@datagrok-libraries/bio 5.28.3 → 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
CHANGED
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@@ -1 +1 @@
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1
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-
{"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;
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1
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+
{"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"}
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@@ -9,7 +9,7 @@ export class UnitsHandler {
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UnitsHandler.setTags(col, splitterAsFasta);
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}
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static setUnitsToSeparatorColumn(col, separator) {
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if (col.semType !== DG.SEMTYPE.MACROMOLECULE || col.getTag(DG.TAGS.UNITS) !== "separator" /* NOTATION.SEPARATOR */
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if (col.semType !== DG.SEMTYPE.MACROMOLECULE || col.getTag(DG.TAGS.UNITS) !== "separator" /* NOTATION.SEPARATOR */)
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throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
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if (!separator)
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throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must have the separator tag.`);
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@@ -101,10 +101,12 @@ export class UnitsHandler {
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}
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}
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getAlphabetIsMultichar() {
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if (this.notation
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return
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-
else
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if (this.notation === "helm" /* NOTATION.HELM */)
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return true;
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else if (this.alphabet !== "UN" /* ALPHABET.UN */)
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return false;
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else
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return this.column.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) === 'true';
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}
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isFasta() { return this.notation === "fasta" /* NOTATION.FASTA */; }
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isSeparator() { return this.notation === "separator" /* NOTATION.SEPARATOR */; }
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@@ -213,8 +215,8 @@ export class UnitsHandler {
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}
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constructor(col) {
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this._column = col;
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const units = this._column.
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if (units !== null)
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const units = this._column.getTag(DG.TAGS.UNITS);
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if (units !== null && units !== undefined)
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this._units = units;
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else
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throw new Error('Units are not specified in column');
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@@ -222,7 +224,10 @@ export class UnitsHandler {
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this._defaultGapSymbol = (this.isFasta()) ? UnitsHandler._defaultGapSymbolsDict.FASTA :
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(this.isHelm()) ? UnitsHandler._defaultGapSymbolsDict.HELM :
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UnitsHandler._defaultGapSymbolsDict.SEPARATOR;
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-
if (!this.column.tags.has("aligned" /* TAGS.aligned */) || !this.column.tags.has("alphabet" /* TAGS.alphabet */)
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if (!this.column.tags.has("aligned" /* TAGS.aligned */) || !this.column.tags.has("alphabet" /* TAGS.alphabet */) ||
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(!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) && !this.isHelm() && this.alphabet === "UN" /* ALPHABET.UN */)) {
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// The following detectors and setters are to be called because the column is likely
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// as the UnitsHandler constructor was called on the column.
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if (this.isFasta()) {
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UnitsHandler.setUnitsToFastaColumn(this.column);
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}
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@@ -247,8 +252,7 @@ export class UnitsHandler {
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// }
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if (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */)) {
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if (this.isHelm()) {
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-
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`tag '${".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */}' is mandatory.`);
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this.column.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, 'true');
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}
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else if (['UN'].includes(this.alphabet)) {
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throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' ` +
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@@ -1 +1 @@
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1
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-
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