@datagrok-libraries/bio 5.43.1 → 5.44.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +20 -3
- package/package.json +4 -3
- package/src/helm/helm-helper.d.ts +17 -2
- package/src/helm/helm-helper.d.ts.map +1 -1
- package/src/helm/helm-helper.js +22 -0
- package/src/helm/helm-helper.js.map +1 -1
- package/src/helm/types.d.ts +4 -2
- package/src/helm/types.d.ts.map +1 -1
- package/src/monomer-works/consts.d.ts +13 -3
- package/src/monomer-works/consts.d.ts.map +1 -1
- package/src/monomer-works/consts.js +3 -3
- package/src/monomer-works/consts.js.map +1 -1
- package/src/monomer-works/monomer-hover.d.ts +10 -0
- package/src/monomer-works/monomer-hover.d.ts.map +1 -0
- package/src/monomer-works/monomer-hover.js +123 -0
- package/src/monomer-works/monomer-hover.js.map +1 -0
- package/src/monomer-works/monomer-utils.d.ts.map +1 -1
- package/src/monomer-works/monomer-utils.js +3 -2
- package/src/monomer-works/monomer-utils.js.map +1 -1
- package/src/monomer-works/seq-to-molfile-worker.js +5 -5
- package/src/monomer-works/seq-to-molfile-worker.js.map +1 -1
- package/src/monomer-works/seq-to-molfile.d.ts +14 -5
- package/src/monomer-works/seq-to-molfile.d.ts.map +1 -1
- package/src/monomer-works/seq-to-molfile.js +56 -12
- package/src/monomer-works/seq-to-molfile.js.map +1 -1
- package/src/monomer-works/to-atomic-level-utils.d.ts +7 -7
- package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
- package/src/monomer-works/to-atomic-level-utils.js +50 -25
- package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
- package/src/monomer-works/to-atomic-level.d.ts +8 -9
- package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
- package/src/monomer-works/to-atomic-level.js +40 -47
- package/src/monomer-works/to-atomic-level.js.map +1 -1
- package/src/monomer-works/types.d.ts +44 -0
- package/src/monomer-works/types.d.ts.map +1 -1
- package/src/monomer-works/types.js +25 -1
- package/src/monomer-works/types.js.map +1 -1
- package/src/monomer-works/utils.d.ts +15 -0
- package/src/monomer-works/utils.d.ts.map +1 -0
- package/src/monomer-works/utils.js +34 -0
- package/src/monomer-works/utils.js.map +1 -0
- package/src/types/index.d.ts +10 -10
- package/src/types/index.d.ts.map +1 -1
- package/src/types/index.js +1 -7
- package/src/types/index.js.map +1 -1
- package/src/utils/cell-renderer-back-base.d.ts +1 -1
- package/src/utils/cell-renderer-back-base.d.ts.map +1 -1
- package/src/utils/cell-renderer-back-base.js +1 -1
- package/src/utils/cell-renderer-back-base.js.map +1 -1
- package/src/utils/cell-renderer-monomer-placer.js +10 -11
- package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
- package/src/utils/generator.d.ts.map +1 -1
- package/src/utils/generator.js +2 -1
- package/src/utils/generator.js.map +1 -1
- package/src/utils/macromolecule/alignment.d.ts.map +1 -1
- package/src/utils/macromolecule/alignment.js +6 -6
- package/src/utils/macromolecule/alignment.js.map +1 -1
- package/src/utils/macromolecule/consts.d.ts +5 -0
- package/src/utils/macromolecule/consts.d.ts.map +1 -1
- package/src/utils/macromolecule/consts.js +7 -0
- package/src/utils/macromolecule/consts.js.map +1 -1
- package/src/utils/macromolecule/scoring.d.ts.map +1 -1
- package/src/utils/macromolecule/scoring.js +1 -1
- package/src/utils/macromolecule/scoring.js.map +1 -1
- package/src/utils/macromolecule/types.d.ts +0 -4
- package/src/utils/macromolecule/types.d.ts.map +1 -1
- package/src/utils/macromolecule/types.js +0 -2
- package/src/utils/macromolecule/types.js.map +1 -1
- package/src/utils/macromolecule/utils.d.ts +0 -4
- package/src/utils/macromolecule/utils.d.ts.map +1 -1
- package/src/utils/macromolecule/utils.js +11 -13
- package/src/utils/macromolecule/utils.js.map +1 -1
- package/src/utils/seq-handler.d.ts +0 -3
- package/src/utils/seq-handler.d.ts.map +1 -1
- package/src/utils/seq-handler.js +7 -10
- package/src/utils/seq-handler.js.map +1 -1
- package/src/utils/seq-helper.d.ts +4 -15
- package/src/utils/seq-helper.d.ts.map +1 -1
- package/src/utils/seq-helper.js +0 -1
- package/src/utils/seq-helper.js.map +1 -1
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@@ -5,7 +5,7 @@ import { IRenderer } from '../types/renderer';
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type GridCellRendererTemp<TBack> = {
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rendererBack: TBack;
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};
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export declare function
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export declare function getGridCellColTemp<TValue, TBack extends CellRendererBackBase<TValue>>(gridCell: DG.GridCell): [DG.GridColumn | null, DG.Column<TValue>, GridCellRendererTemp<TBack>];
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export declare abstract class CellRendererBackBase<TValue> implements IRenderer {
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/** Not null if rendered on a grid */
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protected readonly gridCol: DG.GridColumn | null;
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@@ -1 +1 @@
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-
{"version":3,"file":"cell-renderer-back-base.d.ts","sourceRoot":"","sources":["cell-renderer-back-base.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAE,OAAO,EAAE,cAAc,EAAC,MAAM,MAAM,CAAC;AAIzD,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AACjC,OAAO,EAAC,SAAS,EAAC,MAAM,mBAAmB,CAAC;AAE5C,KAAK,oBAAoB,CAAC,KAAK,IAAI;IACjC,YAAY,EAAE,KAAK,CAAC;CACrB,CAAA;AAED,wBAAgB,
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+
{"version":3,"file":"cell-renderer-back-base.d.ts","sourceRoot":"","sources":["cell-renderer-back-base.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAE,OAAO,EAAE,cAAc,EAAC,MAAM,MAAM,CAAC;AAIzD,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AACjC,OAAO,EAAC,SAAS,EAAC,MAAM,mBAAmB,CAAC;AAE5C,KAAK,oBAAoB,CAAC,KAAK,IAAI;IACjC,YAAY,EAAE,KAAK,CAAC;CACrB,CAAA;AAED,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,KAAK,SAAS,oBAAoB,CAAC,MAAM,CAAC,EACnF,QAAQ,EAAE,EAAE,CAAC,QAAQ,GACpB,CAAC,EAAE,CAAC,UAAU,GAAG,IAAI,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,oBAAoB,CAAC,KAAK,CAAC,CAAC,CAcxE;AAED,8BAAsB,oBAAoB,CAAC,MAAM,CAAE,YAAW,SAAS;IAOnE,qCAAqC;IACrC,SAAS,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI;IAChD,SAAS,CAAC,QAAQ,CAAC,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC;aAC9B,MAAM,EAAE,OAAO;IATjC,SAAS,CAAC,IAAI,EAAE,cAAc,EAAE,CAAM;IACtC,SAAS,CAAC,KAAK,EAAE,OAAO,CAAQ;IAChC,SAAS,CAAC,SAAS,EAAE,OAAO,CAAS;IAErC,2DAA2D;IAC3D,SAAS;IACP,qCAAqC;IAClB,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAC7B,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAC9B,MAAM,EAAE,OAAO;IAgCjC,OAAO,CAAC,MAAM,CAAC,aAAa,CAAc;IAC1C,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAgD;IAEzE,SAAS,CAAC,KAAK,IAAI,MAAM;IAIzB,SAAS,CAAC,OAAO,IAAI,IAAI;IAMzB,SAAS,CAAC,cAAc,IAAI,IAAI;IAIhC,SAAS,CAAC,KAAK,IAAI,IAAI;IAMhB,MAAM,EAAE,KAAK,EAAE,CAAM;IAE5B,SAAS,CAAC,WAAW,EAAE,OAAO,CAAC,IAAI,CAAC,CAAuB;IAE3D,IAAI,UAAU,IAAI,UAAU,CAAC,IAAI,CAAC,CAA6B;IAE/D,UAAU,CAAC,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI;IAI3B,aAAa,CACjB,OAAO,GAAE,MAAc,EAAE,MAAM,GAAE,MAA6B,GAC7D,OAAO,CAAC,IAAI,CAAC;CAejB"}
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@@ -1,7 +1,7 @@
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import * as grok from 'datagrok-api/grok';
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import { Subject } from 'rxjs';
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import { testEvent } from '@datagrok-libraries/utils/src/test';
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export function
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export function getGridCellColTemp(gridCell) {
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let temp = null;
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let gridCol = null;
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try {
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{"version":3,"file":"cell-renderer-back-base.js","sourceRoot":"","sources":["cell-renderer-back-base.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAI1C,OAAO,EAAa,OAAO,EAAiB,MAAM,MAAM,CAAC;AAEzD,OAAO,EAAC,SAAS,EAAC,MAAM,oCAAoC,CAAC;AAS7D,MAAM,UAAU,
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{"version":3,"file":"cell-renderer-back-base.js","sourceRoot":"","sources":["cell-renderer-back-base.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAI1C,OAAO,EAAa,OAAO,EAAiB,MAAM,MAAM,CAAC;AAEzD,OAAO,EAAC,SAAS,EAAC,MAAM,oCAAoC,CAAC;AAS7D,MAAM,UAAU,kBAAkB,CAChC,QAAqB;IAErB,IAAI,IAAI,GAAuC,IAAI,CAAC;IACpD,IAAI,OAAO,GAAyB,IAAI,CAAC;IACzC,IAAI,CAAC;QACH,OAAO,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC;QACrD,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,IAAmC,CAAC,CAAC,CAAC,IAAI,CAAC;IACtE,CAAC;IAAC,MAAM,CAAC;QAAC,CAAC,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;IAAC,CAAC;IAE3C,MAAM,QAAQ,GAAsB,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC;IACzD,IAAI,GAAG,IAAI,IAAI,QAAQ,CAAC,IAAI,CAAC;IAE7B,IAAI,CAAC,IAAI;QACP,MAAM,IAAI,KAAK,CAAC,iEAAiE,CAAC,CAAC;IACrF,OAAO,CAAC,OAAO,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAC;AACnC,CAAC;AAED,MAAM,OAAgB,oBAAoB;IAKxC,2DAA2D;IAC3D;IACE,qCAAqC;IAClB,OAA6B,EAC7B,QAA2B,EAC9B,MAAe;QAFZ,YAAO,GAAP,OAAO,CAAsB;QAC7B,aAAQ,GAAR,QAAQ,CAAmB;QAC9B,WAAM,GAAN,MAAM,CAAS;QATvB,SAAI,GAAqB,EAAE,CAAC;QAC5B,UAAK,GAAY,IAAI,CAAC;QACtB,cAAS,GAAY,KAAK,CAAC;QAwCpB,aAAQ,GAAW,EAAE,oBAAoB,CAAC,aAAa,CAAC;QAoBzE,kBAAkB;QAEX,WAAM,GAAY,EAAE,CAAC;QAElB,gBAAW,GAAkB,IAAI,OAAO,EAAQ,CAAC;QAvDzD,IAAI,IAAI,CAAC,QAAQ,IAAI,IAAI,CAAC,QAAQ,CAAC,SAAS,EAAE,CAAC;YAC7C,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,aAAa,CAAC,SAAS,CAAC,GAAG,EAAE;gBAClE,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;YACpB,CAAC,CAAC,CAAC,CAAC;QACN,CAAC;QAED,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,cAAc,CAAC,SAAS,CAAC,CAAC,SAAS,EAAE,EAAE;gBAChE,IAAI,CAAC;oBACH,MAAM,OAAO,GAAiB,SAAS,CAAC,IAAI,CAAC,SAAS,CAAC;oBACvD,IAAI,IAAI,CAAC,QAAQ,EAAE,SAAS,CAAC,EAAE,KAAK,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,SAAS;wBAC/D,IAAI,CAAC,OAAO,EAAE,CAAC;gBACnB,CAAC;gBAAC,OAAO,GAAG,EAAE,CAAC;oBAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;gBAAC,CAAC;YAC3C,CAAC,CAAC,CAAC,CAAC;QACN,CAAC;QAED,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;YACjB,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,cAAc,CAAC,SAAS,CAAC,CAAC,SAAS,EAAE,EAAE;gBAChE,IAAI,CAAC;oBACH,MAAM,SAAS,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC;oBACtC,IACE,IAAI,CAAC,OAAO,EAAE,IAAI;wBAClB,IAAI,CAAC,OAAO,CAAC,IAAI,IAAI,IAAI,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI;wBAC7C,IAAI,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,KAAK,SAAS,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,SAAS;wBAChE,IAAI,CAAC,OAAO,EAAE,CAAC;gBACnB,CAAC;gBAAC,OAAO,GAAQ,EAAE,CAAC;oBAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;gBAAC,CAAC;YAChD,CAAC,CAAC,CAAC,CAAC;QACN,CAAC;IACH,CAAC;IAKS,KAAK;QACb,OAAO,GAAG,IAAI,CAAC,WAAW,CAAC,IAAI,IAAI,IAAI,CAAC,QAAQ,GAAG,CAAC;IACtD,CAAC;IAES,OAAO;QACf,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI;YACzB,GAAG,CAAC,WAAW,EAAE,CAAC;QACpB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC;IACxB,CAAC;IAES,cAAc;QACtB,IAAI,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,CAAC,IAAI;YAAE,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,UAAU,EAAE,CAAC;IACzE,CAAC;IAES,KAAK;QACb,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC;IACrB,CAAC;IAQD,IAAI,UAAU,KAAuB,OAAO,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC;IAE/D,UAAU,CAAC,MAAe;QACxB,IAAI,CAAC,cAAc,EAAE,CAAC;IACxB,CAAC;IAED,KAAK,CAAC,aAAa,CACjB,UAAkB,KAAK,EAAE,SAAiB,GAAG,OAAO,UAAU;QAE9D,MAAM,SAAS,GAAG,GAAG,IAAI,CAAC,KAAK,EAAE,kBAAkB,CAAC;QACpD,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,2BAA2B,CAAC,CAAC;QAC3D,MAAM,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,EAAE;YAC/C,IAAI,CAAC,UAAU,EAAE,CAAC;QACpB,CAAC,EAAE,OAAO,EAAE,GAAG,SAAS,KAAK,MAAM,EAAE,CAAC,CAAC;QAEvC,kDAAkD;QAClD,IAAI,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,MAAM,GAAG,EAAE,CAAC;YACjB,MAAM,GAAG,CAAC;QACZ,CAAC;QACD,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,OAAO,CAAC,CAAC;IACzC,CAAC;;AAjDc,kCAAa,GAAW,CAAC,CAAC,AAAb,CAAc"}
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import * as DG from 'datagrok-api/dg';
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import { CellRendererBackBase } from './cell-renderer-back-base';
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const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
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|
-
{"version":3,"file":"cell-renderer-monomer-placer.js","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;
|
|
1
|
+
{"version":3,"file":"cell-renderer-monomer-placer.js","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AAGzC,OAAO,EAAC,oBAAoB,EAAC,MAAM,2BAA2B,CAAC;AAE/D,OAAO,EAAC,mBAAmB,EAAC,MAAM,gCAAgC,CAAC;AACnE,OAAO,EAAC,OAAO,EAAC,MAAM,YAAY,CAAC;AAQnC,MAAM,UAAU,SAAS,CAAC,MAAgB,EAAE,CAAS;IACnD,IAAI,cAAc,GAAW,GAAG,CAAC;IACjC,IAAI,KAAK,GAAW,CAAC,CAAC;IACtB,IAAI,MAAM,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC;IAC/B,IAAI,IAAI,CAAC;IACT,OAAO,KAAK,IAAI,MAAM,EAAE,CAAC;QACvB,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC;QACxC,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,IAAI,GAAG,CAAC,CAAC;YAC3C,OAAO,IAAI,CAAC;aACT,IAAI,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC;YACvB,MAAM,GAAG,IAAI,GAAG,CAAC,CAAC;aACf,gCAAgC;YACnC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC;QAEnB,IAAI,EAAE,cAAc,IAAI,CAAC,EAAE,CAAC;YAC1B,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,+BAA+B;gBAC9E,MAAM,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QACtC,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,MAAM,OAAO,aAAc,SAAQ,oBAA4B;IAa7D,sEAAsE;IACtE,YACE,OAA6B,EAC7B,QAA2B,EAC3B,MAAe,EACR,kBAA0B,EAChB,aAAuC;QAExD,KAAK,CAAC,OAAO,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;QAH1B,uBAAkB,GAAlB,kBAAkB,CAAQ;QAChB,kBAAa,GAAb,aAAa,CAA0B;QAlBlD,aAAQ,GAAW,CAAC,CAAC;QACrB,uBAAkB,GAAsB,IAAI,CAAC;QAErD,4BAA4B;QACpB,mBAAc,GAAG,CAAC,CAAC;QAGnB,kCAA6B,GAAW,CAAC,CAAC;QAE3C,sBAAiB,GAAmC,EAAE,CAAC,CAAC,mDAAmD;QAC3G,yBAAoB,GAAmC,EAAE,CAAC,CAAC,2CAA2C;QAW3G,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,aAAa,EAAE,CAAC;QAClC,IAAI,CAAC,cAAc,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,QAAS,CAAC,MAAM,CAAC,CAAC;QAE9D,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;YACjB,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,GAAG,EAAE;gBACjE,IAAI,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC;YAC1B,CAAC,CAAC,CAAC,CAAC;QACN,CAAC;QAED,mBAAmB,EAAE,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,EAAE;YACvC,IAAI,IAAI,CAAC,SAAS;gBAAE,OAAO;YAC3B,MAAM,UAAU,GAAG,SAAS,CAAC,aAAa,EAAE,CAAC;YAC7C,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,SAAS,CAAC,GAAG,EAAE;gBACjD,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;gBAClB,IAAI,CAAC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;YACnC,CAAC,CAAC,CAAC,CAAC;QACN,CAAC,CAAC,CAAC;IACL,CAAC;IAEkB,KAAK;QACtB,IAAI,IAAI,CAAC,aAAa;YAAE,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,aAAa,EAAE,CAAC;QAC1D,IAAI,CAAC,cAAc,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,QAAS,CAAC,MAAM,CAAC,CAAC;QAC9D,IAAI,CAAC,kBAAkB,GAAG,IAAI,CAAC;QAC/B,IAAI,CAAC,iBAAiB,GAAG,EAAE,CAAC;QAC5B,IAAI,CAAC,oBAAoB,GAAG,EAAE,CAAC;QAC/B,KAAK,CAAC,KAAK,EAAE,CAAC;IAChB,CAAC;IAED,qGAAqG;IAC9F,qBAAqB,CAAC,MAAc,EAAE,QAAgB;QAC3D,IAAI,IAAI,CAAC,QAAQ,GAAG,QAAQ,EAAE,CAAC;YAC7B,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;YACzB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;QACpB,CAAC;QACD,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;YACf,IAAI,CAAC;gBAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAAC,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACjC,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC;gBACxC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,QAAQ,CAAC,CAAC;YACjD,CAAC;QACH,CAAC;QAED,MAAM,GAAG,GAAa,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,8BAA8B,EAAE,CAAC,CAAC;YAC3F,IAAI,CAAC,2BAA2B,CAAC,MAAM,CAAC,CAAC;QAE3C,MAAM,MAAM,GAAa,IAAI,KAAK,CAAS,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;QAC3D,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU;QACzB,KAAK,IAAI,GAAG,GAAW,CAAC,EAAE,GAAG,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,EAAE;YAClD,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC;QAC/C,OAAO,CAAC,GAAG,EAAE,MAAM,CAAC,CAAC;IACvB,CAAC;IAEO,2BAA2B,CAAC,MAAc;QAChD,MAAM,SAAS,GAAG,GAAG,IAAI,CAAC,KAAK,EAAE,mCAAmC,CAAC;QACrE,4CAA4C;QAE5C,IAAI,IAAI,CAAC,kBAAkB,KAAK,IAAI,EAAE,CAAC;YACrC,IAAI,CAAC,kBAAkB,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACvE,CAAC;QAED,MAAM,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,gBAAgB,CAAC;QAChF,MAAM,mBAAmB,GAAW,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,WAAW,CAAC,CAAC;QAC3E,MAAM,KAAK,GAAiB,UAAU,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QACpF,MAAM,gBAAgB,GAAW,IAAI,CAAC,GAAG,CAAC,mBAAmB,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;QAE7E,IAAI,GAAG,GAAa,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC;QACpD,IAAI,GAAG,KAAK,IAAI,IAAI,GAAG,CAAC,MAAM,GAAG,gBAAgB,EAAE,CAAC;YAClD,GAAG,GAAG,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAS,KAAK,CAAC,MAAM,CAAC,CAAC;YAExE,IAAI,QAAQ,GAAW,CAAC,CAAC;YACzB,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,gBAAgB,EAAE,EAAE,OAAO,EAAE,CAAC;gBAC5D,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC;gBAC/C,MAAM,QAAQ,GAAW,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,WAAW,EAAE,IAAI,CAAC,kBAAkB,CAAC,CAAC;gBACzF,MAAM,cAAc,GAAG,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC;gBAC7G,MAAM,WAAW,GAAW,cAAc,GAAG,QAAQ,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,gBAAgB,CAAC;gBAC3F,GAAG,CAAC,OAAO,CAAC,GAAG,WAAW,CAAC;gBAC3B,QAAQ,IAAI,WAAW,CAAC;gBACxB,IAAI,QAAQ,GAAG,IAAI,CAAC,QAAQ;oBAAE,MAAM;YACtC,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAC;IACb,CAAC;IAEO,8BAA8B;;QACpC,MAAM,SAAS,GAAG,GAAG,IAAI,CAAC,KAAK,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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"generator.d.ts","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAe,QAAQ,EAAO,MAAM,iBAAiB,CAAC;AAGtE,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;
|
|
1
|
+
{"version":3,"file":"generator.d.ts","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAe,QAAQ,EAAO,MAAM,iBAAiB,CAAC;AAGtE,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAI3C,wBAAgB,qBAAqB,IAAI,EAAE,CAAC,MAAM,EAAE,CAQnD;AAED,sGAAsG;AACtG,wBAAgB,oBAAoB,CAAC,MAAM,GAAE,MAAgB,GAAG,EAAE,CAAC,MAAM,EAAE,CAc1E;AAED,wBAAgB,qBAAqB,CACnC,QAAQ,GAAE,QAA6B,EAAE,QAAQ,GAAE,QAAsB,EACzE,SAAS,GAAE,MAAM,GAAG,SAA+D,EACnF,UAAU,GAAE,WAAW,GAAG,SAAqB,EAC/C,OAAO,GAAE,MAAc,EAAE,QAAQ,GAAE,MAAY,EAAE,SAAS,GAAE,MAAgB,GAC3E,EAAE,CAAC,MAAM,CAqBX"}
|
package/src/utils/generator.js
CHANGED
|
@@ -1,8 +1,9 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import wu from 'wu';
|
|
3
3
|
import { ALPHABET, getAlphabet, NOTATION, TAGS } from './macromolecule';
|
|
4
|
-
import {
|
|
4
|
+
import { SeqHandler } from './seq-handler';
|
|
5
5
|
import { StringListSeqSplitted } from './macromolecule/utils';
|
|
6
|
+
import { GapOriginals } from './macromolecule/consts';
|
|
6
7
|
export function generateManySequences() {
|
|
7
8
|
const columns = [];
|
|
8
9
|
columns.push(DG.Column.fromList('string', 'MSA', new Array(10 ** 6).fill('meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me')));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"generator.js","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAE,QAAQ,EAAE,IAAI,EAAC,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAC,
|
|
1
|
+
{"version":3,"file":"generator.js","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAE,QAAQ,EAAE,IAAI,EAAC,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AACzC,OAAO,EAAC,qBAAqB,EAAC,MAAM,uBAAuB,CAAC;AAG5D,OAAO,EAAC,YAAY,EAAC,MAAM,wBAAwB,CAAC;AAEpD,MAAM,UAAU,qBAAqB;IACnC,MAAM,OAAO,GAAgB,EAAE,CAAC;IAChC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,QAAQ,EAAE,KAAK,EAC7C,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CACrB,0FAA0F,CAAC,CAAC,CAC/F,CAAC;IACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACrG,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,sGAAsG;AACtG,MAAM,UAAU,oBAAoB,CAAC,SAAiB,EAAE,IAAI,CAAC;IAC3D,MAAM,YAAY,GAChB,4DAA4D,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC3G,MAAM,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,KAAK,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;IACvG,MAAM,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;IAC1C,MAAM,CAAC,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC;IACvC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IACnC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,QAAQ,CAAC,EAAE,CAAC,CAAC;IAC1C,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,mBAAmB,EAAE,MAAM,CAAC,CAAC;IAEhD,MAAM,OAAO,GAAgB,EAAE,CAAC;IAChC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACrB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACrG,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,qBAAqB,CACnC,WAAqB,QAAQ,CAAC,SAAS,EAAE,WAAqB,QAAQ,CAAC,EAAE,EACzE,YAAgC,CAAC,QAAQ,KAAK,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,EACnF,aAAsC,SAAS,EAC/C,UAAkB,KAAK,EAAE,WAAmB,GAAG,EAAE,YAAoB,EAAE,IAAI,CAAC;IAE5E,MAAM,WAAW,GAAa,QAAQ,KAAK,QAAQ,CAAC,EAAE,CAAC,CAAC;QACtD,UAAU,EAAE,uBAAuB,sCAAsB,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;IACtG,MAAM,YAAY,GAAG,WAAW,CAAC,MAAM,CAAC;IAExC,MAAM,GAAG,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,CAAC;IACzE,GAAG,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;IACvC,GAAG,CAAC,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC;IAC1B,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;IACpC,IAAI,QAAQ,IAAI,QAAQ,CAAC,SAAS;QAAE,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,EAAE,SAAU,CAAC,CAAC;IAE3E,MAAM,EAAE,GAAG,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;IACrC,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,QAAQ,EAAE,IAAI,EAAE,EAAE,CAAC;QAC3C,MAAM,QAAQ,GAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC;aACnD,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;aAC7E,OAAO,EAAE,CAAC;QACb,MAAM,GAAG,GAAG,EAAE,CAAC,MAAM,CAAC,IAAI,qBAAqB,CAAC,QAAQ,EAAE,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnF,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;IACrB,CAAC;IAED,OAAO,GAAG,CAAC;AACb,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"alignment.d.ts","sourceRoot":"","sources":["alignment.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"alignment.d.ts","sourceRoot":"","sources":["alignment.ts"],"names":[],"mappings":"AAEA,OAAO,EAAC,YAAY,EAAC,MAAM,SAAS,CAAC;AAIrC,MAAM,MAAM,gBAAgB,GAAG;IAC7B,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,OAAO,CAAC;CACzB,CAAA;AAED,eAAO,MAAM,uBAAuB,EAAE,gBAKrC,CAAC;AAEF,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,YAAY,EAAE,GAAG,EAAE,YAAY,EACzE,gBAAgB,GAAE,OAAO,CAAC,gBAAgB,CAAM,GAC/C;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,YAAY,EAAE,YAAY,CAAC;IAAC,YAAY,EAAE,YAAY,CAAA;CAAE,CAoFxF"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import
|
|
2
|
-
import { NOTATION } from './consts';
|
|
1
|
+
import wu from 'wu';
|
|
2
|
+
import { GapOriginals, NOTATION } from './consts';
|
|
3
3
|
import { StringListSeqSplitted } from './utils';
|
|
4
4
|
export const defaultAlignmentOptions = {
|
|
5
5
|
gapPenalty: 1,
|
|
@@ -59,10 +59,10 @@ export function alignSequencePair(template, seq, alignmentOptions = {}) {
|
|
|
59
59
|
}
|
|
60
60
|
}
|
|
61
61
|
}
|
|
62
|
-
alignedTemplate = [...
|
|
63
|
-
...(options.localAlignment ?
|
|
64
|
-
alignedSeq = [...
|
|
65
|
-
...(options.localAlignment ?
|
|
62
|
+
alignedTemplate = [...wu.count(0).take(i).map((pos) => template.getCanonical(pos)), ...alignedTemplate.reverse(),
|
|
63
|
+
...(options.localAlignment ? wu.count(index[0]).take(templateLen).map((pos) => template.getCanonical(pos)) : [])];
|
|
64
|
+
alignedSeq = [...wu.count(0).take(j).map((pos) => seq.getCanonical(pos)), ...alignedSeq.reverse(),
|
|
65
|
+
...(options.localAlignment ? wu.count(index[1]).take(seqLen).map((pos) => seq.getCanonical(pos)) : [])];
|
|
66
66
|
const templateStart = i;
|
|
67
67
|
const seqStart = j;
|
|
68
68
|
if (templateStart > seqStart)
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"alignment.js","sourceRoot":"","sources":["alignment.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"alignment.js","sourceRoot":"","sources":["alignment.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAC;AAGpB,OAAO,EAAC,YAAY,EAAE,QAAQ,EAAC,MAAM,UAAU,CAAC;AAChD,OAAO,EAAC,qBAAqB,EAAC,MAAM,SAAS,CAAC;AAS9C,MAAM,CAAC,MAAM,uBAAuB,GAAqB;IACvD,UAAU,EAAE,CAAC;IACb,UAAU,EAAE,CAAC;IACb,SAAS,EAAE,YAAY,CAAC,QAAQ,CAAC,KAAK,CAAC;IACvC,cAAc,EAAE,KAAK;CACtB,CAAC;AAEF,MAAM,UAAU,iBAAiB,CAAC,QAAsB,EAAE,GAAiB,EACzE,mBAA8C,EAAE;IAEhD,MAAM,OAAO,GAAG,EAAC,GAAG,uBAAuB,EAAE,GAAG,gBAAgB,EAAC,CAAC;IAElE,SAAS,OAAO,CAAC,GAAW,EAAE,GAAW;QACvC,OAAO,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC;IAChE,CAAC;IAED,MAAM,WAAW,GAAG,QAAQ,CAAC,MAAM,CAAC;IACpC,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC;IAE1B,MAAM,MAAM,GAAG,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;IAEnF,IAAI,QAAQ,GAAG,CAAC,IAAI,CAAC;IACrB,IAAI,KAAK,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YACpC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EACvB,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EACrF,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,UAAU,EACrC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,OAAO,CAAC,UAAU,CAAC,CAAC;YACzC,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,QAAQ,EAAE,CAAC;gBAC7B,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBACxB,KAAK,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YACjB,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,CAAC,GAAG,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC;IACxD,IAAI,CAAC,GAAG,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IACnD,IAAI,eAAe,GAAG,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC;IAC3C,IAAI,UAAU,GAAG,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC;IAEtC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QACtB,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QAE9E,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,OAAO,CAAC,UAAU,IAAI,EAAE,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YAC5F,eAAe,CAAC,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;YACnD,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;YACzC,CAAC,IAAI,CAAC,CAAC;YACP,CAAC,IAAI,CAAC,CAAC;QACT,CAAC;aAAM,CAAC;YACN,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,UAAU,EAAE,CAAC;gBAC1D,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;gBACnC,eAAe,CAAC,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;gBACnD,CAAC,IAAI,CAAC,CAAC;YACT,CAAC;iBAAM,CAAC;gBACN,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,OAAO,CAAC,UAAU,EAAE,CAAC;oBAC1D,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;oBACxC,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;oBACzC,CAAC,IAAI,CAAC,CAAC;gBACT,CAAC;qBAAM,CAAC;oBACN,eAAe,CAAC,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;oBACnD,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;oBACzC,CAAC,IAAI,CAAC,CAAC;oBACP,CAAC,IAAI,CAAC,CAAC;gBACT,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,eAAe,GAAG,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,eAAe,CAAC,OAAO,EAAE;QAC9G,GAAG,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IACpH,UAAU,GAAG,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,UAAU,CAAC,OAAO,EAAE;QAC/F,GAAG,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IAE1G,MAAM,aAAa,GAAG,CAAC,CAAC;IACxB,MAAM,QAAQ,GAAG,CAAC,CAAC;IAEnB,IAAI,aAAa,GAAG,QAAQ;QAC1B,UAAU,GAAG,CAAC,GAAG,IAAI,KAAK,CAAC,aAAa,GAAG,QAAQ,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC,EAAE,GAAG,UAAU,CAAC,CAAC;;QAEvG,eAAe,GAAG,CAAC,GAAG,IAAI,KAAK,CAAC,QAAQ,GAAG,aAAa,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC,EAAE,GAAG,eAAe,CAAC,CAAC;IAGnH,IAAI,UAAU,CAAC,MAAM,GAAG,eAAe,CAAC,MAAM;QAC5C,eAAe,CAAC,IAAI,CAAC,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,eAAe,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC;;QAEjH,UAAU,CAAC,IAAI,CAAC,GAAG,IAAI,KAAK,CAAC,eAAe,CAAC,MAAM,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC;IAE9G,OAAO;QACL,IAAI,EAAE,eAAe,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9B,IAAI,EAAE,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,YAAY,EAAE,IAAI,qBAAqB,CAAC,eAAe,EAAE,OAAO,CAAC,SAAS,CAAC;QAC3E,YAAY,EAAE,IAAI,qBAAqB,CAAC,UAAU,EAAE,OAAO,CAAC,SAAS,CAAC;KACvE,CAAC;AACJ,CAAC"}
|
|
@@ -39,4 +39,9 @@ export declare const Alphabets: {
|
|
|
39
39
|
};
|
|
40
40
|
};
|
|
41
41
|
export declare const candidateAlphabets: CandidateType[];
|
|
42
|
+
/** Canonical gap symbol */
|
|
43
|
+
export declare const GAP_SYMBOL: string;
|
|
44
|
+
export declare const GapOriginals: {
|
|
45
|
+
[units: string]: string;
|
|
46
|
+
};
|
|
42
47
|
//# sourceMappingURL=consts.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,oBAAY,QAAQ;IAClB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;CACrB;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,MAA0C,CAAC;AAChE,eAAO,MAAM,SAAS,EAAE,MAAyB,CAAC;AAElD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC;AAEF,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,eAAO,MAAM,YAAY,EAAE;IACzB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAKxB,CAAC"}
|
|
@@ -47,4 +47,11 @@ export const candidateAlphabets = [
|
|
|
47
47
|
new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),
|
|
48
48
|
new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),
|
|
49
49
|
];
|
|
50
|
+
/** Canonical gap symbol */
|
|
51
|
+
export const GAP_SYMBOL = '';
|
|
52
|
+
export const GapOriginals = {
|
|
53
|
+
[NOTATION.FASTA]: '-',
|
|
54
|
+
[NOTATION.SEPARATOR]: '',
|
|
55
|
+
[NOTATION.HELM]: '*',
|
|
56
|
+
};
|
|
50
57
|
//# sourceMappingURL=consts.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,MAAM,CAAN,IAAY,QAIX;AAJD,WAAY,QAAQ;IAClB,2BAAe,CAAA;IACf,mCAAuB,CAAA;IACvB,yBAAa,CAAA;AACf,CAAC,EAJW,QAAQ,KAAR,QAAQ,QAInB;AAOD,MAAM,CAAN,IAAY,QAMX;AAND,WAAY,QAAQ;IAClB,uBAAW,CAAA;IACX,uBAAW,CAAA;IACX,qBAAS,CAAA;IACT,cAAc;IACd,qBAAS,CAAA;AACX,CAAC,EANW,QAAQ,KAAR,QAAQ,QAMnB;AAED,MAAM,CAAN,IAAY,IAUX;AAVD,WAAY,IAAI;IACd,2BAAmB,CAAA;IACnB,6BAAqB,CAAA;IACrB,sCAA8B,CAAA;IAC9B,oDAA4C,CAAA;IAC5C,+BAAuB,CAAA;IACvB,8CAAsC,CAAA;IACtC,wCAAgC,CAAA;IAChC,0CAAkC,CAAA;IAClC,4BAAoB,CAAA;AACtB,CAAC,EAVW,IAAI,KAAJ,IAAI,QAUf;AAED,MAAM,CAAC,MAAM,iBAAiB,GAAW,IAAI,CAAC;AAE9C,MAAM,CAAC,MAAM,SAAS,GAAW,4CAA4C,CAAC;AAE9E,MAAM,CAAC,MAAM,MAAM,GAAW,iCAAiC,CAAC;AAChE,MAAM,CAAC,MAAM,SAAS,GAAW,gBAAgB,CAAC;AAElD,MAAM,CAAC,MAAM,SAAS,GAAG,IAAI;IAAA;QAC3B,UAAK,GAAG;YACN,OAAO,EAAE,IAAI,GAAG,CAAS;gBACvB,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;gBAChD,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;aACjD,CAAC;YACF,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC1C,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;SAC3C,CAAC;IACJ,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAC,MAAM,kBAAkB,GAAoB;IACjD,IAAI,aAAa,CAAC,QAAQ,CAAC,EAAE,EAAE,SAAS,CAAC,KAAK,CAAC,OAAO,EAAE,IAAI,CAAC;IAC7D,IAAI,aAAa,CAAC,QAAQ,CAAC,GAAG,EAAE,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;IAC1D,IAAI,aAAa,CAAC,QAAQ,CAAC,GAAG,EAAE,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;CAC3D,CAAC;AAEF,2BAA2B;AAC3B,MAAM,CAAC,MAAM,UAAU,GAAW,EAAE,CAAC;AAErC,MAAM,CAAC,MAAM,YAAY,GAErB;IACF,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,GAAG;IACrB,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,EAAE;IACxB,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,GAAG;CACrB,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"scoring.d.ts","sourceRoot":"","sources":["scoring.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,
|
|
1
|
+
{"version":3,"file":"scoring.d.ts","sourceRoot":"","sources":["scoring.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,YAAY,EAAC,MAAM,iCAAiC,CAAC;AAK7D,oBAAY,KAAK;IACf,QAAQ,aAAa;IACrB,UAAU,eAAe;CAC1B;AAED;;;;;iDAKiD;AACjD,wBAAsB,eAAe,CACnC,KAAK,EAAE,EAAE,CAAC,SAAS,EAAE,GAAG,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,OAAO,EAAE,KAAK,GACvE,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAc5B;AAED;;;iDAGiD;AACjD,wBAAgB,iBAAiB,CAAC,SAAS,EAAE,YAAY,EAAE,WAAW,EAAE,EAAE,CAAC,SAAS,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CA4BvG;AAED;;;gDAGgD;AAChD,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,YAAY,EAAE,WAAW,EAAE,EAAE,CAAC,SAAS,GACjD,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAI5B"}
|
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import { sequenceChemSimilarity } from '../../monomer-works/monomer-utils';
|
|
3
|
-
import { GAP_SYMBOL } from '../../utils/macromolecule/types';
|
|
4
3
|
import { splitAlignedSequences } from '../splitter';
|
|
5
4
|
import { SeqHandler } from '../seq-handler';
|
|
5
|
+
import { GAP_SYMBOL } from './consts';
|
|
6
6
|
export var SCORE;
|
|
7
7
|
(function (SCORE) {
|
|
8
8
|
SCORE["IDENTITY"] = "identity";
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"scoring.js","sourceRoot":"","sources":["scoring.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,sBAAsB,EAAC,MAAM,mCAAmC,CAAC;
|
|
1
|
+
{"version":3,"file":"scoring.js","sourceRoot":"","sources":["scoring.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,sBAAsB,EAAC,MAAM,mCAAmC,CAAC;AAEzE,OAAO,EAAC,qBAAqB,EAAC,MAAM,aAAa,CAAC;AAClD,OAAO,EAAC,UAAU,EAAC,MAAM,gBAAgB,CAAC;AAC1C,OAAO,EAAC,UAAU,EAAC,MAAM,UAAU,CAAC;AAEpC,MAAM,CAAN,IAAY,KAGX;AAHD,WAAY,KAAK;IACf,8BAAqB,CAAA;IACrB,kCAAyB,CAAA;AAC3B,CAAC,EAHW,KAAK,KAAL,KAAK,QAGhB;AAED;;;;;iDAKiD;AACjD,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,KAAmB,EAAE,GAAsB,EAAE,GAAW,EAAE,OAAc;IAExE,MAAM,UAAU,GAAG,qBAAqB,CAAC,GAAG,CAAC,CAAC;IAC9C,MAAM,KAAK,GAAG,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;IACxC,MAAM,MAAM,GAAG,KAAK,CAAC,oBAAoB,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC;IACxD,MAAM,KAAK,GAAG,UAAU,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC;IAC3C,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,cAAc;IAExD,MAAM,SAAS,GAAG,OAAO,KAAK,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC;QACzF,OAAO,KAAK,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,mBAAmB,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3F,IAAI,SAAS,KAAK,IAAI;QACpB,MAAM,IAAI,KAAK,CAAC,oDAAoD,OAAO,EAAE,CAAC,CAAC;IACjF,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,aAAa,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IAC7D,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;IAC7B,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;iDAGiD;AACjD,MAAM,UAAU,iBAAiB,CAAC,SAAuB,EAAE,WAAyB;IAClF,MAAM,YAAY,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC;IAChD,MAAM,YAAY,GAAkB,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAC5D,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAClE,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAElE,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,YAAY,EAAE,EAAE,MAAM,EAAE,CAAC;QACrD,MAAM,MAAM,GAAG,WAAW,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACnD,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,EAAiB,CAAC;QAC1D,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QAChE,MAAM,IAAI,GAAG,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC;QACpF,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACpE,CAAC;IAED,MAAM,iBAAiB,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,WAAW,CAAC,QAAQ,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,UAAU,EAAE,CAAC;IAC1D,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,WAAW,CAAC,QAAQ,EAAE,EAAE,QAAQ,EAAE,CAAC;QACnE,kBAAkB,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;QACjC,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;YACzD,MAAM,WAAW,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC;YACzC,MAAM,aAAa,GAAW,WAAW,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC/E,IAAI,aAAa,KAAK,uBAAuB,CAAC,MAAM,CAAC;gBACnD,EAAE,kBAAkB,CAAC,QAAQ,CAAC,CAAC;QACnC,CAAC;QACD,kBAAkB,CAAC,QAAQ,CAAC,IAAI,SAAS,CAAC,MAAM,CAAC;IACnD,CAAC;IAED,OAAO,iBAAiB,CAAC;AAC3B,CAAC;AAED;;;gDAGgD;AAChD,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,SAAuB,EAAE,WAAyB;IAElD,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,EAAyB,CAAC;IAC3E,MAAM,SAAS,GAAG,MAAM,sBAAsB,CAAC,cAAc,EAAE,SAAS,CAAC,CAAC;IAC1E,OAAO,SAAS,CAAC;AACnB,CAAC"}
|
|
@@ -1,10 +1,6 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
|
-
/** Canonical gap symbol */
|
|
3
|
-
export declare const GAP_SYMBOL: string;
|
|
4
2
|
export type SeqSplittedBase = ArrayLike<string> & Iterable<string>;
|
|
5
3
|
export interface ISeqSplitted {
|
|
6
|
-
get canonicals(): SeqSplittedBase;
|
|
7
|
-
get originals(): SeqSplittedBase;
|
|
8
4
|
isGap(posIdx: number): boolean;
|
|
9
5
|
/** */
|
|
10
6
|
getCanonical(posIdx: number): string;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;
|
|
1
|
+
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,MAAM,MAAM,eAAe,GAAG,SAAS,CAAC,MAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;AAEnE,MAAM,WAAW,YAAY;IAC3B,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B,MAAM;IACN,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAErC,uEAAuE;IACvE,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAEpC,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,QAAQ,IAAI,YAAY,CAAC;IAE7B,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;CAC/E;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,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AA4BA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}
|
|
@@ -6,8 +6,6 @@ export declare class StringListSeqSplitted implements ISeqSplitted {
|
|
|
6
6
|
private readonly mList;
|
|
7
7
|
private readonly gapOriginalMonomer;
|
|
8
8
|
get length(): number;
|
|
9
|
-
get canonicals(): SeqSplittedBase;
|
|
10
|
-
get originals(): SeqSplittedBase;
|
|
11
9
|
isGap(posIdx: number): boolean;
|
|
12
10
|
getCanonical(posIdx: number): string;
|
|
13
11
|
getOriginal(posIdx: number): string;
|
|
@@ -16,8 +14,6 @@ export declare class StringListSeqSplitted implements ISeqSplitted {
|
|
|
16
14
|
export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
|
|
17
15
|
private readonly seqS;
|
|
18
16
|
get length(): number;
|
|
19
|
-
get canonicals(): string;
|
|
20
|
-
get originals(): string;
|
|
21
17
|
isGap(posIdx: number): boolean;
|
|
22
18
|
getCanonical(posIdx: number): string;
|
|
23
19
|
getOriginal(posIdx: number): string;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAEL,aAAa,
|
|
1
|
+
{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAEL,aAAa,EAAE,YAAY,EAC3B,YAAY,EACZ,WAAW,EAAE,eAAe,EAC5B,YAAY,EACb,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,QAAQ,EAA+E,MAAM,UAAU,CAAC;AAIhH,OAAO,EAAC,UAAU,EAAC,MAAM,oBAAoB,CAAC;AAK9C,qBAAa,qBAAsB,YAAW,YAAY;IAqBtD,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,kBAAkB;IArBrC,IAAI,MAAM,IAAI,MAAM,CAA8B;IAElD,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO;IAI9B,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;IAOpC,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;gBAOhB,KAAK,EAAE,eAAe,EACtB,kBAAkB,EAAE,MAAM;CAE9C;AAED,qBAAa,sBAAuB,YAAW,YAAY;IAsBvD,OAAO,CAAC,QAAQ,CAAC,IAAI;IArBvB,IAAI,MAAM,IAAI,MAAM,CAA6B;IAEjD,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO;IAI9B,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;IAQpC,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;gBAOhB,IAAI,EAAE,MAAM;CAEhC;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,YAAY,GAAG,WAAW,CAKhH;AAyBD;;;;GAIG;AACH,eAAO,MAAM,eAAe,EAAE,YAc7B,CAAC;AAEF,eAAO,MAAM,qBAAqB,EAAE,YAEnC,CAAC;AAEF;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,GAAE,MAAM,GAAG,SAAqB,GAAG,YAAY,CAuB/G;AAMD;;;;;GAKG;AACH,eAAO,MAAM,cAAc,EAAE,YAgB5B,CAAC;AAEF,4EAA4E;AAC5E,MAAM,MAAM,kBAAkB,GAAG,CAAC,YAAY,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,MAAM,CAAC;AAEjF;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,KAAK,GAAE,MAAM,GAAG,SAAqB,GAAG,YAAY,CAWjH;AAID,+CAA+C;AAC/C,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,MAAM,CAQhF;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,+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,CAWhE;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,IAAI,CASvE"}
|
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import wu from 'wu';
|
|
3
|
-
import { CandidateSimType
|
|
4
|
-
import { ALPHABET, Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
|
|
5
|
-
import {
|
|
3
|
+
import { CandidateSimType } from './types';
|
|
4
|
+
import { ALPHABET, Alphabets, candidateAlphabets, GAP_SYMBOL, GapOriginals, monomerRe, NOTATION } from './consts';
|
|
5
|
+
import { SeqHandler } from '../seq-handler';
|
|
6
6
|
import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
|
|
7
7
|
import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
|
|
8
8
|
import { AminoacidsPalettes } from '../../aminoacids';
|
|
@@ -10,15 +10,14 @@ import { NucleotidesPalettes } from '../../nucleotides';
|
|
|
10
10
|
import { UnknownSeqPalettes } from '../../unknown';
|
|
11
11
|
export class StringListSeqSplitted {
|
|
12
12
|
get length() { return this.mList.length; }
|
|
13
|
-
get canonicals() { return this.mList; }
|
|
14
|
-
get originals() { return this.mList; }
|
|
15
13
|
isGap(posIdx) {
|
|
16
14
|
return this.getOriginal(posIdx) === this.gapOriginalMonomer;
|
|
17
15
|
}
|
|
18
16
|
getCanonical(posIdx) {
|
|
19
17
|
if (this.length <= posIdx)
|
|
20
18
|
throw new Error('Index out of bounds');
|
|
21
|
-
|
|
19
|
+
const om = this.mList[posIdx];
|
|
20
|
+
return om !== this.gapOriginalMonomer ? om : GAP_SYMBOL;
|
|
22
21
|
}
|
|
23
22
|
getOriginal(posIdx) {
|
|
24
23
|
if (this.length <= posIdx)
|
|
@@ -32,8 +31,6 @@ export class StringListSeqSplitted {
|
|
|
32
31
|
}
|
|
33
32
|
export class FastaSimpleSeqSplitted {
|
|
34
33
|
get length() { return this.seqS.length; }
|
|
35
|
-
get canonicals() { return this.seqS; }
|
|
36
|
-
get originals() { return this.seqS; }
|
|
37
34
|
isGap(posIdx) {
|
|
38
35
|
return this.getOriginal(posIdx) === GapOriginals[NOTATION.FASTA];
|
|
39
36
|
}
|
|
@@ -69,13 +66,14 @@ function getStats(splitted, minLength) {
|
|
|
69
66
|
const freq = {};
|
|
70
67
|
let sameLength = true;
|
|
71
68
|
let firstLength = null;
|
|
72
|
-
for (const
|
|
69
|
+
for (const seqSS of splitted) {
|
|
73
70
|
if (firstLength == null)
|
|
74
|
-
firstLength =
|
|
75
|
-
else if (
|
|
71
|
+
firstLength = seqSS.length;
|
|
72
|
+
else if (seqSS.length !== firstLength)
|
|
76
73
|
sameLength = false;
|
|
77
|
-
if (
|
|
78
|
-
for (
|
|
74
|
+
if (seqSS.length >= minLength) {
|
|
75
|
+
for (let posIdx = 0; posIdx < seqSS.length; ++posIdx) {
|
|
76
|
+
const cm = seqSS.getCanonical(posIdx);
|
|
79
77
|
if (!(cm in freq))
|
|
80
78
|
freq[cm] = 0;
|
|
81
79
|
freq[cm] += 1;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
|
@@ -8,9 +8,6 @@ export declare const SeqTemps: {
|
|
|
8
8
|
seqHandler: string;
|
|
9
9
|
notationProvider: string;
|
|
10
10
|
};
|
|
11
|
-
export declare const GapOriginals: {
|
|
12
|
-
[units: string]: string;
|
|
13
|
-
};
|
|
14
11
|
export type ConvertFunc = (src: string) => string;
|
|
15
12
|
export type JoinerFunc = (src: ISeqSplitted) => string;
|
|
16
13
|
/** Class for handling notation units in Macromolecule columns and
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"seq-handler.d.ts","sourceRoot":"","sources":["seq-handler.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,
|
|
1
|
+
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|
package/src/utils/seq-handler.js
CHANGED
|
@@ -1,11 +1,11 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import wu from 'wu';
|
|
3
3
|
import { ALPHABET, candidateAlphabets, getSplitterWithSeparator, NOTATION, positionSeparator, splitterAsFasta, splitterAsHelm, TAGS } from './macromolecule';
|
|
4
|
-
import { GAP_SYMBOL, } from './macromolecule/types';
|
|
5
4
|
import { detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted } from './macromolecule/utils';
|
|
6
5
|
import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
|
|
7
6
|
import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
|
|
8
7
|
import { HELM_WRAPPERS_REGEXP, PHOSPHATE_SYMBOL } from './const';
|
|
8
|
+
import { GAP_SYMBOL, GapOriginals } from './macromolecule/consts';
|
|
9
9
|
export const SeqTemps = new class {
|
|
10
10
|
constructor() {
|
|
11
11
|
/** Column's temp slot name for a SeqHandler object */
|
|
@@ -13,11 +13,6 @@ export const SeqTemps = new class {
|
|
|
13
13
|
this.notationProvider = `seq-handler.notation-provider`;
|
|
14
14
|
}
|
|
15
15
|
}();
|
|
16
|
-
export const GapOriginals = {
|
|
17
|
-
[NOTATION.FASTA]: '-',
|
|
18
|
-
[NOTATION.SEPARATOR]: '',
|
|
19
|
-
[NOTATION.HELM]: '*',
|
|
20
|
-
};
|
|
21
16
|
/** Class for handling notation units in Macromolecule columns and
|
|
22
17
|
* conversion of notation systems in Macromolecule columns
|
|
23
18
|
*/
|
|
@@ -245,7 +240,8 @@ export class SeqHandler {
|
|
|
245
240
|
firstLength = mSeq.length;
|
|
246
241
|
else if (mSeq.length !== firstLength)
|
|
247
242
|
sameLength = false;
|
|
248
|
-
for (
|
|
243
|
+
for (let posIdx = 0; posIdx < mSeq.length; ++posIdx) {
|
|
244
|
+
const cm = mSeq.getCanonical(posIdx);
|
|
249
245
|
if (!(cm in freq))
|
|
250
246
|
freq[cm] = 0;
|
|
251
247
|
freq[cm] += 1;
|
|
@@ -324,7 +320,7 @@ export class SeqHandler {
|
|
|
324
320
|
getNewColumn(tgtNotation, tgtSeparator, colName, data) {
|
|
325
321
|
const col = this.column;
|
|
326
322
|
const name = tgtNotation.toLowerCase() + '(' + col.name + ')';
|
|
327
|
-
const newColName = colName ?? col.dataFrame
|
|
323
|
+
const newColName = colName ?? col.dataFrame?.columns.getUnusedName(name) ?? name;
|
|
328
324
|
const newColumn = DG.Column.fromList('string', newColName, data ?? new Array(this.column.length).fill(''));
|
|
329
325
|
newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
|
|
330
326
|
newColumn.meta.units = tgtNotation;
|
|
@@ -473,8 +469,9 @@ export class SeqHandler {
|
|
|
473
469
|
const catI = colRawData[rowIdx];
|
|
474
470
|
if (!(catI in catIdxSet)) {
|
|
475
471
|
catIdxSet.add(catI);
|
|
476
|
-
const
|
|
477
|
-
for (
|
|
472
|
+
const seqSS = this.getSplitted(rowIdx);
|
|
473
|
+
for (let posIdx = 0; posIdx < seqSS.length; ++posIdx) {
|
|
474
|
+
const cm = seqSS.getCanonical(posIdx);
|
|
478
475
|
if (!peptidesSet.has(cm)) {
|
|
479
476
|
this.column.setTag(TAGS.isHelmCompatible, 'false');
|
|
480
477
|
return false;
|