gff-nostream 3.0.1 → 3.0.4

package/dist/util.js

@@ -14,15 +14,10 @@ exports.parseAttributesJBrowse = parseAttributesJBrowse;
 exports.parseAttributesJBrowseNoUnescape = parseAttributesJBrowseNoUnescape;
 exports.parseFeatureJBrowse = parseFeatureJBrowse;
 exports.parseFeatureJBrowseNoUnescape = parseFeatureJBrowseNoUnescape;
-const escapeRegex = /%([0-9A-Fa-f]{2})/g;
 const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
 const lineEndRegex = /\r?\n$/;
 const whitespaceRegex = /\s+/;
 const nonDigitRegex = /\D/g;
-// eslint-disable-next-line no-control-regex
-const attrEscapeRegex = /[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g;
-// eslint-disable-next-line no-control-regex
-const columnEscapeRegex = /[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g;
 const HEX_LOOKUP = {};
 for (let i = 0; i < 256; i++) {
     const hex = i.toString(16).toUpperCase().padStart(2, '0');
@@ -35,16 +30,35 @@ for (let i = 0; i < 256; i++) {
  * @param stringVal - Escaped GFF3 string value
  * @returns An unescaped string value
  */
-function unescape(s) {
-    return s.indexOf('%') === -1 ? s : decodeURIComponent(s);
+function unescape(stringVal) {
+    const idx = stringVal.indexOf('%');
+    if (idx === -1) {
+        return stringVal;
+    }
+    let result = '';
+    let lastIdx = 0;
+    let i = idx;
+    while (i < stringVal.length) {
+        if (stringVal[i] === '%' && i + 2 < stringVal.length) {
+            result += stringVal.slice(lastIdx, i);
+            const hex = stringVal.slice(i + 1, i + 3);
+            const char = HEX_LOOKUP[hex];
+            if (char !== undefined) {
+                result += char;
+            }
+            else {
+                result += stringVal.slice(i, i + 3);
+            }
+            i += 3;
+            lastIdx = i;
+        }
+        else {
+            i++;
+        }
+    }
+    return result + stringVal.slice(lastIdx);
 }
-/**
- * Parse the 9th column (attributes) of a GFF3 feature line.
- *
- * @param attrString - String of GFF3 9th column
- * @returns Parsed attributes
- */
-function parseAttributes(attrString) {
+function parseAttributesImpl(attrString, shouldUnescape) {
     if (attrString.length === 0 || attrString === '.') {
         return {};
     }
@@ -77,7 +91,7 @@ function parseAttributes(attrString) {
                     }
                     if (commaIdx > valStart) {
                         const val = attrString.slice(valStart, commaIdx);
-                        arec.push(unescape(val));
+                        arec.push(shouldUnescape ? unescape(val) : val);
                     }
                     valStart = commaIdx + 1;
                 }
@@ -87,6 +101,15 @@ function parseAttributes(attrString) {
     }
     return attrs;
 }
+/**
+ * Parse the 9th column (attributes) of a GFF3 feature line.
+ *
+ * @param attrString - String of GFF3 9th column
+ * @returns Parsed attributes
+ */
+function parseAttributes(attrString) {
+    return parseAttributesImpl(attrString, true);
+}
 /**
  * Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
  * Fast path for data known to contain no escaped characters.
@@ -95,64 +118,16 @@ function parseAttributes(attrString) {
  * @returns Parsed attributes
  */
 function parseAttributesNoUnescape(attrString) {
-    if (attrString.length === 0 || attrString === '.') {
-        return {};
-    }
-    const attrs = {};
-    let len = attrString.length;
-    if (attrString[len - 1] === '\n') {
-        len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
-        attrString = attrString.slice(0, len);
-    }
-    let start = 0;
-    while (start < len) {
-        let semiIdx = attrString.indexOf(';', start);
-        if (semiIdx === -1) {
-            semiIdx = len;
-        }
-        if (semiIdx > start) {
-            const eqIdx = attrString.indexOf('=', start);
-            if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
-                const tag = attrString.slice(start, eqIdx);
-                let arec = attrs[tag];
-                if (!arec) {
-                    arec = [];
-                    attrs[tag] = arec;
-                }
-                let valStart = eqIdx + 1;
-                while (valStart < semiIdx) {
-                    let commaIdx = attrString.indexOf(',', valStart);
-                    if (commaIdx === -1 || commaIdx > semiIdx) {
-                        commaIdx = semiIdx;
-                    }
-                    if (commaIdx > valStart) {
-                        arec.push(attrString.slice(valStart, commaIdx));
-                    }
-                    valStart = commaIdx + 1;
-                }
-            }
-        }
-        start = semiIdx + 1;
-    }
-    return attrs;
+    return parseAttributesImpl(attrString, false);
 }
-function normUnescape(s) {
-    return s.length === 0 || s === '.' ? null : unescape(s);
-}
-function norm(s) {
-    return s.length === 0 || s === '.' ? null : s;
+function normImpl(s, shouldUnescape) {
+    if (s.length === 0 || s === '.') {
+        return null;
+    }
+    return shouldUnescape ? unescape(s) : s;
 }
-/**
- * Parse a GFF3 feature line
- *
- * @param line - GFF3 feature line
- * @returns The parsed feature
- */
-function parseFeature(line) {
+function parseFeatureImpl(line, shouldUnescape) {
     const f = line.split('\t');
-    const seq_id = f[0];
-    const source = f[1];
-    const type = f[2];
     const startStr = f[3];
     const endStr = f[4];
     const scoreStr = f[5];
@@ -160,17 +135,28 @@ function parseFeature(line) {
     const phase = f[7];
     const attrString = f[8];
     return {
-        seq_id: normUnescape(seq_id),
-        source: normUnescape(source),
-        type: normUnescape(type),
+        seq_id: normImpl(f[0], shouldUnescape),
+        source: normImpl(f[1], shouldUnescape),
+        type: normImpl(f[2], shouldUnescape),
         start: startStr.length === 0 || startStr === '.' ? null : +startStr,
         end: endStr.length === 0 || endStr === '.' ? null : +endStr,
         score: scoreStr.length === 0 || scoreStr === '.' ? null : +scoreStr,
-        strand: norm(strand),
-        phase: norm(phase),
-        attributes: attrString.length === 0 || attrString === '.' ? null : parseAttributes(attrString),
+        strand: normImpl(strand, false),
+        phase: normImpl(phase, false),
+        attributes: attrString.length === 0 || attrString === '.'
+            ? null
+            : parseAttributesImpl(attrString, shouldUnescape),
     };
 }
+/**
+ * Parse a GFF3 feature line
+ *
+ * @param line - GFF3 feature line
+ * @returns The parsed feature
+ */
+function parseFeature(line) {
+    return parseFeatureImpl(line, true);
+}
 /**
  * Parse a GFF3 feature line without unescaping.
  * Fast path for data known to contain no escaped characters.
@@ -179,7 +165,9 @@ function parseFeature(line) {
  * @returns The parsed feature
  */
 function parseFeatureNoUnescape(line) {
-    const f = line.split('\t');
+    return parseFeatureImpl(line, false);
+}
+function parseFieldsArrayImpl(f, shouldUnescape) {
     const seq_id = f[0];
     const source = f[1];
     const type = f[2];
@@ -190,15 +178,17 @@ function parseFeatureNoUnescape(line) {
     const phase = f[7];
     const attrString = f[8];
     return {
-        seq_id: norm(seq_id),
-        source: norm(source),
-        type: norm(type),
-        start: startStr.length === 0 || startStr === '.' ? null : +startStr,
-        end: endStr.length === 0 || endStr === '.' ? null : +endStr,
-        score: scoreStr.length === 0 || scoreStr === '.' ? null : +scoreStr,
-        strand: norm(strand),
-        phase: norm(phase),
-        attributes: attrString.length === 0 || attrString === '.' ? null : parseAttributesNoUnescape(attrString),
+        seq_id: seq_id ? normImpl(seq_id, shouldUnescape) : null,
+        source: source ? normImpl(source, shouldUnescape) : null,
+        type: type ? normImpl(type, shouldUnescape) : null,
+        start: !startStr || startStr === '.' ? null : +startStr,
+        end: !endStr || endStr === '.' ? null : +endStr,
+        score: !scoreStr || scoreStr === '.' ? null : +scoreStr,
+        strand: strand && strand !== '.' ? strand : null,
+        phase: phase && phase !== '.' ? phase : null,
+        attributes: !attrString || attrString === '.'
+            ? null
+            : parseAttributesImpl(attrString, shouldUnescape),
     };
 }
 /**
@@ -208,26 +198,7 @@ function parseFeatureNoUnescape(line) {
  * @returns The parsed feature
  */
 function parseFieldsArray(f) {
-    const seq_id = f[0];
-    const source = f[1];
-    const type = f[2];
-    const startStr = f[3];
-    const endStr = f[4];
-    const scoreStr = f[5];
-    const strand = f[6];
-    const phase = f[7];
-    const attrString = f[8];
-    return {
-        seq_id: seq_id ? normUnescape(seq_id) : null,
-        source: source ? normUnescape(source) : null,
-        type: type ? normUnescape(type) : null,
-        start: !startStr || startStr === '.' ? null : +startStr,
-        end: !endStr || endStr === '.' ? null : +endStr,
-        score: !scoreStr || scoreStr === '.' ? null : +scoreStr,
-        strand: strand && strand !== '.' ? strand : null,
-        phase: phase && phase !== '.' ? phase : null,
-        attributes: !attrString || attrString === '.' ? null : parseAttributes(attrString),
-    };
+    return parseFieldsArrayImpl(f, true);
 }
 /**
  * Parse a GFF3 feature from a pre-split fields array without unescaping.
@@ -237,26 +208,7 @@ function parseFieldsArray(f) {
  * @returns The parsed feature
  */
 function parseFieldsArrayNoUnescape(f) {
-    const seq_id = f[0];
-    const source = f[1];
-    const type = f[2];
-    const startStr = f[3];
-    const endStr = f[4];
-    const scoreStr = f[5];
-    const strand = f[6];
-    const phase = f[7];
-    const attrString = f[8];
-    return {
-        seq_id: seq_id && seq_id !== '.' ? seq_id : null,
-        source: source && source !== '.' ? source : null,
-        type: type && type !== '.' ? type : null,
-        start: !startStr || startStr === '.' ? null : +startStr,
-        end: !endStr || endStr === '.' ? null : +endStr,
-        score: !scoreStr || scoreStr === '.' ? null : +scoreStr,
-        strand: strand && strand !== '.' ? strand : null,
-        phase: phase && phase !== '.' ? phase : null,
-        attributes: !attrString || attrString === '.' ? null : parseAttributesNoUnescape(attrString),
-    };
+    return parseFieldsArrayImpl(f, false);
 }
 /**
  * Parse a GFF3 directive line.
@@ -276,7 +228,6 @@ function parseDirective(line) {
         contents = contents.replace(lineEndRegex, '');
         parsed.value = contents;
     }
-    // do a little additional parsing for sequence-region and genome-build directives
     if (name === 'sequence-region') {
         const c = contents.split(whitespaceRegex, 3);
         return {
@@ -307,19 +258,30 @@ const JBROWSE_DEFAULT_FIELDS = new Set([
     'phase',
     'strand',
 ]);
-function parseStrand(s) {
-    if (s === '+') {
-        return 1;
-    }
-    if (s === '-') {
-        return -1;
-    }
-    if (s === '.') {
-        return 0;
-    }
-    return undefined;
-}
-function parseAttributesJBrowse(attrString, result) {
+// Pre-computed lowercase for common GFF3 spec attribute names to avoid
+// toLowerCase() calls in the hot path
+const COMMON_ATTRS = {
+    ID: 'id',
+    Name: 'name',
+    Parent: 'parent',
+    Note: 'note',
+    Dbxref: 'dbxref',
+    Ontology_term: 'ontology_term',
+    Is_circular: 'is_circular',
+    Alias: 'alias',
+    Target: 'target',
+    Gap: 'gap',
+    Derives_from: 'derives_from',
+    id: 'id',
+    name: 'name',
+    parent: 'parent',
+    note: 'note',
+    dbxref: 'dbxref',
+    alias: 'alias',
+    target: 'target',
+    gap: 'gap',
+};
+function parseAttributesJBrowseImpl(attrString, result, shouldUnescape) {
     if (attrString.length === 0 || attrString === '.') {
         return;
     }
@@ -342,9 +304,12 @@ function parseAttributesJBrowse(attrString, result) {
                     start = semiIdx + 1;
                     continue;
                 }
-                let key = tag.toLowerCase();
-                if (JBROWSE_DEFAULT_FIELDS.has(key)) {
-                    key += '2';
+                let key = COMMON_ATTRS[tag];
+                if (key === undefined) {
+                    key = tag.toLowerCase();
+                    if (JBROWSE_DEFAULT_FIELDS.has(key)) {
+                        key += '2';
+                    }
                 }
                 const values = [];
                 let valStart = eqIdx + 1;
@@ -355,7 +320,7 @@ function parseAttributesJBrowse(attrString, result) {
                     }
                     if (commaIdx > valStart) {
                         const val = attrString.slice(valStart, commaIdx);
-                        values.push(unescape(val));
+                        values.push(shouldUnescape ? unescape(val) : val);
                     }
                     valStart = commaIdx + 1;
                 }
@@ -365,52 +330,13 @@ function parseAttributesJBrowse(attrString, result) {
         start = semiIdx + 1;
     }
 }
+function parseAttributesJBrowse(attrString, result) {
+    parseAttributesJBrowseImpl(attrString, result, true);
+}
 function parseAttributesJBrowseNoUnescape(attrString, result) {
-    if (attrString.length === 0 || attrString === '.') {
-        return;
-    }
-    let len = attrString.length;
-    if (attrString[len - 1] === '\n') {
-        len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
-        attrString = attrString.slice(0, len);
-    }
-    let start = 0;
-    while (start < len) {
-        let semiIdx = attrString.indexOf(';', start);
-        if (semiIdx === -1) {
-            semiIdx = len;
-        }
-        if (semiIdx > start) {
-            const eqIdx = attrString.indexOf('=', start);
-            if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
-                const tag = attrString.slice(start, eqIdx);
-                if (tag === '_lineHash') {
-                    start = semiIdx + 1;
-                    continue;
-                }
-                let key = tag.toLowerCase();
-                if (JBROWSE_DEFAULT_FIELDS.has(key)) {
-                    key += '2';
-                }
-                const values = [];
-                let valStart = eqIdx + 1;
-                while (valStart < semiIdx) {
-                    let commaIdx = attrString.indexOf(',', valStart);
-                    if (commaIdx === -1 || commaIdx > semiIdx) {
-                        commaIdx = semiIdx;
-                    }
-                    if (commaIdx > valStart) {
-                        values.push(attrString.slice(valStart, commaIdx));
-                    }
-                    valStart = commaIdx + 1;
-                }
-                result[key] = values.length === 1 ? values[0] : values;
-            }
-        }
-        start = semiIdx + 1;
-    }
+    parseAttributesJBrowseImpl(attrString, result, false);
 }
-function parseFeatureJBrowse(line) {
+function parseFeatureJBrowseImpl(line, shouldUnescape) {
     const f = line.split('\t');
     const seq_id = f[0];
     const source = f[1];
@@ -422,42 +348,35 @@ function parseFeatureJBrowse(line) {
     const phase = f[7];
     const attrString = f[8];
     const result = {
-        refName: seq_id.length === 0 || seq_id === '.' ? '' : unescape(seq_id),
-        source: source.length === 0 || source === '.' ? null : unescape(source),
-        type: type.length === 0 || type === '.' ? null : unescape(type),
+        refName: seq_id.length === 0 || seq_id === '.'
+            ? ''
+            : shouldUnescape
+                ? unescape(seq_id)
+                : seq_id,
+        source: source.length === 0 || source === '.'
+            ? null
+            : shouldUnescape
+                ? unescape(source)
+                : source,
+        type: type.length === 0 || type === '.'
+            ? null
+            : shouldUnescape
+                ? unescape(type)
+                : type,
         start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
         end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
         score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
-        strand: parseStrand(strand),
+        strand: strand === '+' ? 1 : strand === '-' ? -1 : strand === '.' ? 0 : undefined,
         phase: phase.length === 0 || phase === '.' ? undefined : +phase,
         subfeatures: [],
     };
-    parseAttributesJBrowse(attrString, result);
+    parseAttributesJBrowseImpl(attrString, result, shouldUnescape);
     return result;
 }
+function parseFeatureJBrowse(line) {
+    return parseFeatureJBrowseImpl(line, true);
+}
 function parseFeatureJBrowseNoUnescape(line) {
-    const f = line.split('\t');
-    const seq_id = f[0];
-    const source = f[1];
-    const type = f[2];
-    const startStr = f[3];
-    const endStr = f[4];
-    const scoreStr = f[5];
-    const strand = f[6];
-    const phase = f[7];
-    const attrString = f[8];
-    const result = {
-        refName: seq_id.length === 0 || seq_id === '.' ? '' : seq_id,
-        source: source.length === 0 || source === '.' ? null : source,
-        type: type.length === 0 || type === '.' ? null : type,
-        start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
-        end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
-        score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
-        strand: parseStrand(strand),
-        phase: phase.length === 0 || phase === '.' ? undefined : +phase,
-        subfeatures: [],
-    };
-    parseAttributesJBrowseNoUnescape(attrString, result);
-    return result;
+    return parseFeatureJBrowseImpl(line, false);
 }
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/api.js

@@ -21,15 +21,14 @@ export function parseStringSyncJBrowse(str) {
 function stringToRecords(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] === '#') {
+    for (const line of lines) {
+        if (line.length === 0 || line.startsWith('#')) {
             if (line.startsWith('##FASTA')) {
                 break;
             }
             continue;
         }
-        if (line[0] === '>') {
+        if (line.startsWith('>')) {
             break;
         }
         records.push({
@@ -52,17 +51,14 @@ export function parseRecords(records) {
     const items = [];
     const byId = new Map();
     const orphans = new Map();
-    for (let i = 0; i < records.length; i++) {
-        const record = records[i];
+    for (const record of records) {
         const featureLine = (record.hasEscapes
             ? parseFeature(record.line)
             : parseFeatureNoUnescape(record.line));
         featureLine.child_features = [];
         featureLine.derived_features = [];
         if (record.lineHash !== undefined) {
-            if (!featureLine.attributes) {
-                featureLine.attributes = {};
-            }
+            featureLine.attributes ??= {};
             featureLine.attributes._lineHash = [String(record.lineHash)];
         }
         const attrs = featureLine.attributes;
@@ -88,8 +84,8 @@ export function parseRecords(records) {
                 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]);
+                    for (const w of waiting) {
+                        featureLine.child_features.push(w);
                     }
                     orphans.delete(id);
                 }
@@ -99,12 +95,11 @@ export function parseRecords(records) {
             feature = [featureLine];
         }
         if (parents) {
-            for (let j = 0; j < parents.length; j++) {
-                const parentId = parents[j];
+            for (const parentId of parents) {
                 const parent = byId.get(parentId);
                 if (parent) {
-                    for (let k = 0; k < parent.length; k++) {
-                        parent[k].child_features.push(feature);
+                    for (const p of parent) {
+                        p.child_features.push(feature);
                     }
                 }
                 else {
@@ -131,8 +126,7 @@ export function parseRecordsJBrowse(records) {
     const items = [];
     const byId = new Map();
     const orphans = new Map();
-    for (let i = 0; i < records.length; i++) {
-        const record = records[i];
+    for (const record of records) {
         const feature = record.hasEscapes
             ? parseFeatureJBrowse(record.line)
             : parseFeatureJBrowseNoUnescape(record.line);
@@ -154,8 +148,8 @@ export function parseRecordsJBrowse(records) {
                 byId.set(id, feature);
                 const waiting = orphans.get(id);
                 if (waiting) {
-                    for (let j = 0; j < waiting.length; j++) {
-                        feature.subfeatures.push(waiting[j]);
+                    for (const w of waiting) {
+                        feature.subfeatures.push(w);
                     }
                     orphans.delete(id);
                 }
@@ -163,8 +157,7 @@ export function parseRecordsJBrowse(records) {
         }
         if (parent) {
             const parents = Array.isArray(parent) ? parent : [parent];
-            for (let j = 0; j < parents.length; j++) {
-                const parentId = parents[j];
+            for (const parentId of parents) {
                 const parentFeature = byId.get(parentId);
                 if (parentFeature) {
                     parentFeature.subfeatures.push(feature);