@datagrok-libraries/bio 5.40.8 → 5.41.1

package/src/utils/cell-renderer-monomer-placer.js

@@ -1,96 +1,84 @@
-import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { SeqHandler } from './seq-handler';
-export class MonomerPlacer {
+import { CellRendererBackBase } from './cell-renderer-back-base';
+import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
+export class MonomerPlacer extends CellRendererBackBase {
     get updated() { return this._updated; }
     /** View is required to subscribe and handle for data frame changes */
-    constructor(grid, col, propsProvider) {
-        this.grid = grid;
-        this.col = col;
+    constructor(gridCol, tableCol, logger, propsProvider) {
+        super(gridCol, tableCol, logger);
         this.propsProvider = propsProvider;
         this._monomerLengthList = null;
         // width of separator symbol
         this.separatorWidth = 5;
+        this._processedMaxVisibleSeqLength = 0;
         this._updated = false;
         this._monomerLengthMap = {}; // caches the lengths to save time on g.measureText
         this._monomerStructureMap = {}; // caches the atomic structures of monomers
-        this.subs = [];
-        this.destroyed = false;
         this.props = this.propsProvider();
-        this._rowsProcessed = DG.BitSet.create(this.col.length);
-        if (this.grid) {
-            // Changes handling is available only in with a view
-            this.subs.push(col.dataFrame.onDataChanged.subscribe(() => {
-                try {
-                    this.props = this.propsProvider();
-                    this._monomerLengthList = null;
-                    this._rowsProcessed = DG.BitSet.create(this.col.length);
-                }
-                catch (err) {
-                    console.error(err);
-                }
-            }));
-            this.subs.push(this.props.monomerLib.onChanged.subscribe(() => {
-                this._monomerStructureMap = {};
-            }));
-            this.subs.push(grok.events.onViewRemoving.subscribe((eventData) => {
-                try {
-                    const eventView = eventData.args.view;
-                    if (this.grid?.dart && this.grid.view?.id === eventView.id && !this.destroyed)
-                        this.destroy();
-                }
-                catch (err) {
-                    console.error(err);
-                }
-            }));
-            this.subs.push(grok.events.onTableRemoved.subscribe((eventData) => {
-                try {
-                    const eventDf = eventData.args.dataFrame;
-                    if (this.col.dataFrame?.dart && this.col.dataFrame.id === eventDf.id && !this.destroyed)
-                        this.destroy();
-                }
-                catch (err) {
-                    console.error(err);
-                }
+        this._processedRows = DG.BitSet.create(this.tableCol.length);
+        if (this.gridCol) {
+            this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe(() => {
+                this._onRendered.next();
             }));
         }
+        getMonomerLibHelper().then((libHelper) => {
+            if (this.destroyed)
+                return;
+            const monomerLib = libHelper.getBioLib();
+            this.subs.push(monomerLib.onChanged.subscribe(() => {
+                this.reset();
+                this.gridCol?.grid?.invalidate();
+            }));
+        });
     }
-    destroy() {
-        for (const sub of this.subs)
-            sub.unsubscribe();
-        this.destroyed = true;
+    reset() {
+        if (this.propsProvider)
+            this.props = this.propsProvider();
+        this._processedRows = DG.BitSet.create(this.tableCol.length);
+        this._monomerLengthList = null;
+        this._monomerLengthMap = {};
+        this._monomerStructureMap = {};
     }
     /** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
-    getCellMonomerLengths(rowIdx) {
-        const res = this.props.seqHandler.isMsa() ? this.getCellMonomerLengthsForSeqMsa() :
-            this.getCellMonomerLengthsForSeq(rowIdx);
+    getCellMonomerLengths(rowIdx, width) {
+        const res = this.props.seqHandler.isMsa() ? this.getCellMonomerLengthsForSeqMsa(width) :
+            this.getCellMonomerLengthsForSeq(rowIdx, width);
         const resSum = new Array(res.length + 1);
         resSum[0] = 5; // padding
         for (let pos = 1; pos < resSum.length; pos++)
             resSum[pos] = resSum[pos - 1] + res[pos - 1];
         return [res, resSum];
     }
-    getCellMonomerLengthsForSeq(rowIdx) {
+    getCellMonomerLengthsForSeq(rowIdx, width) {
         if (this._monomerLengthList === null) {
-            this._monomerLengthList = new Array(this.col.length).fill(null);
+            this._monomerLengthList = new Array(this.tableCol.length).fill(null);
             this._updated = true;
         }
+        const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
+        const maxVisibleSeqLength = Math.ceil(width / minMonWidth);
+        const seqMonList = SeqHandler.forColumn(this.tableCol).getSplitted(rowIdx).originals;
+        const visibleSeqLength = Math.min(maxVisibleSeqLength, seqMonList.length);
         let res = this._monomerLengthList[rowIdx];
-        if (res === null) {
-            const seqMonList = SeqHandler.forColumn(this.col).getSplitted(rowIdx).originals;
+        if (res === null || res.length < visibleSeqLength) {
             res = this._monomerLengthList[rowIdx] = new Array(seqMonList.length);
-            for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
+            let seqWidth = 0;
+            for (let seqMonI = 0; seqMonI < visibleSeqLength; ++seqMonI) {
+                const seqMonLabel = seqMonList[seqMonI];
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.props.monomerLengthLimit);
                 const separatorWidth = this.props.seqHandler.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
                 const seqMonWidth = separatorWidth + shortMon.length * this.props.monomerCharWidth;
                 res[seqMonI] = seqMonWidth;
+                seqWidth += seqMonWidth;
+                if (seqWidth > width)
+                    break;
             }
             this._updated = true;
         }
         return res;
     }
-    getCellMonomerLengthsForSeqMsa() {
+    getCellMonomerLengthsForSeqMsa(width) {
         var _a;
         if (this._monomerLengthList === null) {
             this._monomerLengthList = new Array(1).fill(null);
@@ -102,38 +90,49 @@ export class MonomerPlacer {
         // const endIdx = Math.min(Math.ceil((this.grid?.vertScroll.max ?? 0) + 10), this.col.length);
         const { startIdx, endIdx } = (() => {
             try {
-                if (this.grid && this.grid.dart) {
+                const grid = this.gridCol && this.gridCol.dart ? this.gridCol.grid : null;
+                if (grid && grid.dart) {
                     return {
-                        startIdx: Math.max(Math.floor((this.grid?.vertScroll.min ?? 0) - 10), 0),
-                        endIdx: Math.min(Math.ceil((this.grid?.vertScroll.max ?? 0) + 10), this.col.length)
+                        startIdx: Math.max(Math.floor((grid?.vertScroll.min ?? 0) - 10), 0),
+                        endIdx: Math.min(Math.ceil((grid?.vertScroll.max ?? 0) + 10), this.tableCol.length)
                     };
                 }
                 else
-                    return { startIdx: 0, endIdx: Math.min(this.col.length, 10) };
+                    return { startIdx: 0, endIdx: Math.min(this.tableCol.length, 10) };
             }
             catch (_e) {
-                return { startIdx: 0, endIdx: Math.min(this.col.length, 10) };
+                return { startIdx: 0, endIdx: Math.min(this.tableCol.length, 10) };
             }
         })();
+        const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
+        const maxVisibleSeqLength = Math.ceil(width / minMonWidth);
         for (let seqIdx = startIdx; seqIdx < endIdx; seqIdx++) {
-            if (this._rowsProcessed.get(seqIdx))
+            if (this._processedRows.get(seqIdx) && maxVisibleSeqLength <= this._processedMaxVisibleSeqLength)
                 continue;
-            const seqMonList = SeqHandler.forColumn(this.col).getSplitted(seqIdx).originals;
-            if (seqMonList.length > res.length)
-                res.push(...new Array(seqMonList.length - res.length).fill(0));
-            for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
+            const seqMonList = SeqHandler.forColumn(this.tableCol)
+                .getSplitted(seqIdx, maxVisibleSeqLength).originals;
+            const visibleSeqLength = Math.min(maxVisibleSeqLength, seqMonList.length);
+            if (visibleSeqLength > res.length)
+                res.push(...new Array(visibleSeqLength - res.length).fill(minMonWidth));
+            let seqWidth = 0;
+            for (let seqMonI = 0; seqMonI < visibleSeqLength; ++seqMonI) {
+                const seqMonLabel = seqMonList[seqMonI];
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.props.monomerLengthLimit);
                 const seqMonWidth = this.props.separatorWidth + shortMon.length * this.props.monomerCharWidth;
                 res[seqMonI] = Math.max(res[seqMonI] ?? 0, seqMonWidth);
+                seqWidth += seqMonWidth;
+                if (seqWidth >= width)
+                    break;
             }
             this._updated = true;
+            this._processedMaxVisibleSeqLength = Math.max(this._processedMaxVisibleSeqLength, maxVisibleSeqLength);
         }
         return res; // first (and single) row of data
     }
     /** Returns seq position for pointer x */
-    getPosition(rowIdx, x) {
-        const [_monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx);
-        const sh = SeqHandler.forColumn(this.col);
+    getPosition(rowIdx, x, width) {
+        const [_monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx, width);
+        const sh = SeqHandler.forColumn(this.tableCol);
         const seqMonList = wu(sh.getSplitted(rowIdx).originals).toArray();
         if (seqMonList.length === 0)
             return null;

package/src/utils/cell-renderer-monomer-placer.js.map

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+{"version":3,"file":"cell-renderer-monomer-placer.js","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AAIzC,OAAO,EAAC,oBAAoB,EAAC,MAAM,2BAA2B,CAAC;AAE/D,OAAO,EAAC,mBAAmB,EAAC,MAAM,gCAAgC,CAAC;AAQnE,MAAM,OAAO,aAAc,SAAQ,oBAA4B;IAU7D,IAAW,OAAO,KAAc,OAAO,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC;IAKvD,sEAAsE;IACtE,YACE,OAA6B,EAC7B,QAA2B,EAC3B,MAAe,EACE,aAAuC;QAExD,KAAK,CAAC,OAAO,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;QAFhB,kBAAa,GAAb,aAAa,CAA0B;QAnBlD,uBAAkB,GAAsB,IAAI,CAAC;QAErD,4BAA4B;QACpB,mBAAc,GAAG,CAAC,CAAC;QAGnB,kCAA6B,GAAW,CAAC,CAAC;QAE1C,aAAQ,GAAY,KAAK,CAAC;QAG3B,sBAAiB,GAAmC,EAAE,CAAC,CAAC,mDAAmD;QAC3G,yBAAoB,GAAmC,EAAE,CAAC,CAAC,2CAA2C;QAU3G,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;YAChB,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;SACL;QAED,mBAAmB,EAAE,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,EAAE;YACvC,IAAI,IAAI,CAAC,SAAS;gBAAE,OAAO;YAC3B,MAAM,UAAU,GAAG,SAAS,CAAC,SAAS,EAAE,CAAC;YACzC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,SAAS,CAAC,GAAG,EAAE;gBACjD,IAAI,CAAC,KAAK,EAAE,CAAC;gBACb,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;IACjC,CAAC;IAED,qGAAqG;IAC9F,qBAAqB,CAAC,MAAc,EAAE,KAAa;QACxD,MAAM,GAAG,GAAa,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,8BAA8B,CAAC,KAAK,CAAC,CAAC,CAAC;YAChG,IAAI,CAAC,2BAA2B,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;QAElD,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,EAAE,KAAa;QAC/D,IAAI,IAAI,CAAC,kBAAkB,KAAK,IAAI,EAAE;YACpC,IAAI,CAAC,kBAAkB,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACrE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC;SACtB;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,KAAK,GAAG,WAAW,CAAC,CAAC;QACnE,MAAM,UAAU,GAAoB,UAAU,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,SAAS,CAAC;QACtG,MAAM,gBAAgB,GAAW,IAAI,CAAC,GAAG,CAAC,mBAAmB,EAAE,UAAU,CAAC,MAAM,CAAC,CAAC;QAElF,IAAI,GAAG,GAAa,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC;QACpD,IAAI,GAAG,KAAK,IAAI,IAAI,GAAG,CAAC,MAAM,GAAG,gBAAgB,EAAE;YACjD,GAAG,GAAG,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAS,UAAU,CAAC,MAAM,CAAC,CAAC;YAE7E,IAAI,QAAQ,GAAW,CAAC,CAAC;YACzB,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,gBAAgB,EAAE,EAAE,OAAO,EAAE;gBAC3D,MAAM,WAAW,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC;gBACxC,MAAM,QAAQ,GAAW,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,WAAW,EAAE,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC;gBAC/F,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,KAAK;oBAAE,MAAM;aAC7B;YACD,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC;SACtB;QACD,OAAO,GAAG,CAAC;IACb,CAAC;IAEO,8BAA8B,CAAC,KAAa;;QAClD,IAAI,IAAI,CAAC,kBAAkB,KAAK,IAAI,EAAE;YACpC,IAAI,CAAC,kBAAkB,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YAClD,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC;SACtB;QACD,MAAA,IAAI,CAAC,kBAAkB,EAAC,CAAC,SAAD,CAAC,IAAM,IAAI,KAAK,CAAC,CAAC,CAAC,EAAC;QAC5C,MAAM,GAAG,GAAG,IAAI,CAAC,kBAAkB,CAAC,CAAC,CAAC,CAAC;QACvC,mFAAmF;QACnF,8FAA8F;QAE9F,MAAM,EAAC,QAAQ,EAAE,MAAM,EAAC,GAAG,CAAC,GAAG,EAAE;YAC/B,IAAI;gBACF,MAAM,IAAI,GAAmB,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC;gBAC1F,IAAI,IAAI,IAAI,IAAI,CAAC,IAAI,EAAE;oBACrB,OAAO;wBACL,QAAQ,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,EAAE,UAAU,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC;wBACnE,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,UAAU,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;qBACpF,CAAC;iBACH;;oBAAM,OAAO,EAAC,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,EAAC,CAAC;aACzE;YAAC,OAAO,EAAE,EAAE;gBACX,OAAO,EAAC,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,EAAC,CAAC;aAClE;QACH,CAAC,CAAC,EAAE,CAAC;QAEL,MAAM,WAAW,GAAG,IAAI,CA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package/src/utils/const.d.ts

@@ -1,3 +1,12 @@
+import '../types/helm';
+import * as org from 'org';
+import PolymerTypes = org.helm.PolymerTypes;
+import HelmTypes = org.helm.HelmTypes;
+import MonomerTypes = org.helm.MonomerTypes;
+export { PolymerTypes, HelmTypes, MonomerTypes };
+import HELM_POLYMER_TYPE = org.helm.PolymerTypes;
+import HELM_MONOMER_TYPE = org.helm.MonomerTypes;
+export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
 /** Required HELM library monomer fields:
  * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
 export declare const enum HELM_REQUIRED_FIELD {
@@ -13,7 +22,7 @@ export declare const enum HELM_REQUIRED_FIELD {
     CREATE_DATE = "createDate"
 }
 export declare const enum HELM_RGROUP_FIELDS {
-    CAP_GROUP_SMILES = "capGroupSMILES",
+    CAP_GROUP_SMILES = "capGroupSmiles",
     CAP_GROUP_SMILES_UPPERCASE = "capGroupSMILES",
     ALTERNATE_ID = "alternateId",
     CAP_GROUP_NAME = "capGroupName",
@@ -36,15 +45,6 @@ export declare const enum HELM_FIELDS {
     POLYMER_TYPE = "polymerType",
     SYMBOL = "symbol"
 }
-export declare const enum HELM_POLYMER_TYPE {
-    PEPTIDE = "PEPTIDE",
-    RNA = "RNA"
-}
-export declare const enum HELM_MONOMER_TYPE {
-    BACKBONE = "Backbone",
-    TERMINAL = "Terminal",
-    BRANCH = "Branch"
-}
 export declare const HELM_CORE_FIELDS: HELM_FIELDS[];
 export declare const SDF_MONOMER_NAME = "MonomerName";
 export declare const jsonSdfMonomerLibDict: {

package/src/utils/const.d.ts.map

@@ -1 +1 @@
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package/src/utils/const.js

@@ -1,3 +1,4 @@
+import '../types/helm';
 // core fields of HELM library object used in toAtomicLevel function
 export const HELM_CORE_FIELDS = [
     "symbol" /* HELM_FIELDS.SYMBOL */,

package/src/utils/const.js.map

@@ -1 +1 @@
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package/src/utils/macromolecule/utils.d.ts.map

@@ -1 +1 @@
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package/src/utils/macromolecule/utils.js

@@ -114,7 +114,20 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
         if (!seq)
             return new StringListSeqSplitted([], GapOriginals[NOTATION.SEPARATOR]);
         else {
-            const mmList = seq.replaceAll('\"-\"', '').replaceAll('\'-\'', '').split(separator, limit);
+            let mmList;
+            const mRe = new RegExp(String.raw `"-"|'-'|[^${separator}]+`, 'g'); // depends on separator args
+            if (limit !== undefined) {
+                mRe.lastIndex = 0;
+                mmList = new Array(limit);
+                let mEa = null;
+                let mI = 0;
+                while ((mEa = mRe.exec(seq)) !== null && mI < limit) {
+                    mmList[mI++] = mEa[0].replace(`"-"`, '').replace(`'-'`, '');
+                }
+                mmList.splice(mI);
+            }
+            else
+                mmList = seq.replaceAll('\"-\"', '').replaceAll('\'-\'', '').split(separator, limit);
             return new StringListSeqSplitted(mmList, GapOriginals[NOTATION.SEPARATOR]);
         }
     };

package/src/utils/macromolecule/utils.js.map

@@ -1 +1 @@
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package/src/utils/seq-handler.d.ts

@@ -44,7 +44,7 @@ export declare class SeqHandler {
     private cached;
     private _splitted;
     private columnVersion;
-    getSplitted(rowIdx: number): ISeqSplitted;
+    getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
     private _stats;
     get stats(): SeqColStats;
     private _maxLength;

package/src/utils/seq-handler.d.ts.map

@@ -1 +1 @@
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package/src/utils/seq-handler.js

@@ -206,10 +206,10 @@ export class SeqHandler {
     //   }
     //   return this._splitted;
     // }
-    getSplitted(rowIdx) {
-        if (!this.cached) {
+    getSplitted(rowIdx, limit) {
+        if (!this.cached || limit !== undefined) {
             const seq = this.column.get(rowIdx);
-            return this.splitter(seq);
+            return this.getSplitter(limit)(seq);
         }
         else {
             if (this.column.version !== this.columnVersion || this._splitted === null) {
@@ -450,7 +450,7 @@ export class SeqHandler {
         const monomerLibHelper = await getMonomerLibHelper();
         const bioLib = monomerLibHelper.getBioLib();
         // retrieve peptides
-        const peptides = bioLib.getMonomerSymbolsByType("PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */.toString());
+        const peptides = bioLib.getMonomerSymbolsByType("PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */);
         // convert the peptides list to a set for faster lookup
         const peptidesSet = new Set(peptides);
         // get splitter for given separator and check if all monomers are in the lib

package/src/utils/seq-handler.js.map

@@ -1 +1 @@
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package/src/viewers/helm-service.d.ts

@@ -0,0 +1,17 @@
+import * as DG from 'datagrok-api/dg';
+import '../types/jsdraw2';
+import * as JSDraw2 from 'JSDraw2';
+import { PropsBase, RenderServiceBase } from '../utils/cell-renderer-async-base';
+export declare class HelmProps extends PropsBase {
+    readonly helm: string;
+    constructor(helm: string, backColor: number, width: number, height: number);
+}
+export type HelmAux = {
+    /** The molecule made of atoms (monomers) and bonds */ mol: JSDraw2.IEditorMol;
+    /** SVG bounding box */ bBox: DG.Rect;
+    /** Cell box {0, 0, w, h} */ cBox: DG.Rect;
+};
+export declare abstract class HelmServiceBase extends RenderServiceBase<HelmProps, HelmAux> {
+}
+export declare function getHelmService(): Promise<HelmServiceBase>;
+//# sourceMappingURL=helm-service.d.ts.map

package/src/viewers/helm-service.d.ts.map

@@ -0,0 +1 @@
+{"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"}