@datagrok/bio 2.14.1 → 2.15.0

package/CHANGELOG.md

@@ -1,5 +1,47 @@
 # Bio changelog
 
+## 2.15.0 (2024-09-04)
+
+Monomer manager
+
+### Features
+
+* Add getHelm for Cyclized notation provider
+* Add detector for Dimerized notation provider
+* Add Monomer library manager view with duplicate preferences
+* Add Monomer manager for editing/adding/removing monomers
+* Add monomer lib for PolyTool rules
+
+### Bug fixes
+
+* Fix tests benchmark
+* Fix typo Needleman-Wunsch
+* Fix test flapping benchmark separatorDnaShorts50Few50
+* Fix toAtomicLevel workers error DG is not defined
+* Fix biosubstructure filter
+* Fix SeqHandler.getHelm lost cycles, add tests
+* Fix SeqlHelper.helmToAtomicLevel to work without table
+
+## 2.14.3 (2024-08-27)
+
+### Bug fixes
+
+* Order Top menu
+* Fix to Atomic Level hide highlight column
+* Fix to Atomic Level for column
+* Bump dependencies version, fix tests
+
+## 2.14.2 (2024-08-23)
+
+### Features
+
+* Add highlighting monomer at atomic level
+
+### Bug fixes
+
+* Add tests for toAtomicLevel UI
+* Fix demo Helm, MSA, Sequence Space viewer adding
+
 ## 2.14.1 (2024-08-14)
 
 Fix monomer substitution matrix calculation

package/css/monomer-manager.css

@@ -0,0 +1,66 @@
+.monomer-manager-root .grok-sketcher {
+    min-width: unset !important;
+}
+
+.monomer-manager-root {
+    width: 100% !important;
+    height: 100% !important;
+}
+
+.monomer-manager-sketcher .ketcher-host {
+    height: 100% !important;
+} 
+
+.monomer-manager-root > div:first-child {
+    flex-basis: 40% !important;
+}
+.monomer-manager-root > div:nth-child(2) {
+    flex-basis: 60% !important;
+}
+
+.monomer-manager-root > div:first-child > .ui-form {
+    max-width: unset !important;
+}
+
+.monomer-card-info-row {
+    width: 100%;
+    overflow: hidden;
+    text-overflow: ellipsis;
+    margin-bottom: 10px;
+}
+
+.monomer-card-info-row > div:nth-child(2) {
+    white-space: nowrap;
+    overflow: hidden;
+    text-overflow: ellipsis;
+}
+
+.monomer-card-info-row > div:nth-child(1) {
+    font-weight: bold;
+    margin-right: 5px;
+    text-wrap: nowrap;
+}
+
+.duplicate-monomer-symbol-row {
+    visibility: visible !important;
+}
+
+.monomer-card-root {
+    border: 2px solid var(--grey-2);
+    border-radius: 5px;
+    padding: 5px;
+    margin: 5px;
+    overflow: hidden;
+    align-items: center;
+    cursor: pointer;
+    width: 200px;
+    height: 300px;
+    min-width: 200px;
+    min-height: 300px;
+}
+
+.duplicate-monomers-virtual-view {
+    width: 100% !important;
+    overflow-x: clip;
+    overflow-y: auto;
+}

package/detectors.js

@@ -615,12 +615,17 @@ class BioPackageDetectors extends DG.Package {
 
 async function refineSeqSplitter(col, stats, separator) {
   let invalidateRequired = false;
-  const isCyclized = Object.keys(stats.freq).some((om) => om.match(/.+\(\d+\)/));
-  if (isCyclized) {
+  const isCyclized = Object.keys(stats.freq).some((om) => om.match(/^.+\(\d+\)$/));
+  const isDimerized = Object.keys(stats.freq).some((om) => om.match(/^\(#\d\).+$/));
+
+  if (isCyclized && !isDimerized) {
     await grok.functions.call('Bio:applyNotationProviderForCyclized', {col: col, separator: separator});
     // SeqHandler will be recreated and replaced with the next call .forColumn()
     // because of changing tags of the column
     invalidateRequired = true;
+  } else if (isDimerized) {
+    await grok.functions.call('Bio: applyNotationProviderForDimerized', {col: col, separator: separator});
+    invalidateRequired = true;
   }
 
   if (invalidateRequired) {

package/dist/111.js

@@ -1,2 +1,2 @@
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+var bio;(()=>{"use strict";var e,r,t={4111:(e,r,t)=>{var n=t(6066);const o=e=>null==e;var a=t(2780),s=t(8774);onmessage=async e=>{const{values:r,startIdx:t,endIdx:i,threshold:c,fnNames:l,opts:p,aggregationMethod:h,weights:u}=e.data;try{const e=[],f=[],g=[],v=i-t,d=function(e,r){return e===n.G.MANHATTAN?e=>e.reduce(((e,t,n)=>e+t*r[n]),0):e=>{const t=e.reduce(((e,t,n)=>e+(t*r[n])**2),0);return Math.sqrt(t)}}(h,u);r.forEach(((e,t)=>{if((0,a.lW)(l[t]))for(let n=0;n<e.length;++n)o(e[n])||(r[t][n]=new s.A(r[t][n]._data,r[t][n]._length))}));let b=0;const w=new Array(l.length).fill(null).map(((e,r)=>new a.t$(l[r]).getMeasure(p[r]))),m=r[0].length-2-Math.floor(Math.sqrt(-8*t+4*r[0].length*(r[0].length-1)-7)/2-.5),y=t-r[0].length*m+Math.floor((m+1)*(m+2)/2);let x=m,O=y;for(;b<v;){const t=w.map(((e,t)=>o(r[t][x])||o(r[t][O])?1:e(r[t][x],r[t][O]))),n=1===t.length?t[0]:d(t);1-n>=c&&(e.push(x),f.push(O),g.push(n)),b++,O++,O===r[0].length&&(x++,O=x+1)}const A=new Int32Array(e),M=new Int32Array(f),j=new Float32Array(g);postMessage({i:A,j:M,distance:j})}catch(e){postMessage({error:e})}}}},n={};function o(e){var r=n[e];if(void 0!==r)return r.exports;var a=n[e]={exports:{}};return t[e](a,a.exports,o),a.exports}o.m=t,o.x=()=>{var e=o.O(void 0,[242,589],(()=>o(4111)));return o.O(e)},e=[],o.O=(r,t,n,a)=>{if(!t){var s=1/0;for(p=0;p<e.length;p++){for(var[t,n,a]=e[p],i=!0,c=0;c<t.length;c++)(!1&a||s>=a)&&Object.keys(o.O).every((e=>o.O[e](t[c])))?t.splice(c--,1):(i=!1,a<s&&(s=a));if(i){e.splice(p--,1);var l=n();void 0!==l&&(r=l)}}return r}a=a||0;for(var p=e.length;p>0&&e[p-1][2]>a;p--)e[p]=e[p-1];e[p]=[t,n,a]},o.d=(e,r)=>{for(var t in r)o.o(r,t)&&!o.o(e,t)&&Object.defineProperty(e,t,{enumerable:!0,get:r[t]})},o.f={},o.e=e=>Promise.all(Object.keys(o.f).reduce(((r,t)=>(o.f[t](e,r),r)),[])),o.u=e=>e+".js",o.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(e){if("object"==typeof window)return window}}(),o.o=(e,r)=>Object.prototype.hasOwnProperty.call(e,r),(()=>{var e;o.g.importScripts&&(e=o.g.location+"");var r=o.g.document;if(!e&&r&&(r.currentScript&&"SCRIPT"===r.currentScript.tagName.toUpperCase()&&(e=r.currentScript.src),!e)){var t=r.getElementsByTagName("script");if(t.length)for(var n=t.length-1;n>-1&&(!e||!/^http(s?):/.test(e));)e=t[n--].src}if(!e)throw new Error("Automatic publicPath is not supported in this browser");e=e.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),o.p=e})(),(()=>{var e={111:1};o.f.i=(r,t)=>{e[r]||importScripts(o.p+o.u(r))};var r=self.webpackChunkbio=self.webpackChunkbio||[],t=r.push.bind(r);r.push=r=>{var[n,a,s]=r;for(var i in a)o.o(a,i)&&(o.m[i]=a[i]);for(s&&s(o);n.length;)e[n.pop()]=1;t(r)}})(),r=o.x,o.x=()=>Promise.all([o.e(242),o.e(589)]).then(r);var a=o.x();bio=a})();
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priority];\n\t\treturn;\n\t}\n\tvar notFulfilled = Infinity;\n\tfor (var i = 0; i < deferred.length; i++) {\n\t\tvar [chunkIds, fn, priority] = deferred[i];\n\t\tvar fulfilled = true;\n\t\tfor (var j = 0; j < chunkIds.length; j++) {\n\t\t\tif ((priority & 1 === 0 || notFulfilled >= priority) && Object.keys(__webpack_require__.O).every((key) => (__webpack_require__.O[key](chunkIds[j])))) {\n\t\t\t\tchunkIds.splice(j--, 1);\n\t\t\t} else {\n\t\t\t\tfulfilled = false;\n\t\t\t\tif(priority < notFulfilled) notFulfilled = priority;\n\t\t\t}\n\t\t}\n\t\tif(fulfilled) {\n\t\t\tdeferred.splice(i--, 1)\n\t\t\tvar r = fn();\n\t\t\tif (r !== undefined) result = r;\n\t\t}\n\t}\n\treturn result;\n};","var next = __webpack_require__.x;\n__webpack_require__.x = () => {\n\treturn Promise.all([\n\t\t__webpack_require__.e(242),\n\t\t__webpack_require__.e(589)\n\t]).then(next);\n};","import { DistanceAggregationMethods } from './types';\nexport const isNil = (x) => x === null || x === undefined;\nexport function insertSmaller(distancesAr, indexes, num, index) {\n    if (num > distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num < v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n    if (num < distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num > v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function getAggregationFunction(aggregationMethod, weights) {\n    switch (aggregationMethod) {\n        case DistanceAggregationMethods.MANHATTAN:\n            return (vs) => vs.reduce((acc, val, idx) => acc + val * weights[idx], 0);\n        default:\n            return (vs) => {\n                // euclidean\n                const sum = vs.reduce((acc, val, idx) => acc + (val * weights[idx]) ** 2, 0);\n                return Math.sqrt(sum);\n            };\n    }\n}\n//# 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{ getAggregationFunction, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, threshold, fnNames, opts, aggregationMethod, weights } = event.data;\n    try {\n        // if (startIdx != -1)\n        //   throw new Error('Error in sparse matrix worker'); // TODO: remove this line\n        const i = [];\n        const j = [];\n        const distances = [];\n        const chunkSize = endIdx - startIdx;\n        //const mi = startRow;\n        //const mj = startCol;\n        const aggregate = getAggregationFunction(aggregationMethod, weights);\n        values.forEach((v, colIdx) => {\n            if (isBitArrayMetric(fnNames[colIdx])) {\n                for (let i = 0; i < v.length; ++i) {\n                    if (isNil(v[i]))\n                        continue;\n                    values[colIdx][i] = new 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