@datagrok/sequence-translator 1.0.17 → 1.1.4

package/src/tests/formats-support.ts

@@ -0,0 +1,40 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {DEFAULT_FORMATS} from '../model/const';
+import {FormatConverter} from '../model/format-translation/format-converter';
+import {getJsonData} from '../model/data-loading-utils/json-loader';
+import {formatsToHelm} from './const';
+import {SequenceValidator} from '../model/parsing-validation/sequence-validator';
+import {getTranslatedSequences} from '../model/format-translation/conversion-utils';
+import {_package} from '../package';
+
+function getTranslationObject(sequence: string, format: string): {[format: string]: string} {
+  const indexOfInvalidChar = (new SequenceValidator(sequence)).getInvalidCodeIndex(format);
+  return getTranslatedSequences(sequence, indexOfInvalidChar, format);
+}
+
+const inputs = {
+  [DEFAULT_FORMATS.AXOLABS]: 'Afcgacsu',
+  [DEFAULT_FORMATS.HELM]: 'RNA1{[fR](A)p.[25r](C)p.[25r](G)p.[25r](A)p.[25r](C)[sp].[25r](U)}$$$$'
+}
+
+category('Formats support', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  Object.entries(inputs).forEach(([format, sequence]) => {
+    test(`All formats for ${format}`, async () => {
+      const output = getTranslationObject(sequence, format);
+      const result = Object.keys(output).length;
+      // +1 due to nucleotides
+      const expected = Object.keys(formatsToHelm).length + 1;
+      expect(result, expected);
+    });
+  });
+});

package/src/tests/formats-to-helm.ts

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+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {DEFAULT_FORMATS} from '../model/const';
+import {FormatConverter} from '../model/format-translation/format-converter';
+import {getJsonData} from '../model/data-loading-utils/json-loader';
+import {formatsToHelm} from './const';
+import {_package} from '../package';
+
+function getHelm(strand: string, format: string): string {
+  return (new FormatConverter(strand, format).convertTo(DEFAULT_FORMATS.HELM));
+}
+
+function getFromat(helm: string, format: string): string {
+  return (new FormatConverter(helm, DEFAULT_FORMATS.HELM).convertTo(format));
+}
+
+category('Formats to HELM', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  for (const format of Object.keys(formatsToHelm)) {
+    for (const [strand, helm] of Object.entries(formatsToHelm[format])) {
+      test(`${format} to HELM`, async () => {
+        const expected = helm;
+        const result = getHelm(strand, format);
+        expect(result, expected);
+      });
+    }
+  }
+});
+
+category('HELM to Formats', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  for (const format of Object.keys(formatsToHelm)) {
+    for (const [strand, helm] of Object.entries(formatsToHelm[format])) {
+      test(`${format} to HELM`, async () => {
+        const expected = strand;
+        const result = getFromat(helm, format);
+        expect(result, expected);
+      });
+    }
+  }
+});

package/src/tests/helm-to-nucleotides.ts

@@ -0,0 +1,28 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {DEFAULT_FORMATS} from '../model/const';
+import {FormatConverter} from '../model/format-translation/format-converter';
+import {getNucleotidesSequence} from '../model/format-translation/conversion-utils';
+import {getJsonData} from '../model/data-loading-utils/json-loader';
+import {helmToNucleotides} from './const';
+import {_package} from '../package';
+import {MonomerLibWrapper} from '../model/monomer-lib/lib-wrapper';
+
+category('HELM to Nucleotides', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  Object.entries(helmToNucleotides).forEach(([helm, nucleotide], idx) => {
+    test(`Sequence ${idx + 1} to nucleotides`, async () => {
+      const expected = nucleotide;
+      const result = getNucleotidesSequence(helm, MonomerLibWrapper.getInstance());
+      expect(result, expected);
+    });
+  })
+});

package/src/view/const/main-tab.ts

@@ -0,0 +1,3 @@
+export const DEFAULT_INPUT = 'fAmCmGmAmCpsmU';
+export const SEQUENCE_COPIED_MSG = 'Copied';
+export const SEQ_TOOLTIP_MSG = 'Copy sequence';

package/src/view/const/view.ts

@@ -0,0 +1,10 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+export const MAIN_TAB = 'SEQUENCE';
+export const AXOLABS_TAB = 'PATTERN';
+export const SDF_TAB = 'SDF';
+
+export const DEFAULT_AXOLABS_INPUT = 'Afcgacsu';

package/src/view/css/axolabs-tab.css

@@ -0,0 +1 @@
+/* Naming convention: class names should begin with st and tab name (main, axo, sdf) to avoid naming collitions */

package/src/view/css/colored-text-input.css

@@ -0,0 +1,27 @@
+.colored-text-input > textarea {
+  width: 100%;
+  -webkit-text-fill-color: transparent;
+  background-color: transparent;
+  position: relative;
+  z-index: 1;
+  resize: none;
+  height: 22px; /* Fine tuned value to avoid "jumping" of the textarea upon autoresize */
+}
+
+.colored-text-input > div {
+  /* The values here are fine tuned to those of the ui.input textarea in order
+   * to achieve precise overlap */
+  overflow: auto;
+  position: absolute;
+  pointer-events: none;
+  cursor: text;
+  z-index: 0;
+  max-width: 100%;
+  padding: 2px;
+  line-height: normal;
+  font-family: 'Roboto Mono', 'Roboto Mono Local', monospace;
+  font-size: 12px;
+  color: transparent;
+  white-space: pre-wrap;
+  word-wrap: break-word;
+}

package/src/view/css/main-tab.css

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+/* Naming convention: class names should begin with st and tab name (main, axo, sdf) to avoid naming collitions */
+.st-main-input-table {
+  width: 100%;
+}
+
+.st-main-input-table td:has(textarea) {
+  width: 100%;
+  padding-right: 20px;
+}
+
+.st-main-input-table td:has(select) {
+  min-width: 120px;
+  vertical-align: top;
+}
+
+.st-main-output-table {
+  margin-top: 20px;
+  margin-right: 20px;
+  margin-bottom: 10px;
+}
+
+.st-main-output-table table {
+  width: 100%;
+  table-layout: fixed;
+}
+
+/* .st-main-output-table table tbody tr td { */
+/*   max-width: 20%; */
+/* } */
+
+.st-main-output-table td {
+  padding-top: 6px;
+  padding-bottom: 6px;
+}
+.st-main-output-table tr:nth-child(even) {
+  background-color: var(--grey-1);
+}
+
+.st-main-output-table td:nth-child(odd) {
+  width: 120px;
+  vertical-align: top;
+}
+
+.st-main-output-table td a {
+  overflow-wrap: break-word;
+}

package/src/view/css/sdf-tab.css

@@ -0,0 +1,39 @@
+/* Naming convention: class names should begin with st and tab name (main, axo, sdf) to avoid naming collitions */
+
+.st-sdf-body {
+  padding-right: 20px;
+}
+
+.st-sdf-input-form {
+  text-align: right;
+  vertical-align: top;
+  min-width: 95px;
+}
+
+.st-sdf-direction-choice label {
+  min-width: 100px;
+  float: right;
+}
+
+.st-sdf-direction-choice div {
+  justify-content: right;
+}
+
+.st-sdf-text-input-td { /* Style for td containing textarea */
+  width: 100%;
+}
+
+.st-sdf-mol-img {
+  margin-right: 30px;
+  float: right;
+}
+
+.st-sdf-bool-button-block {
+  justify-content: right;
+  margin-bottom: 10px;
+}
+
+.st-sdf-bottom {
+  flex-direction: row-reverse;
+  padding-top: 20px;
+}

package/src/view/monomer-lib-viewer/viewer.ts

@@ -0,0 +1,22 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {drawZoomedInMolecule} from '../utils/draw-molecule';
+import {MonomerLibWrapper} from '../../model/monomer-lib/lib-wrapper';
+
+export class MonomerLibViewer {
+  static async view(): Promise<void> {
+    const table = MonomerLibWrapper.getInstance().getTableForViewer();
+    table.name = 'Monomer Library';
+    const view = grok.shell.addTableView(table);
+    view.grid.props.allowEdit = false;
+    const onDoubleClick = view.grid.onCellDoubleClick;
+    onDoubleClick.subscribe(async (gridCell: DG.GridCell) => {
+      const molfile = gridCell.cell.value;
+      if (gridCell.tableColumn?.semType === 'Molecule')
+        await drawZoomedInMolecule(molfile);
+    });
+  }
+}