@datagrok/peptides 1.12.0 → 1.13.0

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.12.0",
+  "version": "1.13.0",
   "author": {
     "name": "Volodymyr Dyma",
     "email": "vdyma@datagrok.ai"
@@ -13,13 +13,13 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.37.0",
-    "@datagrok-libraries/ml": "^6.3.39",
-    "@datagrok-libraries/statistics": "^1.2.2",
-    "@datagrok-libraries/utils": "^4.1.4",
-    "@datagrok-libraries/tutorials": "^1.3.6",
+    "@datagrok-libraries/bio": "^5.38.2",
+    "@datagrok-libraries/ml": "^6.3.40",
+    "@datagrok-libraries/statistics": "^1.2.7",
+    "@datagrok-libraries/utils": "^4.1.13",
+    "@datagrok-libraries/tutorials": "^1.3.7",
     "cash-dom": "^8.1.5",
-    "datagrok-api": "^1.16.1",
+    "datagrok-api": "^1.16.5",
     "file-loader": "^6.2.0",
     "rxjs": "^6.5.5",
     "wu": "latest",

package/src/demo/fasta.ts

@@ -6,11 +6,10 @@ import {startAnalysis} from '../widgets/peptides';
 import * as C from '../utils/constants';
 import {scaleActivity} from '../utils/misc';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
 import {PeptidesModel} from '../model';
 
 export async function macromoleculeSarFastaDemoUI(): Promise<void> {
-  const demo = new DemoScript('Macromolecule SAR analysis', '');
+  grok.shell.windows.showContextPanel = true;
   const alignedSequenceCol = 'AlignedSequence';
   const simpleActivityColName = 'IC50';
   const simpleTable = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
@@ -21,27 +20,9 @@ export async function macromoleculeSarFastaDemoUI(): Promise<void> {
   simpleAlignedSeqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
   simpleAlignedSeqCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
   const simpleScaledCol = scaleActivity(simpleActivityCol, C.SCALING_METHODS.MINUS_LG);
-
-  demo.step('Load data', async () => {grok.shell.addTableView(simpleTable);},
-    {description: 'Load the dataset containing macromolecule sequences. Notice how Datagrok detects macromolecules ' +
-      'and applies renderer for better visual understanding of the data', delay: 2000});
-
-  let alignedCol: DG.Column<string>;
-  demo.step('Align sequences', async () => {
-    const clustersCol = DG.Column.string('Cluster', simpleTable.rowCount).init('0');
-    alignedCol = await grok.functions.call('Bio:alignSequences', {sequenceCol: simpleAlignedSeqCol, clustersCol});
-  }, {description: 'Align sequences with our Multiple Sequence Alignment tool. This tool can be found in the top ' +
-    'menu Bio -> Alignment -> MSA... New msa column will be added to the table', delay: 2000});
-
-  let model: PeptidesModel;
-  demo.step('Run SAR analysis', async () => {
-    model = await startAnalysis(simpleActivityCol, alignedCol, null, simpleTable, simpleScaledCol,
-      C.SCALING_METHODS.MINUS_LG) as PeptidesModel;
-    model.analysisView.addViewer('WebLogo');
-  }, {description: 'Run SAR analysis on aligned sequences from top menu: Bio -> SAR -> Peptides...', delay: 2000});
-
-  demo.step('Browse Mutation Cliffs', async () => {model.modifyMonomerPositionSelection('D', '13', false);},
-    {description: 'Browse Mutation Cliffs by selecting corresponding cells in Mutation Cliffs viewer in the bottom',
-      delay: 2000});
-  await demo.start();
+  const clustersCol = DG.Column.string('Cluster', simpleTable.rowCount).init('0');
+  const alignedCol: DG.Column<string> = await grok.functions.call('Bio:alignSequences', {sequenceCol: simpleAlignedSeqCol, clustersCol});
+  const model: PeptidesModel = await startAnalysis(simpleActivityCol, alignedCol, null, simpleTable, simpleScaledCol,
+    C.SCALING_METHODS.MINUS_LG) as PeptidesModel;
+  model.modifyMutationCliffsSelection({monomerOrCluster: 'D', positionOrClusterType: '13'});
 }