msa-parsers 5.0.6 → 5.0.12
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/gffToInterPro.d.ts +0 -4
- package/dist/gff/gffToInterPro.js +0 -7
- package/dist/gff/gffToInterPro.js.map +1 -1
- package/dist/msa/A3mMSA.d.ts +2 -21
- package/dist/msa/A3mMSA.js +5 -69
- package/dist/msa/A3mMSA.js.map +1 -1
- package/dist/msa/A3mMSA.test.js +46 -14
- package/dist/msa/A3mMSA.test.js.map +1 -1
- package/dist/msa/BaseMSA.d.ts +19 -0
- package/dist/msa/BaseMSA.js +36 -0
- package/dist/msa/BaseMSA.js.map +1 -0
- package/dist/msa/ClustalMSA.d.ts +2 -8
- package/dist/msa/ClustalMSA.js +3 -28
- package/dist/msa/ClustalMSA.js.map +1 -1
- package/dist/msa/EmfMSA.d.ts +2 -9
- package/dist/msa/EmfMSA.js +3 -31
- package/dist/msa/EmfMSA.js.map +1 -1
- package/dist/msa/FastaMSA.d.ts +3 -10
- package/dist/msa/FastaMSA.js +11 -36
- package/dist/msa/FastaMSA.js.map +1 -1
- package/dist/msa/StockholmMSA.d.ts +2 -2
- package/dist/msa/StockholmMSA.js +18 -34
- package/dist/msa/StockholmMSA.js.map +1 -1
- package/dist/msa/index.test.js +37 -1
- package/dist/msa/index.test.js.map +1 -1
- package/dist/msa/parseNewick.js +10 -2
- package/dist/msa/parseNewick.js.map +1 -1
- package/package.json +8 -3
- package/src/gff/gffToInterPro.ts +0 -11
- package/src/msa/A3mMSA.test.ts +47 -14
- package/src/msa/A3mMSA.ts +5 -78
- package/src/msa/BaseMSA.ts +49 -0
- package/src/msa/ClustalMSA.ts +3 -34
- package/src/msa/EmfMSA.ts +3 -38
- package/src/msa/FastaMSA.ts +17 -45
- package/src/msa/StockholmMSA.ts +18 -39
- package/src/msa/index.test.ts +50 -1
- package/src/msa/parseNewick.ts +14 -2
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@@ -10,10 +10,6 @@ import type { GFFRecord, InterProScanResponse, InterProScanResults } from '../ty
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* - Attributes: Name (accession), signature_desc (name), Dbxref, etc.
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*/
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export declare function gffToInterProResults(gffRecords: GFFRecord[]): Record<string, InterProScanResults>;
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-
/**
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* Convert GFF string directly to InterProScan format
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*/
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export declare function parseGFFToInterPro(gffStr: string, parseGFFfn: (str: string) => GFFRecord[]): Record<string, InterProScanResults>;
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/**
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* Create a full InterProScanResponse from GFF records
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*/
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@@ -64,13 +64,6 @@ export function gffToInterProResults(gffRecords) {
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}
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return results;
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}
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-
/**
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* Convert GFF string directly to InterProScan format
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*/
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export function parseGFFToInterPro(gffStr, parseGFFfn) {
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const records = parseGFFfn(gffStr);
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-
return gffToInterProResults(records);
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-
}
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/**
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* Create a full InterProScanResponse from GFF records
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*/
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"gffToInterPro.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.ts"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,MAAM,UAAU,oBAAoB,CAClC,UAAuB;IAEvB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAuB,CAAA;IAEjD,KAAK,MAAM,MAAM,IAAI,UAAU,EAAE,CAAC;QAChC,MAAM,QAAQ,GAAG,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC9C,IAAI,QAAQ,EAAE,CAAC;YACb,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACvB,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACzC,CAAC;IACH,CAAC;IAED,MAAM,OAAO,GAAwC,EAAE,CAAA;IAEvD,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,UAAU,EAAE,CAAC;QAC1C,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAG/B,CAAA;QACH,MAAM,SAAS,GAAG,IAAI,GAAG,EAGtB,CAAA;QAEH,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,EAAa;gBACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;YAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB;gBAChC,MAAM,CAAC,IAAe;gBACvB,SAAS,CAAA;YACX,MAAM,WAAW,GACd,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI,CAAA;YAEN,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9B,SAAS,CAAC,GAAG,CAAC,SAAS,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,SAAS,EAAE,CAAC,CAAA;YAC5D,CAAC;YAED,MAAM,SAAS,GAAG,kBAAkB,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YACnD,IAAI,SAAS,EAAE,CAAC;gBACd,SAAS,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAA;YAC1D,CAAC;iBAAM,CAAC;gBACN,kBAAkB,CAAC,GAAG,CAAC,SAAS,EAAE;oBAChC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE;iBACzC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;QAED,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,KAAK,MAAM,CAAC,SAAS,EAAE,SAAS,CAAC,IAAI,kBAAkB,EAAE,CAAC;YACxD,MAAM,IAAI,GAAG,SAAS,CAAC,GAAG,CAAC,SAAS,CAAE,CAAA;YACtC,OAAO,CAAC,IAAI,CAAC;gBACX,SAAS,EAAE;oBACT,KAAK,EAAE,IAAI;iBACZ;gBACD,SAAS;aACV,CAAC,CAAA;QACJ,CAAC;QAED,OAAO,CAAC,KAAK,CAAC,GAAG;YACf,OAAO;YACP,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;SACtB,CAAA;IACH,CAAC;IAED,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,
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{"version":3,"file":"gffToInterPro.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.ts"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,MAAM,UAAU,oBAAoB,CAClC,UAAuB;IAEvB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAuB,CAAA;IAEjD,KAAK,MAAM,MAAM,IAAI,UAAU,EAAE,CAAC;QAChC,MAAM,QAAQ,GAAG,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC9C,IAAI,QAAQ,EAAE,CAAC;YACb,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACvB,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACzC,CAAC;IACH,CAAC;IAED,MAAM,OAAO,GAAwC,EAAE,CAAA;IAEvD,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,UAAU,EAAE,CAAC;QAC1C,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAG/B,CAAA;QACH,MAAM,SAAS,GAAG,IAAI,GAAG,EAGtB,CAAA;QAEH,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,EAAa;gBACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;YAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB;gBAChC,MAAM,CAAC,IAAe;gBACvB,SAAS,CAAA;YACX,MAAM,WAAW,GACd,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI,CAAA;YAEN,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9B,SAAS,CAAC,GAAG,CAAC,SAAS,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,SAAS,EAAE,CAAC,CAAA;YAC5D,CAAC;YAED,MAAM,SAAS,GAAG,kBAAkB,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YACnD,IAAI,SAAS,EAAE,CAAC;gBACd,SAAS,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAA;YAC1D,CAAC;iBAAM,CAAC;gBACN,kBAAkB,CAAC,GAAG,CAAC,SAAS,EAAE;oBAChC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE;iBACzC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;QAED,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,KAAK,MAAM,CAAC,SAAS,EAAE,SAAS,CAAC,IAAI,kBAAkB,EAAE,CAAC;YACxD,MAAM,IAAI,GAAG,SAAS,CAAC,GAAG,CAAC,SAAS,CAAE,CAAA;YACtC,OAAO,CAAC,IAAI,CAAC;gBACX,SAAS,EAAE;oBACT,KAAK,EAAE,IAAI;iBACZ;gBACD,SAAS;aACV,CAAC,CAAA;QACJ,CAAC;QAED,OAAO,CAAC,KAAK,CAAC,GAAG;YACf,OAAO;YACP,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;SACtB,CAAA;IACH,CAAC;IAED,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB,CACnC,UAAuB;IAEvB,MAAM,UAAU,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAA;IACnD,OAAO;QACL,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC;KACnC,CAAA;AACH,CAAC"}
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package/dist/msa/A3mMSA.d.ts
CHANGED
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@@ -1,33 +1,14 @@
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import
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export default class A3mMSA {
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import BaseMSA from './BaseMSA.ts';
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export default class A3mMSA extends BaseMSA {
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private MSA;
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private orderedNames;
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constructor(text: string);
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/**
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* Detect if text is likely A3M format
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*/
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static sniff(text: string): boolean;
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/**
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* Expand A3M format to standard aligned format.
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*
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* In A3M, lowercase characters are insertions that implicitly introduce
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* gaps in sequences that don't have an insert at that position.
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* Gaps (-) following match columns in sequences without inserts align
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* with lowercase inserts in other sequences.
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*/
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private expandA3M;
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getMSA(): {
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seqdata: Record<string, string>;
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};
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getRowData(): undefined;
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getNames(): string[];
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getRow(name: string): string;
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getWidth(): number;
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getStructures(): {};
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get alignmentNames(): never[];
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getHeader(): {};
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getTree(): NodeWithIds;
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get seqConsensus(): undefined;
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get secondaryStructureConsensus(): undefined;
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get tracks(): never[];
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}
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package/dist/msa/A3mMSA.js
CHANGED
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import BaseMSA from "./BaseMSA.js";
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/**
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* A3M Format Parser
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*
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@@ -19,7 +20,6 @@
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*
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* @see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html
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*/
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// Char code helpers for fast character classification
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const CODE_A = 65; // 'A'
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const CODE_Z = 90; // 'Z'
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const CODE_a = 97; // 'a'
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@@ -29,13 +29,13 @@ const CODE_DOT = 46; // '.'
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function isLower(code) {
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return code >= CODE_a && code <= CODE_z;
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}
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export default class A3mMSA {
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export default class A3mMSA extends BaseMSA {
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MSA;
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orderedNames;
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constructor(text) {
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super();
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const rawSeqs = [];
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const names = [];
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// First pass: parse sequences (like FASTA), preserving order
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for (const entry of text.split('>')) {
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if (!/\S/.test(entry)) {
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continue;
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this.orderedNames = names;
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this.MSA = { seqdata: this.expandA3M(rawSeqs, names) };
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}
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/**
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* Detect if text is likely A3M format
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*/
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static sniff(text) {
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if (!text.startsWith('>')) {
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return false;
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@@ -79,8 +76,6 @@ export default class A3mMSA {
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if (seqs.length < 2) {
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return false;
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}
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// Check for lowercase and compute match column lengths in single pass per sequence
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// In A3M, match columns = uppercase letters + dashes (deletions)
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let hasLowercase = false;
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let firstMatchLen = -1;
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let sameMatchLength = true;
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@@ -91,8 +86,7 @@ export default class A3mMSA {
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if (isLower(code)) {
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hasLowercase = true;
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}
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else if (code >= CODE_A && code <= CODE_Z || code === CODE_DASH) {
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// Uppercase letters and dashes are match columns
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else if ((code >= CODE_A && code <= CODE_Z) || code === CODE_DASH) {
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matchLen++;
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}
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}
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@@ -107,21 +101,11 @@ export default class A3mMSA {
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}
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return hasLowercase && sameMatchLength;
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}
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/**
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* Expand A3M format to standard aligned format.
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*
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* In A3M, lowercase characters are insertions that implicitly introduce
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* gaps in sequences that don't have an insert at that position.
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* Gaps (-) following match columns in sequences without inserts align
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* with lowercase inserts in other sequences.
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*/
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expandA3M(rawSeqs, names) {
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const numSeqs = names.length;
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if (numSeqs === 0) {
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return {};
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}
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// Parse sequences: extract match chars (uppercase only) and insert content
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// For each sequence, track: matchChars, insertContent (after each match)
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const matchChars = [];
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const insertContent = [];
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for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
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@@ -131,11 +115,8 @@ export default class A3mMSA {
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let i = 0;
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while (i < seq.length) {
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const code = seq.charCodeAt(i);
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if (code >= CODE_A && code <= CODE_Z || code === CODE_DASH) {
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// Uppercase letter or dash - match column (dash = deletion)
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if ((code >= CODE_A && code <= CODE_Z) || code === CODE_DASH) {
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matches.push(seq[i]);
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// Collect following lowercase/dot characters as insert content
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// Note: dash is NOT insert content, it's a match column
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let ins = '';
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let j = i + 1;
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while (j < seq.length) {
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@@ -152,17 +133,14 @@ export default class A3mMSA {
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i = j;
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}
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else if (code === CODE_DOT) {
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// Leading dot (gap aligned to insert) - skip
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i++;
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}
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else if (isLower(code)) {
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// Leading insert before first match
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let ins = '';
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while (i < seq.length && isLower(seq.charCodeAt(i))) {
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ins += seq[i];
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i++;
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}
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// Add empty match with this insert
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matches.push('');
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inserts.push(ins);
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}
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@@ -173,14 +151,11 @@ export default class A3mMSA {
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matchChars.push(matches);
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insertContent.push(inserts);
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}
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// Find number of match positions (should be same for all valid A3M)
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const numPositions = Math.max(...matchChars.map(m => m.length), 0);
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// Find max insert length at each position (only count lowercase, not gaps)
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155
|
const maxInserts = new Array(numPositions).fill(0);
|
|
180
156
|
for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
|
|
181
157
|
const inserts = insertContent[seqIdx];
|
|
182
158
|
for (let pos = 0; pos < inserts.length; pos++) {
|
|
183
|
-
// Count only lowercase characters as actual inserts
|
|
184
159
|
let lcCount = 0;
|
|
185
160
|
for (const c of inserts[pos]) {
|
|
186
161
|
if (isLower(c.charCodeAt(0))) {
|
|
@@ -192,7 +167,6 @@ export default class A3mMSA {
|
|
|
192
167
|
}
|
|
193
168
|
}
|
|
194
169
|
}
|
|
195
|
-
// Build expanded sequences
|
|
196
170
|
const expanded = {};
|
|
197
171
|
for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
|
|
198
172
|
const matches = matchChars[seqIdx];
|
|
@@ -203,25 +177,20 @@ export default class A3mMSA {
|
|
|
203
177
|
if (pos < matches.length) {
|
|
204
178
|
const matchChar = matches[pos];
|
|
205
179
|
const insContent = inserts[pos] || '';
|
|
206
|
-
// Add match character (or gap if empty)
|
|
207
180
|
result.push(matchChar || '-');
|
|
208
|
-
// Process insert content
|
|
209
181
|
let lcContent = '';
|
|
210
182
|
for (const c of insContent) {
|
|
211
183
|
if (isLower(c.charCodeAt(0))) {
|
|
212
184
|
lcContent += c.toUpperCase();
|
|
213
185
|
}
|
|
214
186
|
}
|
|
215
|
-
// Add the insert content (uppercased)
|
|
216
187
|
result.push(lcContent);
|
|
217
|
-
// Pad with gaps to match max insert length
|
|
218
188
|
const padding = maxIns - lcContent.length;
|
|
219
189
|
if (padding > 0) {
|
|
220
190
|
result.push('.'.repeat(padding));
|
|
221
191
|
}
|
|
222
192
|
}
|
|
223
193
|
else {
|
|
224
|
-
// This sequence is shorter - add gaps
|
|
225
194
|
result.push('-');
|
|
226
195
|
if (maxIns > 0) {
|
|
227
196
|
result.push('.'.repeat(maxIns));
|
|
@@ -235,9 +204,6 @@ export default class A3mMSA {
|
|
|
235
204
|
getMSA() {
|
|
236
205
|
return this.MSA;
|
|
237
206
|
}
|
|
238
|
-
getRowData() {
|
|
239
|
-
return undefined;
|
|
240
|
-
}
|
|
241
207
|
getNames() {
|
|
242
208
|
return this.orderedNames;
|
|
243
209
|
}
|
|
@@ -248,35 +214,5 @@ export default class A3mMSA {
|
|
|
248
214
|
const name = Object.keys(this.MSA.seqdata)[0];
|
|
249
215
|
return name ? this.getRow(name).length : 0;
|
|
250
216
|
}
|
|
251
|
-
getStructures() {
|
|
252
|
-
return {};
|
|
253
|
-
}
|
|
254
|
-
get alignmentNames() {
|
|
255
|
-
return [];
|
|
256
|
-
}
|
|
257
|
-
getHeader() {
|
|
258
|
-
return {};
|
|
259
|
-
}
|
|
260
|
-
getTree() {
|
|
261
|
-
return {
|
|
262
|
-
id: 'root',
|
|
263
|
-
name: 'root',
|
|
264
|
-
noTree: true,
|
|
265
|
-
children: this.getNames().map(name => ({
|
|
266
|
-
id: name,
|
|
267
|
-
children: [],
|
|
268
|
-
name,
|
|
269
|
-
})),
|
|
270
|
-
};
|
|
271
|
-
}
|
|
272
|
-
get seqConsensus() {
|
|
273
|
-
return undefined;
|
|
274
|
-
}
|
|
275
|
-
get secondaryStructureConsensus() {
|
|
276
|
-
return undefined;
|
|
277
|
-
}
|
|
278
|
-
get tracks() {
|
|
279
|
-
return [];
|
|
280
|
-
}
|
|
281
217
|
}
|
|
282
218
|
//# sourceMappingURL=A3mMSA.js.map
|
package/dist/msa/A3mMSA.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"A3mMSA.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.ts"],"names":[],"mappings":"
|
|
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;YAC1C,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/A3mMSA.test.js
CHANGED
|
@@ -1,5 +1,17 @@
|
|
|
1
1
|
import { describe, expect, test } from 'vitest';
|
|
2
2
|
import A3mMSA from "./A3mMSA.js";
|
|
3
|
+
// A3M format rules (see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html):
|
|
4
|
+
//
|
|
5
|
+
// - Uppercase letters = "match columns" (aligned positions shared by all seqs)
|
|
6
|
+
// - Lowercase letters = insertions (extra residues in one seq, not a match column)
|
|
7
|
+
// - Dashes '-' = deletions (missing residue at a match column, counts as match)
|
|
8
|
+
// - Dots '.' = gaps aligned to insertions in other sequences
|
|
9
|
+
//
|
|
10
|
+
// Key constraint: all sequences must have the same number of match columns
|
|
11
|
+
// (uppercase + dashes). Lowercase chars don't count toward this total.
|
|
12
|
+
//
|
|
13
|
+
// When expanded to a standard alignment, lowercase inserts become new columns
|
|
14
|
+
// (uppercased), and sequences without inserts at that position get '.' gaps.
|
|
3
15
|
describe('A3mMSA', () => {
|
|
4
16
|
describe('sniff', () => {
|
|
5
17
|
test('returns false for non-FASTA text', () => {
|
|
@@ -14,10 +26,13 @@ ACDEFGHIKLMNPQRSTVWY`;
|
|
|
14
26
|
expect(A3mMSA.sniff(fasta)).toBe(false);
|
|
15
27
|
});
|
|
16
28
|
test('returns true for A3M format', () => {
|
|
29
|
+
// seq1: match=ACDEFKLMNPQ (11), insert=ghi (3)
|
|
30
|
+
// seq2: match=ACDEFKLMNPQ (11)
|
|
31
|
+
// Same match count + has lowercase → detected as A3M
|
|
17
32
|
const a3m = `>seq1
|
|
18
33
|
ACDEFghiKLMNPQ
|
|
19
34
|
>seq2
|
|
20
|
-
|
|
35
|
+
ACDEFKLMNPQ`;
|
|
21
36
|
expect(A3mMSA.sniff(a3m)).toBe(true);
|
|
22
37
|
});
|
|
23
38
|
test('returns false for single sequence', () => {
|
|
@@ -26,11 +41,13 @@ ACDEFghiKLMNPQ`;
|
|
|
26
41
|
expect(A3mMSA.sniff(a3m)).toBe(false);
|
|
27
42
|
});
|
|
28
43
|
test('counts dashes as match columns in sniff', () => {
|
|
29
|
-
//
|
|
44
|
+
// seq1: match=ACDEF (5), insert=ghi (3)
|
|
45
|
+
// seq2: match=AC--F (5, where -- are deletions that count as match columns)
|
|
46
|
+
// Same match count + has lowercase → detected as A3M
|
|
30
47
|
const a3m = `>seq1
|
|
31
48
|
ACDEFghi
|
|
32
49
|
>seq2
|
|
33
|
-
--
|
|
50
|
+
AC--F`;
|
|
34
51
|
expect(A3mMSA.sniff(a3m)).toBe(true);
|
|
35
52
|
});
|
|
36
53
|
test('returns false when match column counts differ', () => {
|
|
@@ -46,10 +63,14 @@ ACDEF---`;
|
|
|
46
63
|
});
|
|
47
64
|
describe('parsing', () => {
|
|
48
65
|
test('parses simple A3M', () => {
|
|
66
|
+
// Both have 11 match columns. seq1 has 3 lowercase inserts (ghi) after F.
|
|
67
|
+
// After expansion, ghi becomes 3 new columns (uppercased in seq1, dots in seq2):
|
|
68
|
+
// seq1: ACDEF + GHI + KLMNPQ = ACDEFGHIKLMNPQ (14 chars)
|
|
69
|
+
// seq2: ACDEF + ... + KLMNPQ = ACDEF...KLMNPQ (14 chars)
|
|
49
70
|
const a3m = `>seq1
|
|
50
71
|
ACDEFghiKLMNPQ
|
|
51
72
|
>seq2
|
|
52
|
-
|
|
73
|
+
ACDEFKLMNPQ`;
|
|
53
74
|
const msa = new A3mMSA(a3m);
|
|
54
75
|
expect(msa.getNames()).toEqual(['seq1', 'seq2']);
|
|
55
76
|
const seq1 = msa.getRow('seq1');
|
|
@@ -145,26 +166,37 @@ A-FG`;
|
|
|
145
166
|
expect(seq1).toBe('A-..FG');
|
|
146
167
|
});
|
|
147
168
|
test('realistic a3m with insertions and deletions', () => {
|
|
148
|
-
//
|
|
169
|
+
// All 3 sequences have 11 match columns (uppercase + dashes).
|
|
170
|
+
// seq1 has 3 lowercase insertions (ghi) after the 5th match column.
|
|
171
|
+
// seq2 uses dashes for deletions at match positions 1-2 and 9-10.
|
|
172
|
+
//
|
|
173
|
+
// A3M input (match columns marked with ^, inserts unmarked):
|
|
174
|
+
// query: A C D E F K L M N P Q
|
|
175
|
+
// ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ = 11 match cols
|
|
176
|
+
// seq1: A C D E F g h i K L M N P Q
|
|
177
|
+
// ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ = 11 match cols, ghi = inserts
|
|
178
|
+
// seq2: - - D E F K L M - - Q
|
|
179
|
+
// ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ = 11 match cols (dashes are deletions)
|
|
180
|
+
//
|
|
181
|
+
// After expansion (inserts become new columns, '.' fills gaps):
|
|
182
|
+
// query: ACDEF...KLMNPQ (14 chars)
|
|
183
|
+
// seq1: ACDEFGHIKLMNPQ (14 chars, ghi uppercased)
|
|
184
|
+
// seq2: --DEF...KLM--Q (14 chars)
|
|
149
185
|
const a3m = `>query
|
|
150
|
-
|
|
186
|
+
ACDEFKLMNPQ
|
|
151
187
|
>seq1
|
|
152
188
|
ACDEFghiKLMNPQ
|
|
153
189
|
>seq2
|
|
154
|
-
--
|
|
190
|
+
--DEFKLM--Q`;
|
|
155
191
|
const msa = new A3mMSA(a3m);
|
|
156
192
|
const query = msa.getRow('query');
|
|
157
193
|
const seq1 = msa.getRow('seq1');
|
|
158
194
|
const seq2 = msa.getRow('seq2');
|
|
159
195
|
expect(query.length).toBe(seq1.length);
|
|
160
196
|
expect(query.length).toBe(seq2.length);
|
|
161
|
-
|
|
162
|
-
|
|
163
|
-
|
|
164
|
-
// seq2: --DEF + ... + ---KLMNPQ = --DEF...---KLMNPQ
|
|
165
|
-
expect(query).toBe('ACDEF...GHIKLMNPQ');
|
|
166
|
-
expect(seq1).toBe('ACDEFGHIGHIKLMNPQ');
|
|
167
|
-
expect(seq2).toBe('--DEF...---KLMNPQ');
|
|
197
|
+
expect(query).toBe('ACDEF...KLMNPQ');
|
|
198
|
+
expect(seq1).toBe('ACDEFGHIKLMNPQ');
|
|
199
|
+
expect(seq2).toBe('--DEF...KLM--Q');
|
|
168
200
|
});
|
|
169
201
|
test('getWidth returns correct width', () => {
|
|
170
202
|
const a3m = `>seq1
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"A3mMSA.test.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAEhC,QAAQ,CAAC,QAAQ,EAAE,GAAG,EAAE;IACtB,QAAQ,CAAC,OAAO,EAAE,GAAG,EAAE;QACrB,IAAI,CAAC,kCAAkC,EAAE,GAAG,EAAE;YAC5C,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAC7C,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC/C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,iCAAiC,EAAE,GAAG,EAAE;YAC3C,MAAM,KAAK,GAAG;;;qBAGC,CAAA;YACf,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACzC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;YACvC,MAAM,GAAG,GAAG;;;
|
|
1
|
+
{"version":3,"file":"A3mMSA.test.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAEhC,kFAAkF;AAClF,EAAE;AACF,+EAA+E;AAC/E,mFAAmF;AACnF,uFAAuF;AACvF,sEAAsE;AACtE,EAAE;AACF,2EAA2E;AAC3E,uEAAuE;AACvE,EAAE;AACF,8EAA8E;AAC9E,6EAA6E;AAE7E,QAAQ,CAAC,QAAQ,EAAE,GAAG,EAAE;IACtB,QAAQ,CAAC,OAAO,EAAE,GAAG,EAAE;QACrB,IAAI,CAAC,kCAAkC,EAAE,GAAG,EAAE;YAC5C,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAC7C,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC/C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,iCAAiC,EAAE,GAAG,EAAE;YAC3C,MAAM,KAAK,GAAG;;;qBAGC,CAAA;YACf,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACzC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;YACvC,+CAA+C;YAC/C,+BAA+B;YAC/B,qDAAqD;YACrD,MAAM,GAAG,GAAG;;;YAGN,CAAA;YACN,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACtC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,mCAAmC,EAAE,GAAG,EAAE;YAC7C,MAAM,GAAG,GAAG;eACH,CAAA;YACT,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACvC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,yCAAyC,EAAE,GAAG,EAAE;YACnD,wCAAwC;YACxC,4EAA4E;YAC5E,qDAAqD;YACrD,MAAM,GAAG,GAAG;;;MAGZ,CAAA;YACA,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACtC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,+CAA+C,EAAE,GAAG,EAAE;YACzD,gCAAgC;YAChC,mCAAmC;YACnC,8DAA8D;YAC9D,MAAM,MAAM,GAAG;;;SAGZ,CAAA;YACH,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC1C,CAAC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,QAAQ,CAAC,SAAS,EAAE,GAAG,EAAE;QACvB,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;YAC7B,0EAA0E;YAC1E,iFAAiF;YACjF,2DAA2D;YAC3D,2DAA2D;YAC3D,MAAM,GAAG,GAAG;;;YAGN,CAAA;YACN,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;YAChD,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAC/B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YACrC,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;QAC/B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;YACxC,iEAAiE;YACjE,kDAAkD;YAClD,MAAM,GAAG,GAAG;;;GAGf,CAAA;YACG,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAC/B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,iDAAiD;YACjD,uDAAuD;YACvD,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC1B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC5B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;YACvC,6DAA6D;YAC7D,kDAAkD;YAClD,MAAM,GAAG,GAAG;;;IAGd,CAAA;YACE,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAC/B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YACrC,0CAA0C;YAC1C,0CAA0C;YAC1C,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;YAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;QAChC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,4CAA4C,EAAE,GAAG,EAAE;YACtD,kCAAkC;YAClC,iEAAiE;YACjE,MAAM,GAAG,GAAG;;;OAGX,CAAA;YACD,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;YACjC,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YACtC,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC5B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QAC7B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,kCAAkC,EAAE,GAAG,EAAE;YAC5C,yBAAyB;YACzB,gDAAgD;YAChD,MAAM,GAAG,GAAG;;;OAGX,CAAA;YACD,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;YACjC,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YACtC,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC5B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QAC7B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,mCAAmC,EAAE,GAAG,EAAE;YAC7C,MAAM,GAAG,GAAG;;;OAGX,CAAA;YACD,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;YACjC,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YACtC,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC5B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QAC7B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,gCAAgC,EAAE,GAAG,EAAE;YAC1C,yDAAyD;YACzD,oDAAoD;YACpD,MAAM,GAAG,GAAG;;;KAGb,CAAA;YACC,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;YACjC,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YACtC,qCAAqC;YACrC,oCAAoC;YACpC,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC5B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QAC7B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,6C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|
|
@@ -0,0 +1,19 @@
|
|
|
1
|
+
import type { NodeWithIds } from '../types.ts';
|
|
2
|
+
export default abstract class BaseMSA {
|
|
3
|
+
abstract getMSA(): unknown;
|
|
4
|
+
abstract getRow(name: string): string;
|
|
5
|
+
abstract getWidth(): number;
|
|
6
|
+
abstract getNames(): string[];
|
|
7
|
+
getTree(): NodeWithIds;
|
|
8
|
+
getRowData(_name: string): {
|
|
9
|
+
name?: string;
|
|
10
|
+
accession?: string;
|
|
11
|
+
dbxref?: string;
|
|
12
|
+
} | undefined;
|
|
13
|
+
getStructures(): Record<string, unknown>;
|
|
14
|
+
getHeader(): unknown;
|
|
15
|
+
get alignmentNames(): string[];
|
|
16
|
+
get seqConsensus(): string | undefined;
|
|
17
|
+
get secondaryStructureConsensus(): string | undefined;
|
|
18
|
+
get tracks(): unknown[];
|
|
19
|
+
}
|
|
@@ -0,0 +1,36 @@
|
|
|
1
|
+
export default class BaseMSA {
|
|
2
|
+
getTree() {
|
|
3
|
+
return {
|
|
4
|
+
id: 'root',
|
|
5
|
+
name: 'root',
|
|
6
|
+
noTree: true,
|
|
7
|
+
children: this.getNames().map(name => ({
|
|
8
|
+
id: name,
|
|
9
|
+
children: [],
|
|
10
|
+
name,
|
|
11
|
+
})),
|
|
12
|
+
};
|
|
13
|
+
}
|
|
14
|
+
getRowData(_name) {
|
|
15
|
+
return undefined;
|
|
16
|
+
}
|
|
17
|
+
getStructures() {
|
|
18
|
+
return {};
|
|
19
|
+
}
|
|
20
|
+
getHeader() {
|
|
21
|
+
return {};
|
|
22
|
+
}
|
|
23
|
+
get alignmentNames() {
|
|
24
|
+
return [];
|
|
25
|
+
}
|
|
26
|
+
get seqConsensus() {
|
|
27
|
+
return undefined;
|
|
28
|
+
}
|
|
29
|
+
get secondaryStructureConsensus() {
|
|
30
|
+
return undefined;
|
|
31
|
+
}
|
|
32
|
+
get tracks() {
|
|
33
|
+
return [];
|
|
34
|
+
}
|
|
35
|
+
}
|
|
36
|
+
//# sourceMappingURL=BaseMSA.js.map
|
|
@@ -0,0 +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,SAA+E,CAAA;IACxF,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;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
|
package/dist/msa/ClustalMSA.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import
|
|
2
|
-
export default class ClustalMSA {
|
|
1
|
+
import BaseMSA from './BaseMSA.ts';
|
|
2
|
+
export default class ClustalMSA extends BaseMSA {
|
|
3
3
|
private MSA;
|
|
4
4
|
constructor(text: string);
|
|
5
5
|
getMSA(): {
|
|
@@ -15,16 +15,10 @@ export default class ClustalMSA {
|
|
|
15
15
|
};
|
|
16
16
|
getRow(name: string): string;
|
|
17
17
|
getWidth(): number;
|
|
18
|
-
getRowData(): undefined;
|
|
19
18
|
getHeader(): {
|
|
20
19
|
info: string;
|
|
21
20
|
version: string | undefined;
|
|
22
21
|
};
|
|
23
22
|
getNames(): string[];
|
|
24
|
-
getStructures(): {};
|
|
25
|
-
get alignmentNames(): never[];
|
|
26
|
-
getTree(): NodeWithIds;
|
|
27
23
|
get seqConsensus(): string;
|
|
28
|
-
get secondaryStructureConsensus(): undefined;
|
|
29
|
-
get tracks(): never[];
|
|
30
24
|
}
|
package/dist/msa/ClustalMSA.js
CHANGED
|
@@ -1,7 +1,9 @@
|
|
|
1
1
|
import { parse } from 'clustal-js';
|
|
2
|
-
|
|
2
|
+
import BaseMSA from "./BaseMSA.js";
|
|
3
|
+
export default class ClustalMSA extends BaseMSA {
|
|
3
4
|
MSA;
|
|
4
5
|
constructor(text) {
|
|
6
|
+
super();
|
|
5
7
|
this.MSA = parse(text);
|
|
6
8
|
}
|
|
7
9
|
getMSA() {
|
|
@@ -13,41 +15,14 @@ export default class ClustalMSA {
|
|
|
13
15
|
getWidth() {
|
|
14
16
|
return this.MSA.alns[0].seq.length;
|
|
15
17
|
}
|
|
16
|
-
getRowData() {
|
|
17
|
-
return undefined;
|
|
18
|
-
}
|
|
19
18
|
getHeader() {
|
|
20
19
|
return this.MSA.header;
|
|
21
20
|
}
|
|
22
21
|
getNames() {
|
|
23
22
|
return this.MSA.alns.map(aln => aln.id);
|
|
24
23
|
}
|
|
25
|
-
getStructures() {
|
|
26
|
-
return {};
|
|
27
|
-
}
|
|
28
|
-
get alignmentNames() {
|
|
29
|
-
return [];
|
|
30
|
-
}
|
|
31
|
-
getTree() {
|
|
32
|
-
return {
|
|
33
|
-
id: 'root',
|
|
34
|
-
name: 'root',
|
|
35
|
-
noTree: true,
|
|
36
|
-
children: this.getNames().map(name => ({
|
|
37
|
-
id: name,
|
|
38
|
-
name,
|
|
39
|
-
children: [],
|
|
40
|
-
})),
|
|
41
|
-
};
|
|
42
|
-
}
|
|
43
24
|
get seqConsensus() {
|
|
44
25
|
return this.MSA.consensus;
|
|
45
26
|
}
|
|
46
|
-
get secondaryStructureConsensus() {
|
|
47
|
-
return undefined;
|
|
48
|
-
}
|
|
49
|
-
get tracks() {
|
|
50
|
-
return [];
|
|
51
|
-
}
|
|
52
27
|
}
|
|
53
28
|
//# sourceMappingURL=ClustalMSA.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/msa/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;
|
|
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,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IACrC,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
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import
|
|
2
|
-
export default class EmfMSA {
|
|
1
|
+
import BaseMSA from './BaseMSA.ts';
|
|
2
|
+
export default class EmfMSA extends BaseMSA {
|
|
3
3
|
private MSA;
|
|
4
4
|
constructor(text: string);
|
|
5
5
|
getMSA(): {
|
|
@@ -15,13 +15,6 @@ export default class EmfMSA {
|
|
|
15
15
|
}[];
|
|
16
16
|
getRow(name: string): string;
|
|
17
17
|
getWidth(): number;
|
|
18
|
-
getRowData(): undefined;
|
|
19
18
|
getHeader(): string;
|
|
20
19
|
getNames(): string[];
|
|
21
|
-
getStructures(): {};
|
|
22
|
-
get alignmentNames(): never[];
|
|
23
|
-
getTree(): NodeWithIds;
|
|
24
|
-
get seqConsensus(): undefined;
|
|
25
|
-
get secondaryStructureConsensus(): undefined;
|
|
26
|
-
get tracks(): never[];
|
|
27
20
|
}
|