@datagrok/bio - npm Package Compare versions

Comparing version 1.5.8 to 1.5.9

detectors.js

@@ -78,4 +78,4 @@ /**
 
-      const forbidden = BioPackageDetectors.checkForbiddenWoSeparator(stats.freq);
-      if (separator || !forbidden) {
+      // const forbidden = BioPackageDetectors.checkForbiddenWoSeparator(stats.freq);
+      if (separator || alphabet != 'UN') {
         const units = `${format}:${seqType}:${alphabet}`;
@@ -127,7 +127,7 @@ col.setTag(DG.TAGS.UNITS, units);
 
-  /** Without a separator, special symbols or digits are not allowed as monomers. */
-  static checkForbiddenWoSeparator(freq) {
-    const forbiddenRe = /[\d!@#$%^&*()_+\-=\[\]{};':"\\|,.<>\/?]/i;
-    return Object.keys(freq).filter((m) => forbiddenRe.test(m)).length > 0;
-  }
+  // /** Without a separator, special symbols or digits are not allowed as monomers. */
+  // static checkForbiddenWoSeparator(freq) {
+  //   const forbiddenRe = /[\d!@#$%^&*()_+\-=\[\]{};':"\\|,.<>\/?]/i;
+  //   return Object.keys(freq).filter((m) => forbiddenRe.test(m)).length > 0;
+  // }
 
@@ -134,0 +134,0 @@ /** Stats of sequences with specified splitter func, returns { freq, sameLength } */

package.json

@@ -5,3 +5,3 @@ {
   "friendlyName": "Bio",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
@@ -8,0 +8,0 @@ "repository": {

src/tests/detectors-test.ts

@@ -108,5 +108,7 @@ import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
     msaComplex = 'msaComplex',
-    idCsv = 'idCsv',
-    sarSmallCsv = 'sarSmallCsv',
     helmCsv = 'helmCsv',
+    testIdCsv = 'testIdCsv',
+    testSmilesCsv = 'testSmilesCsv',
+    testHelmCsv = 'testHelmCsv',
+    testDemogCsv = 'testDemogCsv',
   }
@@ -119,5 +121,7 @@
     'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
-    'idCsv': 'System:AppData/Bio/samples/id.csv',
-    'sarSmallCsv': 'System:AppData/Bio/samples/sar-small.csv',
     'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
+    'testDemogCsv': 'System:AppData/Bio/samples/testDemog.csv',
+    'testIdCsv': 'System:AppData/Bio/samples/id.csv',
+    'testHelmCsv': 'System:AppData/Bio/samples/testHelm.csv',
+    'testSmilesCsv': 'System:AppData/Bio/samples/testSmiles.csv',
   };
@@ -243,7 +247,7 @@
   test('samplesIdCsvNegativeID', async () => {
-    await _testNeg(readSamples(Samples.idCsv), 'ID');
+    await _testNeg(readSamples(Samples.testIdCsv), 'ID');
   });
 
   test('samplesSarSmallCsvNegativeSmiles', async () => {
-    await _testNeg(readSamples(Samples.sarSmallCsv), 'smiles');
+    await _testNeg(readSamples(Samples.testSmilesCsv), 'smiles');
   });
@@ -258,2 +262,34 @@
   });
+
+  // sample_testHelm.csb
+  // columns: ID,Test type,HELM string,Valid?,Mol Weight,Mol Formula,SMILES
+  test('samplesTestHelmNegativeID', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'ID');
+  });
+  test('samplesTestHelmNegativeTestType', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Test type');
+  });
+  test('samplesTestHelmPositiveHelmString', async () => {
+    await _testPos(readSamples(Samples.testHelmCsv), 'HELM string', 'HELM');
+  });
+  test('samplesTestHelmNegativeValid', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Valid?');
+  });
+  test('samplesTestHelmNegativeMolWeight', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Mol Weight');
+  });
+  test('samplesTestHelmNegativeMolFormula', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Mol Formula');
+  });
+  test('samplesTestHelmNegativeSmiles', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Smiles');
+  });
+
+  test('samplesTestDemogNegativeAll', async () => {
+    const dfFunc: DfReaderFunc = readSamples(Samples.testDemogCsv);
+    const df: DG.DataFrame = await dfFunc();
+
+    for (const col of df.columns.toList())
+      await _testNeg(dfFunc, col.name);
+  });
 });
@@ -260,0 +296,0 @@

src/utils/cell-renderer.ts

@@ -12,3 +12,3 @@ import * as C from "./constants";
 
-const lru = new DG.LruCache<any, any>(); 
+const lru = new DG.LruCache<any, any>();
 
@@ -131,5 +131,2 @@ function getPalleteByType(paletteType: string): SeqPalette  {
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
-  constructor() {
-    super();
-  }
 
@@ -167,3 +164,3 @@ get name(): string {return 'macromoleculeSequence';}
       host.setAttribute('data', gridCell.cell.value);
-      
+      gridCell.element = host;
       //@ts-ignore
@@ -192,17 +189,17 @@ var canvas = new JSDraw2.Editor(host, { width: w, height: h, skin: "w8", viewonly: true });
       const s: string = cell.value ?? '';
-  
+
       //TODO: can this be replaced/merged with splitSequence?
       const units = gridCell.cell.column.getTag(DG.TAGS.UNITS);
-  
+
       const palette = getPalleteByType(paletteType);
-  
+
       const separator = gridCell.cell.column.getTag('separator') ?? '';
       const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, gridCell.cell.column.getTag('separator') );// splitter,
-  
+
       const subParts:string[] =  splitterFunc(cell.value);
       console.log(subParts);
-  
+
       const textSize = g.measureText(subParts.join(''));
       let x1 = Math.max(x, x + (w - textSize.width) / 2);
-  
+
       subParts.forEach((amino, index) => {
@@ -214,3 +211,3 @@ let [color, outerAmino,, pivot] = ChemPalette.getColorAAPivot(amino);
       });
-  
+
       g.restore();
@@ -217,0 +214,0 @@ }

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Improved metrics

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12142728

increased by5.24%

Number of package files

67

increased by3.08%

Lines of code

96363

increased by0.06%

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Published versions last months

4

decreased by-20%

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