@datagrok/bio 2.1.0 → 2.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (6) hide show
  1. package/dist/package-test.js +276 -246
  2. package/dist/package.js +276 -246
  3. package/package.json +2 -2
  4. package/src/package.ts +21 -65
  5. package/src/widgets/representations.ts +1 -1
  6. package/{test-Bio-3afbd4014fa1-de511bfe.html → test-Bio-3afbd4014fa1-8c5a0df5.html} +98 -98
package/package.json CHANGED
@@ -5,7 +5,7 @@
5
5
  "name": "Leonid Stolbov",
6
6
  "email": "lstolbov@datagrok.ai"
7
7
  },
8
- "version": "2.1.0",
8
+ "version": "2.1.1",
9
9
  "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
10
10
  "repository": {
11
11
  "type": "git",
@@ -14,7 +14,7 @@
14
14
  },
15
15
  "dependencies": {
16
16
  "@biowasm/aioli": "^3.1.0",
17
- "@datagrok-libraries/bio": "^5.9.12",
17
+ "@datagrok-libraries/bio": "^5.9.13",
18
18
  "@datagrok-libraries/chem-meta": "1.0.1",
19
19
  "@datagrok-libraries/ml": "^6.2.2",
20
20
  "@datagrok-libraries/utils": "^1.14.1",
package/src/package.ts CHANGED
@@ -2,7 +2,6 @@
2
2
  import * as grok from 'datagrok-api/grok';
3
3
  import * as ui from 'datagrok-api/ui';
4
4
  import * as DG from 'datagrok-api/dg';
5
- import * as bio from '@datagrok-libraries/bio';
6
5
 
7
6
  export const _package = new DG.Package();
8
7
 
@@ -13,7 +12,7 @@ import {SequenceAlignment, Aligned} from './seq_align';
13
12
  import {getEmbeddingColsNames, sequenceSpace, sequenceSpaceByFingerprints} from './analysis/sequence-space';
14
13
  import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
15
14
  import {createLinesGrid, createPropPanelElement, createTooltipElement, getChemSimilaritiesMarix, getSimilaritiesMarix} from './analysis/sequence-activity-cliffs';
16
- import {createJsonMonomerLibFromSdf, encodeMonomers, getMolfilesFromSeq} from '@datagrok-libraries/bio/src/utils/monomer-utils';
15
+ import {createJsonMonomerLibFromSdf, encodeMonomers, getMolfilesFromSeq} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
17
16
  import {HELM_CORE_LIB_FILENAME} from '@datagrok-libraries/bio/src/utils/const';
18
17
  import {getMacroMol} from './utils/atomic-works';
19
18
  import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
@@ -39,16 +38,17 @@ import {saveAsFastaUI} from './utils/save-as-fasta';
39
38
  import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
40
39
  import { getMonomericMols } from './calculations/monomerLevelMols';
41
40
  import { delay } from '@datagrok-libraries/utils/src/test';
42
- import {Observable, Subject} from 'rxjs';
41
+ import {from, Observable, Subject} from 'rxjs';
42
+ import {Monomer, IMonomerLib, MonomerWorks, MonomerLib, readLibrary,
43
+ SeqPalette, UnitsHandler, WebLogoViewer, getStats, splitterAsHelm} from '@datagrok-libraries/bio';
43
44
 
44
45
  const STORAGE_NAME = 'Libraries';
45
- const LIB_PATH = 'libraries/';
46
- const expectedMonomerData = ['symbol', 'name', 'molfile', 'rgroups', 'polymerType', 'monomerType'];
46
+ const LIB_PATH = 'System:AppData/Bio/libraries';
47
47
 
48
- let monomerLib: bio.IMonomerLib | null = null;
48
+ let monomerLib: IMonomerLib | null = null;
49
49
  export let hydrophobPalette: SeqPaletteCustom | null = null;
50
50
 
51
- export class SeqPaletteCustom implements bio.SeqPalette {
51
+ export class SeqPaletteCustom implements SeqPalette {
52
52
  private readonly _palette: { [m: string]: string };
53
53
  constructor(palette: { [m: string]: string }) {
54
54
  this._palette = palette;
@@ -67,7 +67,7 @@ export async function initBio() {
67
67
  const module = await grok.functions.call('Chem:getRdKitModule');
68
68
 
69
69
 
70
- const series = monomerLib!.getMonomersByType('PEPTIDE')!;
70
+ const series = monomerLib!.getMonomerMolsByType('PEPTIDE')!;
71
71
  Object.keys(series).forEach(symbol => {
72
72
  monomers.push(symbol);
73
73
  const block = series[symbol].replaceAll('#R', 'O ');
@@ -90,67 +90,23 @@ export async function initBio() {
90
90
 
91
91
  async function loadLibraries() {
92
92
  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
93
- for (let i = 0; i < 1; ++i)
93
+ for (let i = 0; i < uploadedLibraries.length; ++i)
94
94
  await monomerManager(uploadedLibraries[i]);
95
95
  }
96
96
 
97
97
  //name: monomerManager
98
98
  //input: string value
99
99
  export async function monomerManager(value: string) {
100
- let data: any[] = [];
101
- let file;
102
- let dfSdf;
103
- if (value.endsWith('.sdf')) {
104
- const funcList: DG.Func[] = DG.Func.find({package: 'Chem', name: 'importSdf'});
105
- if (funcList.length === 1) {
106
- file = await _package.files.readAsBytes(`${LIB_PATH}${value}`);
107
- dfSdf = await grok.functions.call('Chem:importSdf', {bytes: file});
108
- data = createJsonMonomerLibFromSdf(dfSdf[0]);
109
- } else {
110
- grok.shell.warning('Chem package is not installed');
111
- }
112
- } else {
113
- const file = await _package.files.readAsText(`${LIB_PATH}${value}`);
114
- data = JSON.parse(file);
115
- }
116
-
117
- let monomers: { [type: string]: { [name: string]: bio.Monomer } } = {};
118
- const types: string[] = [];
119
- //group monomers by their type
120
- data.forEach(monomer => {
121
- let monomerAdd: bio.Monomer = {
122
- 'symbol': monomer['symbol'],
123
- 'name': monomer['name'],
124
- 'naturalAnalog': monomer['naturalAnalog'],
125
- 'molfile': monomer['molfile'],
126
- 'rgroups': monomer['rgroups'],
127
- 'polymerType': monomer['polymerType'],
128
- 'monomerType': monomer['monomerType'],
129
- 'data': {}
130
- };
131
-
132
- Object.keys(monomer).forEach(prop => {
133
- if (!expectedMonomerData.includes(prop))
134
- monomerAdd.data[prop] = monomer[prop];
135
- });
136
-
137
- if (!types.includes(monomer['polymerType'])) {
138
- monomers[monomer['polymerType']] = {};
139
- types.push(monomer['polymerType']);
140
- }
141
-
142
- monomers[monomer['polymerType']][monomer['symbol']] = monomerAdd;
143
- });
144
-
145
100
  if (monomerLib == null)
146
- monomerLib = new bio.MonomerLib();
147
-
148
- monomerLib!.update(monomers);
101
+ monomerLib = await readLibrary(LIB_PATH, value);
102
+ else {
103
+ monomerLib!.update(await readLibrary(LIB_PATH, value));
104
+ }
149
105
  }
150
106
 
151
107
  //name: getBioLib
152
108
  //output: object monomerLib
153
- export function getBioLib(): bio.IMonomerLib | null {
109
+ export function getBioLib(): IMonomerLib | null {
154
110
  return monomerLib;
155
111
  }
156
112
 
@@ -245,7 +201,7 @@ export function checkInputColumn(
245
201
  let res: boolean = true;
246
202
  let msg: string = '';
247
203
 
248
- const uh = new bio.UnitsHandler(col);
204
+ const uh = new UnitsHandler(col);
249
205
  if (col.semType !== DG.SEMTYPE.MACROMOLECULE) {
250
206
  grok.shell.warning(name + ' analysis is allowed for Macromolecules semantic type');
251
207
  res = false;
@@ -295,7 +251,7 @@ export function sequenceAlignment(alignType: string, alignTable: string, gap: nu
295
251
  //tags: viewer, panel
296
252
  //output: viewer result
297
253
  export function webLogoViewer() {
298
- return new bio.WebLogoViewer();
254
+ return new WebLogoViewer();
299
255
  }
300
256
 
301
257
  //name: VdRegions
@@ -475,7 +431,7 @@ export async function compositionAnalysis(): Promise<void> {
475
431
  if (col.semType != DG.SEMTYPE.MACROMOLECULE)
476
432
  return false;
477
433
 
478
- const colUH = new bio.UnitsHandler(col);
434
+ const colUH = new UnitsHandler(col);
479
435
  // TODO: prevent for cyclic, branched or multiple chains in Helm
480
436
  return true;
481
437
  });
@@ -494,7 +450,7 @@ export async function compositionAnalysis(): Promise<void> {
494
450
  return;
495
451
  } else if (colList.length > 1) {
496
452
  const colListNames: string [] = colList.map((col) => col.name);
497
- const selectedCol = colList.find((c) => { return (new bio.UnitsHandler(c)).isMsa(); });
453
+ const selectedCol = colList.find((c) => { return (new UnitsHandler(c)).isMsa(); });
498
454
  const colInput: DG.InputBase = ui.choiceInput(
499
455
  'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
500
456
  ui.dialog({
@@ -546,7 +502,7 @@ export async function peptideMolecule(macroMolecule: DG.Cell): Promise<DG.Widget
546
502
  //input: string fileContent
547
503
  //output: list tables
548
504
  export function importFasta(fileContent: string): DG.DataFrame [] {
549
- const ffh = new bio.FastaFileHandler(fileContent);
505
+ const ffh = new FastaFileHandler(fileContent);
550
506
  return ffh.importFasta();
551
507
  }
552
508
 
@@ -621,7 +577,7 @@ export async function testDetectMacromolecule(path: string): Promise<DG.DataFram
621
577
  //tags: panel, bio
622
578
  //input: column col {semType: Macromolecule}
623
579
  export function splitToMonomers(col: DG.Column<string>): void {
624
- if (!col.getTag(bio.TAGS.aligned).includes(C.MSA))
580
+ if (!col.getTag(TAGS.aligned).includes(C.MSA))
625
581
  return grok.shell.error('Splitting is applicable only for aligned sequences');
626
582
 
627
583
  const tempDf = splitAlignedSequences(col);
@@ -638,7 +594,7 @@ export function splitToMonomers(col: DG.Column<string>): void {
638
594
  //name: Bio: getHelmMonomers
639
595
  //input: column sequence {semType: Macromolecule}
640
596
  export function getHelmMonomers(sequence: DG.Column<string>): string[] {
641
- const stats = bio.getStats(sequence, 1, bio.splitterAsHelm);
597
+ const stats = getStats(sequence, 1, splitterAsHelm);
642
598
  return Object.keys(stats.freq);
643
599
  }
644
600
 
package/src/widgets/representations.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import * as grok from 'datagrok-api/grok';
2
2
  import * as ui from 'datagrok-api/ui';
3
3
  import * as DG from 'datagrok-api/dg';
4
- import {getMolfilesFromSingleSeq} from '@datagrok-libraries/bio/src/utils/monomer-utils';
4
+ import {getMolfilesFromSingleSeq} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
5
5
  import {HELM_CORE_LIB_FILENAME} from '@datagrok-libraries/bio/src/utils/const';
6
6
 
7
7
  /**
package/{test-Bio-3afbd4014fa1-de511bfe.html → test-Bio-3afbd4014fa1-8c5a0df5.html} RENAMED
@@ -1,4 +1,4 @@
1
- <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=3afbd4014fa1. Commit de511bfe.</title><style type="text/css">html,
1
+ <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=3afbd4014fa1. Commit 8c5a0df5.</title><style type="text/css">html,
2
2
  body {
3
3
  font-family: Arial, Helvetica, sans-serif;
4
4
  font-size: 1rem;
@@ -229,17 +229,17 @@ header {
229
229
  font-size: 1rem;
230
230
  padding: 0 0.5rem;
231
231
  }
232
- </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=3afbd4014fa1. Commit de511bfe.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-07 13:45:52</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">36.52s</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">22.685s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 230 : Bio.splitters.splitToMonomers : TypeError: Cannot read properties of undefined (reading 'push')
232
+ </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=3afbd4014fa1. Commit 8c5a0df5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-08 13:09:19</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">28.64s</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">19.009s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 180 : Bio.splitters.splitToMonomers : TypeError: Cannot read properties of undefined (reading 'push')
233
233
  Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot read properties of undefined (reading 'forEach')
234
- Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot read properties of undefined (reading 'endsWith')
235
- Test result : Failed : 265 : Bio.renderers.rendererMacromoleculeFasta : TypeError: Cannot read properties of undefined (reading 'push')
236
- Test result : Failed : 174 : Bio.renderers.rendererMacromoleculeSeparator : TypeError: Cannot read properties of undefined (reading 'push')
237
- Test result : Failed : 59 : Bio.renderers.rendererMacromoleculeDifference : TypeError: Cannot read properties of undefined (reading 'push')
238
- Test result : Failed : 329 : Bio.renderers.afterMsa : TypeError: Cannot read properties of undefined (reading 'push')
239
- Test result : Failed : 238 : Bio.renderers.afterConvert : TypeError: Cannot read properties of undefined (reading 'push')
240
- Test result : Failed : 63 : Bio.renderers.selectRendererBySemType : TypeError: Cannot read properties of undefined (reading 'push')
234
+ Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot read properties of null (reading 'getMonomerMolsByType')
235
+ Test result : Failed : 311 : Bio.renderers.rendererMacromoleculeFasta : TypeError: Cannot read properties of undefined (reading 'push')
236
+ Test result : Failed : 184 : Bio.renderers.rendererMacromoleculeSeparator : TypeError: Cannot read properties of undefined (reading 'push')
237
+ Test result : Failed : 54 : Bio.renderers.rendererMacromoleculeDifference : TypeError: Cannot read properties of undefined (reading 'push')
238
+ Test result : Failed : 311 : Bio.renderers.afterMsa : TypeError: Cannot read properties of undefined (reading 'push')
239
+ Test result : Failed : 186 : Bio.renderers.afterConvert : TypeError: Cannot read properties of undefined (reading 'push')
240
+ Test result : Failed : 58 : Bio.renderers.selectRendererBySemType : TypeError: Cannot read properties of undefined (reading 'push')
241
241
  Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read properties of undefined (reading 'forEach')
242
- Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read properties of undefined (reading 'endsWith')
242
+ Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read properties of null (reading 'getMonomerMolsByType')
243
243
 
244
244
  at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:70:20
245
245
  at Generator.next (&lt;anonymous&gt;)
@@ -259,131 +259,131 @@ Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read propertie
259
259
  at Generator.next (&lt;anonymous&gt;)
260
260
  at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
261
261
  at runMicrotasks (&lt;anonymous&gt;)
262
- at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
263
- Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
262
+ at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 0 : Bio.Palettes.testPaletteN : OK
263
+ Test result : Success : 1 : Bio.Palettes.testPaletteAA : OK
264
264
  Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
265
- Test result : Success : 49 : Bio.detectors.NegativeEmpty : OK
265
+ Test result : Success : 83 : Bio.detectors.NegativeEmpty : OK
266
266
  Test result : Success : 15 : Bio.detectors.Negative1 : OK
267
- Test result : Success : 21 : Bio.detectors.Negative2 : OK
268
- Test result : Success : 14 : Bio.detectors.Negative3 : OK
269
- Test result : Success : 53 : Bio.detectors.NegativeSmiles : OK
270
- Test result : Success : 21 : Bio.detectors.Dna1 : OK
271
- Test result : Success : 23 : Bio.detectors.Rna1 : OK
272
- Test result : Success : 17 : Bio.detectors.AA1 : OK
273
- Test result : Success : 8 : Bio.detectors.MsaDna1 : OK
267
+ Test result : Success : 27 : Bio.detectors.Negative2 : OK
268
+ Test result : Success : 18 : Bio.detectors.Negative3 : OK
269
+ Test result : Success : 372 : Bio.detectors.NegativeSmiles : OK
270
+ Test result : Success : 27 : Bio.detectors.Dna1 : OK
271
+ Test result : Success : 16 : Bio.detectors.Rna1 : OK
272
+ Test result : Success : 8 : Bio.detectors.AA1 : OK
273
+ Test result : Success : 16 : Bio.detectors.MsaDna1 : OK
274
274
  Test result : Success : 13 : Bio.detectors.MsaAA1 : OK
275
- Test result : Success : 13 : Bio.detectors.SepDna : OK
276
- Test result : Success : 28 : Bio.detectors.SepRna : OK
277
- Test result : Success : 25 : Bio.detectors.SepPt : OK
275
+ Test result : Success : 28 : Bio.detectors.SepDna : OK
276
+ Test result : Success : 24 : Bio.detectors.SepRna : OK
277
+ Test result : Success : 26 : Bio.detectors.SepPt : OK
278
278
  Test result : Success : 9 : Bio.detectors.SepUn1 : OK
279
279
  Test result : Success : 7 : Bio.detectors.SepUn2 : OK
280
- Test result : Success : 7 : Bio.detectors.SepMsaN1 : OK
281
- Test result : Success : 392 : Bio.detectors.SamplesFastaCsvPt : OK
282
- Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
283
- Test result : Success : 5 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
284
- Test result : Success : 38 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
285
- Test result : Success : 272 : Bio.detectors.SamplesFastaFastaPt : OK
286
- Test result : Success : 879 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
287
- Test result : Success : 16 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
288
- Test result : Success : 114 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
289
- Test result : Success : 349 : Bio.detectors.samplesMsaComplexUn : OK
290
- Test result : Success : 55 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
291
- Test result : Success : 705 : Bio.detectors.samplesIdCsvNegativeID : OK
292
- Test result : Success : 631 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
293
- Test result : Success : 192 : Bio.detectors.samplesHelmCsvHELM : OK
294
- Test result : Success : 28 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
295
- Test result : Success : 149 : Bio.detectors.samplesTestHelmNegativeID : OK
296
- Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeTestType : OK
297
- Test result : Success : 12 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
298
- Test result : Success : 8 : Bio.detectors.samplesTestHelmNegativeValid : OK
299
- Test result : Success : 25 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
300
- Test result : Success : 18 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
301
- Test result : Success : 9 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
302
- Test result : Success : 1413 : Bio.detectors.samplesTestDemogNegativeAll : OK
303
- Test result : Success : 503 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
304
- Test result : Success : 152 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
305
- Test result : Success : 133 : Bio.detectors.samplesFastaPtPosSequence : OK
306
- Test result : Success : 143 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
307
- Test result : Success : 281 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
308
- Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
309
- Test result : Success : 4 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
310
- Test result : Success : 12 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
311
- Test result : Success : 193 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
312
- Test result : Success : 11 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
313
- Test result : Success : 181 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
314
- Test result : Success : 6 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
315
- Test result : Success : 188 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
316
- Test result : Success : 1740 : Bio.MSA.isCorrect : OK
317
- Test result : Success : 162 : Bio.MSA.isCorrectLong : OK
318
- Test result : Success : 1243 : Bio.sequenceSpace.sequenceSpaceOpens : OK
319
- Test result : Success : 532 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
320
- Test result : Success : 768 : Bio.activityCliffs.activityCliffsOpens : OK
321
- Test result : Success : 1159 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
280
+ Test result : Success : 19 : Bio.detectors.SepMsaN1 : OK
281
+ Test result : Success : 425 : Bio.detectors.SamplesFastaCsvPt : OK
282
+ Test result : Success : 4 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
283
+ Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
284
+ Test result : Success : 78 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
285
+ Test result : Success : 195 : Bio.detectors.SamplesFastaFastaPt : OK
286
+ Test result : Success : 636 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
287
+ Test result : Success : 7 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
288
+ Test result : Success : 94 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
289
+ Test result : Success : 189 : Bio.detectors.samplesMsaComplexUn : OK
290
+ Test result : Success : 39 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
291
+ Test result : Success : 128 : Bio.detectors.samplesIdCsvNegativeID : OK
292
+ Test result : Success : 142 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
293
+ Test result : Success : 140 : Bio.detectors.samplesHelmCsvHELM : OK
294
+ Test result : Success : 5 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
295
+ Test result : Success : 85 : Bio.detectors.samplesTestHelmNegativeID : OK
296
+ Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeTestType : OK
297
+ Test result : Success : 4 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
298
+ Test result : Success : 3 : Bio.detectors.samplesTestHelmNegativeValid : OK
299
+ Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
300
+ Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
301
+ Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
302
+ Test result : Success : 459 : Bio.detectors.samplesTestDemogNegativeAll : OK
303
+ Test result : Success : 214 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
304
+ Test result : Success : 122 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
305
+ Test result : Success : 90 : Bio.detectors.samplesFastaPtPosSequence : OK
306
+ Test result : Success : 102 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
307
+ Test result : Success : 136 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
308
+ Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
309
+ Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
310
+ Test result : Success : 4 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
311
+ Test result : Success : 128 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
312
+ Test result : Success : 3 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
313
+ Test result : Success : 106 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
314
+ Test result : Success : 5 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
315
+ Test result : Success : 116 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
316
+ Test result : Success : 1104 : Bio.MSA.isCorrect : OK
317
+ Test result : Success : 134 : Bio.MSA.isCorrectLong : OK
318
+ Test result : Success : 920 : Bio.sequenceSpace.sequenceSpaceOpens : OK
319
+ Test result : Success : 498 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
320
+ Test result : Success : 730 : Bio.activityCliffs.activityCliffsOpens : OK
321
+ Test result : Success : 793 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
322
322
  Test result : Success : 1 : Bio.splitters.fastaMulti : OK
323
- Test result : Success : 0 : Bio.splitters.helm1 : OK
323
+ Test result : Success : 1 : Bio.splitters.helm1 : OK
324
324
  Test result : Success : 0 : Bio.splitters.helm2 : OK
325
325
  Test result : Success : 0 : Bio.splitters.helm3-multichar : OK
326
326
  Test result : Success : 0 : Bio.splitters.testHelm1 : OK
327
- Test result : Success : 0 : Bio.splitters.testHelm2 : OK
327
+ Test result : Success : 1 : Bio.splitters.testHelm2 : OK
328
328
  Test result : Success : 1 : Bio.splitters.testHelm3 : OK
329
329
  Test result : Success : 1 : Bio.splitters.getHelmMonomers : OK
330
- Test result : Success : 74 : Bio.renderers.long sequence performance : OK
331
- Test result : Success : 732 : Bio.renderers.many sequence performance : OK
330
+ Test result : Success : 70 : Bio.renderers.long sequence performance : OK
331
+ Test result : Success : 615 : Bio.renderers.many sequence performance : OK
332
332
  Test result : Success : 0 : Bio.renderers.setRendererManually : GROK-11212
333
- Test result : Success : 5 : Bio.converters.testFastaPtToSeparator : OK
333
+ Test result : Success : 4 : Bio.converters.testFastaPtToSeparator : OK
334
334
  Test result : Success : 3 : Bio.converters.testFastaDnaToSeparator : OK
335
- Test result : Success : 3 : Bio.converters.testFastaRnaToSeparator : OK
336
- Test result : Success : 2 : Bio.converters.testFastaGapsToSeparator : OK
337
- Test result : Success : 1 : Bio.converters.testFastaPtToHelm : OK
338
- Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
339
- Test result : Success : 1 : Bio.converters.testFastaRnaToHelm : OK
340
- Test result : Success : 2 : Bio.converters.testFastaGapsToHelm : OK
341
- Test result : Success : 0 : Bio.converters.testSeparatorPtToFasta : OK
342
- Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
343
- Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
335
+ Test result : Success : 2 : Bio.converters.testFastaRnaToSeparator : OK
336
+ Test result : Success : 3 : Bio.converters.testFastaGapsToSeparator : OK
337
+ Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
338
+ Test result : Success : 1 : Bio.converters.testFastaDnaToHelm : OK
339
+ Test result : Success : 2 : Bio.converters.testFastaRnaToHelm : OK
340
+ Test result : Success : 1 : Bio.converters.testFastaGapsToHelm : OK
341
+ Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
342
+ Test result : Success : 0 : Bio.converters.testSeparatorDnaToFasta : OK
343
+ Test result : Success : 1 : Bio.converters.testSeparatorRnaToFasta : OK
344
344
  Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
345
345
  Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
346
346
  Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
347
- Test result : Success : 1 : Bio.converters.testSeparatorRnaToHelm : OK
348
- Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
349
- Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
350
- Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
347
+ Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
348
+ Test result : Success : 1 : Bio.converters.testSeparatorGapsToHelm : OK
349
+ Test result : Success : 0 : Bio.converters.testHelmDnaToFasta : OK
350
+ Test result : Success : 0 : Bio.converters.testHelmRnaToFasta : OK
351
351
  Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
352
- Test result : Success : 1 : Bio.converters.testHelmDnaToSeparator : OK
352
+ Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
353
353
  Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
354
354
  Test result : Success : 1 : Bio.converters.testHelmPtToSeparator : OK
355
355
  Test result : Success : 1 : Bio.converters.testHelmLoneRibose : OK
356
- Test result : Success : 11 : Bio.converters.testHelmLoneDeoxyribose : OK
356
+ Test result : Success : 2 : Bio.converters.testHelmLoneDeoxyribose : OK
357
357
  Test result : Success : 1 : Bio.converters.testHelmLonePhosphorus : OK
358
- Test result : Success : 9 : Bio.fastaFileHandler.testNormalFormatting : OK
358
+ Test result : Success : 1 : Bio.fastaFileHandler.testNormalFormatting : OK
359
359
  Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
360
360
  Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
361
361
  Test result : Success : 0 : Bio.fastaExport.wrapSequenceSingle : OK
362
362
  Test result : Success : 0 : Bio.fastaExport.wrapSequenceMulti : OK
363
- Test result : Success : 2 : Bio.fastaExport.saveAsFastaTest1 : OK
363
+ Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest1 : OK
364
364
  Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest2 : OK
365
365
  Test result : Success : 1 : Bio.bio.testGetStatsHelm1 : OK
366
366
  Test result : Success : 1 : Bio.bio.testGetStatsN1 : OK
367
367
  Test result : Success : 0 : Bio.bio.testGetAlphabetSimilarity : OK
368
368
  Test result : Success : 1 : Bio.bio.testPickupPaletteN1 : OK
369
369
  Test result : Success : 1 : Bio.bio.testPickupPaletteN1e : OK
370
- Test result : Success : 8 : Bio.bio.testPickupPaletteAA1 : OK
370
+ Test result : Success : 1 : Bio.bio.testPickupPaletteAA1 : OK
371
371
  Test result : Success : 1 : Bio.bio.testPickupPaletteX : OK
372
372
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerSingle : OK
373
- Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
374
- Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
373
+ Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
374
+ Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
375
375
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
376
376
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : OK
377
- Test result : Success : 247 : Bio.WebLogo-positions.allPositions : OK
378
- Test result : Success : 136 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
379
- Test result : Success : 87 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
377
+ Test result : Success : 92 : Bio.WebLogo-positions.allPositions : OK
378
+ Test result : Success : 73 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
379
+ Test result : Success : 77 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
380
380
  Test result : Success : 3 : Bio.checkInputColumn.testMsaPos : OK
381
381
  Test result : Success : 1 : Bio.checkInputColumn.testMsaNegHelm : OK
382
382
  Test result : Success : 1 : Bio.checkInputColumn.testMsaNegUN : OK
383
- Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
384
- Test result : Success : 372 : Bio.similarity/diversity.similaritySearchViewer : OK
385
- Test result : Success : 430 : Bio.similarity/diversity.diversitySearchViewer : OK
386
- Test result : Success : 194 : Bio.substructureFilters.fasta : OK
383
+ Test result : Success : 0 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
384
+ Test result : Success : 360 : Bio.similarity/diversity.similaritySearchViewer : OK
385
+ Test result : Success : 214 : Bio.similarity/diversity.diversitySearchViewer : OK
386
+ Test result : Success : 190 : Bio.substructureFilters.fasta : OK
387
387
  Test result : Success : 394 : Bio.substructureFilters.separator : OK
388
- Test result : Success : 1714 : Bio.substructureFilters.helm : OK
388
+ Test result : Success : 1950 : Bio.substructureFilters.helm : OK
389
389
  </pre></div></div></div></div></body></html>