@rnacanvas/search 2.0.0 → 3.0.1

package/README.md

@@ -12,37 +12,7 @@ All exports of this package can be accessed as named imports.
 
 ```javascript
 // some example imports
-import { Motif, SequenceCharacter } from '@rnacanvas/search';
-```
-
-## `class Motif`
-
-Represents a motif.
-
-```javascript
-var CUGCCA = new Motif('CUGCCA');
-
-CUGCCA.toString(); // "CUGCCA"
-
-// a single character motif
-var A = new Motif('A');
-
-A.toString(); // "A"
-
-// empty motifs are accepted
-var emptyMotif = new Motif('');
-
-emptyMotif.toString(); // ""
-```
-
-### `toString()`
-
-Returns the motif as a string.
-
-```javascript
-var CUGCCA = new Motif('CUGCCA');
-
-CUGCCA.toString(); // "CUGCCA"
+import { removeGapCharacters, SequenceCharacter } from '@rnacanvas/search';
 ```
 
 ## `function removeGapCharacters()`
@@ -150,17 +120,17 @@ N.matches('.'); // false
 N.matches('-'); // false
 ```
 
-Throws for empty strings and strings containing more than one character.
+Returns `false` for empty strings and strings containing more than one character.
 
 ```javascript
 var A = new SequenceCharacter('A');
 
 // empty string
-A.matches(''); // throws
+A.matches(''); // false
 
 // strings containing more than one character
-A.matches('AG'); // throws
-A.matches('asdf'); // throws
+A.matches('AG'); // false
+A.matches('asdf'); // false
 ```
 
 ### `complements()`
@@ -217,17 +187,18 @@ Note that the special IUPAC codes
 `S`, `W`, `K`, `M`, `B`, `D`, `H` and `V`
 have no complements.
 
-This method throws for empty strings and strings containing more than one character.
+This method returns `false` for empty strings
+and strings containing more than one character.
 
 ```javascript
 var A = new SequenceCharacter('A');
 
 // empty string
-A.complements(''); // throws
+A.complements(''); // false
 
 // strings containing more than one character
-A.complements('AG'); // throws
-A.complements('asdf'); // throws
+A.complements('AG'); // false
+A.complements('asdf'); // false
 ```
 
 ## `function isWobblePair()`

package/dist/AlignmentCell.d.ts

@@ -0,0 +1,16 @@
+/**
+ * A cell in an alignment matrix.
+ */
+export declare class AlignmentCell {
+    readonly score: number;
+    /**
+     * The change in I index to get to this cell (from the previous cell).
+     */
+    readonly deltaI: number;
+    /**
+     * The change in J index to get to this cell (from the previous cell).
+     */
+    readonly deltaJ: number;
+    constructor(score: number, deltaI: number, deltaJ: number);
+}
+//# sourceMappingURL=AlignmentCell.d.ts.map

package/dist/AlignmentCell.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AlignmentCell.d.ts","sourceRoot":"","sources":["../src/AlignmentCell.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,qBAAa,aAAa;IACxB,QAAQ,CAAC,KAAK,SAAC;IAEf;;OAEG;IACH,QAAQ,CAAC,MAAM,SAAC;IAEhB;;OAEG;IACH,QAAQ,CAAC,MAAM,SAAC;gBAEJ,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAM1D"}

package/dist/AlignmentMatrix.d.ts

@@ -0,0 +1,7 @@
+import { AlignmentCell } from './AlignmentCell';
+export declare class AlignmentMatrix {
+    #private;
+    get(i: number, j: number): AlignmentCell | never;
+    set(i: number, j: number, cell: AlignmentCell): void;
+}
+//# sourceMappingURL=AlignmentMatrix.d.ts.map

package/dist/AlignmentMatrix.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AlignmentMatrix.d.ts","sourceRoot":"","sources":["../src/AlignmentMatrix.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAEhD,qBAAa,eAAe;;IAG1B,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,GAAG,aAAa,GAAG,KAAK;IAsBhD,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,aAAa,GAAG,IAAI;CAarD"}

package/dist/SequenceCharacter.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"SequenceCharacter.d.ts","sourceRoot":"","sources":["../src/SequenceCharacter.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,qBAAa,iBAAiB;;gBAGhB,SAAS,EAAE,MAAM;IAU7B,QAAQ,IAAI,MAAM;IAIlB,OAAO,CAAC,cAAc,EAAE,iBAAiB,GAAG,MAAM,GAAG,OAAO;IAkC5D,WAAW,CAAC,cAAc,EAAE,iBAAiB,GAAG,MAAM,GAAG,OAAO;CAiCjE"}
+{"version":3,"file":"SequenceCharacter.d.ts","sourceRoot":"","sources":["../src/SequenceCharacter.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,qBAAa,iBAAiB;;gBAGhB,SAAS,EAAE,MAAM;IAU7B,QAAQ,IAAI,MAAM;IAIlB,OAAO,CAAC,cAAc,EAAE,iBAAiB,GAAG,MAAM,GAAG,OAAO;IAgC5D,WAAW,CAAC,cAAc,EAAE,iBAAiB,GAAG,MAAM,GAAG,OAAO;CA+BjE"}

package/dist/index.js

@@ -1 +1 @@
-!function(e,t){"object"==typeof exports&&"object"==typeof module?module.exports=t():"function"==typeof define&&define.amd?define([],t):"object"==typeof exports?exports.search=t():e.search=t()}(this,()=>(()=>{"use strict";var e={d:(t,r)=>{for(var n in r)e.o(r,n)&&!e.o(t,n)&&Object.defineProperty(t,n,{enumerable:!0,get:r[n]})},o:(e,t)=>Object.prototype.hasOwnProperty.call(e,t),r:e=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})}},t={};function r(e){return e.replace(/[\.-]/g,"")}e.r(t),e.d(t,{SequenceCharacter:()=>a,removeGapCharacters:()=>r});var n,o=function(e,t,r,n){if("a"===r&&!n)throw new TypeError("Private accessor was defined without a getter");if("function"==typeof t?e!==t||!n:!t.has(e))throw new TypeError("Cannot read private member from an object whose class did not declare it");return"m"===r?n:"a"===r?n.call(e):n?n.value:t.get(e)};class a{constructor(e){if(n.set(this,void 0),0==e.length)throw new Error("Character cannot be an empty string.");if(e.length>1)throw new Error("Character must be a single character.");!function(e,t,r,n,o){if("m"===n)throw new TypeError("Private method is not writable");if("a"===n&&!o)throw new TypeError("Private accessor was defined without a setter");if("function"==typeof t?e!==t||!o:!t.has(e))throw new TypeError("Cannot write private member to an object whose class did not declare it");"a"===n?o.call(e,r):o?o.value=r:t.set(e,r)}(this,n,e,"f")}toString(){return o(this,n,"f")}matches(e){var t,r;if("string"!=typeof e&&(e=e.toString()),0==e.length)throw new Error("Other character cannot be an empty string.");if(e.length>1)throw new Error("Other character cannot be multiple characters.");let a=o(this,n,"f").toUpperCase();return e=e.toUpperCase(),!(!i.includes(a)||!i.includes(e))||!i.includes(a)&&!i.includes(e)&&("N"===a&&!i.includes(e)||"N"===e&&!i.includes(a)||(a in c?null!==(r=null===(t=c[a])||void 0===t?void 0:t.includes(e))&&void 0!==r&&r:a===e))}complements(e){var t,r;if("string"!=typeof e&&(e=e.toString()),0==e.length)throw new Error("Other character cannot be an empty string.");if(e.length>1)throw new Error("Other character cannot be multiple characters.");let a=o(this,n,"f").toUpperCase();return e=e.toUpperCase(),!(!i.includes(a)||!i.includes(e))||!i.includes(a)&&!i.includes(e)&&("N"===a&&!i.includes(e)||"N"===e&&!i.includes(a)||a in s&&null!==(r=null===(t=s[a])||void 0===t?void 0:t.includes(e))&&void 0!==r&&r)}}n=new WeakMap;const i=[...".-"],c={A:[..."A"],C:[..."C"],G:[..."G"],U:[..."UT"],T:[..."TU"],R:[..."AG"],Y:[..."CUT"],S:[..."GC"],W:[..."AUT"],K:[..."GUT"],M:[..."AC"],B:[..."CGUTYSK"],D:[..."AGUTRWK"],H:[..."ACUTYWM"],V:[..."ACGRSM"]},s={A:[..."UT"],C:[..."G"],G:[..."CUTY"],U:[..."AGR"],T:[..."AGR"],R:[..."UT"],Y:[..."G"]};return t})());
+!function(e,t){"object"==typeof exports&&"object"==typeof module?module.exports=t():"function"==typeof define&&define.amd?define([],t):"object"==typeof exports?exports.search=t():e.search=t()}(this,()=>(()=>{"use strict";var e={d:(t,r)=>{for(var n in r)e.o(r,n)&&!e.o(t,n)&&Object.defineProperty(t,n,{enumerable:!0,get:r[n]})},o:(e,t)=>Object.prototype.hasOwnProperty.call(e,t),r:e=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})}},t={};function r(e){return e.replace(/[\.-]/g,"")}e.r(t),e.d(t,{SequenceCharacter:()=>i,removeGapCharacters:()=>r});var n,o=function(e,t,r,n){if("a"===r&&!n)throw new TypeError("Private accessor was defined without a getter");if("function"==typeof t?e!==t||!n:!t.has(e))throw new TypeError("Cannot read private member from an object whose class did not declare it");return"m"===r?n:"a"===r?n.call(e):n?n.value:t.get(e)};class i{constructor(e){if(n.set(this,void 0),0==e.length)throw new Error("Character cannot be an empty string.");if(e.length>1)throw new Error("Character must be a single character.");!function(e,t,r,n,o){if("m"===n)throw new TypeError("Private method is not writable");if("a"===n&&!o)throw new TypeError("Private accessor was defined without a setter");if("function"==typeof t?e!==t||!o:!t.has(e))throw new TypeError("Cannot write private member to an object whose class did not declare it");"a"===n?o.call(e,r):o?o.value=r:t.set(e,r)}(this,n,e,"f")}toString(){return o(this,n,"f")}matches(e){var t,r;if("string"!=typeof e&&(e=e.toString()),1!=e.length)return!1;let i=o(this,n,"f").toUpperCase();return e=e.toUpperCase(),!(!a.includes(i)||!a.includes(e))||!a.includes(i)&&!a.includes(e)&&("N"===i&&!a.includes(e)||"N"===e&&!a.includes(i)||(i in s?null!==(r=null===(t=s[i])||void 0===t?void 0:t.includes(e))&&void 0!==r&&r:i===e))}complements(e){var t,r;if("string"!=typeof e&&(e=e.toString()),1!=e.length)return!1;let i=o(this,n,"f").toUpperCase();return e=e.toUpperCase(),!(!a.includes(i)||!a.includes(e))||!a.includes(i)&&!a.includes(e)&&("N"===i&&!a.includes(e)||"N"===e&&!a.includes(i)||i in c&&null!==(r=null===(t=c[i])||void 0===t?void 0:t.includes(e))&&void 0!==r&&r)}}n=new WeakMap;const a=[...".-"],s={A:[..."A"],C:[..."C"],G:[..."G"],U:[..."UT"],T:[..."TU"],R:[..."AG"],Y:[..."CUT"],S:[..."GC"],W:[..."AUT"],K:[..."GUT"],M:[..."AC"],B:[..."CGUTYSK"],D:[..."AGUTRWK"],H:[..."ACUTYWM"],V:[..."ACGRSM"]},c={A:[..."UT"],C:[..."G"],G:[..."CUTY"],U:[..."AGR"],T:[..."AGR"],R:[..."UT"],Y:[..."G"]};return t})());

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rnacanvas/search",
-  "version": "2.0.0",
+  "version": "3.0.1",
   "description": "Find motifs and complements",
   "repository": {
     "type": "git",