msa-parsers 8.0.0 → 8.2.0

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 (5) hide show
  1. package/dist/msa/stockholmParser.js +3 -0
  2. package/dist/msa/stockholmParser.js.map +1 -1
  3. package/package.json +1 -1
  4. package/src/msa/stockholmParser.test.ts +11 -0
  5. package/src/msa/stockholmParser.ts +3 -0
package/dist/msa/stockholmParser.js CHANGED
@@ -49,6 +49,9 @@ export function parseAll(text, opts) {
49
49
  for (const line of lines) {
50
50
  let match;
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51
  if (formatStartRegex.test(line)) {
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+ if (stock) {
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+ db.push(stock);
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+ }
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  stock = createStockholm();
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  treeContinues = false;
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  }
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,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;KAC7B,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,8EAA8E;AAC9E,yEAAyE;AACzE,6EAA6E;AAC7E,MAAM,SAAS,GAAG,6BAA6B,CAAA;AAC/C,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,IAA2B;IAE3B,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IACtC,wEAAwE;IACxE,6CAA6C;IAC7C,IAAI,aAAa,GAAG,KAAK,CAAA;IAEzB,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;YACzB,aAAa,GAAG,KAAK,CAAA;QACvB,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,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,CAAA;YACrC,IAAI,GAAG,KAAK,IAAI,IAAI,aAAa,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACvD,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;YACxC,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;YACxB,CAAC;YACD,aAAa,GAAG,GAAG,KAAK,IAAI,CAAA;QAC9B,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,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC/D,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,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAC3D;YAAA,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC7C,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,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAA;YAC5D,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC3D,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,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,KAAK,SAAS,EAAE,CAAC;gBACzC,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,IAA2B;IAE3B,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,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;KAC7B,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,8EAA8E;AAC9E,yEAAyE;AACzE,6EAA6E;AAC7E,MAAM,SAAS,GAAG,6BAA6B,CAAA;AAC/C,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,IAA2B;IAE3B,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IACtC,wEAAwE;IACxE,6CAA6C;IAC7C,IAAI,aAAa,GAAG,KAAK,CAAA;IAEzB,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,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,eAAe,EAAE,CAAA;YACzB,aAAa,GAAG,KAAK,CAAA;QACvB,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,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,CAAA;YACrC,IAAI,GAAG,KAAK,IAAI,IAAI,aAAa,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACvD,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;YACxC,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;YACxB,CAAC;YACD,aAAa,GAAG,GAAG,KAAK,IAAI,CAAA;QAC9B,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,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC/D,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,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAC3D;YAAA,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC7C,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,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAA;YAC5D,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC3D,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,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,KAAK,SAAS,EAAE,CAAC;gBACzC,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,IAA2B;IAE3B,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": "8.0.0",
3
+ "version": "8.2.0",
4
4
  "license": "MIT",
5
5
  "type": "module",
6
6
  "repository": {
package/src/msa/stockholmParser.test.ts CHANGED
@@ -133,6 +133,17 @@ seq2 GHIKL
133
133
  })
134
134
  })
135
135
 
136
+ test('a header ends the open alignment when its // is missing', () => {
137
+ const db = parseAll(`# STOCKHOLM 1.0
138
+ seq1 ACDEF
139
+ # STOCKHOLM 1.0
140
+ seq2 GHIKL
141
+ //`)
142
+ expect(db).toHaveLength(2)
143
+ expect(db[0]?.seqdata).toEqual({ seq1: 'ACDEF' })
144
+ expect(db[1]?.seqdata).toEqual({ seq2: 'GHIKL' })
145
+ })
146
+
136
147
  test('joins a tree split across #=GF NH lines, starting a new one at TN', () => {
137
148
  const [aln] = parseAll(`# STOCKHOLM 1.0
138
149
  #=GF TN first
package/src/msa/stockholmParser.ts CHANGED
@@ -71,6 +71,9 @@ export function parseAll(
71
71
  let match: RegExpExecArray | null
72
72
 
73
73
  if (formatStartRegex.test(line)) {
74
+ if (stock) {
75
+ db.push(stock)
76
+ }
74
77
  stock = createStockholm()
75
78
  treeContinues = false
76
79
  } else if (formatEndRegex.test(line)) {