@datagrok-libraries/bio 2.1.0 → 2.1.1
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/package.json
CHANGED
|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
export declare function _testPaletteN(): void
|
|
2
|
-
export declare function _testPaletteAA(): void
|
|
1
|
+
export declare function _testPaletteN(): Promise<void>;
|
|
2
|
+
export declare function _testPaletteAA(): Promise<void>;
|
|
3
3
|
//# sourceMappingURL=palettes.test.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"palettes.test.d.ts","sourceRoot":"","sources":["palettes.test.ts"],"names":[],"mappings":"AAUA,
|
|
1
|
+
{"version":3,"file":"palettes.test.d.ts","sourceRoot":"","sources":["palettes.test.ts"],"names":[],"mappings":"AAUA,wBAAsB,aAAa,kBASlC;AAED,wBAAsB,cAAc,kBAiBnC"}
|
|
@@ -1,27 +1,40 @@
|
|
|
1
|
+
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
|
|
2
|
+
function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
|
|
3
|
+
return new (P || (P = Promise))(function (resolve, reject) {
|
|
4
|
+
function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
|
|
5
|
+
function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
|
|
6
|
+
function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
|
|
7
|
+
step((generator = generator.apply(thisArg, _arguments || [])).next());
|
|
8
|
+
});
|
|
9
|
+
};
|
|
1
10
|
import { expect } from '@datagrok-libraries/utils/src/test';
|
|
2
11
|
import { AminoacidsPalettes } from '../aminoacids';
|
|
3
12
|
import { SeqPaletteBase } from '../seq-palettes';
|
|
4
13
|
import { NucleotidesPalettes } from '../nucleotides';
|
|
5
14
|
export function _testPaletteN() {
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
15
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
16
|
+
const cpChromatogram = NucleotidesPalettes.Chromatogram;
|
|
17
|
+
// TODO: Check palettes implement SeqPalette interface
|
|
18
|
+
// expect(cpChromatogram instanceof SeqPalette, true);
|
|
19
|
+
expect(cpChromatogram instanceof SeqPaletteBase, true);
|
|
20
|
+
expect(cpChromatogram instanceof NucleotidesPalettes, true);
|
|
21
|
+
});
|
|
11
22
|
}
|
|
12
23
|
export function _testPaletteAA() {
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
24
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
25
|
+
const cpLest = AminoacidsPalettes.Lesk;
|
|
26
|
+
const cpRasMol = AminoacidsPalettes.RasMol;
|
|
27
|
+
const cpGrokGroups = AminoacidsPalettes.GrokGroups;
|
|
28
|
+
// TODO: Check palettes implement SeqPalette interface
|
|
29
|
+
// expect(cpLest instanceof SeqPalette, true);
|
|
30
|
+
// expect(cpRasMol instanceof SeqPalette, true);
|
|
31
|
+
// expect(cpGrokGroups instanceof SeqPalette, true);
|
|
32
|
+
expect(cpLest instanceof SeqPaletteBase, true);
|
|
33
|
+
expect(cpRasMol instanceof SeqPaletteBase, true);
|
|
34
|
+
expect(cpGrokGroups instanceof SeqPaletteBase, true);
|
|
35
|
+
expect(cpLest instanceof AminoacidsPalettes, true);
|
|
36
|
+
expect(cpRasMol instanceof AminoacidsPalettes, true);
|
|
37
|
+
expect(cpGrokGroups instanceof AminoacidsPalettes, true);
|
|
38
|
+
});
|
|
26
39
|
}
|
|
27
|
-
//# sourceMappingURL=data:application/json;base64,
|
|
40
|
+
//# sourceMappingURL=data:application/json;base64,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
|
package/detectors.js
DELETED
|
@@ -1,56 +0,0 @@
|
|
|
1
|
-
import * as grok from 'datagrok-api/grok';
|
|
2
|
-
import * as ui from 'datagrok-api/ui';
|
|
3
|
-
import * as DG from 'datagrok-api/dg';
|
|
4
|
-
import {Aminoacids} from './src/aminoacids';
|
|
5
|
-
import {Nucleotides} from './src/nucleotides';
|
|
6
|
-
|
|
7
|
-
/**
|
|
8
|
-
* The class contains semantic type detectors.
|
|
9
|
-
* Detectors are functions tagged with `DG.FUNC_TYPES.SEM_TYPE_DETECTOR`.
|
|
10
|
-
* See also: https://datagrok.ai/help/develop/how-to/define-semantic-type-detectors
|
|
11
|
-
* The class name is comprised of <PackageName> and the `PackageDetectors` suffix.
|
|
12
|
-
* Follow this naming convention to ensure that your detectors are properly loaded.
|
|
13
|
-
*/
|
|
14
|
-
class BioPackageDetectors extends DG.Package {
|
|
15
|
-
//tags: semTypeDetector
|
|
16
|
-
//input: column col
|
|
17
|
-
//output: string semType
|
|
18
|
-
detectNucleotidesSeq(col) {
|
|
19
|
-
const alphabet = Nucleotides.Names + {'-': 'gap'};
|
|
20
|
-
return DG.Detector.sampleCategories(col, (s) => {
|
|
21
|
-
return s.split('').every((n) => n in alphabet);
|
|
22
|
-
}) ? Nucleotides.SemType : null;
|
|
23
|
-
}
|
|
24
|
-
|
|
25
|
-
//tags: semTypeDetector
|
|
26
|
-
//input: column col
|
|
27
|
-
//output: string semType
|
|
28
|
-
detectAminoacidsSeq(col) {
|
|
29
|
-
const alphabet = Aminoacids.Names + {'-': 'gap'};
|
|
30
|
-
return DG.Detector.sampleCategories(col, (s) => {
|
|
31
|
-
return s.split('').every((aa) => aa in alphabet);
|
|
32
|
-
}) ? Aminoacids.SemType : null;
|
|
33
|
-
}
|
|
34
|
-
|
|
35
|
-
//tags: semTypeDetector
|
|
36
|
-
//input: column col
|
|
37
|
-
//output: string semType
|
|
38
|
-
detectMultipleAlignmentNucleotidesSeq(col) {
|
|
39
|
-
const alphabet = Nucleotides.Names + {'-': 'gap'};
|
|
40
|
-
const len = col.get(0).length;
|
|
41
|
-
return DG.Detector.sampleCategories(col, (s) => {
|
|
42
|
-
return s.length == len && s.split('').every((n) => n in alphabet);
|
|
43
|
-
}) ? Nucleotides.SemTypeMultipleAlignment : null;
|
|
44
|
-
}
|
|
45
|
-
|
|
46
|
-
//tags: semTypeDetector
|
|
47
|
-
//input: column col
|
|
48
|
-
//output: string semType
|
|
49
|
-
detectMultipleAlignmentAminoacidsSeq(col) {
|
|
50
|
-
const alphabet = Aminoacids.Names + {'-': 'gap'};
|
|
51
|
-
const len = col.get(0).length;
|
|
52
|
-
return DG.Detector.sampleCategories(col, (s) => {
|
|
53
|
-
return s.length == len && s.split('').every((aa) => aa in alphabet);
|
|
54
|
-
}) ? Aminoacids.SemTypeMultipleAlignment : null;
|
|
55
|
-
}
|
|
56
|
-
}
|