@datagrok-libraries/bio 5.9.2 → 5.9.4

package/index.d.ts

@@ -4,7 +4,7 @@ import { Aminoacids, AminoacidsPalettes } from './src/aminoacids';
 import { MonomerWorks } from './src/monomer-works';
 import { Nucleotides, NucleotidesPalettes } from './src/nucleotides';
 import { SeqPalette, SeqPaletteBase } from './src/seq-palettes';
-import { IMonomerLib, Monomer, MonomerType, NodeType, isLeaf, NodeCuttedType } from './src/types';
+import { IMonomerLib, Monomer, NodeType, isLeaf, NodeCuttedType } from './src/types';
 import { UnknownSeqPalette, UnknownSeqPalettes } from './src/unknown';
 import { DrawStyle, printLeftOrCentered } from './src/utils/cell-renderer';
 import { FastaFileHandler } from './src/utils/fasta-handler';
@@ -19,5 +19,5 @@ import { VdRegion, VdRegionType } from './src/vd-regions';
 import { CanvasCallback, getPhylocanvasGlService, IPhylocanvasGlViewer, NodeStyleType, PhylocanvasGlServiceBase, PhylocanvasGlTask, StylesType, TreeTypesNames } from './src/viewers/phylocanvas-gl-viewer';
 import { IVdRegionsViewer } from './src/viewers/vd-regions-viewer';
 import { PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer } from './src/viewers/web-logo-viewer';
-export { ALIGNMENT, ALPHABET, NOTATION, TAGS, NotationConverter, SplitterFunc, getStats, getAlphabetSimilarity, getSplitter, splitterAsFasta, splitterAsHelm, getSplitterForColumn, monomerToShort, splitAlignedSequences, SeqPalette, SeqPaletteBase, Aminoacids, AminoacidsPalettes, Nucleotides, NucleotidesPalettes, UnknownSeqPalettes, UnknownSeqPalette, pickUpPalette, getPaletteByType, PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer, UnitsHandler, DrawStyle, printLeftOrCentered, FastaFileHandler, VdRegionType, VdRegion, IVdRegionsViewer, NodeType, isLeaf, NodeCuttedType, PhylocanvasTreeNode, NodeStyleType, StylesType, IPhylocanvasGlViewer, TreeTypesNames, PhylocanvasGlServiceBase, CanvasCallback, PhylocanvasGlTask, getPhylocanvasGlService, PhylocanvasGL, Shapes, TreeTypes, Utils, Newick, INewickHelper, ITreeHelper, getTreeHelper, Monomer, IMonomerLib, MonomerType, getMonomerLib, MonomerWorks, };
+export { ALIGNMENT, ALPHABET, NOTATION, TAGS, NotationConverter, SplitterFunc, getStats, getAlphabetSimilarity, getSplitter, splitterAsFasta, splitterAsHelm, getSplitterForColumn, monomerToShort, splitAlignedSequences, SeqPalette, SeqPaletteBase, Aminoacids, AminoacidsPalettes, Nucleotides, NucleotidesPalettes, UnknownSeqPalettes, UnknownSeqPalette, pickUpPalette, getPaletteByType, PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer, UnitsHandler, DrawStyle, printLeftOrCentered, FastaFileHandler, VdRegionType, VdRegion, IVdRegionsViewer, NodeType, isLeaf, NodeCuttedType, PhylocanvasTreeNode, NodeStyleType, StylesType, IPhylocanvasGlViewer, TreeTypesNames, PhylocanvasGlServiceBase, CanvasCallback, PhylocanvasGlTask, getPhylocanvasGlService, PhylocanvasGL, Shapes, TreeTypes, Utils, Newick, INewickHelper, ITreeHelper, getTreeHelper, Monomer, IMonomerLib, getMonomerLib, MonomerWorks, };
 //# sourceMappingURL=index.d.ts.map

package/index.d.ts.map

@@ -1 +1 @@
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package/index.js

@@ -20,4 +20,4 @@ import { VdRegion, VdRegionType } from './src/vd-regions';
 import { getPhylocanvasGlService, PhylocanvasGlServiceBase, TreeTypesNames } from './src/viewers/phylocanvas-gl-viewer';
 import { PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer } from './src/viewers/web-logo-viewer';
 export { NotationConverter, getStats, getAlphabetSimilarity, getSplitter, splitterAsFasta, splitterAsHelm, getSplitterForColumn, monomerToShort, splitAlignedSequences, SeqPaletteBase, Aminoacids, AminoacidsPalettes, Nucleotides, NucleotidesPalettes, UnknownSeqPalettes, UnknownSeqPalette, pickUpPalette, getPaletteByType, PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer, UnitsHandler, DrawStyle, printLeftOrCentered, FastaFileHandler, VdRegionType, VdRegion, isLeaf, TreeTypesNames, PhylocanvasGlServiceBase, getPhylocanvasGlService, PhylocanvasGL, Shapes, TreeTypes, Utils, Newick, getTreeHelper, getMonomerLib, MonomerWorks, };
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

package/index.ts

@@ -7,7 +7,7 @@ import {Aminoacids, AminoacidsPalettes} from './src/aminoacids';
 import {MonomerWorks} from './src/monomer-works';
 import {Nucleotides, NucleotidesPalettes} from './src/nucleotides';
 import {SeqPalette, SeqPaletteBase} from './src/seq-palettes';
-import {IMonomerLib, Monomer, MonomerType, NodeType, isLeaf, NodeCuttedType} from './src/types';
+import {IMonomerLib, Monomer, NodeType, isLeaf, NodeCuttedType} from './src/types';
 import {UnknownSeqPalette, UnknownSeqPalettes} from './src/unknown';
 import {DrawStyle, printLeftOrCentered} from './src/utils/cell-renderer';
 import {FastaFileHandler} from './src/utils/fasta-handler';
@@ -106,7 +106,6 @@ export {
 
   Monomer,
   IMonomerLib,
-  MonomerType,
   getMonomerLib,
   MonomerWorks,
 };

package/package.json

@@ -4,7 +4,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.9.2",
+  "version": "5.9.4",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/utils": "^1.10.1",

package/src/monomer-works.d.ts

@@ -1,7 +1,7 @@
-import { IMonomerLib, Monomer, MonomerType } from './types';
+import { IMonomerLib, Monomer } from './types';
 export declare class MonomerWorks {
     monomerLib: IMonomerLib;
     constructor(monomerLib: IMonomerLib);
-    getCappedMonomer(monomerType: MonomerType, monomerName: string): Monomer | null;
+    getCappedMonomer(monomerType: string, monomerName: string): Monomer | null;
 }
 //# sourceMappingURL=monomer-works.d.ts.map

package/src/monomer-works.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-works.d.ts","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,WAAW,EAAE,OAAO,EAAE,WAAW,EAAC,MAAM,SAAS,CAAC;AAI1D,qBAAa,YAAY;IACvB,UAAU,EAAE,WAAW,CAAC;gBAEZ,UAAU,EAAE,WAAW;IAK5B,gBAAgB,CAAC,WAAW,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI;CAOvF"}
+{"version":3,"file":"monomer-works.d.ts","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,WAAW,EAAE,OAAO,EAAC,MAAM,SAAS,CAAC;AAI7C,qBAAa,YAAY;IACvB,UAAU,EAAE,WAAW,CAAC;gBAEZ,UAAU,EAAE,WAAW;IAK5B,gBAAgB,CAAC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI;CAIlF"}

package/src/monomer-works.js

@@ -4,10 +4,8 @@ export class MonomerWorks {
     }
     //types according to Monomer possible
     getCappedMonomer(monomerType, monomerName) {
-        if (!this.monomerLib.types.includes(monomerType))
-            throw new Error(`MonomerWorksError: monomer type \`${monomerType}\` is incorrect`);
-        //return capTheMonomer(this.monomerLib!.get(type, name));
-        return this.monomerLib.get(monomerType, monomerName);
+        //TODO
+        return null;
     }
 }
-//# sourceMappingURL=data:application/json;base64,eyJ2ZXJzaW9uIjozLCJmaWxlIjoibW9ub21lci13b3Jrcy5qcyIsInNvdXJjZVJvb3QiOiIiLCJzb3VyY2VzIjpbIm1vbm9tZXItd29ya3MudHMiXSwibmFtZXMiOltdLCJtYXBwaW5ncyI6IkFBUUEsTUFBTSxPQUFPLFlBQVk7SUFHdkIsWUFBWSxVQUF1QjtRQUNqQyxJQUFJLENBQUMsVUFBVSxHQUFHLFVBQVUsQ0FBQztJQUMvQixDQUFDO0lBRUQscUNBQXFDO0lBQzlCLGdCQUFnQixDQUFDLFdBQXdCLEVBQUUsV0FBbUI7UUFDbkUsSUFBSSxDQUFDLElBQUksQ0FBQyxVQUFVLENBQUMsS0FBSyxDQUFDLFFBQVEsQ0FBQyxXQUFXLENBQUM7WUFDOUMsTUFBTSxJQUFJLEtBQUssQ0FBQyxxQ0FBcUMsV0FBVyxpQkFBaUIsQ0FBQyxDQUFDO1FBRXJGLHlEQUF5RDtRQUN6RCxPQUFPLElBQUksQ0FBQyxVQUFVLENBQUMsR0FBRyxDQUFDLFdBQVcsRUFBRSxXQUFXLENBQUMsQ0FBQztJQUN2RCxDQUFDO0NBQ0YiLCJzb3VyY2VzQ29udGVudCI6WyJpbXBvcnQgKiBhcyBncm9rIGZyb20gJ2RhdGFncm9rLWFwaS9ncm9rJztcbmltcG9ydCAqIGFzIHVpIGZyb20gJ2RhdGFncm9rLWFwaS91aSc7XG5pbXBvcnQgKiBhcyBERyBmcm9tICdkYXRhZ3Jvay1hcGkvZGcnO1xuXG5pbXBvcnQge0lNb25vbWVyTGliLCBNb25vbWVyLCBNb25vbWVyVHlwZX0gZnJvbSAnLi90eXBlcyc7XG5pbXBvcnQge2NhcFRoZU1vbm9tZXJ9IGZyb20gJy4vdXRpbHMvdG8tYXRvbWljLWxldmVsJztcblxuXG5leHBvcnQgY2xhc3MgTW9ub21lcldvcmtzIHtcbiAgbW9ub21lckxpYjogSU1vbm9tZXJMaWI7XG5cbiAgY29uc3RydWN0b3IobW9ub21lckxpYjogSU1vbm9tZXJMaWIpIHtcbiAgICB0aGlzLm1vbm9tZXJMaWIgPSBtb25vbWVyTGliO1xuICB9XG5cbiAgLy90eXBlcyBhY2NvcmRpbmcgdG8gTW9ub21lciBwb3NzaWJsZVxuICBwdWJsaWMgZ2V0Q2FwcGVkTW9ub21lcihtb25vbWVyVHlwZTogTW9ub21lclR5cGUsIG1vbm9tZXJOYW1lOiBzdHJpbmcpOiBNb25vbWVyIHwgbnVsbCB7XG4gICAgaWYgKCF0aGlzLm1vbm9tZXJMaWIudHlwZXMuaW5jbHVkZXMobW9ub21lclR5cGUpKVxuICAgICAgdGhyb3cgbmV3IEVycm9yKGBNb25vbWVyV29ya3NFcnJvcjogbW9ub21lciB0eXBlIFxcYCR7bW9ub21lclR5cGV9XFxgIGlzIGluY29ycmVjdGApO1xuXG4gICAgLy9yZXR1cm4gY2FwVGhlTW9ub21lcih0aGlzLm1vbm9tZXJMaWIhLmdldCh0eXBlLCBuYW1lKSk7XG4gICAgcmV0dXJuIHRoaXMubW9ub21lckxpYi5nZXQobW9ub21lclR5cGUsIG1vbm9tZXJOYW1lKTtcbiAgfVxufVxuIl19
+//# sourceMappingURL=data:application/json;base64,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

package/src/types/index.d.ts

@@ -10,19 +10,33 @@ export interface NodeCuttedType extends NodeType {
     cuttedChildren?: NodeType[];
 }
 export declare type Monomer = {
-    at: {
-        [R: string]: string;
+    symbol: string;
+    name: string;
+    naturalAnalog: string;
+    molfile: string;
+    polymerType: string;
+    monomerType: string;
+    rgroups: {
+        capGroupSmiles: string;
+        alternateId: string;
+        capGroupName: string;
+        label: string;
+    }[];
+    data: {
+        [property: string]: any;
     };
-    id: string;
-    m: string;
-    n: string;
-    na: string;
-    rs: number;
 };
-export declare type MonomerType = 'HELM_AA' | 'HELM_BASE' | 'HELM_CHEM' | 'HELM_LINKER' | 'HELM_SUGAR';
 export interface IMonomerLib {
-    get(monomerType: MonomerType, monomerName: string): Monomer | null;
-    get types(): MonomerType[];
+    getMonomer(monomerType: string, monomerName: string): Monomer | null;
+    getMonomersByType(type: string): {
+        [symbol: string]: string;
+    } | null;
+    getTypes(): string[];
+    update(monomers: {
+        [type: string]: {
+            [name: string]: Monomer;
+        };
+    }): void;
     get onChanged(): Observable<any>;
 }
 //# sourceMappingURL=index.d.ts.map

package/src/types/index.d.ts.map

@@ -1 +1 @@
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package/src/types/index.js

@@ -2,4 +2,4 @@
 export function isLeaf(node) {
     return !node.children || node.children.length == 0;
 }
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