@datagrok-libraries/bio 5.28.2 → 5.28.4
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/package.json +3 -3
- package/src/utils/fasta-handler.d.ts.map +1 -1
- package/src/utils/fasta-handler.js +1 -0
- package/src/utils/fasta-handler.js.map +1 -1
- package/src/utils/macromolecule.d.ts +6 -1
- package/src/utils/macromolecule.d.ts.map +1 -1
- package/src/utils/macromolecule.js +23 -19
- package/src/utils/macromolecule.js.map +1 -1
- package/src/utils/notation-converter.d.ts.map +1 -1
- package/src/utils/notation-converter.js +2 -3
- package/src/utils/notation-converter.js.map +1 -1
- package/src/utils/units-handler.d.ts +6 -2
- package/src/utils/units-handler.d.ts.map +1 -1
- package/src/utils/units-handler.js +75 -22
- package/src/utils/units-handler.js.map +1 -1
package/package.json
CHANGED
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@@ -8,15 +8,15 @@
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"access": "public"
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},
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"friendlyName": "Datagrok bio library",
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-
"version": "5.28.
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+
"version": "5.28.4",
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"description": "",
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"dependencies": {
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"@datagrok-libraries/gridext": "^1.3.22",
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"@datagrok-libraries/utils": "^2.5.0",
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+
"@deck.gl/core": "8.8.12",
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"cash-dom": "latest",
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"datagrok-api": "^1.10.2",
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"dayjs": "latest",
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-
"@deck.gl/core": "8.8.12",
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"mjolnir.js": "^2.7.0",
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"rxjs": "^6.5.5",
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"wu": "latest"
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@@ -28,7 +28,7 @@
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"eslint": "latest",
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"eslint-config-google": "latest",
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"ts-loader": "^9.2.6",
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-
"typescript": "^4.
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"typescript": "^4.9.5"
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},
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"scripts": {
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"link": "npm link",
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"fasta-handler.d.ts","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;
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1
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+
{"version":3,"file":"fasta-handler.d.ts","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,oCAAoC;AACpC,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,YAAY,CAAS;IAC7B,OAAO,CAAC,kBAAkB,CAAgB;IAC1C,OAAO,CAAC,eAAe,CAAgB;IAGvC,IAAW,iBAAiB,IAAI,MAAM,EAAE,CAAoC;IAE5E,IAAW,cAAc,IAAI,MAAM,EAAE,CAAiC;IAEtE;;;;;;;OAOG;IACH,OAAO,CAAC,kBAAkB;IAS1B,2DAA2D;IAC3D,OAAO,CAAC,YAAY;IAiBpB;;;;OAIG;IACI,WAAW,IAAI,EAAE,CAAC,SAAS,EAAG;gBAezB,WAAW,EAAE,MAAM;CAIhC"}
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@@ -42,6 +42,7 @@ export class FastaFileHandler {
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const descriptionsArrayCol = DG.Column.fromStrings('description', this.descriptionsArray);
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const sequenceCol = DG.Column.fromStrings('sequence', this.sequencesArray);
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sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
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sequenceCol.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
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// here should go the code from units handler
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UnitsHandler.setUnitsToFastaColumn(sequenceCol);
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return [DG.DataFrame.fromColumns([
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"fasta-handler.js","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;
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+
{"version":3,"file":"fasta-handler.js","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAG7C,oCAAoC;AACpC,MAAM,OAAO,gBAAgB;IAI3B,2CAA2C;IAE3C,IAAW,iBAAiB,KAAe,OAAO,IAAI,CAAC,kBAAkB,CAAC,CAAC,CAAC;IAE5E,IAAW,cAAc,KAAe,OAAO,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC;IAEtE;;;;;;;OAOG;IACK,kBAAkB,CACxB,eAAuB,EACvB,aAAqB;QAErB,MAAM,GAAG,GAAG,IAAI,CAAC,YAAY,CAAC,KAAK,CAAC,eAAe,EAAE,aAAa,CAAC,CAAC;QACpE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACjC,OAAO,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC;IAED,2DAA2D;IACnD,YAAY;QAClB,MAAM,KAAK,GAAG,WAAW,CAAC,CAAC,4CAA4C;QAEvE,IAAI,eAAe,GAAG,CAAC,CAAC;QACxB,IAAI,KAAK,CAAC,CAAC,mDAAmD;QAC9D,OAAO,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,EAAE;YAC5C,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,SAAS,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC,CAAC;YAClF,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;YAC1C,IAAI,eAAe,KAAK,CAAC;gBACvB,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,kBAAkB,CAAC,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;YACnF,eAAe,GAAG,KAAK,CAAC,SAAS,GAAG,CAAC,CAAC;SACvC;QACD,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,kBAAkB,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;QAExE,8BAA8B;IAChC,CAAC;IAED;;;;OAIG;IACI,WAAW;QAChB,MAAM,oBAAoB,GAAG,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,aAAa,EAAE,IAAI,CAAC,iBAAiB,CAAC,CAAC;QAC1F,MAAM,WAAW,GAAG,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,UAAU,EAAE,IAAI,CAAC,cAAc,CAAC,CAAC;QAC3E,WAAW,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;QAC/C,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,+BAAiB,CAAC;QAElD,6CAA6C;QAC7C,YAAY,CAAC,qBAAqB,CAAC,WAAW,CAAC,CAAC;QAEhD,OAAO,CAAC,EAAE,CAAC,SAAS,CAAC,WAAW,CAAC;gBAC/B,oBAAoB;gBACpB,WAAW;aACZ,CAAC,CAAC,CAAC;IACN,CAAC;IAED,YAAY,WAAmB;QA/DvB,uBAAkB,GAAa,EAAE,CAAC,CAAC,4BAA4B;QAC/D,oBAAe,GAAa,EAAE,CAAC,CAAC,wBAAwB;QA+D9D,IAAI,CAAC,YAAY,GAAG,WAAW,CAAC;QAChC,IAAI,CAAC,YAAY,EAAE,CAAC;IACtB,CAAC;CACF"}
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@@ -79,7 +79,11 @@ export declare function getAlphabet(alphabet: ALPHABET): Set<string>;
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* @return {number} Cosine similarity
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*/
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export declare function getAlphabetSimilarity(freq: MonomerFreqs, alphabet: Set<string>, gapSymbol?: string): number;
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-
export declare
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export declare const candidateAlphabets: [string, Set<string>, number][];
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/** Alphabet candidate type */
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type CandidateType = [string, Set<string>, number];
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/** From detectMacromolecule */
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export declare function detectAlphabet(freq: MonomerFreqs, candidates: CandidateType[], gapSymbol?: string): string;
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/** Selects a suitable palette based on column data
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* @param {DG.Column} seqCol Column to look for a palette
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* @param {number} minLength minimum length of sequence to detect palette (empty strings are allowed)
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@@ -88,4 +92,5 @@ export declare function detectAlphabet(stats: SeqColStats): string;
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export declare function pickUpPalette(seqCol: DG.Column, minLength?: number): SeqPalette;
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export declare function getPaletteByType(paletteType: string): SeqPalette;
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export declare function pickUpSeqCol(df: DG.DataFrame): DG.Column | null;
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export {};
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//# sourceMappingURL=macromolecule.d.ts.map
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@@ -1 +1 @@
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-
{"version":3,"file":"macromolecule.d.ts","sourceRoot":"","sources":["macromolecule.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,UAAU,EAAC,MAAM,iBAAiB,CAAC;AAO3C,0EAA0E;AAC1E,0BAAkB,QAAQ;IACxB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,QAAQ;IACxB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,EAAE,OAAO;CACV;AAED,0BAAkB,IAAI;IACpB,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;CACxB;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,EAAE,CAAC;AACrD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD;;;;;GAKG;AACH,wBAAgB,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,YAAY,GAAG,WAAW,CAsBlG;AAED,eAAO,MAAM,SAAS,EAAE,MAA8B,CAAC;AAEvD;;;GAGG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,GAAG,GAAG,MAAM,EAAE,
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{"version":3,"file":"macromolecule.d.ts","sourceRoot":"","sources":["macromolecule.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,UAAU,EAAC,MAAM,iBAAiB,CAAC;AAO3C,0EAA0E;AAC1E,0BAAkB,QAAQ;IACxB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,QAAQ;IACxB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,EAAE,OAAO;CACV;AAED,0BAAkB,IAAI;IACpB,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;CACxB;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,EAAE,CAAC;AACrD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD;;;;;GAKG;AACH,wBAAgB,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,YAAY,GAAG,WAAW,CAsBlG;AAED,eAAO,MAAM,SAAS,EAAE,MAA8B,CAAC;AAEvD;;;GAGG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,GAAG,GAAG,MAAM,EAAE,CAOlD;AAED;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,GAAE,MAAM,GAAG,SAAqB,GAAG,YAAY,CAI/G;AAKD;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,GAAG,GAAG,MAAM,EAAE,CAgBjD;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,KAAK,GAAE,MAAM,GAAG,SAAqB,GAAG,YAAY,CAWjH;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,YAAY,CAOjE;AAID,+CAA+C;AAC/C,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,MAAM,CAKhF;AAED,MAAM;AACN,wBAAgB,WAAW,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAC,CAW3D;AAED;;;;;GAKG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,YAAY,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,SAAS,GAAE,MAAY,GAAG,MAAM,CAchH;AAED,eAAO,MAAM,kBAAkB,EAAE,CAAC,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC,EAI7D,CAAC;AAEF,8BAA8B;AAC9B,KAAK,aAAa,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC,CAAC;AAInD,+BAA+B;AAC/B,wBAAgB,cAAc,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,aAAa,EAAE,EAAE,SAAS,GAAE,MAAY,UAetG;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,GAAE,MAAU,GAAG,UAAU,CAYlF;AAED,wBAAgB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,UAAU,CAYhE;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAS/D"}
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@@ -41,14 +41,8 @@ export const monomerRe = /\[(\w+)\]|(\w)|(-)/g;
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export function splitterAsFasta(seq) {
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return wu(seq.toString().matchAll(monomerRe))
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.map((ma) => {
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let mRes;
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const m = ma[0];
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mRes = ma[1];
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}
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else {
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mRes = m;
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}
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const mRes = m.length > 1 ? ma[1] : m;
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return mRes;
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}).toArray();
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}
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@@ -154,17 +148,27 @@ export function getAlphabetSimilarity(freq, alphabet, gapSymbol = '-') {
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const alphabetV = new Vector(alphabetA);
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return vectorDotProduct(freqV, alphabetV) / (vectorLength(freqV) * vectorLength(alphabetV));
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}
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export
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export const candidateAlphabets = [
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["PT" /* ALPHABET.PT */, UnitsHandler.PeptideFastaAlphabet, 0.50],
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["DNA" /* ALPHABET.DNA */, UnitsHandler.DnaFastaAlphabet, 0.55],
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["RNA" /* ALPHABET.RNA */, UnitsHandler.RnaFastaAlphabet, 0.55],
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];
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/** From detectMacromolecule */
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export function detectAlphabet(freq, candidates, gapSymbol = '-') {
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const candidatesSims = candidates.map((c) => {
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const sim = getAlphabetSimilarity(freq, c[1], gapSymbol);
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return [c[0], c[1], c[2], freq, sim];
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});
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let alphabetName;
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const maxSim = Math.max(...candidatesSims.map((cs) => cs[4] > cs[2] ? cs[4] : -1));
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if (maxSim > 0) {
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const sim = candidatesSims.find((cs) => cs[4] === maxSim);
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alphabetName = sim[0];
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}
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else {
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alphabetName = "UN" /* ALPHABET.UN */;
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}
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return alphabetName;
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}
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/** Selects a suitable palette based on column data
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* @param {DG.Column} seqCol Column to look for a palette
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@@ -179,7 +183,7 @@ export function pickUpPalette(seqCol, minLength = 5) {
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else {
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const stats = getStats(seqCol, minLength, splitterAsFasta);
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alphabet = detectAlphabet(stats);
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alphabet = detectAlphabet(stats.freq, candidateAlphabets);
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}
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const res = getPaletteByType(alphabet);
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return res;
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|
-
{"version":3,"file":"macromolecule.js","sourceRoot":"","sources":["macromolecule.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,MAAM,EAAC,MAAM,iDAAiD,CAAC;AACvE,OAAO,EAAC,YAAY,EAAE,gBAAgB,EAAC,MAAM,iDAAiD,CAAC;AAE/F,OAAO,EAAa,kBAAkB,EAAC,MAAM,eAAe,CAAC;AAC7D,OAAO,EAAc,mBAAmB,EAAC,MAAM,gBAAgB,CAAC;AAChE,OAAO,EAAC,kBAAkB,EAAC,MAAM,YAAY,CAAC;AAC9C,OAAO,EAAC,YAAY,EAAC,MAAM,wBAAwB,CAAC;AA4BnD,CAAC;AAMF;;;;;GAKG;AACH,MAAM,UAAU,QAAQ,CAAC,MAAiB,EAAE,SAAiB,EAAE,QAAsB;IACnF,MAAM,IAAI,GAA4B,EAAE,CAAC;IACzC,IAAI,UAAU,GAAG,IAAI,CAAC;IACtB,IAAI,WAAW,GAAG,IAAI,CAAC;IAEvB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,UAAU,EAAE;QACnC,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC;QAE3B,IAAI,WAAW,IAAI,IAAI;YACrB,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC;aACvB,IAAI,IAAI,CAAC,MAAM,KAAK,WAAW;YAClC,UAAU,GAAG,KAAK,CAAC;QAErB,IAAI,IAAI,CAAC,MAAM,IAAI,SAAS,EAAE;YAC5B,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE;gBACpB,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC;oBACd,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;gBACd,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;aACd;SACF;KACF;IACD,OAAO,EAAC,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,UAAU,EAAC,CAAC;AAC9C,CAAC;AAED,MAAM,CAAC,MAAM,SAAS,GAAW,qBAAqB,CAAC;AAEvD;;;GAGG;AACH,MAAM,UAAU,eAAe,CAAC,GAAQ;IACtC,OAAO,EAAE,CAAmB,GAAG,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;SAC5D,GAAG,CAAC,CAAC,EAAoB,EAAE,EAAE;QAC5B,
|
|
1
|
+
{"version":3,"file":"macromolecule.js","sourceRoot":"","sources":["macromolecule.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,MAAM,EAAC,MAAM,iDAAiD,CAAC;AACvE,OAAO,EAAC,YAAY,EAAE,gBAAgB,EAAC,MAAM,iDAAiD,CAAC;AAE/F,OAAO,EAAa,kBAAkB,EAAC,MAAM,eAAe,CAAC;AAC7D,OAAO,EAAc,mBAAmB,EAAC,MAAM,gBAAgB,CAAC;AAChE,OAAO,EAAC,kBAAkB,EAAC,MAAM,YAAY,CAAC;AAC9C,OAAO,EAAC,YAAY,EAAC,MAAM,wBAAwB,CAAC;AA4BnD,CAAC;AAMF;;;;;GAKG;AACH,MAAM,UAAU,QAAQ,CAAC,MAAiB,EAAE,SAAiB,EAAE,QAAsB;IACnF,MAAM,IAAI,GAA4B,EAAE,CAAC;IACzC,IAAI,UAAU,GAAG,IAAI,CAAC;IACtB,IAAI,WAAW,GAAG,IAAI,CAAC;IAEvB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,UAAU,EAAE;QACnC,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC;QAE3B,IAAI,WAAW,IAAI,IAAI;YACrB,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC;aACvB,IAAI,IAAI,CAAC,MAAM,KAAK,WAAW;YAClC,UAAU,GAAG,KAAK,CAAC;QAErB,IAAI,IAAI,CAAC,MAAM,IAAI,SAAS,EAAE;YAC5B,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE;gBACpB,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC;oBACd,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;gBACd,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;aACd;SACF;KACF;IACD,OAAO,EAAC,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,UAAU,EAAC,CAAC;AAC9C,CAAC;AAED,MAAM,CAAC,MAAM,SAAS,GAAW,qBAAqB,CAAC;AAEvD;;;GAGG;AACH,MAAM,UAAU,eAAe,CAAC,GAAQ;IACtC,OAAO,EAAE,CAAmB,GAAG,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;SAC5D,GAAG,CAAC,CAAC,EAAoB,EAAE,EAAE;QAC5B,MAAM,CAAC,GAAW,EAAE,CAAC,CAAC,CAAC,CAAC;QACxB,MAAM,IAAI,GAAG,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACtC,OAAO,IAAI,CAAC;IACd,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC;AACjB,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,wBAAwB,CAAC,SAAiB,EAAE,QAA4B,SAAS;IAC/F,OAAO,CAAC,GAAW,EAAE,EAAE;QACrB,OAAO,GAAG,CAAC,KAAK,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC;IACrC,CAAC,CAAC;AACJ,CAAC;AAED,MAAM,MAAM,GAAW,iCAAiC,CAAC;AACzD,MAAM,SAAS,GAAW,gBAAgB,CAAC;AAE3C;;;;GAIG;AACH,MAAM,UAAU,cAAc,CAAC,GAAQ;IACrC,MAAM,CAAC,SAAS,GAAG,CAAC,CAAC;IACrB,MAAM,EAAE,GAA2B,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC/D,MAAM,KAAK,GAAkB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAE/C,MAAM,aAAa,GAAG,CAAC,EAAU,EAAU,EAAE;QAC3C,SAAS,CAAC,SAAS,GAAG,CAAC,CAAC;QACxB,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChC,IAAI,IAAI,IAAI,IAAI,CAAC,MAAM,IAAI,CAAC;YAC1B,OAAO,IAAI,CAAC,CAAC,CAAC,CAAC;;YAEf,OAAO,EAAE,CAAC;IACd,CAAC,CAAC;IAEF,MAAM,MAAM,GAAa,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACvD,OAAO,MAAM,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;AACnC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CAAC,KAAa,EAAE,SAAiB,EAAE,QAA4B,SAAS;IACjG,IAAI,KAAK,CAAC,WAAW,EAAE,CAAC,UAAU,8BAAgB;QAChD,OAAO,eAAe,CAAC;SACpB,IAAI,KAAK,CAAC,WAAW,EAAE,CAAC,UAAU,sCAAoB;QACzD,OAAO,wBAAwB,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC;SAC/C,IAAI,KAAK,CAAC,WAAW,EAAE,CAAC,UAAU,4BAAe;QACpD,OAAO,cAAc,CAAC;;QAEtB,MAAM,IAAI,KAAK,CAAC,oBAAoB,KAAK,IAAI,CAAC,CAAC;IAEjD,0BAA0B;AAC5B,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,oBAAoB,CAAC,GAAc;IACjD,IAAI,GAAG,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,CAAC,aAAa;QAC1C,MAAM,IAAI,KAAK,CAAC,6BAA6B,EAAE,CAAC,OAAO,CAAC,aAAa,SAAS,CAAC,CAAC;IAElF,MAAM,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACxC,MAAM,SAAS,GAAG,GAAG,CAAC,MAAM,kCAAgB,CAAC;IAC7C,OAAO,WAAW,CAAC,KAAK,EAAE,SAAS,CAAC,CAAC;AACvC,CAAC;AAED,MAAM,iBAAiB,GAAW,QAAQ,CAAC;AAE3C,+CAA+C;AAC/C,MAAM,UAAU,cAAc,CAAC,KAAa,EAAE,kBAA0B;;IACtE,MAAM,eAAe,GAA4B,KAAK,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAC;IAChF,MAAM,WAAW,GAAY,KAAK,CAAC,MAAM,GAAG,kBAAkB,IAAI,CAAC,MAAA,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,MAAM,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAC;IACrG,MAAM,UAAU,GAAG,MAAA,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAG,CAAC,CAAC,mCAAI,GAAG,CAAC;IAC/C,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,UAAU,CAAC,SAAS,CAAC,CAAC,EAAE,kBAAkB,CAAC,GAAG,GAAG,CAAC;AACvF,CAAC;AAED,MAAM;AACN,MAAM,UAAU,WAAW,CAAC,QAAkB;IAC5C,QAAQ,QAAQ,EAAE;QAClB;YACE,OAAO,YAAY,CAAC,gBAAgB,CAAC;QACvC;YACE,OAAO,YAAY,CAAC,gBAAgB,CAAC;QACvC;YACE,OAAO,YAAY,CAAC,oBAAoB,CAAC;QAC3C;YACE,MAAM,IAAI,KAAK,CAAC,yBAAyB,QAAQ,IAAI,CAAC,CAAC;KACxD;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,qBAAqB,CAAC,IAAkB,EAAE,QAAqB,EAAE,YAAoB,GAAG;IACtG,MAAM,IAAI,GAAG,IAAI,GAAG,CAAS,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,GAAG,QAAQ,CAAC,CAAC,CAAC;IAC3E,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IAEvB,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,MAAM,SAAS,GAAa,EAAE,CAAC;IAC/B,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE;QACpB,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACpC,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;KACzC;IACD,0FAA0F;IAC1F,MAAM,KAAK,GAAW,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC;IACxC,MAAM,SAAS,GAAW,IAAI,MAAM,CAAC,SAAS,CAAC,CAAC;IAChD,OAAO,gBAAgB,CAAC,KAAK,EAAE,SAAS,CAAC,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,GAAG,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC;AAC9F,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAoC;IACjE,yBAAc,YAAY,CAAC,oBAAoB,EAAE,IAAI,CAAC;IACtD,2BAAe,YAAY,CAAC,gBAAgB,EAAE,IAAI,CAAC;IACnD,2BAAe,YAAY,CAAC,gBAAgB,EAAE,IAAI,CAAC;CACpD,CAAC;AAOF,+BAA+B;AAC/B,MAAM,UAAU,cAAc,CAAC,IAAkB,EAAE,UAA2B,EAAE,YAAoB,GAAG;IACrG,MAAM,cAAc,GAAuB,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;QAC9D,MAAM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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"notation-converter.d.ts","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAC7C,OAAO,EAAiC,QAAQ,EAAe,YAAY,EAAO,MAAM,iBAAiB,CAAC;AAE1G,iFAAiF;AACjF,qBAAa,iBAAkB,SAAQ,YAAY;IACjD,OAAO,CAAC,SAAS,CAA6B;IAE9C,SAAS,KAAK,QAAQ,IAAI,YAAY,CAIrC;IAEM,OAAO,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE1C,WAAW,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE9C,MAAM,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAEhD;;;;;;OAMG;IACH,OAAO,CAAC,uBAAuB;
|
|
1
|
+
{"version":3,"file":"notation-converter.d.ts","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAC7C,OAAO,EAAiC,QAAQ,EAAe,YAAY,EAAO,MAAM,iBAAiB,CAAC;AAE1G,iFAAiF;AACjF,qBAAa,iBAAkB,SAAQ,YAAY;IACjD,OAAO,CAAC,SAAS,CAA6B;IAE9C,SAAS,KAAK,QAAQ,IAAI,YAAY,CAIrC;IAEM,OAAO,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE1C,WAAW,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE9C,MAAM,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAEhD;;;;;;OAMG;IACH,OAAO,CAAC,uBAAuB;IAmB/B;;;;;OAKG;IACH,OAAO,CAAC,eAAe;IAiBvB,OAAO,CAAC,mBAAmB;IAkB3B;;;;;;;OAOG;IACI,mBAAmB,CACxB,aAAa,EAAE,MAAM,EACrB,eAAe,GAAE,MAAM,GAAG,IAAW,GACpC,MAAM;IAOT;;;;;OAKG;IACH,OAAO,CAAC,aAAa;IAgBrB;;;;;OAKG;IACH,OAAO,CAAC,uBAAuB;IA6B/B;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GACrF,MAAM;IAgCT;;;;;;;;OAQG;IACH,OAAO,CAAC,WAAW;IAsBnB,OAAO,CAAC,sBAAsB;IAK9B;;;;;OAKG;IACI,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,GAAE,MAAM,GAAG,IAAW,GAAG,EAAE,CAAC,MAAM;gBAsBjE,GAAG,EAAE,EAAE,CAAC,MAAM;CAGlC"}
|
|
@@ -21,7 +21,7 @@ export class NotationConverter extends UnitsHandler {
|
|
|
21
21
|
convertFastaToSeparator(separator, fastaGapSymbol = null) {
|
|
22
22
|
if (fastaGapSymbol === null)
|
|
23
23
|
fastaGapSymbol = this.defaultGapSymbol;
|
|
24
|
-
const newColumn = this.getNewColumn("separator" /* NOTATION.SEPARATOR
|
|
24
|
+
const newColumn = this.getNewColumn("separator" /* NOTATION.SEPARATOR */, separator);
|
|
25
25
|
// assign the values to the newly created empty column
|
|
26
26
|
newColumn.init((idx) => {
|
|
27
27
|
const fastaPolymer = this.column.get(idx);
|
|
@@ -33,7 +33,6 @@ export class NotationConverter extends UnitsHandler {
|
|
|
33
33
|
return fastaMonomersArray.join(separator);
|
|
34
34
|
});
|
|
35
35
|
newColumn.setTag(DG.TAGS.UNITS, "separator" /* NOTATION.SEPARATOR */);
|
|
36
|
-
newColumn.setTag("separator" /* TAGS.separator */, separator);
|
|
37
36
|
return newColumn;
|
|
38
37
|
}
|
|
39
38
|
/**
|
|
@@ -188,7 +187,7 @@ export class NotationConverter extends UnitsHandler {
|
|
|
188
187
|
convertHelm(tgtNotation, tgtSeparator, tgtGapSymbol) {
|
|
189
188
|
// This function must not contain calls of isDna() and isRna(), for
|
|
190
189
|
// source helm columns may contain RNA, DNA and PT across different rows
|
|
191
|
-
const newColumn = this.getNewColumn(tgtNotation);
|
|
190
|
+
const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
|
|
192
191
|
// assign the values to the empty column
|
|
193
192
|
newColumn.init((idx) => {
|
|
194
193
|
const helmPolymer = this.column.get(idx);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"notation-converter.js","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAC7C,OAAO,EAAC,oBAAoB,EAAE,QAAQ,EAA4C,MAAM,iBAAiB,CAAC;AAE1G,iFAAiF;AACjF,MAAM,OAAO,iBAAkB,SAAQ,YAAY;IAGjD,IAAc,QAAQ;QACpB,IAAI,IAAI,CAAC,SAAS,KAAK,IAAI;YACzB,IAAI,CAAC,SAAS,GAAG,oBAAoB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACrD,OAAO,IAAI,CAAC,SAAS,CAAC;IACxB,CAAC;IAEM,OAAO,CAAC,cAAwB,IAAa,OAAO,cAAc,iCAAmB,CAAC,CAAC,CAAC;IAExF,WAAW,CAAC,cAAwB,IAAa,OAAO,cAAc,yCAAuB,CAAC,CAAC,CAAC;IAEhG,MAAM,CAAC,cAAwB,IAAa,OAAO,cAAc,+BAAkB,CAAC,CAAC,CAAC;IAE7F;;;;;;OAMG;IACK,uBAAuB,CAAC,SAAiB,EAAE,iBAAgC,IAAI;QACrF,IAAI,cAAc,KAAK,IAAI;YACzB,cAAc,GAAG,IAAI,CAAC,gBAAgB,CAAC;QAEzC,MAAM,SAAS,GAAG,IAAI,CAAC,YAAY,
|
|
1
|
+
{"version":3,"file":"notation-converter.js","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAC7C,OAAO,EAAC,oBAAoB,EAAE,QAAQ,EAA4C,MAAM,iBAAiB,CAAC;AAE1G,iFAAiF;AACjF,MAAM,OAAO,iBAAkB,SAAQ,YAAY;IAGjD,IAAc,QAAQ;QACpB,IAAI,IAAI,CAAC,SAAS,KAAK,IAAI;YACzB,IAAI,CAAC,SAAS,GAAG,oBAAoB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACrD,OAAO,IAAI,CAAC,SAAS,CAAC;IACxB,CAAC;IAEM,OAAO,CAAC,cAAwB,IAAa,OAAO,cAAc,iCAAmB,CAAC,CAAC,CAAC;IAExF,WAAW,CAAC,cAAwB,IAAa,OAAO,cAAc,yCAAuB,CAAC,CAAC,CAAC;IAEhG,MAAM,CAAC,cAAwB,IAAa,OAAO,cAAc,+BAAkB,CAAC,CAAC,CAAC;IAE7F;;;;;;OAMG;IACK,uBAAuB,CAAC,SAAiB,EAAE,iBAAgC,IAAI;QACrF,IAAI,cAAc,KAAK,IAAI;YACzB,cAAc,GAAG,IAAI,CAAC,gBAAgB,CAAC;QAEzC,MAAM,SAAS,GAAG,IAAI,CAAC,YAAY,uCAAqB,SAAS,CAAC,CAAC;QACnE,sDAAsD;QACtD,SAAS,CAAC,IAAI,CAAC,CAAC,GAAW,EAAE,EAAE;YAC7B,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;YAC1C,MAAM,kBAAkB,GAAG,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC;YACvD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,kBAAkB,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBAClD,IAAI,kBAAkB,CAAC,CAAC,CAAC,KAAK,cAAc;oBAC1C,kBAAkB,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,sBAAsB,CAAC,SAAS,CAAC;aACzE;YACD,OAAO,kBAAkB,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QAC5C,CAAC,CAAC,CAAC;QACH,SAAS,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,uCAAqB,CAAC;QACpD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED;;;;;OAKG;IACK,eAAe;QACrB,MAAM,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;YACvC,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;gBACxB,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;oBAChC,SAAS,CAAC,CAAC,6CAA6C;QAE9D,IAAI,MAAM,KAAK,SAAS;YACtB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;QAErD,MAAM,OAAO,GAAG,MAAM,CAAC;QACvB,MAAM,WAAW,GAAG,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;YACzC,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,0BAA0B;QACxD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,0BAA0B;QAC3F,OAAO,CAAC,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,OAAO,CAAC,CAAC;IACtD,CAAC;IAED,mDAAmD;IAC3C,mBAAmB,CACzB,aAAqB,EACrB,eAAuB,EACvB,MAAc,EACd,WAAmB,EACnB,YAAoB,EACpB,OAAe;QAEf,MAAM,YAAY,GAAG,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC;QAClD,MAAM,gBAAgB,GAAa,YAAY,CAAC,GAAG,CAAC,CAAC,EAAU,EAAE,EAAE;YACjE,IAAI,EAAE,KAAK,eAAe;gBACxB,OAAO,YAAY,CAAC,sBAAsB,CAAC,IAAI,CAAC;;gBAEhD,OAAO,GAAG,WAAW,GAAG,EAAE,GAAG,YAAY,EAAE,CAAC;QAChD,CAAC,CAAC,CAAC;QACH,OAAO,GAAG,MAAM,GAAG,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,OAAO,EAAE,CAAC;IAC5D,CAAC;IAED;;;;;;;OAOG;IACI,mBAAmB,CACxB,aAAqB,EACrB,kBAAiC,IAAI;QAErC,IAAI,eAAe,KAAK,IAAI;YAC1B,eAAe,GAAG,IAAI,CAAC,gBAAgB,CAAC;QAC1C,MAAM,CAAC,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC,eAAe,EAAE,CAAC;QAC5E,OAAO,IAAI,CAAC,mBAAmB,CAAC,aAAa,EAAE,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,OAAO,CAAC,CAAC;IAC9G,CAAC;IAED;;;;;OAKG;IACK,aAAa,CAAC,kBAAiC,IAAI;QACzD,IAAI,eAAe,KAAK,IAAI;YAC1B,eAAe,GAAG,IAAI,CAAC,gBAAgB,CAAC;QAE1C,MAAM,CAAC,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC,eAAe,EAAE,CAAC;QAE5E,MAAM,SAAS,GAAG,IAAI,CAAC,YAAY,4BAAe,CAAC;QACnD,wCAAwC;QACxC,SAAS,CAAC,IAAI,CAAC,CAAC,GAAW,EAAE,EAAE;YAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;YAC3C,OAAO,IAAI,CAAC,mBAAmB,CAAC,aAAa,EAAE,eAAgB,EAAE,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,OAAO,CAAC,CAAC;QAC/G,CAAC,CAAC,CAAC;QACH,SAAS,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,6BAAgB,CAAC;QAC/C,OAAO,SAAS,CAAC;IACnB,CAAC;IAED;;;;;OAKG;IACK,uBAAuB,CAAC,iBAAgC,IAAI;QAClE,IAAI,cAAc,KAAK,IAAI;YACzB,cAAc,GAAG,YAAY,CAAC,sBAAsB,CAAC,KAAK,CAAC;QAE7D,MAAM,SAAS,GAAG,IAAI,CAAC,YAAY,8BAAgB,CAAC;QACpD,wCAAwC;QACxC,SAAS,CAAC,IAAI,CAAC,CAAC,GAAW,EAAE,EAAE;YAC7B,MAAM,gBAAgB,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;YAC9C,sCAAsC;YACtC,MAAM,mBAAmB,GAAG,IAAI,CAAC,QAAQ,CAAC,gBAAgB,CAAC,CAAC;YAC5D,MAAM,kBAAkB,GAAa,EAAE,CAAC;YACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,mBAAmB,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACnD,MAAM,IAAI,GAAG,mBAAmB,CAAC,CAAC,CAAC,CAAC;gBACpC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;oBACrB,kBAAkB,CAAC,IAAI,CAAC,cAAe,CAAC,CAAC;iBAC1C;qBAAM,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;oBAC1B,wCAAwC;oBACxC,MAAM,OAAO,GAAG,GAAG,GAAG,IAAI,GAAG,GAAG,CAAC;oBACjC,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;iBAClC;qBAAM;oBACL,kBAAkB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;iBAC/B;aACF;YACD,OAAO,kBAAkB,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACrC,CAAC,CAAC,CAAC;QACH,SAAS,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,+BAAiB,CAAC;QAChD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAmB,EAAE,WAAmB,EAAE,YAAqB,EAAE,YAAqB;QAEtF,IAAI,CAAC,YAAY,EAAE;YACjB,YAAY,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,WAAuB,CAAC,CAAC,CAAC,CAAC;gBACtD,YAAY,CAAC,sBAAsB,CAAC,KAAK,CAAC,CAAC;gBAC3C,YAAY,CAAC,sBAAsB,CAAC,SAAS,CAAC;SACjD;QAED,IAAI,CAAC,YAAY,EAAE;YACjB,YAAY,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,WAAuB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC;SAC9E;QACD,MAAM,cAAc,GAAG,iBAAiB,CAAC;QACzC,MAAM,YAAY,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,CAAC,IAAI,WAAW,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QACpF,iCAAiC;QACjC,MAAM,cAAc,GAAG,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC;QAClD,MAAM,gBAAgB,GAAa,EAAE,CAAC;QACtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC9C,IAAI,IAAI,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;YAC7B,IAAI,YAAY;gBACd,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC,CAAC;YAC1C,IAAI,IAAI,KAAK,YAAY,CAAC,sBAAsB,CAAC,IAAI,EAAE;gBACrD,gBAAgB,CAAC,IAAI,CAAC,YAAa,CAAC,CAAC;aACtC;iBAAM,IAAI,IAAI,CAAC,OAAO,CAAC,WAAuB,CAAC,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;gBACnE,2DAA2D;gBAC3D,MAAM,OAAO,GAAG,GAAG,GAAG,IAAI,GAAG,GAAG,CAAC;gBACjC,gBAAgB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;aAChC;iBAAM;gBACL,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;aAC7B;SACF;QACD,OAAO,gBAAgB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IAC7C,CAAC;IAED;;;;;;;;OAQG;IACK,WAAW,CAAC,WAAmB,EAAE,YAAqB,EAAE,YAAqB;QACnF,mEAAmE;QACnE,wEAAwE;QACxE,MAAM,SAAS,GAAG,IAAI,CAAC,YAAY,CAAC,WAAuB,EAAE,YAAY,CAAC,CAAC;QAC3E,wCAAwC;QACxC,SAAS,CAAC,IAAI,CAAC,CAAC,GAAW,EAAE,EAAE;YAC7B,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;YACzC,OAAO,IAAI,CAAC,2BAA2B,CAAC,WAAW,EAAE,WAAW,EAAE,YAAY,EAAE,YAAY,CAAC,CAAC;YAC9F,mEAAmE;YACnE,mEAAmE;YACnE,0CAA0C;QAC5C,CAAC,CAAC,CAAC;QAEH,iFAAiF;QACjF,MAAM,QAAQ,GAAiB,oBAAoB,CAAC,SAAS,CAAC,CAAC;QAC/D,MAAM,KAAK,GAAgB,QAAQ,CAAC,SAAS,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAC;QAC5D,MAAM,OAAO,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC;QACrD,SAAS,CAAC,MAAM,+BAAe,OAAO,CAAC,CAAC;QAExC,OAAO,SAAS,CAAC;IACnB,CAAC;IAEO,sBAAsB;QAC5B,iDAAiD;QACjD,OAAO,IAAI,CAAC,YAAY,sCAAoB,CAAC;IAC/C,CAAC;IAED;;;;;OAKG;IACI,OAAO,CAAC,WAAqB,EAAE,eAA8B,IAAI;QACtE,sBAAsB;QACtB,IAAI,IAAI,CAAC,QAAQ,KAAK,WAAW;YAC/B,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;QAC7C,IAAI,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,IAAI,YAAY,KAAK,IAAI;YACxD,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;QAEpD,IAAI,IAAI,CAAC,OAAO,EAAE,IAAI,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,IAAI,YAAY,KAAK,IAAI;YAC1E,OAAO,IAAI,CAAC,uBAAuB,CAAC,YAAY,CAAC,CAAC;aAC/C,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC;YACzE,OAAO,IAAI,CAAC,aAAa,EAAE,CAAC;aACzB,IAAI,IAAI,CAAC,WAAW,EAAE,IAAI,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC;YACtD,OAAO,IAAI,CAAC,uBAAuB,EAAE,CAAC;aACnC,IAAI,IAAI,CAAC,MAAM,EAAE,IAAI,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE,mBAAmB;YACtE,OAAO,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,CAAC;aAClC,IAAI,IAAI,CAAC,MAAM,EAAE,IAAI,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC;YACrD,OAAO,IAAI,CAAC,WAAW,CAAC,WAAW,EAAE,YAAa,CAAC,CAAC;;YAEpD,MAAM,IAAI,KAAK,CAAC,2BAA2B;gBACzC,yBAAyB,IAAI,CAAC,QAAQ,yBAAyB,WAAW,IAAI,CAAC,CAAC;IACtF,CAAC;IAED,YAAmB,GAAc;QAC/B,KAAK,CAAC,GAAG,CAAC,CAAC;QAzQL,cAAS,GAAwB,IAAI,CAAC;IA0Q9C,CAAC;CACF"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
|
-
import { NOTATION } from './macromolecule';
|
|
2
|
+
import { NOTATION, SplitterFunc } from './macromolecule';
|
|
3
3
|
/** Class for handling notation units in Macromolecule columns */
|
|
4
4
|
export declare class UnitsHandler {
|
|
5
5
|
protected readonly _column: DG.Column;
|
|
@@ -15,6 +15,10 @@ export declare class UnitsHandler {
|
|
|
15
15
|
static readonly DnaFastaAlphabet: Set<string>;
|
|
16
16
|
static readonly RnaFastaAlphabet: Set<string>;
|
|
17
17
|
static setUnitsToFastaColumn(col: DG.Column): void;
|
|
18
|
+
static setUnitsToSeparatorColumn(col: DG.Column, separator?: string): void;
|
|
19
|
+
static setUnitsToHelmColumn(col: DG.Column): void;
|
|
20
|
+
/** From detectMacromolecule */
|
|
21
|
+
static setTags(col: DG.Column, splitter: SplitterFunc): void;
|
|
18
22
|
protected get units(): string;
|
|
19
23
|
protected get column(): DG.Column;
|
|
20
24
|
get notation(): NOTATION;
|
|
@@ -44,7 +48,7 @@ export declare class UnitsHandler {
|
|
|
44
48
|
* @param {NOTATION} targetNotation
|
|
45
49
|
* @return {DG.Column}
|
|
46
50
|
*/
|
|
47
|
-
protected getNewColumn(targetNotation: NOTATION): DG.Column;
|
|
51
|
+
protected getNewColumn(targetNotation: NOTATION, separator?: string): DG.Column;
|
|
48
52
|
/**
|
|
49
53
|
* Create a new empty column using templateCol as a template
|
|
50
54
|
*
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"units-handler.d.ts","sourceRoot":"","sources":["units-handler.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,
|
|
1
|
+
{"version":3,"file":"units-handler.d.ts","sourceRoot":"","sources":["units-handler.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EACgB,QAAQ,EAG7B,YAAY,EAEb,MAAM,iBAAiB,CAAC;AAEzB,iEAAiE;AACjE,qBAAa,YAAY;IACvB,SAAS,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC;IACtC,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC;IACzB,SAAS,CAAC,SAAS,EAAE,QAAQ,CAAC;IAC9B,SAAS,CAAC,iBAAiB,EAAE,MAAM,CAAC;IACpC,SAAS,CAAC,MAAM,CAAC,QAAQ,CAAC,sBAAsB;;;;MAI9C;IAEF,gBAAuB,oBAAoB,cAGxC;IACH,gBAAuB,gBAAgB,cAAyC;IAChF,gBAAuB,gBAAgB,cAAyC;WAElE,qBAAqB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM;WAQpC,yBAAyB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM;WAW5D,oBAAoB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM;IAQjD,+BAA+B;WACjB,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,QAAQ,EAAE,YAAY,GAAG,IAAI;IAuBnE,SAAS,KAAK,KAAK,IAAI,MAAM,CAAwB;IAErD,SAAS,KAAK,MAAM,IAAI,EAAE,CAAC,MAAM,CAAyB;IAE1D,IAAW,QAAQ,IAAI,QAAQ,CAA2B;IAE1D,IAAW,gBAAgB,IAAI,MAAM,CAAmC;IAExE,IAAW,SAAS,IAAI,MAAM,GAAG,SAAS,CAKzC;IAED,IAAW,OAAO,IAAI,MAAM,CAQ3B;IAED,iCAAiC;IACjC,IAAW,QAAQ,IAAI,MAAM,CAQ5B;IAEM,eAAe,IAAI,MAAM;IA6BzB,sBAAsB,IAAI,OAAO;IASjC,OAAO,IAAI,OAAO;IAElB,WAAW,IAAI,OAAO;IAEtB,MAAM,IAAI,OAAO;IAEjB,KAAK,IAAI,OAAO;IAEhB,KAAK,IAAI,OAAO;IAEhB,SAAS,IAAI,OAAO;IAEpB,KAAK,IAAI,OAAO;IAEvB,4DAA4D;IAC5D;;OAEG;IACH,SAAS,CAAC,WAAW,IAAI,QAAQ;IAWjC;;;;;;OAMG;IACH,SAAS,CAAC,YAAY,CAAC,cAAc,EAAE,QAAQ,EAAE,SAAS,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM;IAsC/E;;;;;;OAMG;WACW,YAAY,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM;IAM7D;;;;;OAKG;WACW,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO;IASxD;;;;;;;;OAQG;WACW,sBAAsB,CAClC,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,GACZ,EAAE,CAAC,MAAM;gBAYO,GAAG,EAAE,EAAE,CAAC,MAAM;CA+ClC"}
|
|
@@ -1,16 +1,48 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
|
-
import { detectAlphabet, getSplitterForColumn, getStats,
|
|
2
|
+
import { candidateAlphabets, detectAlphabet, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getSplitterForColumn, getStats, } from './macromolecule';
|
|
3
3
|
/** Class for handling notation units in Macromolecule columns */
|
|
4
4
|
export class UnitsHandler {
|
|
5
5
|
static setUnitsToFastaColumn(col) {
|
|
6
|
-
if (col.semType !== DG.SEMTYPE.MACROMOLECULE)
|
|
7
|
-
throw new Error(
|
|
8
|
-
const stats = getStats(col, 5, splitterAsFasta);
|
|
9
|
-
const aligned = stats.sameLength ? 'SEQ.MSA' : 'SEQ';
|
|
10
|
-
const alphabet = detectAlphabet(stats);
|
|
6
|
+
if (col.semType !== DG.SEMTYPE.MACROMOLECULE || col.getTag(DG.TAGS.UNITS) !== "fasta" /* NOTATION.FASTA */)
|
|
7
|
+
throw new Error(`The column of notation '${"fasta" /* NOTATION.FASTA */}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
|
|
11
8
|
col.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
|
|
12
|
-
|
|
13
|
-
|
|
9
|
+
UnitsHandler.setTags(col, splitterAsFasta);
|
|
10
|
+
}
|
|
11
|
+
static setUnitsToSeparatorColumn(col, separator) {
|
|
12
|
+
if (col.semType !== DG.SEMTYPE.MACROMOLECULE || col.getTag(DG.TAGS.UNITS) !== "separator" /* NOTATION.SEPARATOR */)
|
|
13
|
+
throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
|
|
14
|
+
if (!separator)
|
|
15
|
+
throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must have the separator tag.`);
|
|
16
|
+
col.setTag(DG.TAGS.UNITS, "separator" /* NOTATION.SEPARATOR */);
|
|
17
|
+
col.setTag("separator" /* TAGS.separator */, separator);
|
|
18
|
+
UnitsHandler.setTags(col, getSplitterWithSeparator(separator));
|
|
19
|
+
}
|
|
20
|
+
static setUnitsToHelmColumn(col) {
|
|
21
|
+
if (col.semType !== DG.SEMTYPE.MACROMOLECULE)
|
|
22
|
+
throw new Error(`The column of notation '${"helm" /* NOTATION.HELM */}' must be '${DG.SEMTYPE.MACROMOLECULE}'`);
|
|
23
|
+
col.setTag(DG.TAGS.UNITS, "helm" /* NOTATION.HELM */);
|
|
24
|
+
UnitsHandler.setTags(col, splitterAsHelm);
|
|
25
|
+
}
|
|
26
|
+
/** From detectMacromolecule */
|
|
27
|
+
static setTags(col, splitter) {
|
|
28
|
+
const units = col.getTag(DG.TAGS.UNITS);
|
|
29
|
+
const stats = getStats(col, 5, splitter);
|
|
30
|
+
const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
|
|
31
|
+
if (["fasta" /* NOTATION.FASTA */, "separator" /* NOTATION.SEPARATOR */].includes(units)) {
|
|
32
|
+
// Empty monomer alphabet is not allowed
|
|
33
|
+
if (Object.keys(stats.freq).length === 0)
|
|
34
|
+
throw new Error('Alphabet is empty');
|
|
35
|
+
const aligned = stats.sameLength ? "SEQ.MSA" /* ALIGNMENT.SEQ_MSA */ : "SEQ" /* ALIGNMENT.SEQ */;
|
|
36
|
+
col.setTag("aligned" /* TAGS.aligned */, aligned);
|
|
37
|
+
const alphabet = detectAlphabet(stats.freq, candidateAlphabets);
|
|
38
|
+
col.setTag("alphabet" /* TAGS.alphabet */, alphabet);
|
|
39
|
+
if (alphabet === "UN" /* ALPHABET.UN */) {
|
|
40
|
+
const alphabetSize = Object.keys(stats.freq).length;
|
|
41
|
+
const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
|
|
42
|
+
col.setTag(".alphabetSize" /* TAGS.alphabetSize */, alphabetSize.toString());
|
|
43
|
+
col.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, alphabetIsMultichar ? 'true' : 'false');
|
|
44
|
+
}
|
|
45
|
+
}
|
|
14
46
|
}
|
|
15
47
|
get units() { return this._units; }
|
|
16
48
|
get column() { return this._column; }
|
|
@@ -69,10 +101,12 @@ export class UnitsHandler {
|
|
|
69
101
|
}
|
|
70
102
|
}
|
|
71
103
|
getAlphabetIsMultichar() {
|
|
72
|
-
if (this.notation
|
|
73
|
-
return
|
|
74
|
-
else
|
|
104
|
+
if (this.notation === "helm" /* NOTATION.HELM */)
|
|
105
|
+
return true;
|
|
106
|
+
else if (this.alphabet !== "UN" /* ALPHABET.UN */)
|
|
75
107
|
return false;
|
|
108
|
+
else
|
|
109
|
+
return this.column.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) === 'true';
|
|
76
110
|
}
|
|
77
111
|
isFasta() { return this.notation === "fasta" /* NOTATION.FASTA */; }
|
|
78
112
|
isSeparator() { return this.notation === "separator" /* NOTATION.SEPARATOR */; }
|
|
@@ -102,7 +136,7 @@ export class UnitsHandler {
|
|
|
102
136
|
* @param {NOTATION} targetNotation
|
|
103
137
|
* @return {DG.Column}
|
|
104
138
|
*/
|
|
105
|
-
getNewColumn(targetNotation) {
|
|
139
|
+
getNewColumn(targetNotation, separator) {
|
|
106
140
|
const col = this.column;
|
|
107
141
|
const len = col.length;
|
|
108
142
|
const name = targetNotation.toLowerCase() + '(' + col.name + ')';
|
|
@@ -110,6 +144,11 @@ export class UnitsHandler {
|
|
|
110
144
|
const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill(''));
|
|
111
145
|
newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
|
|
112
146
|
newColumn.setTag(DG.TAGS.UNITS, targetNotation);
|
|
147
|
+
if (targetNotation === "separator" /* NOTATION.SEPARATOR */) {
|
|
148
|
+
if (!separator)
|
|
149
|
+
throw new Error(`Notation \'${"separator" /* NOTATION.SEPARATOR */}\' requires separator value.`);
|
|
150
|
+
newColumn.setTag("separator" /* TAGS.separator */, separator);
|
|
151
|
+
}
|
|
113
152
|
newColumn.setTag(DG.TAGS.CELL_RENDERER, 'Macromolecule');
|
|
114
153
|
const srcAligned = col.getTag("aligned" /* TAGS.aligned */);
|
|
115
154
|
if (srcAligned)
|
|
@@ -176,8 +215,8 @@ export class UnitsHandler {
|
|
|
176
215
|
}
|
|
177
216
|
constructor(col) {
|
|
178
217
|
this._column = col;
|
|
179
|
-
const units = this._column.
|
|
180
|
-
if (units !== null)
|
|
218
|
+
const units = this._column.getTag(DG.TAGS.UNITS);
|
|
219
|
+
if (units !== null && units !== undefined)
|
|
181
220
|
this._units = units;
|
|
182
221
|
else
|
|
183
222
|
throw new Error('Units are not specified in column');
|
|
@@ -185,10 +224,23 @@ export class UnitsHandler {
|
|
|
185
224
|
this._defaultGapSymbol = (this.isFasta()) ? UnitsHandler._defaultGapSymbolsDict.FASTA :
|
|
186
225
|
(this.isHelm()) ? UnitsHandler._defaultGapSymbolsDict.HELM :
|
|
187
226
|
UnitsHandler._defaultGapSymbolsDict.SEPARATOR;
|
|
188
|
-
if (!this.column.tags.has("aligned" /* TAGS.aligned */))
|
|
189
|
-
|
|
190
|
-
|
|
191
|
-
|
|
227
|
+
if (!this.column.tags.has("aligned" /* TAGS.aligned */) || !this.column.tags.has("alphabet" /* TAGS.alphabet */) ||
|
|
228
|
+
(!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) && !this.isHelm() && this.alphabet === "UN" /* ALPHABET.UN */)) {
|
|
229
|
+
// The following detectors and setters are to be called because the column is likely
|
|
230
|
+
// as the UnitsHandler constructor was called on the column.
|
|
231
|
+
if (this.isFasta()) {
|
|
232
|
+
UnitsHandler.setUnitsToFastaColumn(this.column);
|
|
233
|
+
}
|
|
234
|
+
else if (this.isSeparator()) {
|
|
235
|
+
const separator = col.getTag("separator" /* TAGS.separator */);
|
|
236
|
+
UnitsHandler.setUnitsToSeparatorColumn(this.column, separator);
|
|
237
|
+
}
|
|
238
|
+
else if (this.isHelm()) {
|
|
239
|
+
UnitsHandler.setUnitsToHelmColumn(this.column);
|
|
240
|
+
}
|
|
241
|
+
else {
|
|
242
|
+
throw new Error(`Unexpected units '${this.column.getTag(DG.TAGS.UNITS)}'.`);
|
|
243
|
+
}
|
|
192
244
|
}
|
|
193
245
|
// if (!this.column.tags.has(TAGS.alphabetSize)) {
|
|
194
246
|
// if (this.isHelm())
|
|
@@ -199,12 +251,13 @@ export class UnitsHandler {
|
|
|
199
251
|
// `tag '${TAGS.alphabetSize}' is mandatory.`);
|
|
200
252
|
// }
|
|
201
253
|
if (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */)) {
|
|
202
|
-
if (this.isHelm())
|
|
203
|
-
|
|
204
|
-
|
|
205
|
-
else if (['UN'].includes(this.alphabet))
|
|
254
|
+
if (this.isHelm()) {
|
|
255
|
+
this.column.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, 'true');
|
|
256
|
+
}
|
|
257
|
+
else if (['UN'].includes(this.alphabet)) {
|
|
206
258
|
throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' ` +
|
|
207
259
|
`tag '${".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */}' is mandatory.`);
|
|
260
|
+
}
|
|
208
261
|
}
|
|
209
262
|
}
|
|
210
263
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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