@datagrok-libraries/bio 0.0.2 → 0.0.3

package/package.json

@@ -5,10 +5,10 @@
   },
   "beta": true,
   "friendlyName": "Datagrok bio library",
-  "version": "0.0.2",
+  "version": "0.0.3",
   "description": "",
   "dependencies": {
-    "datagrok-api": ">=0.95.8",
+    "datagrok-api": ">=0.108.0",
     "@datagrok-libraries/utils": ">=0.0.13",
     "cash-dom": "latest",
     "dayjs": "latest"
@@ -30,8 +30,8 @@
     "link-all": "npm link datagrok-api @datagrok-libraries/utils",
     "debug-bio": "grok publish --rebuild",
     "release-bio": "grok publish --rebuild --release",
-    "build-bio": "webpack",
-    "build": "webpack",
+    "build-bio": "tsc",
+    "build": "tsc",
     "debug-bio-public": "grok publish public --rebuild",
     "release-bio-public": "grok publish public --rebuild --release",
     "debug-bio-local": "grok publish local --rebuild",

package/src/sequence-encoder.d.ts

@@ -0,0 +1,62 @@
+declare type SideChainScale = {
+    [name: string]: number;
+};
+/**
+ * Class to categorial encode/decode aligned amino acid residues sequence.
+ *
+ * @export
+ * @class AlignedSequenceEncoder
+ */
+export declare class AlignedSequenceEncoder {
+    protected aa2num: SideChainScale;
+    protected num2aa: {
+        [code: number]: string;
+    };
+    constructor(scale?: string);
+    /**
+       * Truncate NH2 and -COOH terminals of the given sequence.
+       *
+       * @static
+       * @param {string} seq The sequence provided.
+       * @return {string} Truncated sequence.
+       * @memberof AlignedSequenceEncoder
+       */
+    static _truncateSequence(seq: string): string;
+    /**
+       * Cuts auxiliary defises before a residue.
+       *
+       * @static
+       * @param {string} seq The sequence to process.
+       * @return {string} Processed sequence.
+       * @memberof AlignedSequenceEncoder
+       */
+    static _dropDefises(seq: string): string;
+    /**
+       * Performs truncation and cutting auxiliary defises.
+       *
+       * @static
+       * @param {string} sequence The sequence work under process.
+       * @return {string} Result of cleaning.
+       * @memberof AlignedSequenceEncoder
+       */
+    static clean(sequence: string): string;
+    /**
+       * Categorial encode of the sequence provided.
+       *
+       * @param {string} sequence The sequence.
+       * @return {number[]} Encoded vector.
+       * @memberof AlignedSequenceEncoder
+       */
+    encode(sequence: string): number[];
+    encodeLettter(letter: string): number;
+    /**
+       * Decode the encoded vector into the sequence back.
+       *
+       * @param {number[]} value The vector encoded.
+       * @return {string} Decoded sequence.
+       * @memberof AlignedSequenceEncoder
+       */
+    decode(value: number[]): string;
+}
+export {};
+//# sourceMappingURL=sequence-encoder.d.ts.map

package/src/sequence-encoder.d.ts.map

@@ -0,0 +1 @@
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package/tsconfig.json

@@ -4,14 +4,14 @@
 
     /* Basic Options */
     // "incremental": true,                         /* Enable incremental compilation */
-    "target": "es2018",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
+    "target": "es6",                                /* 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. */
+     "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": "./",                              /* Redirect output structure to the directory. */
@@ -55,17 +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": false,                          /* Skip type checking of declaration files. */
+    "skipLibCheck": true,                          /* Skip type checking of declaration files. */
     "forceConsistentCasingInFileNames": true        /* Disallow inconsistently-cased references to the same file. */
   }
 }