@datagrok-libraries/bio 5.40.7 → 5.41.0
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 -0
- package/package.json +5 -5
- package/src/helm/helm-helper.d.ts +3 -2
- package/src/helm/helm-helper.d.ts.map +1 -1
- package/src/helm/helm-helper.js.map +1 -1
- package/src/helm/types.d.ts +3 -24
- package/src/helm/types.d.ts.map +1 -1
- package/src/helm/types.js +1 -1
- package/src/helm/types.js.map +1 -1
- package/src/types/dojo.d.ts +4 -0
- package/src/types/dojo.d.ts.map +1 -0
- package/src/types/dojo.js +2 -0
- package/src/types/dojo.js.map +1 -0
- package/src/types/helm.d.ts +83 -0
- package/src/types/helm.d.ts.map +1 -0
- package/src/types/helm.js +2 -0
- package/src/types/helm.js.map +1 -0
- package/src/types/index.d.ts +2 -0
- package/src/types/index.d.ts.map +1 -1
- package/src/types/index.js.map +1 -1
- package/src/types/jsdraw2.d.ts +44 -0
- package/src/types/jsdraw2.d.ts.map +1 -0
- package/src/types/jsdraw2.js +2 -0
- package/src/types/jsdraw2.js.map +1 -0
- package/src/utils/cell-renderer-async-base.d.ts +94 -0
- package/src/utils/cell-renderer-async-base.d.ts.map +1 -0
- package/src/utils/cell-renderer-async-base.js +406 -0
- package/src/utils/cell-renderer-async-base.js.map +1 -0
- package/src/utils/cell-renderer-back-base.d.ts +26 -0
- package/src/utils/cell-renderer-back-base.d.ts.map +1 -0
- package/src/utils/cell-renderer-back-base.js +80 -0
- package/src/utils/cell-renderer-back-base.js.map +1 -0
- package/src/utils/cell-renderer-monomer-placer.d.ts +5 -6
- package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
- package/src/utils/cell-renderer-monomer-placer.js +25 -44
- package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
- package/src/viewers/helm-service.d.ts +17 -0
- package/src/viewers/helm-service.d.ts.map +1 -0
- package/src/viewers/helm-service.js +19 -0
- package/src/viewers/helm-service.js.map +1 -0
- package/src/viewers/ngl-gl-service.d.ts +7 -27
- package/src/viewers/ngl-gl-service.d.ts.map +1 -1
- package/src/viewers/ngl-gl-service.js +8 -1
- package/src/viewers/ngl-gl-service.js.map +1 -1
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@@ -1,13 +1,12 @@
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-
import * as grok from 'datagrok-api/grok';
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import * as DG from 'datagrok-api/dg';
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import wu from 'wu';
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import { SeqHandler } from './seq-handler';
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-
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import { CellRendererBackBase } from './cell-renderer-back-base';
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export class MonomerPlacer extends CellRendererBackBase {
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get updated() { return this._updated; }
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/** View is required to subscribe and handle for data frame changes */
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constructor(
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this.col = col;
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constructor(gridCol, tableCol, logger, propsProvider) {
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super(gridCol, tableCol, logger);
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this.propsProvider = propsProvider;
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this._monomerLengthList = null;
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// width of separator symbol
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@@ -15,38 +14,19 @@ export class MonomerPlacer {
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this._updated = false;
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this._monomerLengthMap = {}; // caches the lengths to save time on g.measureText
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this._monomerStructureMap = {}; // caches the atomic structures of monomers
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this.subs = [];
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this.props = this.propsProvider();
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this._rowsProcessed = DG.BitSet.create(this.
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try {
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this.props = this.propsProvider();
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this._monomerLengthList = null;
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this._rowsProcessed = DG.BitSet.create(this.col.length);
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}
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catch (err) {
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console.error(err);
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}
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}));
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this.subs.push(this.props.monomerLib.onChanged.subscribe(() => {
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this._monomerStructureMap = {};
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}));
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this.subs.push(grok.events.onViewRemoved.subscribe((view) => {
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try {
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if (this.grid?.view?.id === view.id)
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this.destroy();
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}
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catch (err) {
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console.error(err);
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}
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}));
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}
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this._rowsProcessed = DG.BitSet.create(this.tableCol.length);
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this.subs.push(this.props.monomerLib.onChanged.subscribe(() => {
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this.reset();
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}));
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}
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reset() {
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if (this.propsProvider)
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this.props = this.propsProvider();
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this._rowsProcessed = DG.BitSet.create(this.tableCol.length);
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this._monomerLengthList = null;
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this._monomerLengthMap = {};
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this._monomerStructureMap = {};
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}
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/** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
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getCellMonomerLengths(rowIdx) {
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@@ -60,12 +40,12 @@ export class MonomerPlacer {
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}
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getCellMonomerLengthsForSeq(rowIdx) {
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if (this._monomerLengthList === null) {
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this._monomerLengthList = new Array(this.
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this._monomerLengthList = new Array(this.tableCol.length).fill(null);
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this._updated = true;
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}
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let res = this._monomerLengthList[rowIdx];
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if (res === null) {
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const seqMonList = SeqHandler.forColumn(this.
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const seqMonList = SeqHandler.forColumn(this.tableCol).getSplitted(rowIdx).originals;
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res = this._monomerLengthList[rowIdx] = new Array(seqMonList.length);
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for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
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const shortMon = this.props.monomerToShort(seqMonLabel, this.props.monomerLengthLimit);
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@@ -89,23 +69,24 @@ export class MonomerPlacer {
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// const endIdx = Math.min(Math.ceil((this.grid?.vertScroll.max ?? 0) + 10), this.col.length);
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const { startIdx, endIdx } = (() => {
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try {
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const grid = this.gridCol && this.gridCol.dart ? this.gridCol.grid : null;
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if (grid && grid.dart) {
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return {
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startIdx: Math.max(Math.floor((
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endIdx: Math.min(Math.ceil((
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startIdx: Math.max(Math.floor((grid?.vertScroll.min ?? 0) - 10), 0),
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endIdx: Math.min(Math.ceil((grid?.vertScroll.max ?? 0) + 10), this.tableCol.length)
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};
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}
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else
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return { startIdx: 0, endIdx: Math.min(this.
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return { startIdx: 0, endIdx: Math.min(this.tableCol.length, 10) };
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}
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catch (_e) {
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return { startIdx: 0, endIdx: Math.min(this.
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return { startIdx: 0, endIdx: Math.min(this.tableCol.length, 10) };
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}
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})();
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for (let seqIdx = startIdx; seqIdx < endIdx; seqIdx++) {
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if (this._rowsProcessed.get(seqIdx))
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continue;
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const seqMonList = SeqHandler.forColumn(this.
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const seqMonList = SeqHandler.forColumn(this.tableCol).getSplitted(seqIdx).originals;
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if (seqMonList.length > res.length)
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res.push(...new Array(seqMonList.length - res.length).fill(0));
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for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
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@@ -120,7 +101,7 @@ export class MonomerPlacer {
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/** Returns seq position for pointer x */
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getPosition(rowIdx, x) {
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const [_monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx);
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const sh = SeqHandler.forColumn(this.
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const sh = SeqHandler.forColumn(this.tableCol);
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const seqMonList = wu(sh.getSplitted(rowIdx).originals).toArray();
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if (seqMonList.length === 0)
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return null;
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@@ -1 +1 @@
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{"version":3,"file":"cell-renderer-monomer-placer.js","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"
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+
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@@ -0,0 +1,17 @@
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import * as DG from 'datagrok-api/dg';
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import '../types/jsdraw2';
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import * as JSDraw2 from 'JSDraw2';
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import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
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export declare class HelmProps extends PropsBase {
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readonly helm: string;
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constructor(helm: string, backColor: number, width: number, height: number);
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}
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export type HelmAux = {
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/** The molecule made of atoms (monomers) and bonds */ mol: JSDraw2.IEditorMol;
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/** SVG bounding box */ bBox: DG.Rect;
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/** Cell box {0, 0, w, h} */ cBox: DG.Rect;
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};
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export declare abstract class HelmServiceBase extends RenderServiceBase<HelmProps, HelmAux> {
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}
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16
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export declare function getHelmService(): Promise<HelmServiceBase>;
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//# sourceMappingURL=helm-service.d.ts.map
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@@ -0,0 +1 @@
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1
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{"version":3,"file":"helm-service.d.ts","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,kBAAkB,CAAC;AAC1B,OAAO,KAAK,OAAO,MAAM,SAAS,CAAC;AAEnC,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,qBAAa,SAAU,SAAQ,SAAS;aAEpB,IAAI,EAAE,MAAM;gBAAZ,IAAI,EAAE,MAAM,EAC5B,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAInD;AAED,MAAM,MAAM,OAAO,GAAG;IACpB,sDAAsD,CAAC,GAAG,EAAE,OAAO,CAAC,UAAU,CAAC;IAC/E,uBAAuB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;IACtC,4BAA4B,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;CAC5C,CAAA;AAED,8BAAsB,eAAgB,SAAQ,iBAAiB,CAAC,SAAS,EAAE,OAAO,CAAC;CAAG;AAEtF,wBAAsB,cAAc,IAAI,OAAO,CAAC,eAAe,CAAC,CAO/D"}
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@@ -0,0 +1,19 @@
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1
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+
import * as DG from 'datagrok-api/dg';
|
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2
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+
import '../types/jsdraw2';
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3
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+
import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
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4
|
+
export class HelmProps extends PropsBase {
|
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5
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+
constructor(helm, backColor, width, height) {
|
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6
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super(backColor, width, height);
|
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7
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this.helm = helm;
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8
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}
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}
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10
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export class HelmServiceBase extends RenderServiceBase {
|
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}
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+
export async function getHelmService() {
|
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13
|
+
const funcList = DG.Func.find({ package: 'Helm', name: 'getHelmService' });
|
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14
|
+
if (funcList.length === 0)
|
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15
|
+
throw new Error('Package "Helm" must be installed for Helm services.');
|
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16
|
+
const svc = (await funcList[0].prepare().call()).getOutputParamValue();
|
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17
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return svc;
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}
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//# sourceMappingURL=helm-service.js.map
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@@ -0,0 +1 @@
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1
|
+
{"version":3,"file":"helm-service.js","sourceRoot":"","sources":["helm-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,kBAAkB,CAAC;AAG1B,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,MAAM,OAAO,SAAU,SAAQ,SAAS;IACtC,YACkB,IAAY,EAC5B,SAAiB,EAAE,KAAa,EAAE,MAAc;QAEhD,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;QAHhB,SAAI,GAAJ,IAAI,CAAQ;IAI9B,CAAC;CACF;AAQD,MAAM,OAAgB,eAAgB,SAAQ,iBAAqC;CAAG;AAEtF,MAAM,CAAC,KAAK,UAAU,cAAc;IAClC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC;IACzE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;IAEzE,MAAM,GAAG,GAAoB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAqB,CAAC;IAC3G,OAAO,GAAG,CAAC;AACb,CAAC"}
|
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@@ -1,30 +1,10 @@
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1
|
-
import
|
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2
|
-
export
|
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3
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-
|
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4
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-
backColor: number;
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5
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-
|
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6
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-
|
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7
|
-
|
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8
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-
} & {
|
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9
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-
[propName: string]: any;
|
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10
|
-
};
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11
|
-
onAfterRender: (canvas: HTMLCanvasElement) => void;
|
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12
|
-
};
|
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13
|
-
export declare abstract class NglGlServiceBase {
|
|
14
|
-
abstract get errorCount(): number;
|
|
15
|
-
/** Disposes MolstarViewer to free WebGL context */
|
|
16
|
-
abstract reset(): Promise<void>;
|
|
17
|
-
/** Queues NglGl render task
|
|
18
|
-
* @param key Specify to skip previously queued tasks with the same key
|
|
19
|
-
*/
|
|
20
|
-
abstract render(args: NglGlTask, key?: keyof any): void;
|
|
21
|
-
/** Default implementation of rendering tree on grid cell
|
|
22
|
-
* @param gCtx Context to draw on grid
|
|
23
|
-
* @param bd Bound rect to clip drawing on task moment
|
|
24
|
-
* @param gCell Grid cell to draw
|
|
25
|
-
* @param canvas Image of the tree rendered
|
|
26
|
-
*/
|
|
27
|
-
abstract renderOnGridCell(gCtx: CanvasRenderingContext2D, bd: DG.Rect, gCell: DG.GridCell, canvas: CanvasImageSource): void;
|
|
1
|
+
import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
|
|
2
|
+
export declare class NglGlProps extends PropsBase {
|
|
3
|
+
readonly pdb: string;
|
|
4
|
+
constructor(pdb: string, backColor: number, width: number, height: number);
|
|
5
|
+
}
|
|
6
|
+
export type NglGlAux = void;
|
|
7
|
+
export declare abstract class NglGlServiceBase extends RenderServiceBase<NglGlProps, void> {
|
|
28
8
|
}
|
|
29
9
|
export declare function getNglGlService(): Promise<NglGlServiceBase>;
|
|
30
10
|
//# sourceMappingURL=ngl-gl-service.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ngl-gl-service.d.ts","sourceRoot":"","sources":["ngl-gl-service.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"ngl-gl-service.d.ts","sourceRoot":"","sources":["ngl-gl-service.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,qBAAa,UAAW,SAAQ,SAAS;aAErB,GAAG,EAAE,MAAM;gBAAX,GAAG,EAAE,MAAM,EAC3B,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAInD;AAED,MAAM,MAAM,QAAQ,GAAG,IAAI,CAAC;AAE5B,8BAAsB,gBAAiB,SAAQ,iBAAiB,CAAC,UAAU,EAAE,IAAI,CAAC;CAAG;AAGrF,wBAAsB,eAAe,IAAI,OAAO,CAAC,gBAAgB,CAAC,CAOjE"}
|
|
@@ -1,5 +1,12 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
|
-
|
|
2
|
+
import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
|
|
3
|
+
export class NglGlProps extends PropsBase {
|
|
4
|
+
constructor(pdb, backColor, width, height) {
|
|
5
|
+
super(backColor, width, height);
|
|
6
|
+
this.pdb = pdb;
|
|
7
|
+
}
|
|
8
|
+
}
|
|
9
|
+
export class NglGlServiceBase extends RenderServiceBase {
|
|
3
10
|
}
|
|
4
11
|
export async function getNglGlService() {
|
|
5
12
|
const funcList = DG.Func.find({ package: 'BiostructureViewer', name: 'getNglGlService' });
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ngl-gl-service.js","sourceRoot":"","sources":["ngl-gl-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;
|
|
1
|
+
{"version":3,"file":"ngl-gl-service.js","sourceRoot":"","sources":["ngl-gl-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,SAAS,EAAE,iBAAiB,EAAC,MAAM,mCAAmC,CAAC;AAE/E,MAAM,OAAO,UAAW,SAAQ,SAAS;IACvC,YACkB,GAAW,EAC3B,SAAiB,EAAE,KAAa,EAAE,MAAc;QAEhD,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;QAHhB,QAAG,GAAH,GAAG,CAAQ;IAI7B,CAAC;CACF;AAID,MAAM,OAAgB,gBAAiB,SAAQ,iBAAmC;CAAG;AAGrF,MAAM,CAAC,KAAK,UAAU,eAAe;IACnC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,oBAAoB,EAAE,IAAI,EAAE,iBAAiB,EAAC,CAAC,CAAC;IACxF,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,oEAAoE,CAAC,CAAC;IAExF,MAAM,GAAG,GAAqB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAsB,CAAC;IAC7G,OAAO,GAAG,CAAC;AACb,CAAC"}
|