massbank 0.0.2 → 0.2.0

package/lib/validation/rules/non-standard-chars-rule.js

@@ -0,0 +1,61 @@
+import { PositionUtils } from '../../parser/index.js';
+/**
+ * Pattern for allowed characters (from Java Validator).
+ * Note: We deliberately allow both LF (`\n`) and CR (`\r`) here so CRLF
+ * line endings do not trigger non-standard character warnings. The Java CLI
+ * treats CR as non-standard only via logging; for this library we avoid
+ * warning on platform-specific line endings while still flagging real
+ * non-ASCII issues.
+ */
+const NON_STANDARD_CHARS_PATTERN = /[^\w\r\n\-[\]."\\ ;:–=+,|(){}/$%@'°!?#`^*&<>µáćÉéóäöü©]/;
+/**
+ * Validates non-standard characters in the record
+ * Only validates character set.
+ * This rule is warning-only and never produces blocking validation errors.
+ */
+export class NonStandardCharsRule {
+    validate(_record, _originalText, _filename, _options) {
+        void _record;
+        void _originalText;
+        void _filename;
+        void _options;
+        return [];
+    }
+    getWarnings(record, originalText, filename, 
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _options) {
+        const warnings = [];
+        // Skip deprecated records
+        if (record.DEPRECATED) {
+            return warnings;
+        }
+        const match = NON_STANDARD_CHARS_PATTERN.exec(originalText);
+        if (match?.index !== undefined) {
+            const { line, column } = PositionUtils.getLineColumn(originalText, match.index);
+            const char = match[0] || '';
+            const codePoint = char.codePointAt(0);
+            const hex = codePoint
+                ? `U+${codePoint.toString(16).toUpperCase().padStart(4, '0')}`
+                : '';
+            // Common replacements
+            const suggestions = new Map([
+                ['\u2014', 'Replace em-dash with hyphen'],
+                ['\u201C', 'Replace fancy opening quote with straight quote (")'],
+                ['\u201D', 'Replace fancy closing quote with straight quote (")'],
+                ['\u2018', "Replace fancy opening apostrophe with straight quote (')"],
+                ['\u2019', "Replace fancy closing apostrophe with straight quote (')"],
+                ['\u2022', 'Replace bullet point with hyphen (-)'],
+                ['\u00AE', 'Replace registered symbol with (R)'],
+            ]);
+            const suggestion = suggestions.get(char) || 'Replace with standard ASCII character';
+            warnings.push({
+                file: filename,
+                line,
+                column,
+                message: `Non-standard character '${char}' (${hex}) found. ${suggestion}`,
+            });
+        }
+        return warnings;
+    }
+}
+//# sourceMappingURL=non-standard-chars-rule.js.map

package/lib/validation/rules/non-standard-chars-rule.js.map

@@ -0,0 +1 @@
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package/lib/validation/rules/serialization-rule.d.ts

@@ -0,0 +1,14 @@
+import type { Record } from '../../record.js';
+import type { ValidationError, ValidationWarning } from '../../types.js';
+import type { IValidationRule, ValidationRuleOptions } from '../interfaces.js';
+/**
+ * Validates serialization round-trip (parse -> serialize -> compare)
+ * Only validates serialization consistency.
+ * This rule produces blocking validation errors but no warnings.
+ */
+export declare class SerializationRule implements IValidationRule {
+    validate(record: Record, originalText: string, filename: string, _options: ValidationRuleOptions): ValidationError[];
+    getWarnings(): ValidationWarning[];
+    private findFirstDifference;
+}
+//# sourceMappingURL=serialization-rule.d.ts.map

package/lib/validation/rules/serialization-rule.d.ts.map

@@ -0,0 +1 @@
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package/lib/validation/rules/serialization-rule.js

@@ -0,0 +1,78 @@
+import { PositionUtils } from '../../parser/index.js';
+import { serializeRecord } from '../../serializer/index.js';
+/**
+ * Validates serialization round-trip (parse -> serialize -> compare)
+ * Only validates serialization consistency.
+ * This rule produces blocking validation errors but no warnings.
+ */
+export class SerializationRule {
+    validate(record, originalText, filename, 
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _options) {
+        const errors = [];
+        try {
+            const serialized = serializeRecord(record);
+            // eslint-disable-next-line unicorn/prefer-string-replace-all
+            const normalizedOriginal = originalText.replace(/\r\n?/g, '\n');
+            // Find first difference
+            const diffPosition = this.findFirstDifference(normalizedOriginal, serialized);
+            if (diffPosition !== -1) {
+                const { line, column } = PositionUtils.getLineColumn(normalizedOriginal, diffPosition);
+                // Get context around the difference for better error message
+                const originalLine = normalizedOriginal.split('\n')[line - 1] || '';
+                const serializedLine = serialized.split('\n')[line - 1] || '';
+                let message = 'File formatting issue detected (round-trip validation failed).';
+                // Provide specific guidance based on common issues
+                if (originalLine !== serializedLine) {
+                    if (originalLine.includes('  ') && serializedLine.includes(' ')) {
+                        message += ' Check for extra spaces or inconsistent spacing.';
+                    }
+                    else if (!serializedLine.trim()) {
+                        message +=
+                            ' This line may contain unrecognized fields that were ignored during parsing.';
+                    }
+                    else {
+                        const expectedPreview = serializedLine.length > 80
+                            ? `${serializedLine.slice(0, 77)}...`
+                            : serializedLine;
+                        const foundPreview = originalLine.length > 80
+                            ? `${originalLine.slice(0, 77)}...`
+                            : originalLine;
+                        message += ` Expected (${serializedLine.length} chars): "${expectedPreview}" but found (${originalLine.length} chars): "${foundPreview}"`;
+                    }
+                }
+                errors.push({
+                    file: filename,
+                    line,
+                    column,
+                    message,
+                    type: 'serialization',
+                });
+            }
+        }
+        catch (error) {
+            errors.push({
+                file: filename,
+                message: `Serialization failed: ${error instanceof Error ? error.message : 'Unknown error'}`,
+                type: 'serialization',
+            });
+        }
+        return errors;
+    }
+    getWarnings() {
+        return [];
+    }
+    findFirstDifference(str1, str2) {
+        const minLength = Math.min(str1.length, str2.length);
+        for (let i = 0; i < minLength; i++) {
+            if (str1[i] !== str2[i]) {
+                return i;
+            }
+        }
+        if (str1.length !== str2.length) {
+            return minLength;
+        }
+        return -1;
+    }
+}
+//# sourceMappingURL=serialization-rule.js.map

package/lib/validation/rules/serialization-rule.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"serialization-rule.js","sourceRoot":"","sources":["../../../src/validation/rules/serialization-rule.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAEtD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAI5D;;;;GAIG;AACH,MAAM,OAAO,iBAAiB;IAC5B,QAAQ,CACN,MAAc,EACd,YAAoB,EACpB,QAAgB;IAChB,6DAA6D;IAC7D,QAA+B;QAE/B,MAAM,MAAM,GAAsB,EAAE,CAAC;QAErC,IAAI,CAAC;YACH,MAAM,UAAU,GAAG,eAAe,CAAC,MAAM,CAAC,CAAC;YAC3C,6DAA6D;YAC7D,MAAM,kBAAkB,GAAG,YAAY,CAAC,OAAO,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC;YAEhE,wBAAwB;YACxB,MAAM,YAAY,GAAG,IAAI,CAAC,mBAAmB,CAC3C,kBAAkB,EAClB,UAAU,CACX,CAAC;YAEF,IAAI,YAAY,KAAK,CAAC,CAAC,EAAE,CAAC;gBACxB,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,aAAa,CAAC,aAAa,CAClD,kBAAkB,EAClB,YAAY,CACb,CAAC;gBAEF,6DAA6D;gBAC7D,MAAM,YAAY,GAAG,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBACpE,MAAM,cAAc,GAAG,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAE9D,IAAI,OAAO,GACT,gEAAgE,CAAC;gBAEnE,mDAAmD;gBACnD,IAAI,YAAY,KAAK,cAAc,EAAE,CAAC;oBACpC,IAAI,YAAY,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;wBAChE,OAAO,IAAI,kDAAkD,CAAC;oBAChE,CAAC;yBAAM,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,EAAE,CAAC;wBAClC,OAAO;4BACL,8EAA8E,CAAC;oBACnF,CAAC;yBAAM,CAAC;wBACN,MAAM,eAAe,GACnB,cAAc,CAAC,MAAM,GAAG,EAAE;4BACxB,CAAC,CAAC,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK;4BACrC,CAAC,CAAC,cAAc,CAAC;wBACrB,MAAM,YAAY,GAChB,YAAY,CAAC,MAAM,GAAG,EAAE;4BACtB,CAAC,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK;4BACnC,CAAC,CAAC,YAAY,CAAC;wBACnB,OAAO,IAAI,cAAc,cAAc,CAAC,MAAM,aAAa,eAAe,gBAAgB,YAAY,CAAC,MAAM,aAAa,YAAY,GAAG,CAAC;oBAC5I,CAAC;gBACH,CAAC;gBAED,MAAM,CAAC,IAAI,CAAC;oBACV,IAAI,EAAE,QAAQ;oBACd,IAAI;oBACJ,MAAM;oBACN,OAAO;oBACP,IAAI,EAAE,eAAe;iBACtB,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,QAAQ;gBACd,OAAO,EAAE,yBAAyB,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,eAAe,EAAE;gBAC5F,IAAI,EAAE,eAAe;aACtB,CAAC,CAAC;QACL,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,WAAW;QACT,OAAO,EAAE,CAAC;IACZ,CAAC;IAEO,mBAAmB,CAAC,IAAY,EAAE,IAAY;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QACrD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE,CAAC;YACnC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;gBACxB,OAAO,CAAC,CAAC;YACX,CAAC;QACH,CAAC;QACD,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,EAAE,CAAC;YAChC,OAAO,SAAS,CAAC;QACnB,CAAC;QACD,OAAO,CAAC,CAAC,CAAC;IACZ,CAAC;CACF"}

package/lib/validation/rules/unrecognized-field-rule.d.ts

@@ -0,0 +1,25 @@
+import type { Record } from '../../record.js';
+import type { ValidationWarning } from '../../types.js';
+import type { IValidationRule, ValidationRuleOptions } from '../interfaces.js';
+/**
+ * Validation rule that warns about unrecognized fields
+ * Helps catch typos and unsupported field names
+ */
+export declare class UnrecognizedFieldRule implements IValidationRule {
+    /**
+     * List of all recognized MassBank 2.6.0 field names
+     */
+    private readonly recognizedFields;
+    validate(_record: Record, _originalText: string, _filename: string, _options?: ValidationRuleOptions): never[];
+    getWarnings(_record: Record, originalText: string, filename: string, _options?: ValidationRuleOptions): ValidationWarning[];
+    /**
+     * Find a similar field name for typo suggestions
+     * Uses simple Levenshtein distance for similarity
+     */
+    private findSimilarField;
+    /**
+     * Calculate Levenshtein distance between two strings
+     */
+    private levenshteinDistance;
+}
+//# sourceMappingURL=unrecognized-field-rule.d.ts.map

package/lib/validation/rules/unrecognized-field-rule.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"unrecognized-field-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/unrecognized-field-rule.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACxD,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAE/E;;;GAGG;AACH,qBAAa,qBAAsB,YAAW,eAAe;IAC3D;;OAEG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAsC9B;IAEH,QAAQ,CAEN,OAAO,EAAE,MAAM,EAEf,aAAa,EAAE,MAAM,EAErB,SAAS,EAAE,MAAM,EAEjB,QAAQ,CAAC,EAAE,qBAAqB,GAC/B,KAAK,EAAE;IAKV,WAAW,CACT,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,CAAC,EAAE,qBAAqB,GAC/B,iBAAiB,EAAE;IA0CtB;;;OAGG;IACH,OAAO,CAAC,gBAAgB;IAgBxB;;OAEG;IACH,OAAO,CAAC,mBAAmB;CAkC5B"}

package/lib/validation/rules/unrecognized-field-rule.js

@@ -0,0 +1,149 @@
+/**
+ * Validation rule that warns about unrecognized fields
+ * Helps catch typos and unsupported field names
+ */
+export class UnrecognizedFieldRule {
+    /**
+     * List of all recognized MassBank 2.6.0 field names
+     */
+    recognizedFields = new Set([
+        // Header fields
+        'ACCESSION',
+        'RECORD_TITLE',
+        'DATE',
+        'AUTHORS',
+        'LICENSE',
+        'COPYRIGHT',
+        'PUBLICATION',
+        'PROJECT',
+        'COMMENT',
+        'DEPRECATED',
+        // Chemical compound fields
+        'CH$NAME',
+        'CH$COMPOUND_CLASS',
+        'CH$FORMULA',
+        'CH$EXACT_MASS',
+        'CH$SMILES',
+        'CH$IUPAC',
+        'CH$LINK',
+        // Analytical chemistry fields
+        'AC$INSTRUMENT',
+        'AC$INSTRUMENT_TYPE',
+        'AC$MASS_SPECTROMETRY',
+        'AC$CHROMATOGRAPHY',
+        // Mass spectrometry fields
+        'MS$FOCUSED_ION',
+        'MS$DATA_PROCESSING',
+        // Peak data fields
+        'PK$SPLASH',
+        'PK$NUM_PEAK',
+        'PK$PEAK',
+        'PK$ANNOTATION',
+        // Sample/species fields
+        'SP$SCIENTIFIC_NAME',
+        'SP$LINEAGE',
+        'SP$LINK',
+        'SP$SAMPLE',
+    ]);
+    validate(
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _record, 
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _originalText, 
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _filename, 
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _options) {
+        // This rule only produces warnings, not errors
+        return [];
+    }
+    getWarnings(_record, originalText, filename, 
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    _options) {
+        const warnings = [];
+        const lines = originalText.split('\n');
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i]?.trim();
+            if (!line || line === '//' || line.startsWith('//')) {
+                continue;
+            }
+            const colonIndex = line.indexOf(':');
+            if (colonIndex === -1) {
+                continue;
+            }
+            const key = line.slice(0, colonIndex).trim();
+            // Check if this is an unrecognized field
+            if (!this.recognizedFields.has(key)) {
+                // Suggest similar field names for common typos
+                // Normalize to uppercase for comparison to catch case errors
+                const suggestion = this.findSimilarField(key.toUpperCase());
+                let message = `Unrecognized field '${key}'. Not a valid MassBank 2.6.0 field.`;
+                if (suggestion) {
+                    message += ` Did you mean '${suggestion}'?`;
+                }
+                else {
+                    message +=
+                        ' Remove this line or check the MassBank format specification.';
+                }
+                warnings.push({
+                    file: filename,
+                    line: i + 1,
+                    message,
+                });
+            }
+        }
+        return warnings;
+    }
+    /**
+     * Find a similar field name for typo suggestions
+     * Uses simple Levenshtein distance for similarity
+     */
+    findSimilarField(input) {
+        let bestMatch = null;
+        let bestDistance = Number.POSITIVE_INFINITY;
+        for (const field of this.recognizedFields) {
+            const distance = this.levenshteinDistance(input, field);
+            // Only suggest if very similar (distance <= 2)
+            if (distance <= 2 && distance < bestDistance) {
+                bestDistance = distance;
+                bestMatch = field;
+            }
+        }
+        return bestMatch;
+    }
+    /**
+     * Calculate Levenshtein distance between two strings
+     */
+    levenshteinDistance(a, b) {
+        const matrix = [];
+        for (let i = 0; i <= b.length; i++) {
+            matrix[i] = [i];
+        }
+        const firstRow = matrix[0];
+        if (firstRow) {
+            for (let j = 0; j <= a.length; j++) {
+                firstRow[j] = j;
+            }
+        }
+        for (let i = 1; i <= b.length; i++) {
+            const currentRow = matrix[i];
+            const prevRow = matrix[i - 1];
+            if (!currentRow || !prevRow)
+                continue;
+            for (let j = 1; j <= a.length; j++) {
+                if (b.charAt(i - 1) === a.charAt(j - 1)) {
+                    currentRow[j] = prevRow[j - 1] ?? 0;
+                }
+                else {
+                    const substitution = (prevRow[j - 1] ?? 0) + 1;
+                    const insertion = (currentRow[j - 1] ?? 0) + 1;
+                    const deletion = (prevRow[j] ?? 0) + 1;
+                    currentRow[j] = Math.min(substitution, insertion, deletion);
+                }
+            }
+        }
+        const lastRow = matrix[b.length];
+        return lastRow?.[a.length] ?? Number.POSITIVE_INFINITY;
+    }
+}
+//# sourceMappingURL=unrecognized-field-rule.js.map

package/lib/validation/rules/unrecognized-field-rule.js.map

@@ -0,0 +1 @@
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package/lib/validation/validator.d.ts

@@ -0,0 +1,18 @@
+import type { IValidationRule } from './interfaces.js';
+/**
+ * Validator that applies all validation rules to a record
+ */
+export declare class RecordValidator {
+    private readonly rules;
+    constructor(rules?: IValidationRule[]);
+    /**
+     * Add a validation rule
+     * @param rule
+     */
+    addRule(rule: IValidationRule): void;
+    /**
+     * Get all validation rules
+     */
+    getRules(): readonly IValidationRule[];
+}
+//# sourceMappingURL=validator.d.ts.map

package/lib/validation/validator.d.ts.map

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package/lib/validation/validator.js

@@ -0,0 +1,30 @@
+import { AccessionMatchRule, NonStandardCharsRule, SerializationRule, UnrecognizedFieldRule, } from './rules/index.js';
+/**
+ * Validator that applies all validation rules to a record
+ */
+export class RecordValidator {
+    rules;
+    constructor(rules) {
+        // Default rules (can be overridden via dependency injection)
+        this.rules = rules || [
+            new AccessionMatchRule(),
+            new NonStandardCharsRule(),
+            new SerializationRule(),
+            new UnrecognizedFieldRule(),
+        ];
+    }
+    /**
+     * Add a validation rule
+     * @param rule
+     */
+    addRule(rule) {
+        this.rules.push(rule);
+    }
+    /**
+     * Get all validation rules
+     */
+    getRules() {
+        return this.rules;
+    }
+}
+//# sourceMappingURL=validator.js.map

package/lib/validation/validator.js.map

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package/lib/validator/file-utils.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Utility functions for file operations
+ * Simplified for single-file validation
+ */
+export declare const FileUtils: {
+    /**
+     * Read a file as UTF-8 text
+     * @param filePath - Absolute path to the file
+     * @returns File content as string
+     */
+    readFile(filePath: string): Promise<string>;
+};
+//# sourceMappingURL=file-utils.d.ts.map

package/lib/validator/file-utils.d.ts.map

@@ -0,0 +1 @@
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package/lib/validator/file-utils.js

@@ -0,0 +1,24 @@
+import { readFile } from 'node:fs/promises';
+/**
+ * Utility functions for file operations
+ * Simplified for single-file validation
+ */
+export const FileUtils = {
+    /**
+     * Read a file as UTF-8 text
+     * @param filePath - Absolute path to the file
+     * @returns File content as string
+     */
+    async readFile(filePath) {
+        try {
+            return await readFile(filePath, 'utf8');
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : 'Unknown error';
+            const wrappedError = new Error(`Error reading file ${filePath}: ${message}`);
+            wrappedError.cause = error;
+            throw wrappedError;
+        }
+    },
+};
+//# sourceMappingURL=file-utils.js.map

package/lib/validator/file-utils.js.map

@@ -0,0 +1 @@
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package/lib/validator/index.d.ts

@@ -0,0 +1,2 @@
+export { validate, validateContent } from './validator.js';
+//# sourceMappingURL=index.d.ts.map

package/lib/validator/index.d.ts.map

@@ -0,0 +1 @@
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package/lib/validator/index.js

@@ -0,0 +1,2 @@
+export { validate, validateContent } from './validator.js';
+//# sourceMappingURL=index.js.map

package/lib/validator/index.js.map

@@ -0,0 +1 @@
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package/lib/validator/validator.d.ts

@@ -0,0 +1,19 @@
+import type { ValidationOptions, ValidationResult } from '../types.js';
+/**
+ * Validate a single MassBank record file
+ * @param filePath - Path to the .txt file
+ * @param options - Validation options (legacy mode, logger)
+ * @returns ValidationResult with errors, warnings, and accession
+ */
+export declare function validate(filePath: string, options?: ValidationOptions): Promise<ValidationResult>;
+/**
+ * Validate in-memory MassBank record content
+ * Useful for browser or API use-cases where the record content is not
+ * coming from the filesystem.
+ * @param content - Full record text to validate
+ * @param filename - Logical filename for error reporting (e.g. 'user-upload.txt')
+ * @param options - Validation options (legacy mode, logger)
+ * @returns ValidationResult with errors, warnings, and accession
+ */
+export declare function validateContent(content: string, filename: string, options?: ValidationOptions): Promise<ValidationResult>;
+//# sourceMappingURL=validator.d.ts.map

package/lib/validator/validator.d.ts.map

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