@datagrok-libraries/bio 5.9.7 → 5.9.10
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 +3 -1
- package/package.json +1 -1
- package/src/monomer-works/monomer-lib.d.ts +18 -0
- package/src/monomer-works/monomer-lib.d.ts.map +1 -0
- package/src/monomer-works/monomer-lib.js +38 -0
package/index.d.ts
CHANGED
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@@ -19,5 +19,6 @@ import { VdRegion, VdRegionType } from './src/vd-regions';
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import { CanvasCallback, getPhylocanvasGlService, IPhylocanvasGlViewer, NodeStyleType, PhylocanvasGlServiceBase, PhylocanvasGlTask, StylesType, TreeTypesNames } from './src/viewers/phylocanvas-gl-viewer';
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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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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, MonomerLib };
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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,qBAAqB,CAAC;AACjD,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,qBAAqB,EACrB,QAAQ,EACR,QAAQ,EACR,IAAI,EACJ,SAAS,EACV,MAAM,2BAA2B,CAAC;AACnC,OAAO,EAAC,aAAa,EAAC,MAAM,yBAAyB,CAAC;AACtD,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;AAE3D,OAAO,EACL,SAAS,EACT,QAAQ,EACR,QAAQ,EACR,IAAI,EACJ,iBAAiB,EACjB,YAAY,EACZ,QAAQ,EACR,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,EAGb,OAAO,EACP,WAAW,EACX,aAAa,EACb,YAAY,EACZ,UAAU,EACX,CAAC"}
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package/index.js
CHANGED
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@@ -19,5 +19,6 @@ import { UnitsHandler } from './src/utils/units-handler';
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import { VdRegion, VdRegionType } from './src/vd-regions';
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import { getPhylocanvasGlService, PhylocanvasGlServiceBase, TreeTypesNames } from './src/viewers/phylocanvas-gl-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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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, MonomerLib };
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//# 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package/index.ts
CHANGED
|
@@ -46,7 +46,7 @@ import {
|
|
|
46
46
|
} from './src/viewers/phylocanvas-gl-viewer';
|
|
47
47
|
import {IVdRegionsViewer} from './src/viewers/vd-regions-viewer';
|
|
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
|
|
|
51
51
|
export {
|
|
52
52
|
ALIGNMENT,
|
|
@@ -104,8 +104,10 @@ export {
|
|
|
104
104
|
ITreeHelper,
|
|
105
105
|
getTreeHelper,
|
|
106
106
|
|
|
107
|
+
//Monomer lib and features
|
|
107
108
|
Monomer,
|
|
108
109
|
IMonomerLib,
|
|
109
110
|
getMonomerLib,
|
|
110
111
|
MonomerWorks,
|
|
112
|
+
MonomerLib
|
|
111
113
|
};
|
package/package.json
CHANGED
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
import { Observable } from 'rxjs';
|
|
2
|
+
import { IMonomerLib, Monomer } from '../types/index';
|
|
3
|
+
export declare class MonomerLib implements IMonomerLib {
|
|
4
|
+
private _monomers;
|
|
5
|
+
private _onChanged;
|
|
6
|
+
getMonomer(monomerType: string, monomerName: string): Monomer | null;
|
|
7
|
+
getTypes(): string[];
|
|
8
|
+
getMonomersByType(type: string): {
|
|
9
|
+
[symbol: string]: string;
|
|
10
|
+
};
|
|
11
|
+
get onChanged(): Observable<any>;
|
|
12
|
+
update(monomers: {
|
|
13
|
+
[type: string]: {
|
|
14
|
+
[name: string]: Monomer;
|
|
15
|
+
};
|
|
16
|
+
}): void;
|
|
17
|
+
}
|
|
18
|
+
//# sourceMappingURL=monomer-lib.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"monomer-lib.d.ts","sourceRoot":"","sources":["monomer-lib.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,UAAU,EAAU,MAAM,MAAM,CAAC;AACzC,OAAO,EAAC,WAAW,EAAE,OAAO,EAAC,MAAM,gBAAgB,CAAC;AAEpD,qBAAa,UAAW,YAAW,WAAW;IAC5C,OAAO,CAAC,SAAS,CAAuD;IACxE,OAAO,CAAC,UAAU,CAAsB;IAExC,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI;IAOpE,QAAQ,IAAI,MAAM,EAAE;IAIpB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG;QAAC,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAA;KAAC;IAU3D,IAAI,SAAS,IAAI,UAAU,CAAC,GAAG,CAAC,CAE/B;IAEM,MAAM,CAAC,QAAQ,EAAE;QAAE,CAAC,IAAI,EAAE,MAAM,GAAG;YAAE,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAA;SAAE,CAAA;KAAE,GAAG,IAAI;CAc/E"}
|
|
@@ -0,0 +1,38 @@
|
|
|
1
|
+
import { Subject } from 'rxjs';
|
|
2
|
+
export class MonomerLib {
|
|
3
|
+
constructor() {
|
|
4
|
+
this._monomers = {};
|
|
5
|
+
this._onChanged = new Subject();
|
|
6
|
+
}
|
|
7
|
+
getMonomer(monomerType, monomerName) {
|
|
8
|
+
if (monomerType in this._monomers && monomerName in this._monomers[monomerType])
|
|
9
|
+
return this._monomers[monomerType][monomerName];
|
|
10
|
+
else
|
|
11
|
+
return null;
|
|
12
|
+
}
|
|
13
|
+
getTypes() {
|
|
14
|
+
return Object.keys(this._monomers);
|
|
15
|
+
}
|
|
16
|
+
getMonomersByType(type) {
|
|
17
|
+
let res = {};
|
|
18
|
+
Object.keys(this._monomers[type]).forEach(monomerSymbol => {
|
|
19
|
+
res[monomerSymbol] = this._monomers[type][monomerSymbol].molfile;
|
|
20
|
+
});
|
|
21
|
+
return res;
|
|
22
|
+
}
|
|
23
|
+
get onChanged() {
|
|
24
|
+
return this._onChanged;
|
|
25
|
+
}
|
|
26
|
+
update(monomers) {
|
|
27
|
+
Object.keys(monomers).forEach(type => {
|
|
28
|
+
//could possibly rewrite -> TODO: check duplicated monomer symbol
|
|
29
|
+
if (!this.getTypes().includes(type))
|
|
30
|
+
this._monomers[type] = {};
|
|
31
|
+
Object.keys(monomers[type]).forEach(monomerName => {
|
|
32
|
+
this._monomers[type][monomerName] = monomers[type][monomerName];
|
|
33
|
+
});
|
|
34
|
+
});
|
|
35
|
+
this._onChanged.next();
|
|
36
|
+
}
|
|
37
|
+
}
|
|
38
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