diff --git a/CHANGELOG.md b/CHANGELOG.md index a74188e1..2a20c24e 100644 --- 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 index cb2c488c..94c478ea 100644 --- 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 index 0b2daf48..bc9cca81 100644 --- 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 index 6b7b46e4..efe269fc 100644 --- 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