@datagrok/sequence-translator 1.0.13 → 1.0.15

package/src/structures-works/save-sense-antisense.ts

@@ -1,11 +1,14 @@
+import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
 import {download} from '../helpers';
 import {sequenceToMolV3000} from '../structures-works/from-monomers';
 import {linkStrandsV3000} from '../structures-works/mol-transformations';
 import {getFormat} from '../structures-works/sequence-codes-tools';
 
-export function saveSdf(as: string, ss: string, 
-                        oneEntity: boolean, useChirality: boolean, 
+export function saveSdf(as: string, ss: string,
+                        oneEntity: boolean, useChirality: boolean,
                         invertSS: boolean, invertAS: boolean,
                         as2: string | null = null, invertAS2: boolean | null) {
   const formatAs = getFormat(as);
@@ -25,7 +28,7 @@ export function saveSdf(as: string, ss: string,
   if (oneEntity) {
     const antiStrands = molAS2 == null ? [molAS] : [molAS, molAS2];
     result = linkStrandsV3000({senseStrands: [molSS], antiStrands: antiStrands}, useChirality) + '\n$$$$\n';
-  
+
   } else {
     result =
     molSS + '\n' +

package/src/structures-works/sequence-codes-tools.ts

@@ -1,5 +1,5 @@
 
-import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, delimiter, gcrsCodesWithoutSmiles} from './map';
+import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, DELIMITER, gcrsCodesWithoutSmiles, NUCLEOTIDES} from './map';
 import {sortByStringLengthInDescendingOrder} from '../helpers';
 import {asoGapmersNucleotidesToBioSpring, asoGapmersNucleotidesToGcrs,
   asoGapmersBioSpringToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12, siRnaNucleotideToBioSpringSenseStrand,
@@ -20,7 +20,6 @@ export function getFormat(sequence: string): string | null {
   let outputIndex = 0;
 
   const firstUniqueCharacters = ['r', 'd'];
-  const nucleotides = ['A', 'U', 'T', 'C', 'G'];
 
   possibleSynthesizers.forEach((synthesizer) => {
     const codes = getAllCodesOfSynthesizer(synthesizer);
@@ -32,13 +31,13 @@ export function getFormat(sequence: string): string | null {
 
       if ( // for mistake pattern 'rAA'
         outputIndex > 1 &&
-        nucleotides.includes(sequence[outputIndex]) &&
+        NUCLEOTIDES.includes(sequence[outputIndex]) &&
         firstUniqueCharacters.includes(sequence[outputIndex - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
         firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-        nucleotides.includes(sequence[outputIndex])
+        NUCLEOTIDES.includes(sequence[outputIndex])
       ) {
         outputIndex++;
         break;
@@ -69,13 +68,13 @@ export function getFormat(sequence: string): string | null {
 
       if ( // for mistake pattern 'rAA'
         outputIndex > 1 &&
-        nucleotides.includes(sequence[outputIndex]) &&
+        NUCLEOTIDES.includes(sequence[outputIndex]) &&
         firstUniqueCharacters.includes(sequence[outputIndex - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
         firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-        nucleotides.includes(sequence[outputIndex])
+        NUCLEOTIDES.includes(sequence[outputIndex])
       ) {
         outputIndex++;
         break;
@@ -116,7 +115,6 @@ export function isValidSequence(sequence: string, format: string | null): {
   const outputIndices = Array(possibleSynthesizers.length).fill(0);
 
   const firstUniqueCharacters = ['r', 'd'];
-  const nucleotides = ['A', 'U', 'T', 'C', 'G'];
   possibleSynthesizers.forEach(function(synthesizer, i) {
     const codes = sortByStringLengthInDescendingOrder(getAllCodesOfSynthesizer(synthesizer));
     while (outputIndices[i] < sequence.length) {
@@ -127,13 +125,13 @@ export function isValidSequence(sequence: string, format: string | null): {
 
       if ( // for mistake pattern 'rAA'
         outputIndices[i] > 1 &&
-        nucleotides.includes(sequence[outputIndices[i]]) &&
+        NUCLEOTIDES.includes(sequence[outputIndices[i]]) &&
         firstUniqueCharacters.includes(sequence[outputIndices[i] - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
         firstUniqueCharacters.includes(sequence[outputIndices[i] + 1]) &&
-        nucleotides.includes(sequence[outputIndices[i]])
+        NUCLEOTIDES.includes(sequence[outputIndices[i]])
       ) {
         outputIndices[i]++;
         break;
@@ -211,7 +209,7 @@ export function getAllCodesOfSynthesizer(synthesizer: string): string[] {
   let codes: string[] = [];
   for (const technology of Object.keys(map[synthesizer]))
     codes = codes.concat(Object.keys(map[synthesizer][technology]));
-  return codes.concat(Object.keys(MODIFICATIONS)).concat(delimiter);
+  return codes.concat(Object.keys(MODIFICATIONS)).concat(DELIMITER);
 }
 
 function getListOfPossibleSynthesizersByFirstMatchedCode(sequence: string): string[] {

package/{test-SequenceTranslator-62cc009524f3-4a9916b0.html → test-SequenceTranslator-91c83d8913ff-f94596bc.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 4a9916b0.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=91c83d8913ff. Commit f94596bc.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 4a9916b0.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-16 19:29:02</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 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">1 passed</div><div class="summary-failed summary-empty">0 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/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">15.773s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">2.692s</div></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/SequenceTranslator/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=91c83d8913ff. Commit f94596bc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-29 11:55:21</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 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">1 passed</div><div class="summary-failed summary-empty">0 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/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">18.993s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">5.501s</div></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/SequenceTranslator/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:40:11
@@ -243,16 +243,16 @@ header {
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.acacacsacsac : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.cccgggusug : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.acacacsacsac : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.cccgggusug : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
 </pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:74:11
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)