@rnacanvas/search 1.2.3 → 1.3.0

package/README.md

@@ -50,18 +50,19 @@ new SequenceCharacter('AG'); // throws
 new SequenceCharacter('asdf'); // throws
 ```
 
-Any character may be input to the constructor, though.
+A `SequenceCharacter` instance may be created for any character, though.
 
 ### `toString()`
 
-Simply returns the character as a string.
+Returns the character as a string.
 
 ```javascript
 var A = new SequenceCharacter('A');
 A.toString(); // "A"
 
-var R = new SequenceCharacter('R');
-R.toString(); // "R"
+// preserves case
+var r = new SequenceCharacter('r');
+r.toString(); // "r"
 ```
 
 ### `matches()`
@@ -95,16 +96,19 @@ var N = new SequenceCharacter('N');
 N.matches('A'); // true
 N.matches('p'); // true
 
+// gap characters
 var period = new SequenceCharacter('.');
 var dash = new SequenceCharacter('-');
 
 // gap characters only match other gap characters
 period.matches('.'); // true
 dash.matches('-'); // true
-period.matches('N'); // false
+
+N.matches('.'); // false
+N.matches('-'); // false
 ```
 
-Will throw for empty strings and strings containing more than one character.
+Throws for empty strings and strings containing more than one character.
 
 ```javascript
 var A = new SequenceCharacter('A');
@@ -116,3 +120,70 @@ A.matches(''); // throws
 A.matches('AG'); // throws
 A.matches('asdf'); // throws
 ```
+
+### `complements()`
+
+Returns `true` if the character complements the specified character.
+
+```javascript
+var A = new SequenceCharacter('A');
+
+A.complements('U'); // true
+A.complements('A'); // false
+
+// T and U are interchangeable
+A.complements('T'); // true
+
+// case doesn't matter
+A.complements('u'); // true
+
+// sequence character instances can also be input
+A.complements(new SequenceCharacter('U')); // true
+```
+
+[IUPAC nucleic acid codes](https://www.bioinformatics.org/sms/iupac.html) are recognized.
+
+```javascript
+var G = new SequenceCharacter('G');
+
+// since G can pair with C, U and T
+G.complements('Y'); // true
+
+var U = new SequenceCharacter('U');
+
+// since U can pair with A or G
+U.complements('R'); // true
+
+var N = new SequenceCharacter('N');
+
+// the any character complements any non-gap character
+N.complements('A'); // true
+
+// gap characters
+var period = new SequenceCharacter('.');
+var dash = new SequenceCharacter('-');
+
+// gap characters only complement other gap characters
+period.complements('.'); // true
+period.complements('-'); // true
+
+N.complements('.'); // false
+N.complements('-'); // false
+```
+
+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.
+
+```javascript
+var A = new SequenceCharacter('A');
+
+// empty string
+A.complements(''); // throws
+
+// strings containing more than one character
+A.complements('AG'); // throws
+A.complements('asdf'); // throws
+```

package/dist/Motif.d.ts

@@ -0,0 +1,6 @@
+export declare class Motif {
+    #private;
+    constructor(motif: string);
+    toString(): string;
+}
+//# sourceMappingURL=Motif.d.ts.map

package/dist/Motif.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"Motif.d.ts","sourceRoot":"","sources":["../src/Motif.ts"],"names":[],"mappings":"AAAA,qBAAa,KAAK;;gBAGJ,KAAK,EAAE,MAAM;IAIzB,QAAQ,IAAI,MAAM;CAGnB"}

package/dist/index.d.ts

@@ -1,3 +1,5 @@
+import { Motif } from './Motif';
+export { Motif };
 import { SequenceCharacter } from './SequenceCharacter';
 export { SequenceCharacter };
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AACxD,OAAO,EAAE,iBAAiB,EAAE,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAC;AAChC,OAAO,EAAE,KAAK,EAAE,CAAC;AAEjB,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AACxD,OAAO,EAAE,iBAAiB,EAAE,CAAC"}

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={};e.r(t),e.d(t,{SequenceCharacter:()=>o});var r,n=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 o{constructor(e){if(r.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,r,e,"f")}toString(){return n(this,r,"f")}matches(e){var t,o;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 c=n(this,r,"f").toUpperCase();return e=e.toUpperCase(),!(!i.includes(c)||!i.includes(e))||!i.includes(c)&&!i.includes(e)&&("N"===c&&!i.includes(e)||"N"===e&&!i.includes(c)||(c in a?null!==(o=null===(t=a[c])||void 0===t?void 0:t.includes(e))&&void 0!==o&&o:c===e))}complements(e){var t,o;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=n(this,r,"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!==(o=null===(t=c[a])||void 0===t?void 0:t.includes(e))&&void 0!==o&&o)}}r=new WeakMap;const i=[...".-"],a={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})());
+!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 o in r)e.o(r,o)&&!e.o(t,o)&&Object.defineProperty(t,o,{enumerable:!0,get:r[o]})},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={};e.r(t),e.d(t,{Motif:()=>o,SequenceCharacter:()=>i});var r;class o{constructor(e){r.set(this,void 0),function(e,t,r,o,n){if("m"===o)throw new TypeError("Private method is not writable");if("a"===o&&!n)throw new TypeError("Private accessor was defined without a setter");if("function"==typeof t?e!==t||!n:!t.has(e))throw new TypeError("Cannot write private member to an object whose class did not declare it");"a"===o?n.call(e,r):n?n.value=r:t.set(e,r)}(this,r,e,"f")}toString(){return function(e,t,r,o){if("a"===r&&!o)throw new TypeError("Private accessor was defined without a getter");if("function"==typeof t?e!==t||!o:!t.has(e))throw new TypeError("Cannot read private member from an object whose class did not declare it");return"m"===r?o:"a"===r?o.call(e):o?o.value:t.get(e)}(this,r,"f")}}r=new WeakMap;var n,a=function(e,t,r,o){if("a"===r&&!o)throw new TypeError("Private accessor was defined without a getter");if("function"==typeof t?e!==t||!o:!t.has(e))throw new TypeError("Cannot read private member from an object whose class did not declare it");return"m"===r?o:"a"===r?o.call(e):o?o.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,o,n){if("m"===o)throw new TypeError("Private method is not writable");if("a"===o&&!n)throw new TypeError("Private accessor was defined without a setter");if("function"==typeof t?e!==t||!n:!t.has(e))throw new TypeError("Cannot write private member to an object whose class did not declare it");"a"===o?n.call(e,r):n?n.value=r:t.set(e,r)}(this,n,e,"f")}toString(){return a(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 o=a(this,n,"f").toUpperCase();return e=e.toUpperCase(),!(!c.includes(o)||!c.includes(e))||!c.includes(o)&&!c.includes(e)&&("N"===o&&!c.includes(e)||"N"===e&&!c.includes(o)||(o in s?null!==(r=null===(t=s[o])||void 0===t?void 0:t.includes(e))&&void 0!==r&&r:o===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 o=a(this,n,"f").toUpperCase();return e=e.toUpperCase(),!(!c.includes(o)||!c.includes(e))||!c.includes(o)&&!c.includes(e)&&("N"===o&&!c.includes(e)||"N"===e&&!c.includes(o)||o in l&&null!==(r=null===(t=l[o])||void 0===t?void 0:t.includes(e))&&void 0!==r&&r)}}n=new WeakMap;const c=[...".-"],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"]},l={A:[..."UT"],C:[..."G"],G:[..."CUTY"],U:[..."AGR"],T:[..."AGR"],R:[..."UT"],Y:[..."G"]};return t})());

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@rnacanvas/search",
-  "version": "1.2.3",
-  "description": "Find motifs",
+  "version": "1.3.0",
+  "description": "Find motifs and complements",
   "repository": {
     "type": "git",
     "url": "https://github.com/pzhaojohnson/rnacanvas.search.git"