gff-nostream 2.0.1 → 3.0.0

package/dist/api.d.ts

@@ -1,42 +1,25 @@
 import type { GFF3Feature } from './util.ts';
 export interface LineRecord {
-    fields: string[];
+    line: string;
     lineHash?: string | number;
+    start: number;
+    end: number;
+    hasEscapes: boolean;
 }
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
  * parsed items.
  *
  * @param str - GFF3 string
- * @param inputOptions - Parsing options
- * @returns array of parsed features, directives, comments and/or sequences
- */
-export declare function parseStringSync(str: string): GFF3Feature[];
-/**
- * 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 declare function parseStringSync(str: string): GFF3Feature[];
 /**
- * Synchronously parse an array of LineRecord objects containing pre-split GFF3
- * fields and return an array of the parsed items. Uses a fast path that skips
- * unescaping when hasEscapes is false.
+ * Parse an array of LineRecord objects containing raw GFF3 lines.
+ * Supports parent/child relationships.
  *
- * @param records - Array of LineRecord objects with fields array and optional lineHash
- * @param hasEscapes - Whether the records contain percent-encoded characters
+ * @param records - Array of LineRecord objects with raw line and metadata
  * @returns array of parsed features
  */
-export declare function parseRecordsSyncFast(records: LineRecord[], hasEscapes: boolean): GFF3Feature[];
+export declare function parseRecords(records: LineRecord[]): GFF3Feature[];
 export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, } from './util.ts';

package/dist/api.js

@@ -1,119 +1,115 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseStringSync = parseStringSync;
-exports.parseArraySync = parseArraySync;
-exports.parseRecordsSync = parseRecordsSync;
-exports.parseRecordsSyncFast = parseRecordsSyncFast;
-const parse_ts_1 = __importDefault(require("./parse.js"));
+exports.parseRecords = parseRecords;
 const util_ts_1 = require("./util.js");
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
  * parsed items.
  *
  * @param str - GFF3 string
- * @param inputOptions - Parsing options
- * @returns array of parsed features, directives, comments and/or sequences
- */
-function parseStringSync(str) {
-    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 str.split(/\r?\n/)) {
-        parser.addLine(line);
-    }
-    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 = {};
+function parseStringSync(str) {
+    const lines = str.split(/\r?\n/);
+    const records = [];
+    for (let i = 0; i < lines.length; i++) {
+        const line = lines[i];
+        if (line.length === 0 || line[0] === '#') {
+            if (line.startsWith('##FASTA')) {
+                break;
             }
-            featureLine.attributes._lineHash = [String(record.lineHash)];
+            continue;
         }
-        parser.addParsedFeatureLine(featureLine);
+        if (line[0] === '>') {
+            break;
+        }
+        records.push({
+            line,
+            start: 0,
+            end: 0,
+            hasEscapes: line.includes('%'),
+        });
     }
-    parser.finish();
-    return items;
+    return parseRecords(records);
 }
 /**
- * Synchronously parse an array of LineRecord objects containing pre-split GFF3
- * fields and return an array of the parsed items. Uses a fast path that skips
- * unescaping when hasEscapes is false.
+ * Parse an array of LineRecord objects containing raw GFF3 lines.
+ * Supports parent/child relationships.
  *
- * @param records - Array of LineRecord objects with fields array and optional lineHash
- * @param hasEscapes - Whether the records contain percent-encoded characters
+ * @param records - Array of LineRecord objects with raw line and metadata
  * @returns array of parsed features
  */
-function parseRecordsSyncFast(records, hasEscapes) {
+function parseRecords(records) {
     const items = [];
-    const parser = new parse_ts_1.default({
-        featureCallback: arg => items.push(arg),
-        disableDerivesFromReferences: true,
-        errorCallback: err => {
-            throw new Error(err);
-        },
-    });
-    const parseFunc = hasEscapes ? util_ts_1.parseFieldsArray : util_ts_1.parseFieldsArrayNoUnescape;
-    for (const record of records) {
-        const featureLine = parseFunc(record.fields);
+    const byId = new Map();
+    const orphans = new Map();
+    for (let i = 0; i < records.length; i++) {
+        const record = records[i];
+        const featureLine = (record.hasEscapes
+            ? (0, util_ts_1.parseFeature)(record.line)
+            : (0, util_ts_1.parseFeatureNoUnescape)(record.line));
+        featureLine.child_features = [];
+        featureLine.derived_features = [];
         if (record.lineHash !== undefined) {
             if (!featureLine.attributes) {
                 featureLine.attributes = {};
             }
             featureLine.attributes._lineHash = [String(record.lineHash)];
         }
-        parser.addParsedFeatureLine(featureLine);
+        const attrs = featureLine.attributes;
+        const ids = attrs?.ID;
+        const parents = attrs?.Parent;
+        if (!ids && !parents) {
+            items.push([featureLine]);
+            continue;
+        }
+        let feature;
+        if (ids) {
+            const id = ids[0];
+            const existing = byId.get(id);
+            if (existing) {
+                existing.push(featureLine);
+                feature = existing;
+            }
+            else {
+                feature = [featureLine];
+                if (!parents) {
+                    items.push(feature);
+                }
+                byId.set(id, feature);
+                const waiting = orphans.get(id);
+                if (waiting) {
+                    for (let j = 0; j < waiting.length; j++) {
+                        featureLine.child_features.push(waiting[j]);
+                    }
+                    orphans.delete(id);
+                }
+            }
+        }
+        else {
+            feature = [featureLine];
+        }
+        if (parents) {
+            for (let j = 0; j < parents.length; j++) {
+                const parentId = parents[j];
+                const parent = byId.get(parentId);
+                if (parent) {
+                    for (let k = 0; k < parent.length; k++) {
+                        parent[k].child_features.push(feature);
+                    }
+                }
+                else {
+                    let arr = orphans.get(parentId);
+                    if (!arr) {
+                        arr = [];
+                        orphans.set(parentId, arr);
+                    }
+                    arr.push(feature);
+                }
+            }
+        }
     }
-    parser.finish();
     return items;
 }
 //# sourceMappingURL=api.js.map

package/dist/api.js.map

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

@@ -1,3 +1,2 @@
-import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from './api.ts';
-export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync };
+export { parseRecords, parseStringSync } from './api.ts';
 export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, LineRecord, } from './api.ts';

package/dist/index.js

@@ -1,9 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseStringSync = exports.parseRecordsSyncFast = 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, "parseRecordsSyncFast", { enumerable: true, get: function () { return api_ts_1.parseRecordsSyncFast; } });
+exports.parseStringSync = exports.parseRecords = void 0;
+var api_ts_1 = require("./api.js");
+Object.defineProperty(exports, "parseRecords", { enumerable: true, get: function () { return api_ts_1.parseRecords; } });
 Object.defineProperty(exports, "parseStringSync", { enumerable: true, get: function () { return api_ts_1.parseStringSync; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,mCAAwD;AAA/C,sGAAA,YAAY,OAAA;AAAE,yGAAA,eAAe,OAAA"}

package/dist/util.d.ts

@@ -4,21 +4,7 @@
  * @param stringVal - Escaped GFF3 string value
  * @returns An unescaped string value
  */
-export declare function unescape(stringVal: string): string;
-/**
- * Escape a value for use in a GFF3 attribute value.
- *
- * @param rawVal - Raw GFF3 attribute value
- * @returns An escaped string value
- */
-export declare function escape(rawVal: string | number): string;
-/**
- * Escape a value for use in a GFF3 column value.
- *
- * @param rawVal - Raw GFF3 column value
- * @returns An escaped column value
- */
-export declare function escapeColumn(rawVal: string | number): string;
+export declare function unescape(s: string): string;
 /**
  * Parse the 9th column (attributes) of a GFF3 feature line.
  *
@@ -41,6 +27,20 @@ export declare function parseAttributesNoUnescape(attrString: string): GFF3Attri
  * @returns The parsed feature
  */
 export declare function parseFeature(line: string): GFF3FeatureLine;
+/**
+ * Parse a GFF3 feature line without unescaping.
+ * Fast path for data known to contain no escaped characters.
+ *
+ * @param line - GFF3 feature line
+ * @returns The parsed feature
+ */
+export declare function parseFeatureNoUnescape(line: string): GFF3FeatureLine;
+/**
+ * Parse a GFF3 feature from a pre-split fields array
+ *
+ * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
+ * @returns The parsed feature
+ */
 export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
 /**
  * Parse a GFF3 feature from a pre-split fields array without unescaping.
@@ -57,51 +57,6 @@ export declare function parseFieldsArrayNoUnescape(f: (string | null | undefined
  * @returns The parsed directive
  */
 export declare function parseDirective(line: string): GFF3Directive | GFF3SequenceRegionDirective | GFF3GenomeBuildDirective | null;
-/**
- * Format an attributes object into a string suitable for the 9th column of GFF3.
- *
- * @param attrs - Attributes
- * @returns GFF3 9th column string
- */
-export declare function formatAttributes(attrs: GFF3Attributes): string;
-/**
- * Format a feature object or array of feature objects into one or more lines of
- * GFF3.
- *
- * @param featureOrFeatures - A feature object or array of feature objects
- * @returns A string of one or more GFF3 lines
- */
-export declare function formatFeature(featureOrFeatures: GFF3FeatureLine | GFF3FeatureLineWithRefs | (GFF3FeatureLine | GFF3FeatureLineWithRefs)[]): string;
-/**
- * Format a directive into a line of GFF3.
- *
- * @param directive - A directive object
- * @returns A directive line string
- */
-export declare function formatDirective(directive: GFF3Directive): string;
-/**
- * Format a comment into a GFF3 comment.
- * Yes I know this is just adding a # and a newline.
- *
- * @param comment - A comment object
- * @returns A comment line string
- */
-export declare function formatComment(comment: GFF3Comment): string;
-/**
- * Format a sequence object as FASTA
- *
- * @param seq - A sequence object
- * @returns Formatted single FASTA sequence string
- */
-export declare function formatSequence(seq: GFF3Sequence): string;
-/**
- * Format a directive, comment, sequence, or feature, or array of such items,
- * into one or more lines of GFF3.
- *
- * @param itemOrItems - A comment, sequence, or feature, or array of such items
- * @returns A formatted string or array of strings
- */
-export declare function formatItem(itemOrItems: GFF3FeatureLineWithRefs | GFF3Directive | GFF3Comment | GFF3Sequence | (GFF3FeatureLineWithRefs | GFF3Directive | GFF3Comment | GFF3Sequence)[]): string | string[];
 /** A record of GFF3 attribute identifiers and the values of those identifiers */
 export type GFF3Attributes = Record<string, string[] | undefined>;
 /** A representation of a single line of a GFF3 file */