Merge branch 'master' of https://github.com/ryan-stackwave/tg-oss

ryan-stackwave · Feb 27, 2024 · 31250ca · 31250ca
2 parents 8f1b721 + b16db18
commit 31250ca
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Showing 4 changed files with 13 additions and 24 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,6 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
 - genbank ss-DNA should not be overwirte to DNA [`#1`](https://github.com/TeselaGen/tg-oss/pull/1)
 - Added fix for clipboard commands when there are multiple editors on a page to resolve https://github.com/TeselaGen/tg-oss/issues/24 [`#24`](https://github.com/TeselaGen/tg-oss/issues/24)
 - closes #35 [`#35`](https://github.com/TeselaGen/tg-oss/issues/35)
-- reverting seq data change [`073aba6`](https://github.com/TeselaGen/tg-oss/commit/073aba63090ca69eeaa134a1efa0563aa65a9af1)
 - making upload accept handle async values [`5c8dfd8`](https://github.com/TeselaGen/tg-oss/commit/5c8dfd8a91defd00773329d9dbfc2e15beb01bbb)
 - fixing issue with annotationsToSupport and adding test [`2f885dc`](https://github.com/TeselaGen/tg-oss/commit/2f885dc53fd4441a4473eb0b3194dc82d1922a30)
+- adding download table as csv button to editable tables, more csv wizard fixing [`9f4989e`](https://github.com/TeselaGen/tg-oss/commit/9f4989e2fda4f7542b96cb2f1ec3d3c97c386245)
diff --git a/packages/sequence-utils/package.json b/packages/sequence-utils/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.18",
+  "version": "0.3.19",
   "type": "commonjs",
   "dependencies": {
     "bson-objectid": "^2.0.4",

diff --git a/packages/sequence-utils/src/calculateTm.js b/packages/sequence-utils/src/calculateTm.js
@@ -16,12 +16,12 @@ const calcTmMethods = {
 
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
-   * @param  {String} sequence The DNA sequence to use.
-   * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-   * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-   * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-   * @return {Double} Temperature for the given sequence, in Celsius.
+   * sequence - The DNA sequence to use.
+   * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+   * A - Helix initation for deltaS. Defaults to -10.8.
+   * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * return - Temperature for the given sequence, in Celsius.
    */
   calculateTemperature: function (sequence, type, A, R, C, Na) {
     if (typeof type === "undefined") {

diff --git a/packages/sequence-utils/src/getOrfsFromSequence.js b/packages/sequence-utils/src/getOrfsFromSequence.js
@@ -4,21 +4,13 @@ import getReverseComplementSequenceString from "./getReverseComplementSequenceSt
 /**
  * @private
  * Finds ORFs in a given DNA forward in a given frame.
- * @param  {Int} frame The frame to look in.
- * @param  {String}sequence The dna sequence.
- * @param  {Int} minimumOrfSize The minimum length of ORF to return.
- * @param  {boolean} forward Should we find forward facing orfs or reverse facing orfs
- * @return {Teselagen.bio.orf.ORF[]} The list of ORFs found.
+ * frame - The frame to look in.
+ * sequence - The dna sequence.
+ * minimumOrfSize - The minimum length of ORF to return.
+ * forward - Should we find forward facing orfs or reverse facing orfs
+ * return - The list of ORFs found.
  */
 export default function getOrfsFromSequence(options) {
-  // ac.throw([ac.shape({
-  //     sequence: ac.string,
-  //     minimumOrfSize: ac.posInt,
-  //     forward: ac.bool,
-  //     circular: ac.bool
-  // })], arguments);
-
-  // const frame = options.frame;
   let sequence = options.sequence;
   const minimumOrfSize = options.minimumOrfSize;
   const forward = options.forward;
@@ -38,7 +30,6 @@ export default function getOrfsFromSequence(options) {
   const re = useAdditionalOrfStartCodons
     ? /(?=((?:A[TU]G|G[TU]G|C[TU]G)(?:.{3})*?(?:[TU]AG|[TU]AA|[TU]GA)))/gi
     : /(?=((?:A[TU]G)(?:.{3})*?(?:[TU]AG|[TU]AA|[TU]GA)))/gi;
-  // const str = 'tatgaatgaatgffffffatgfftaaftaafatgfatgfffffsdfatgffatgfffstaafftaafffffffffffffffatgtaaataa\n\natgffftaaf\n\natgffatgftaafftaa\n\natgatgftaafftaa\n\natgatgtaataa\n\ntttttttttttttaatgatgfffffffffftaa';
   let m;
   const orfRanges = [];
   //loop through orf hits!
@@ -103,8 +94,6 @@ export default function getOrfsFromSequence(options) {
     } else {
       orfEnds[orf.end] = index;
       if (!forward) {
-        // if (originalSequenceLength - orf.end - 1 == 3657) {
-        // }
         //this check needs to come after the above assignment of orfEnds
         //flip the start and ends
         const endHolder = orf.end; //temp variable