@intact-ebi/cytoscape-lumina 0.1.0

package/LICENSE

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+ISC License
+
+Copyright (c) 2026 EMBL-EBI
+
+Permission to use, copy, modify, and/or distribute this software for any
+purpose with or without fee is hereby granted, provided that the above
+copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
+AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
+LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
+OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THIS SOFTWARE.

package/README.md

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+# LUMINA: 
+
+## Usage
+
+### Installation
+
+```zsh
+npm install @intact-portal/sub-structure-cyto-layout cytoscape
+```
+
+### Minimal import
+
+```js
+import cytoscape from 'cytoscape';
+import registerSubstructureLayout from '@intact-portal/sub-structure-cyto-layout';
+
+registerSubstructureLayout(cytoscape);
+
+const cy = cytoscape({
+container: document.getElementById('cy'),
+elements
+});
+
+cy.layout({
+name: 'substructure-layout'
+}).run();
+```
+
+### Demo project
+
+```js
+<!doctype html>
+<html lang="en">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>Cytoscape LUMINA demo</title>
+  <style>
+    html,
+    body {
+      height: 100%;
+      margin: 0;
+      font-family: system-ui, sans-serif;
+    }
+
+    body {
+      display: grid;
+      grid-template-rows: auto 1fr;
+    }
+  </style>
+
+  <script type="importmap">
+    {
+      "imports": {
+        "cytoscape": "./node_modules/cytoscape/dist/cytoscape.esm.min.mjs",
+        "@intact-ebi/cytoscape-lumina": "./node_modules/@intact-ebi/cytoscape-lumina/dist/index.js"
+      }
+    }
+  </script>
+</head>
+<body>
+  <header>
+    <h1>LUMINA layout demo</h1>
+  </header>
+  <main id="cy" aria-label="Interactive network graph"></main>
+
+  <script type="module">
+    import cytoscape from 'cytoscape';
+    import registerSubstructureLayout from '@intact-ebi/cytoscape-lumina';
+
+    registerSubstructureLayout(cytoscape);
+
+    const elements = [
+      { data: { id: 'a' } },
+      { data: { id: 'b' } },
+      { data: { id: 'c' } },
+      { data: { id: 'd' } },
+      { data: { id: 'hub' } },
+      { data: { id: 'leaf-1' } },
+      { data: { id: 'leaf-2' } },
+      { data: { id: 'leaf-3' } },
+      { data: { id: 'chain-1' } },
+      { data: { id: 'chain-2' } },
+      { data: { id: 'ab', source: 'a', target: 'b' } },
+      { data: { id: 'bc', source: 'b', target: 'c' } },
+      { data: { id: 'cd', source: 'c', target: 'd' } },
+      { data: { id: 'da', source: 'd', target: 'a' } },
+      { data: { id: 'c-hub', source: 'c', target: 'hub' } },
+      { data: { id: 'hub-leaf-1', source: 'hub', target: 'leaf-1' } },
+      { data: { id: 'hub-leaf-2', source: 'hub', target: 'leaf-2' } },
+      { data: { id: 'hub-leaf-3', source: 'hub', target: 'leaf-3' } },
+      { data: { id: 'd-chain-1', source: 'd', target: 'chain-1' } },
+      { data: { id: 'chain-1-chain-2', source: 'chain-1', target: 'chain-2' } }
+    ];
+
+    const cy = cytoscape({
+      container: document.getElementById('cy'),
+      elements,
+      style: [
+        {
+          selector: 'node',
+          style: {
+            'label': 'data(id)',
+          }
+        },
+      ]
+    });
+
+    cy.layout({
+      name: 'substructure-layout',
+    }).run();
+  </script>
+</body>
+</html>
+```
+
+## Configuration
+
+TODO
+
+## Development
+
+TODO

package/dist/index.d.ts

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+import cytoscape from 'cytoscape';
+export type LayoutAlgorithm = 'force' | 'stress';
+export interface LayoutParameters {
+    LAYOUT_ALGORITHM: LayoutAlgorithm;
+    IDEAL_LENGTH: number;
+    REPULSION: number;
+    SPRING_K: number;
+    ITERATIONS: number;
+    ANGULAR_STRENGTH: number;
+    CENTER_GRAVITY: number;
+    USE_ANGULAR_FORCE: boolean;
+    RANDOMIZE_INITIAL_POSITIONS: boolean;
+    MIN_STAR_LEAVES: number;
+    MIN_CYCLE_LENGTH: number;
+    MAX_CYCLE_LENGTH: number;
+    MIN_CHAIN_LENGTH: number;
+    MIN_PARALLEL_NEIGHBORS: number;
+    CYCLE_NODE_SPACING: number;
+    STAR_RING_SPACING: number;
+    STAR_BASE_NODES_PER_RING: number;
+    CHAIN_MIN_RADIUS: number;
+    PARALLEL_GAP: number;
+    LEAF_NODE_DISTANCE: number;
+    VNODE_RADIUS_MULTIPLIER: number;
+    VNODE_REPULSION: number;
+    VNODE_SPRING_K: number;
+    VNODE_ITERATIONS: number;
+    VNODE_ANGULAR_STRENGTH: number;
+    SPREAD_V_NODES: boolean;
+    SUBSTRUCTURE_LAYOUT: boolean;
+    ENABLE_INITIAL_FORCE_LAYOUT: boolean;
+    STEP_BY_STEP: boolean;
+    SHOW_ALL_EDGES: boolean;
+}
+export declare const DEFAULT_PARAMS: LayoutParameters;
+export interface LayoutStep {
+    stepNumber: number;
+    stepName: string;
+    description: string;
+    nodePositions: {
+        [nodeId: string]: {
+            x: number;
+            y: number;
+        };
+    };
+    virtualNodes?: VNode[];
+    virtualEdges?: VEdge[];
+    metadata?: any;
+}
+export type SubstructureType = 'Normal' | 'Cycle' | 'Chain' | 'Star-Center' | 'Star-Member' | 'Parallel' | 'LeafButNotChain';
+type Node = cytoscape.NodeSingular;
+declare class VNode {
+    id: string;
+    type: any;
+    center_x: number;
+    center_y: number;
+    radius: number;
+    rotate_angle: number;
+    nodes: Node[];
+    neighbors: VNode[];
+    _permanentOrder?: string[];
+    constructor(id: string, x: number, y: number, radius: number);
+    get position(): {
+        x: number;
+        y: number;
+    };
+    setPosition(x: number, y: number): void;
+    addNode(node: Node): void;
+    setPermanentOrder(order: string[]): void;
+    getPermanentOrder(): string[] | undefined;
+    toSnapshot(): {
+        id: string;
+        type: any;
+        center_x: number;
+        center_y: number;
+        radius: number;
+        rotate_angle: number;
+        nodeIds: cytoscape.NodeSingular[];
+    };
+}
+declare class VEdge {
+    source: VNode;
+    target: VNode;
+    weight: number;
+    constructor(source: VNode, target: VNode, weight?: number);
+    toSnapshot(): {
+        source: string;
+        target: string;
+        weight: number;
+    };
+}
+/**
+ * Register this layout as a Cytoscape.js layout extension.
+ *
+ * Usage:
+ *   import cytoscape from 'cytoscape';
+ *   import substructureLayout from './cytoscape-substructure-layout';
+ *
+ *   substructureLayout(cytoscape);
+ *
+ *   cy.layout({
+ *       name: 'substructure-layout',
+ *       layoutAlgorithm: 'force',
+ *       idealLength: 100,
+ *       repulsion: 10000,
+ *       springK: 0.15,
+ *       iterations: 400
+ *   }).run();
+ */
+export default function register(cytoscapeInstance: any): void;
+export { SubstructureLayout };
+/**
+ * Enhanced force-directed layout with structure awareness
+ */
+declare function SubstructureLayout(this: any, options: any): void;