msa-parsers 5.2.0 → 5.3.0
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.
- package/dist/gff/parseGFF.js +19 -5
- package/dist/gff/parseGFF.js.map +1 -1
- package/dist/gff/parseGFF.test.js +10 -0
- package/dist/gff/parseGFF.test.js.map +1 -1
- package/dist/msa/A3mMSA.js +1 -1
- package/dist/msa/A3mMSA.js.map +1 -1
- package/dist/msa/BaseMSA.d.ts +7 -2
- package/dist/msa/BaseMSA.js.map +1 -1
- package/dist/msa/ClustalMSA.js +4 -2
- package/dist/msa/ClustalMSA.js.map +1 -1
- package/dist/msa/EmfMSA.d.ts +0 -1
- package/dist/msa/EmfMSA.js +3 -5
- package/dist/msa/EmfMSA.js.map +1 -1
- package/dist/msa/FastaMSA.js +1 -1
- package/dist/msa/FastaMSA.js.map +1 -1
- package/dist/msa/StockholmMSA.d.ts +4 -15
- package/dist/msa/StockholmMSA.js +1 -1
- package/dist/msa/StockholmMSA.js.map +1 -1
- package/dist/msa/index.test.js +7 -0
- package/dist/msa/index.test.js.map +1 -1
- package/package.json +2 -2
- package/src/gff/parseGFF.test.ts +12 -0
- package/src/gff/parseGFF.ts +19 -5
- package/src/msa/A3mMSA.ts +1 -1
- package/src/msa/BaseMSA.ts +7 -2
- package/src/msa/ClustalMSA.ts +4 -2
- package/src/msa/EmfMSA.ts +3 -6
- package/src/msa/FastaMSA.ts +1 -1
- package/src/msa/StockholmMSA.ts +7 -2
- package/src/msa/index.test.ts +8 -0
package/dist/gff/parseGFF.js
CHANGED
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@@ -1,3 +1,13 @@
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1
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+
// decodeURIComponent throws on a stray '%' (common in unescaped GFF3 values);
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2
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+
// fall back to the raw value rather than aborting the whole parse
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3
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+
function safeDecode(val) {
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4
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try {
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5
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return decodeURIComponent(val);
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6
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+
}
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7
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+
catch {
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8
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return val;
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9
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+
}
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10
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+
}
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1
11
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function parseAttributes(col9) {
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2
12
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if (!col9) {
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3
13
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return {};
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@@ -6,11 +16,15 @@ function parseAttributes(col9) {
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6
16
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.split(';')
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7
17
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.map(f => f.trim())
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8
18
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.filter(f => !!f)
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9
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-
.map(f =>
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10
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-
.
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11
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-
key
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12
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val ?
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13
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-
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19
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+
.map(f => {
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20
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const eq = f.indexOf('=');
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21
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const key = (eq === -1 ? f : f.slice(0, eq)).trim();
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22
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const val = eq === -1 ? undefined : f.slice(eq + 1);
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23
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return [
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24
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key,
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25
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val ? safeDecode(val).trim().split(',').join(' ') : undefined,
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26
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];
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27
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})
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14
28
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.filter(([key]) => key !== ''));
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15
29
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}
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16
30
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export function parseGFF(str) {
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package/dist/gff/parseGFF.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,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,
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1
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+
{"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"}
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@@ -78,6 +78,16 @@ seq2\tSource\ttype\t20\t30\t.\t.\t.\tName=test2`;
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78
78
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const result = parseGFF(gff);
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79
79
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expect(result[0]?.Ontology_term).toBe('GO:0001 GO:0002');
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80
80
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});
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81
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+
test('does not throw on a stray percent sign', () => {
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82
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const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=100%done';
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83
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const result = parseGFF(gff);
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84
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expect(result[0]?.Note).toBe('100%done');
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85
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});
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86
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test('keeps text after a second equals sign', () => {
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87
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const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=a=b';
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88
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const result = parseGFF(gff);
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89
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expect(result[0]?.Note).toBe('a=b');
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90
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});
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81
91
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test('parses multiple lines', () => {
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82
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const gff = `seq1\tPfam\tprotein_match\t10\t50\t.\t.\t.\tName=PF00001
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83
93
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seq1\tSMART\tprotein_match\t60\t100\t.\t.\t.\tName=SM00001
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"parseGFF.test.js","sourceRoot":"","sources":["../../src/gff/parseGFF.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QAChC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,GAAG,GACP,kEAAkE,CAAA;QACpE,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;YACxB,MAAM,EAAE,MAAM;YACd,MAAM,EAAE,cAAc;YACtB,IAAI,EAAE,eAAe;YACrB,KAAK,EAAE,EAAE;YACT,GAAG,EAAE,EAAE;YACP,KAAK,EAAE,CAAC;YACR,MAAM,EAAE,GAAG;YACX,KAAK,EAAE,GAAG;YACV,IAAI,EAAE,SAAS;SAChB,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,GAAG,GACP,kGAAkG,CAAA;QACpG,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;YAC9B,IAAI,EAAE,SAAS;YACf,cAAc,EAAE,OAAO;YACvB,WAAW,EAAE,MAAM;SACpB,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,GAAG,GAAG,8DAA8D,CAAA;QAC1E,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,GAAG,GAAG;;8CAE8B,CAAA;QAC1C,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;gDAEgC,CAAA;QAC5C,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;IAChC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mCAAmC,EAAE,GAAG,EAAE;QAC7C,MAAM,GAAG,GAAG,oCAAoC,CAAA;QAChD,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,GAAG,GAAG,oBAAoB,CAAA;QAChC,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;YAC9B,MAAM,EAAE,MAAM;YACd,MAAM,EAAE,QAAQ;YAChB,IAAI,EAAE,MAAM;YACZ,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,CAAC;SACP,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,GAAG,GAAG,kDAAkD,CAAA;QAC9D,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GACP,mEAAmE,CAAA;QACrE,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,GAAG,GAAG;;wDAEwC,CAAA;QACpD,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
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1
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+
{"version":3,"file":"parseGFF.test.js","sourceRoot":"","sources":["../../src/gff/parseGFF.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QAChC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,GAAG,GACP,kEAAkE,CAAA;QACpE,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;YACxB,MAAM,EAAE,MAAM;YACd,MAAM,EAAE,cAAc;YACtB,IAAI,EAAE,eAAe;YACrB,KAAK,EAAE,EAAE;YACT,GAAG,EAAE,EAAE;YACP,KAAK,EAAE,CAAC;YACR,MAAM,EAAE,GAAG;YACX,KAAK,EAAE,GAAG;YACV,IAAI,EAAE,SAAS;SAChB,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,GAAG,GACP,kGAAkG,CAAA;QACpG,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;YAC9B,IAAI,EAAE,SAAS;YACf,cAAc,EAAE,OAAO;YACvB,WAAW,EAAE,MAAM;SACpB,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,GAAG,GAAG,8DAA8D,CAAA;QAC1E,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,GAAG,GAAG;;8CAE8B,CAAA;QAC1C,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;gDAEgC,CAAA;QAC5C,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;IAChC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mCAAmC,EAAE,GAAG,EAAE;QAC7C,MAAM,GAAG,GAAG,oCAAoC,CAAA;QAChD,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,GAAG,GAAG,oBAAoB,CAAA;QAChC,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;YAC9B,MAAM,EAAE,MAAM;YACd,MAAM,EAAE,QAAQ;YAChB,IAAI,EAAE,MAAM;YACZ,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,CAAC;SACP,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,GAAG,GAAG,kDAAkD,CAAA;QAC9D,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GACP,mEAAmE,CAAA;QACrE,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAClD,MAAM,GAAG,GAAG,mDAAmD,CAAA;QAC/D,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uCAAuC,EAAE,GAAG,EAAE;QACjD,MAAM,GAAG,GAAG,8CAA8C,CAAA;QAC1D,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,GAAG,GAAG;;wDAEwC,CAAA;QACpD,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
|
package/dist/msa/A3mMSA.js
CHANGED
|
@@ -44,7 +44,7 @@ export default class A3mMSA extends BaseMSA {
|
|
|
44
44
|
if (newlineIdx === -1) {
|
|
45
45
|
continue;
|
|
46
46
|
}
|
|
47
|
-
const defLine = entry.slice(0, newlineIdx);
|
|
47
|
+
const defLine = entry.slice(0, newlineIdx).replace(/\r$/, '');
|
|
48
48
|
const spaceIdx = defLine.indexOf(' ');
|
|
49
49
|
const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
|
|
50
50
|
if (id) {
|
package/dist/msa/A3mMSA.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"A3mMSA.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,GAAG,CAAA,CAAC,MAAM;AACzB,MAAM,SAAS,GAAG,EAAE,CAAA,CAAC,MAAM;AAC3B,MAAM,QAAQ,GAAG,EAAE,CAAA,CAAC,MAAM;AAE1B,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAA;AACzC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACjC,GAAG,CAAqC;IACxC,YAAY,CAAU;IAE9B,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAAa,EAAE,CAAA;QAC5B,MAAM,KAAK,GAAa,EAAE,CAAA;QAE1B,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,CAAA;
|
|
1
|
+
{"version":3,"file":"A3mMSA.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,GAAG,CAAA,CAAC,MAAM;AACzB,MAAM,SAAS,GAAG,EAAE,CAAA,CAAC,MAAM;AAC3B,MAAM,QAAQ,GAAG,EAAE,CAAA,CAAC,MAAM;AAE1B,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAA;AACzC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACjC,GAAG,CAAqC;IACxC,YAAY,CAAU;IAE9B,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAAa,EAAE,CAAA;QAC5B,MAAM,KAAK,GAAa,EAAE,CAAA;QAE1B,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,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAA;gBAC/D,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QAED,IAAI,CAAC,YAAY,GAAG,KAAK,CAAA;QACzB,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,CAAA;IACxD,CAAC;IAED,MAAM,CAAC,KAAK,CAAC,IAAY;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC1B,OAAO,KAAK,CAAA;QACd,CAAC;QAED,MAAM,IAAI,GAAa,EAAE,CAAA;QACzB,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,GAAG,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YAC7D,IAAI,GAAG,EAAE,CAAC;gBACR,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QAED,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACpB,OAAO,KAAK,CAAA;QACd,CAAC;QAED,IAAI,YAAY,GAAG,KAAK,CAAA;QACxB,IAAI,aAAa,GAAG,CAAC,CAAC,CAAA;QACtB,IAAI,eAAe,GAAG,IAAI,CAAA;QAE1B,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;YACvB,IAAI,QAAQ,GAAG,CAAC,CAAA;YAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACpC,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;gBAC9B,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;oBAClB,YAAY,GAAG,IAAI,CAAA;gBACrB,CAAC;qBAAM,IAAI,CAAC,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACpE,QAAQ,EAAE,CAAA;gBACZ,CAAC;YACH,CAAC;YAED,IAAI,aAAa,KAAK,CAAC,CAAC,EAAE,CAAC;gBACzB,aAAa,GAAG,QAAQ,CAAA;YAC1B,CAAC;iBAAM,CAAC;gBACN,IAAI,QAAQ,KAAK,aAAa,EAAE,CAAC;oBAC/B,eAAe,GAAG,KAAK,CAAA;gBACzB,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,YAAY,IAAI,eAAe,CAAA;IACxC,CAAC;IAEO,SAAS,CACf,OAAiB,EACjB,KAAe;QAEf,MAAM,OAAO,GAAG,KAAK,CAAC,MAAM,CAAA;QAC5B,IAAI,OAAO,KAAK,CAAC,EAAE,CAAC;YAClB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,UAAU,GAAe,EAAE,CAAA;QACjC,MAAM,aAAa,GAAe,EAAE,CAAA;QAEpC,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,EAAE,MAAM,EAAE,EAAE,CAAC;YAChD,MAAM,GAAG,GAAG,OAAO,CAAC,MAAM,CAAE,CAAA;YAC5B,MAAM,OAAO,GAAa,EAAE,CAAA;YAC5B,MAAM,OAAO,GAAa,EAAE,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,CAAA;YAET,OAAO,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;gBACtB,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;gBAE9B,IAAI,CAAC,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBAC7D,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAE,CAAC,CAAA;oBACrB,IAAI,GAAG,GAAG,EAAE,CAAA;oBACZ,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;oBACb,OAAO,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;wBACtB,MAAM,CAAC,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;wBAC3B,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ,EAAE,CAAC;4BACjC,GAAG,IAAI,GAAG,CAAC,CAAC,CAAE,CAAA;4BACd,CAAC,EAAE,CAAA;wBACL,CAAC;6BAAM,CAAC;4BACN,MAAK;wBACP,CAAC;oBACH,CAAC;oBACD,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;oBACjB,CAAC,GAAG,CAAC,CAAA;gBACP,CAAC;qBAAM,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;oBAC7B,CAAC,EAAE,CAAA;gBACL,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;oBACzB,IAAI,GAAG,GAAG,EAAE,CAAA;oBACZ,OAAO,CAAC,GAAG,GAAG,CAAC,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;wBACpD,GAAG,IAAI,GAAG,CAAC,CAAC,CAAE,CAAA;wBACd,CAAC,EAAE,CAAA;oBACL,CAAC;oBACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBAChB,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACnB,CAAC;qBAAM,CAAC;oBACN,CAAC,EAAE,CAAA;gBACL,CAAC;YACH,CAAC;YAED,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACxB,aAAa,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC7B,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,CAAA;QAElE,MAAM,UAAU,GAAG,IAAI,KAAK,CAAS,YAAY,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAC1D,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,EAAE,MAAM,EAAE,EAAE,CAAC;YAChD,MAAM,OAAO,GAAG,aAAa,CAAC,MAAM,CAAE,CAAA;YACtC,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC;gBAC9C,IAAI,OAAO,GAAG,CAAC,CAAA;gBACf,KAAK,MAAM,CAAC,IAAI,OAAO,CAAC,GAAG,CAAE,EAAE,CAAC;oBAC9B,IAAI,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;wBAC7B,OAAO,EAAE,CAAA;oBACX,CAAC;gBACH,CAAC;gBACD,IAAI,OAAO,GAAG,UAAU,CAAC,GAAG,CAAE,EAAE,CAAC;oBAC/B,UAAU,CAAC,GAAG,CAAC,GAAG,OAAO,CAAA;gBAC3B,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAE3C,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,EAAE,MAAM,EAAE,EAAE,CAAC;YAChD,MAAM,OAAO,GAAG,UAAU,CAAC,MAAM,CAAE,CAAA;YACnC,MAAM,OAAO,GAAG,aAAa,CAAC,MAAM,CAAE,CAAA;YACtC,MAAM,MAAM,GAAa,EAAE,CAAA;YAE3B,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,YAAY,EAAE,GAAG,EAAE,EAAE,CAAC;gBAC5C,MAAM,MAAM,GAAG,UAAU,CAAC,GAAG,CAAE,CAAA;gBAE/B,IAAI,GAAG,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;oBACzB,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAE,CAAA;oBAC/B,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAA;oBAErC,MAAM,CAAC,IAAI,CAAC,SAAS,IAAI,GAAG,CAAC,CAAA;oBAE7B,IAAI,SAAS,GAAG,EAAE,CAAA;oBAClB,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;wBAC3B,IAAI,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;4BAC7B,SAAS,IAAI,CAAC,CAAC,WAAW,EAAE,CAAA;wBAC9B,CAAC;oBACH,CAAC;oBAED,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;oBAEtB,MAAM,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;oBACzC,IAAI,OAAO,GAAG,CAAC,EAAE,CAAC;wBAChB,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAA;oBAClC,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;oBAChB,IAAI,MAAM,GAAG,CAAC,EAAE,CAAC;wBACf,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAA;oBACjC,CAAC;gBACH,CAAC;YACH,CAAC;YAED,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAE,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QAC5C,CAAC;QAED,OAAO,QAAQ,CAAA;IACjB,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,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,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5C,CAAC;CACF"}
|
package/dist/msa/BaseMSA.d.ts
CHANGED
|
@@ -11,9 +11,14 @@ export default abstract class BaseMSA {
|
|
|
11
11
|
dbxref?: string;
|
|
12
12
|
} | undefined;
|
|
13
13
|
getStructures(): Record<string, unknown>;
|
|
14
|
-
getHeader(): unknown
|
|
14
|
+
getHeader(): Record<string, unknown>;
|
|
15
15
|
get alignmentNames(): string[];
|
|
16
16
|
get seqConsensus(): string | undefined;
|
|
17
17
|
get secondaryStructureConsensus(): string | undefined;
|
|
18
|
-
get tracks():
|
|
18
|
+
get tracks(): {
|
|
19
|
+
id: string;
|
|
20
|
+
name: string;
|
|
21
|
+
data?: string;
|
|
22
|
+
customColorScheme?: Record<string, string>;
|
|
23
|
+
}[];
|
|
19
24
|
}
|
package/dist/msa/BaseMSA.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;
|
|
1
|
+
{"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
CHANGED
|
@@ -10,10 +10,12 @@ export default class ClustalMSA extends BaseMSA {
|
|
|
10
10
|
return this.MSA;
|
|
11
11
|
}
|
|
12
12
|
getRow(name) {
|
|
13
|
-
return this.MSA.alns.find(aln => aln.id === name)?.seq
|
|
13
|
+
return this.MSA.alns.find(aln => aln.id === name)?.seq ?? '';
|
|
14
14
|
}
|
|
15
15
|
getWidth() {
|
|
16
|
-
|
|
16
|
+
// 0 for an empty alignment (e.g. unrecognized text routed here as fallback)
|
|
17
|
+
// rather than crashing on alns[0]
|
|
18
|
+
return this.MSA.alns[0]?.seq.length ?? 0;
|
|
17
19
|
}
|
|
18
20
|
getHeader() {
|
|
19
21
|
return this.MSA.header;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/msa/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IACrC,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/msa/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IACrC,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,4EAA4E;QAC5E,kCAAkC;QAClC,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,MAAM,IAAI,CAAC,CAAA;IAC1C,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;CACF"}
|
package/dist/msa/EmfMSA.d.ts
CHANGED
package/dist/msa/EmfMSA.js
CHANGED
|
@@ -10,13 +10,11 @@ export default class EmfMSA extends BaseMSA {
|
|
|
10
10
|
return this.MSA;
|
|
11
11
|
}
|
|
12
12
|
getRow(name) {
|
|
13
|
-
return this.MSA.find(aln => aln.protein === name)?.seq
|
|
13
|
+
return this.MSA.find(aln => aln.protein === name)?.seq ?? '';
|
|
14
14
|
}
|
|
15
15
|
getWidth() {
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
getHeader() {
|
|
19
|
-
return '';
|
|
16
|
+
// 0 for an empty alignment rather than crashing on MSA[0]
|
|
17
|
+
return this.MSA[0]?.seq.length ?? 0;
|
|
20
18
|
}
|
|
21
19
|
getNames() {
|
|
22
20
|
return this.MSA.map(aln => aln.protein);
|
package/dist/msa/EmfMSA.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"EmfMSA.js","sourceRoot":"","sources":["../../src/msa/EmfMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAEpC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACjC,GAAG,CAAgC;IAE3C,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"EmfMSA.js","sourceRoot":"","sources":["../../src/msa/EmfMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAEpC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACjC,GAAG,CAAgC;IAE3C,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,0DAA0D;QAC1D,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,MAAM,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACzC,CAAC;CACF"}
|
package/dist/msa/FastaMSA.js
CHANGED
|
@@ -13,7 +13,7 @@ export default class FastaMSA extends BaseMSA {
|
|
|
13
13
|
if (newlineIdx === -1) {
|
|
14
14
|
continue;
|
|
15
15
|
}
|
|
16
|
-
const defLine = entry.slice(0, newlineIdx);
|
|
16
|
+
const defLine = entry.slice(0, newlineIdx).replace(/\r$/, '');
|
|
17
17
|
const spaceIdx = defLine.indexOf(' ');
|
|
18
18
|
const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
|
|
19
19
|
if (id) {
|
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,CAAA;
|
|
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"}
|
|
@@ -33,22 +33,11 @@ export default class StockholmMSA extends BaseMSA {
|
|
|
33
33
|
getTree(): NodeWithIds;
|
|
34
34
|
get seqConsensus(): string | undefined;
|
|
35
35
|
get secondaryStructureConsensus(): string | undefined;
|
|
36
|
-
get tracks():
|
|
36
|
+
get tracks(): {
|
|
37
37
|
id: string;
|
|
38
38
|
name: string;
|
|
39
|
-
data
|
|
40
|
-
customColorScheme
|
|
41
|
-
|
|
42
|
-
'<'?: undefined;
|
|
43
|
-
};
|
|
44
|
-
} | {
|
|
45
|
-
id: string;
|
|
46
|
-
name: string;
|
|
47
|
-
data: string | undefined;
|
|
48
|
-
customColorScheme: {
|
|
49
|
-
'>': string;
|
|
50
|
-
'<': string;
|
|
51
|
-
};
|
|
52
|
-
})[];
|
|
39
|
+
data?: string;
|
|
40
|
+
customColorScheme?: Record<string, string>;
|
|
41
|
+
}[];
|
|
53
42
|
}
|
|
54
43
|
export { sniff as stockholmSniff } from './stockholmParser.ts';
|
package/dist/msa/StockholmMSA.js
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;
|
|
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,iBAAiB,EAAE;oBACjB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,WAAW;iBACjB;aACF;SACF,CAAA;IACH,CAAC;CACF;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}
|
package/dist/msa/index.test.js
CHANGED
|
@@ -56,6 +56,13 @@ MNPQRSTVWY`;
|
|
|
56
56
|
expect(msa.getRow('seq2')).toBe('MNPQRSTVWY');
|
|
57
57
|
});
|
|
58
58
|
});
|
|
59
|
+
describe('FastaMSA CRLF line endings', () => {
|
|
60
|
+
test('strips trailing carriage return from sequence names', () => {
|
|
61
|
+
const msa = new FastaMSA('>seq1\r\nACDEF\r\n>seq2\r\nGHIKL\r\n');
|
|
62
|
+
expect(msa.getNames()).toEqual(['seq1', 'seq2']);
|
|
63
|
+
expect(msa.getRow('seq1')).toBe('ACDEF');
|
|
64
|
+
});
|
|
65
|
+
});
|
|
59
66
|
describe('parseNewick single-quoted names', () => {
|
|
60
67
|
test('parses quoted name containing a colon', () => {
|
|
61
68
|
const tree = parseNewick("('EU105457.1|chr09:67680268..67675529_LTR/Copia':0.5,seq2:0.3);");
|
|
@@ -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;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,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,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;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/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "msa-parsers",
|
|
3
|
-
"version": "5.
|
|
3
|
+
"version": "5.3.0",
|
|
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.
|
|
31
|
+
"vitest": "^4.1.8"
|
|
32
32
|
},
|
|
33
33
|
"scripts": {
|
|
34
34
|
"clean": "rimraf dist",
|
package/src/gff/parseGFF.test.ts
CHANGED
|
@@ -93,6 +93,18 @@ seq2\tSource\ttype\t20\t30\t.\t.\t.\tName=test2`
|
|
|
93
93
|
expect(result[0]?.Ontology_term).toBe('GO:0001 GO:0002')
|
|
94
94
|
})
|
|
95
95
|
|
|
96
|
+
test('does not throw on a stray percent sign', () => {
|
|
97
|
+
const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=100%done'
|
|
98
|
+
const result = parseGFF(gff)
|
|
99
|
+
expect(result[0]?.Note).toBe('100%done')
|
|
100
|
+
})
|
|
101
|
+
|
|
102
|
+
test('keeps text after a second equals sign', () => {
|
|
103
|
+
const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=a=b'
|
|
104
|
+
const result = parseGFF(gff)
|
|
105
|
+
expect(result[0]?.Note).toBe('a=b')
|
|
106
|
+
})
|
|
107
|
+
|
|
96
108
|
test('parses multiple lines', () => {
|
|
97
109
|
const gff = `seq1\tPfam\tprotein_match\t10\t50\t.\t.\t.\tName=PF00001
|
|
98
110
|
seq1\tSMART\tprotein_match\t60\t100\t.\t.\t.\tName=SM00001
|
package/src/gff/parseGFF.ts
CHANGED
|
@@ -1,5 +1,15 @@
|
|
|
1
1
|
import type { GFFRecord } from '../types.ts'
|
|
2
2
|
|
|
3
|
+
// decodeURIComponent throws on a stray '%' (common in unescaped GFF3 values);
|
|
4
|
+
// fall back to the raw value rather than aborting the whole parse
|
|
5
|
+
function safeDecode(val: string) {
|
|
6
|
+
try {
|
|
7
|
+
return decodeURIComponent(val)
|
|
8
|
+
} catch {
|
|
9
|
+
return val
|
|
10
|
+
}
|
|
11
|
+
}
|
|
12
|
+
|
|
3
13
|
function parseAttributes(col9?: string): Record<string, string | undefined> {
|
|
4
14
|
if (!col9) {
|
|
5
15
|
return {}
|
|
@@ -9,11 +19,15 @@ function parseAttributes(col9?: string): Record<string, string | undefined> {
|
|
|
9
19
|
.split(';')
|
|
10
20
|
.map(f => f.trim())
|
|
11
21
|
.filter(f => !!f)
|
|
12
|
-
.map(f =>
|
|
13
|
-
|
|
14
|
-
key
|
|
15
|
-
val ?
|
|
16
|
-
|
|
22
|
+
.map(f => {
|
|
23
|
+
const eq = f.indexOf('=')
|
|
24
|
+
const key = (eq === -1 ? f : f.slice(0, eq)).trim()
|
|
25
|
+
const val = eq === -1 ? undefined : f.slice(eq + 1)
|
|
26
|
+
return [
|
|
27
|
+
key,
|
|
28
|
+
val ? safeDecode(val).trim().split(',').join(' ') : undefined,
|
|
29
|
+
]
|
|
30
|
+
})
|
|
17
31
|
.filter(([key]) => key !== ''),
|
|
18
32
|
)
|
|
19
33
|
}
|
package/src/msa/A3mMSA.ts
CHANGED
|
@@ -50,7 +50,7 @@ export default class A3mMSA extends BaseMSA {
|
|
|
50
50
|
if (newlineIdx === -1) {
|
|
51
51
|
continue
|
|
52
52
|
}
|
|
53
|
-
const defLine = entry.slice(0, newlineIdx)
|
|
53
|
+
const defLine = entry.slice(0, newlineIdx).replace(/\r$/, '')
|
|
54
54
|
const spaceIdx = defLine.indexOf(' ')
|
|
55
55
|
const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx)
|
|
56
56
|
if (id) {
|
package/src/msa/BaseMSA.ts
CHANGED
|
@@ -29,7 +29,7 @@ export default abstract class BaseMSA {
|
|
|
29
29
|
return {}
|
|
30
30
|
}
|
|
31
31
|
|
|
32
|
-
getHeader(): unknown {
|
|
32
|
+
getHeader(): Record<string, unknown> {
|
|
33
33
|
return {}
|
|
34
34
|
}
|
|
35
35
|
|
|
@@ -45,7 +45,12 @@ export default abstract class BaseMSA {
|
|
|
45
45
|
return undefined
|
|
46
46
|
}
|
|
47
47
|
|
|
48
|
-
get tracks():
|
|
48
|
+
get tracks(): {
|
|
49
|
+
id: string
|
|
50
|
+
name: string
|
|
51
|
+
data?: string
|
|
52
|
+
customColorScheme?: Record<string, string>
|
|
53
|
+
}[] {
|
|
49
54
|
return []
|
|
50
55
|
}
|
|
51
56
|
}
|
package/src/msa/ClustalMSA.ts
CHANGED
|
@@ -15,11 +15,13 @@ export default class ClustalMSA extends BaseMSA {
|
|
|
15
15
|
}
|
|
16
16
|
|
|
17
17
|
getRow(name: string): string {
|
|
18
|
-
return this.MSA.alns.find(aln => aln.id === name)?.seq
|
|
18
|
+
return this.MSA.alns.find(aln => aln.id === name)?.seq ?? ''
|
|
19
19
|
}
|
|
20
20
|
|
|
21
21
|
getWidth() {
|
|
22
|
-
|
|
22
|
+
// 0 for an empty alignment (e.g. unrecognized text routed here as fallback)
|
|
23
|
+
// rather than crashing on alns[0]
|
|
24
|
+
return this.MSA.alns[0]?.seq.length ?? 0
|
|
23
25
|
}
|
|
24
26
|
|
|
25
27
|
getHeader() {
|
package/src/msa/EmfMSA.ts
CHANGED
|
@@ -15,15 +15,12 @@ export default class EmfMSA extends BaseMSA {
|
|
|
15
15
|
}
|
|
16
16
|
|
|
17
17
|
getRow(name: string): string {
|
|
18
|
-
return this.MSA.find(aln => aln.protein === name)?.seq
|
|
18
|
+
return this.MSA.find(aln => aln.protein === name)?.seq ?? ''
|
|
19
19
|
}
|
|
20
20
|
|
|
21
21
|
getWidth() {
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
getHeader() {
|
|
26
|
-
return ''
|
|
22
|
+
// 0 for an empty alignment rather than crashing on MSA[0]
|
|
23
|
+
return this.MSA[0]?.seq.length ?? 0
|
|
27
24
|
}
|
|
28
25
|
|
|
29
26
|
getNames() {
|
package/src/msa/FastaMSA.ts
CHANGED
|
@@ -18,7 +18,7 @@ export default class FastaMSA extends BaseMSA {
|
|
|
18
18
|
if (newlineIdx === -1) {
|
|
19
19
|
continue
|
|
20
20
|
}
|
|
21
|
-
const defLine = entry.slice(0, newlineIdx)
|
|
21
|
+
const defLine = entry.slice(0, newlineIdx).replace(/\r$/, '')
|
|
22
22
|
const spaceIdx = defLine.indexOf(' ')
|
|
23
23
|
const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx)
|
|
24
24
|
if (id) {
|
package/src/msa/StockholmMSA.ts
CHANGED
|
@@ -22,7 +22,7 @@ export default class StockholmMSA extends BaseMSA {
|
|
|
22
22
|
}
|
|
23
23
|
|
|
24
24
|
getRow(name: string) {
|
|
25
|
-
return this.MSA.seqdata[name]
|
|
25
|
+
return this.MSA.seqdata[name] ?? ''
|
|
26
26
|
}
|
|
27
27
|
|
|
28
28
|
getWidth() {
|
|
@@ -96,7 +96,12 @@ export default class StockholmMSA extends BaseMSA {
|
|
|
96
96
|
return this.MSA.gc.SS_cons
|
|
97
97
|
}
|
|
98
98
|
|
|
99
|
-
get tracks() {
|
|
99
|
+
get tracks(): {
|
|
100
|
+
id: string
|
|
101
|
+
name: string
|
|
102
|
+
data?: string
|
|
103
|
+
customColorScheme?: Record<string, string>
|
|
104
|
+
}[] {
|
|
100
105
|
return [
|
|
101
106
|
{
|
|
102
107
|
id: 'seqConsensus',
|
package/src/msa/index.test.ts
CHANGED
|
@@ -74,6 +74,14 @@ MNPQRSTVWY`
|
|
|
74
74
|
})
|
|
75
75
|
})
|
|
76
76
|
|
|
77
|
+
describe('FastaMSA CRLF line endings', () => {
|
|
78
|
+
test('strips trailing carriage return from sequence names', () => {
|
|
79
|
+
const msa = new FastaMSA('>seq1\r\nACDEF\r\n>seq2\r\nGHIKL\r\n')
|
|
80
|
+
expect(msa.getNames()).toEqual(['seq1', 'seq2'])
|
|
81
|
+
expect(msa.getRow('seq1')).toBe('ACDEF')
|
|
82
|
+
})
|
|
83
|
+
})
|
|
84
|
+
|
|
77
85
|
describe('parseNewick single-quoted names', () => {
|
|
78
86
|
test('parses quoted name containing a colon', () => {
|
|
79
87
|
const tree = parseNewick(
|