@datagrok-libraries/bio 2.0.2 → 2.1.1

package/package.json

@@ -5,13 +5,13 @@
   },
   "beta": true,
   "friendlyName": "Datagrok bio library",
-  "version": "2.0.2",
+  "version": "2.1.1",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/utils": "^0.4.2",
     "@types/wu": "latest",
     "cash-dom": "latest",
-    "datagrok-api": "^1.1.5",
+    "datagrok-api": "^1.3.5",
     "dayjs": "latest",
     "rxjs": "^6.5.5",
     "wu": "latest"

package/src/nucleotides.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"nucleotides.d.ts","sourceRoot":"","sources":["nucleotides.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,gBAAgB,EAAC,MAAM,iDAAiD,CAAC;AACjF,OAAO,EAAC,UAAU,EAAE,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAE1D,qBAAa,mBAAoB,SAAQ,cAAc;IACrD,OAAO,CAAC,MAAM,CAAC,YAAY,CAAa;IAExC,WAAkB,YAAY,IAAI,UAAU,CAW3C;CACF;AAED,qBAAa,WAAW;IACtB,MAAM,CAAC,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAiB;IAEhD,MAAM,CAAC,QAAQ,CAAC,wBAAwB,EAAE,MAAM,CAAkC;IAElF,OAAc,KAAK,EAAE,gBAAgB,CAMnC;CACH"}

package/src/nucleotides.js

@@ -15,7 +15,7 @@ export class NucleotidesPalettes extends SeqPaletteBase {
 }
 export class Nucleotides {
 }
-Nucleotides.SemType = 'MultipleAlignment';
+Nucleotides.SemType = 'Nucleotides';
 Nucleotides.SemTypeMultipleAlignment = 'NucleotidesMultipleAlignment';
 Nucleotides.Names = {
     'A': 'Adenine',
@@ -24,4 +24,4 @@ Nucleotides.Names = {
     'T': 'Thymine',
     'U': 'Uracil',
 };
-//# sourceMappingURL=data:application/json;base64,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
+//# sourceMappingURL=data:application/json;base64,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

package/src/tests/palettes.test.d.ts

@@ -1,3 +1,3 @@
-export declare function _testPaletteN(): void;
-export declare function _testPaletteAA(): void;
+export declare function _testPaletteN(): Promise<void>;
+export declare function _testPaletteAA(): Promise<void>;
 //# sourceMappingURL=palettes.test.d.ts.map

package/src/tests/palettes.test.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"palettes.test.d.ts","sourceRoot":"","sources":["palettes.test.ts"],"names":[],"mappings":"AAUA,wBAAgB,aAAa,SAS5B;AAED,wBAAgB,cAAc,SAiB7B"}
+{"version":3,"file":"palettes.test.d.ts","sourceRoot":"","sources":["palettes.test.ts"],"names":[],"mappings":"AAUA,wBAAsB,aAAa,kBASlC;AAED,wBAAsB,cAAc,kBAiBnC"}

package/src/tests/palettes.test.js

@@ -1,27 +1,40 @@
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
 import { expect } from '@datagrok-libraries/utils/src/test';
 import { AminoacidsPalettes } from '../aminoacids';
 import { SeqPaletteBase } from '../seq-palettes';
 import { NucleotidesPalettes } from '../nucleotides';
 export function _testPaletteN() {
-    const cpChromatogram = NucleotidesPalettes.Chromatogram;
-    // TODO: Check palettes implement SeqPalette interface
-    // expect(cpChromatogram instanceof SeqPalette, true);
-    expect(cpChromatogram instanceof SeqPaletteBase, true);
-    expect(cpChromatogram instanceof NucleotidesPalettes, true);
+    return __awaiter(this, void 0, void 0, function* () {
+        const cpChromatogram = NucleotidesPalettes.Chromatogram;
+        // TODO: Check palettes implement SeqPalette interface
+        // expect(cpChromatogram instanceof SeqPalette, true);
+        expect(cpChromatogram instanceof SeqPaletteBase, true);
+        expect(cpChromatogram instanceof NucleotidesPalettes, true);
+    });
 }
 export function _testPaletteAA() {
-    const cpLest = AminoacidsPalettes.Lesk;
-    const cpRasMol = AminoacidsPalettes.RasMol;
-    const cpGrokGroups = AminoacidsPalettes.GrokGroups;
-    // TODO: Check palettes implement SeqPalette interface
-    // expect(cpLest instanceof SeqPalette, true);
-    // expect(cpRasMol instanceof SeqPalette, true);
-    // expect(cpGrokGroups instanceof SeqPalette, true);
-    expect(cpLest instanceof SeqPaletteBase, true);
-    expect(cpRasMol instanceof SeqPaletteBase, true);
-    expect(cpGrokGroups instanceof SeqPaletteBase, true);
-    expect(cpLest instanceof AminoacidsPalettes, true);
-    expect(cpRasMol instanceof AminoacidsPalettes, true);
-    expect(cpGrokGroups instanceof AminoacidsPalettes, true);
+    return __awaiter(this, void 0, void 0, function* () {
+        const cpLest = AminoacidsPalettes.Lesk;
+        const cpRasMol = AminoacidsPalettes.RasMol;
+        const cpGrokGroups = AminoacidsPalettes.GrokGroups;
+        // TODO: Check palettes implement SeqPalette interface
+        // expect(cpLest instanceof SeqPalette, true);
+        // expect(cpRasMol instanceof SeqPalette, true);
+        // expect(cpGrokGroups instanceof SeqPalette, true);
+        expect(cpLest instanceof SeqPaletteBase, true);
+        expect(cpRasMol instanceof SeqPaletteBase, true);
+        expect(cpGrokGroups instanceof SeqPaletteBase, true);
+        expect(cpLest instanceof AminoacidsPalettes, true);
+        expect(cpRasMol instanceof AminoacidsPalettes, true);
+        expect(cpGrokGroups instanceof AminoacidsPalettes, true);
+    });
 }
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package/src/utils.js

@@ -7,9 +7,9 @@ export function getColumnSeparator(col) {
     const categories = col.categories;
     const catLen = categories.length;
     for (const potentialSeparator of defaultSeparators) {
-        if (categories.filter(sequence => sequence.includes(potentialSeparator) || sequence == '').length == catLen)
+        if (categories.every((sequence) => sequence.includes(potentialSeparator) || sequence == ''))
             return potentialSeparator;
     }
     return separator !== null && separator !== void 0 ? separator : '';
 }
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package/src/vd-regions.d.ts

@@ -0,0 +1,27 @@
+export declare enum VdRegionType {
+    Unknown = "unknown",
+    FR = "framework",
+    CDR = "cdr"
+}
+/** Describes V-DOMAIN (IG and TR) region (of multiple alignment)
+ * https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
+ */
+export declare class VdRegion {
+    type: VdRegionType;
+    name: string;
+    chain: string;
+    order: number;
+    positionStartName: string;
+    positionEndName: string;
+    /**
+     * start and position are strings because they correspond to position names as column names in ANARCI output
+     * @param {VdRegionType} type  Type of the region
+     * @param {string} name  Name of the region
+     * @param {string} chain
+     * @param {string} order
+     * @param {string} positionStartName  Region start position (inclusive)
+     * @param {string} positionEndName  Region end position (inclusive)
+     */
+    constructor(type: VdRegionType, name: string, chain: string, order: number, positionStartName: string, positionEndName: string);
+}
+//# sourceMappingURL=vd-regions.d.ts.map

package/src/vd-regions.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"vd-regions.d.ts","sourceRoot":"","sources":["vd-regions.ts"],"names":[],"mappings":"AAEA,oBAAY,YAAY;IACtB,OAAO,YAAY;IACnB,EAAE,cAAc;IAChB,GAAG,QAAQ;CACZ;AAED;;GAEG;AACH,qBAAa,QAAQ;IACnB,IAAI,EAAE,YAAY,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,eAAe,EAAE,MAAM,CAAC;IAExB;;;;;;;;OAQG;gBACS,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EACxE,iBAAiB,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM;CAQrD"}

package/src/vd-regions.js

@@ -0,0 +1,30 @@
+// Data structures for V-Domain regions of antibodies
+export var VdRegionType;
+(function (VdRegionType) {
+    VdRegionType["Unknown"] = "unknown";
+    VdRegionType["FR"] = "framework";
+    VdRegionType["CDR"] = "cdr";
+})(VdRegionType || (VdRegionType = {}));
+/** Describes V-DOMAIN (IG and TR) region (of multiple alignment)
+ * https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
+ */
+export class VdRegion {
+    /**
+     * start and position are strings because they correspond to position names as column names in ANARCI output
+     * @param {VdRegionType} type  Type of the region
+     * @param {string} name  Name of the region
+     * @param {string} chain
+     * @param {string} order
+     * @param {string} positionStartName  Region start position (inclusive)
+     * @param {string} positionEndName  Region end position (inclusive)
+     */
+    constructor(type, name, chain, order, positionStartName, positionEndName) {
+        this.type = type;
+        this.name = name;
+        this.chain = chain;
+        this.order = order;
+        this.positionStartName = positionStartName;
+        this.positionEndName = positionEndName;
+    }
+}
+//# sourceMappingURL=data:application/json;base64,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

package/detectors.js

@@ -1,56 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-import {Aminoacids} from './src/aminoacids';
-import {Nucleotides} from './src/nucleotides';
-
-/**
- * The class contains semantic type detectors.
- * Detectors are functions tagged with `DG.FUNC_TYPES.SEM_TYPE_DETECTOR`.
- * See also: https://datagrok.ai/help/develop/how-to/define-semantic-type-detectors
- * The class name is comprised of <PackageName> and the `PackageDetectors` suffix.
- * Follow this naming convention to ensure that your detectors are properly loaded.
- */
-class BioPackageDetectors extends DG.Package {
-  //tags: semTypeDetector
-  //input: column col
-  //output: string semType
-  detectNucleotidesSeq(col) {
-    const alphabet = Nucleotides.Names + {'-': 'gap'};
-    return DG.Detector.sampleCategories(col, (s) => {
-      return s.split('').every((n) => n in alphabet);
-    }) ? Nucleotides.SemType : null;
-  }
-
-  //tags: semTypeDetector
-  //input: column col
-  //output: string semType
-  detectAminoacidsSeq(col) {
-    const alphabet = Aminoacids.Names + {'-': 'gap'};
-    return DG.Detector.sampleCategories(col, (s) => {
-      return s.split('').every((aa) => aa in alphabet);
-    }) ? Aminoacids.SemType : null;
-  }
-
-  //tags: semTypeDetector
-  //input: column col
-  //output: string semType
-  detectMultipleAlignmentNucleotidesSeq(col) {
-    const alphabet = Nucleotides.Names + {'-': 'gap'};
-    const len = col.get(0).length;
-    return DG.Detector.sampleCategories(col, (s) => {
-      return s.length == len && s.split('').every((n) => n in alphabet);
-    }) ? Nucleotides.SemTypeMultipleAlignment : null;
-  }
-
-  //tags: semTypeDetector
-  //input: column col
-  //output: string semType
-  detectMultipleAlignmentAminoacidsSeq(col) {
-    const alphabet = Aminoacids.Names + {'-': 'gap'};
-    const len = col.get(0).length;
-    return DG.Detector.sampleCategories(col, (s) => {
-      return s.length == len && s.split('').every((aa) => aa in alphabet);
-    }) ? Aminoacids.SemTypeMultipleAlignment : null;
-  }
-}