@datagrok/bio 1.5.1 → 1.5.4

package/src/utils/notation-converter.ts

@@ -0,0 +1,131 @@
+import * as DG from 'datagrok-api/dg';
+
+// export const enum NOTATION {
+//   // these values can be changed to "user-friendly" ones later on
+//   FASTA = 'fasta',
+//   SEPARATOR = 'separator',
+//   HELM = 'helm'
+// }
+
+export class NotationConverter {
+  private _sourceColumn: DG.Column; // the column to be converted
+  private _currentUnits: string; // units of the form fasta:SEQ:NT, etc.
+  private _sourceNotation: string; // current notation (without :SEQ:NT, etc.)
+  private _targetNotation: string;
+
+  private get sourceColumn(): DG.Column { return this._sourceColumn; }
+  private get currentUnits(): string { return this._currentUnits; }
+  private get sourceNotation(): string { return this._sourceNotation; }
+  private get targetNotation(): string { return this._targetNotation; }
+
+  // these values can be changed to "user-friendly" ones later on
+  private _fasta = 'fasta';
+  private _separator = 'separator';
+  private _helm = 'helm';
+
+  public isFasta(): boolean { return this.sourceNotation == this._fasta; }
+  public isSeparator(): boolean { return this.sourceNotation == this._separator; }
+  public isHelm(): boolean { return this.sourceNotation == this._helm; }
+
+  private determineSourceNotation() : string {
+    if (this.currentUnits.toLowerCase().startsWith('fasta'))
+      return 'fasta';
+    else if (this.currentUnits.toLowerCase().startsWith('separator'))
+      return 'separator';
+    else
+      // TODO: handle possible exceptions
+      return 'HELM';
+  }
+
+  private convertFastaToSeparator(): DG.Column {
+    // TODO: implementation
+    const len = this.sourceColumn.length;
+    const newColName = 'converted';
+    const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill('fasta2sep'));
+    newColumn.semType = 'Macromolecule';
+    return newColumn;
+  }
+
+  private convertFastaToHelm(): DG.Column {
+    // TODO: implementation
+    const len = this.sourceColumn.length;
+    const newColName = 'converted';
+    const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill('fasta2helm'));
+    newColumn.semType = 'Macromolecule';
+    return newColumn;
+  }
+
+  private convertSeparatorToFasta(): DG.Column {
+    // TODO: implementation
+    const len = this.sourceColumn.length;
+    const newColName = 'converted';
+    const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill('sep2fasta'));
+    newColumn.semType = 'Macromolecule';
+    return newColumn;
+  }
+
+  private convertSeparatorToHelm(): DG.Column {
+    // TODO: implementation
+    const len = this.sourceColumn.length;
+    const newColName = 'converted';
+    const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill('sep2helm'));
+    newColumn.semType = 'Macromolecule';
+    return newColumn;
+  }
+
+  private convertHelmToFasta(): DG.Column {
+    // TODO: implementation
+    const len = this.sourceColumn.length;
+    const newColName = 'converted';
+    const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill('helm2fasta'));
+    newColumn.semType = 'Macromolecule';
+    return newColumn;
+  }
+
+  private convertHelmToSeparator(): DG.Column {
+    // TODO: implementation
+    const len = this.sourceColumn.length;
+    const newColName = 'converted';
+    const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill('helm2sep'));
+    newColumn.semType = 'Macromolecule';
+    return newColumn;
+  }
+
+  // TODO: write the bodies of converter methods
+  public convert() : DG.Column {
+    if (
+      this.sourceNotation == this._fasta &&
+      this.targetNotation == this._separator
+    )
+      return this.convertFastaToSeparator();
+    else if (
+      this.sourceNotation == this._fasta &&
+      this.targetNotation == this._helm
+    )
+      return this.convertFastaToHelm();
+    else if (
+      this.sourceNotation == this._separator &&
+      this.targetNotation == this._fasta
+    )
+      return this.convertSeparatorToFasta();
+    else if (
+      this.sourceNotation == this._separator &&
+      this.targetNotation == this._helm
+    )
+      return this.convertSeparatorToHelm();
+    else if (
+      this.sourceNotation == this._helm &&
+      this.targetNotation == this._fasta
+    )
+      return this.convertHelmToFasta();
+    else
+      return this.convertHelmToSeparator();
+  }
+
+  public constructor(col: DG.Column, target: string) {
+    this._sourceColumn = col;
+    this._currentUnits = this._sourceColumn.tags[DG.TAGS.UNITS];
+    this._sourceNotation = this.determineSourceNotation();
+    this._targetNotation = target;
+  }
+}

package/src/utils/sequence-activity-cliffs.ts

@@ -1,9 +1,15 @@
 import {IDrawTooltipParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
+import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarity-metrics';
+import { AvailableMetrics } from '@datagrok-libraries/ml/src/typed-metrics';
 
-export async function sequenceGetSimilarities(col: DG.Column, seq: string): Promise<DG.Column | null> {
-  return null;
+export async function sequenceGetSimilarities(col: DG.Column, seq: string): Promise<DG.Column | null>{ 
+  const stringArray = col.toList();
+  const distances = new Array(stringArray.length).fill(0.0);
+  for (let i = 0; i < stringArray.length; ++i)
+    distances[i] = getSimilarityFromDistance(AvailableMetrics['String']['Levenshtein'](stringArray[i], seq));
+  return DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances);
 }
 
 export function drawTooltip(params: IDrawTooltipParams) {

package/src/utils/sequence-space.ts

@@ -18,9 +18,9 @@ export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<
     const sepFinal = sep ? sep === '.' ? '\\\.' : sep : '-';
     const regex = new RegExp(sepFinal, 'g');
     if (Object.keys(AvailableMetrics['String']).includes(spaceParams.similarityMetric))
-      preparedData = spaceParams.seqCol.toList().map((v) => v.replace(regex, '')) as string[];
+      preparedData = spaceParams.seqCol.toList().map((v: string) => v.replace(regex, '')) as string[];
     else
-      preparedData = spaceParams.seqCol.toList().map((v) => v.replace(regex, '')) as string[];
+      preparedData = spaceParams.seqCol.toList().map((v: string) => v.replace(regex, '')) as string[];
   } else {
     preparedData = spaceParams.seqCol.toList();
   }
@@ -31,13 +31,13 @@ export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<
     spaceParams.similarityMetric as StringMetrics | BitArrayMetrics,
     spaceParams.options);
   const cols: DG.Column[] = spaceParams.embedAxesNames.map(
-    (name, index) => DG.Column.fromFloat32Array(name, sequenceSpaceResult.embedding[index]));
+    (name: string, index: number) => DG.Column.fromFloat32Array(name, sequenceSpaceResult.embedding[index]));
   return {distance: sequenceSpaceResult.distance, coordinates: new DG.ColumnList(cols)};
 }
 
 
 export function getEmbeddingColsNames(df: DG.DataFrame) {
   const axes = ['Embed_X', 'Embed_Y'];
-  const colNameInd = df.columns.names().filter((it) => it.includes(axes[0])).length + 1;
+  const colNameInd = df.columns.names().filter((it: string) => it.includes(axes[0])).length + 1;
   return axes.map((it) => `${it}_${colNameInd}`);
 }

package/src/utils/split-to-monomers.ts

@@ -0,0 +1,8 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+export function splitToMonomers() {
+
+}