@datagrok/peptides 0.0.1 → 0.4.2

package/tsconfig.json

@@ -4,17 +4,17 @@
 
     /* Basic Options */
     // "incremental": true,                         /* Enable incremental compilation */
-    "target": "es2017",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', 'ES2021', or 'ESNEXT'. */
-    "module": "es2020",                           /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
-    // "lib": [],                                   /* Specify library files to be included in the compilation. */
-    "allowJs": true,                             /* Allow javascript files to be compiled. */
+    "target": "es2018",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
+    "module": "es2020",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
+    "lib": ["es2020", "dom"],      /* Specify library files to be included in the compilation. */
+    // "allowJs": true,                             /* Allow javascript files to be compiled. */
     // "checkJs": true,                             /* Report errors in .js files. */
     // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
     // "declaration": true,                         /* Generates corresponding '.d.ts' file. */
     // "declarationMap": true,                      /* Generates a sourcemap for each corresponding '.d.ts' file. */
     // "sourceMap": true,                           /* Generates corresponding '.map' file. */
     // "outFile": "./",                             /* Concatenate and emit output to single file. */
-    "outDir": "./dist",                              /* Redirect output structure to the directory. */
+    // "outDir": "./",                              /* Redirect output structure to the directory. */
     // "rootDir": "./",                             /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */
     // "composite": true,                           /* Enable project compilation */
     // "tsBuildInfoFile": "./",                     /* Specify file to store incremental compilation information */
@@ -26,7 +26,7 @@
 
     /* Strict Type-Checking Options */
     "strict": true,                                 /* Enable all strict type-checking options. */
-    "noImplicitAny": true,                       /* Raise error on expressions and declarations with an implied 'any' type. */
+    // "noImplicitAny": true,                       /* Raise error on expressions and declarations with an implied 'any' type. */
     // "strictNullChecks": true,                    /* Enable strict null checks. */
     // "strictFunctionTypes": true,                 /* Enable strict checking of function types. */
     // "strictBindCallApply": true,                 /* Enable strict 'bind', 'call', and 'apply' methods on functions. */
@@ -40,11 +40,10 @@
     // "noImplicitReturns": true,                   /* Report error when not all code paths in function return a value. */
     // "noFallthroughCasesInSwitch": true,          /* Report errors for fallthrough cases in switch statement. */
     // "noUncheckedIndexedAccess": true,            /* Include 'undefined' in index signature results */
-    // "noImplicitOverride": true,                  /* Ensure overriding members in derived classes are marked with an 'override' modifier. */
     // "noPropertyAccessFromIndexSignature": true,  /* Require undeclared properties from index signatures to use element accesses. */
 
     /* Module Resolution Options */
-    "moduleResolution": "node",                  /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */
+    "moduleResolution": "node",                     /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */
     // "baseUrl": "./",                             /* Base directory to resolve non-absolute module names. */
     // "paths": {},                                 /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */
     // "rootDirs": [],                              /* List of root folders whose combined content represents the structure of the project at runtime. */
@@ -56,17 +55,17 @@
     // "allowUmdGlobalAccess": true,                /* Allow accessing UMD globals from modules. */
 
     /* Source Map Options */
-    // "sourceRoot": "",                            /* Specify the location where debugger should locate TypeScript files instead of source locations. */
-    // "mapRoot": "",                               /* Specify the location where debugger should locate map files instead of generated locations. */
-    // "inlineSourceMap": true,                     /* Emit a single file with source maps instead of having a separate file. */
-    // "inlineSources": true,                       /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */
+    "sourceRoot": "",                            /* Specify the location where debugger should locate TypeScript files instead of source locations. */
+    "mapRoot": "",                               /* Specify the location where debugger should locate map files instead of generated locations. */
+    "inlineSourceMap": true,                     /* Emit a single file with source maps instead of having a separate file. */
+    "inlineSources": true,                       /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */
 
     /* Experimental Options */
     // "experimentalDecorators": true,              /* Enables experimental support for ES7 decorators. */
     // "emitDecoratorMetadata": true,               /* Enables experimental support for emitting type metadata for decorators. */
 
     /* Advanced Options */
-    "skipLibCheck": true,                           /* Skip type checking of declaration files. */
+    "skipLibCheck": true,                          /* Skip type checking of declaration files. */
     "forceConsistentCasingInFileNames": true        /* Disallow inconsistently-cased references to the same file. */
   }
 }

package/webpack.config.js

@@ -3,19 +3,19 @@ const path = require('path');
 module.exports = {
   mode: 'development',
   entry: {
-    package: './src/package.ts'
+    package: './src/package.ts',
   },
   module: {
     rules: [
       {
-        test: /\.tsx?$/,
+        test: /\.ts?$/,
         use: 'ts-loader',
         exclude: /node_modules/,
       },
     ],
   },
   resolve: {
-    extensions: ['.tsx', '.ts', '.js'],
+    extensions: ['.tsx', '.js', '.ts'],
   },
   devtool: 'inline-source-map',
   externals: {
@@ -24,7 +24,7 @@ module.exports = {
     'datagrok-api/ui': 'ui',
     'openchemlib/full.js': 'OCL',
     'rxjs': 'rxjs',
-    'rxjs/operators': 'rxjs.operators'
+    'rxjs/operators': 'rxjs.operators',
   },
   output: {
     filename: '[name].js',

package/src/split-aligned.ts

@@ -1,42 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-
-export function splitAlignedPeptides(peptideColumn: DG.Column) {
-  let splitPeptidesArray: string[][] = [];
-  let isFirstRun = true;
-  let splitted: string[];
-
-  for (const peptideStr of peptideColumn.toList()) {
-    splitted = peptideStr.split('-');
-
-    if (isFirstRun) {
-      for (let i = 0; i < splitted.length; i++) {
-        splitPeptidesArray.push([]);
-      }
-      isFirstRun = false;
-    }
-
-    splitted.forEach((value, index) => {
-      splitPeptidesArray[index].push(value === '' ? '-' : value);
-    });
-  }
-
-  //create column names list
-  let columnNames = ['N'];
-  columnNames = columnNames.concat(splitPeptidesArray.map((_, index) => `${index + 1 < 10 ? 0 : ''}${index +1 }`));
-  columnNames.push('C');
-
-  // filter out the columns with the same values
-  splitPeptidesArray = splitPeptidesArray.filter((positionArray, index) => {
-    const isRetained = new Set(positionArray).size > 1;
-    if (!isRetained) {
-      columnNames.splice(index, 1);
-    }
-    return isRetained;
-  });
-
-  const columnsArray = splitPeptidesArray.map((positionArray, index) => {
-    return DG.Column.fromList('string', columnNames[index], positionArray);
-  });
-
-  return DG.DataFrame.fromColumns(columnsArray);
-}

package/src/utils/misc.ts

@@ -1,101 +0,0 @@
-//@ts-ignore: no types
-import * as jStat from 'jstat';
-
-type testStats = {
-  'p-value': number,
-  'Mean difference'?: number,
-  'Median difference'?: number,
-  'p-value more': number,
-  'p-value less': number,
-};
-
-export function tTest(arr1: number[], arr2: number[], alpha=0.05, devKnown=false, devEqual=false): testStats {
-  const m1: number = jStat.mean(arr1);
-  const m2: number = jStat.mean(arr2);
-  const v1: number = jStat.variance(arr1);
-  const v2: number = jStat.variance(arr2);
-  const n1 = arr1.length;
-  const n2 = arr2.length;
-
-  let wv1;
-  let wv2;
-  let wv;
-  let Z;
-  let K;
-  let pMore;
-  let pLess;
-  let pTot;
-
-  if (!devKnown) {
-    if (!devEqual) {
-      wv1 = v1 / n1;
-      wv2 = v2 / n2;
-      Z = (m1 - m2) / Math.sqrt(wv1 + wv2);
-      K = Math.pow((wv1 + wv2), 2) / (wv1 * wv1 / (n1 - 1) + wv2 * wv2 / (n2 - 1));
-
-      pLess = jStat.studentt.cdf(Z, K);
-      pMore = 1 - pLess;
-      pTot = 2 * (pLess < pMore ? pLess : pMore);
-    } else {
-      K = n1 + n2 - 2;
-      wv = (v1 * (n1 - 1) + v2 * (n2 - 1)) / K;
-      Z = Math.sqrt(n1 * n2 / (n1 + n2)) * (m1 - m2) / wv;
-
-      pMore = 1 - jStat.studentt.cdf(Z, K);
-      pLess = jStat.studentt.cdf(Z, K);
-      pTot = 2 * (pLess < pMore ? pLess : pMore);
-    }
-  } else {
-    wv1 = v1 / n1;
-    wv2 = v2 / n2;
-    Z = (m1 - m2) / Math.sqrt(wv1 + wv2);
-
-    pLess = jStat.normal.pdf(Z, 0, 1);
-    pMore = 1 - pLess;
-    pTot = 2 * (pLess < pMore ? pLess : pMore);
-  }
-  return {'p-value': pTot, 'Mean difference': m1 - m2, 'p-value more': pMore, 'p-value less': pLess};
-}
-
-export function uTest(x: number[], y: number[], continuity=true): testStats {
-  const xy = x.concat(y);
-  const n1 = x.length;
-  const n2 = y.length;
-  const med1 = jStat.median(x);
-  const med2 = jStat.median(y);
-
-  const ranks = jStat.rank(xy);
-
-  const R1 = jStat.sum(ranks.slice(0, n1));
-  const U1 = R1 - n1 * (n1 + 1) / 2;
-  const U2 = n1 * n2 - U1;
-  const U = U1 > U2 ? U1 : U2;
-
-  const mu = n1 * n2 / 2;
-  const n = n1 + n2;
-
-  const tieTerm = _tieTerm(ranks);
-  const s = Math.sqrt(n1 * n2 / 12 * ((n + 1) - tieTerm / (n* (n - 1))));
-
-  let numerator = U - mu;
-
-  if (continuity) {
-    numerator -= 0.5;
-  }
-
-  const z = numerator / s;
-
-  const p = 2 * (1 - jStat.normal.cdf(z, 0, 1));
-
-  return {'p-value': p, 'Median difference': med1 - med2, 'p-value more': p, 'p-value less': p};
-}
-
-function _tieTerm(ranks: number[]): number {
-  const ties: {[key: number]: number} = {};
-
-  ranks.forEach((num) => {
-    ties[num] = (ties[num] || 0) + 1;
-  });
-
-  return jStat.sum(Object.values(ties));
-}