@rnacanvas/draw.bases.bonds 10.0.2

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 pzhaojohnson
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# Installation
+
+With `npm`:
+
+```
+npm install @rnacanvas/draw.bases.bonds
+```
+
+# Usage
+
+All exports of this package can be accessed as named imports.
+
+```javascript
+// an example import
+import { StraightBond } from '@rnacanvas/draw.bases.bonds';
+```

package/_config.yml

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+theme: jekyll-theme-minimal

package/babel.config.js

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+module.exports = {
+  presets: [
+    ['@babel/preset-env', { targets: { node: 'current' } }],
+    '@babel/preset-typescript',
+  ],
+};

package/dist/InvertedStraightBondsHider.d.ts

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+interface StraightBond {
+    /**
+     * The DOM node corresponding to the straight bond.
+     */
+    domNode: Node;
+    /**
+     * Returns true if the straight bond is inverted and returns false otherwise.
+     */
+    isInverted(): boolean;
+    setAttribute(name: 'opacity', value: string): void;
+}
+/**
+ * A live collection of items that may change over time
+ * and whose contents are expected to always be up-to-date.
+ */
+interface LiveCollection<T> extends Iterable<T> {
+}
+/**
+ * Automatically hides straight bonds that become inverted
+ * by setting their `opacity` attributes to zero.
+ *
+ * Also automatically unhides straight bonds that have stopped being inverted
+ * by setting their `opacity` attributes to one.
+ *
+ * This class will overwrite any previously set `opacity` attribute values on straight bonds.
+ */
+export declare class InvertedStraightBondsHider {
+    private targetStraightBonds;
+    /**
+     * @param targetStraightBonds The straight bonds to hide when they become inverted.
+     * @param parentSVGDoc The SVG document that the target straight bonds are in.
+     */
+    constructor(targetStraightBonds: LiveCollection<StraightBond>, parentSVGDoc: SVGSVGElement);
+    private updateOpacities;
+}
+export {};
+//# sourceMappingURL=InvertedStraightBondsHider.d.ts.map

package/dist/InvertedStraightBondsHider.d.ts.map

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package/dist/Nucleobase.d.ts

@@ -0,0 +1,19 @@
+/**
+ * A two-dimensional point.
+ */
+export type Point = {
+    x: number;
+    y: number;
+};
+/**
+ * The nucleobase interface used by bonds.
+ */
+export interface Nucleobase {
+    readonly id: string;
+    readonly centerPoint: Point;
+    /**
+     * Allows one to listen for when the nucleobase moves (i.e., its center point changes).
+     */
+    addEventListener(eventName: 'move', listener: () => void): void;
+}
+//# sourceMappingURL=Nucleobase.d.ts.map

package/dist/Nucleobase.d.ts.map

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package/dist/SavableStraightBond.d.ts

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+import type { StraightBond } from './StraightBond';
+import type { Nucleobase } from './Nucleobase';
+type NonNullObject = {
+    [name: string]: unknown;
+};
+/**
+ * Represents a straight bond that can be saved (e.g., in a file)
+ * for future drawing.
+ */
+export declare class SavableStraightBond<B extends Nucleobase> {
+    #private;
+    /**
+     * @param straightBond A straight bond to wrap.
+     */
+    constructor(straightBond: StraightBond<B>);
+    /**
+     * Returns an object that can be serialized to a JSON string
+     * and that is the saved representation of the straight bond.
+     *
+     * Throws if the straight bond has a falsy ID
+     * or if base 1 or 2 of the straight bond has a falsy ID.
+     */
+    toJSONSerializable(): NonNullObject | never;
+}
+export {};
+//# sourceMappingURL=SavableStraightBond.d.ts.map

package/dist/SavableStraightBond.d.ts.map

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package/dist/SavedStraightBond.d.ts

@@ -0,0 +1,36 @@
+import { StraightBond } from './StraightBond';
+import type { Nucleobase } from './Nucleobase';
+type NonNullObject = {
+    [name: string]: unknown;
+};
+interface Drawing<B extends Nucleobase> {
+    /**
+     * The actual DOM node corresponding to the drawing and that is the drawing
+     * (in this case an SVG document).
+     */
+    readonly domNode: SVGSVGElement;
+    /**
+     * All nucleobases in the drawing.
+     */
+    readonly bases: Iterable<B>;
+}
+/**
+ * Represents a straight bond that has been saved (e.g., in a file)
+ * and that can be recreated.
+ */
+export declare class SavedStraightBond<B extends Nucleobase> {
+    #private;
+    /**
+     * @param jsonSerializable The saved form of the straight bond (e.g., parsed from a file).
+     * @param parentDrawing
+     */
+    constructor(jsonSerializable: NonNullObject | unknown, parentDrawing: Drawing<B>);
+    /**
+     * Recreates the saved straight bond.
+     *
+     * Throws if unable to do so.
+     */
+    recreate(): StraightBond<B> | never;
+}
+export {};
+//# sourceMappingURL=SavedStraightBond.d.ts.map

package/dist/SavedStraightBond.d.ts.map

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package/dist/StraightBond.d.ts

@@ -0,0 +1,181 @@
+import type { Nucleobase } from './Nucleobase';
+/**
+ * A two-dimensional point.
+ */
+export type Point = {
+    x: number;
+    y: number;
+};
+/**
+ * A bond that is a straight line between two bases.
+ */
+export declare class StraightBond<B extends Nucleobase> {
+    private line;
+    readonly base1: B;
+    readonly base2: B;
+    /**
+     * Default values for newly created straight bonds.
+     */
+    static defaultValues: {
+        attributes: {
+            stroke: string;
+            'stroke-width': string;
+        };
+        basePadding1: number;
+        basePadding2: number;
+    };
+    /**
+     * Creates a new straight bond connecting bases 1 and 2.
+     *
+     * Applies the default values contained in the `defaultValues` static property object
+     * to the newly created straight bond.
+     */
+    static between<B extends Nucleobase>(base1: B, base2: B): StraightBond<B>;
+    private cachedBasePadding1;
+    private cachedBasePadding2;
+    /**
+     * Note that this constructor will not apply any default values to the newly created straight bond.
+     *
+     * @param line The line element that is the straight bond.
+     * @param base1 Base 1 connected by the bond.
+     * @param base2 Base 2 connected by the bond.
+     */
+    constructor(line: SVGLineElement, base1: B, base2: B);
+    /**
+     * The two bases bound by the straight bond.
+     *
+     * In the returned base-pair, the two bases bound by the straight bond
+     * will be ordered base 1 and then base 2.
+     */
+    get basePair(): [B, B];
+    /**
+     * The actual DOM node of the line element that is the straight bond.
+     */
+    get domNode(): SVGLineElement;
+    /**
+     * Get an attribute of the line element that is the straight bond.
+     */
+    getAttribute(name: string): string | null;
+    /**
+     * Set an attribute of the line element that is the straight bond.
+     */
+    setAttribute(name: string, value: string): void;
+    /**
+     * This method is meant to receive as input an object of attribute values
+     * keyed by attribute name.
+     *
+     * Invalid inputs are ignored.
+     */
+    setAttributes(attributes: {
+        [name: string]: unknown;
+    } | unknown): void;
+    /**
+     * The `id` property of the line element that is the straight bond.
+     */
+    get id(): string;
+    /**
+     * Assigns a new UUID to the straight bond.
+     *
+     * (Overwrites any preexisting ID that the straight bond had.)
+     */
+    assignUUID(): void;
+    /**
+     * Appends the line element that is the straight bond to the given container node.
+     */
+    appendTo(container: Node): void;
+    /**
+     * Removes the line element that is the straight bond from its parent container node.
+     *
+     * Has no effect if the straight bond (line element) had no parent container node to begin with.
+     */
+    remove(): void;
+    /**
+     * Returns true if the line element that is the straight bond is a child (or grandchild, great-grandchild, etc.)
+     * of the given container node.
+     *
+     * Returns false otherwise, including if the given container node is the straight bond (line element) itself.
+     */
+    isIn(container: Node): boolean;
+    /**
+     * Returns true if the line element that is the straight bond is a child of any sort of parent container node.
+     *
+     * Returns false otherwise.
+     */
+    hasParent(): boolean;
+    /**
+     * The length of the line element that is the straight bond.
+     *
+     * Note that this method might throw if the straight bond has not been added to the document of the webpage.
+     */
+    getTotalLength(): number | never;
+    /**
+     * Get a point along the length of the straight bond (going from point 1 to point 2).
+     *
+     * Note that this method might throw if the straight bond has not been added to the document of the webpage.
+     */
+    getPointAtLength(length: number): Point | never;
+    /**
+     * The point connecting with base 1 of the straight bond.
+     */
+    get point1(): Point;
+    /**
+     * The point connecting with base 2 of the straight bond.
+     */
+    get point2(): Point;
+    /**
+     * The distance that point 1 is meant to be from base 1 of the straight bond.
+     *
+     * Note that this is not the same thing as the current distance between point 1 and base 1 of the straight bond.
+     *
+     * (This is to allow for proper repositioning of the straight bond after its bases have been moved.)
+     */
+    get basePadding1(): number;
+    /**
+     * Will reposition the straight bond.
+     */
+    set basePadding1(basePadding1: number);
+    /**
+     * Values that are not finite numbers are ignored.
+     *
+     * Negative values are clamped to zero.
+     */
+    setBasePadding1(basePadding1: number | unknown): void;
+    /**
+     * The distance that point 2 is meant to be from base 2 of the straight bond.
+     *
+     * Note that this is not the same thing as the current distance between point 2 and base 2 of the straight bond.
+     *
+     * (This is to allow for proper repositioning of the straight bond after its bases have been moved.)
+     */
+    get basePadding2(): number;
+    /**
+     * Will reposition the straight bond.
+     */
+    set basePadding2(basePadding2: number);
+    /**
+     * Values that are not finite numbers are ignored.
+     *
+     * Negative values are clamped to zero.
+     */
+    setBasePadding2(basePadding2: number | unknown): void;
+    /**
+     * Returns true if the sum of base paddings 1 and 2 is greater than
+     * the distance between the center points of bases 1 and 2 for the straight bond.
+     *
+     * Returns false otherwise.
+     */
+    isInverted(): boolean;
+    /**
+     * Sets values of the straight bond.
+     *
+     * Is supposed to receive as input an object of property values (keyed by property name).
+     *
+     * The input object can also contain an attributes child object (with key `attributes`).
+     */
+    set(values: unknown): void;
+    /**
+     * Repositions the straight bond based on the current positions of bases 1 and 2.
+     */
+    private reposition;
+}
+//# sourceMappingURL=StraightBond.d.ts.map

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package/dist/index.d.ts

@@ -0,0 +1,11 @@
+import { StraightBond } from './StraightBond';
+export { StraightBond };
+import type { Nucleobase } from './Nucleobase';
+export type { Nucleobase };
+import { SavableStraightBond } from './SavableStraightBond';
+export { SavableStraightBond };
+import { SavedStraightBond } from './SavedStraightBond';
+export { SavedStraightBond };
+import { InvertedStraightBondsHider } from './InvertedStraightBondsHider';
+export { InvertedStraightBondsHider };
+//# sourceMappingURL=index.d.ts.map

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package/dist/index.js

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package/package.json

@@ -0,0 +1,34 @@
+{
+  "name": "@rnacanvas/draw.bases.bonds",
+  "version": "10.0.2",
+  "description": "Draw bonds between bases",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/pzhaojohnson/rnacanvas.draw.bases.bonds.git"
+  },
+  "main": "./dist/index.js",
+  "scripts": {
+    "test": "jest",
+    "build": "webpack"
+  },
+  "author": "pzhaojohnson",
+  "license": "MIT",
+  "devDependencies": {
+    "@babel/core": "^7.23.7",
+    "@babel/preset-env": "^7.23.7",
+    "@babel/preset-typescript": "^7.23.3",
+    "babel-jest": "^29.7.0",
+    "jest": "^29.7.0",
+    "jest-environment-jsdom": "^29.7.0",
+    "ts-loader": "^9.5.1",
+    "typescript": "^5.3.3",
+    "webpack": "^5.89.0",
+    "webpack-cli": "^5.1.4"
+  },
+  "dependencies": {
+    "@rnacanvas/draw.svg": "^3.3.0",
+    "@rnacanvas/points": "^1.12.0",
+    "@rnacanvas/value-check": "^1.6.2",
+    "@svgdotjs/svg.js": "^3.2.0"
+  }
+}

package/tsconfig.json

@@ -0,0 +1,13 @@
+{
+  "compilerOptions": {
+    "strict": true,
+    "outDir": "./dist/",
+    "sourceMap": true,
+    "declaration": true,
+    "declarationDir": "./dist/",
+    "declarationMap": true,
+    "module": "es6",
+    "target": "es6",
+    "moduleResolution": "node"
+  }
+}

package/webpack.config.js

@@ -0,0 +1,28 @@
+const path = require('path');
+
+module.exports = {
+  entry: './src/index.ts',
+  mode: 'production',
+  module: {
+    rules: [
+      {
+        test: /\.tsx?$/,
+        use: 'ts-loader',
+        exclude: /node_modules/,
+      },
+    ],
+  },
+  resolve: {
+    extensions: ['.tsx', '.ts', '.js'],
+  },
+  output: {
+    path: path.resolve(__dirname, 'dist'),
+    filename: 'index.js',
+    globalObject: 'this',
+    library: {
+      name: 'draw.bases.bonds',
+      type: 'umd',
+    },
+    clean: true,
+  },
+};