2 -2
- package/dist/index.js +2 -1
- package/dist/index.js.map +1 -1
- package/dist/parse.js +4 -6
- package/dist/parse.js.map +1 -1
- package/dist/util.d.ts +16 -0
- package/dist/util.js +68 -0
- package/dist/util.js.map +1 -1
- package/esm/api.d.ts +10 -0
- package/esm/api.js +33 -1
- package/esm/api.js.map +1 -1
- package/esm/index.d.ts +2 -2
- package/esm/index.js +2 -2
- package/esm/index.js.map +1 -1
- package/esm/parse.js +4 -6
- package/esm/parse.js.map +1 -1
- package/esm/util.d.ts +16 -0
- package/esm/util.js +66 -0
- package/esm/util.js.map +1 -1
- package/package.json +1 -1
- package/src/api.ts +37 -1
- package/src/index.ts +2 -2
- package/src/parse.ts +6 -7
- package/src/util.ts +74 -0
package/dist/api.d.ts
CHANGED
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@@ -29,4 +29,14 @@ export declare function parseArraySync(arr: string[]): GFF3Feature[];
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* @returns array of parsed features
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*/
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export declare function parseRecordsSync(records: LineRecord[]): GFF3Feature[];
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32
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+
/**
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* Synchronously parse an array of LineRecord objects containing pre-split GFF3
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* fields and return an array of the parsed items. Uses a fast path that skips
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* unescaping when hasEscapes is false.
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*
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* @param records - Array of LineRecord objects with fields array and optional lineHash
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* @param hasEscapes - Whether the records contain percent-encoded characters
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* @returns array of parsed features
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*/
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export declare function parseRecordsSyncFast(records: LineRecord[], hasEscapes: boolean): GFF3Feature[];
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export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, } from './util.ts';
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package/dist/api.js
CHANGED
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@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
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exports.parseStringSync = parseStringSync;
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exports.parseArraySync = parseArraySync;
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exports.parseRecordsSync = parseRecordsSync;
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9
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exports.parseRecordsSyncFast = parseRecordsSyncFast;
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const parse_ts_1 = __importDefault(require("./parse.js"));
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const util_ts_1 = require("./util.js");
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/**
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@@ -83,4 +84,36 @@ function parseRecordsSync(records) {
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parser.finish();
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return items;
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}
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+
/**
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* Synchronously parse an array of LineRecord objects containing pre-split GFF3
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* fields and return an array of the parsed items. Uses a fast path that skips
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* unescaping when hasEscapes is false.
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*
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* @param records - Array of LineRecord objects with fields array and optional lineHash
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* @param hasEscapes - Whether the records contain percent-encoded characters
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* @returns array of parsed features
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*/
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function parseRecordsSyncFast(records, hasEscapes) {
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const items = [];
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const parser = new parse_ts_1.default({
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featureCallback: arg => items.push(arg),
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disableDerivesFromReferences: true,
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errorCallback: err => {
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throw new Error(err);
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},
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});
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const parseFunc = hasEscapes ? util_ts_1.parseFieldsArray : util_ts_1.parseFieldsArrayNoUnescape;
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for (const record of records) {
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const featureLine = parseFunc(record.fields);
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if (record.lineHash !== undefined) {
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if (!featureLine.attributes) {
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featureLine.attributes = {};
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}
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featureLine.attributes._lineHash = [String(record.lineHash)];
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}
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parser.addParsedFeatureLine(featureLine);
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}
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parser.finish();
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return items;
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}
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//# sourceMappingURL=api.js.map
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package/dist/api.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":";;;;;AAkBA,0CAgBC;AAUD,wCAgBC;AASD,4CAuBC;
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{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":";;;;;AAkBA,0CAgBC;AAUD,wCAgBC;AASD,4CAuBC;AAWD,oDAyBC;AAhID,0DAA+B;AAC/B,uCAAwE;AASxE;;;;;;;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;AAED;;;;;;;;GAQG;AACH,SAAgB,oBAAoB,CAAC,OAAqB,EAAE,UAAmB;IAC7E,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,MAAM,SAAS,GAAG,UAAU,CAAC,CAAC,CAAC,0BAAgB,CAAC,CAAC,CAAC,oCAA0B,CAAA;IAE5E,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,WAAW,GAAoB,SAAS,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC7D,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"}
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package/dist/index.d.ts
CHANGED
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@@ -1,3 +1,3 @@
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import { parseArraySync, parseRecordsSync, parseStringSync } from './api.ts';
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export { parseArraySync, parseRecordsSync, parseStringSync };
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import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from './api.ts';
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export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync };
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export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, LineRecord, } from './api.ts';
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package/dist/index.js
CHANGED
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@@ -1,8 +1,9 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.parseStringSync = exports.parseRecordsSync = exports.parseArraySync = void 0;
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exports.parseStringSync = exports.parseRecordsSyncFast = exports.parseRecordsSync = exports.parseArraySync = void 0;
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const api_ts_1 = require("./api.js");
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Object.defineProperty(exports, "parseArraySync", { enumerable: true, get: function () { return api_ts_1.parseArraySync; } });
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Object.defineProperty(exports, "parseRecordsSync", { enumerable: true, get: function () { return api_ts_1.parseRecordsSync; } });
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Object.defineProperty(exports, "parseRecordsSyncFast", { enumerable: true, get: function () { return api_ts_1.parseRecordsSyncFast; } });
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Object.defineProperty(exports, "parseStringSync", { enumerable: true, get: function () { return api_ts_1.parseStringSync; } });
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//# sourceMappingURL=index.js.map
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package/dist/index.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,qCAAkG;AACzF,+FADA,uBAAc,OACA;AAAE,iGADA,yBAAgB,OACA;AAAE,qGADA,6BAAoB,OACA;AAAE,gGADA,wBAAe,OACA"}
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package/dist/parse.js
CHANGED
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@@ -34,10 +34,6 @@ var __importStar = (this && this.__importStar) || (function () {
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})();
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Object.defineProperty(exports, "__esModule", { value: true });
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const GFF3 = __importStar(require("./util.js"));
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const containerAttributes = {
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Parent: 'child_features',
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Derives_from: 'derived_features',
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};
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const featureLineRegex = /^\s*[^#\s>]/;
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const commentOrDirectiveRegex = /^\s*(#+)(.*)/;
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const blankLineRegex = /^\s*$/;
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@@ -255,7 +251,8 @@ class Parser {
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let dominated = false;
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for (const id of ids) {
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const domKey = `Parent,${toId}`;
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const rec = this._completedReferences[id] ||
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const rec = this._completedReferences[id] ||
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(this._completedReferences[id] = {});
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if (rec[domKey]) {
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dominated = true;
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}
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let dominated = false;
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for (const id of ids) {
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const domKey = `Derives_from,${toId}`;
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const rec = this._completedReferences[id] ||
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const rec = this._completedReferences[id] ||
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(this._completedReferences[id] = {});
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if (rec[domKey]) {
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dominated = true;
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}
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package/dist/parse.js.map
CHANGED
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{"version":3,"file":"parse.js","sourceRoot":"","sources":["../src/parse.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAiC;AAEjC,MAAM,
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|
+
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|
package/dist/util.d.ts
CHANGED
|
@@ -26,6 +26,14 @@ export declare function escapeColumn(rawVal: string | number): string;
|
|
|
26
26
|
* @returns Parsed attributes
|
|
27
27
|
*/
|
|
28
28
|
export declare function parseAttributes(attrString: string): GFF3Attributes;
|
|
29
|
+
/**
|
|
30
|
+
* Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
|
|
31
|
+
* Fast path for data known to contain no escaped characters.
|
|
32
|
+
*
|
|
33
|
+
* @param attrString - String of GFF3 9th column
|
|
34
|
+
* @returns Parsed attributes
|
|
35
|
+
*/
|
|
36
|
+
export declare function parseAttributesNoUnescape(attrString: string): GFF3Attributes;
|
|
29
37
|
/**
|
|
30
38
|
* Parse a GFF3 feature line
|
|
31
39
|
*
|
|
@@ -34,6 +42,14 @@ export declare function parseAttributes(attrString: string): GFF3Attributes;
|
|
|
34
42
|
*/
|
|
35
43
|
export declare function parseFeature(line: string): GFF3FeatureLine;
|
|
36
44
|
export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
|
|
45
|
+
/**
|
|
46
|
+
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
|
47
|
+
* Fast path for data known to contain no escaped characters.
|
|
48
|
+
*
|
|
49
|
+
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
50
|
+
* @returns The parsed feature
|
|
51
|
+
*/
|
|
52
|
+
export declare function parseFieldsArrayNoUnescape(f: (string | null | undefined)[]): GFF3FeatureLine;
|
|
37
53
|
/**
|
|
38
54
|
* Parse a GFF3 directive line.
|
|
39
55
|
*
|
package/dist/util.js
CHANGED
|
@@ -6,8 +6,10 @@ exports.unescape = unescape;
|
|
|
6
6
|
exports.escape = escape;
|
|
7
7
|
exports.escapeColumn = escapeColumn;
|
|
8
8
|
exports.parseAttributes = parseAttributes;
|
|
9
|
+
exports.parseAttributesNoUnescape = parseAttributesNoUnescape;
|
|
9
10
|
exports.parseFeature = parseFeature;
|
|
10
11
|
exports.parseFieldsArray = parseFieldsArray;
|
|
12
|
+
exports.parseFieldsArrayNoUnescape = parseFieldsArrayNoUnescape;
|
|
11
13
|
exports.parseDirective = parseDirective;
|
|
12
14
|
exports.formatAttributes = formatAttributes;
|
|
13
15
|
exports.formatFeature = formatFeature;
|
|
@@ -96,6 +98,43 @@ function parseAttributes(attrString) {
|
|
|
96
98
|
}
|
|
97
99
|
return attrs;
|
|
98
100
|
}
|
|
101
|
+
/**
|
|
102
|
+
* Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
|
|
103
|
+
* Fast path for data known to contain no escaped characters.
|
|
104
|
+
*
|
|
105
|
+
* @param attrString - String of GFF3 9th column
|
|
106
|
+
* @returns Parsed attributes
|
|
107
|
+
*/
|
|
108
|
+
function parseAttributesNoUnescape(attrString) {
|
|
109
|
+
if (!attrString.length || attrString === '.') {
|
|
110
|
+
return {};
|
|
111
|
+
}
|
|
112
|
+
const attrs = {};
|
|
113
|
+
let str = attrString;
|
|
114
|
+
if (str.endsWith('\n')) {
|
|
115
|
+
str = str.slice(0, str.endsWith('\r\n') ? -2 : -1);
|
|
116
|
+
}
|
|
117
|
+
for (const a of str.split(';')) {
|
|
118
|
+
const eqIdx = a.indexOf('=');
|
|
119
|
+
if (eqIdx === -1) {
|
|
120
|
+
continue;
|
|
121
|
+
}
|
|
122
|
+
const value = a.slice(eqIdx + 1);
|
|
123
|
+
if (!value.length) {
|
|
124
|
+
continue;
|
|
125
|
+
}
|
|
126
|
+
const tag = a.slice(0, eqIdx).trim();
|
|
127
|
+
let arec = attrs[tag];
|
|
128
|
+
if (!arec) {
|
|
129
|
+
arec = [];
|
|
130
|
+
attrs[tag] = arec;
|
|
131
|
+
}
|
|
132
|
+
for (const s of value.split(',')) {
|
|
133
|
+
arec.push(s.trim());
|
|
134
|
+
}
|
|
135
|
+
}
|
|
136
|
+
return attrs;
|
|
137
|
+
}
|
|
99
138
|
/**
|
|
100
139
|
* Parse a GFF3 feature line
|
|
101
140
|
*
|
|
@@ -136,6 +175,35 @@ function parseFieldsArray(f) {
|
|
|
136
175
|
attributes: attrString === null ? null : parseAttributes(attrString),
|
|
137
176
|
};
|
|
138
177
|
}
|
|
178
|
+
/**
|
|
179
|
+
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
|
180
|
+
* Fast path for data known to contain no escaped characters.
|
|
181
|
+
*
|
|
182
|
+
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
183
|
+
* @returns The parsed feature
|
|
184
|
+
*/
|
|
185
|
+
function parseFieldsArrayNoUnescape(f) {
|
|
186
|
+
const seq_id = norm(f[0]);
|
|
187
|
+
const source = norm(f[1]);
|
|
188
|
+
const type = norm(f[2]);
|
|
189
|
+
const start = norm(f[3]);
|
|
190
|
+
const end = norm(f[4]);
|
|
191
|
+
const score = norm(f[5]);
|
|
192
|
+
const strand = norm(f[6]);
|
|
193
|
+
const phase = norm(f[7]);
|
|
194
|
+
const attrString = norm(f[8]);
|
|
195
|
+
return {
|
|
196
|
+
seq_id,
|
|
197
|
+
source,
|
|
198
|
+
type,
|
|
199
|
+
start: start === null ? null : parseInt(start, 10),
|
|
200
|
+
end: end === null ? null : parseInt(end, 10),
|
|
201
|
+
score: score === null ? null : parseFloat(score),
|
|
202
|
+
strand,
|
|
203
|
+
phase,
|
|
204
|
+
attributes: attrString === null ? null : parseAttributesNoUnescape(attrString),
|
|
205
|
+
};
|
|
206
|
+
}
|
|
139
207
|
/**
|
|
140
208
|
* Parse a GFF3 directive line.
|
|
141
209
|
*
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";AAAA,6DAA6D;AAC7D,qEAAqE;;AAmBrE,4BAOC;AAeD,wBAEC;AAQD,oCAEC;AAQD,0CAkCC;AAQD,oCAEC;AAYD,4CAsBC;AAQD,wCAwCC;AAQD,4CASC;AA+DD,sCAQC;AAQD,0CAOC;AASD,sCAEC;AAQD,wCAIC;AASD,gCA8BC;AA9VD,MAAM,WAAW,GAAG,oBAAoB,CAAA;AACxC,MAAM,cAAc,GAAG,uBAAuB,CAAA;AAC9C,MAAM,YAAY,GAAG,QAAQ,CAAA;AAC7B,MAAM,eAAe,GAAG,KAAK,CAAA;AAC7B,MAAM,aAAa,GAAG,KAAK,CAAA;AAC3B,4CAA4C;AAC5C,MAAM,eAAe,GAAG,0CAA0C,CAAA;AAClE,4CAA4C;AAC5C,MAAM,iBAAiB,GAAG,sCAAsC,CAAA;AAEhE;;;;;GAKG;AAEH,SAAgB,QAAQ,CAAC,SAAiB;IACxC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,OAAO,SAAS,CAAC,UAAU,CAAC,WAAW,EAAE,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CACvD,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CACvC,CAAA;AACH,CAAC;AAED,SAAS,OAAO,CAAC,KAAa,EAAE,CAAkB;IAChD,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,EAAE;QACnC,MAAM,GAAG,GAAG,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QACxE,OAAO,IAAI,GAAG,EAAE,CAAA;IAClB,CAAC,CAAC,CAAA;AACJ,CAAC;AAED;;;;;GAKG;AACH,SAAgB,MAAM,CAAC,MAAuB;IAC5C,OAAO,OAAO,CAAC,eAAe,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC;AAED;;;;;GAKG;AACH,SAAgB,YAAY,CAAC,MAAuB;IAClD,OAAO,OAAO,CAAC,iBAAiB,EAAE,MAAM,CAAC,CAAA;AAC3C,CAAC;AAED;;;;;GAKG;AACH,SAAgB,eAAe,CAAC,UAAkB;IAChD,IAAI,CAAC,UAAU,CAAC,MAAM,IAAI,UAAU,KAAK,GAAG,EAAE,CAAC;QAC7C,OAAO,EAAE,CAAA;IACX,CAAC;IAED,MAAM,KAAK,GAAmB,EAAE,CAAA;IAEhC,IAAI,GAAG,GAAG,UAAU,CAAA;IACpB,IAAI,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QACvB,GAAG,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACpD,CAAC;IAED,KAAK,MAAM,CAAC,IAAI,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QAC/B,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QAC5B,IAAI,KAAK,KAAK,CAAC,CAAC,EAAE,CAAC;YACjB,SAAQ;QACV,CAAC;QACD,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAChC,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YAClB,SAAQ;QACV,CAAC;QAED,MAAM,GAAG,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,IAAI,EAAE,CAAA;QACpC,IAAI,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,IAAI,GAAG,EAAE,CAAA;YACT,KAAK,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;QACnB,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACjC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;QAC/B,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;GAKG;AACH,SAAgB,YAAY,CAAC,IAAY;IACvC,OAAO,gBAAgB,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED;;;;;GAKG;AACH,SAAS,IAAI,CAAC,CAA4B;IACxC,OAAO,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AAC5D,CAAC;AAED,SAAgB,gBAAgB,CAAC,CAAgC;IAC/D,MAAM,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACzB,MAAM,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACzB,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvB,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACtB,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACzB,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,UAAU,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAE7B,OAAO;QACL,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI;QACxC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI;QACxC,IAAI,EAAE,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI;QAClC,KAAK,EAAE,KAAK,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,EAAE,EAAE,CAAC;QAClD,GAAG,EAAE,GAAG,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,EAAE,EAAE,CAAC;QAC5C,KAAK,EAAE,KAAK,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC;QAChD,MAAM;QACN,KAAK;QACL,UAAU,EAAE,UAAU,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,UAAU,CAAC;KACrE,CAAA;AACH,CAAC;AAED;;;;;GAKG;AACH,SAAgB,cAAc,CAC5B,IAAY;IAMZ,MAAM,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACvC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,IAAI,CAAA;IACb,CAAC;IAED,MAAM,CAAC,EAAE,IAAI,CAAC,GAAG,KAAK,CAAA;IACtB,IAAI,CAAC,EAAE,AAAD,EAAG,QAAQ,CAAC,GAAG,KAAK,CAAA;IAE1B,MAAM,MAAM,GAAkB,EAAE,SAAS,EAAE,IAAI,EAAE,CAAA;IACjD,IAAI,QAAS,CAAC,MAAM,EAAE,CAAC;QACrB,QAAQ,GAAG,QAAS,CAAC,OAAO,CAAC,YAAY,EAAE,EAAE,CAAC,CAAA;QAC9C,MAAM,CAAC,KAAK,GAAG,QAAQ,CAAA;IACzB,CAAC;IAED,iFAAiF;IACjF,IAAI,IAAI,KAAK,iBAAiB,EAAE,CAAC;QAC/B,MAAM,CAAC,GAAG,QAAS,CAAC,KAAK,CAAC,eAAe,EAAE,CAAC,CAAC,CAAA;QAC7C,OAAO;YACL,GAAG,MAAM;YACT,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC;YACZ,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,aAAa,EAAE,EAAE,CAAC;YAC1C,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,aAAa,EAAE,EAAE,CAAC;SACV,CAAA;IAClC,CAAC;SAAM,IAAI,IAAI,KAAK,cAAc,EAAE,CAAC;QACnC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAS,CAAC,KAAK,CAAC,eAAe,EAAE,CAAC,CAAC,CAAA;QAC/D,OAAO;YACL,GAAG,MAAM;YACT,MAAM;YACN,SAAS;SACkB,CAAA;IAC/B,CAAC;IAED,OAAO,MAAM,CAAA;AACf,CAAC;AAED;;;;;GAKG;AACH,SAAgB,gBAAgB,CAAC,KAAqB;IACpD,MAAM,SAAS,G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|
|
1
|
+
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|
package/esm/api.d.ts
CHANGED
|
@@ -29,4 +29,14 @@ export declare function parseArraySync(arr: string[]): GFF3Feature[];
|
|
|
29
29
|
* @returns array of parsed features
|
|
30
30
|
*/
|
|
31
31
|
export declare function parseRecordsSync(records: LineRecord[]): GFF3Feature[];
|
|
32
|
+
/**
|
|
33
|
+
* Synchronously parse an array of LineRecord objects containing pre-split GFF3
|
|
34
|
+
* fields and return an array of the parsed items. Uses a fast path that skips
|
|
35
|
+
* unescaping when hasEscapes is false.
|
|
36
|
+
*
|
|
37
|
+
* @param records - Array of LineRecord objects with fields array and optional lineHash
|
|
38
|
+
* @param hasEscapes - Whether the records contain percent-encoded characters
|
|
39
|
+
* @returns array of parsed features
|
|
40
|
+
*/
|
|
41
|
+
export declare function parseRecordsSyncFast(records: LineRecord[], hasEscapes: boolean): GFF3Feature[];
|
|
32
42
|
export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, } from './util.ts';
|
package/esm/api.js
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import Parser from "./parse.js";
|
|
2
|
-
import { parseFieldsArray } from "./util.js";
|
|
2
|
+
import { parseFieldsArray, parseFieldsArrayNoUnescape } from "./util.js";
|
|
3
3
|
/**
|
|
4
4
|
* Synchronously parse a string containing GFF3 and return an array of the
|
|
5
5
|
* parsed items.
|
|
@@ -75,4 +75,36 @@ export function parseRecordsSync(records) {
|
|
|
75
75
|
parser.finish();
|
|
76
76
|
return items;
|
|
77
77
|
}
|
|
78
|
+
/**
|
|
79
|
+
* Synchronously parse an array of LineRecord objects containing pre-split GFF3
|
|
80
|
+
* fields and return an array of the parsed items. Uses a fast path that skips
|
|
81
|
+
* unescaping when hasEscapes is false.
|
|
82
|
+
*
|
|
83
|
+
* @param records - Array of LineRecord objects with fields array and optional lineHash
|
|
84
|
+
* @param hasEscapes - Whether the records contain percent-encoded characters
|
|
85
|
+
* @returns array of parsed features
|
|
86
|
+
*/
|
|
87
|
+
export function parseRecordsSyncFast(records, hasEscapes) {
|
|
88
|
+
const items = [];
|
|
89
|
+
const parser = new Parser({
|
|
90
|
+
featureCallback: arg => items.push(arg),
|
|
91
|
+
disableDerivesFromReferences: true,
|
|
92
|
+
errorCallback: err => {
|
|
93
|
+
throw new Error(err);
|
|
94
|
+
},
|
|
95
|
+
});
|
|
96
|
+
const parseFunc = hasEscapes ? parseFieldsArray : parseFieldsArrayNoUnescape;
|
|
97
|
+
for (const record of records) {
|
|
98
|
+
const featureLine = parseFunc(record.fields);
|
|
99
|
+
if (record.lineHash !== undefined) {
|
|
100
|
+
if (!featureLine.attributes) {
|
|
101
|
+
featureLine.attributes = {};
|
|
102
|
+
}
|
|
103
|
+
featureLine.attributes._lineHash = [String(record.lineHash)];
|
|
104
|
+
}
|
|
105
|
+
parser.addParsedFeatureLine(featureLine);
|
|
106
|
+
}
|
|
107
|
+
parser.finish();
|
|
108
|
+
return items;
|
|
109
|
+
}
|
|
78
110
|
//# sourceMappingURL=api.js.map
|
package/esm/api.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,YAAY,CAAA;AAC/B,OAAO,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;
|
|
1
|
+
{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,YAAY,CAAA;AAC/B,OAAO,EAAE,gBAAgB,EAAE,0BAA0B,EAAE,MAAM,WAAW,CAAA;AASxE;;;;;;;GAOG;AACH,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,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,MAAM,UAAU,cAAc,CAAC,GAAa;IAC1C,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,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,MAAM,UAAU,gBAAgB,CAAC,OAAqB;IACpD,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,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,gBAAgB,CAAC,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;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,oBAAoB,CAAC,OAAqB,EAAE,UAAmB;IAC7E,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,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,MAAM,SAAS,GAAG,UAAU,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,0BAA0B,CAAA;IAE5E,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,WAAW,GAAoB,SAAS,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC7D,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/esm/index.d.ts
CHANGED
|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
import { parseArraySync, parseRecordsSync, parseStringSync } from './api.ts';
|
|
2
|
-
export { parseArraySync, parseRecordsSync, parseStringSync };
|
|
1
|
+
import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from './api.ts';
|
|
2
|
+
export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync };
|
|
3
3
|
export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, LineRecord, } from './api.ts';
|
package/esm/index.js
CHANGED
|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
import { parseArraySync, parseRecordsSync, parseStringSync } from "./api.js";
|
|
2
|
-
export { parseArraySync, parseRecordsSync, parseStringSync };
|
|
1
|
+
import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from "./api.js";
|
|
2
|
+
export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync };
|
|
3
3
|
//# sourceMappingURL=index.js.map
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,eAAe,EAAE,MAAM,UAAU,CAAA;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,eAAe,EAAE,MAAM,UAAU,CAAA;AAClG,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,eAAe,EAAE,CAAA"}
|
package/esm/parse.js
CHANGED
|
@@ -1,8 +1,4 @@
|
|
|
1
1
|
import * as GFF3 from "./util.js";
|
|
2
|
-
const containerAttributes = {
|
|
3
|
-
Parent: 'child_features',
|
|
4
|
-
Derives_from: 'derived_features',
|
|
5
|
-
};
|
|
6
2
|
const featureLineRegex = /^\s*[^#\s>]/;
|
|
7
3
|
const commentOrDirectiveRegex = /^\s*(#+)(.*)/;
|
|
8
4
|
const blankLineRegex = /^\s*$/;
|
|
@@ -227,7 +223,8 @@ export default class Parser {
|
|
|
227
223
|
let dominated = false;
|
|
228
224
|
for (const id of ids) {
|
|
229
225
|
const domKey = `Parent,${toId}`;
|
|
230
|
-
const rec = this._completedReferences[id] ||
|
|
226
|
+
const rec = this._completedReferences[id] ||
|
|
227
|
+
(this._completedReferences[id] = {});
|
|
231
228
|
if (rec[domKey]) {
|
|
232
229
|
dominated = true;
|
|
233
230
|
}
|
|
@@ -254,7 +251,8 @@ export default class Parser {
|
|
|
254
251
|
let dominated = false;
|
|
255
252
|
for (const id of ids) {
|
|
256
253
|
const domKey = `Derives_from,${toId}`;
|
|
257
|
-
const rec = this._completedReferences[id] ||
|
|
254
|
+
const rec = this._completedReferences[id] ||
|
|
255
|
+
(this._completedReferences[id] = {});
|
|
258
256
|
if (rec[domKey]) {
|
|
259
257
|
dominated = true;
|
|
260
258
|
}
|
package/esm/parse.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"parse.js","sourceRoot":"","sources":["../src/parse.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,WAAW,CAAA;AAEjC,MAAM,
|
|
1
|
+
{"version":3,"file":"parse.js","sourceRoot":"","sources":["../src/parse.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,WAAW,CAAA;AAEjC,MAAM,gBAAgB,GAAG,aAAa,CAAA;AACtC,MAAM,uBAAuB,GAAG,cAAc,CAAA;AAC9C,MAAM,cAAc,GAAG,OAAO,CAAA;AAC9B,MAAM,eAAe,GAAG,OAAO,CAAA;AAC/B,MAAM,eAAe,GAAG,UAAU,CAAA;AAiBlC,MAAM,CAAC,OAAO,OAAO,MAAM;IACzB,eAAe,CAAqC;IACpD,WAAW,CAAY;IACvB,eAAe,CAAqC;IACpD,aAAa,CAAyB;IACtC,4BAA4B,CAAS;IACrC,iBAAiB,CAAyC;IAC1D,UAAU,CAAQ;IAClB,GAAG,GAAG,KAAK,CAAA;IACX,UAAU,GAAG,CAAC,CAAA;IACd,6DAA6D;IAC7D,wCAAwC;IAChC,0BAA0B,GAAuB,EAAE,CAAA;IAC3D,2BAA2B;IACnB,sBAAsB,GAC5B,EAAE,CAAA;IACI,oBAAoB,GAGxB,EAAE,CAAA;IACN,yDAAyD;IACzD,iBAAiB;IACjB,mBAAmB;IACnB,qEAAqE;IACrE,iFAAiF;IACjF,OAAO;IACP,IAAI;IACI,yBAAyB,GAA2C,EAAE,CAAA;IAE9E,YAAY,IAAgB;QAC1B,gEAAgE;QAChE,MAAM,QAAQ,GAAG,GAAG,EAAE,GAAE,CAAC,CAAA;QAEzB,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,eAAe,IAAI,QAAQ,CAAA;QACvD,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,IAAI,QAAQ,CAAA;QAC/C,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,eAAe,IAAI,QAAQ,CAAA;QACvD,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,QAAQ,CAAA;QACnD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAC,iBAAiB,IAAI,QAAQ,CAAA;QAC3D,IAAI,CAAC,4BAA4B;YAC/B,IAAI,CAAC,4BAA4B,IAAI,KAAK,CAAA;QAE5C,4BAA4B;QAC5B,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAA;IAC9E,CAAC;IAED,OAAO,CAAC,IAAY;QAClB,IAAI,IAAI,CAAC,GAAG,EAAE,CAAC;YACb,OAAM;QACR,CAAC;QAED,IAAI,CAAC,UAAU,IAAI,CAAC,CAAA;QAEpB,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,iCAAiC;YACjC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YACtB,OAAM;QACR,CAAC;QAED,MAAM,KAAK,GAAG,uBAAuB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAChD,IAAI,KAAK,EAAE,CAAC;YACV,uBAAuB;YACvB,MAAM,CAAC,EAAE,SAAS,CAAC,GAAG,KAAK,CAAA;YAC3B,IAAI,CAAC,EAAE,AAAD,EAAG,QAAQ,CAAC,GAAG,KAAK,CAAA;YAE1B,IAAI,SAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC5B,uDAAuD;gBACvD,IAAI,CAAC,iCAAiC,EAAE,CAAA;YAC1C,CAAC;iBAAM,IAAI,SAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACnC,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;gBAC3C,IAAI,SAAS,EAAE,CAAC;oBACd,IAAI,SAAS,CAAC,SAAS,KAAK,OAAO,EAAE,CAAC;wBACpC,IAAI,CAAC,iCAAiC,EAAE,CAAA;wBACxC,IAAI,CAAC,GAAG,GAAG,IAAI,CAAA;oBACjB,CAAC;yBAAM,CAAC;wBACN,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;oBAC3B,CAAC;gBACH,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,QAAS,CAAC,SAAS,EAAE,EAAE,CAAC,CAAA;YACpD,CAAC;QACH,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,yBAAyB;QAC3B,CAAC;aAAM,IAAI,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,sDAAsD;YACtD,IAAI,CAAC,iCAAiC,EAAE,CAAA;YACxC,IAAI,CAAC,GAAG,GAAG,IAAI,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,qBAAqB;YACrB,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,EAAE,EAAE,CAAC,CAAA;YACpD,MAAM,IAAI,KAAK,CAAC,oCAAoC,OAAO,IAAI,CAAC,CAAA;QAClE,CAAC;IACH,CAAC;IAED,oBAAoB,CAAC,WAAiC;QACpD,IAAI,IAAI,CAAC,GAAG,EAAE,CAAC;YACb,OAAM;QACR,CAAC;QACD,IAAI,CAAC,UAAU,IAAI,CAAC,CAAA;QACpB,IAAI,CAAC,iBAAiB,CAAC,WAAW,CAAC,CAAA;IACrC,CAAC;IAED,MAAM;QACJ,IAAI,CAAC,iCAAiC,EAAE,CAAA;QACxC,IAAI,CAAC,WAAW,EAAE,CAAA;IACpB,CAAC;IAEO,SAAS,CACf,CAA2D;QAE3D,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC,CAAA;QACzB,CAAC;aAAM,IAAI,WAAW,IAAI,CAAC,EAAE,CAAC;YAC5B,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC,CAAA;QAC3B,CAAC;aAAM,IAAI,SAAS,IAAI,CAAC,EAAE,CAAC;YAC1B,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC,CAAA;QACzB,CAAC;IACH,CAAC;IAEO,uBAAuB,CAAC,mBAAmB,GAAG,CAAC;QACrD,MAAM,aAAa,GAAG,CAAC,IAAuB,EAAE,EAAE;YAChD,IAAI,IAAI,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAC/D,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,EAAE,CAAA;gBACjC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,EAAE;oBACf,OAAO,IAAI,CAAC,sBAAsB,CAAC,EAAE,CAAC,CAAA;oBACtC,OAAO,IAAI,CAAC,oBAAoB,CAAC,EAAE,CAAC,CAAA;gBACtC,CAAC,CAAC,CAAA;gBACF,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;oBACf,uEAAuE;oBACvE,IAAI,CAAC,CAAC,cAAc,EAAE,CAAC;wBACrB,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;4BAC3B,aAAa,CAAC,CAAC,CAAC,CAAA;wBAClB,CAAC,CAAC,CAAA;oBACJ,CAAC;oBACD,uEAAuE;oBACvE,IAAI,CAAC,CAAC,gBAAgB,EAAE,CAAC;wBACvB,CAAC,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;4BAC7B,aAAa,CAAC,CAAC,CAAC,CAAA;wBAClB,CAAC,CAAC,CAAA;oBACJ,CAAC;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC,CAAA;QAED,OACE,IAAI,CAAC,0BAA0B,CAAC,MAAM,GAAG,mBAAmB;YAC5D,IAAI,CAAC,UAAU,EACf,CAAC;YACD,MAAM,IAAI,GAAG,IAAI,CAAC,0BAA0B,CAAC,KAAK,EAAE,CAAA;YACpD,IAAI,IAAI,EAAE,CAAC;gBACT,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;gBACpB,aAAa,CAAC,IAAI,CAAC,CAAA;YACrB,CAAC;QACH,CAAC;IACH,CAAC;IAED;;;OAGG;IACK,iCAAiC;QACvC,IAAI,CAAC,0BAA0B,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;QAElE,IAAI,CAAC,0BAA0B,GAAG,EAAE,CAAA;QACpC,IAAI,CAAC,sBAAsB,GAAG,EAAE,CAAA;QAChC,IAAI,CAAC,oBAAoB,GAAG,EAAE,CAAA;QAE9B,yDAAyD;QACzD,kCAAkC;QAClC,MAAM,UAAU,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAA;QAC9D,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC;YACtB,MAAM,IAAI,KAAK,CACb,sGAAsG,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAC7H,CAAA;QACH,CAAC;IACH,CAAC;IAEO,WAAW,CAAC,IAAY;QAC9B,IAAI,CAAC,iBAAiB,CAAC,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAA;IACjD,CAAC;IAEO,iBAAiB,CAAC,cAAoC;QAC5D,MAAM,WAAW,GAAG,cAA8C,CAAA;QAClE,WAAW,CAAC,cAAc,GAAG,EAAE,CAAA;QAC/B,WAAW,CAA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|
package/esm/util.d.ts
CHANGED
|
@@ -26,6 +26,14 @@ export declare function escapeColumn(rawVal: string | number): string;
|
|
|
26
26
|
* @returns Parsed attributes
|
|
27
27
|
*/
|
|
28
28
|
export declare function parseAttributes(attrString: string): GFF3Attributes;
|
|
29
|
+
/**
|
|
30
|
+
* Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
|
|
31
|
+
* Fast path for data known to contain no escaped characters.
|
|
32
|
+
*
|
|
33
|
+
* @param attrString - String of GFF3 9th column
|
|
34
|
+
* @returns Parsed attributes
|
|
35
|
+
*/
|
|
36
|
+
export declare function parseAttributesNoUnescape(attrString: string): GFF3Attributes;
|
|
29
37
|
/**
|
|
30
38
|
* Parse a GFF3 feature line
|
|
31
39
|
*
|
|
@@ -34,6 +42,14 @@ export declare function parseAttributes(attrString: string): GFF3Attributes;
|
|
|
34
42
|
*/
|
|
35
43
|
export declare function parseFeature(line: string): GFF3FeatureLine;
|
|
36
44
|
export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
|
|
45
|
+
/**
|
|
46
|
+
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
|
47
|
+
* Fast path for data known to contain no escaped characters.
|
|
48
|
+
*
|
|
49
|
+
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
50
|
+
* @returns The parsed feature
|
|
51
|
+
*/
|
|
52
|
+
export declare function parseFieldsArrayNoUnescape(f: (string | null | undefined)[]): GFF3FeatureLine;
|
|
37
53
|
/**
|
|
38
54
|
* Parse a GFF3 directive line.
|
|
39
55
|
*
|
package/esm/util.js
CHANGED
|
@@ -81,6 +81,43 @@ export function parseAttributes(attrString) {
|
|
|
81
81
|
}
|
|
82
82
|
return attrs;
|
|
83
83
|
}
|
|
84
|
+
/**
|
|
85
|
+
* Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
|
|
86
|
+
* Fast path for data known to contain no escaped characters.
|
|
87
|
+
*
|
|
88
|
+
* @param attrString - String of GFF3 9th column
|
|
89
|
+
* @returns Parsed attributes
|
|
90
|
+
*/
|
|
91
|
+
export function parseAttributesNoUnescape(attrString) {
|
|
92
|
+
if (!attrString.length || attrString === '.') {
|
|
93
|
+
return {};
|
|
94
|
+
}
|
|
95
|
+
const attrs = {};
|
|
96
|
+
let str = attrString;
|
|
97
|
+
if (str.endsWith('\n')) {
|
|
98
|
+
str = str.slice(0, str.endsWith('\r\n') ? -2 : -1);
|
|
99
|
+
}
|
|
100
|
+
for (const a of str.split(';')) {
|
|
101
|
+
const eqIdx = a.indexOf('=');
|
|
102
|
+
if (eqIdx === -1) {
|
|
103
|
+
continue;
|
|
104
|
+
}
|
|
105
|
+
const value = a.slice(eqIdx + 1);
|
|
106
|
+
if (!value.length) {
|
|
107
|
+
continue;
|
|
108
|
+
}
|
|
109
|
+
const tag = a.slice(0, eqIdx).trim();
|
|
110
|
+
let arec = attrs[tag];
|
|
111
|
+
if (!arec) {
|
|
112
|
+
arec = [];
|
|
113
|
+
attrs[tag] = arec;
|
|
114
|
+
}
|
|
115
|
+
for (const s of value.split(',')) {
|
|
116
|
+
arec.push(s.trim());
|
|
117
|
+
}
|
|
118
|
+
}
|
|
119
|
+
return attrs;
|
|
120
|
+
}
|
|
84
121
|
/**
|
|
85
122
|
* Parse a GFF3 feature line
|
|
86
123
|
*
|
|
@@ -121,6 +158,35 @@ export function parseFieldsArray(f) {
|
|
|
121
158
|
attributes: attrString === null ? null : parseAttributes(attrString),
|
|
122
159
|
};
|
|
123
160
|
}
|
|
161
|
+
/**
|
|
162
|
+
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
|
163
|
+
* Fast path for data known to contain no escaped characters.
|
|
164
|
+
*
|
|
165
|
+
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
166
|
+
* @returns The parsed feature
|
|
167
|
+
*/
|
|
168
|
+
export function parseFieldsArrayNoUnescape(f) {
|
|
169
|
+
const seq_id = norm(f[0]);
|
|
170
|
+
const source = norm(f[1]);
|
|
171
|
+
const type = norm(f[2]);
|
|
172
|
+
const start = norm(f[3]);
|
|
173
|
+
const end = norm(f[4]);
|
|
174
|
+
const score = norm(f[5]);
|
|
175
|
+
const strand = norm(f[6]);
|
|
176
|
+
const phase = norm(f[7]);
|
|
177
|
+
const attrString = norm(f[8]);
|
|
178
|
+
return {
|
|
179
|
+
seq_id,
|
|
180
|
+
source,
|
|
181
|
+
type,
|
|
182
|
+
start: start === null ? null : parseInt(start, 10),
|
|
183
|
+
end: end === null ? null : parseInt(end, 10),
|
|
184
|
+
score: score === null ? null : parseFloat(score),
|
|
185
|
+
strand,
|
|
186
|
+
phase,
|
|
187
|
+
attributes: attrString === null ? null : parseAttributesNoUnescape(attrString),
|
|
188
|
+
};
|
|
189
|
+
}
|
|
124
190
|
/**
|
|
125
191
|
* Parse a GFF3 directive line.
|
|
126
192
|
*
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
package/src/api.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import Parser from './parse.ts'
|
|
2
|
-
import { parseFieldsArray } from './util.ts'
|
|
2
|
+
import { parseFieldsArray, parseFieldsArrayNoUnescape } from './util.ts'
|
|
3
3
|
|
|
4
4
|
import type { GFF3Feature, GFF3FeatureLine } from './util.ts'
|
|
5
5
|
|
|
@@ -92,6 +92,42 @@ export function parseRecordsSync(records: LineRecord[]): GFF3Feature[] {
|
|
|
92
92
|
return items
|
|
93
93
|
}
|
|
94
94
|
|
|
95
|
+
/**
|
|
96
|
+
* Synchronously parse an array of LineRecord objects containing pre-split GFF3
|
|
97
|
+
* fields and return an array of the parsed items. Uses a fast path that skips
|
|
98
|
+
* unescaping when hasEscapes is false.
|
|
99
|
+
*
|
|
100
|
+
* @param records - Array of LineRecord objects with fields array and optional lineHash
|
|
101
|
+
* @param hasEscapes - Whether the records contain percent-encoded characters
|
|
102
|
+
* @returns array of parsed features
|
|
103
|
+
*/
|
|
104
|
+
export function parseRecordsSyncFast(records: LineRecord[], hasEscapes: boolean): GFF3Feature[] {
|
|
105
|
+
const items: GFF3Feature[] = []
|
|
106
|
+
const parser = new Parser({
|
|
107
|
+
featureCallback: arg => items.push(arg),
|
|
108
|
+
disableDerivesFromReferences: true,
|
|
109
|
+
errorCallback: err => {
|
|
110
|
+
throw new Error(err)
|
|
111
|
+
},
|
|
112
|
+
})
|
|
113
|
+
|
|
114
|
+
const parseFunc = hasEscapes ? parseFieldsArray : parseFieldsArrayNoUnescape
|
|
115
|
+
|
|
116
|
+
for (const record of records) {
|
|
117
|
+
const featureLine: GFF3FeatureLine = parseFunc(record.fields)
|
|
118
|
+
if (record.lineHash !== undefined) {
|
|
119
|
+
if (!featureLine.attributes) {
|
|
120
|
+
featureLine.attributes = {}
|
|
121
|
+
}
|
|
122
|
+
featureLine.attributes._lineHash = [String(record.lineHash)]
|
|
123
|
+
}
|
|
124
|
+
parser.addParsedFeatureLine(featureLine)
|
|
125
|
+
}
|
|
126
|
+
parser.finish()
|
|
127
|
+
|
|
128
|
+
return items
|
|
129
|
+
}
|
|
130
|
+
|
|
95
131
|
export type {
|
|
96
132
|
GFF3Comment,
|
|
97
133
|
GFF3Directive,
|
package/src/index.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { parseArraySync, parseRecordsSync, parseStringSync } from './api.ts'
|
|
2
|
-
export { parseArraySync, parseRecordsSync, parseStringSync }
|
|
1
|
+
import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from './api.ts'
|
|
2
|
+
export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync }
|
|
3
3
|
|
|
4
4
|
export type {
|
|
5
5
|
GFF3Comment,
|
package/src/parse.ts
CHANGED
|
@@ -1,10 +1,5 @@
|
|
|
1
1
|
import * as GFF3 from './util.ts'
|
|
2
2
|
|
|
3
|
-
const containerAttributes = {
|
|
4
|
-
Parent: 'child_features' as const,
|
|
5
|
-
Derives_from: 'derived_features' as const,
|
|
6
|
-
}
|
|
7
|
-
|
|
8
3
|
const featureLineRegex = /^\s*[^#\s>]/
|
|
9
4
|
const commentOrDirectiveRegex = /^\s*(#+)(.*)/
|
|
10
5
|
const blankLineRegex = /^\s*$/
|
|
@@ -284,7 +279,9 @@ export default class Parser {
|
|
|
284
279
|
let dominated = false
|
|
285
280
|
for (const id of ids) {
|
|
286
281
|
const domKey = `Parent,${toId}`
|
|
287
|
-
const rec =
|
|
282
|
+
const rec =
|
|
283
|
+
this._completedReferences[id] ||
|
|
284
|
+
(this._completedReferences[id] = {})
|
|
288
285
|
if (rec[domKey]) {
|
|
289
286
|
dominated = true
|
|
290
287
|
}
|
|
@@ -311,7 +308,9 @@ export default class Parser {
|
|
|
311
308
|
let dominated = false
|
|
312
309
|
for (const id of ids) {
|
|
313
310
|
const domKey = `Derives_from,${toId}`
|
|
314
|
-
const rec =
|
|
311
|
+
const rec =
|
|
312
|
+
this._completedReferences[id] ||
|
|
313
|
+
(this._completedReferences[id] = {})
|
|
315
314
|
if (rec[domKey]) {
|
|
316
315
|
dominated = true
|
|
317
316
|
}
|
package/src/util.ts
CHANGED
|
@@ -96,6 +96,49 @@ export function parseAttributes(attrString: string): GFF3Attributes {
|
|
|
96
96
|
return attrs
|
|
97
97
|
}
|
|
98
98
|
|
|
99
|
+
/**
|
|
100
|
+
* Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
|
|
101
|
+
* Fast path for data known to contain no escaped characters.
|
|
102
|
+
*
|
|
103
|
+
* @param attrString - String of GFF3 9th column
|
|
104
|
+
* @returns Parsed attributes
|
|
105
|
+
*/
|
|
106
|
+
export function parseAttributesNoUnescape(attrString: string): GFF3Attributes {
|
|
107
|
+
if (!attrString.length || attrString === '.') {
|
|
108
|
+
return {}
|
|
109
|
+
}
|
|
110
|
+
|
|
111
|
+
const attrs: GFF3Attributes = {}
|
|
112
|
+
|
|
113
|
+
let str = attrString
|
|
114
|
+
if (str.endsWith('\n')) {
|
|
115
|
+
str = str.slice(0, str.endsWith('\r\n') ? -2 : -1)
|
|
116
|
+
}
|
|
117
|
+
|
|
118
|
+
for (const a of str.split(';')) {
|
|
119
|
+
const eqIdx = a.indexOf('=')
|
|
120
|
+
if (eqIdx === -1) {
|
|
121
|
+
continue
|
|
122
|
+
}
|
|
123
|
+
const value = a.slice(eqIdx + 1)
|
|
124
|
+
if (!value.length) {
|
|
125
|
+
continue
|
|
126
|
+
}
|
|
127
|
+
|
|
128
|
+
const tag = a.slice(0, eqIdx).trim()
|
|
129
|
+
let arec = attrs[tag]
|
|
130
|
+
if (!arec) {
|
|
131
|
+
arec = []
|
|
132
|
+
attrs[tag] = arec
|
|
133
|
+
}
|
|
134
|
+
|
|
135
|
+
for (const s of value.split(',')) {
|
|
136
|
+
arec.push(s.trim())
|
|
137
|
+
}
|
|
138
|
+
}
|
|
139
|
+
return attrs
|
|
140
|
+
}
|
|
141
|
+
|
|
99
142
|
/**
|
|
100
143
|
* Parse a GFF3 feature line
|
|
101
144
|
*
|
|
@@ -140,6 +183,37 @@ export function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureL
|
|
|
140
183
|
}
|
|
141
184
|
}
|
|
142
185
|
|
|
186
|
+
/**
|
|
187
|
+
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
|
188
|
+
* Fast path for data known to contain no escaped characters.
|
|
189
|
+
*
|
|
190
|
+
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
191
|
+
* @returns The parsed feature
|
|
192
|
+
*/
|
|
193
|
+
export function parseFieldsArrayNoUnescape(f: (string | null | undefined)[]): GFF3FeatureLine {
|
|
194
|
+
const seq_id = norm(f[0])
|
|
195
|
+
const source = norm(f[1])
|
|
196
|
+
const type = norm(f[2])
|
|
197
|
+
const start = norm(f[3])
|
|
198
|
+
const end = norm(f[4])
|
|
199
|
+
const score = norm(f[5])
|
|
200
|
+
const strand = norm(f[6])
|
|
201
|
+
const phase = norm(f[7])
|
|
202
|
+
const attrString = norm(f[8])
|
|
203
|
+
|
|
204
|
+
return {
|
|
205
|
+
seq_id,
|
|
206
|
+
source,
|
|
207
|
+
type,
|
|
208
|
+
start: start === null ? null : parseInt(start, 10),
|
|
209
|
+
end: end === null ? null : parseInt(end, 10),
|
|
210
|
+
score: score === null ? null : parseFloat(score),
|
|
211
|
+
strand,
|
|
212
|
+
phase,
|
|
213
|
+
attributes: attrString === null ? null : parseAttributesNoUnescape(attrString),
|
|
214
|
+
}
|
|
215
|
+
}
|
|
216
|
+
|
|
143
217
|
/**
|
|
144
218
|
* Parse a GFF3 directive line.
|
|
145
219
|
*
|