@datagrok/bio 1.4.2 → 1.5.1

package/src/utils/sequence-space.ts

@@ -1,43 +1,43 @@
 import * as DG from 'datagrok-api/dg';
-import { AvailableMetrics } from '@datagrok-libraries/ml/src/typed-metrics';
+import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {reduceDimensinalityWithNormalization} from '@datagrok-libraries/ml/src/sequence-space';
 import {BitArrayMetrics, StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
-import { Matrix } from '@datagrok-libraries/utils/src/type-declarations';
+import {Matrix} from '@datagrok-libraries/utils/src/type-declarations';
 import BitArray from '@datagrok-libraries/utils/src/bit-array';
+import {ISequenceSpaceParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 
 export interface ISequenceSpaceResult {
   distance: Matrix;
   coordinates: DG.ColumnList;
 }
 
-export async function sequenceSpace(molColumn: DG.Column, methodName: string, similarityMetric: string,
-    axes: string[], options?: any): Promise<ISequenceSpaceResult> {
-    let preparedData: any;
-    if (!(molColumn!.tags[DG.TAGS.UNITS] === 'HELM')) {
-      const sep = molColumn.getTag('separator');
-      const sepFinal = sep ? sep === '.' ? '\\\.' : sep: '-';  
-      var regex = new RegExp(sepFinal, "g");
-      if (Object.keys(AvailableMetrics['String']).includes(similarityMetric)) {
-          preparedData = molColumn.toList().map((v) => v.replace(regex, '')) as string[];
-      } else {
-          preparedData = molColumn.toList().map((v) => v.replace(regex, '')) as string[];
-      }
-    } else {
-      preparedData = molColumn.toList();
-    }
-    
-    const sequenceSpaceResult = await reduceDimensinalityWithNormalization(
-      preparedData,
-      methodName,
-      similarityMetric as StringMetrics|BitArrayMetrics,
-      options);
-    const cols: DG.Column[] = axes.map((name, index) => DG.Column.fromFloat32Array(name, sequenceSpaceResult.embedding[index]))
-    return {distance: sequenceSpaceResult.distance, coordinates: new DG.ColumnList(cols)};
+export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<ISequenceSpaceResult> {
+  let preparedData: any;
+  if (!(spaceParams.seqCol!.tags[DG.TAGS.UNITS] === 'HELM')) {
+    const sep = spaceParams.seqCol.getTag('separator');
+    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[];
+    else
+      preparedData = spaceParams.seqCol.toList().map((v) => v.replace(regex, '')) as string[];
+  } else {
+    preparedData = spaceParams.seqCol.toList();
   }
 
+  const sequenceSpaceResult = await reduceDimensinalityWithNormalization(
+    preparedData,
+    spaceParams.methodName,
+    spaceParams.similarityMetric as StringMetrics | BitArrayMetrics,
+    spaceParams.options);
+  const cols: DG.Column[] = spaceParams.embedAxesNames.map(
+    (name, index) => 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;
-    return axes.map((it) => `${it}_${colNameInd}`);
-  }
+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;
+  return axes.map((it) => `${it}_${colNameInd}`);
+}