@datagrok-libraries/bio 2.0.3 → 2.1.0

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.
Files changed (6) hide show
  1. package/package.json +1 -1
  2. package/src/nucleotides.d.ts.map +1 -1
  3. package/src/nucleotides.js +2 -2
  4. package/src/vd-regions.d.ts +27 -0
  5. package/src/vd-regions.d.ts.map +1 -0
  6. package/src/vd-regions.js +30 -0
package/package.json CHANGED
@@ -5,7 +5,7 @@
5
5
  },
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  "beta": true,
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  "friendlyName": "Datagrok bio library",
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- "version": "2.0.3",
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+ "version": "2.1.0",
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  "description": "",
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  "dependencies": {
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  "@datagrok-libraries/utils": "^0.4.2",
package/src/nucleotides.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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,CAAuB;IAEtD,MAAM,CAAC,QAAQ,CAAC,wBAAwB,EAAE,MAAM,CAAkC;IAElF,OAAc,KAAK,EAAE,gBAAgB,CAMnC;CACH"}
1
+ {"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 CHANGED
@@ -15,7 +15,7 @@ export class NucleotidesPalettes extends SeqPaletteBase {
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  }
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  export class Nucleotides {
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  }
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- Nucleotides.SemType = 'MultipleAlignment';
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+ Nucleotides.SemType = 'Nucleotides';
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  Nucleotides.SemTypeMultipleAlignment = 'NucleotidesMultipleAlignment';
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  Nucleotides.Names = {
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  'A': 'Adenine',
@@ -24,4 +24,4 @@ Nucleotides.Names = {
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  'T': 'Thymine',
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  'U': 'Uracil',
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  };
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- //# sourceMappingURL=data:application/json;base64,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
27
+ //# sourceMappingURL=data:application/json;base64,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
package/src/vd-regions.d.ts ADDED
@@ -0,0 +1,27 @@
1
+ export declare enum VdRegionType {
2
+ Unknown = "unknown",
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+ FR = "framework",
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+ CDR = "cdr"
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+ }
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+ /** Describes V-DOMAIN (IG and TR) region (of multiple alignment)
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+ * https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
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+ */
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+ export declare class VdRegion {
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+ type: VdRegionType;
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+ name: string;
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+ chain: string;
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+ order: number;
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+ positionStartName: string;
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+ positionEndName: string;
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+ /**
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+ * start and position are strings because they correspond to position names as column names in ANARCI output
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+ * @param {VdRegionType} type Type of the region
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+ * @param {string} name Name of the region
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+ * @param {string} chain
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+ * @param {string} order
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+ * @param {string} positionStartName Region start position (inclusive)
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+ * @param {string} positionEndName Region end position (inclusive)
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+ */
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+ constructor(type: VdRegionType, name: string, chain: string, order: number, positionStartName: string, positionEndName: string);
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+ }
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+ //# sourceMappingURL=vd-regions.d.ts.map
package/src/vd-regions.d.ts.map ADDED
@@ -0,0 +1 @@
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 ADDED
@@ -0,0 +1,30 @@
1
+ // Data structures for V-Domain regions of antibodies
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+ export var VdRegionType;
3
+ (function (VdRegionType) {
4
+ VdRegionType["Unknown"] = "unknown";
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+ VdRegionType["FR"] = "framework";
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+ VdRegionType["CDR"] = "cdr";
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+ })(VdRegionType || (VdRegionType = {}));
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+ /** Describes V-DOMAIN (IG and TR) region (of multiple alignment)
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+ * https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
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+ */
11
+ export class VdRegion {
12
+ /**
13
+ * start and position are strings because they correspond to position names as column names in ANARCI output
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+ * @param {VdRegionType} type Type of the region
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+ * @param {string} name Name of the region
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+ * @param {string} chain
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+ * @param {string} order
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+ * @param {string} positionStartName Region start position (inclusive)
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+ * @param {string} positionEndName Region end position (inclusive)
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+ */
21
+ constructor(type, name, chain, order, positionStartName, positionEndName) {
22
+ this.type = type;
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+ this.name = name;
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+ this.chain = chain;
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+ this.order = order;
26
+ this.positionStartName = positionStartName;
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+ this.positionEndName = positionEndName;
28
+ }
29
+ }
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+ //# sourceMappingURL=data:application/json;base64,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