massbank 0.2.0 → 0.3.0

package/lib/get-variables.d.ts

@@ -0,0 +1,3 @@
+import type { MeasurementXY, TextData } from 'cheminfo-types';
+export declare function getVariables(blob: TextData): MeasurementXY;
+//# sourceMappingURL=get-variables.d.ts.map

package/lib/get-variables.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"get-variables.d.ts","sourceRoot":"","sources":["../src/get-variables.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAM9D,wBAAgB,YAAY,CAAC,IAAI,EAAE,QAAQ,GAAG,aAAa,CA0B1D"}

package/lib/get-variables.js

@@ -0,0 +1,27 @@
+import { ensureString } from 'ensure-string';
+import { parseRecord } from "./parser/parse-record.js";
+import { postParsing } from "./parser/post-parsing.js";
+export function getVariables(blob) {
+    const text = ensureString(blob);
+    const parsed = parseRecord(text);
+    const enhanced = postParsing(parsed);
+    const { peakData, recordTitle, ...meta } = enhanced;
+    // peakData could in fact also contain annotations that we are ignoring here
+    const measurementXY = {
+        variables: {
+            x: {
+                label: 'm/z',
+                data: peakData?.peak?.map((p) => p.mz) ?? [],
+            },
+            y: {
+                label: 'intensity',
+                data: peakData?.peak?.map((p) => p.intensity) ?? [],
+            },
+        },
+        dataType: 'Mass spectrum',
+        title: recordTitle ?? '',
+        meta,
+    };
+    return measurementXY;
+}
+//# sourceMappingURL=get-variables.js.map

package/lib/get-variables.js.map

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

@@ -2,6 +2,8 @@
  * MassBank validation library
  * Main entry point for the package
  */
-export { validate, validateContent } from './validator/index.js';
+export * from './validator/validate.ts';
+export * from './validator/validateContent.ts';
+export * from './get-variables.ts';
 export type { ValidationError, ValidationOptions, ValidationResult, ValidationWarning, } from './types.js';
 //# sourceMappingURL=index.d.ts.map

package/lib/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAC/C,cAAc,oBAAoB,CAAC;AAGnC,YAAY,EACV,eAAe,EACf,iBAAiB,EACjB,gBAAgB,EAChB,iBAAiB,GAClB,MAAM,YAAY,CAAC"}

package/lib/index.js

@@ -2,6 +2,7 @@
  * MassBank validation library
  * Main entry point for the package
  */
-// Validation functions
-export { validate, validateContent } from './validator/index.js';
+export * from "./validator/validate.js";
+export * from "./validator/validateContent.js";
+export * from "./get-variables.js";
 //# sourceMappingURL=index.js.map

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAC/C,cAAc,oBAAoB,CAAC"}

package/lib/parser/field-parsers.d.ts

@@ -1,53 +1,53 @@
-import type { Record } from '../record.js';
+import type { InternalRecord } from '../record.js';
 import type { IFieldParser } from './interfaces.js';
 /**
  * Base class for field parsers
  */
 declare abstract class BaseFieldParser implements IFieldParser {
     abstract canParse(key: string): boolean;
-    abstract parse(key: string, value: string, record: Record): void;
+    abstract parse(key: string, value: string, record: InternalRecord): void;
 }
 /**
  * Header field parser
  */
 export declare class HeaderFieldParser extends BaseFieldParser {
     canParse(key: string): boolean;
-    parse(key: string, value: string, record: Record): void;
+    parse(key: string, value: string, record: InternalRecord): void;
 }
 /**
  * Compound (CH$) field parser
  */
 export declare class CompoundFieldParser extends BaseFieldParser {
     canParse(key: string): boolean;
-    parse(key: string, value: string, record: Record): void;
+    parse(key: string, value: string, record: InternalRecord): void;
 }
 /**
  * Analytical conditions (AC$) field parser
  */
 export declare class AnalyticalConditionsFieldParser extends BaseFieldParser {
     canParse(key: string): boolean;
-    parse(key: string, value: string, record: Record): void;
+    parse(key: string, value: string, record: InternalRecord): void;
 }
 /**
  * Mass spectrometry (MS$) field parser
  */
 export declare class MassSpectrometryFieldParser extends BaseFieldParser {
     canParse(key: string): boolean;
-    parse(key: string, value: string, record: Record): void;
+    parse(key: string, value: string, record: InternalRecord): void;
 }
 /**
  * Peak (PK$) field parser (non-table fields)
  */
 export declare class PeakFieldParser extends BaseFieldParser {
     canParse(key: string): boolean;
-    parse(key: string, value: string, record: Record): void;
+    parse(key: string, value: string, record: InternalRecord): void;
 }
 /**
  * Species (SP$) field parser
  */
 export declare class SpeciesFieldParser extends BaseFieldParser {
     canParse(key: string): boolean;
-    parse(key: string, value: string, record: Record): void;
+    parse(key: string, value: string, record: InternalRecord): void;
 }
 export {};
 //# sourceMappingURL=field-parsers.d.ts.map

package/lib/parser/field-parsers.d.ts.map

@@ -1 +1 @@
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package/lib/parser/index.d.ts

@@ -1,4 +1,4 @@
-export { RecordParser, createParser, parseRecord } from './record-parser.js';
+export { RecordParser, createParser, parseRecord } from './parse-record.ts';
 export { ParseException } from './exceptions.js';
 export type { IFieldParser, IRecordParser, ITableParser, } from './interfaces.js';
 export { PositionUtils } from './position-utils.js';

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

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/parser/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAC5E,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACjD,YAAY,EACV,YAAY,EACZ,aAAa,EACb,YAAY,GACb,MAAM,iBAAiB,CAAC;AACzB,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC"}

package/lib/parser/index.js

@@ -1,4 +1,4 @@
-export { RecordParser, createParser, parseRecord } from './record-parser.js';
+export { RecordParser, createParser, parseRecord } from "./parse-record.js";
 export { ParseException } from './exceptions.js';
 export { PositionUtils } from './position-utils.js';
 //# sourceMappingURL=index.js.map

package/lib/parser/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/parser/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AAC7E,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AAMjD,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/parser/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAC5E,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AAMjD,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC"}

package/lib/parser/interfaces.d.ts

@@ -1,15 +1,15 @@
-import type { Record } from '../record.js';
+import type { InternalRecord } from '../record.js';
 /**
  * Interface for parsing MassBank records
  */
 export interface IRecordParser {
     /**
-     * Parse a MassBank record string into a Record object
+     * Parse a MassBank record string into a InternalRecord object
      * @param text - The MassBank record text
-     * @returns The parsed Record object
+     * @returns The parsed InternalRecord object
      * @throws {import('./exceptions.js').ParseException} if parsing fails
      */
-    parse(text: string): Record;
+    parse(text: string): InternalRecord;
 }
 /**
  * Interface for parsing field values
@@ -22,7 +22,7 @@ export interface IFieldParser {
     /**
      * Parse the field value
      */
-    parse(key: string, value: string, record: Record): void;
+    parse(key: string, value: string, record: InternalRecord): void;
 }
 /**
  * Interface for parsing table data (peaks, annotations)
@@ -37,10 +37,10 @@ export interface ITableParser {
      * @param key - The field key
      * @param lines - All lines
      * @param startIndex - Index of first data line (header is at startIndex - 1)
-     * @param record - Record to populate
+     * @param record - InternalRecord to populate
      * @param headerLine - The full header line (e.g., "PK$ANNOTATION: m/z ion")
      * @returns The number of lines consumed
      */
-    parse(key: string, lines: string[], startIndex: number, record: Record, headerLine?: string): number;
+    parse(key: string, lines: string[], startIndex: number, record: InternalRecord, headerLine?: string): number;
 }
 //# sourceMappingURL=interfaces.d.ts.map

package/lib/parser/interfaces.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"interfaces.d.ts","sourceRoot":"","sources":["../../src/parser/interfaces.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AAEnD;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B;;;;;OAKG;IACH,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CAAC;CACrC;AAED;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B;;OAEG;IACH,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B;;OAEG;IACH,KAAK,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,cAAc,GAAG,IAAI,CAAC;CACjE;AAED;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B;;OAEG;IACH,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B;;;;;;;;OAQG;IACH,KAAK,CACH,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EAAE,EACf,UAAU,EAAE,MAAM,EAClB,MAAM,EAAE,cAAc,EACtB,UAAU,CAAC,EAAE,MAAM,GAClB,MAAM,CAAC;CACX"}

package/lib/parser/{record-parser.d.ts → parse-record.d.ts}

@@ -1,5 +1,5 @@
-import type { Record } from '../record.js';
-import type { IRecordParser } from './interfaces.js';
+import type { InternalRecord } from '../record.ts';
+import type { IRecordParser } from './interfaces.ts';
 /**
  * Main MassBank record parser
  * responsible for parsing
@@ -11,10 +11,10 @@ export declare class RecordParser implements IRecordParser {
     private readonly tableParsers;
     constructor();
     /**
-     * Parse a MassBank record string into a Record object
+     * Parse a MassBank record string into a InternalRecord object
      * @param text
      */
-    parse(text: string): Record;
+    parse(text: string): InternalRecord;
 }
 /**
  * Factory function to create a parser instance
@@ -23,7 +23,8 @@ export declare class RecordParser implements IRecordParser {
 export declare function createParser(): IRecordParser;
 /**
  * Convenience function to parse a record
- * @param text
+ * @param text - MassBank record as string
+ * @returns Parsed InternalRecord object
  */
-export declare function parseRecord(text: string): Record;
-//# sourceMappingURL=record-parser.d.ts.map
+export declare function parseRecord(text: string): InternalRecord;
+//# sourceMappingURL=parse-record.d.ts.map

package/lib/parser/parse-record.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"parse-record.d.ts","sourceRoot":"","sources":["../../src/parser/parse-record.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AAWnD,OAAO,KAAK,EAEV,aAAa,EAEd,MAAM,iBAAiB,CAAC;AAIzB;;;;;GAKG;AACH,qBAAa,YAAa,YAAW,aAAa;IAChD,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAiB;IAC9C,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAiB;;IAgB9C;;;OAGG;IACH,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc;CA0FpC;AAED;;;GAGG;AACH,wBAAgB,YAAY,IAAI,aAAa,CAE5C;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CAGxD"}

package/lib/parser/{record-parser.js → parse-record.js}

@@ -1,7 +1,7 @@
-import { ParseException } from './exceptions.js';
-import { AnalyticalConditionsFieldParser, CompoundFieldParser, HeaderFieldParser, MassSpectrometryFieldParser, PeakFieldParser, SpeciesFieldParser, } from './field-parsers.js';
-import { PositionUtils } from './position-utils.js';
-import { AnnotationTableParser, PeakTableParser } from './table-parsers.js';
+import { ParseException } from "./exceptions.js";
+import { AnalyticalConditionsFieldParser, CompoundFieldParser, HeaderFieldParser, MassSpectrometryFieldParser, PeakFieldParser, SpeciesFieldParser, } from "./field-parsers.js";
+import { PositionUtils } from "./position-utils.js";
+import { AnnotationTableParser, PeakTableParser } from "./table-parsers.js";
 /**
  * Main MassBank record parser
  * responsible for parsing
@@ -24,7 +24,7 @@ export class RecordParser {
         this.tableParsers = [new PeakTableParser(), new AnnotationTableParser()];
     }
     /**
-     * Parse a MassBank record string into a Record object
+     * Parse a MassBank record string into a InternalRecord object
      * @param text
      */
     parse(text) {
@@ -95,10 +95,11 @@ export function createParser() {
 }
 /**
  * Convenience function to parse a record
- * @param text
+ * @param text - MassBank record as string
+ * @returns Parsed InternalRecord object
  */
 export function parseRecord(text) {
     const parser = createParser();
     return parser.parse(text);
 }
-//# sourceMappingURL=record-parser.js.map
+//# sourceMappingURL=parse-record.js.map

package/lib/parser/parse-record.js.map

@@ -0,0 +1 @@
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package/lib/parser/post-parsing.d.ts

@@ -0,0 +1,7 @@
+import type { InternalRecord, MassBankRecord } from '../record.ts';
+/**
+ * InternalRecord is a nearly flat structure; convert it to a camel-cased Record.
+ * @param parsed
+ */
+export declare function postParsing(parsed: InternalRecord): MassBankRecord;
+//# sourceMappingURL=post-parsing.d.ts.map

package/lib/parser/post-parsing.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"post-parsing.d.ts","sourceRoot":"","sources":["../../src/parser/post-parsing.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAEV,cAAc,EACd,cAAc,EAEf,MAAM,cAAc,CAAC;AActB;;;GAGG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,cAAc,GAAG,cAAc,CAqClE"}

package/lib/parser/post-parsing.js

@@ -0,0 +1,63 @@
+import camelcase from 'camelcase';
+/**
+ * InternalRecord is a nearly flat struture, we will organize it
+ * @param parsed
+ */
+const groupKeyMap = {
+    CH: 'compound',
+    AC: 'analyticalConditions',
+    MS: 'massSpectrometryData',
+    PK: 'peakData',
+    SP: 'species',
+};
+/**
+ * InternalRecord is a nearly flat structure; convert it to a camel-cased Record.
+ * @param parsed
+ */
+export function postParsing(parsed) {
+    const result = { accession: parsed.ACCESSION };
+    for (const [rawKey, value] of Object.entries(parsed)) {
+        if (rawKey === 'ACCESSION' || rawKey.startsWith('_'))
+            continue;
+        if (rawKey.includes('$')) {
+            const [mainKey, subKey] = rawKey.split('$');
+            const groupKey = groupKeyMap[mainKey];
+            if (!groupKey)
+                continue;
+            result[groupKey] ??= {};
+            const camelSubKey = camelcase(subKey, { pascalCase: false });
+            let normalizedValue = value;
+            if (mainKey === 'PK' && subKey === 'PEAK' && Array.isArray(value)) {
+                normalizedValue = stripPeakOriginal(value);
+            }
+            else if (mainKey === 'PK' &&
+                subKey === 'ANNOTATION' &&
+                Array.isArray(value)) {
+                normalizedValue = stripAnnotationOriginal(value);
+            }
+            result[groupKey][camelSubKey] =
+                normalizedValue;
+            continue;
+        }
+        const camelKey = camelcase(rawKey, { pascalCase: false });
+        //@ts-expect-error don't know how to fix this
+        result[camelKey] = value;
+    }
+    return result;
+}
+function stripPeakOriginal(peaks) {
+    return peaks.map(({ mz, intensity, relativeIntensity }) => ({
+        mz,
+        intensity,
+        relativeIntensity,
+    }));
+}
+function stripAnnotationOriginal(annotations) {
+    return annotations.map(({ mz, annotation, exactMass, errorPpm }) => ({
+        mz,
+        annotation,
+        exactMass,
+        errorPpm,
+    }));
+}
+//# sourceMappingURL=post-parsing.js.map

package/lib/parser/post-parsing.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"post-parsing.js","sourceRoot":"","sources":["../../src/parser/post-parsing.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,WAAW,CAAC;AASlC;;;GAGG;AACH,MAAM,WAAW,GAAG;IAClB,EAAE,EAAE,UAAU;IACd,EAAE,EAAE,sBAAsB;IAC1B,EAAE,EAAE,sBAAsB;IAC1B,EAAE,EAAE,UAAU;IACd,EAAE,EAAE,SAAS;CACL,CAAC;AAEX;;;GAGG;AACH,MAAM,UAAU,WAAW,CAAC,MAAsB;IAChD,MAAM,MAAM,GAAmB,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,CAAC;IAE/D,KAAK,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;QACrD,IAAI,MAAM,KAAK,WAAW,IAAI,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC;YAAE,SAAS;QAE/D,IAAI,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,OAAO,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,CAAqB,CAAC;YAChE,MAAM,QAAQ,GAAG,WAAW,CAAC,OAAmC,CAAC,CAAC;YAClE,IAAI,CAAC,QAAQ;gBAAE,SAAS;YAExB,MAAM,CAAC,QAAQ,CAAC,KAAK,EAAE,CAAC;YAExB,MAAM,WAAW,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,UAAU,EAAE,KAAK,EAAE,CAAC,CAAC;YAE7D,IAAI,eAAe,GAAG,KAAK,CAAC;YAC5B,IAAI,OAAO,KAAK,IAAI,IAAI,MAAM,KAAK,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;gBAClE,eAAe,GAAG,iBAAiB,CAAC,KAAK,CAAC,CAAC;YAC7C,CAAC;iBAAM,IACL,OAAO,KAAK,IAAI;gBAChB,MAAM,KAAK,YAAY;gBACvB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EACpB,CAAC;gBACD,eAAe,GAAG,uBAAuB,CAAC,KAAK,CAAC,CAAC;YACnD,CAAC;YAEA,MAAM,CAAC,QAAQ,CAA6B,CAAC,WAAW,CAAC;gBACxD,eAAe,CAAC;YAClB,SAAS;QACX,CAAC;QAED,MAAM,QAAQ,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,UAAU,EAAE,KAAK,EAAE,CAAC,CAAC;QAC1D,6CAA6C;QAC7C,MAAM,CAAC,QAAQ,CAAC,GAAG,KAAK,CAAC;IAC3B,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,iBAAiB,CAAC,KAAyB;IAClD,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,SAAS,EAAE,iBAAiB,EAAE,EAAE,EAAE,CAAC,CAAC;QAC1D,EAAE;QACF,SAAS;QACT,iBAAiB;KAClB,CAAC,CAAC,CAAC;AACN,CAAC;AAED,SAAS,uBAAuB,CAAC,WAAqC;IACpE,OAAO,WAAW,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,UAAU,EAAE,SAAS,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC,CAAC;QACnE,EAAE;QACF,UAAU;QACV,SAAS;QACT,QAAQ;KACT,CAAC,CAAC,CAAC;AACN,CAAC"}

package/lib/parser/table-parsers.d.ts

@@ -1,18 +1,18 @@
-import type { Record } from '../record.js';
+import type { InternalRecord } from '../record.js';
 import type { ITableParser } from './interfaces.js';
 /**
  * Base class for table parsers
  */
 declare abstract class BaseTableParser implements ITableParser {
     abstract canParse(key: string): boolean;
-    abstract parse(key: string, lines: string[], startIndex: number, record: Record, headerLine?: string): number;
+    abstract parse(key: string, lines: string[], startIndex: number, record: InternalRecord, headerLine?: string): number;
 }
 /**
  * Peak table parser
  */
 export declare class PeakTableParser extends BaseTableParser {
     canParse(key: string): boolean;
-    parse(key: string, lines: string[], startIndex: number, record: Record, _headerLine?: string): number;
+    parse(key: string, lines: string[], startIndex: number, record: InternalRecord, _headerLine?: string): number;
     private parsePeakLine;
 }
 /**
@@ -20,7 +20,7 @@ export declare class PeakTableParser extends BaseTableParser {
  */
 export declare class AnnotationTableParser extends BaseTableParser {
     canParse(key: string): boolean;
-    parse(key: string, lines: string[], startIndex: number, record: Record, headerLine?: string): number;
+    parse(key: string, lines: string[], startIndex: number, record: InternalRecord, headerLine?: string): number;
     private parseAnnotationLine;
 }
 export {};

package/lib/parser/table-parsers.d.ts.map

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package/lib/record.d.ts

@@ -1,24 +1,28 @@
 /**
- * MassBank Record structure
+ * MassBank InternalRecord structure
  */
 export interface Peak {
     mz: number;
     intensity: number;
     relativeIntensity: number;
-    _original?: {
-        mz: string;
-        intensity: string;
-        relativeIntensity: string;
-    };
 }
 export interface Annotation {
     mz: number;
     annotation?: string;
     exactMass?: number;
     errorPpm?: number;
+}
+export interface PeakWithOriginal extends Peak {
+    _original?: {
+        mz: string;
+        intensity: string;
+        relativeIntensity: string;
+    };
+}
+export interface AnnotationWithOriginal extends Annotation {
     _original?: string;
 }
-export interface Record {
+export interface InternalRecord {
     ACCESSION: string;
     RECORD_TITLE?: string;
     DATE?: string;
@@ -44,12 +48,55 @@ export interface Record {
     MS$DATA_PROCESSING?: string[];
     PK$SPLASH?: string;
     PK$NUM_PEAK?: number;
-    PK$PEAK?: Peak[];
-    PK$ANNOTATION?: Annotation[];
+    PK$PEAK?: PeakWithOriginal[];
+    PK$ANNOTATION?: AnnotationWithOriginal[];
     _PK$ANNOTATION_HEADER?: string;
     SP$SCIENTIFIC_NAME?: string;
     SP$LINEAGE?: string;
     SP$LINK?: string[];
     SP$SAMPLE?: string;
 }
+export interface MassBankRecord {
+    accession: string;
+    recordTitle?: string;
+    date?: string;
+    authors?: string;
+    license?: string;
+    copyright?: string;
+    publication?: string;
+    project?: string;
+    comment?: string[];
+    deprecated?: string;
+    compound?: {
+        name?: string[];
+        compoundClass?: string;
+        formula?: string;
+        exactMass?: string;
+        smiles?: string;
+        iupac?: string;
+        link?: string[];
+    };
+    analyticalConditions?: {
+        instrument?: string;
+        instrumentType?: string;
+        massSpectrometry?: string[];
+        chromatography?: string[];
+    };
+    massSpectrometryData?: {
+        focusedIon?: string[];
+        dataProcessing?: string[];
+    };
+    peakData?: {
+        splash?: string;
+        numPeak?: number;
+        peak?: Peak[];
+        annotation?: Annotation[];
+    };
+    species?: {
+        scientificName?: string;
+        lineage?: string;
+        link?: string[];
+        sample?: string;
+    };
+}
 //# sourceMappingURL=record.d.ts.map

package/lib/record.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"record.d.ts","sourceRoot":"","sources":["../src/record.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,MAAM,WAAW,IAAI;IACnB,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,MAAM,CAAC;IAClB,iBAAiB,EAAE,MAAM,CAAC;CAC3B;AAED,MAAM,WAAW,UAAU;IACzB,EAAE,EAAE,MAAM,CAAC;IACX,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,gBAAiB,SAAQ,IAAI;IAE5C,SAAS,CAAC,EAAE;QACV,EAAE,EAAE,MAAM,CAAC;QACX,SAAS,EAAE,MAAM,CAAC;QAClB,iBAAiB,EAAE,MAAM,CAAC;KAC3B,CAAC;CACH;AAED,MAAM,WAAW,sBAAuB,SAAQ,UAAU;IAExD,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,cAAc;IAE7B,SAAS,EAAE,MAAM,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,UAAU,CAAC,EAAE,MAAM,CAAC;IAGpB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IAGnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,oBAAoB,CAAC,EAAE,MAAM,EAAE,CAAC;IAChC,iBAAiB,CAAC,EAAE,MAAM,EAAE,CAAC;IAG7B,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B,kBAAkB,CAAC,EAAE,MAAM,EAAE,CAAC;IAG9B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,gBAAgB,EAAE,CAAC;IAC7B,aAAa,CAAC,EAAE,sBAAsB,EAAE,CAAC;IAEzC,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAG/B,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,cAAc;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,UAAU,CAAC,EAAE,MAAM,CAAC;IAEpB,QAAQ,CAAC,EAAE;QACT,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;QAChB,aAAa,CAAC,EAAE,MAAM,CAAC;QACvB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;KACjB,CAAC;IAEF,oBAAoB,CAAC,EAAE;QACrB,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC;QAC5B,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;KAC3B,CAAC;IAEF,oBAAoB,CAAC,EAAE;QACrB,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;QACtB,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;KAC3B,CAAC;IAEF,QAAQ,CAAC,EAAE;QACT,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,IAAI,CAAC,EAAE,IAAI,EAAE,CAAC;QACd,UAAU,CAAC,EAAE,UAAU,EAAE,CAAC;KAC3B,CAAC;IAEF,OAAO,CAAC,EAAE;QACR,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;QAChB,MAAM,CAAC,EAAE,MAAM,CAAC;KACjB,CAAC;CACH"}

package/lib/record.js

@@ -1,5 +1,5 @@
 /**
- * MassBank Record structure
+ * MassBank InternalRecord structure
  */
 export {};
 //# sourceMappingURL=record.js.map

package/lib/serializer/interfaces.d.ts

@@ -1,4 +1,4 @@
-import type { Record } from '../record.js';
+import type { InternalRecord } from '../record.js';
 /**
  * Interface for serializing MassBank records
  *
@@ -9,6 +9,6 @@ export interface IRecordSerializer {
      * @param record - The record to serialize
      * @returns The serialized record string
      */
-    serialize(record: Record): string;
+    serialize(record: InternalRecord): string;
 }
 //# sourceMappingURL=interfaces.d.ts.map

package/lib/serializer/interfaces.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"interfaces.d.ts","sourceRoot":"","sources":["../../src/serializer/interfaces.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAE3C;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC;;;;OAIG;IACH,SAAS,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;CACnC"}
+{"version":3,"file":"interfaces.d.ts","sourceRoot":"","sources":["../../src/serializer/interfaces.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AAEnD;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC;;;;OAIG;IACH,SAAS,CAAC,MAAM,EAAE,cAAc,GAAG,MAAM,CAAC;CAC3C"}