@datagrok-libraries/bio 5.26.0 → 5.27.0

package/package.json

@@ -4,7 +4,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.26.0",
+  "version": "5.27.0",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.22",

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

@@ -0,0 +1,39 @@
+import * as DG from 'datagrok-api/dg';
+import { IViewer } from './viewer';
+import { PositionHeight } from './web-logo';
+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
+ * Attributes {@link positionStartName} and {@link positionEndName} are strings because
+ * they correspond to position names as column names in ANARCI output (with a character index possible).
+ */
+export interface VdRegion {
+    readonly type: VdRegionType;
+    readonly name: string;
+    readonly chain: string;
+    readonly order: number;
+    /** Name of the column containing sequence */
+    readonly sequenceColumnName: string;
+    /** Region start position (inclusive) */
+    readonly positionStartName: string;
+    /** Region end position (inclusive) */
+    readonly positionEndName: string;
+}
+export declare class VdRegionsPropsDefault {
+    regionTypes: VdRegionType[];
+    chains: string[];
+    skipEmptyPositions: boolean;
+    positionWidth: number;
+    positionHeight: PositionHeight;
+}
+export type VdRegionsProps = Required<VdRegionsPropsDefault>;
+/** Interface for VdRegionsViewer from @datagrok/bio to unbind dependency to Bio package */
+export interface IVdRegionsViewer extends VdRegionsProps, IViewer {
+    init(): Promise<void>;
+    setData(mlbDf: DG.DataFrame, regions: VdRegion[]): void;
+}
+//# sourceMappingURL=vd-regions.d.ts.map

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

@@ -0,0 +1 @@
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package/src/viewers/vd-regions.js

@@ -0,0 +1,19 @@
+import { PositionHeight } from './web-logo';
+// Data structures for V-Domain regions of antibodies
+export var VdRegionType;
+(function (VdRegionType) {
+    VdRegionType["Unknown"] = "unknown";
+    VdRegionType["FR"] = "framework";
+    VdRegionType["CDR"] = "cdr";
+})(VdRegionType || (VdRegionType = {}));
+export class VdRegionsPropsDefault {
+    constructor() {
+        this.regionTypes = [VdRegionType.CDR];
+        this.chains = ['Heavy', 'Light'];
+        //sequenceColumnNamePostfix: string = 'chain sequence';
+        this.skipEmptyPositions = false;
+        this.positionWidth = 16;
+        this.positionHeight = PositionHeight.Entropy;
+    }
+}
+//# sourceMappingURL=vd-regions.js.map

package/src/viewers/vd-regions.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"vd-regions.js","sourceRoot":"","sources":["vd-regions.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,cAAc,EAAC,MAAM,YAAY,CAAC;AAE1C,qDAAqD;AAErD,MAAM,CAAN,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,mCAAmB,CAAA;IACnB,gCAAgB,CAAA;IAChB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,KAAZ,YAAY,QAIvB;AAwBD,MAAM,OAAO,qBAAqB;IAAlC;QACE,gBAAW,GAAmB,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC;QACjD,WAAM,GAAa,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QACtC,uDAAuD;QAEvD,uBAAkB,GAAY,KAAK,CAAC;QACpC,kBAAa,GAAW,EAAE,CAAC;QAC3B,mBAAc,GAAmB,cAAc,CAAC,OAAO,CAAC;IAC1D,CAAC;CAAA"}

package/src/viewers/web-logo.d.ts

@@ -1,5 +1,22 @@
+import { IViewer } from './viewer';
 export declare enum PositionHeight {
     Entropy = "Entropy",
     full = "100%"
 }
+export declare class WebLogoPropsDefault {
+    sequenceColumnName: string | null;
+    startPositionName: string | null;
+    endPositionName: string | null;
+    skipEmptySequences: boolean;
+    skipEmptyPositions: boolean;
+    shrinkEmptyTail: boolean;
+}
+export type WebLogoProps = Required<WebLogoPropsDefault>;
+export interface IWebLogoViewer extends WebLogoProps, IViewer {
+}
+export declare const positionSeparator: string;
+export declare const positionRe: RegExp;
+export declare enum TAGS {
+    positionNames = ".positionNames"
+}
 //# sourceMappingURL=web-logo.d.ts.map

package/src/viewers/web-logo.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"web-logo.d.ts","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAIA,oBAAY,cAAc;IACxB,OAAO,YAAY;IACnB,IAAI,SAAS;CACd"}
+{"version":3,"file":"web-logo.d.ts","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAEjC,oBAAY,cAAc;IACxB,OAAO,YAAY;IACnB,IAAI,SAAS;CACd;AAED,qBAAa,mBAAmB;IAE9B,kBAAkB,EAAE,MAAM,GAAG,IAAI,CAAQ;IACzC,iBAAiB,EAAE,MAAM,GAAG,IAAI,CAAQ;IACxC,eAAe,EAAE,MAAM,GAAG,IAAI,CAAQ;IACtC,kBAAkB,EAAE,OAAO,CAAQ;IACnC,kBAAkB,EAAE,OAAO,CAAS;IACpC,eAAe,EAAE,OAAO,CAAQ;CACjC;AAED,MAAM,MAAM,YAAY,GAAG,QAAQ,CAAC,mBAAmB,CAAC,CAAC;AAEzD,MAAM,WAAW,cAAe,SAAQ,YAAY,EAAE,OAAO;CAE5D;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAC9C,eAAO,MAAM,UAAU,EAAE,MAAwB,CAAC;AAElD,oBAAY,IAAI;IACd,aAAa,mBAAmB;CACjC"}

package/src/viewers/web-logo.js

@@ -3,4 +3,21 @@ export var PositionHeight;
     PositionHeight["Entropy"] = "Entropy";
     PositionHeight["full"] = "100%";
 })(PositionHeight || (PositionHeight = {}));
+export class WebLogoPropsDefault {
+    constructor() {
+        // -- Data --
+        this.sequenceColumnName = null;
+        this.startPositionName = null;
+        this.endPositionName = null;
+        this.skipEmptySequences = true;
+        this.skipEmptyPositions = false;
+        this.shrinkEmptyTail = true;
+    }
+}
+export const positionSeparator = ', ';
+export const positionRe = /(\d+)([A-Z]?)/;
+export var TAGS;
+(function (TAGS) {
+    TAGS["positionNames"] = ".positionNames";
+})(TAGS || (TAGS = {}));
 //# sourceMappingURL=web-logo.js.map

package/src/viewers/web-logo.js.map

@@ -1 +1 @@
-{"version":3,"file":"web-logo.js","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAIA,MAAM,CAAN,IAAY,cAGX;AAHD,WAAY,cAAc;IACxB,qCAAmB,CAAA;IACnB,+BAAa,CAAA;AACf,CAAC,EAHW,cAAc,KAAd,cAAc,QAGzB"}
+{"version":3,"file":"web-logo.js","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAKA,MAAM,CAAN,IAAY,cAGX;AAHD,WAAY,cAAc;IACxB,qCAAmB,CAAA;IACnB,+BAAa,CAAA;AACf,CAAC,EAHW,cAAc,KAAd,cAAc,QAGzB;AAED,MAAM,OAAO,mBAAmB;IAAhC;QACE,aAAa;QACb,uBAAkB,GAAkB,IAAI,CAAC;QACzC,sBAAiB,GAAkB,IAAI,CAAC;QACxC,oBAAe,GAAkB,IAAI,CAAC;QACtC,uBAAkB,GAAY,IAAI,CAAC;QACnC,uBAAkB,GAAY,KAAK,CAAC;QACpC,oBAAe,GAAY,IAAI,CAAC;IAClC,CAAC;CAAA;AAQD,MAAM,CAAC,MAAM,iBAAiB,GAAW,IAAI,CAAC;AAC9C,MAAM,CAAC,MAAM,UAAU,GAAW,eAAe,CAAC;AAElD,MAAM,CAAN,IAAY,IAEX;AAFD,WAAY,IAAI;IACd,wCAAgC,CAAA;AAClC,CAAC,EAFW,IAAI,KAAJ,IAAI,QAEf"}

package/src/vd-regions.d.ts

@@ -1,34 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-import { IViewer } from './viewers/viewer';
-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);
-}
-/** Interface for VdRegionsViewer from @datagrok/bio to unbind dependency to Bio package */
-export interface IVdRegionsViewer extends IViewer {
-    init(): Promise<void>;
-    setData(mlbDf: DG.DataFrame, regions: VdRegion[]): void;
-}
-//# sourceMappingURL=vd-regions.d.ts.map

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

@@ -1 +0,0 @@
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package/src/vd-regions.js

@@ -1,30 +0,0 @@
-// 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=vd-regions.js.map

package/src/vd-regions.js.map

@@ -1 +0,0 @@
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