@datagrok-libraries/bio 5.10.0 → 5.11.0
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/index.d.ts +2 -1
- package/index.d.ts.map +1 -1
- package/index.js +3 -2
- package/index.ts +9 -0
- package/package.json +1 -1
- package/src/viewers/ngl-gl-viewer.d.ts +52 -0
- package/src/viewers/ngl-gl-viewer.d.ts.map +1 -0
- package/src/viewers/ngl-gl-viewer.js +26 -0
package/index.d.ts
CHANGED
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@@ -20,5 +20,6 @@ import { IVdRegionsViewer } from './src/viewers/vd-regions-viewer';
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import { PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer } from './src/viewers/web-logo-viewer';
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import { MonomerLib } from './src/monomer-works/monomer-lib';
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import { readLibrary } from './src/monomer-works/monomer-utils';
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-
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import { getNglGlService, NglGlServiceBase, NglGlTask } from './src/viewers/ngl-gl-viewer';
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export { ALIGNMENT, ALPHABET, NOTATION, TAGS, NotationConverter, SplitterFunc, getStats, getAlphabet, 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, getNglGlService, NglGlServiceBase, NglGlTask, Monomer, IMonomerLib, MonomerWorks, MonomerLib, readLibrary };
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//# sourceMappingURL=index.d.ts.map
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package/index.d.ts.map
CHANGED
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@@ -1 +1 @@
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-
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,mBAAmB,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,SAAS,EAAC,MAAM,6BAA6B,CAAC;AAElG,OAAO,EAAC,aAAa,EAAC,MAAM,6BAA6B,CAAC;AAE1D,OAAO,EAAC,UAAU,EAAE,kBAAkB,EAAC,MAAM,kBAAkB,CAAC;AAChE,OAAO,EAAC,YAAY,EAAC,MAAM,mCAAmC,CAAC;AAC/D,OAAO,EAAC,WAAW,EAAE,mBAAmB,EAAC,MAAM,mBAAmB,CAAC;AACnE,OAAO,EAAC,UAAU,EAAE,cAAc,EAAC,MAAM,oBAAoB,CAAC;AAC9D,OAAO,EAAC,WAAW,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,cAAc,EAAC,MAAM,aAAa,CAAC;AACnF,OAAO,EAAC,iBAAiB,EAAE,kBAAkB,EAAC,MAAM,eAAe,CAAC;AACpE,OAAO,EAAC,SAAS,EAAE,mBAAmB,EAAC,MAAM,2BAA2B,CAAC;AACzE,OAAO,EAAC,gBAAgB,EAAC,MAAM,2BAA2B,CAAC;AAC3D,OAAO,EACL,WAAW,EACX,eAAe,EACf,oBAAoB,EACpB,YAAY,EACZ,cAAc,EACd,cAAc,EACd,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,WAAW,EACX,qBAAqB,EACrB,QAAQ,EACR,QAAQ,EACR,IAAI,EACJ,SAAS,EACV,MAAM,2BAA2B,CAAC;AACnC,OAAO,EAAC,aAAa,EAAC,MAAM,2BAA2B,CAAC;AACxD,OAAO,EAAC,iBAAiB,EAAC,MAAM,gCAAgC,CAAC;AACjE,OAAO,EAAC,qBAAqB,EAAC,MAAM,sBAAsB,CAAC;AAC3D,OAAO,EAAC,aAAa,EAAE,WAAW,EAAC,MAAM,yBAAyB,CAAC;AACnE,OAAO,EAAC,YAAY,EAAC,MAAM,2BAA2B,CAAC;AACvD,OAAO,EAAC,QAAQ,EAAE,YAAY,EAAC,MAAM,kBAAkB,CAAC;AACxD,OAAO,EACL,cAAc,EACd,uBAAuB,EACvB,oBAAoB,EACpB,aAAa,EACb,wBAAwB,EACxB,iBAAiB,EACjB,UAAU,EACV,cAAc,EACf,MAAM,qCAAqC,CAAC;AAC7C,OAAO,EAAC,gBAAgB,EAAC,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAC,cAAc,EAAE,YAAY,EAAE,mBAAmB,EAAE,aAAa,EAAC,MAAM,+BAA+B,CAAC;AAC/G,OAAO,EAAC,UAAU,EAAC,MAAM,iCAAiC,CAAC;AAC3D,OAAO,EAAC,WAAW,EAAC,MAAM,mCAAmC,CAAC;AAC9D,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,SAAS,EACV,MAAM,6BAA6B,CAAC;AAErC,OAAO,EACL,SAAS,EACT,QAAQ,EACR,QAAQ,EACR,IAAI,EACJ,iBAAiB,EACjB,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,qBAAqB,EACrB,WAAW,EACX,eAAe,EACf,cAAc,EACd,oBAAoB,EACpB,cAAc,EACd,qBAAqB,EACrB,UAAU,EACV,cAAc,EACd,UAAU,EACV,kBAAkB,EAClB,WAAW,EACX,mBAAmB,EACnB,kBAAkB,EAClB,iBAAiB,EACjB,aAAa,EACb,gBAAgB,EAChB,cAAc,EACd,YAAY,EACZ,mBAAmB,EACnB,aAAa,EACb,YAAY,EACZ,SAAS,EACT,mBAAmB,EACnB,gBAAgB,EAChB,YAAY,EACZ,QAAQ,EACR,gBAAgB,EAEhB,QAAQ,EAAE,MAAM,EAAE,cAAc,EAChC,mBAAmB,EACnB,aAAa,EAAE,UAAU,EAEzB,oBAAoB,EACpB,cAAc,EACd,wBAAwB,EACxB,cAAc,EACd,iBAAiB,EACjB,uBAAuB,EAEvB,aAAa,EACb,MAAM,EAAE,SAAS,EACjB,KAAK,EACL,MAAM,EACN,aAAa,EACb,WAAW,EACX,aAAa,EAEb,eAAe,EACf,gBAAgB,EAChB,SAAS,EAGT,OAAO,EACP,WAAW,EACX,YAAY,EACZ,UAAU,EACV,WAAW,EACZ,CAAC"}
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package/index.js
CHANGED
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@@ -20,5 +20,6 @@ import { getPhylocanvasGlService, PhylocanvasGlServiceBase, TreeTypesNames } fro
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import { PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer } from './src/viewers/web-logo-viewer';
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import { MonomerLib } from './src/monomer-works/monomer-lib';
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import { readLibrary } from './src/monomer-works/monomer-utils';
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import { getNglGlService, NglGlServiceBase } from './src/viewers/ngl-gl-viewer';
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export { NotationConverter, getStats, getAlphabet, 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, getNglGlService, NglGlServiceBase, MonomerWorks, MonomerLib, readLibrary };
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package/index.ts
CHANGED
|
@@ -48,6 +48,11 @@ import {IVdRegionsViewer} from './src/viewers/vd-regions-viewer';
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|
|
48
48
|
import {PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer} from './src/viewers/web-logo-viewer';
|
|
49
49
|
import {MonomerLib} from './src/monomer-works/monomer-lib';
|
|
50
50
|
import {readLibrary} from './src/monomer-works/monomer-utils';
|
|
51
|
+
import {
|
|
52
|
+
getNglGlService,
|
|
53
|
+
NglGlServiceBase,
|
|
54
|
+
NglGlTask
|
|
55
|
+
} from './src/viewers/ngl-gl-viewer';
|
|
51
56
|
|
|
52
57
|
export {
|
|
53
58
|
ALIGNMENT,
|
|
@@ -106,6 +111,10 @@ export {
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|
|
106
111
|
ITreeHelper,
|
|
107
112
|
getTreeHelper,
|
|
108
113
|
|
|
114
|
+
getNglGlService,
|
|
115
|
+
NglGlServiceBase,
|
|
116
|
+
NglGlTask,
|
|
117
|
+
|
|
109
118
|
//Monomer lib and features
|
|
110
119
|
Monomer,
|
|
111
120
|
IMonomerLib,
|
package/package.json
CHANGED
|
@@ -0,0 +1,52 @@
|
|
|
1
|
+
import * as DG from 'datagrok-api/dg';
|
|
2
|
+
import { IViewer } from './viewer';
|
|
3
|
+
import { Observable } from 'rxjs';
|
|
4
|
+
import { MjolnirPointerEvent } from 'mjolnir.js';
|
|
5
|
+
import { PickingInfo } from '@deck.gl/core/typed';
|
|
6
|
+
export declare type NodeStyleType = {
|
|
7
|
+
[propName: string]: any;
|
|
8
|
+
};
|
|
9
|
+
export declare type StylesType = {
|
|
10
|
+
[nodeName: string]: NodeStyleType;
|
|
11
|
+
};
|
|
12
|
+
export interface INglGlViewer extends IViewer {
|
|
13
|
+
get nwkDf(): DG.DataFrame;
|
|
14
|
+
set nwkDf(value: DG.DataFrame);
|
|
15
|
+
setProps(updater: {
|
|
16
|
+
[propName: string]: any;
|
|
17
|
+
}): void;
|
|
18
|
+
get onAfterRender(): Observable<{
|
|
19
|
+
gl: WebGLRenderingContext;
|
|
20
|
+
}>;
|
|
21
|
+
get onHover(): Observable<{
|
|
22
|
+
info: PickingInfo;
|
|
23
|
+
event: MjolnirPointerEvent;
|
|
24
|
+
}>;
|
|
25
|
+
}
|
|
26
|
+
export declare type NglGlTask = {
|
|
27
|
+
name: string;
|
|
28
|
+
backColor: number;
|
|
29
|
+
props: {
|
|
30
|
+
[propName: string]: any;
|
|
31
|
+
};
|
|
32
|
+
onAfterRender: (canvas: HTMLCanvasElement) => Promise<void>;
|
|
33
|
+
};
|
|
34
|
+
export declare abstract class NglGlServiceBase {
|
|
35
|
+
static noneSource: {
|
|
36
|
+
type: string;
|
|
37
|
+
data: any;
|
|
38
|
+
};
|
|
39
|
+
/** Queues NglGl render task
|
|
40
|
+
* @param key Specify to skip previously queued tasks with the same key
|
|
41
|
+
*/
|
|
42
|
+
abstract render(args: NglGlTask, key?: keyof any): void;
|
|
43
|
+
/** Default implementation of rendering tree on grid cell
|
|
44
|
+
* @param gCtx Context to draw on grid
|
|
45
|
+
* @param bd Bound rect to clip drawing on task moment
|
|
46
|
+
* @param gCell Grid cell to draw
|
|
47
|
+
* @param canvas Image of the tree rendered
|
|
48
|
+
*/
|
|
49
|
+
abstract renderOnGridCell(gCtx: CanvasRenderingContext2D, bd: DG.Rect, gCell: DG.GridCell, canvas: CanvasImageSource): void;
|
|
50
|
+
}
|
|
51
|
+
export declare function getNglGlService(): Promise<NglGlServiceBase>;
|
|
52
|
+
//# sourceMappingURL=ngl-gl-viewer.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ngl-gl-viewer.d.ts","sourceRoot":"","sources":["ngl-gl-viewer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AACjC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAChC,OAAO,EAAC,mBAAmB,EAAC,MAAM,YAAY,CAAC;AAC/C,OAAO,EAAC,WAAW,EAAC,MAAM,qBAAqB,CAAC;AAGhD,oBAAY,aAAa,GAAG;IAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;CAAE,CAAC;AACxD,oBAAY,UAAU,GAAG;IAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,aAAa,CAAA;CAAE,CAAC;AAE/D,MAAM,WAAW,YAAa,SAAQ,OAAO;IAC3C,IAAI,KAAK,IAAI,EAAE,CAAC,SAAS,CAAC;IAE1B,IAAI,KAAK,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,EAAE;IAE/B,QAAQ,CAAC,OAAO,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,GAAG,IAAI,CAAC;IAErD,IAAI,aAAa,IAAI,UAAU,CAAC;QAAE,EAAE,EAAE,qBAAqB,CAAA;KAAE,CAAC,CAAC;IAE/D,IAAI,OAAO,IAAI,UAAU,CAAC;QAAE,IAAI,EAAE,WAAW,CAAC;QAAC,KAAK,EAAE,mBAAmB,CAAA;KAAE,CAAC,CAAC;CAC9E;AAGD,oBAAY,SAAS,GAAG;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAC;IACnC,aAAa,EAAE,CAAC,MAAM,EAAE,iBAAiB,KAAK,OAAO,CAAC,IAAI,CAAC,CAAA;CAC5D,CAAC;AAEF,8BAAsB,gBAAgB;IACpC,OAAc,UAAU,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,GAAG,CAAA;KAAE,CAGnD;IAEF;;OAEG;IACH,QAAQ,CAAC,MAAM,CAAC,IAAI,EAAE,SAAS,EAAE,GAAG,CAAC,EAAE,MAAM,GAAG,GAAG,IAAI;IAEvD;;;;;OAKG;IACH,QAAQ,CAAC,gBAAgB,CACvB,IAAI,EAAE,wBAAwB,EAAE,EAAE,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,iBAAiB,GAAG,IAAI;CACpG;AAGD,wBAAsB,eAAe,IAAI,OAAO,CAAC,gBAAgB,CAAC,CAOjE"}
|
|
@@ -0,0 +1,26 @@
|
|
|
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
|
+
};
|
|
10
|
+
import * as DG from 'datagrok-api/dg';
|
|
11
|
+
export class NglGlServiceBase {
|
|
12
|
+
}
|
|
13
|
+
NglGlServiceBase.noneSource = {
|
|
14
|
+
type: 'biojs',
|
|
15
|
+
data: { name: 'none', branch_length: 1, children: [] }
|
|
16
|
+
};
|
|
17
|
+
export function getNglGlService() {
|
|
18
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
19
|
+
const funcList = DG.Func.find({ package: 'PhyloTreeViewer', name: 'getNglGlService' });
|
|
20
|
+
if (funcList.length === 0)
|
|
21
|
+
throw new Error('Package "PhyloTreeViewer"" must be installed for NglGl services.');
|
|
22
|
+
const svc = (yield funcList[0].prepare().call()).getOutputParamValue();
|
|
23
|
+
return svc;
|
|
24
|
+
});
|
|
25
|
+
}
|
|
26
|
+
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|