@datagrok-libraries/bio 5.34.3 → 5.36.0

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 (42) hide show
  1. package/.eslintrc.json +4 -3
  2. package/CHANGELOG.md +18 -9
  3. package/package.json +1 -1
  4. package/src/monomer-works/monomer-utils.d.ts +9 -0
  5. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  6. package/src/monomer-works/monomer-utils.js +58 -13
  7. package/src/monomer-works/monomer-utils.js.map +1 -1
  8. package/src/monomer-works/to-atomic-level.d.ts +1 -1
  9. package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
  10. package/src/monomer-works/to-atomic-level.js +7 -8
  11. package/src/monomer-works/to-atomic-level.js.map +1 -1
  12. package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
  13. package/src/utils/cell-renderer-monomer-placer.js +7 -8
  14. package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
  15. package/src/utils/cell-renderer.d.ts +3 -2
  16. package/src/utils/cell-renderer.d.ts.map +1 -1
  17. package/src/utils/cell-renderer.js +1 -1
  18. package/src/utils/cell-renderer.js.map +1 -1
  19. package/src/utils/macromolecule/consts.d.ts.map +1 -1
  20. package/src/utils/macromolecule/consts.js +1 -1
  21. package/src/utils/macromolecule/consts.js.map +1 -1
  22. package/src/utils/macromolecule/index.d.ts +1 -1
  23. package/src/utils/macromolecule/index.d.ts.map +1 -1
  24. package/src/utils/macromolecule/index.js +1 -1
  25. package/src/utils/macromolecule/index.js.map +1 -1
  26. package/src/utils/macromolecule/types.d.ts +5 -1
  27. package/src/utils/macromolecule/types.d.ts.map +1 -1
  28. package/src/utils/macromolecule/types.js.map +1 -1
  29. package/src/utils/macromolecule/utils.d.ts +1 -7
  30. package/src/utils/macromolecule/utils.d.ts.map +1 -1
  31. package/src/utils/macromolecule/utils.js +18 -31
  32. package/src/utils/macromolecule/utils.js.map +1 -1
  33. package/src/utils/notation-converter.d.ts.map +1 -1
  34. package/src/utils/notation-converter.js +5 -7
  35. package/src/utils/notation-converter.js.map +1 -1
  36. package/src/utils/splitter.d.ts.map +1 -1
  37. package/src/utils/splitter.js +3 -2
  38. package/src/utils/splitter.js.map +1 -1
  39. package/src/utils/units-handler.d.ts +3 -3
  40. package/src/utils/units-handler.d.ts.map +1 -1
  41. package/src/utils/units-handler.js +26 -18
  42. package/src/utils/units-handler.js.map +1 -1
package/src/utils/cell-renderer.d.ts.map CHANGED
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package/src/utils/cell-renderer.js CHANGED
@@ -25,7 +25,7 @@ export var DrawStyle;
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  * @param {number[]}maxWord {{[pos: number]: number}} Max word lengths per position.
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  * @param {number}wordIdx Is index of word we currently draw.
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  * @param {DG.GridCell}gridCell Is grid cell.
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- * @param {string[]}referenceSequence Is reference sequence for diff mode.
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+ * @param {ISeqSplitted}referenceSequence Is reference sequence for diff mode.
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  * @param {number}maxLengthOfMonomer Is max length of monomer.
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  * @param {{[key: string]: TextMetrics}}monomerTextSizeMap Is map of monomer text sizes.
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  * @return {number} x coordinate to start printing at.*/
package/src/utils/cell-renderer.js.map CHANGED
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+ {"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,QAAQ;IACxB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,0BAAkB,IAAI;IACpB,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;CACvC;AAED,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC"}
package/src/utils/macromolecule/consts.js CHANGED
@@ -6,7 +6,7 @@ export var NOTATION;
6
6
  NOTATION["SEPARATOR"] = "separator";
7
7
  NOTATION["HELM"] = "helm";
8
8
  })(NOTATION || (NOTATION = {}));
9
- export const monomerRe = /(\[[A-Za-z0-9-_]+\]|.)/g;
9
+ export const monomerRe = /(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g;
10
10
  export const Alphabets = new class {
11
11
  constructor() {
12
12
  this.fasta = {
package/src/utils/macromolecule/consts.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,MAAM,CAAN,IAAY,QAIX;AAJD,WAAY,QAAQ;IAClB,2BAAe,CAAA;IACf,mCAAuB,CAAA;IACvB,yBAAa,CAAA;AACf,CAAC,EAJW,QAAQ,KAAR,QAAQ,QAInB;AAwBD,MAAM,CAAC,MAAM,SAAS,GAAW,yBAAyB,CAAC;AAE3D,MAAM,CAAC,MAAM,SAAS,GAAG,IAAI;IAAA;QAC3B,UAAK,GAAG;YACN,OAAO,EAAE,IAAI,GAAG,CAAS;gBACvB,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;gBAChD,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;aACjD,CAAC;YACF,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC1C,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;SAC3C,CAAC;IACJ,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAC,MAAM,kBAAkB,GAAoB;IACjD,IAAI,aAAa,yBAAc,SAAS,CAAC,KAAK,CAAC,OAAO,EAAE,IAAI,CAAC;IAC7D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;IAC1D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;CAC3D,CAAC"}
1
+ {"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,MAAM,CAAN,IAAY,QAIX;AAJD,WAAY,QAAQ;IAClB,2BAAe,CAAA;IACf,mCAAuB,CAAA;IACvB,yBAAa,CAAA;AACf,CAAC,EAJW,QAAQ,KAAR,QAAQ,QAInB;AAwBD,MAAM,CAAC,MAAM,SAAS,GAAW,4CAA4C,CAAC;AAE9E,MAAM,CAAC,MAAM,SAAS,GAAG,IAAI;IAAA;QAC3B,UAAK,GAAG;YACN,OAAO,EAAE,IAAI,GAAG,CAAS;gBACvB,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;gBAChD,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;aACjD,CAAC;YACF,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC1C,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;SAC3C,CAAC;IACJ,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAC,MAAM,kBAAkB,GAAoB;IACjD,IAAI,aAAa,yBAAc,SAAS,CAAC,KAAK,CAAC,OAAO,EAAE,IAAI,CAAC;IAC7D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;IAC1D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;CAC3D,CAAC"}
package/src/utils/macromolecule/index.d.ts CHANGED
@@ -1,4 +1,4 @@
1
1
  export { SplitterFunc, } from './types';
2
2
  export { TAGS, NOTATION, ALPHABET, ALIGNMENT, } from './consts';
3
- export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, MonomerToShortFunc, getSplitterForColumn } from './utils';
3
+ export { splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, MonomerToShortFunc, getSplitterForColumn } from './utils';
4
4
  //# sourceMappingURL=index.d.ts.map
package/src/utils/macromolecule/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EACL,YAAY,GAEb,MAAM,SAAS,CAAC;AAEjB,OAAO,EACL,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,SAAS,GACV,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAChB,kBAAkB,EAClB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EACL,YAAY,GAEb,MAAM,SAAS,CAAC;AAEjB,OAAO,EACL,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,SAAS,GACV,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAChB,kBAAkB,EAClB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}
package/src/utils/macromolecule/index.js CHANGED
@@ -1,3 +1,3 @@
1
1
  export { NOTATION, } from './consts';
2
- export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, getSplitterForColumn } from './utils';
2
+ export { splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, getSplitterForColumn } from './utils';
3
3
  //# sourceMappingURL=index.js.map
package/src/utils/macromolecule/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,EAEL,QAAQ,GAGT,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEhB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,EAEL,QAAQ,GAGT,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEhB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}
package/src/utils/macromolecule/types.d.ts CHANGED
@@ -1,8 +1,12 @@
1
+ export interface ISeqSplitted extends Iterable<string> {
2
+ [jPos: number]: string;
3
+ length: number;
4
+ }
1
5
  export type SeqColStats = {
2
6
  freq: MonomerFreqs;
3
7
  sameLength: boolean;
4
8
  };
5
- export type SplitterFunc = (seq: string) => string[];
9
+ export type SplitterFunc = (seq: string) => ISeqSplitted;
6
10
  export type MonomerFreqs = {
7
11
  [m: string]: number;
8
12
  };
package/src/utils/macromolecule/types.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAOA,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,EAAE,CAAC;AACrD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}
1
+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,YAAa,SAAQ,QAAQ,CAAC,MAAM,CAAC;IACpD,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAC;IACvB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}
package/src/utils/macromolecule/types.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAWA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}
1
+ {"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAgBA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}
package/src/utils/macromolecule/utils.d.ts CHANGED
@@ -14,6 +14,7 @@ export declare function getStatsForCol(seqCol: DG.Column, minLength: number, spl
14
14
  * @return {string[]} array of monomers
15
15
  */
16
16
  export declare function splitterAsFasta(seq: any): string[];
17
+ export declare function splitterAsFastaSimple(seq: any): string[];
17
18
  /** Gets method to split sequence by separator
18
19
  * @param {string} separator
19
20
  * @param limit
@@ -28,13 +29,6 @@ export declare function getSplitterWithSeparator(separator: string, limit?: numb
28
29
  export declare function splitterAsHelm(seq: any): string[];
29
30
  /** Func type to shorten a {@link monomerLabel} with length {@link limit} */
30
31
  export type MonomerToShortFunc = (monomerLabel: string, limit: number) => string;
31
- /** Get splitter method to split sequences to monomers
32
- * @param {string} units
33
- * @param {string} separator
34
- * @param limit
35
- * @return {SplitterFunc}
36
- */
37
- export declare function getSplitter(units: string, separator: string, limit?: number | undefined): SplitterFunc;
38
32
  /** Generate splitter function for sequence column
39
33
  * @param {DG.Column} col
40
34
  * @return {SplitterFunc} Splitter function
package/src/utils/macromolecule/utils.d.ts.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAmB,aAAa,EAAgB,YAAY,EAAE,WAAW,EAAE,YAAY,EAAC,MAAM,SAAS,CAAC;AAC/G,OAAO,EAAC,QAAQ,EAA2D,MAAM,UAAU,CAAC;AAI5F,OAAO,EAAC,UAAU,EAAC,MAAM,oBAAoB,CAAC;AAK9C;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,YAAY,GAAG,WAAW,CAKxG;AAwBD;;;GAGG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,GAAG,GAAG,MAAM,EAAE,CAclD;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,GAAG,MAAM,EAAE,CAExD;AAED;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,GAAE,MAAM,GAAG,SAAqB,GAAG,YAAY,CAI/G;AAKD;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,GAAG,GAAG,MAAM,EAAE,CAgBjD;AAED,4EAA4E;AAC5E,MAAM,MAAM,kBAAkB,GAAG,CAAC,YAAY,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,MAAM,CAAC;AAGjF;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,YAAY,CAGjE;AAID,+CAA+C;AAC/C,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,MAAM,CAQhF;AAED,MAAM;AACN,wBAAgB,WAAW,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAC,CAW3D;AAED;;;;;GAKG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,YAAY,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,SAAS,GAAE,MAAY,GAAG,MAAM,CAchH;AAED,+BAA+B;AAC/B,wBAAgB,cAAc,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,aAAa,EAAE,EAAE,SAAS,GAAE,MAAY,UAgBtG;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,GAAE,MAAU,GAAG,UAAU,CAYlF;AAED,wBAAgB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,UAAU,CAWhE;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,IAAI,CASvE"}
package/src/utils/macromolecule/utils.js CHANGED
@@ -1,7 +1,7 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import wu from 'wu';
3
3
  import { CandidateSimType } from './types';
4
- import { Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
4
+ import { Alphabets, candidateAlphabets, monomerRe } from './consts';
5
5
  import { UnitsHandler } from '../units-handler';
6
6
  import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
7
7
  import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
@@ -44,14 +44,21 @@ function getStats(splitted, minLength) {
44
44
  * @return {string[]} array of monomers
45
45
  */
46
46
  export function splitterAsFasta(seq) {
47
- return seq.toString().replace(monomerRe, '.$1').slice(1).split('.').map((monomer) => {
48
- if (monomer.startsWith('[') && monomer.endsWith(']'))
49
- return monomer.slice(1, -1);
50
- else if (monomer === '-')
51
- return '';
52
- else
53
- return monomer;
54
- });
47
+ // return seq.toString().replace(monomerRe, '.$1').slice(1).split('.').map((monomer: string) => {
48
+ // if (monomer.startsWith('[') && monomer.endsWith(']'))
49
+ // return monomer.slice(1, -1);
50
+ // else if (monomer === '-')
51
+ // return '';
52
+ // else
53
+ // return monomer;
54
+ // });
55
+ return wu(seq.toString().matchAll(monomerRe))
56
+ .map((ma) => {
57
+ return ma[2] ?? ma[1]; // preserve '-' as gap symbol for compatibility with simpleAsFastaSimple
58
+ }).toArray();
59
+ }
60
+ export function splitterAsFastaSimple(seq) {
61
+ return !seq ? [] : seq;
55
62
  }
56
63
  /** Gets method to split sequence by separator
57
64
  * @param {string} separator
@@ -85,33 +92,13 @@ export function splitterAsHelm(seq) {
85
92
  const mmList = inSeq ? inSeq.split('.') : [];
86
93
  return mmList.map(mmPostProcess);
87
94
  }
88
- /** Get splitter method to split sequences to monomers
89
- * @param {string} units
90
- * @param {string} separator
91
- * @param limit
92
- * @return {SplitterFunc}
93
- */
94
- export function getSplitter(units, separator, limit = undefined) {
95
- if (units.toLowerCase().startsWith(NOTATION.FASTA))
96
- return splitterAsFasta;
97
- else if (units.toLowerCase().startsWith(NOTATION.SEPARATOR))
98
- return getSplitterWithSeparator(separator, limit);
99
- else if (units.toLowerCase().startsWith(NOTATION.HELM))
100
- return splitterAsHelm;
101
- else
102
- throw new Error(`Unexpected units ${units} .`);
103
- // TODO: Splitter for HELM
104
- }
105
95
  /** Generate splitter function for sequence column
106
96
  * @param {DG.Column} col
107
97
  * @return {SplitterFunc} Splitter function
108
98
  */
109
99
  export function getSplitterForColumn(col) {
110
- if (col.semType !== DG.SEMTYPE.MACROMOLECULE)
111
- throw new Error(`Get splitter for semType "${DG.SEMTYPE.MACROMOLECULE}" only.`);
112
- const units = col.getTag(DG.TAGS.UNITS);
113
- const separator = col.getTag("separator" /* TAGS.separator */);
114
- return getSplitter(units, separator);
100
+ const uh = UnitsHandler.getOrCreate(col);
101
+ return uh.getSplitter();
115
102
  }
116
103
  const longMonomerPartRe = /([^\W_]+)/g;
117
104
  /** Convert long monomer names to short ones */
package/src/utils/macromolecule/utils.js.map CHANGED
@@ -1 +1 @@
1
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package/src/utils/notation-converter.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"notation-converter.d.ts","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAa,YAAY,EAAC,MAAM,iBAAiB,CAAC;AACzD,OAAO,EAAC,YAAY,EAAC,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAC,QAAQ,EAAO,MAAM,wBAAwB,CAAC;AAGtD,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;AAElD,iFAAiF;AACjF,qBAAa,iBAAkB,SAAQ,YAAY;IACjD,OAAO,CAAC,SAAS,CAA6B;IAE9C,SAAS,KAAK,QAAQ,IAAI,YAAY,CAIrC;IAEM,OAAO,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE1C,WAAW,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE9C,MAAM,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAEhD;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GACrF,MAAM;IAgCT;;;;;OAKG;IACI,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM;gBAUpD,GAAG,EAAE,EAAE,CAAC,MAAM;IAI1B,YAAY,CAAC,QAAQ,EAAE,QAAQ,EAAE,YAAY,GAAE,MAAM,GAAG,IAAW,GAAG,WAAW;CAczF"}
1
+ {"version":3,"file":"notation-converter.d.ts","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAa,YAAY,EAAC,MAAM,iBAAiB,CAAC;AACzD,OAAO,EAAe,YAAY,EAAC,MAAM,uBAAuB,CAAC;AACjE,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAGhD,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;AAElD,iFAAiF;AACjF,qBAAa,iBAAkB,SAAQ,YAAY;IACjD,OAAO,CAAC,SAAS,CAA6B;IAE9C,SAAS,KAAK,QAAQ,IAAI,YAAY,CAIrC;IAEM,OAAO,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE1C,WAAW,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE9C,MAAM,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAEhD;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GACrF,MAAM;IA+BT;;;;;OAKG;IACI,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM;gBASpD,GAAG,EAAE,EAAE,CAAC,MAAM;IAI1B,YAAY,CAAC,QAAQ,EAAE,QAAQ,EAAE,YAAY,GAAE,MAAM,GAAG,IAAW,GAAG,WAAW;CAczF"}
package/src/utils/notation-converter.js CHANGED
@@ -39,17 +39,15 @@ export class NotationConverter extends UnitsHandler {
39
39
  let item = helmItemsArray[i];
40
40
  if (isNucleotide)
41
41
  item = item.replace(helmWrappersRe, '');
42
- if (item === GapSymbols[NOTATION.HELM]) {
42
+ if (item === GapSymbols[NOTATION.HELM])
43
43
  tgtMonomersArray.push(tgtGapSymbol);
44
- }
45
44
  else if (this.toFasta(tgtNotation) && item.length > 1) {
46
45
  // the case of a multi-character monomer converted to FASTA
47
46
  const monomer = '[' + item + ']';
48
47
  tgtMonomersArray.push(monomer);
49
48
  }
50
- else {
49
+ else
51
50
  tgtMonomersArray.push(item);
52
- }
53
51
  }
54
52
  return tgtMonomersArray.join(tgtSeparator);
55
53
  }
@@ -117,8 +115,8 @@ function convertToHelm(srcUh, src) {
117
115
  const isDna = src.startsWith('DNA');
118
116
  const isRna = src.startsWith('RNA');
119
117
  const [prefix, leftWrapper, rightWrapper, postfix] = srcUh.getHelmWrappers();
120
- const srcMList = srcUh.getSplitter()(src);
121
- const tgtMList = srcMList.map((srcM) => {
118
+ const srcS = srcUh.getSplitter()(src);
119
+ const tgtMList = wu(srcS).map((srcM) => {
122
120
  let m = srcM;
123
121
  if (srcUh.isGap(m))
124
122
  m = GapSymbols[NOTATION.HELM];
@@ -127,7 +125,7 @@ function convertToHelm(srcUh, src) {
127
125
  else
128
126
  m = srcM.length == 1 ? `${leftWrapper}${srcM}${rightWrapper}` : `${leftWrapper}[${srcM}]${rightWrapper}`;
129
127
  return m;
130
- });
128
+ }).toArray();
131
129
  return `${prefix}${tgtMList.join('.')}${postfix}`;
132
130
  }
133
131
  /** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */
package/src/utils/notation-converter.js.map CHANGED
@@ -1 +1 @@
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package/src/utils/splitter.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"splitter.d.ts","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,wBAAgB,qBAAqB,CAAC,cAAc,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,SAAS,CA0BrF"}
1
+ {"version":3,"file":"splitter.d.ts","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,wBAAgB,qBAAqB,CAAC,cAAc,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,SAAS,CA0BrF"}
package/src/utils/splitter.js CHANGED
@@ -1,4 +1,5 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
+ import wu from 'wu';
2
3
  import { getSplitterForColumn } from './macromolecule/utils';
3
4
  export function splitAlignedSequences(sequenceColumn) {
4
5
  const splitter = getSplitterForColumn(sequenceColumn);
@@ -16,10 +17,10 @@ export function splitAlignedSequences(sequenceColumn) {
16
17
  if (sequence == null)
17
18
  continue;
18
19
  const currentMonomerList = splitter(sequence);
19
- currentMonomerList.forEach((monomer, positionIndex) => {
20
+ for (const [monomer, positionIndex] of wu.enumerate(currentMonomerList)) {
20
21
  const col = getCol(positionIndex) || createCol(positionIndex);
21
22
  col.set(rowIndex, monomer || '-', false);
22
- });
23
+ }
23
24
  }
24
25
  return resultDf;
25
26
  }
package/src/utils/splitter.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"splitter.js","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,oBAAoB,EAAC,MAAM,uBAAuB,CAAC;AAG3D,MAAM,UAAU,qBAAqB,CAAC,cAAiC;IACrE,MAAM,QAAQ,GAAG,oBAAoB,CAAC,cAAc,CAAC,CAAC;IACtD,MAAM,MAAM,GAAG,CAAC,KAAa,EAA4B,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC;IACtF,MAAM,SAAS,GAAG,CAAC,KAAa,EAAqB,EAAE;QACrD,MAAM,WAAW,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC1E,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;QAC7B,OAAO,WAAW,CAAC;IACrB,CAAC,CAAC;IAEF,MAAM,UAAU,GAAwB,EAAE,CAAC;IAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,CAAC;IACvC,MAAM,QAAQ,GAAG,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;IAE/C,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,EAAE,QAAQ,EAAE;QACtD,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9C,IAAI,QAAQ,IAAI,IAAI;YAClB,SAAS;QAEX,MAAM,kBAAkB,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC;QAC9C,kBAAkB,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,aAAa,EAAE,EAAE;YACpD,MAAM,GAAG,GAAG,MAAM,CAAC,aAAa,CAAC,IAAI,SAAS,CAAC,aAAa,CAAC,CAAC;YAC9D,GAAG,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,IAAI,GAAG,EAAE,KAAK,CAAC,CAAC;QAC3C,CAAC,CAAC,CAAC;KACJ;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC"}
1
+ {"version":3,"file":"splitter.js","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,oBAAoB,EAAC,MAAM,uBAAuB,CAAC;AAG3D,MAAM,UAAU,qBAAqB,CAAC,cAAiC;IACrE,MAAM,QAAQ,GAAG,oBAAoB,CAAC,cAAc,CAAC,CAAC;IACtD,MAAM,MAAM,GAAG,CAAC,KAAa,EAA4B,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC;IACtF,MAAM,SAAS,GAAG,CAAC,KAAa,EAAqB,EAAE;QACrD,MAAM,WAAW,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC1E,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;QAC7B,OAAO,WAAW,CAAC;IACrB,CAAC,CAAC;IAEF,MAAM,UAAU,GAAwB,EAAE,CAAC;IAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,CAAC;IACvC,MAAM,QAAQ,GAAG,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;IAE/C,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,EAAE,QAAQ,EAAE;QACtD,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9C,IAAI,QAAQ,IAAI,IAAI;YAClB,SAAS;QAEX,MAAM,kBAAkB,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC;QAC9C,KAAK,MAAM,CAAC,OAAO,EAAE,aAAa,CAAC,IAAI,EAAE,CAAC,SAAS,CAAC,kBAAkB,CAAC,EAAE;YACvE,MAAM,GAAG,GAAG,MAAM,CAAC,aAAa,CAAC,IAAI,SAAS,CAAC,aAAa,CAAC,CAAC;YAC9D,GAAG,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,IAAI,GAAG,EAAE,KAAK,CAAC,CAAC;SAC1C;KACF;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC"}
package/src/utils/units-handler.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { NOTATION } from './macromolecule/consts';
3
- import { SeqColStats, SplitterFunc } from './macromolecule/types';
3
+ import { ISeqSplitted, SeqColStats, SplitterFunc } from './macromolecule/types';
4
4
  import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
5
5
  import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
6
6
  export declare const Tags: {
@@ -34,7 +34,7 @@ export declare class UnitsHandler {
34
34
  getAlphabetIsMultichar(): boolean;
35
35
  private _splitted;
36
36
  /** */
37
- get splitted(): string[][];
37
+ get splitted(): ISeqSplitted[];
38
38
  private _stats;
39
39
  get stats(): SeqColStats;
40
40
  isFasta(): boolean;
@@ -92,7 +92,7 @@ export declare class UnitsHandler {
92
92
  */
93
93
  static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
94
94
  /** Gets function to split seq value to monomers */
95
- getSplitter(): SplitterFunc;
95
+ getSplitter(limit?: number): SplitterFunc;
96
96
  getDistanceFunctionName(): MmDistanceFunctionsNames;
97
97
  getDistanceFunction(): mmDistanceFunctionType;
98
98
  checkHelmCompatibility(): Promise<boolean>;
package/src/utils/units-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/src/utils/units-handler.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { candidateAlphabets, NOTATION } from './macromolecule/consts';
3
- import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator } from './macromolecule/utils';
3
+ import { detectAlphabet, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, splitterAsFastaSimple } from './macromolecule/utils';
4
4
  import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
5
5
  import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
6
6
  export const Tags = new class {
@@ -90,9 +90,8 @@ export class UnitsHandler {
90
90
  if (this.notation == NOTATION.HELM || this.alphabet == "UN" /* ALPHABET.UN */) {
91
91
  const alphabetSizeStr = this.column.getTag(".alphabetSize" /* TAGS.alphabetSize */);
92
92
  let alphabetSize;
93
- if (alphabetSizeStr) {
93
+ if (alphabetSizeStr)
94
94
  alphabetSize = parseInt(alphabetSizeStr);
95
- }
96
95
  else {
97
96
  // calculate alphabetSize on demand
98
97
  const stats = this.stats;
@@ -167,8 +166,8 @@ export class UnitsHandler {
167
166
  isMsa() { return this.aligned ? this.aligned.toUpperCase().includes('MSA') : false; }
168
167
  isHelmCompatible() { return this.helmCompatible === 'true'; }
169
168
  isGap(m) {
170
- return !m || (this.units === NOTATION.FASTA && m === GapSymbols.FASTA) ||
171
- (this.units === NOTATION.HELM && m === GapSymbols.HELM);
169
+ return !m || (this.units === NOTATION.FASTA && m === GapSymbols[NOTATION.FASTA]) ||
170
+ (this.units === NOTATION.HELM && m === GapSymbols[NOTATION.HELM]);
172
171
  }
173
172
  /** Associate notation types with the corresponding units */
174
173
  /**
@@ -224,13 +223,13 @@ export class UnitsHandler {
224
223
  if (srcAligned)
225
224
  newColumn.setTag("aligned" /* TAGS.aligned */, srcAligned);
226
225
  const srcAlphabet = col.getTag("alphabet" /* TAGS.alphabet */);
227
- if (srcAlphabet)
226
+ if (srcAlphabet != null)
228
227
  newColumn.setTag("alphabet" /* TAGS.alphabet */, srcAlphabet);
229
228
  let srcAlphabetSize = col.getTag(".alphabetSize" /* TAGS.alphabetSize */);
230
- if (srcAlphabetSize)
229
+ if (srcAlphabet != null && srcAlphabetSize)
231
230
  newColumn.setTag(".alphabetSize" /* TAGS.alphabetSize */, srcAlphabetSize);
232
231
  const srcAlphabetIsMultichar = col.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */);
233
- if (srcAlphabetIsMultichar !== undefined)
232
+ if (srcAlphabet != null && srcAlphabetIsMultichar !== undefined)
234
233
  newColumn.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, srcAlphabetIsMultichar);
235
234
  if (tgtNotation == NOTATION.HELM) {
236
235
  srcAlphabetSize = this.getAlphabetSize().toString();
@@ -284,8 +283,21 @@ export class UnitsHandler {
284
283
  return newColumn;
285
284
  }
286
285
  /** Gets function to split seq value to monomers */
287
- getSplitter() {
288
- return getSplitterForColumn(this._column);
286
+ getSplitter(limit) {
287
+ if (this.units.toLowerCase().startsWith(NOTATION.FASTA)) {
288
+ const alphabet = this.column.getTag("alphabet" /* TAGS.alphabet */);
289
+ if (alphabet !== null && !this.getAlphabetIsMultichar())
290
+ return splitterAsFastaSimple;
291
+ else
292
+ return splitterAsFasta;
293
+ }
294
+ else if (this.units.toLowerCase().startsWith(NOTATION.SEPARATOR))
295
+ return getSplitterWithSeparator(this.separator, limit);
296
+ else if (this.units.toLowerCase().startsWith(NOTATION.HELM))
297
+ return splitterAsHelm;
298
+ else
299
+ throw new Error(`Unexpected units ${this.units} .`);
300
+ // TODO: Splitter for HELM
289
301
  }
290
302
  getDistanceFunctionName() {
291
303
  // TODO add support for helm and separator notation
@@ -357,19 +369,16 @@ export class UnitsHandler {
357
369
  (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) && !this.isHelm() && this.alphabet === "UN" /* ALPHABET.UN */)) {
358
370
  // The following detectors and setters are to be called because the column is likely
359
371
  // as the UnitsHandler constructor was called on the column.
360
- if (this.isFasta()) {
372
+ if (this.isFasta())
361
373
  UnitsHandler.setUnitsToFastaColumn(this);
362
- }
363
374
  else if (this.isSeparator()) {
364
375
  const separator = col.getTag("separator" /* TAGS.separator */);
365
376
  UnitsHandler.setUnitsToSeparatorColumn(this, separator);
366
377
  }
367
- else if (this.isHelm()) {
378
+ else if (this.isHelm())
368
379
  UnitsHandler.setUnitsToHelmColumn(this);
369
- }
370
- else {
380
+ else
371
381
  throw new Error(`Unexpected units '${this.column.getTag(DG.TAGS.UNITS)}'.`);
372
- }
373
382
  }
374
383
  // if (!this.column.tags.has(TAGS.alphabetSize)) {
375
384
  // if (this.isHelm())
@@ -380,9 +389,8 @@ export class UnitsHandler {
380
389
  // `tag '${TAGS.alphabetSize}' is mandatory.`);
381
390
  // }
382
391
  if (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */)) {
383
- if (this.isHelm()) {
392
+ if (this.isHelm())
384
393
  this.column.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, 'true');
385
- }
386
394
  else if (['UN'].includes(this.alphabet)) {
387
395
  throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' ` +
388
396
  `tag '${".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */}' is mandatory.`);
package/src/utils/units-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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