msa-parsers 5.8.0 → 5.10.0
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/msa/A3mMSA.js +7 -1
- package/dist/msa/A3mMSA.js.map +1 -1
- package/dist/msa/ClustalMSA.js +3 -1
- package/dist/msa/ClustalMSA.js.map +1 -1
- package/dist/msa/EmfMSA.js +3 -1
- package/dist/msa/EmfMSA.js.map +1 -1
- package/dist/msa/index.test.js +5 -1
- package/dist/msa/index.test.js.map +1 -1
- package/package.json +1 -1
- package/src/msa/A3mMSA.ts +7 -1
- package/src/msa/ClustalMSA.ts +3 -1
- package/src/msa/EmfMSA.ts +3 -1
- package/src/msa/index.test.ts +5 -1
package/dist/msa/A3mMSA.js
CHANGED
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@@ -100,7 +100,13 @@ export default class A3mMSA extends BaseMSA {
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100
100
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*/
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101
101
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function expandA3M(rawSeqs, names) {
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102
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const rows = rawSeqs.map(parseRow);
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103
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-
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103
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+
// a loop, not Math.max(...): an a3m from an hhblits search routinely carries
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104
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+
// six figures of hits, and spreading one argument per row throws
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105
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+
// "Maximum call stack size exceeded" somewhere past ~125k of them
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106
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+
let numPositions = 0;
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107
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+
for (const { matches } of rows) {
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108
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+
numPositions = Math.max(numPositions, matches.length);
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109
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+
}
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104
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// one insert slot before each match column, plus one trailing slot
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const maxInserts = new Array(numPositions + 1).fill(0);
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106
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for (const { inserts } of rows) {
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package/dist/msa/A3mMSA.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"A3mMSA.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD;;;;;;;;;;;;;;;;;;;;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;AAE3B,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAA;AACzC,CAAC;AAED,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,CAAC,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,IAAI,KAAK,SAAS,CAAA;AACjE,CAAC;AAYD,SAAS,QAAQ,CAAC,GAAW;IAC3B,MAAM,OAAO,GAAa,EAAE,CAAA;IAC5B,MAAM,OAAO,GAAG,CAAC,EAAE,CAAC,CAAA;IAEpB,KAAK,MAAM,EAAE,IAAI,GAAG,EAAE,CAAC;QACrB,MAAM,IAAI,GAAG,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;QAC7B,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YAClB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;YAChB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAA;QACjD,CAAC;QACD,0EAA0E;QAC1E,wDAAwD;IAC1D,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,CAAA;AAC7B,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,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;QAC1C,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,SAAS,CAChB,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,EACvB,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,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,GAAG,iBAAiB,CAAC,IAAI,CAAC;aACjC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;aACf,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEnB,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACpB,OAAO,KAAK,CAAA;QACd,CAAC;QAED,sEAAsE;QACtE,4EAA4E;QAC5E,6EAA6E;QAC7E,4EAA4E;QAC5E,2BAA2B;QAC3B,IAAI,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,EAAE,CAAC;YAChD,OAAO,KAAK,CAAA;QACd,CAAC;QAED,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;QAC/B,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAC7D,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;QAE3E,OAAO,YAAY,IAAI,eAAe,CAAA;IACxC,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;CACF;AAED;;;;GAIG;AACH,SAAS,SAAS,CAAC,OAAiB,EAAE,KAAe;IACnD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;IAClC,
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1
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+
{"version":3,"file":"A3mMSA.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD;;;;;;;;;;;;;;;;;;;;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;AAE3B,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAA;AACzC,CAAC;AAED,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,CAAC,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,IAAI,KAAK,SAAS,CAAA;AACjE,CAAC;AAYD,SAAS,QAAQ,CAAC,GAAW;IAC3B,MAAM,OAAO,GAAa,EAAE,CAAA;IAC5B,MAAM,OAAO,GAAG,CAAC,EAAE,CAAC,CAAA;IAEpB,KAAK,MAAM,EAAE,IAAI,GAAG,EAAE,CAAC;QACrB,MAAM,IAAI,GAAG,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;QAC7B,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YAClB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;YAChB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAA;QACjD,CAAC;QACD,0EAA0E;QAC1E,wDAAwD;IAC1D,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,CAAA;AAC7B,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,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;QAC1C,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,SAAS,CAChB,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,EACvB,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,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,GAAG,iBAAiB,CAAC,IAAI,CAAC;aACjC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;aACf,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEnB,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACpB,OAAO,KAAK,CAAA;QACd,CAAC;QAED,sEAAsE;QACtE,4EAA4E;QAC5E,6EAA6E;QAC7E,4EAA4E;QAC5E,2BAA2B;QAC3B,IAAI,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,EAAE,CAAC;YAChD,OAAO,KAAK,CAAA;QACd,CAAC;QAED,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;QAC/B,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAC7D,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;QAE3E,OAAO,YAAY,IAAI,eAAe,CAAA;IACxC,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;CACF;AAED;;;;GAIG;AACH,SAAS,SAAS,CAAC,OAAiB,EAAE,KAAe;IACnD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;IAClC,6EAA6E;IAC7E,iEAAiE;IACjE,kEAAkE;IAClE,IAAI,YAAY,GAAG,CAAC,CAAA;IACpB,KAAK,MAAM,EAAE,OAAO,EAAE,IAAI,IAAI,EAAE,CAAC;QAC/B,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,EAAE,OAAO,CAAC,MAAM,CAAC,CAAA;IACvD,CAAC;IAED,mEAAmE;IACnE,MAAM,UAAU,GAAG,IAAI,KAAK,CAAS,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC9D,KAAK,MAAM,EAAE,OAAO,EAAE,IAAI,IAAI,EAAE,CAAC;QAC/B,KAAK,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAC3C,UAAU,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAE,EAAE,GAAG,CAAC,MAAM,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;IAED,MAAM,QAAQ,GAA2B,EAAE,CAAA;IAE3C,KAAK,MAAM,CAAC,MAAM,EAAE,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;QAC5D,MAAM,MAAM,GAAa,EAAE,CAAA;QAC3B,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,IAAI,YAAY,EAAE,GAAG,EAAE,EAAE,CAAC;YAC7C,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAA;YAC9B,MAAM,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAA;YAC3D,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;gBACvB,+DAA+D;gBAC/D,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;QACD,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAE,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAC5C,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC"}
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package/dist/msa/ClustalMSA.js
CHANGED
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@@ -25,8 +25,10 @@ export default class ClustalMSA extends BaseMSA {
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25
25
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getHeader() {
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26
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return this.MSA.header;
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}
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28
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+
// deduped, matching the first-wins byName map: emitting a repeated id twice
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+
// renders a phantom duplicate row showing the first record's residues
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getNames() {
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29
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-
return this.
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+
return [...this.byName.keys()];
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}
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get seqConsensus() {
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return this.MSA.consensus;
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@@ -1 +1 @@
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1
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-
{"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,2EAA2E;IAC3E,oDAAoD;IAC5C,MAAM,CAAqB;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;QACtB,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC;YAChC,8CAA8C;YAC9C,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBAC7B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACpC,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,
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1
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+
{"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,2EAA2E;IAC3E,oDAAoD;IAC5C,MAAM,CAAqB;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;QACtB,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC;YAChC,8CAA8C;YAC9C,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBAC7B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACpC,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,4EAA4E;IAC5E,sEAAsE;IACtE,QAAQ;QACN,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,CAAA;IAChC,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;CACF"}
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package/dist/msa/EmfMSA.js
CHANGED
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@@ -22,8 +22,10 @@ export default class EmfMSA extends BaseMSA {
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22
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getRow(name) {
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23
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return this.byName.get(name) ?? '';
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24
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}
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25
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+
// deduped, matching the first-wins byName map: emitting a repeated id twice
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26
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+
// renders a phantom duplicate row showing the first record's residues
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25
27
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getNames() {
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26
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-
return this.
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28
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+
return [...this.byName.keys()];
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}
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}
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//# sourceMappingURL=EmfMSA.js.map
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package/dist/msa/EmfMSA.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"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,2EAA2E;IAC3E,6DAA6D;IACrD,MAAM,CAAqB;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;QAC5B,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,GAAG,EAAE,CAAC;YAC3B,8CAA8C;YAC9C,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;gBAClC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACpC,CAAC;IAED,QAAQ;QACN,OAAO,
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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,2EAA2E;IAC3E,6DAA6D;IACrD,MAAM,CAAqB;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;QAC5B,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,GAAG,EAAE,CAAC;YAC3B,8CAA8C;YAC9C,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;gBAClC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACpC,CAAC;IAED,4EAA4E;IAC5E,sEAAsE;IACtE,QAAQ;QACN,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,CAAA;IAChC,CAAC;CACF"}
|
package/dist/msa/index.test.js
CHANGED
|
@@ -122,7 +122,11 @@ seq2 MNPQRSTVWY
|
|
|
122
122
|
seq1 AAAAAAAAAA
|
|
123
123
|
seq1 CCCCCCCCCC
|
|
124
124
|
`;
|
|
125
|
-
|
|
125
|
+
const msa = new ClustalMSA(dup);
|
|
126
|
+
expect(msa.getRow('seq1')).toBe('AAAAAAAAAA');
|
|
127
|
+
// and the name is listed once: getNames drives the row layout, so a
|
|
128
|
+
// repeated id would otherwise draw a phantom second row of the same residues
|
|
129
|
+
expect(msa.getNames()).toEqual(['seq1']);
|
|
126
130
|
});
|
|
127
131
|
});
|
|
128
132
|
describe('StockholmMSA row order', () => {
|
|
@@ -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;AAI1C,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,6BAA6B,EAAE,GAAG,EAAE;IAC3C,IAAI,CAAC,2DAA2D,EAAE,GAAG,EAAE;QACrE,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,iCAAiC,CAAC,CAAA;QAC3D,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACvC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,uBAAuB,EAAE,GAAG,EAAE;IACrC,MAAM,OAAO,GAAG;;;;CAIjB,CAAA;IAEC,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACxC,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC,OAAO,CAAC,CAAA;QACnC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAC7C,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAC7C,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,2CAA2C,EAAE,GAAG,EAAE;QACrD,uEAAuE;QACvE,sEAAsE;QACtE,yEAAyE;QACzE,0DAA0D;QAC1D,MAAM,GAAG,GAAG;;;;CAIf,CAAA;QACG,MAAM,
|
|
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;AAI1C,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,6BAA6B,EAAE,GAAG,EAAE;IAC3C,IAAI,CAAC,2DAA2D,EAAE,GAAG,EAAE;QACrE,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,iCAAiC,CAAC,CAAA;QAC3D,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACvC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,uBAAuB,EAAE,GAAG,EAAE;IACrC,MAAM,OAAO,GAAG;;;;CAIjB,CAAA;IAEC,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACxC,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC,OAAO,CAAC,CAAA;QACnC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAC7C,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAC7C,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,2CAA2C,EAAE,GAAG,EAAE;QACrD,uEAAuE;QACvE,sEAAsE;QACtE,yEAAyE;QACzE,0DAA0D;QAC1D,MAAM,GAAG,GAAG;;;;CAIf,CAAA;QACG,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAC7C,oEAAoE;QACpE,6EAA6E;QAC7E,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,wBAAwB,EAAE,GAAG,EAAE;IACtC,IAAI,CAAC,iDAAiD,EAAE,GAAG,EAAE;QAC3D,2EAA2E;QAC3E,wDAAwD;QACxD,MAAM,SAAS,GAAG;;;;GAInB,CAAA;QACC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG,CAAC,IAAgB,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;AAE9E,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,SAAS,CAAC,IAAI,CAAC,CAAA;QAC7B,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,+CAA+C,CAAC,CAAA;IAC1E,CAAC,CA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|
package/package.json
CHANGED
package/src/msa/A3mMSA.ts
CHANGED
|
@@ -131,7 +131,13 @@ export default class A3mMSA extends BaseMSA {
|
|
|
131
131
|
*/
|
|
132
132
|
function expandA3M(rawSeqs: string[], names: string[]): Record<string, string> {
|
|
133
133
|
const rows = rawSeqs.map(parseRow)
|
|
134
|
-
|
|
134
|
+
// a loop, not Math.max(...): an a3m from an hhblits search routinely carries
|
|
135
|
+
// six figures of hits, and spreading one argument per row throws
|
|
136
|
+
// "Maximum call stack size exceeded" somewhere past ~125k of them
|
|
137
|
+
let numPositions = 0
|
|
138
|
+
for (const { matches } of rows) {
|
|
139
|
+
numPositions = Math.max(numPositions, matches.length)
|
|
140
|
+
}
|
|
135
141
|
|
|
136
142
|
// one insert slot before each match column, plus one trailing slot
|
|
137
143
|
const maxInserts = new Array<number>(numPositions + 1).fill(0)
|
package/src/msa/ClustalMSA.ts
CHANGED
|
@@ -33,8 +33,10 @@ export default class ClustalMSA extends BaseMSA {
|
|
|
33
33
|
return this.MSA.header
|
|
34
34
|
}
|
|
35
35
|
|
|
36
|
+
// deduped, matching the first-wins byName map: emitting a repeated id twice
|
|
37
|
+
// renders a phantom duplicate row showing the first record's residues
|
|
36
38
|
getNames() {
|
|
37
|
-
return this.
|
|
39
|
+
return [...this.byName.keys()]
|
|
38
40
|
}
|
|
39
41
|
|
|
40
42
|
get seqConsensus() {
|
package/src/msa/EmfMSA.ts
CHANGED
|
@@ -29,7 +29,9 @@ export default class EmfMSA extends BaseMSA {
|
|
|
29
29
|
return this.byName.get(name) ?? ''
|
|
30
30
|
}
|
|
31
31
|
|
|
32
|
+
// deduped, matching the first-wins byName map: emitting a repeated id twice
|
|
33
|
+
// renders a phantom duplicate row showing the first record's residues
|
|
32
34
|
getNames() {
|
|
33
|
-
return this.
|
|
35
|
+
return [...this.byName.keys()]
|
|
34
36
|
}
|
|
35
37
|
}
|
package/src/msa/index.test.ts
CHANGED
|
@@ -150,7 +150,11 @@ seq2 MNPQRSTVWY
|
|
|
150
150
|
seq1 AAAAAAAAAA
|
|
151
151
|
seq1 CCCCCCCCCC
|
|
152
152
|
`
|
|
153
|
-
|
|
153
|
+
const msa = new ClustalMSA(dup)
|
|
154
|
+
expect(msa.getRow('seq1')).toBe('AAAAAAAAAA')
|
|
155
|
+
// and the name is listed once: getNames drives the row layout, so a
|
|
156
|
+
// repeated id would otherwise draw a phantom second row of the same residues
|
|
157
|
+
expect(msa.getNames()).toEqual(['seq1'])
|
|
154
158
|
})
|
|
155
159
|
})
|
|
156
160
|
|