@datagrok/bio 2.0.8 → 2.0.10

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.0.8",
+  "version": "2.0.10",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "^4.3.0",
+    "@datagrok-libraries/bio": "^4.4.0",
     "@datagrok-libraries/chem-meta": "1.0.0",
     "@datagrok-libraries/ml": "^6.2.0",
     "@datagrok-libraries/utils": "^1.6.2",

package/src/package.ts

@@ -315,9 +315,11 @@ export async function compositionAnalysis(): Promise<void> {
     return;
   } else if (colList.length > 1) {
     const colListNames: string [] = colList.map((col) => col.name);
-    const colInput: DG.InputBase = ui.choiceInput('Column', colListNames[0], colListNames);
+    const selectedCol = colList.find((c) => { return (new UnitsHandler(c)).isMsa(); });
+    const colInput: DG.InputBase = ui.choiceInput(
+      'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
     ui.dialog({
-      title: 'R-Groups Analysis',
+      title: 'Composition Analysis',
       helpUrl: '/help/domains/bio/macromolecules.md#composition-analysis'
     })
       .add(ui.div([

package/src/tests/detectors-test.ts

@@ -131,8 +131,8 @@ MWRSWY-CKHP
 
   const samples: { [key: string]: string } = {
     'fastaCsv': 'System:AppData/Bio/samples/sample_FASTA.csv',
-    'fastaFasta': 'System:AppData/Bio/samples/sample_FASTA.fasta',
-    'fastaPtCsv': 'System:AppData/Bio/samples/sample_FASTA_PT.csv',
+    'fastaFasta': 'System:AppData/Bio/data/sample_FASTA.fasta',
+    'fastaPtCsv': 'System:AppData/Bio/data/sample_FASTA_PT.csv',
     'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
     'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
     'peptidesComplex': 'System:AppData/Bio/tests/peptides_complex_msa.csv',

package/src/utils/cell-renderer.ts

@@ -274,7 +274,8 @@ export function drawMoleculeDifferenceOnCanvas(
   s: string,
   units: string,
   separator: string,
-  fullStringLength?: boolean) {
+  fullStringLength?: boolean,
+  molDifferences?:{[key: number]: HTMLCanvasElement}) {
 
   //TODO: can this be replaced/merged with splitSequence?
   const [s1, s2] = s.split('#');
@@ -314,9 +315,34 @@ export function drawMoleculeDifferenceOnCanvas(
       const subX0 = printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
       const subX1 = printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
       updatedX = Math.max(subX1, subX0);
+      if (molDifferences) {        
+        molDifferences[i] = createDifferenceCanvas(amino1, amino2, color1, color2, updatedY, vShift, h);
+      }
     } else
       updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5);
     updatedX += 4;
   }
   g.restore();
 }
+
+function createDifferenceCanvas(
+  amino1: string, 
+  amino2: string, 
+  color1: string, 
+  color2: string, 
+  y: number,
+  shift: number, 
+  h: number): HTMLCanvasElement {
+    const canvas = document.createElement('canvas');
+    const context = canvas.getContext('2d')!;
+    const width1 = context.measureText(processSequence([amino1]).join('')).width;
+    const width2 = context.measureText(processSequence([amino2]).join('')).width;
+    const width = Math.max(width1, width2);
+    canvas.height = h;
+    canvas.width = width + 20;
+    context.font = '12px monospace';
+    context.textBaseline = 'top';
+    printLeftOrCentered(0, y - shift, width, h, context, amino1, color1, 0, true);
+    printLeftOrCentered(0, y + shift, width, h, context, amino2, color2, 0, true);
+    return canvas;
+}

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

@@ -88,8 +88,24 @@ export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivE
   canvas.height = 30;
   const units = params.seqCol.getTag(DG.TAGS.UNITS);
   const separator = params.seqCol.getTag(TAGS.SEPARATOR);
-  drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30, sequencesArray.join('#'), units, separator, true);
+  const molDifferences: {[key: number]: HTMLCanvasElement} = {};
+  drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30, sequencesArray.join('#'), units, separator, true, molDifferences);
   propPanel.append(ui.div(canvas, { style: { width: '300px', overflow: 'scroll' } }));
+  
+  if (Object.keys(molDifferences).length > 0) {
+    const diffsPanel = ui.divV([]);
+    diffsPanel.append(ui.divH([
+      ui.divText('Pos', { style: { fontWeight: 'bold', width: '30px' } }),
+      ui.divText('Difference', { style: { fontWeight: 'bold' } }) 
+    ]))
+    for (let key of Object.keys(molDifferences)) {
+      diffsPanel.append(ui.divH([
+        ui.divText(key, { style: { width: '30px' } }),
+        molDifferences[key as any]
+      ]));
+    }
+    propPanel.append(diffsPanel);
+  }
 
   function addFiledToPropPanel(name: string, value: number) {
     propPanel.append(ui.divH([

package/test-Bio-7770371320b2-1095ee64.html

@@ -1,374 +0,0 @@
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 1095ee64.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-19 08:10:18</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">40.792s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">25.775s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 183 : Bio.renderers.setRendererManually : Error: Tag 'cell.renderer' has been manually set to 'MacromoleculeDifference' for column but after df was added as table, tag 'cell.renderer' has reset to 'sequence' instead of manual 'MacromoleculeDifference'.
-
-    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:68:20
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
-    at runMicrotasks (&lt;anonymous&gt;)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:40:11
-    at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
-    at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
-    at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Bio package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:66:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
-    at runMicrotasks (&lt;anonymous&gt;)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 6 : Bio.WebLogo.testGetStats : OK
-Test result : Success : 0 : Bio.WebLogo.testGetAlphabetSimilarity : OK
-Test result : Success : 2 : Bio.WebLogo.testPickupPaletteN1 : OK
-Test result : Success : 2 : Bio.WebLogo.testPickupPaletteN1e : OK
-Test result : Success : 2 : Bio.WebLogo.testPickupPaletteAA1 : OK
-Test result : Success : 2 : Bio.WebLogo.testPickupPaletteX : OK
-Test result : Success : 1 : Bio.WebLogo.monomerToText.longMonomerSingle : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerShort : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
-Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
-Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
-Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
-Test result : Success : 49 : Bio.detectors.NegativeEmpty : OK
-Test result : Success : 15 : Bio.detectors.Negative1 : OK
-Test result : Success : 22 : Bio.detectors.Negative2 : OK
-Test result : Success : 16 : Bio.detectors.Negative3 : OK
-Test result : Success : 14 : Bio.detectors.NegativeSmiles : OK
-Test result : Success : 9 : Bio.detectors.Dna1 : OK
-Test result : Success : 26 : Bio.detectors.Rna1 : OK
-Test result : Success : 41 : Bio.detectors.AA1 : OK
-Test result : Success : 26 : Bio.detectors.MsaDna1 : OK
-Test result : Success : 20 : Bio.detectors.MsaAA1 : OK
-Test result : Success : 40 : Bio.detectors.SepDna : OK
-Test result : Success : 21 : Bio.detectors.SepRna : OK
-Test result : Success : 17 : Bio.detectors.SepPt : OK
-Test result : Success : 15 : Bio.detectors.SepUn1 : OK
-Test result : Success : 19 : Bio.detectors.SepUn2 : OK
-Test result : Success : 18 : Bio.detectors.SepMsaN1 : OK
-Test result : Success : 653 : Bio.detectors.SamplesFastaCsvPt : OK
-Test result : Success : 17 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
-Test result : Success : 20 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
-Test result : Success : 89 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
-Test result : Success : 417 : Bio.detectors.SamplesFastaFastaPt : OK
-Test result : Success : 1139 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
-Test result : Success : 28 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
-Test result : Success : 211 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
-Test result : Success : 285 : Bio.detectors.samplesMsaComplexUn : OK
-Test result : Success : 38 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
-Test result : Success : 212 : Bio.detectors.samplesIdCsvNegativeID : OK
-Test result : Success : 242 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
-Test result : Success : 208 : Bio.detectors.samplesHelmCsvHELM : OK
-Test result : Success : 13 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
-Test result : Success : 248 : Bio.detectors.samplesTestHelmNegativeID : OK
-Test result : Success : 15 : Bio.detectors.samplesTestHelmNegativeTestType : OK
-Test result : Success : 9 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
-Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeValid : OK
-Test result : Success : 5 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
-Test result : Success : 8 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
-Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
-Test result : Success : 1095 : Bio.detectors.samplesTestDemogNegativeAll : OK
-Test result : Success : 889 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
-Test result : Success : 274 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
-Test result : Success : 273 : Bio.detectors.samplesFastaPtPosSequence : OK
-Test result : Success : 216 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
-Test result : Success : 348 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
-Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
-Test result : Success : 14 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
-Test result : Success : 29 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
-Test result : Success : 231 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
-Test result : Success : 5 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
-Test result : Success : 219 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
-Test result : Success : 24 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
-Test result : Success : 249 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
-Test result : Success : 1661 : Bio.MSA.isCorrect : OK
-Test result : Success : 306 : Bio.MSA.isCorrectLong : OK
-Test result : Success : 1216 : Bio.sequenceSpace.sequenceSpaceOpens : OK
-Test result : Success : 4269 : Bio.sequenceSpace.sequenceSpaceOpensWithEmptyRows : OK
-Test result : Success : 947 : Bio.activityCliffs.activityCliffsOpen : OK
-Test result : Success : 853 : Bio.activityCliffs.activityCliffsOpenWithEmptyRows : OK
-Test result : Success : 1 : Bio.splitters.helm1 : OK
-Test result : Success : 1 : Bio.splitters.helm2 : OK
-Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
-Test result : Success : 1 : Bio.splitters.testHelm1 : OK
-Test result : Success : 1 : Bio.splitters.testHelm2 : OK
-Test result : Success : 1 : Bio.splitters.testHelm3 : OK
-Test result : Success : 335 : Bio.splitters.splitToMonomers : OK
-Test result : Success : 2 : Bio.splitters.getHelmMonomers : OK
-Test result : Success : 93 : Bio.renderers.long sequence performance  : OK
-Test result : Success : 676 : Bio.renderers.many sequence performance : OK
-Test result : Success : 269 : Bio.renderers.rendererMacromoleculeFasta : OK
-Test result : Success : 218 : Bio.renderers.rendererMacromoleculeSeparator : OK
-Test result : Success : 72 : Bio.renderers.rendererMacromoleculeDifference : OK
-Test result : Success : 534 : Bio.renderers.afterMsa : OK
-Test result : Success : 238 : Bio.renderers.afterConvert : OK
-Test result : Success : 207 : Bio.renderers.selectRendererBySemType : OK
-Test result : Success : 6 : Bio.converters.testFastaPtToSeparator : OK
-Test result : Success : 10 : Bio.converters.testFastaDnaToSeparator : OK
-Test result : Success : 6 : Bio.converters.testFastaRnaToSeparator : OK
-Test result : Success : 5 : Bio.converters.testFastaGapsToSeparator : OK
-Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
-Test result : Success : 1 : Bio.converters.testFastaDnaToHelm : OK
-Test result : Success : 1 : Bio.converters.testFastaRnaToHelm : OK
-Test result : Success : 2 : Bio.converters.testFastaGapsToHelm : OK
-Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
-Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
-Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
-Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
-Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
-Test result : Success : 1 : Bio.converters.testSeparatorDnaToHelm : OK
-Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
-Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
-Test result : Success : 0 : Bio.converters.testHelmDnaToFasta : OK
-Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
-Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
-Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
-Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
-Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
-Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
-Test result : Success : 3 : Bio.converters.testHelmLoneDeoxyribose : OK
-Test result : Success : 1 : Bio.converters.testHelmLonePhosphorus : OK
-Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
-Test result : Success : 1 : Bio.fastaFileHandler.testExtraSpaces : OK
-Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
-Test result : Success : 111 : Bio.WebLogo-positions.allPositions : OK
-Test result : Success : 116 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
-Test result : Success : 126 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
-Test result : Success : 8 : Bio.checkInputColumn.testMsaPos : OK
-Test result : Success : 2 : Bio.checkInputColumn.testMsaNegHelm : OK
-Test result : Success : 2 : Bio.checkInputColumn.testMsaNegUN : OK
-Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
-</pre></div></div></div></div></body></html>