@datagrok/bio 2.0.27 → 2.0.28

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Files changed (8) hide show
  1. package/dist/package-test.js +114 -61
  2. package/dist/package.js +112 -59
  3. package/package.json +2 -2
  4. package/scripts/admet-run.py +27 -0
  5. package/src/analysis/sequence-similarity-viewer.ts +1 -2
  6. package/src/substructure-search/substructure-search.ts +4 -5
  7. package/src/tests/checkInputColumn-tests.ts +2 -4
  8. package/test-Bio-49ff04f38f57-8ab13d10.html +385 -0
package/package.json CHANGED
@@ -5,7 +5,7 @@
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  "name": "Leonid Stolbov",
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  "email": "lstolbov@datagrok.ai"
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  },
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- "version": "2.0.27",
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+ "version": "2.0.28",
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  "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
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  "repository": {
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  "type": "git",
@@ -14,7 +14,7 @@
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  },
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  "dependencies": {
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  "@biowasm/aioli": "^3.1.0",
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- "@datagrok-libraries/bio": "^5.5.0",
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+ "@datagrok-libraries/bio": "^5.7.0",
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  "@datagrok-libraries/chem-meta": "1.0.1",
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  "@datagrok-libraries/ml": "^6.2.0",
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  "@datagrok-libraries/utils": "^1.11.1",
package/scripts/admet-run.py ADDED
@@ -0,0 +1,27 @@
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+ #!/usr/bin/env python2
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+ # -*- coding: utf-8 -*-
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+ """
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+ Created on Mon Feb 19 17:30:46 2018
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+
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+ @author: cbdd
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+ """
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+ from sklearn.externals import joblib
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+ import numpy as np
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+ import pandas as pd
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+ import os
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+
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+ ###################################### Load model ##########
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+ # current_path = os.path.split(os.path.realpath(__file__))[0]
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+ cf = joblib.load('CYP3A4-substrate.pkl')
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+
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+ ###################################### Load descriptors ##########
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+ fingerprint_content = pd.read_csv('des.csv').ix[:, 1:]
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+ des_list = np.array(fingerprint_content)
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+
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+ ###################################### Prediction ##########
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+ y_predict_label = cf.predict(des_list)
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+ y_predict_proba = cf.predict_proba(des_list)
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+ print('#' * 10 + 'Results labels' + '#' * 10)
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+ print(y_predict_label)
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+ print('#' * 10 + 'Results probabilities' + '#' * 10)
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+ print(y_predict_proba)
package/src/analysis/sequence-similarity-viewer.ts CHANGED
@@ -8,7 +8,6 @@ import {getMonomericMols} from '../calculations/monomerLevelMols';
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  import * as C from '../utils/constants';
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  import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
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  import {updateDivInnerHTML} from '../utils/ui-utils';
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- import {TableView} from 'datagrok-api/dg';
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  import {Subject} from 'rxjs';
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  export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
@@ -70,7 +69,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
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  const targetMolRow = this.idxs?.getRawData().findIndex((it) => it == this.targetMoleculeIdx);
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  const targetScoreCell = grid.cell('score', targetMolRow!);
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  targetScoreCell.cell.value = null;
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- (grok.shell.v as TableView).grid.root.addEventListener('click', (event: MouseEvent) => {
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+ (grok.shell.v as DG.TableView).grid.root.addEventListener('click', (event: MouseEvent) => {
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  this.gridSelect = false;
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  });
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  updateDivInnerHTML(this.root, grid.root);
package/src/substructure-search/substructure-search.ts CHANGED
@@ -5,12 +5,11 @@ import * as bio from '@datagrok-libraries/bio';
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5
 
6
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  import * as C from '../utils/constants';
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  import {getMonomericMols} from '../calculations/monomerLevelMols';
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- import {BitSet} from 'datagrok-api/dg';
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  import {updateDivInnerHTML} from '../utils/ui-utils';
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9
 
11
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  export const MONOMER_MOLS_COL = 'monomeric-mols';
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13
- const enum MONOMERIC_COL_TAGS{
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+ const enum MONOMERIC_COL_TAGS {
14
13
  MONOMERIC_MOLS = 'monomeric-mols',
15
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  LAST_INVALIDATED_VERSION = 'last-invalidated-version',
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  MONOMERS_DICT = 'monomers-dict'
@@ -64,7 +63,7 @@ export function substructureSearchDialog(col: DG.Column): void {
64
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  const colExists = col.dataFrame.columns.names()
65
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  .filter((it) => it.toLocaleLowerCase() === matchesColName.toLocaleLowerCase()).length > 0;
66
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  if (!colExists) {
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- let matches: BitSet;
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+ let matches: DG.BitSet;
68
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  if (units === bio.NOTATION.HELM)
69
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  matches = await helmSubstructureSearch(substructure, col);
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  else
@@ -92,13 +91,13 @@ function prepareSubstructureRegex(substructure: string, separator: string) {
92
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  const endsWithSep = substructure.charAt(substructure.length - 1) === separator;
93
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  const substrWithoutSep = substructure.replace(new RegExp(`^${char}|${char}$`, 'g'), '');
94
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  const re = startsWithSep ? endsWithSep ? `${char}${substrWithoutSep}${char}` :
95
- `${char}${substrWithoutSep}${char}|${char}${substrWithoutSep}$` :
94
+ `${char}${substrWithoutSep}${char}|${char}${substrWithoutSep}$` :
96
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  endsWithSep ? `^${substrWithoutSep}${char}|${char}${substrWithoutSep}${char}` :
97
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  `^${substrWithoutSep}${char}|${char}${substrWithoutSep}${char}|${char}${substrWithoutSep}$`;
98
97
  return re;
99
98
  }
100
99
 
101
- export async function helmSubstructureSearch(substructure: string, col: DG.Column): Promise<BitSet> {
100
+ export async function helmSubstructureSearch(substructure: string, col: DG.Column): Promise<DG.BitSet> {
102
101
  if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
103
102
  await invalidateHelmMols(col);
104
103
  const substructureCol = DG.Column.string('helm', 1).init((i) => substructure);
package/src/tests/checkInputColumn-tests.ts CHANGED
@@ -7,8 +7,6 @@ import * as bio from '@datagrok-libraries/bio';
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  import {after, before, category, test, expect, expectArray} from '@datagrok-libraries/utils/src/test';
8
8
 
9
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  import {checkInputColumn, multipleSequenceAlignmentAny} from '../package';
10
- import {UNITS} from 'datagrok-api/dg';
11
- import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
12
10
 
13
11
  category('checkInputColumn', () => {
14
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  const csv = `seq
@@ -41,7 +39,7 @@ seq4`;
41
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  const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
42
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  const col: DG.Column = df.getCol('seq');
43
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  col.semType = DG.SEMTYPE.MACROMOLECULE;
44
- col.setTag(DG.TAGS.UNITS, NOTATION.HELM);
42
+ col.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
45
43
  col.setTag(bio.TAGS.alphabetSize, '11');
46
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  col.setTag(bio.TAGS.alphabetIsMultichar, 'true');
47
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@@ -56,7 +54,7 @@ seq4`;
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  const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
57
55
  const col: DG.Column = df.getCol('seq');
58
56
  col.semType = DG.SEMTYPE.MACROMOLECULE;
59
- col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
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+ col.setTag(DG.TAGS.UNITS, bio.NOTATION.FASTA);
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58
  col.setTag(bio.TAGS.alphabet, 'UN');
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  col.setTag(bio.TAGS.alphabetSize, '11');
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  col.setTag(bio.TAGS.alphabetIsMultichar, 'true');
package/test-Bio-49ff04f38f57-8ab13d10.html ADDED
@@ -0,0 +1,385 @@
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+ <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=49ff04f38f57. Commit 8ab13d10.</title><style type="text/css">html,
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+ body {
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+ font-family: Arial, Helvetica, sans-serif;
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+ font-size: 1rem;
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+ margin: 0;
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+ padding: 0;
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+ color: #333;
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+ }
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+ body {
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+ padding: 2rem 1rem;
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+ font-size: 0.85rem;
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+ }
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+ #jesthtml-content {
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+ margin: 0 auto;
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+ max-width: 70rem;
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+ }
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+ header {
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+ display: flex;
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+ align-items: center;
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+ }
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+ #title {
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+ margin: 0;
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+ flex-grow: 1;
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+ }
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+ #logo {
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+ height: 4rem;
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+ }
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+ #timestamp {
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+ color: #777;
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+ margin-top: 0.5rem;
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+ }
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+
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+ /** SUMMARY */
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+ #summary {
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+ color: #333;
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+ margin: 2rem 0;
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+ display: flex;
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+ font-family: monospace;
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+ font-size: 1rem;
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+ }
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+ #summary > div {
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+ margin-right: 2rem;
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+ background: #eee;
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+ padding: 1rem;
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+ min-width: 15rem;
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+ }
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+ #summary > div:last-child {
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+ margin-right: 0;
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+ }
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+ @media only screen and (max-width: 720px) {
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+ #summary {
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+ flex-direction: column;
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+ }
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+ #summary > div {
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+ margin-right: 0;
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+ margin-top: 2rem;
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+ }
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+ #summary > div:first-child {
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+ margin-top: 0;
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+ }
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+ }
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+
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+ .summary-total {
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+ font-weight: bold;
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+ margin-bottom: 0.5rem;
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+ }
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+ .summary-passed {
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+ color: #4f8a10;
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+ border-left: 0.4rem solid #4f8a10;
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+ padding-left: 0.5rem;
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+ }
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+ .summary-failed,
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+ .summary-obsolete-snapshots {
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+ color: #d8000c;
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+ border-left: 0.4rem solid #d8000c;
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+ padding-left: 0.5rem;
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+ }
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+ .summary-pending {
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+ color: #9f6000;
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+ border-left: 0.4rem solid #9f6000;
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+ padding-left: 0.5rem;
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+ }
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+ .summary-empty {
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+ color: #999;
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+ border-left: 0.4rem solid #999;
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+ }
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+
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+ .test-result {
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+ padding: 1rem;
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+ margin-bottom: 0.25rem;
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+ }
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+ .test-result:last-child {
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+ border: 0;
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+ }
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+ .test-result.passed {
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+ background-color: #dff2bf;
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+ color: #4f8a10;
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+ }
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+ .test-result.failed {
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+ background-color: #ffbaba;
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+ color: #d8000c;
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+ }
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+ .test-result.pending {
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+ background-color: #ffdf61;
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+ color: #9f6000;
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+ }
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+
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+ .test-info {
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+ display: flex;
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+ justify-content: space-between;
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+ }
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+ .test-suitename {
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+ width: 20%;
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+ text-align: left;
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+ font-weight: bold;
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+ word-break: break-word;
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+ }
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+ .test-title {
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+ width: 40%;
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+ text-align: left;
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+ font-style: italic;
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+ }
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+ .test-status {
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+ width: 20%;
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+ text-align: right;
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+ }
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+ .test-duration {
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+ width: 10%;
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+ text-align: right;
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+ font-size: 0.75rem;
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+ }
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+
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+ .failureMessages {
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+ padding: 0 1rem;
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+ margin-top: 1rem;
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+ border-top: 1px dashed #d8000c;
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+ }
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+ .failureMessages.suiteFailure {
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+ border-top: none;
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+ }
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+ .failureMsg {
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+ white-space: pre-wrap;
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+ white-space: -moz-pre-wrap;
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+ white-space: -pre-wrap;
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+ white-space: -o-pre-wrap;
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+ word-wrap: break-word;
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+ }
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+
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+ .suite-container {
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+ margin-bottom: 2rem;
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+ }
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+ .suite-info {
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+ padding: 1rem;
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+ background-color: #eee;
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+ color: #777;
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+ display: flex;
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+ align-items: center;
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+ margin-bottom: 0.25rem;
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+ }
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+ .suite-info .suite-path {
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+ word-break: break-all;
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+ flex-grow: 1;
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+ font-family: monospace;
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+ font-size: 1rem;
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+ }
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+ .suite-info .suite-time {
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+ margin-left: 0.5rem;
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+ padding: 0.2rem 0.3rem;
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+ font-size: 0.75rem;
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+ }
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+ .suite-info .suite-time.warn {
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+ background-color: #d8000c;
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+ color: #fff;
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+ }
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+
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+ /* CONSOLE LOGS */
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+ .suite-consolelog {
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+ margin-bottom: 0.25rem;
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+ padding: 1rem;
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+ background-color: #efefef;
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+ }
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+ .suite-consolelog-header {
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+ font-weight: bold;
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+ }
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+ .suite-consolelog-item {
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+ padding: 0.5rem;
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+ }
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+ .suite-consolelog-item pre {
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+ margin: 0.5rem 0;
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+ white-space: pre-wrap;
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+ white-space: -moz-pre-wrap;
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+ white-space: -pre-wrap;
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+ white-space: -o-pre-wrap;
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+ word-wrap: break-word;
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+ }
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+ .suite-consolelog-item-origin {
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+ color: #777;
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+ font-weight: bold;
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+ }
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+ .suite-consolelog-item-message {
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+ color: #000;
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+ font-size: 1rem;
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+ padding: 0 0.5rem;
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+ }
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+
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+ /* OBSOLETE SNAPSHOTS */
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+ .suite-obsolete-snapshots {
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+ margin-bottom: 0.25rem;
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+ padding: 1rem;
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+ background-color: #ffbaba;
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+ color: #d8000c;
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+ }
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+ .suite-obsolete-snapshots-header {
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+ font-weight: bold;
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+ }
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+ .suite-obsolete-snapshots-item {
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+ padding: 0.5rem;
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+ }
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+ .suite-obsolete-snapshots-item pre {
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+ margin: 0.5rem 0;
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+ white-space: pre-wrap;
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+ white-space: -moz-pre-wrap;
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+ white-space: -pre-wrap;
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+ white-space: -o-pre-wrap;
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+ word-wrap: break-word;
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+ }
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+ .suite-obsolete-snapshots-item-message {
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+ color: #000;
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+ font-size: 1rem;
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+ padding: 0 0.5rem;
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+ }
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+ </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=49ff04f38f57. Commit 8ab13d10.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-26 12:18:45</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">35.829s</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">25.318s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 1156 : Bio.activityCliffs.activityCliffsOpens : Error: Expected "102 cliffs", got "102 CLIFFS"
233
+ Test result : Failed : 1248 : Bio.activityCliffs.activityCliffsWithEmptyRows : Error: Expected "103 cliffs", got "103 CLIFFS"
234
+ Test result : Failed : 169 : 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'.
235
+
236
+ at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:70:20
237
+ at Generator.next (&lt;anonymous&gt;)
238
+ at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
239
+ at runMicrotasks (&lt;anonymous&gt;)
240
+ 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)
241
+ at Generator.next (&lt;anonymous&gt;)
242
+ at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
243
+ 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
244
+ at Generator.next (&lt;anonymous&gt;)
245
+ at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
246
+ at new Promise (&lt;anonymous&gt;)
247
+ at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
248
+ at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
249
+ at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
250
+ 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:68:11
251
+ at Generator.next (&lt;anonymous&gt;)
252
+ at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
253
+ at runMicrotasks (&lt;anonymous&gt;)
254
+ at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
255
+ Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
256
+ Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
257
+ Test result : Success : 43 : Bio.detectors.NegativeEmpty : OK
258
+ Test result : Success : 10 : Bio.detectors.Negative1 : OK
259
+ Test result : Success : 9 : Bio.detectors.Negative2 : OK
260
+ Test result : Success : 13 : Bio.detectors.Negative3 : OK
261
+ Test result : Success : 37 : Bio.detectors.NegativeSmiles : OK
262
+ Test result : Success : 21 : Bio.detectors.Dna1 : OK
263
+ Test result : Success : 14 : Bio.detectors.Rna1 : OK
264
+ Test result : Success : 8 : Bio.detectors.AA1 : OK
265
+ Test result : Success : 7 : Bio.detectors.MsaDna1 : OK
266
+ Test result : Success : 7 : Bio.detectors.MsaAA1 : OK
267
+ Test result : Success : 7 : Bio.detectors.SepDna : OK
268
+ Test result : Success : 13 : Bio.detectors.SepRna : OK
269
+ Test result : Success : 9 : Bio.detectors.SepPt : OK
270
+ Test result : Success : 14 : Bio.detectors.SepUn1 : OK
271
+ Test result : Success : 7 : Bio.detectors.SepUn2 : OK
272
+ Test result : Success : 6 : Bio.detectors.SepMsaN1 : OK
273
+ Test result : Success : 493 : Bio.detectors.SamplesFastaCsvPt : OK
274
+ Test result : Success : 7 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
275
+ Test result : Success : 5 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
276
+ Test result : Success : 34 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
277
+ Test result : Success : 844 : Bio.detectors.SamplesFastaFastaPt : OK
278
+ Test result : Success : 497 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
279
+ Test result : Success : 19 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
280
+ Test result : Success : 68 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
281
+ Test result : Success : 204 : Bio.detectors.samplesMsaComplexUn : OK
282
+ Test result : Success : 25 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
283
+ Test result : Success : 645 : Bio.detectors.samplesIdCsvNegativeID : OK
284
+ Test result : Success : 399 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
285
+ Test result : Success : 127 : Bio.detectors.samplesHelmCsvHELM : OK
286
+ Test result : Success : 8 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
287
+ Test result : Success : 110 : Bio.detectors.samplesTestHelmNegativeID : OK
288
+ Test result : Success : 18 : Bio.detectors.samplesTestHelmNegativeTestType : OK
289
+ Test result : Success : 11 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
290
+ Test result : Success : 15 : Bio.detectors.samplesTestHelmNegativeValid : OK
291
+ Test result : Success : 22 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
292
+ Test result : Success : 5 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
293
+ Test result : Success : 13 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
294
+ Test result : Success : 1002 : Bio.detectors.samplesTestDemogNegativeAll : OK
295
+ Test result : Success : 321 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
296
+ Test result : Success : 127 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
297
+ Test result : Success : 130 : Bio.detectors.samplesFastaPtPosSequence : OK
298
+ Test result : Success : 130 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
299
+ Test result : Success : 217 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
300
+ Test result : Success : 12 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
301
+ Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
302
+ Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
303
+ Test result : Success : 187 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
304
+ Test result : Success : 15 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
305
+ Test result : Success : 135 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
306
+ Test result : Success : 6 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
307
+ Test result : Success : 196 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
308
+ Test result : Success : 918 : Bio.MSA.isCorrect : OK
309
+ Test result : Success : 154 : Bio.MSA.isCorrectLong : OK
310
+ Test result : Success : 1241 : Bio.sequenceSpace.sequenceSpaceOpens : OK
311
+ Test result : Success : 5367 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
312
+ Test result : Success : 1 : Bio.splitters.fastaMulti : OK
313
+ Test result : Success : 1 : Bio.splitters.helm1 : OK
314
+ Test result : Success : 1 : Bio.splitters.helm2 : OK
315
+ Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
316
+ Test result : Success : 0 : Bio.splitters.testHelm1 : OK
317
+ Test result : Success : 1 : Bio.splitters.testHelm2 : OK
318
+ Test result : Success : 0 : Bio.splitters.testHelm3 : OK
319
+ Test result : Success : 349 : Bio.splitters.splitToMonomers : OK
320
+ Test result : Success : 2 : Bio.splitters.getHelmMonomers : OK
321
+ Test result : Success : 86 : Bio.renderers.long sequence performance : OK
322
+ Test result : Success : 728 : Bio.renderers.many sequence performance : OK
323
+ Test result : Success : 389 : Bio.renderers.rendererMacromoleculeFasta : OK
324
+ Test result : Success : 198 : Bio.renderers.rendererMacromoleculeSeparator : OK
325
+ Test result : Success : 92 : Bio.renderers.rendererMacromoleculeDifference : OK
326
+ Test result : Success : 417 : Bio.renderers.afterMsa : OK
327
+ Test result : Success : 224 : Bio.renderers.afterConvert : OK
328
+ Test result : Success : 167 : Bio.renderers.selectRendererBySemType : OK
329
+ Test result : Success : 4 : Bio.converters.testFastaPtToSeparator : OK
330
+ Test result : Success : 3 : Bio.converters.testFastaDnaToSeparator : OK
331
+ Test result : Success : 3 : Bio.converters.testFastaRnaToSeparator : OK
332
+ Test result : Success : 3 : Bio.converters.testFastaGapsToSeparator : OK
333
+ Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
334
+ Test result : Success : 8 : Bio.converters.testFastaDnaToHelm : OK
335
+ Test result : Success : 2 : Bio.converters.testFastaRnaToHelm : OK
336
+ Test result : Success : 2 : Bio.converters.testFastaGapsToHelm : OK
337
+ Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
338
+ Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
339
+ Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
340
+ Test result : Success : 1 : Bio.converters.testSeparatorGapsToFasta : OK
341
+ Test result : Success : 1 : Bio.converters.testSeparatorPtToHelm : OK
342
+ Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
343
+ Test result : Success : 1 : Bio.converters.testSeparatorRnaToHelm : OK
344
+ Test result : Success : 1 : Bio.converters.testSeparatorGapsToHelm : OK
345
+ Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
346
+ Test result : Success : 0 : Bio.converters.testHelmRnaToFasta : OK
347
+ Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
348
+ Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
349
+ Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
350
+ Test result : Success : 1 : Bio.converters.testHelmPtToSeparator : OK
351
+ Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
352
+ Test result : Success : 2 : Bio.converters.testHelmLoneDeoxyribose : OK
353
+ Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
354
+ Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
355
+ Test result : Success : 1 : Bio.fastaFileHandler.testExtraSpaces : OK
356
+ Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
357
+ Test result : Success : 1 : Bio.fastaExport.wrapSequenceSingle : OK
358
+ Test result : Success : 0 : Bio.fastaExport.wrapSequenceMulti : OK
359
+ Test result : Success : 2 : Bio.fastaExport.saveAsFastaTest1 : OK
360
+ Test result : Success : 2 : Bio.fastaExport.saveAsFastaTest2 : OK
361
+ Test result : Success : 1 : Bio.bio.testGetStatsHelm1 : OK
362
+ Test result : Success : 2 : Bio.bio.testGetStatsN1 : OK
363
+ Test result : Success : 0 : Bio.bio.testGetAlphabetSimilarity : OK
364
+ Test result : Success : 2 : Bio.bio.testPickupPaletteN1 : OK
365
+ Test result : Success : 1 : Bio.bio.testPickupPaletteN1e : OK
366
+ Test result : Success : 1 : Bio.bio.testPickupPaletteAA1 : OK
367
+ Test result : Success : 2 : Bio.bio.testPickupPaletteX : OK
368
+ Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerSingle : OK
369
+ Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
370
+ Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
371
+ Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
372
+ Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : OK
373
+ Test result : Success : 81 : Bio.WebLogo-positions.allPositions : OK
374
+ Test result : Success : 84 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
375
+ Test result : Success : 75 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
376
+ Test result : Success : 2 : Bio.checkInputColumn.testMsaPos : OK
377
+ Test result : Success : 0 : Bio.checkInputColumn.testMsaNegHelm : OK
378
+ Test result : Success : 10 : Bio.checkInputColumn.testMsaNegUN : OK
379
+ Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
380
+ Test result : Success : 790 : Bio.similarity/diversity.similaritySearchViewer : OK
381
+ Test result : Success : 370 : Bio.similarity/diversity.diversitySearchViewer : OK
382
+ Test result : Success : 197 : Bio.substructureFilters.fasta : OK
383
+ Test result : Success : 396 : Bio.substructureFilters.separator : OK
384
+ Test result : Success : 1269 : Bio.substructureFilters.helm : OK
385
+ </pre></div></div></div></div></body></html>