@datagrok/bio 2.0.33 → 2.1.1

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Files changed (6) hide show
  1. package/dist/package-test.js +2529 -2828
  2. package/dist/package.js +2470 -2769
  3. package/package.json +2 -2
  4. package/src/package.ts +35 -129
  5. package/src/widgets/representations.ts +2 -3
  6. package/{test-Bio-3afbd4014fa1-15e7930e.html → test-Bio-3afbd4014fa1-8c5a0df5.html} +104 -104
package/package.json CHANGED
@@ -5,7 +5,7 @@
5
5
  "name": "Leonid Stolbov",
6
6
  "email": "lstolbov@datagrok.ai"
7
7
  },
8
- "version": "2.0.33",
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": "^5.8.0",
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';
@@ -21,7 +20,7 @@ import {convert} from './utils/convert';
21
20
  import {getMacroMolColumnPropertyPanel, representationsWidget} from './widgets/representations';
22
21
  import {MonomerFreqs, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
23
22
  import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule'
24
- import {_toAtomicLevel} from '@datagrok-libraries/bio/src/utils/to-atomic-level';
23
+ import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
25
24
  import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
26
25
  import {removeEmptyStringRows} from '@datagrok-libraries/utils/src/dataframe-utils';
27
26
  import {
@@ -39,80 +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
48
  let monomerLib: IMonomerLib | null = null;
49
49
  export let hydrophobPalette: SeqPaletteCustom | null = null;
50
50
 
51
- class MonomerLib implements IMonomerLib {
52
- private _monomers: { [type: string]: { [name: string]: Monomer } } = {};
53
- private _onChanged = new Subject<any>();
54
-
55
- getMonomer(monomerType: string, monomerName: string): Monomer | null {
56
- if (monomerType in this._monomers! && monomerName in this._monomers![monomerType])
57
- return this._monomers![monomerType][monomerName];
58
- else
59
- return null;
60
- }
61
-
62
- getTypes(): string[] {
63
- return Object.keys(this._monomers);
64
- }
65
-
66
- getMonomersByType(type: string): {[symbol: string]: string} {
67
- let res: {[symbol: string]: string} = {};
68
-
69
- Object.keys(this._monomers[type]).forEach(monomerSymbol => {
70
- res[monomerSymbol] = this._monomers[type][monomerSymbol].molfile;
71
- });
72
-
73
- return res;
74
- }
75
-
76
- get onChanged(): Observable<any> {
77
- return this._onChanged;
78
- }
79
-
80
- public update(monomers: { [type: string]: { [name: string]: Monomer } }): void {
81
- Object.keys(monomers).forEach(type => {
82
- //could possibly rewrite -> TODO: check duplicated monomer symbol
83
-
84
- if (!this.getTypes().includes(type))
85
- this._monomers![type] = {};
86
-
87
- Object.keys(monomers[type]).forEach(monomerName =>{
88
- this._monomers[type][monomerName] = monomers[type][monomerName];
89
- })
90
- });
91
-
92
- this._onChanged.next();
93
- }
94
- }
95
-
96
- export type Monomer = {
97
- symbol: string,
98
- name: string,
99
- molfile: string,
100
- rgroups: {capGroupSmiles: string, alternateId: string, capGroupName: string, label: string }[],
101
- polymerType: string,
102
- monomerType: string,
103
- data: {[property: string]: string}
104
- }
105
-
106
- //expected types: HELM_AA, HELM_BASE, HELM_CHEM, HELM_LINKER, HELM_SUGAR
107
- export interface IMonomerLib {
108
- getMonomer(monomerType: string, monomerName: string): Monomer | null;
109
- getMonomersByType(type: string): {[symbol: string]: string} | null;
110
- getTypes(): string[];
111
- update(monomers: { [type: string]: { [name: string]: Monomer } }): void;
112
- get onChanged(): Observable<any>;
113
- }
114
-
115
- export class SeqPaletteCustom implements bio.SeqPalette {
51
+ export class SeqPaletteCustom implements SeqPalette {
116
52
  private readonly _palette: { [m: string]: string };
117
53
  constructor(palette: { [m: string]: string }) {
118
54
  this._palette = palette;
@@ -131,7 +67,7 @@ export async function initBio() {
131
67
  const module = await grok.functions.call('Chem:getRdKitModule');
132
68
 
133
69
 
134
- const series = monomerLib!.getMonomersByType('PEPTIDE')!;
70
+ const series = monomerLib!.getMonomerMolsByType('PEPTIDE')!;
135
71
  Object.keys(series).forEach(symbol => {
136
72
  monomers.push(symbol);
137
73
  const block = series[symbol].replaceAll('#R', 'O ');
@@ -154,69 +90,40 @@ export async function initBio() {
154
90
 
155
91
  async function loadLibraries() {
156
92
  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
157
- for (let i = 0; i < 1; ++i)
93
+ for (let i = 0; i < uploadedLibraries.length; ++i)
158
94
  await monomerManager(uploadedLibraries[i]);
159
95
  }
160
96
 
161
97
  //name: monomerManager
162
98
  //input: string value
163
99
  export async function monomerManager(value: string) {
164
- let data: any[] = [];
165
- let file;
166
- let dfSdf;
167
- if (value.endsWith('.sdf')) {
168
- const funcList: DG.Func[] = DG.Func.find({package: 'Chem', name: 'importSdf'});
169
- console.debug(`Helm: initHelm() funcList.length = ${funcList.length}`);
170
- if (funcList.length === 1) {
171
- file = await _package.files.readAsBytes(`${LIB_PATH}${value}`);
172
- dfSdf = await grok.functions.call('Chem:importSdf', {bytes: file});
173
- data = createJsonMonomerLibFromSdf(dfSdf[0]);
174
- } else {
175
- grok.shell.warning('Chem package is not installed');
176
- }
177
- } else {
178
- const file = await _package.files.readAsText(`${LIB_PATH}${value}`);
179
- data = JSON.parse(file);
180
- }
181
-
182
100
  if (monomerLib == null)
183
- monomerLib = new MonomerLib();
184
-
185
- let monomers: { [type: string]: { [name: string]: Monomer } } = {};
186
- const types: string[] = [];
187
- //group monomers by their type
188
- data.forEach(monomer => {
189
- let monomerAdd: Monomer = {
190
- 'symbol': monomer['symbol'],
191
- 'name': monomer['name'],
192
- 'molfile': monomer['molfile'],
193
- 'rgroups': monomer['rgroups'],
194
- 'polymerType': monomer['polymerType'],
195
- 'monomerType': monomer['monomerType'],
196
- 'data': {}
197
- };
198
-
199
- Object.keys(monomer).forEach(prop => {
200
- if (!expectedMonomerData.includes(prop))
201
- monomerAdd.data[prop] = monomer[prop];
202
- });
203
-
204
- if (!types.includes(monomer['polymerType'])) {
205
- monomers[monomer['polymerType']] = {};
206
- types.push(monomer['polymerType']);
207
- }
101
+ monomerLib = await readLibrary(LIB_PATH, value);
102
+ else {
103
+ monomerLib!.update(await readLibrary(LIB_PATH, value));
104
+ }
105
+ }
208
106
 
209
- monomers[monomer['polymerType']][monomer['symbol']] = monomerAdd;
210
- });
107
+ //name: getBioLib
108
+ //output: object monomerLib
109
+ export function getBioLib(): IMonomerLib | null {
110
+ return monomerLib;
111
+ }
211
112
 
212
- monomerLib!.update(monomers);
113
+ //name: manageFiles
114
+ export async function manageFiles() {
115
+ const a = ui.dialog({title: 'Manage files'})
116
+ //@ts-ignore
117
+ .add(ui.fileBrowser({path: 'System:AppData/Bio/libraries'}).root)
118
+ .addButton('OK', () => a.close())
119
+ .show();
213
120
  }
214
121
 
215
122
  //name: Manage Libraries
216
123
  //tags: panel, widgets
217
- //input: column helmColumn {semType: Macromolecule}
124
+ //input: column seqColumn {semType: Macromolecule}
218
125
  //output: widget result
219
- export async function libraryPanel(helmColumn: DG.Column): Promise<DG.Widget> {
126
+ export async function libraryPanel(seqColumn: DG.Column): Promise<DG.Widget> {
220
127
  //@ts-ignore
221
128
  let filesButton: HTMLButtonElement = ui.button('Manage', manageFiles);
222
129
  let divInputs: HTMLDivElement = ui.div();
@@ -227,7 +134,6 @@ export async function libraryPanel(helmColumn: DG.Column): Promise<DG.Widget> {
227
134
  divInputs.append(ui.boolInput(libraryName, true, async() => {
228
135
  grok.dapi.userDataStorage.remove(STORAGE_NAME, libraryName, true);
229
136
  await loadLibraries();
230
- grok.shell.tv.grid.invalidate();
231
137
  }).root);
232
138
  }
233
139
  let unusedLibraries: string[] = librariesList.filter(x => !uploadedLibraries.includes(x));
@@ -295,7 +201,7 @@ export function checkInputColumn(
295
201
  let res: boolean = true;
296
202
  let msg: string = '';
297
203
 
298
- const uh = new bio.UnitsHandler(col);
204
+ const uh = new UnitsHandler(col);
299
205
  if (col.semType !== DG.SEMTYPE.MACROMOLECULE) {
300
206
  grok.shell.warning(name + ' analysis is allowed for Macromolecules semantic type');
301
207
  res = false;
@@ -345,7 +251,7 @@ export function sequenceAlignment(alignType: string, alignTable: string, gap: nu
345
251
  //tags: viewer, panel
346
252
  //output: viewer result
347
253
  export function webLogoViewer() {
348
- return new bio.WebLogoViewer();
254
+ return new WebLogoViewer();
349
255
  }
350
256
 
351
257
  //name: VdRegions
@@ -525,7 +431,7 @@ export async function compositionAnalysis(): Promise<void> {
525
431
  if (col.semType != DG.SEMTYPE.MACROMOLECULE)
526
432
  return false;
527
433
 
528
- const colUH = new bio.UnitsHandler(col);
434
+ const colUH = new UnitsHandler(col);
529
435
  // TODO: prevent for cyclic, branched or multiple chains in Helm
530
436
  return true;
531
437
  });
@@ -544,7 +450,7 @@ export async function compositionAnalysis(): Promise<void> {
544
450
  return;
545
451
  } else if (colList.length > 1) {
546
452
  const colListNames: string [] = colList.map((col) => col.name);
547
- const selectedCol = colList.find((c) => { return (new bio.UnitsHandler(c)).isMsa(); });
453
+ const selectedCol = colList.find((c) => { return (new UnitsHandler(c)).isMsa(); });
548
454
  const colInput: DG.InputBase = ui.choiceInput(
549
455
  'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
550
456
  ui.dialog({
@@ -596,7 +502,7 @@ export async function peptideMolecule(macroMolecule: DG.Cell): Promise<DG.Widget
596
502
  //input: string fileContent
597
503
  //output: list tables
598
504
  export function importFasta(fileContent: string): DG.DataFrame [] {
599
- const ffh = new bio.FastaFileHandler(fileContent);
505
+ const ffh = new FastaFileHandler(fileContent);
600
506
  return ffh.importFasta();
601
507
  }
602
508
 
@@ -671,7 +577,7 @@ export async function testDetectMacromolecule(path: string): Promise<DG.DataFram
671
577
  //tags: panel, bio
672
578
  //input: column col {semType: Macromolecule}
673
579
  export function splitToMonomers(col: DG.Column<string>): void {
674
- if (!col.getTag(bio.TAGS.aligned).includes(C.MSA))
580
+ if (!col.getTag(TAGS.aligned).includes(C.MSA))
675
581
  return grok.shell.error('Splitting is applicable only for aligned sequences');
676
582
 
677
583
  const tempDf = splitAlignedSequences(col);
@@ -688,7 +594,7 @@ export function splitToMonomers(col: DG.Column<string>): void {
688
594
  //name: Bio: getHelmMonomers
689
595
  //input: column sequence {semType: Macromolecule}
690
596
  export function getHelmMonomers(sequence: DG.Column<string>): string[] {
691
- const stats = bio.getStats(sequence, 1, bio.splitterAsHelm);
597
+ const stats = getStats(sequence, 1, splitterAsHelm);
692
598
  return Object.keys(stats.freq);
693
599
  }
694
600
 
package/src/widgets/representations.ts CHANGED
@@ -1,9 +1,8 @@
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
- import {getMacroMol} from '@datagrok-libraries/bio/src/utils/atomic-works';
7
6
 
8
7
  /**
9
8
  * @export
@@ -79,7 +78,7 @@ export async function representationsWidget(macroMolecule: DG.Cell, monomersLibO
79
78
  try {
80
79
  try {
81
80
  const atomicCodes = getMolfilesFromSingleSeq(macroMolecule, monomersLibObject);
82
- const result = await getMacroMol(atomicCodes!);
81
+ const result = ''//await getMacroMol(atomicCodes!);
83
82
  const molBlock2D = result[0];
84
83
  molBlock3D = (await grok.functions.call('Bio:Embed', {molBlock2D})) as unknown as string;
85
84
  } catch (e) {
package/{test-Bio-3afbd4014fa1-15e7930e.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 15e7930e.</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 15e7930e.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-04 14:02:19</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">45.144s</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">28.346s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 234 : 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 : 359 : Bio.renderers.rendererMacromoleculeFasta : TypeError: Cannot read properties of undefined (reading 'push')
236
- Test result : Failed : 254 : Bio.renderers.rendererMacromoleculeSeparator : TypeError: Cannot read properties of undefined (reading 'push')
237
- Test result : Failed : 96 : Bio.renderers.rendererMacromoleculeDifference : TypeError: Cannot read properties of undefined (reading 'push')
238
- Test result : Failed : 545 : Bio.renderers.afterMsa : TypeError: Cannot read properties of undefined (reading 'push')
239
- Test result : Failed : 352 : Bio.renderers.afterConvert : TypeError: Cannot read properties of undefined (reading 'push')
240
- Test result : Failed : 104 : 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;)
@@ -262,128 +262,128 @@ Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read propertie
262
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
263
  Test result : Success : 1 : Bio.Palettes.testPaletteAA : OK
264
264
  Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
265
- Test result : Success : 273 : Bio.detectors.NegativeEmpty : OK
266
- Test result : Success : 34 : Bio.detectors.Negative1 : OK
267
- Test result : Success : 36 : Bio.detectors.Negative2 : OK
268
- Test result : Success : 31 : Bio.detectors.Negative3 : OK
269
- Test result : Success : 44 : Bio.detectors.NegativeSmiles : OK
270
- Test result : Success : 24 : Bio.detectors.Dna1 : OK
271
- Test result : Success : 37 : Bio.detectors.Rna1 : OK
272
- Test result : Success : 38 : Bio.detectors.AA1 : OK
273
- Test result : Success : 23 : Bio.detectors.MsaDna1 : OK
274
- Test result : Success : 46 : Bio.detectors.MsaAA1 : OK
275
- Test result : Success : 21 : Bio.detectors.SepDna : OK
276
- Test result : Success : 22 : Bio.detectors.SepRna : OK
277
- Test result : Success : 24 : Bio.detectors.SepPt : OK
278
- Test result : Success : 19 : Bio.detectors.SepUn1 : OK
279
- Test result : Success : 18 : Bio.detectors.SepUn2 : OK
280
- Test result : Success : 29 : Bio.detectors.SepMsaN1 : OK
281
- Test result : Success : 1790 : Bio.detectors.SamplesFastaCsvPt : OK
282
- Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
265
+ Test result : Success : 83 : Bio.detectors.NegativeEmpty : OK
266
+ Test result : Success : 15 : Bio.detectors.Negative1 : 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
+ Test result : Success : 13 : Bio.detectors.MsaAA1 : 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
+ Test result : Success : 9 : Bio.detectors.SepUn1 : OK
279
+ Test result : Success : 7 : Bio.detectors.SepUn2 : 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
283
  Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
284
- Test result : Success : 137 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
285
- Test result : Success : 335 : Bio.detectors.SamplesFastaFastaPt : OK
286
- Test result : Success : 1536 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
287
- Test result : Success : 41 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
288
- Test result : Success : 239 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
289
- Test result : Success : 340 : Bio.detectors.samplesMsaComplexUn : OK
290
- Test result : Success : 65 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
291
- Test result : Success : 241 : Bio.detectors.samplesIdCsvNegativeID : OK
292
- Test result : Success : 222 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
293
- Test result : Success : 217 : Bio.detectors.samplesHelmCsvHELM : OK
294
- Test result : Success : 28 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
295
- Test result : Success : 213 : Bio.detectors.samplesTestHelmNegativeID : OK
296
- Test result : Success : 23 : Bio.detectors.samplesTestHelmNegativeTestType : OK
297
- Test result : Success : 10 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
298
- Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeValid : OK
299
- Test result : Success : 19 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
300
- Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
301
- Test result : Success : 13 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
302
- Test result : Success : 1437 : Bio.detectors.samplesTestDemogNegativeAll : OK
303
- Test result : Success : 698 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
304
- Test result : Success : 185 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
305
- Test result : Success : 136 : Bio.detectors.samplesFastaPtPosSequence : OK
306
- Test result : Success : 162 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
307
- Test result : Success : 216 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : 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
308
  Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
309
- Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
310
- Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
311
- Test result : Success : 210 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
312
- Test result : Success : 9 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
313
- Test result : Success : 192 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
314
- Test result : Success : 28 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
315
- Test result : Success : 168 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
316
- Test result : Success : 2670 : Bio.MSA.isCorrect : OK
317
- Test result : Success : 124 : Bio.MSA.isCorrectLong : OK
318
- Test result : Success : 1279 : Bio.sequenceSpace.sequenceSpaceOpens : OK
319
- Test result : Success : 596 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
320
- Test result : Success : 836 : Bio.activityCliffs.activityCliffsOpens : OK
321
- Test result : Success : 868 : Bio.activityCliffs.activityCliffsWithEmptyRows : 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
323
  Test result : Success : 1 : Bio.splitters.helm1 : OK
324
324
  Test result : Success : 0 : Bio.splitters.helm2 : OK
325
- Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
325
+ Test result : Success : 0 : Bio.splitters.helm3-multichar : OK
326
326
  Test result : Success : 0 : Bio.splitters.testHelm1 : OK
327
327
  Test result : Success : 1 : Bio.splitters.testHelm2 : OK
328
- Test result : Success : 0 : Bio.splitters.testHelm3 : OK
328
+ Test result : Success : 1 : Bio.splitters.testHelm3 : OK
329
329
  Test result : Success : 1 : Bio.splitters.getHelmMonomers : OK
330
- Test result : Success : 109 : Bio.renderers.long sequence performance : OK
331
- Test result : Success : 918 : 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 : 6 : Bio.converters.testFastaPtToSeparator : OK
334
- Test result : Success : 5 : Bio.converters.testFastaDnaToSeparator : OK
335
- Test result : Success : 4 : Bio.converters.testFastaRnaToSeparator : OK
336
- Test result : Success : 5 : Bio.converters.testFastaGapsToSeparator : OK
333
+ Test result : Success : 4 : Bio.converters.testFastaPtToSeparator : OK
334
+ Test result : Success : 3 : Bio.converters.testFastaDnaToSeparator : OK
335
+ Test result : Success : 2 : Bio.converters.testFastaRnaToSeparator : OK
336
+ Test result : Success : 3 : Bio.converters.testFastaGapsToSeparator : OK
337
337
  Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
338
- Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
338
+ Test result : Success : 1 : Bio.converters.testFastaDnaToHelm : OK
339
339
  Test result : Success : 2 : Bio.converters.testFastaRnaToHelm : OK
340
340
  Test result : Success : 1 : Bio.converters.testFastaGapsToHelm : OK
341
- Test result : Success : 0 : Bio.converters.testSeparatorPtToFasta : OK
342
- Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
341
+ Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
342
+ Test result : Success : 0 : Bio.converters.testSeparatorDnaToFasta : OK
343
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
- Test result : Success : 1 : Bio.converters.testSeparatorDnaToHelm : OK
346
+ Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
347
347
  Test result : Success : 0 : 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
351
- Test result : Success : 1 : Bio.converters.testHelmPtToFasta : 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
+ Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
352
352
  Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
353
- Test result : Success : 1 : Bio.converters.testHelmRnaToSeparator : OK
354
- Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
355
- Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
353
+ Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
354
+ Test result : Success : 1 : Bio.converters.testHelmPtToSeparator : OK
355
+ Test result : Success : 1 : Bio.converters.testHelmLoneRibose : OK
356
356
  Test result : Success : 2 : Bio.converters.testHelmLoneDeoxyribose : OK
357
- Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
358
- Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
359
- Test result : Success : 1 : Bio.fastaFileHandler.testExtraSpaces : OK
357
+ Test result : Success : 1 : Bio.converters.testHelmLonePhosphorus : OK
358
+ Test result : Success : 1 : Bio.fastaFileHandler.testNormalFormatting : OK
359
+ Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
360
360
  Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
361
- Test result : Success : 1 : Bio.fastaExport.wrapSequenceSingle : OK
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
- Test result : Success : 2 : Bio.bio.testGetStatsHelm1 : OK
365
+ Test result : Success : 1 : Bio.bio.testGetStatsHelm1 : OK
366
366
  Test result : Success : 1 : Bio.bio.testGetStatsN1 : OK
367
- Test result : Success : 1 : Bio.bio.testGetAlphabetSimilarity : OK
367
+ Test result : Success : 0 : Bio.bio.testGetAlphabetSimilarity : OK
368
368
  Test result : Success : 1 : Bio.bio.testPickupPaletteN1 : OK
369
- Test result : Success : 2 : Bio.bio.testPickupPaletteN1e : OK
369
+ Test result : Success : 1 : Bio.bio.testPickupPaletteN1e : OK
370
370
  Test result : Success : 1 : Bio.bio.testPickupPaletteAA1 : OK
371
- Test result : Success : 2 : Bio.bio.testPickupPaletteX : OK
371
+ Test result : Success : 1 : Bio.bio.testPickupPaletteX : OK
372
372
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerSingle : OK
373
373
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
374
- Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
374
+ Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
375
375
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
376
- Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : OK
377
- Test result : Success : 140 : Bio.WebLogo-positions.allPositions : OK
378
- Test result : Success : 120 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
379
- Test result : Success : 132 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
376
+ Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : 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 : 484 : Bio.similarity/diversity.similaritySearchViewer : OK
385
- Test result : Success : 356 : Bio.similarity/diversity.diversitySearchViewer : OK
386
- Test result : Success : 231 : Bio.substructureFilters.fasta : OK
387
- Test result : Success : 420 : Bio.substructureFilters.separator : OK
388
- Test result : Success : 1913 : Bio.substructureFilters.helm : 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
+ Test result : Success : 394 : Bio.substructureFilters.separator : OK
388
+ Test result : Success : 1950 : Bio.substructureFilters.helm : OK
389
389
  </pre></div></div></div></div></body></html>