msa-parsers 5.4.0 → 5.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (17) hide show
  1. package/dist/gff/parseGFF.js +9 -1
  2. package/dist/gff/parseGFF.js.map +1 -1
  3. package/dist/msa/FastaMSA.d.ts +1 -0
  4. package/dist/msa/FastaMSA.js +7 -3
  5. package/dist/msa/FastaMSA.js.map +1 -1
  6. package/dist/msa/StockholmMSA.js +6 -2
  7. package/dist/msa/StockholmMSA.js.map +1 -1
  8. package/dist/msa/index.test.js +12 -0
  9. package/dist/msa/index.test.js.map +1 -1
  10. package/dist/msa/stockholmParser.js +16 -30
  11. package/dist/msa/stockholmParser.js.map +1 -1
  12. package/package.json +2 -2
  13. package/src/gff/parseGFF.ts +9 -1
  14. package/src/msa/FastaMSA.ts +8 -3
  15. package/src/msa/StockholmMSA.ts +7 -3
  16. package/src/msa/index.test.ts +14 -0
  17. package/src/msa/stockholmParser.ts +20 -30
package/dist/gff/parseGFF.js CHANGED
@@ -20,9 +20,17 @@ function parseAttributes(col9) {
20
20
  const eq = f.indexOf('=');
21
21
  const key = (eq === -1 ? f : f.slice(0, eq)).trim();
22
22
  const val = eq === -1 ? undefined : f.slice(eq + 1);
23
+ // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
24
+ // literal comma encoded as %2C survives the split and isn't mistaken
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+ // for a separator
23
26
  return [
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27
  key,
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- val ? safeDecode(val).trim().split(',').join(' ') : undefined,
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+ val
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+ ? val
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+ .split(',')
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+ .map(v => safeDecode(v).trim())
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+ .join(' ')
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+ : undefined,
26
34
  ];
27
35
  })
28
36
  .filter(([key]) => key !== ''));
package/dist/gff/parseGFF.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,OAAO;YACL,GAAG;YACH,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS;SAC9D,CAAA;IACH,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,OAAO;YACL,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,GAAG,eAAe,CAAC,IAAI,CAAC;SACzB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
1
+ {"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,wEAAwE;QACxE,qEAAqE;QACrE,kBAAkB;QAClB,OAAO;YACL,GAAG;YACH,GAAG;gBACD,CAAC,CAAC,GAAG;qBACA,KAAK,CAAC,GAAG,CAAC;qBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;qBAC9B,IAAI,CAAC,GAAG,CAAC;gBACd,CAAC,CAAC,SAAS;SACd,CAAA;IACH,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,OAAO;YACL,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,GAAG,eAAe,CAAC,IAAI,CAAC;SACzB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
package/dist/msa/FastaMSA.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import BaseMSA from './BaseMSA.ts';
2
2
  export default class FastaMSA extends BaseMSA {
3
3
  private MSA;
4
+ private orderedNames;
4
5
  constructor(text: string);
5
6
  getMSA(): {
6
7
  seqdata: Record<string, string>;
package/dist/msa/FastaMSA.js CHANGED
@@ -1,6 +1,9 @@
1
1
  import BaseMSA from "./BaseMSA.js";
2
2
  export default class FastaMSA extends BaseMSA {
3
3
  MSA;
4
+ // explicit insertion-ordered ids: object key order reorders integer-like
5
+ // keys (e.g. a numeric ">123" defline) to the front, scrambling row order
6
+ orderedNames = [];
4
7
  constructor(text) {
5
8
  super();
6
9
  const seqdata = {};
@@ -18,6 +21,7 @@ export default class FastaMSA extends BaseMSA {
18
21
  const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
19
22
  if (id) {
20
23
  seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
24
+ this.orderedNames.push(id);
21
25
  if (id.includes(':')) {
22
26
  colonNormalized[id.replaceAll(':', '_')] = id;
23
27
  }
@@ -29,7 +33,7 @@ export default class FastaMSA extends BaseMSA {
29
33
  return this.MSA;
30
34
  }
31
35
  getNames() {
32
- return Object.keys(this.MSA.seqdata);
36
+ return this.orderedNames;
33
37
  }
34
38
  getRow(name) {
35
39
  return (this.MSA.seqdata[name] ??
@@ -37,8 +41,8 @@ export default class FastaMSA extends BaseMSA {
37
41
  '');
38
42
  }
39
43
  getWidth() {
40
- const name = Object.keys(this.MSA.seqdata)[0];
41
- return this.getRow(name).length;
44
+ const name = this.orderedNames[0];
45
+ return name === undefined ? 0 : this.getRow(name).length;
42
46
  }
43
47
  }
44
48
  //# sourceMappingURL=FastaMSA.js.map
package/dist/msa/FastaMSA.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/msa/FastaMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,OAAO;IACnC,GAAG,CAGV;IAED,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAA2B,EAAE,CAAA;QAC1C,MAAM,eAAe,GAA2B,EAAE,CAAA;QAClD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YAC7D,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACrC,MAAM,EAAE,GAAG,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,EAAE,EAAE,CAAC;gBACP,OAAO,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;gBAC/D,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,eAAe,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAA;gBAC/C,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,eAAe,EAAE,CAAA;IACzC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,CACL,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC;YACtB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;YACtD,EAAE,CACH,CAAA;IACH,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;CACF"}
1
+ {"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/msa/FastaMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,OAAO;IACnC,GAAG,CAGV;IAED,yEAAyE;IACzE,0EAA0E;IAClE,YAAY,GAAa,EAAE,CAAA;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAA2B,EAAE,CAAA;QAC1C,MAAM,eAAe,GAA2B,EAAE,CAAA;QAClD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YAC7D,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACrC,MAAM,EAAE,GAAG,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,EAAE,EAAE,CAAC;gBACP,OAAO,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;gBAC/D,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC1B,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,eAAe,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAA;gBAC/C,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,eAAe,EAAE,CAAA;IACzC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,CACL,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC;YACtB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;YACtD,EAAE,CACH,CAAA;IACH,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QACjC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;CACF"}
package/dist/msa/StockholmMSA.js CHANGED
@@ -9,7 +9,11 @@ export default class StockholmMSA extends BaseMSA {
9
9
  super();
10
10
  const res = parseAll(text);
11
11
  this.data = res;
12
- this.MSA = res[currentAlignment];
12
+ const aln = res[currentAlignment] ?? res[0];
13
+ if (!aln) {
14
+ throw new Error('No alignments found in Stockholm file');
15
+ }
16
+ this.MSA = aln;
13
17
  }
14
18
  getMSA() {
15
19
  return this.MSA;
@@ -19,7 +23,7 @@ export default class StockholmMSA extends BaseMSA {
19
23
  }
20
24
  getWidth() {
21
25
  const name = Object.keys(this.MSA.seqdata)[0];
22
- return this.getRow(name).length;
26
+ return name === undefined ? 0 : this.getRow(name).length;
23
27
  }
24
28
  get alignmentNames() {
25
29
  return this.data.map((aln, idx) => aln.gf.DE?.[0] ?? `Alignment ${idx + 1}`);
package/dist/msa/StockholmMSA.js.map CHANGED
@@ -1 +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,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAE,CAAA;IACnC,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,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,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"}
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"}
package/dist/msa/index.test.js CHANGED
@@ -14,6 +14,18 @@ GHIKL`;
14
14
  expect(msa).toBeInstanceOf(FastaMSA);
15
15
  expect(msa.getNames()).toEqual(['seq1', 'seq2']);
16
16
  });
17
+ test('preserves row order for numeric FASTA ids', () => {
18
+ // object key order would hoist integer-like keys ('10' before '2'),
19
+ // scrambling the alignment; getNames must keep file order
20
+ const fasta = `>3
21
+ ACDEF
22
+ >1
23
+ GHIKL
24
+ >2
25
+ MNPQR`;
26
+ const msa = parseMSA(fasta);
27
+ expect(msa.getNames()).toEqual(['3', '1', '2']);
28
+ });
17
29
  test('parses A3M format', () => {
18
30
  const a3m = `>seq1
19
31
  ACDEFghiKLMNPQ
package/dist/msa/index.test.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.test.js","sourceRoot":"","sources":["../../src/msa/index.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,EAAE,mBAAmB,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAC1D,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAE1C,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,KAAK,GAAG;;;MAGZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;;YAGJ,CAAA;QACR,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAEzB,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACpC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,OAAO,GAAG;;;;qBAIC,CAAA;QACjB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAClD,MAAM,OAAO,GAAG;4BACQ,CAAA;QACxB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,yCAAyC,EAAE,GAAG,EAAE;QACnD,yEAAyE;QACzE,+CAA+C;QAC/C,MAAM,UAAU,GAAG;;;YAGX,CAAA;QACR,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACnD,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QAEjE,MAAM,YAAY,GAAG;;;MAGnB,CAAA;QACF,MAAM,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACvD,MAAM,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACjE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,+BAA+B,EAAE,GAAG,EAAE;IAC7C,MAAM,KAAK,GAAG;;;WAGL,CAAA;IAET,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,iFAAiF,EAAE,GAAG,EAAE;QAC3F,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8EAA8E,EAAE,GAAG,EAAE;QACxF,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,4BAA4B,EAAE,GAAG,EAAE;IAC1C,IAAI,CAAC,qDAAqD,EAAE,GAAG,EAAE;QAC/D,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,sCAAsC,CAAC,CAAA;QAChE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,iCAAiC,EAAE,GAAG,EAAE;IAC/C,IAAI,CAAC,uCAAuC,EAAE,GAAG,EAAE;QACjD,MAAM,IAAI,GAAG,WAAW,CACtB,iEAAiE,CAClE,CAAA;QACD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,+CAA+C,CAAC,CAAA;IAC1E,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,IAAI,GAAG,WAAW,CAAC,gCAAgC,CAAC,CAAA;QAC1D,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,aAAa,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,IAAI,GAAG,WAAW,CAAC,sBAAsB,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,qBAAqB,EAAE,GAAG,EAAE;IACnC,IAAI,CAAC,gBAAgB,EAAE,GAAG,EAAE;QAC1B,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,cAAc,EAAE,GAAG,EAAE;QACxB,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oBAAoB,EAAE,GAAG,EAAE;QAC9B,MAAM,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACzC,MAAM,CAAC,mBAAmB,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,CAAC,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
1
+ {"version":3,"file":"index.test.js","sourceRoot":"","sources":["../../src/msa/index.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,EAAE,mBAAmB,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAC1D,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAE1C,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,KAAK,GAAG;;;MAGZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,2CAA2C,EAAE,GAAG,EAAE;QACrD,oEAAoE;QACpE,0DAA0D;QAC1D,MAAM,KAAK,GAAG;;;;;MAKZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IACjD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;;YAGJ,CAAA;QACR,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAEzB,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACpC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,OAAO,GAAG;;;;qBAIC,CAAA;QACjB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAClD,MAAM,OAAO,GAAG;4BACQ,CAAA;QACxB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,yCAAyC,EAAE,GAAG,EAAE;QACnD,yEAAyE;QACzE,+CAA+C;QAC/C,MAAM,UAAU,GAAG;;;YAGX,CAAA;QACR,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACnD,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QAEjE,MAAM,YAAY,GAAG;;;MAGnB,CAAA;QACF,MAAM,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACvD,MAAM,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACjE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,+BAA+B,EAAE,GAAG,EAAE;IAC7C,MAAM,KAAK,GAAG;;;WAGL,CAAA;IAET,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,iFAAiF,EAAE,GAAG,EAAE;QAC3F,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8EAA8E,EAAE,GAAG,EAAE;QACxF,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,4BAA4B,EAAE,GAAG,EAAE;IAC1C,IAAI,CAAC,qDAAqD,EAAE,GAAG,EAAE;QAC/D,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,sCAAsC,CAAC,CAAA;QAChE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,iCAAiC,EAAE,GAAG,EAAE;IAC/C,IAAI,CAAC,uCAAuC,EAAE,GAAG,EAAE;QACjD,MAAM,IAAI,GAAG,WAAW,CACtB,iEAAiE,CAClE,CAAA;QACD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,+CAA+C,CAAC,CAAA;IAC1E,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,IAAI,GAAG,WAAW,CAAC,gCAAgC,CAAC,CAAA;QAC1D,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,aAAa,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,IAAI,GAAG,WAAW,CAAC,sBAAsB,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,qBAAqB,EAAE,GAAG,EAAE;IACnC,IAAI,CAAC,gBAAgB,EAAE,GAAG,EAAE;QAC1B,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,cAAc,EAAE,GAAG,EAAE;QACxB,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oBAAoB,EAAE,GAAG,EAAE;QAC9B,MAAM,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACzC,MAAM,CAAC,mBAAmB,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,CAAC,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
package/dist/msa/stockholmParser.js CHANGED
@@ -13,6 +13,17 @@ function createStockholm() {
13
13
  seqdata: {},
14
14
  };
15
15
  }
16
+ // records before a "# STOCKHOLM 1.0" header are an error in strict mode,
17
+ // otherwise they implicitly start a new alignment
18
+ function ensureStock(stock, strict) {
19
+ if (stock) {
20
+ return stock;
21
+ }
22
+ if (strict) {
23
+ throw new Error('No format header: # STOCKHOLM 1.0');
24
+ }
25
+ return createStockholm();
26
+ }
16
27
  const formatStartRegex = /^# STOCKHOLM 1.0/;
17
28
  const formatEndRegex = /^\/\/\s*$/;
18
29
  const gfRegex = /^#=GF\s+(\S+)\s+(.*?)\s*$/;
@@ -41,12 +52,7 @@ export function parseAll(text, opts) {
41
52
  stock = null;
42
53
  }
43
54
  else if ((match = gfRegex.exec(line))) {
44
- if (!stock) {
45
- if (options.strict) {
46
- throw new Error('No format header: # STOCKHOLM 1.0');
47
- }
48
- stock = createStockholm();
49
- }
55
+ stock = ensureStock(stock, !!options.strict);
50
56
  const tag = match[1];
51
57
  if (!stock.gf[tag]) {
52
58
  stock.gf[tag] = [];
@@ -54,12 +60,7 @@ export function parseAll(text, opts) {
54
60
  stock.gf[tag].push(match[2]);
55
61
  }
56
62
  else if ((match = gcRegex.exec(line))) {
57
- if (!stock) {
58
- if (options.strict) {
59
- throw new Error('No format header: # STOCKHOLM 1.0');
60
- }
61
- stock = createStockholm();
62
- }
63
+ stock = ensureStock(stock, !!options.strict);
63
64
  const tag = match[1];
64
65
  if (!stock.gc[tag]) {
65
66
  stock.gc[tag] = '';
@@ -67,12 +68,7 @@ export function parseAll(text, opts) {
67
68
  stock.gc[tag] += match[2];
68
69
  }
69
70
  else if ((match = gsRegex.exec(line))) {
70
- if (!stock) {
71
- if (options.strict) {
72
- throw new Error('No format header: # STOCKHOLM 1.0');
73
- }
74
- stock = createStockholm();
75
- }
71
+ stock = ensureStock(stock, !!options.strict);
76
72
  const seqname = match[1];
77
73
  const tag = match[2];
78
74
  const value = match[3];
@@ -85,12 +81,7 @@ export function parseAll(text, opts) {
85
81
  stock.gs[tag][seqname].push(value);
86
82
  }
87
83
  else if ((match = grRegex.exec(line))) {
88
- if (!stock) {
89
- if (options.strict) {
90
- throw new Error('No format header: # STOCKHOLM 1.0');
91
- }
92
- stock = createStockholm();
93
- }
84
+ stock = ensureStock(stock, !!options.strict);
94
85
  const seqname = match[1];
95
86
  const tag = match[2];
96
87
  const value = match[3];
@@ -103,12 +94,7 @@ export function parseAll(text, opts) {
103
94
  stock.gr[tag][seqname] += value;
104
95
  }
105
96
  else if ((match = lineRegex.exec(line))) {
106
- if (!stock) {
107
- if (options.strict) {
108
- throw new Error('No format header: # STOCKHOLM 1.0');
109
- }
110
- stock = createStockholm();
111
- }
97
+ stock = ensureStock(stock, !!options.strict);
112
98
  const seqname = match[1];
113
99
  const seqdata = match[2];
114
100
  if (!stock.seqdata[seqname]) {
package/dist/msa/stockholmParser.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,EAAE;KACZ,CAAA;AACH,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,SAAS,GAAG,uBAAuB,CAAA;AACzC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA4C;IAE5C,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IAEtC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,GAAG,eAAe,EAAE,CAAA;QAC3B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC/B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;QAC5B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,KAAK,CAAA;QACjC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC1C,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;gBACtD,CAAC;gBACD,KAAK,GAAG,eAAe,EAAE,CAAA;YAC3B,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;gBAC3B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QACnC,CAAC;aAAM,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACpC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IAED,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,KAAK,CACnB,IAAY,EACZ,IAA4C;IAE5C,MAAM,EAAE,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC/B,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;IAClD,CAAC;IACD,OAAO,EAAE,CAAC,CAAC,CAAE,CAAA;AACf,CAAC"}
1
+ {"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,EAAE;KACZ,CAAA;AACH,CAAC;AAED,yEAAyE;AACzE,kDAAkD;AAClD,SAAS,WAAW,CAClB,KAA2B,EAC3B,MAAe;IAEf,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAA;IACd,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;IACtD,CAAC;IACD,OAAO,eAAe,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,SAAS,GAAG,uBAAuB,CAAA;AACzC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA4C;IAE5C,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IAEtC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,GAAG,eAAe,EAAE,CAAA;QAC3B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC/B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;QAC5B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,KAAK,CAAA;QACjC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC1C,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;gBAC3B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QACnC,CAAC;aAAM,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACpC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IAED,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,KAAK,CACnB,IAAY,EACZ,IAA4C;IAE5C,MAAM,EAAE,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC/B,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;IAClD,CAAC;IACD,OAAO,EAAE,CAAC,CAAC,CAAE,CAAA;AACf,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "msa-parsers",
3
- "version": "5.4.0",
3
+ "version": "5.4.1",
4
4
  "license": "MIT",
5
5
  "type": "module",
6
6
  "repository": {
@@ -28,7 +28,7 @@
28
28
  },
29
29
  "devDependencies": {
30
30
  "typescript": "^6.0.3",
31
- "vitest": "^4.1.8"
31
+ "vitest": "^4.1.9"
32
32
  },
33
33
  "scripts": {
34
34
  "clean": "rimraf dist",
package/src/gff/parseGFF.ts CHANGED
@@ -23,9 +23,17 @@ function parseAttributes(col9?: string): Record<string, string | undefined> {
23
23
  const eq = f.indexOf('=')
24
24
  const key = (eq === -1 ? f : f.slice(0, eq)).trim()
25
25
  const val = eq === -1 ? undefined : f.slice(eq + 1)
26
+ // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
27
+ // literal comma encoded as %2C survives the split and isn't mistaken
28
+ // for a separator
26
29
  return [
27
30
  key,
28
- val ? safeDecode(val).trim().split(',').join(' ') : undefined,
31
+ val
32
+ ? val
33
+ .split(',')
34
+ .map(v => safeDecode(v).trim())
35
+ .join(' ')
36
+ : undefined,
29
37
  ]
30
38
  })
31
39
  .filter(([key]) => key !== ''),
package/src/msa/FastaMSA.ts CHANGED
@@ -6,6 +6,10 @@ export default class FastaMSA extends BaseMSA {
6
6
  colonNormalized: Record<string, string>
7
7
  }
8
8
 
9
+ // explicit insertion-ordered ids: object key order reorders integer-like
10
+ // keys (e.g. a numeric ">123" defline) to the front, scrambling row order
11
+ private orderedNames: string[] = []
12
+
9
13
  constructor(text: string) {
10
14
  super()
11
15
  const seqdata: Record<string, string> = {}
@@ -23,6 +27,7 @@ export default class FastaMSA extends BaseMSA {
23
27
  const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx)
24
28
  if (id) {
25
29
  seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '')
30
+ this.orderedNames.push(id)
26
31
  if (id.includes(':')) {
27
32
  colonNormalized[id.replaceAll(':', '_')] = id
28
33
  }
@@ -36,7 +41,7 @@ export default class FastaMSA extends BaseMSA {
36
41
  }
37
42
 
38
43
  getNames() {
39
- return Object.keys(this.MSA.seqdata)
44
+ return this.orderedNames
40
45
  }
41
46
 
42
47
  getRow(name: string) {
@@ -48,7 +53,7 @@ export default class FastaMSA extends BaseMSA {
48
53
  }
49
54
 
50
55
  getWidth() {
51
- const name = Object.keys(this.MSA.seqdata)[0]!
52
- return this.getRow(name).length
56
+ const name = this.orderedNames[0]
57
+ return name === undefined ? 0 : this.getRow(name).length
53
58
  }
54
59
  }
package/src/msa/StockholmMSA.ts CHANGED
@@ -14,7 +14,11 @@ export default class StockholmMSA extends BaseMSA {
14
14
  super()
15
15
  const res = parseAll(text)
16
16
  this.data = res
17
- this.MSA = res[currentAlignment]!
17
+ const aln = res[currentAlignment] ?? res[0]
18
+ if (!aln) {
19
+ throw new Error('No alignments found in Stockholm file')
20
+ }
21
+ this.MSA = aln
18
22
  }
19
23
 
20
24
  getMSA() {
@@ -26,8 +30,8 @@ export default class StockholmMSA extends BaseMSA {
26
30
  }
27
31
 
28
32
  getWidth() {
29
- const name = Object.keys(this.MSA.seqdata)[0]!
30
- return this.getRow(name).length
33
+ const name = Object.keys(this.MSA.seqdata)[0]
34
+ return name === undefined ? 0 : this.getRow(name).length
31
35
  }
32
36
 
33
37
  get alignmentNames() {
package/src/msa/index.test.ts CHANGED
@@ -18,6 +18,20 @@ GHIKL`
18
18
  expect(msa.getNames()).toEqual(['seq1', 'seq2'])
19
19
  })
20
20
 
21
+ test('preserves row order for numeric FASTA ids', () => {
22
+ // object key order would hoist integer-like keys ('10' before '2'),
23
+ // scrambling the alignment; getNames must keep file order
24
+ const fasta = `>3
25
+ ACDEF
26
+ >1
27
+ GHIKL
28
+ >2
29
+ MNPQR`
30
+ const msa = parseMSA(fasta)
31
+
32
+ expect(msa.getNames()).toEqual(['3', '1', '2'])
33
+ })
34
+
21
35
  test('parses A3M format', () => {
22
36
  const a3m = `>seq1
23
37
  ACDEFghiKLMNPQ
package/src/msa/stockholmParser.ts CHANGED
@@ -24,6 +24,21 @@ function createStockholm(): StockholmData {
24
24
  }
25
25
  }
26
26
 
27
+ // records before a "# STOCKHOLM 1.0" header are an error in strict mode,
28
+ // otherwise they implicitly start a new alignment
29
+ function ensureStock(
30
+ stock: StockholmData | null,
31
+ strict: boolean,
32
+ ): StockholmData {
33
+ if (stock) {
34
+ return stock
35
+ }
36
+ if (strict) {
37
+ throw new Error('No format header: # STOCKHOLM 1.0')
38
+ }
39
+ return createStockholm()
40
+ }
41
+
27
42
  const formatStartRegex = /^# STOCKHOLM 1.0/
28
43
  const formatEndRegex = /^\/\/\s*$/
29
44
  const gfRegex = /^#=GF\s+(\S+)\s+(.*?)\s*$/
@@ -57,36 +72,21 @@ export function parseAll(
57
72
  }
58
73
  stock = null
59
74
  } else if ((match = gfRegex.exec(line))) {
60
- if (!stock) {
61
- if (options.strict) {
62
- throw new Error('No format header: # STOCKHOLM 1.0')
63
- }
64
- stock = createStockholm()
65
- }
75
+ stock = ensureStock(stock, !!options.strict)
66
76
  const tag = match[1]!
67
77
  if (!stock.gf[tag]) {
68
78
  stock.gf[tag] = []
69
79
  }
70
80
  stock.gf[tag].push(match[2]!)
71
81
  } else if ((match = gcRegex.exec(line))) {
72
- if (!stock) {
73
- if (options.strict) {
74
- throw new Error('No format header: # STOCKHOLM 1.0')
75
- }
76
- stock = createStockholm()
77
- }
82
+ stock = ensureStock(stock, !!options.strict)
78
83
  const tag = match[1]!
79
84
  if (!stock.gc[tag]) {
80
85
  stock.gc[tag] = ''
81
86
  }
82
87
  stock.gc[tag] += match[2]!
83
88
  } else if ((match = gsRegex.exec(line))) {
84
- if (!stock) {
85
- if (options.strict) {
86
- throw new Error('No format header: # STOCKHOLM 1.0')
87
- }
88
- stock = createStockholm()
89
- }
89
+ stock = ensureStock(stock, !!options.strict)
90
90
  const seqname = match[1]!
91
91
  const tag = match[2]!
92
92
  const value = match[3]!
@@ -98,12 +98,7 @@ export function parseAll(
98
98
  }
99
99
  stock.gs[tag][seqname].push(value)
100
100
  } else if ((match = grRegex.exec(line))) {
101
- if (!stock) {
102
- if (options.strict) {
103
- throw new Error('No format header: # STOCKHOLM 1.0')
104
- }
105
- stock = createStockholm()
106
- }
101
+ stock = ensureStock(stock, !!options.strict)
107
102
  const seqname = match[1]!
108
103
  const tag = match[2]!
109
104
  const value = match[3]!
@@ -115,12 +110,7 @@ export function parseAll(
115
110
  }
116
111
  stock.gr[tag][seqname] += value
117
112
  } else if ((match = lineRegex.exec(line))) {
118
- if (!stock) {
119
- if (options.strict) {
120
- throw new Error('No format header: # STOCKHOLM 1.0')
121
- }
122
- stock = createStockholm()
123
- }
113
+ stock = ensureStock(stock, !!options.strict)
124
114
  const seqname = match[1]!
125
115
  const seqdata = match[2]!
126
116
  if (!stock.seqdata[seqname]) {