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@datagrok/bio

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@datagrok/bio - npm Package Compare versions

Comparing version 1.7.23 to 1.7.24

test-Bio-4f0c8bae6479-367602e1.html

9

package.json
{
"name": "@datagrok/bio",
"beta": false,
"friendlyName": "Bio",

@@ -9,3 +8,3 @@ "author": {

},
"version": "1.7.23",
"version": "1.7.24",
"description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",

@@ -19,5 +18,5 @@ "repository": {

"@biowasm/aioli": ">=2.4.0",
"@datagrok-libraries/bio": "^3.0.2",
"@datagrok-libraries/ml": "^3.0.0",
"@datagrok-libraries/utils": "^1.4.0",
"@datagrok-libraries/bio": "^3.0.3",
"@datagrok-libraries/ml": "^3.0.3",
"@datagrok-libraries/utils": "^1.5.4",
"cash-dom": "latest",

@@ -24,0 +23,0 @@ "datagrok-api": "^1.5.0",

@@ -54,6 +54,6 @@ /**

if (cStatus.get(i)) {
passReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
passReport += `Test result : Success : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
} else {
failed = true;
failReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
failReport += `Test result : Failed : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
}

@@ -60,0 +60,0 @@ }

@@ -27,2 +27,3 @@ /* Do not change these import lines to match external modules in webpack configuration */

import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
import {removeEmptyStringRows} from '@datagrok-libraries/utils/src/dataframe-utils'

@@ -165,4 +166,7 @@

const embedColsNames = getEmbeddingColsNames(table);
const withoutEmptyValues = DG.DataFrame.fromColumns([macroMolecule]).clone();
const emptyValsIdxs = removeEmptyStringRows(withoutEmptyValues, encodedCol);
const chemSpaceParams = {
seqCol: encodedCol,
seqCol: withoutEmptyValues.col(macroMolecule.name)!,
methodName: methodName,

@@ -174,4 +178,7 @@ similarityMetric: similarityMetric,

const embeddings = sequenceSpaceRes.coordinates;
for (const col of embeddings)
table.columns.add(col);
for (const col of embeddings) {
const listValues = col.toList();
emptyValsIdxs.forEach((ind: number) => listValues.splice(ind, 0, null));
table.columns.add(DG.Column.fromFloat32Array(col.name, listValues));
}
if (plotEmbeddings) {

@@ -178,0 +185,0 @@ for (const v of grok.shell.views) {

@@ -69,3 +69,3 @@ import * as C from './constants';

pivot: number = 0, left = false, transparencyRate: number = 1.0,
separator: string = '', last: boolean = false, drawStyle: string = 'classic', maxWord:any={}, maxWordIdx:number=0, gridCell:any = {}): number {
separator: string = '', last: boolean = false, drawStyle: string = 'classic', maxWord: any = {}, maxWordIdx: number = 0, gridCell: any = {}): number {
g.textAlign = 'start';

@@ -216,4 +216,6 @@ const colorPart = s.substring(0);

// обработка новых елементов
const columns = gridCell.cell.column.categories;
let monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = WebLogo.monomerToShort;
let maxLengthOfMonomer = 8;
let maxLengthWords = {};

@@ -226,3 +228,3 @@ // check if gridCell.cell.column.temp is array

//@ts-ignore
let textSizeWidth = g.measureText(WebLogo.monomerToText(amino) + ' ');
let textSizeWidth = g.measureText(monomerToShortFunction(amino, maxLengthOfMonomer));
//@ts-ignore

@@ -246,13 +248,5 @@ if (textSizeWidth.width > (maxLengthWords[index] ?? 0)) {

let tagUnits = gridCell.cell.column.getTag(DG.TAGS.UNITS);
let maxLength = 0;
let maxWord = '';
let drawStyle = 'classic';
if (tagUnits.includes('MSA')) {
subParts.forEach(part => {
if (part.length > maxLength) {
maxLength = part.length;
maxWord = part;
drawStyle = 'msa';
}
});
drawStyle = 'msa';
}

@@ -263,3 +257,3 @@ subParts.forEach((amino, index) => {

let last = index === subParts.length - 1;
x1 = printLeftOrCentered(x1, y, w, h, g, WebLogo.monomerToText(amino), color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell);
x1 = printLeftOrCentered(x1, y, w, h, g, monomerToShortFunction(amino, maxLengthOfMonomer), color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell);
});

@@ -266,0 +260,0 @@

@@ -11,3 +11,3 @@ import {IDrawTooltipParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';

for (let i = 0; i < stringArray.length; ++i)
distances[i] = getSimilarityFromDistance(AvailableMetrics['String']['Levenshtein'](stringArray[i], seq));
distances[i] = stringArray[i] ? getSimilarityFromDistance(AvailableMetrics['String']['Levenshtein'](stringArray[i], seq)) : 0;
return DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances);

@@ -14,0 +14,0 @@ }

Sorry, the diff of this file is too big to display

Sorry, the diff of this file is too big to display

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