msa-parsers 5.6.3 → 5.7.1

package/README.md

@@ -8,9 +8,7 @@ Part of [react-msaview](../) (JBrowseMSA).
 ## Installation
 
 ```bash
-npm install msa-parsers
-# or
-yarn add msa-parsers
+pnpm add msa-parsers
 ```
 
 ## Supported formats

package/dist/gff/gffToInterPro.test.js

@@ -1,5 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import { gffToInterProResponse, gffToInterProResults } from "./gffToInterPro.js";
+import { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.js';
 describe('gffToInterProResults', () => {
     test('converts empty array', () => {
         expect(gffToInterProResults([])).toEqual({});

package/dist/gff/index.js

@@ -1,4 +1,4 @@
-export { parseGFF } from "./parseGFF.js";
-export { gffToInterProResponse, gffToInterProResults } from "./gffToInterPro.js";
-export { interProResponseToGFF, interProToGFF } from "./interProToGFF.js";
+export { parseGFF } from './parseGFF.js';
+export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.js';
+export { interProResponseToGFF, interProToGFF } from './interProToGFF.js';
 //# sourceMappingURL=index.js.map

package/dist/gff/interProToGFF.test.js

@@ -1,5 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import { interProResponseToGFF, interProToGFF } from "./interProToGFF.js";
+import { interProResponseToGFF, interProToGFF } from './interProToGFF.js';
 describe('interProToGFF', () => {
     test('converts empty results', () => {
         const gff = interProToGFF({});

package/dist/gff/parseGFF.test.js

@@ -1,5 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import { parseGFF } from "./parseGFF.js";
+import { parseGFF } from './parseGFF.js';
 describe('parseGFF', () => {
     test('parses empty string', () => {
         expect(parseGFF('')).toEqual([]);

package/dist/index.d.ts

@@ -1,4 +1,4 @@
-export * from './types.ts';
+export type * from './types.ts';
 export { generateNodeIds } from './util.ts';
 export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.ts';
 export type { MSAFormat, MSAParserType } from './msa/index.ts';

package/dist/index.js

@@ -1,9 +1,7 @@
-// Types
-export * from "./types.js";
 // Utilities
-export { generateNodeIds } from "./util.js";
+export { generateNodeIds } from './util.js';
 // MSA parsers
-export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from "./msa/index.js";
+export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.js';
 // GFF parsing
-export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from "./gff/index.js";
+export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.js';
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,QAAQ;AACR,cAAc,YAAY,CAAA;AAE1B,YAAY;AACZ,OAAO,EAAE,eAAe,EAAE,MAAM,WAAW,CAAA;AAE3C,cAAc;AACd,OAAO,EACL,MAAM,EACN,UAAU,EACV,MAAM,EACN,QAAQ,EACR,YAAY,EACZ,mBAAmB,EACnB,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,cAAc,GACf,MAAM,gBAAgB,CAAA;AAGvB,cAAc;AACd,OAAO,EACL,qBAAqB,EACrB,oBAAoB,EACpB,qBAAqB,EACrB,aAAa,EACb,QAAQ,GACT,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,YAAY;AACZ,OAAO,EAAE,eAAe,EAAE,MAAM,WAAW,CAAA;AAE3C,cAAc;AACd,OAAO,EACL,MAAM,EACN,UAAU,EACV,MAAM,EACN,QAAQ,EACR,YAAY,EACZ,mBAAmB,EACnB,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,cAAc,GACf,MAAM,gBAAgB,CAAA;AAGvB,cAAc;AACd,OAAO,EACL,qBAAqB,EACrB,oBAAoB,EACpB,qBAAqB,EACrB,aAAa,EACb,QAAQ,GACT,MAAM,gBAAgB,CAAA"}

package/dist/msa/A3mMSA.js

@@ -1,4 +1,4 @@
-import BaseMSA from "./BaseMSA.js";
+import BaseMSA from './BaseMSA.js';
 /**
  * A3M Format Parser
  *

package/dist/msa/A3mMSA.test.js

@@ -1,5 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import A3mMSA from "./A3mMSA.js";
+import A3mMSA from './A3mMSA.js';
 // A3M format rules (see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html):
 //
 // - Uppercase letters = "match columns" (aligned positions shared by all seqs)

package/dist/msa/BaseMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IAMnC,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,UAAU,CAAC,KAAa;QACtB,OAAO,SAEM,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QAMR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/msa/ClustalMSA.js

@@ -1,5 +1,5 @@
 import { parse } from 'clustal-js';
-import BaseMSA from "./BaseMSA.js";
+import BaseMSA from './BaseMSA.js';
 export default class ClustalMSA extends BaseMSA {
     MSA;
     constructor(text) {

package/dist/msa/EmfMSA.js

@@ -1,5 +1,5 @@
 import { parseEmfAln } from 'emf-js';
-import BaseMSA from "./BaseMSA.js";
+import BaseMSA from './BaseMSA.js';
 export default class EmfMSA extends BaseMSA {
     MSA;
     constructor(text) {

package/dist/msa/FastaMSA.js

@@ -1,4 +1,4 @@
-import BaseMSA from "./BaseMSA.js";
+import BaseMSA from './BaseMSA.js';
 export default class FastaMSA extends BaseMSA {
     MSA;
     // explicit insertion-ordered ids: object key order reorders integer-like

package/dist/msa/StockholmMSA.js

@@ -1,7 +1,7 @@
-import parseNewick from "./parseNewick.js";
-import { parseAll } from "./stockholmParser.js";
-import { generateNodeIds } from "../util.js";
-import BaseMSA from "./BaseMSA.js";
+import { generateNodeIds } from '../util.js';
+import BaseMSA from './BaseMSA.js';
+import parseNewick from './parseNewick.js';
+import { parseAll } from './stockholmParser.js';
 export default class StockholmMSA extends BaseMSA {
     data;
     MSA;
@@ -107,5 +107,5 @@ export default class StockholmMSA extends BaseMSA {
         ];
     }
 }
-export { sniff as stockholmSniff } from "./stockholmParser.js";
+export { sniff as stockholmSniff } from './stockholmParser.js';
 //# sourceMappingURL=StockholmMSA.js.map

package/dist/msa/StockholmMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAKlC,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,OAAO;IACvC,IAAI,CAAiB;IACrB,GAAG,CAAe;IAE1B,YAAY,IAAY,EAAE,gBAAwB;QAChD,KAAK,EAAE,CAAA;QACP,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC1B,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QAC3C,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;QAC1D,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC7C,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,MAAM,CAAC,WAAW,CAC5B,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD;YACD,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7D;SACF,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC;SAC9C,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,MAAM,GAGR,EAAE,CAAA;QACN,KAAK,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC;YACrD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;gBACxB,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,KAAK,EAAE,CAAC;oBACV,CAAC;oBAAA,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC;wBACxB,GAAG,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE;wBAC5B,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE;wBAChB,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;wBACpB,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;IACpE,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAA;IAC5B,CAAC;IAED,IAAI,MAAM;QAMR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,oEAAoE;gBACpE,sEAAsE;gBACtE,sEAAsE;gBACtE,gEAAgE;gBAChE,iBAAiB,EAAE;oBACjB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;iBACZ;aACF;SACF,CAAA;IACH,CAAC;CACF;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}
+{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAK/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,OAAO;IACvC,IAAI,CAAiB;IACrB,GAAG,CAAe;IAE1B,YAAY,IAAY,EAAE,gBAAwB;QAChD,KAAK,EAAE,CAAA;QACP,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC1B,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QAC3C,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;QAC1D,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC7C,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,MAAM,CAAC,WAAW,CAC5B,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD;YACD,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7D;SACF,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC;SAC9C,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,MAAM,GAGR,EAAE,CAAA;QACN,KAAK,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC;YACrD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;gBACxB,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,KAAK,EAAE,CAAC;oBACV,CAAC;oBAAA,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC;wBACxB,GAAG,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE;wBAC5B,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE;wBAChB,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;wBACpB,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;IACpE,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAA;IAC5B,CAAC;IAED,IAAI,MAAM;QAMR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,oEAAoE;gBACpE,sEAAsE;gBACtE,sEAAsE;gBACtE,gEAAgE;gBAChE,iBAAiB,EAAE;oBACjB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;iBACZ;aACF;SACF,CAAA;IACH,CAAC;CACF;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}

package/dist/msa/impgIntegration.test.js

@@ -1,7 +1,7 @@
 import { describe, expect, test } from 'vitest';
-import A3mMSA from "./A3mMSA.js";
-import FastaMSA from "./FastaMSA.js";
-import { parseMSA } from "./index.js";
+import A3mMSA from './A3mMSA.js';
+import FastaMSA from './FastaMSA.js';
+import { parseMSA } from './index.js';
 // impg (https://github.com/pangenome/impg) pipes `impg query -o fasta-aln` into
 // scripts/faln2html.py, which feeds the FASTA string to
 // MSAModelF().create({ data: { msa } }). These tests pin the behavior that

package/dist/msa/index.js

@@ -1,10 +1,10 @@
-import A3mMSA from "./A3mMSA.js";
-import ClustalMSA from "./ClustalMSA.js";
-import EmfMSA from "./EmfMSA.js";
-import FastaMSA from "./FastaMSA.js";
-import StockholmMSA, { stockholmSniff } from "./StockholmMSA.js";
+import A3mMSA from './A3mMSA.js';
+import ClustalMSA from './ClustalMSA.js';
+import EmfMSA from './EmfMSA.js';
+import FastaMSA from './FastaMSA.js';
+import StockholmMSA, { stockholmSniff } from './StockholmMSA.js';
 export { parseEmfTree } from 'emf-js';
-export { default as parseNewick } from "./parseNewick.js";
+export { default as parseNewick } from './parseNewick.js';
 // when `format` is given the heuristic sniffing is bypassed -- callers that
 // already know the format (e.g. impg emitting fasta-aln) can force it rather
 // than rely on auto-detection, which is necessarily ambiguous between formats
@@ -45,9 +45,9 @@ export function parseMSA(text, currentAlignment = 0, format) {
 export function getUngappedSequence(alignedSeq) {
     return alignedSeq.replaceAll(/[.-]/g, '');
 }
-export { default as A3mMSA } from "./A3mMSA.js";
-export { default as ClustalMSA } from "./ClustalMSA.js";
-export { default as EmfMSA } from "./EmfMSA.js";
-export { default as FastaMSA } from "./FastaMSA.js";
-export { default as StockholmMSA, stockholmSniff } from "./StockholmMSA.js";
+export { default as A3mMSA } from './A3mMSA.js';
+export { default as ClustalMSA } from './ClustalMSA.js';
+export { default as EmfMSA } from './EmfMSA.js';
+export { default as FastaMSA } from './FastaMSA.js';
+export { default as StockholmMSA, stockholmSniff } from './StockholmMSA.js';
 //# sourceMappingURL=index.js.map

package/dist/msa/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/msa/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,YAAY,EAAE,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAEhE,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EAAE,OAAO,IAAI,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAWzD,4EAA4E;AAC5E,6EAA6E;AAC7E,8EAA8E;AAC9E,0CAA0C;AAC1C,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,gBAAgB,GAAG,CAAC,EACpB,MAAkB;IAElB,IAAI,MAAM,KAAK,WAAW,EAAE,CAAC;QAC3B,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QACzB,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;IAC7B,CAAC;IACD,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACvB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3B,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;AAC7B,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,UAAkB;IACpD,OAAO,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAA;AAC3C,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,iBAAiB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA"}

package/dist/msa/index.test.js

@@ -1,9 +1,9 @@
 import { describe, expect, test } from 'vitest';
-import A3mMSA from "./A3mMSA.js";
-import ClustalMSA from "./ClustalMSA.js";
-import FastaMSA from "./FastaMSA.js";
-import { getUngappedSequence, parseMSA } from "./index.js";
-import parseNewick from "./parseNewick.js";
+import A3mMSA from './A3mMSA.js';
+import ClustalMSA from './ClustalMSA.js';
+import FastaMSA from './FastaMSA.js';
+import { getUngappedSequence, parseMSA } from './index.js';
+import parseNewick from './parseNewick.js';
 describe('parseMSA', () => {
     test('parses FASTA format', () => {
         const fasta = `>seq1

package/dist/msa/parseNewick.js.map

@@ -1 +1 @@
-{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../../src/msa/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,mFAAmF;IACnF,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,YAAY,GAAG,CAAC,CAAC,OAAO,CAAC,mBAAmB,EAAE,CAAC,CAAC,EAAE,KAAa,EAAE,EAAE;QACvE,MAAM,GAAG,GAAG,WAAW,CAAC,MAAM,CAAA;QAC9B,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;QAC7C,OAAO,MAAM,GAAG,IAAI,CAAA;IACtB,CAAC,CAAC,CAAA;IAEF,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,YAAY,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,GAAG,CAAC,OAAO,CACvB,cAAc,EACd,CAAC,CAAC,EAAE,GAAW,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,CAAC,GAAG,CAAC,CAAE,CAC9C,CAAA;QACD,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,eAAe;gBACvB,IAAI,CAAC,QAAQ,GAAG,CAAC,OAAO,CAAC,CAAA;gBACzB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;gBACxB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../../src/msa/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,mFAAmF;IACnF,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,YAAY,GAAG,CAAC,CAAC,OAAO,CAAC,mBAAmB,EAAE,CAAC,CAAC,EAAE,KAAa,EAAE,EAAE;QACvE,MAAM,GAAG,GAAG,WAAW,CAAC,MAAM,CAAA;QAC9B,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;QAC7C,OAAO,MAAM,GAAG,IAAI,CAAA;IACtB,CAAC,CAAC,CAAA;IAEF,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,YAAY,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,GAAG,CAAC,OAAO,CACvB,cAAc,EACd,CAAC,CAAC,EAAE,GAAW,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,CAAC,GAAG,CAAC,CAAE,CAC9C,CAAA;QACD,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,eAAe;gBACvB,IAAI,CAAC,QAAQ,GAAG,CAAC,OAAO,CAAC,CAAA;gBACzB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,SAAS,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;gBACxB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/msa/stockholmParser.test.js

@@ -1,5 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import { parse, parseAll, sniff } from "./stockholmParser.js";
+import { parse, parseAll, sniff } from './stockholmParser.js';
 describe('stockholmParser', () => {
     describe('sniff', () => {
         test('returns true for Stockholm format', () => {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "msa-parsers",
-  "version": "5.6.3",
+  "version": "5.7.1",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -20,14 +20,14 @@
     "src"
   ],
   "dependencies": {
-    "clustal-js": "^2.0.15",
+    "clustal-js": "^2.0.17",
     "emf-js": "^2.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
   "devDependencies": {
-    "typescript": "^6.0.3",
+    "typescript": "^7.0.2",
     "vitest": "^4.1.10"
   },
   "scripts": {

package/src/index.ts

@@ -1,5 +1,5 @@
 // Types
-export * from './types.ts'
+export type * from './types.ts'
 
 // Utilities
 export { generateNodeIds } from './util.ts'

package/src/msa/BaseMSA.ts

@@ -21,7 +21,8 @@ export default abstract class BaseMSA {
 
   getRowData(_name: string) {
     return undefined as
-      { name?: string; accession?: string; dbxref?: string } | undefined
+      | { name?: string; accession?: string; dbxref?: string }
+      | undefined
   }
 
   getStructures(): Record<string, unknown> {

package/src/msa/StockholmMSA.ts

@@ -1,7 +1,7 @@
-import parseNewick from './parseNewick.ts'
-import { parseAll } from './stockholmParser.ts'
 import { generateNodeIds } from '../util.ts'
 import BaseMSA from './BaseMSA.ts'
+import parseNewick from './parseNewick.ts'
+import { parseAll } from './stockholmParser.ts'
 
 import type { NodeWithIds } from '../types.ts'
 import type { StockholmData } from './stockholmParser.ts'

package/src/msa/index.ts

@@ -8,7 +8,11 @@ export { parseEmfTree } from 'emf-js'
 export { default as parseNewick } from './parseNewick.ts'
 
 export type MSAParserType =
-  StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA
+  | StockholmMSA
+  | A3mMSA
+  | FastaMSA
+  | EmfMSA
+  | ClustalMSA
 
 export type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal'