From e6b549ebcfd4a16f461d4b1e484274224ca61b58 Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 3 Sep 2024 15:06:02 +0200 Subject: [PATCH 1/8] readme test --- README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..e69de29 -- GitLab From d14e4fdb9c7ab534d2aebbf9e751d7ed468a3b88 Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 10 Sep 2024 10:13:18 +0200 Subject: [PATCH 2/8] push initial template --- README.md | 3 + jest.config.js | 4 + package-lock.json | 5595 +++++++++++++++++++++++++++++++++++++ package.json | 24 + src/__tests__/add.test.ts | 6 + src/index.ts | 3 + tsconfig.json | 14 + tsup.config.ts | 10 + 8 files changed, 5659 insertions(+) create mode 100644 jest.config.js create mode 100644 package-lock.json create mode 100644 package.json create mode 100644 src/__tests__/add.test.ts create mode 100644 src/index.ts create mode 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"./dist/index.js", + "module": "./dist/index.mjs", + "types": "./dist/index.d.ts", + "files": [ + "dist" + ], + "license": "Apache-2.0" +} diff --git a/src/__tests__/add.test.ts b/src/__tests__/add.test.ts new file mode 100644 index 0000000..6ba006f --- /dev/null +++ b/src/__tests__/add.test.ts @@ -0,0 +1,6 @@ +import { add } from '../'; + +test('adds two numbers correctly', () => { + const result = add(2, 3); + expect(result).toBe(5); +}); \ No newline at end of file diff --git a/src/index.ts b/src/index.ts new file mode 100644 index 0000000..946a4b8 --- /dev/null +++ b/src/index.ts @@ -0,0 +1,3 @@ +export function add(a: number, b: number): number { + return a + b; +} \ No newline at end of file diff --git a/tsconfig.json b/tsconfig.json new file mode 100644 index 0000000..2a5c28a --- /dev/null +++ b/tsconfig.json @@ -0,0 +1,14 @@ +{ + "compilerOptions": { + /* Language and Environment */ + "target": "es2016", + /* Modules */ + "module": "commonjs", + "esModuleInterop": true, + "forceConsistentCasingInFileNames": true, + /* Type Checking */ + "strict": true, + "skipLibCheck": true, + "outDir": "dist" + } +} diff --git a/tsup.config.ts b/tsup.config.ts new file mode 100644 index 0000000..356c46c --- /dev/null +++ b/tsup.config.ts @@ -0,0 +1,10 @@ +import { defineConfig } from "tsup"; + +export default defineConfig({ + entry: ["src/index.ts"], + format: ["cjs", "esm"], // Build for commonJS and ESmodules + dts: true, // Generate declaration file (.d.ts) + splitting: false, + sourcemap: true, + clean: true, +}); \ No newline at end of file -- GitLab From 2ce8004c2bace83b261ddd03ac626fc14121cf60 Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 10 Sep 2024 10:21:31 +0200 Subject: [PATCH 3/8] essai suppr README --- README.md | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 README.md diff --git a/README.md b/README.md deleted file mode 100644 index af7d0f4..0000000 --- a/README.md +++ /dev/null @@ -1,3 +0,0 @@ -in package.json, change name of project -src -> index.ts -> add all exported methods -src/__tests__/ -> add unit test file \ No newline at end of file -- GitLab From bb1aa12f1157d87f2d80e4bca0b84361f062d83f Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 10 Sep 2024 10:27:20 +0200 Subject: [PATCH 4/8] suppr tous --- jest.config.js | 4 - package-lock.json | 5595 ------------------------------------- package.json | 24 - src/__tests__/add.test.ts | 6 - src/index.ts | 3 - tsconfig.json | 14 - tsup.config.ts | 10 - 7 files changed, 5656 deletions(-) delete mode 100644 jest.config.js delete mode 100644 package-lock.json delete mode 100644 package.json delete mode 100644 src/__tests__/add.test.ts delete mode 100644 src/index.ts delete mode 100644 tsconfig.json delete mode 100644 tsup.config.ts diff --git a/jest.config.js b/jest.config.js deleted file mode 100644 index f7475c3..0000000 --- a/jest.config.js +++ /dev/null @@ -1,4 +0,0 @@ -module.exports = { - preset: "ts-jest", - 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"./dist/index.js", - "module": "./dist/index.mjs", - "types": "./dist/index.d.ts", - "files": [ - "dist" - ], - "license": "Apache-2.0" -} diff --git a/src/__tests__/add.test.ts b/src/__tests__/add.test.ts deleted file mode 100644 index 6ba006f..0000000 --- a/src/__tests__/add.test.ts +++ /dev/null @@ -1,6 +0,0 @@ -import { add } from '../'; - -test('adds two numbers correctly', () => { - const result = add(2, 3); - expect(result).toBe(5); -}); \ No newline at end of file diff --git a/src/index.ts b/src/index.ts deleted file mode 100644 index 946a4b8..0000000 --- a/src/index.ts +++ /dev/null @@ -1,3 +0,0 @@ -export function add(a: number, b: number): number { - return a + b; -} \ No newline at end of file diff --git a/tsconfig.json b/tsconfig.json deleted file mode 100644 index 2a5c28a..0000000 --- a/tsconfig.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "compilerOptions": { - /* Language and Environment */ - "target": "es2016", - /* Modules */ - "module": "commonjs", - "esModuleInterop": true, - "forceConsistentCasingInFileNames": true, - /* Type Checking */ - "strict": true, - "skipLibCheck": true, - "outDir": "dist" - } -} diff --git a/tsup.config.ts b/tsup.config.ts deleted file mode 100644 index 356c46c..0000000 --- a/tsup.config.ts +++ /dev/null @@ -1,10 +0,0 @@ -import { defineConfig } from "tsup"; - -export default defineConfig({ - entry: ["src/index.ts"], - format: ["cjs", "esm"], // Build for commonJS and ESmodules - dts: true, // Generate declaration file (.d.ts) - splitting: false, - sourcemap: true, - clean: true, -}); \ No newline at end of file -- GitLab From 10ba4ec5db6c5eee832612202af1adacd16c0636 Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 10 Sep 2024 10:28:31 +0200 Subject: [PATCH 5/8] push template --- README.md | 3 + jest.config.js | 4 + package-lock.json | 5595 +++++++++++++++++++++++++++++++++++++ package.json | 24 + src/__tests__/add.test.ts | 6 + src/index.ts | 3 + tsconfig.json | 14 + tsup.config.ts | 10 + 8 files changed, 5659 insertions(+) create mode 100644 README.md create mode 100644 jest.config.js create mode 100644 package-lock.json create mode 100644 package.json create mode 100644 src/__tests__/add.test.ts create mode 100644 src/index.ts create mode 100644 tsconfig.json create mode 100644 tsup.config.ts diff --git a/README.md b/README.md new file mode 100644 index 0000000..af7d0f4 --- /dev/null +++ b/README.md @@ -0,0 +1,3 @@ +in package.json, change name of project +src -> index.ts -> add all exported methods +src/__tests__/ -> add unit test file \ No newline at end of file diff --git a/jest.config.js b/jest.config.js new file mode 100644 index 0000000..f7475c3 --- /dev/null +++ b/jest.config.js @@ -0,0 +1,4 @@ +module.exports = { + preset: "ts-jest", + testEnvironment: "node", +}; \ No newline at end of file diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 0000000..e24983c --- /dev/null +++ b/package-lock.json @@ -0,0 +1,5595 @@ +{ + "name": 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"./dist/index.js", + "module": "./dist/index.mjs", + "types": "./dist/index.d.ts", + "files": [ + "dist" + ], + "license": "Apache-2.0" +} diff --git a/src/__tests__/add.test.ts b/src/__tests__/add.test.ts new file mode 100644 index 0000000..6ba006f --- /dev/null +++ b/src/__tests__/add.test.ts @@ -0,0 +1,6 @@ +import { add } from '../'; + +test('adds two numbers correctly', () => { + const result = add(2, 3); + expect(result).toBe(5); +}); \ No newline at end of file diff --git a/src/index.ts b/src/index.ts new file mode 100644 index 0000000..946a4b8 --- /dev/null +++ b/src/index.ts @@ -0,0 +1,3 @@ +export function add(a: number, b: number): number { + return a + b; +} \ No newline at end of file diff --git a/tsconfig.json b/tsconfig.json new file mode 100644 index 0000000..2a5c28a --- /dev/null +++ b/tsconfig.json @@ -0,0 +1,14 @@ +{ + "compilerOptions": { + /* Language and Environment */ + "target": "es2016", + /* Modules */ + "module": "commonjs", + "esModuleInterop": true, + "forceConsistentCasingInFileNames": true, + /* Type Checking */ + "strict": true, + "skipLibCheck": true, + "outDir": "dist" + } +} diff --git a/tsup.config.ts b/tsup.config.ts new file mode 100644 index 0000000..356c46c --- /dev/null +++ b/tsup.config.ts @@ -0,0 +1,10 @@ +import { defineConfig } from "tsup"; + +export default defineConfig({ + entry: ["src/index.ts"], + format: ["cjs", "esm"], // Build for commonJS and ESmodules + dts: true, // Generate declaration file (.d.ts) + splitting: false, + sourcemap: true, + clean: true, +}); \ No newline at end of file -- GitLab From 8b31a14a81c20d304ed12c4c7cb900d4682c8600 Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 10 Sep 2024 11:54:48 +0200 Subject: [PATCH 6/8] all scripts and file necessary from previous repo --- .gitignore | 2 + .npmrc | 1 + env.d.ts | 4 + package-lock.json | 6942 +++++++++++------ package.json | 22 +- src/composables/AlgorithmBFS.ts | 94 + src/composables/AlgorithmDFS.ts | 128 + src/composables/CalculateRelationCycle.ts | 477 ++ src/composables/CalculateSize.ts | 427 + src/composables/CalculateStartNodes.ts | 195 + src/composables/ConvertFromNetwork.ts | 482 ++ src/composables/ConvertToNetwork.ts | 154 + src/composables/GetSetAttributsNodes.ts | 260 + src/composables/LayoutDrawCycle.ts | 1377 ++++ src/composables/LayoutFindCycle.ts | 267 + src/composables/LayoutMain.ts | 232 + src/composables/LayoutMainChain.ts | 391 + src/composables/LayoutManageSideCompounds.ts | 839 ++ src/composables/LayoutReversibleReactions.ts | 458 ++ src/composables/LayoutSugiyamaForce.ts | 225 + src/composables/MetricsApplication.ts | 329 + src/composables/MetricsCalculation.ts | 448 ++ src/composables/SBMLtoJSON.ts | 160 + src/composables/UseSubgraphNetwork.ts | 160 + .../__tests__/2_reac_1_metab_4514.xml | 68 + src/composables/__tests__/SBMLtoJSON.spec.ts | 122 + .../__tests__/countIntersection.spec.ts | 33 + .../__tests__/countIsolatedNodes.spec.ts | 76 + src/composables/countIntersections.ts | 429 + src/composables/countIsolatedNodes.ts | 36 + src/composables/importNetwork.ts | 93 + src/composables/useSubgraphs.ts | 207 + src/index.ts | 6 +- src/types/CoordinatesSize.ts | 11 + src/types/DFS.ts | 6 + src/types/EnumArgs.ts | 35 + src/types/FormatJSONGraphXML.ts | 58 + src/types/FormatJsonStyle.ts | 8 + src/types/FormatJsonViz.ts | 17 + src/types/NetworkLayout.ts | 37 + src/types/Parameters.ts | 72 + src/types/Reaction.ts | 34 + src/types/Subgraph.ts | 42 + src/types/SubgraphNetwork.ts | 37 + src/types/VizType.ts | 37 + 45 files changed, 13271 insertions(+), 2267 deletions(-) create mode 100644 .gitignore create mode 100644 .npmrc create mode 100644 env.d.ts create mode 100644 src/composables/AlgorithmBFS.ts create mode 100644 src/composables/AlgorithmDFS.ts create mode 100644 src/composables/CalculateRelationCycle.ts create mode 100644 src/composables/CalculateSize.ts create mode 100644 src/composables/CalculateStartNodes.ts create mode 100644 src/composables/ConvertFromNetwork.ts create mode 100644 src/composables/ConvertToNetwork.ts create mode 100644 src/composables/GetSetAttributsNodes.ts create mode 100644 src/composables/LayoutDrawCycle.ts create mode 100644 src/composables/LayoutFindCycle.ts create mode 100644 src/composables/LayoutMain.ts create mode 100644 src/composables/LayoutMainChain.ts create mode 100644 src/composables/LayoutManageSideCompounds.ts create mode 100644 src/composables/LayoutReversibleReactions.ts create mode 100644 src/composables/LayoutSugiyamaForce.ts create mode 100644 src/composables/MetricsApplication.ts create mode 100644 src/composables/MetricsCalculation.ts create mode 100644 src/composables/SBMLtoJSON.ts create mode 100644 src/composables/UseSubgraphNetwork.ts create mode 100644 src/composables/__tests__/2_reac_1_metab_4514.xml create mode 100644 src/composables/__tests__/SBMLtoJSON.spec.ts create mode 100644 src/composables/__tests__/countIntersection.spec.ts create mode 100644 src/composables/__tests__/countIsolatedNodes.spec.ts create mode 100644 src/composables/countIntersections.ts create mode 100644 src/composables/countIsolatedNodes.ts create mode 100644 src/composables/importNetwork.ts create mode 100644 src/composables/useSubgraphs.ts create mode 100644 src/types/CoordinatesSize.ts create mode 100644 src/types/DFS.ts create mode 100644 src/types/EnumArgs.ts create mode 100644 src/types/FormatJSONGraphXML.ts create mode 100644 src/types/FormatJsonStyle.ts create mode 100644 src/types/FormatJsonViz.ts create mode 100644 src/types/NetworkLayout.ts create mode 100644 src/types/Parameters.ts create mode 100644 src/types/Reaction.ts create mode 100644 src/types/Subgraph.ts create mode 100644 src/types/SubgraphNetwork.ts create mode 100644 src/types/VizType.ts diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..763301f --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +dist/ +node_modules/ \ No newline at end of file diff --git a/.npmrc b/.npmrc new file mode 100644 index 0000000..7cdc81c --- /dev/null +++ b/.npmrc @@ -0,0 +1 @@ +@metabohub:registry=https://forgemia.inra.fr/api/v4/packages/npm/ diff --git a/env.d.ts b/env.d.ts new file mode 100644 index 0000000..c4d9129 --- /dev/null +++ b/env.d.ts @@ -0,0 +1,4 @@ +declare module '@metabohub/viz-core'; +declare module 'dagrejs'; +declare module '@metabohub/viz-context-menu'; +declare module 'line-intersect'; \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index e24983c..f55e045 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,13 +8,33 @@ "name": "@metabohub/ts-package-name", "version": "0.0.0", "license": "Apache-2.0", + "dependencies": { + "@mdi/font": "^7.4.47", + "@metabohub/viz-context-menu": "^0.0.2", + "@metabohub/viz-core": "^0.6.1", + "cytoscape": "^3.30.2", + "line-intersect": "^3.0.0", + "xml2js": "^0.6.2" + }, "devDependencies": { "@types/jest": "^29.5.12", + "@types/jsdom": "^21.1.6", + "@types/node": "^20.11.14", 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"^29.7.0", + "jsdom": "^24.0.0", + "prettier": "^3.2.4", "ts-jest": "^29.1.2", "ts-node": "^10.9.2", "tsup": "^8.0.2", - "typescript": "^5.4.5" + "typescript": "^5.4.5", + "xml-js": "^1.6.11" }, "main": "./dist/index.js", "module": "./dist/index.mjs", diff --git a/src/composables/AlgorithmBFS.ts b/src/composables/AlgorithmBFS.ts new file mode 100644 index 0000000..fad45dc --- /dev/null +++ b/src/composables/AlgorithmBFS.ts @@ -0,0 +1,94 @@ +// Types imports +import { StartNodesType } from "../types/EnumArgs"; +import { Network } from "@metabohub/viz-core/src/types/Network"; + +// Composable imports +import { getStartNodes } from "./CalculateStartNodes"; +import { networkToAdjacentObject } from "./ConvertFromNetwork"; + + +/** + * This file contains the functions to perform Breadth-First Search (BFS) on a graph. + * + * -> BFS : + * Perform Breadth-First Search (BFS) on a graph represented by an adjacency object. + * + * -> BFSWithSources : + * Perform Breadth-First Search (BFS) on a network with multiple sources. + */ + + +/** + * Perform Breadth-First Search (BFS) on a graph represented by an adjacency object. + * @param adjacency The adjacency object representing the graph. + * @param source The starting node for BFS. + * @param blockedNodes List of nodes that can't be visited (blocked) + * @returns An array of nodes visited in BFS order. + */ +export function BFS(adjacency: { [key: string]: string[] }, source: string, blockedNodes?:string[]): string[] { + const visitedNodes: Set<string> = new Set(); + const nodesToProcess: string[] = [source]; + + while (nodesToProcess.length) { + const currentNode = nodesToProcess.shift()!; + + if (currentNode && !visitedNodes.has(currentNode)) { + visitedNodes.add(currentNode); + const children = adjacency[currentNode] || []; + children.forEach(child => { + if (!visitedNodes.has(child)) { + if ( (blockedNodes && !blockedNodes.includes(child)) || !blockedNodes ){ + nodesToProcess.push(child); + } + } + }); + } + } + + return Array.from(visitedNodes); +} + + +/** + * Perform Breadth-First Search (BFS) on a network with multiple sources. + * @param network The network to perform BFS on. + * @param sources An array of source nodes or a source type. + * Source type : + * RANK_ONLY : sources are nodes of rank 0 + * SOURCE_ONLY : sources are topological sources of the network (nul indegree) + * RANK_SOURCE : sources are node of rank 0, then source nodes + * ALL : sources are all nodes + * SOURCE_ALL : sources are topological sources, then all the others nodes + * RANK_SOURCE_ALL : sources are node of rank 0, then topological sources, then all the other nodes + * @returns An array of nodes visited in BFS order, a node can appear several time if it is a descendant of several sources. + */ +export async function BFSWithSources(network:Network, sources:Array<string>|StartNodesType):Promise<Array<string>>{ + + try{ + let bfsAllSources:string[] =[]; + + // create graph for library from network + const adj=networkToAdjacentObject(network); + + //get sources nodes if no list from user + let sources_list: Array<string>; + if (Array.isArray(sources)) { + sources_list = sources; + } else { + sources_list = await getStartNodes(network, sources); + } + + // apply BFS + sources_list.forEach(source=>{ + // bfs on source only if source not already visited + if( !bfsAllSources.includes(source)){ + const bfs=BFS(adj,source,bfsAllSources); + bfsAllSources = bfsAllSources.concat(bfs); + } + }) + + return bfsAllSources + }catch(error){ + throw error; + } +} diff --git a/src/composables/AlgorithmDFS.ts b/src/composables/AlgorithmDFS.ts new file mode 100644 index 0000000..95b00e0 --- /dev/null +++ b/src/composables/AlgorithmDFS.ts @@ -0,0 +1,128 @@ +import { Network } from '@metabohub/viz-core/src/types/Network'; +import { Node } from '@metabohub/viz-core/src/types/Node'; +import { networkToGDSGraph, networkToSerialized } from './ConvertFromNetwork'; +import { Serialized} from 'graph-data-structure'; +import Graph from "graph-data-structure"; +import { StartNodesType } from '../types/EnumArgs'; +import { getStartNodes } from './CalculateStartNodes'; + +/** + * Take a network and sources, return the dfs result (that is an array of string of node ID) + * @param network + * @param sources to use for dfs : array of node ID or a type of method to get sources automatically + * RANK_ONLY : sources are nodes of rank 0 + * SOURCE_ONLY : sources are topological sources of the network (nul indegree) + * RANK_SOURCE : sources are node of rank 0, then source nodes + * ALL : sources are all nodes + * SOURCE_ALL : sources are topological sources, then all the others nodes + * RANK_SOURCE_ALL : sources are node of rank 0, then topological sources, then all the other nodes + * + * @returns dfs result + */ +export function DFSWithSources(network:Network, sources:Array<string>|StartNodesType):Array<string>{ + + console.log('DFS'); + + // create graph for library from network + const graph=networkToGDSGraph(network); + + //get sources nodes if no list from user + let sources_list: Array<string>; + if (Array.isArray(sources)) { + sources_list = sources; + } else { + sources_list = getStartNodes(network, sources); + } + + // apply DFS (reverse order because DFS is a backward reading) + const dfs= graph.depthFirstSearch(sources_list); + return dfs.reverse(); + +} + + + +/** + * Do a DFS from a source and remove the last edge of cycle to get a "source DAG". + * @param network + * @param sources to use as staring node for DFS + * @returns the reverse dfs order (topological sort) and a graph object without the cycles accessible from the sources + */ +export function DFSsourceDAG(network:Network, sources:Array<string>):{dfs:Array<string>, graph:{[key:string]:Function} } { + let DFS=createGraphForDFS(network); + + sources.forEach(sourceID =>{ + const sourceIndex=DFS.nodesID.indexOf(sourceID); + // if the source exist in the network and it's not already visited : dfs from this source + if (sourceIndex!==-1 && !DFS.visited[sourceIndex]){ + DFS=nodeDagDFS(DFS,sourceIndex,[]); + } + }); + + return { dfs:DFS.dfsOrder.reverse(),graph:DFS.GDSgraph }; +} + +/** + * Initialize a dfs object from the network + * @param network + * @returns initialized DFS object + */ +function createGraphForDFS(network:Network):DFS{ + const nbNode=Object.keys(network.nodes).length; + const graphGDS=networkToGDSGraph(network); + return { + dfsOrder: [], + GDSgraph: graphGDS, + nodesID:graphGDS.nodes(), + visited:Array.from({ length: nbNode }, () => false), + } +} + +/** + * DFS from a node + * @param DFS dfs object with visited nodes, adjacent information ... + * @param nodeIndex of the node ro process + * @param currentPath the dfs path from the source to this node + * @returns the DFS object with visited nodes, adjacent information ... + */ +function nodeDagDFS(DFS:DFS,nodeIndex:number,currentPath:number[]):DFS{ + + // mark the node as visited + DFS.visited[nodeIndex] = true; + + // add node to current path (copy of path, else pointer) + const path=Array.from(currentPath); + path.push(nodeIndex) + + // loop through the children of the node + DFS.GDSgraph.adjacent(DFS.nodesID[nodeIndex]).sort().forEach(childID => { + + // get the index of the child + const childIndex = DFS.nodesID.indexOf(childID); + if(childIndex!==-1){ + + // if the child node had never been visited : the edge is an tree edge + if (!DFS.visited[childIndex]){ + + // dfs through the child node + DFS=nodeDagDFS(DFS,childIndex,path); + + } else { // if the child node had already been visited + // and that the node is in the current path : there is a cycle + if(path.includes(childIndex)){ + const parentID=DFS.nodesID[nodeIndex]; + DFS.GDSgraph.removeEdge(parentID,childID) + } + + } + } + }); + + // add the node to the dfs order + DFS.dfsOrder.push(DFS.nodesID[nodeIndex]); + + return DFS; +} + + + diff --git a/src/composables/CalculateRelationCycle.ts b/src/composables/CalculateRelationCycle.ts new file mode 100644 index 0000000..2266b2b --- /dev/null +++ b/src/composables/CalculateRelationCycle.ts @@ -0,0 +1,477 @@ +// Type imports +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Link } from "@metabohub/viz-core/src/types/Link"; +import { Ordering } from "../types/EnumArgs"; +import { TypeSubgraph } from "../types/Subgraph"; +import { LinkLayout, NetworkLayout } from "../types/NetworkLayout"; + + +// Composable imports +import { inCycle } from "./GetSetAttributsNodes"; + + +/** + * This file contains functions to calculate the order of links for the cycle metanodes. + * + * ********************************* + * 0. Get nodes + * + * -> neighborsGroupCycle + * retrieves the neighboring nodes of a given cycle group, either the parent or child nodes + * + * -> parentNodeNotInCycle + * returns an array of parent nodes, of a list of nodes, that are not part of any cycle in the subgraph network + * + * -> childNodeNotInCycle + * returns an array of child nodes, of a list of nodes, that are not part of any cycle in the subgraph network + * + * -> getNodesIDPlacedInGroupCycle + * retrieves the IDs of nodes placed (with x and y define) in a specific group cycle + * + * -> getNodesPlacedInGroupCycle + * retrieves the nodes (id, x, y) placed in a specific group cycle. If position is fixed it's (id, fx, fy). If there is no posisiton, it's only the id + * + * -> getNodesPlacedInGroupCycleAsObject + * retrieves the nodes (id, x, y) placed in a specific group cycle. If position is fixed it's (id, fx, fy). If there is no posisiton, it's only the id + * + * + * ********************************* + * 1. Get (ordered) links + * + * -> cycleMetanodeLink + * return a link that can take into the count the cycle metanodes. If the end of the link is inside a metanode (group cycle), the end of the link is the group cycle instead of the id of the node + * + * -> sortLinksWithAllGroupCycle + * sorts the links to limit crossing with cycle metanodes (for all group cycles). + * + * -> sortLinksWithGroupCycle + * sorts the links based on the given group cycle + * + * -> getLinksNodeGroupCycle + * finds the links that are associated with the given node and group cycle + * + * -> getLinksForListNodes + * retrieves the links between nodes based on a list of node IDs + * + + * + * ********************************* + * 2. Get graph + * + * -> getListNodeLinksForCycleGroup + * retrieves the list of node and links for a specific cycle group. Position of nodes can be fixed + * + * -> getListNodeLinksForCycleGroupAsObject + * retrieves an object for node and a list for links for a specific cycle group + * + * ********************************* + * 3. Get relation cycle + * + * -> parentCycle + * return the name of the parent cycle of the cycle, if not, return the name of the cycle + * + */ + + + +/*******************************************************************************************************************************************************/ +//___________________________________________________0. Get nodes __________________________________________________________________________ + + + +/** + * Retrieves the neighboring nodes of a given cycle group, either the parent or child nodes. + * + * @param subgraphNetwork - The subgraph network containing the cycle group. + * @param cycleGroupId - The ID of the cycle group. + * @param parentOrChild - Specifies whether to retrieve the parent cycles or the child of the cycle group. Can be either "parent" or "child". + * @param xSort - Optional. Specifies whether to sort the nodes of the group cycle by their x position. Defaults to true. + * The neighboring nodes are added in the order of the x position of the nodes inside the group cycle. + * @returns An array of cycle IDs representing the neighboring cycles. + */ +export function neighborsGroupCycle(subgraphNetwork:SubgraphNetwork,cycleGroupId:string, parentOrChild:"parent"|"child",xSort:boolean=true):string[]{ + if (cycleGroupId in subgraphNetwork[TypeSubgraph.CYCLEGROUP] && subgraphNetwork[TypeSubgraph.CYCLEGROUP][cycleGroupId].precalculatedNodesPosition){ + // get the id of nodes in group cycle + const nodes=getNodesIDPlacedInGroupCycle(subgraphNetwork,cycleGroupId); + // sort nodes of the group cycle by x + if (xSort){ + nodes.sort((nodeIdA, nodeIdB) => { + const nodeA = subgraphNetwork[TypeSubgraph.CYCLEGROUP][cycleGroupId].precalculatedNodesPosition[nodeIdA]; + const nodeB = subgraphNetwork[TypeSubgraph.CYCLEGROUP][cycleGroupId].precalculatedNodesPosition[nodeIdB]; + return nodeA.x - nodeB.x; + }); + } + if (parentOrChild==="parent"){ + // get parent nodes + const parentCycles = Array.from(new Set(parentNodeNotInCycle(subgraphNetwork, nodes).flat())); + return parentCycles; + } else { + // get child nodes + const childCycles = Array.from(new Set(childNodeNotInCycle(subgraphNetwork, nodes).flat())); + return childCycles; + } + }else{ + return []; + } +} + + +/** + * Returns an array of parent nodes, of a list of nodes, that are not part of any cycle in the subgraph network. + * + * @param subgraphNetwork - The subgraph network object. + * @param listNodes - The list of nodes to check for parent nodes. + * @returns An array of arrays containing the parent nodes that are not part of any cycle. + */ +export function parentNodeNotInCycle(subgraphNetwork: SubgraphNetwork, listNodes: string[]): string[][] { + const parentNodes = listNodes.map((node: string) => { + const parentNodesI = subgraphNetwork.network.value.links + .filter(link => link.target.id === node) // get link with those node as child + .map(link => link.source.id) // get the other node + .filter(id => !inCycle(subgraphNetwork.network.value, id)) // no node in a cycle + return parentNodesI; + }); + return parentNodes; +} + + +/** + * Returns an array of child nodes, of a list of nodes, that are not part of any cycle in the subgraph network. + * + * @param subgraphNetwork - The subgraph network object. + * @param listNodes - The list of nodes to check for child nodes. + * @returns An array of arrays containing the child nodes that are not part of any cycle. + */ +export function childNodeNotInCycle(subgraphNetwork: SubgraphNetwork, listNodes: string[]): string[][] { + const childNodes = listNodes.map((node: string) => { + const childNodesI = subgraphNetwork.network.value.links + .filter(link => link.source.id === node) // get link with those node as parent + .map(link => link.target.id) // get the other node + .filter(id => !inCycle(subgraphNetwork.network.value, id)) // no node in a cycle + return childNodesI; + }); + + return childNodes; +} + + + + +/** + * Retrieves the IDs of nodes placed (with x and y define) in a specific group cycle. + * + * @param subgraphNetwork - The subgraph network containing the group cycles. + * @param groupCycleID - The ID of the group cycle to retrieve the nodes from. + * @returns An array of strings representing the IDs of the nodes placed in the group cycle. + */ +export function getNodesIDPlacedInGroupCycle(subgraphNetwork:SubgraphNetwork,groupCycleID:string):string[]{ + if (groupCycleID in subgraphNetwork[TypeSubgraph.CYCLEGROUP] && subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycleID].precalculatedNodesPosition){ + return Object.entries(subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycleID].precalculatedNodesPosition) + .filter(([_,item]) => item.x !== undefined && item.y !== undefined) + .map(([key,_])=>key); + }else{ + return []; + } +} + +/** + * Retrieves the nodes (id, x, y) placed in a specific group cycle. If position is fixed it's (id, fx, fy). + * If there is no posisiton, it's only the id + * + * @param subgraphNetwork - The subgraph network object. + * @param groupCycleID - The ID of the group cycle. + * @param positionAsFixed - Optional. Specifies whether to return the node positions as fixed coordinates. Defaults to false. + * @returns An array of objects representing the nodes placed in the group cycle. Each object contains the node ID and optionally the x and y coordinates if positionAsFixed is true. + * If the group cycle ID is not found or the precalculated node positions are not available, null is returned. + */ +export function getNodesPlacedInGroupCycle(subgraphNetwork:SubgraphNetwork,groupCycleID:string,positionAsFixed:boolean=false):{ id: string,x?:number, y?:number, fx?:number, fy?:number }[]{ + if (groupCycleID in subgraphNetwork[TypeSubgraph.CYCLEGROUP] && subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycleID].precalculatedNodesPosition){ + return Object.entries(subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycleID].precalculatedNodesPosition) + .filter(([_, item]) => { return item.x !== undefined && item.y !== undefined }) + .map(([key, item]) => { + if (item.x!==null || item.y!==null){ + if (positionAsFixed) return { id: key,fx:item.x, fy:item.y } + else return { id: key,x:item.x, y:item.y } + + }else{ + return { id: key } + } + }); + }else{ + return null; + } +} + +/** + * Retrieves the nodes (id, x, y) placed in a specific group cycle. If position is fixed it's (id, fx, fy). + * If there is no posisiton, it's only the id + * + * @param subgraphNetwork - The subgraph network object. + * @param groupCycleID - The ID of the group cycle. + * @param positionAsFixed - Optional. Specifies whether to return the node positions as fixed coordinates. Defaults to false. + * @returns An object representing the nodes placed in the group cycle. Each value contains the x and y coordinates. + * If the group cycle ID is not found or the precalculated node positions are not available, null is returned. + */ +export function getNodesPlacedInGroupCycleAsObject(subgraphNetwork:SubgraphNetwork,groupCycleID:string):{ [key:string]:{x:number,y:number }}{ + if (groupCycleID in subgraphNetwork[TypeSubgraph.CYCLEGROUP] && subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycleID].precalculatedNodesPosition){ + return Object.entries(subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycleID].precalculatedNodesPosition) + .filter(([_, item]) => { return item.x !== undefined && item.y !== undefined }) + .reduce((acc, node) => { + if (node[1].x!==null || node[1].y!==null){ + acc[node[0]]={ x:node[1].x, y:node[1].y } + } + return acc; + },{}); + }else{ + return null; + } +} + + + +/*******************************************************************************************************************************************************/ +//___________________________________________________1. Get (ordered) links__________________________________________________________________________ + + + +/** + * Return a link that can take into the count the cycle metanodes. + * If the end of the link is inside a metanode (group cycle), the end of the link is the group cycle instead of the id of the node. + * + * @param link - The link layout to calculate the relation cycle for. + * @param cycle - Optional. Specifies whether to consider cycleMetanodes in the calculation. Default is true. + * @returns An object containing the inCycle array, tail string, and head string. + * @throws {Error} If tail or head is undefined. + */ +export function cycleMetanodeLink(link:LinkLayout, cycle:boolean=true):{inCycle:string[],tail:string,head:string}{ + + let inCycle:string[]=[]; + let tail:string; + let head:string; + + // source in cycleMetanode ? + if(cycle && link.source.metadataLayout && Object.keys(link.source.metadataLayout).includes(TypeSubgraph.CYCLEGROUP) && link.source.metadataLayout[TypeSubgraph.CYCLEGROUP]){ + tail=link.source.metadataLayout[TypeSubgraph.CYCLEGROUP]; + inCycle.push(tail); + }else{ + tail=link.source.id; + } + + // target in cycleMetanode ? + if(cycle && link.target.metadataLayout && Object.keys(link.target.metadataLayout).includes(TypeSubgraph.CYCLEGROUP) && link.target.metadataLayout[TypeSubgraph.CYCLEGROUP]){ + head=link.target.metadataLayout[TypeSubgraph.CYCLEGROUP]; + inCycle.push(head); + }else{ + head=link.target.id; + } + + if (!tail) throw new Error("tail is undefined"); + if (!head) throw new Error("head is undefined"); + + const newLink={inCycle:inCycle,tail:tail,head:head}; + return newLink; +} + + +/** + * Sorts the links to limit crossing with cycle metanodes (for all group cycles). + * Links that are associated with the left node of the group cycle are placed first, followed by the links associated with the right node of the group cycle. + * Then, all other links are added in the order of the input array. + * + * @param subgraphNetwork - The subgraph network. + * @param orderChange - A boolean indicating whether to change the order with group cycle. Default is false. + * @returns The subgraphNetwork and an array of sorted links. + */ +export function sortLinksWithAllGroupCycle(subgraphNetwork:SubgraphNetwork,orderChange:boolean=false):{subgraphNetwork:SubgraphNetwork,linksOrdered:LinkLayout[]}{ + let links:Link[]=[]; + + // change ordre with group cycle + if (orderChange && subgraphNetwork[TypeSubgraph.CYCLEGROUP]){ + + // adding edge in right order for each group cycle + Object.keys(subgraphNetwork[TypeSubgraph.CYCLEGROUP]).forEach((groupCycle) => { + const resultSorting=sortLinksWithGroupCycle(subgraphNetwork,groupCycle); + subgraphNetwork=resultSorting.subgraphNetwork; + links=links.concat(resultSorting.linksOrdered); + }); + // add other links + Object.values(subgraphNetwork.network.value.links).forEach((link) => { + if (!links.includes(link)){ + links.push(link); + } + }); + return { subgraphNetwork:subgraphNetwork,linksOrdered:links }; + + }else{ // no change + return { subgraphNetwork:subgraphNetwork,linksOrdered:subgraphNetwork.network.value.links }; + } +} + +/** + * Sorts the links based on the given group cycle. + * Links that are associated with the left node of the group cycle are placed first, followed by the links associated with the right node of the group cycle. + * Choose if ordering apply for parent or children of cycle (the one with the most links) + * + * @param subgraphNetwork - The subgraph network containing the cycles group. + * @param groupCycle - The group cycle id to sort the links. + * @returns The subgraphNetwork and an array of sorted links. + */ +function sortLinksWithGroupCycle(subgraphNetwork:SubgraphNetwork,groupCycle:string):{subgraphNetwork:SubgraphNetwork,linksOrdered:LinkLayout[]}{ + let links:LinkLayout[]=[]; + if( groupCycle in subgraphNetwork.cyclesGroup){ + // sort parent of cycle by x of the child in the cycle + // (first : parent of the left node of group cycle) + const parents=neighborsGroupCycle(subgraphNetwork,groupCycle,"parent",true); + const children=neighborsGroupCycle(subgraphNetwork,groupCycle,"child",true); + + let nodeOrder:string[]=[]; + let source:"node"|"groupCycle"; + + // if more parent than children : order parent + if (parents.length>=children.length){ + nodeOrder=parents; + source="node"; + subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycle].ordering=Ordering.IN; + }else{ + // order children + nodeOrder=children; + source="groupCycle"; + subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycle].ordering=Ordering.OUT; + } + + // get links between the parent (or children) and the group cycle in the right order + nodeOrder.forEach((nodeId) => { + // get links for each node + const newLinksOrder = getLinksNodeGroupCycle(subgraphNetwork,nodeId,groupCycle,source); + // add links + newLinksOrder.forEach((newLink) => { + links.push(newLink); + }); + + }); + return { subgraphNetwork:subgraphNetwork,linksOrdered:links }; + }else{ + return { subgraphNetwork:subgraphNetwork,linksOrdered:[] }; + } +} + +/** + * Finds the links that are associated with the given node and group cycle. + * For parent nodes, the source is the node (and the target is the group cycle). + * For child nodes, the source is the group cycle (and the target is the node). + * + * @param subgraphNetwork + * @param nodeId node id + * @param groupCycleId id of cycle group + * @param source "node" if the parent links are needed, "groupCycle" if the child links are needed + * @returns links that are child or parent of a group cycle + */ +function getLinksNodeGroupCycle(subgraphNetwork:SubgraphNetwork,nodeId:string,groupCycleId:string,source:"node"|"groupCycle"):LinkLayout[]{ + if (source==="node"){ + // node to group cycle + return Object.values(subgraphNetwork.network.value.links).filter((link) => { + return link.source.id === nodeId && link.target.metadataLayout && TypeSubgraph.CYCLEGROUP in link.target.metadataLayout && link.target.metadataLayout[TypeSubgraph.CYCLEGROUP] === groupCycleId; + }); + }else{ + // group cycle to node + return Object.values(subgraphNetwork.network.value.links).filter((link) => { + return link.target.id === nodeId && link.source.metadataLayout && TypeSubgraph.CYCLEGROUP in link.source.metadataLayout && link.source.metadataLayout[TypeSubgraph.CYCLEGROUP] === groupCycleId; + }); + } + +} + +/** + * Retrieves the links between nodes based on a list of node IDs. + * + * @param network - The network layout object. + * @param nodes - An array of node IDs. + * @returns An array of link objects containing the source and target IDs. + */ +export function getLinksForListNodes(network: NetworkLayout, nodes: string[]): {source:string,target:string}[] { + return network.links.filter(link => + nodes.includes(link.source.id) && nodes.includes(link.target.id) + ).map(link => { return { source: link.source.id, target: link.target.id } }); +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________2. Get graph __________________________________________________________________________ + + + + +/** + * Retrieves the list of node and links for a specific cycle group. + * Position of nodes can be fixed. + * + * @param subgraphNetwork - The subgraph network object. + * @param groupCycleName - The name of the cycle group. + * @param positionAsFixed - (Optional) Indicates whether the node positions should be fixed. Default is false. + * + * @returns An object containing the list of nodes and links for the cycle group. + */ +export function getListNodeLinksForCycleGroup(subgraphNetwork:SubgraphNetwork,groupCycleName:string,positionAsFixed:boolean=false) +:{nodes:{ id: string,fx?:number, fy?:number,x?:number,y?:number }[],links:{source:string,target:string}[]}{ + const nodesGroupCycle=getNodesPlacedInGroupCycle(subgraphNetwork,groupCycleName,positionAsFixed); + const nodesGroupCycleName=Object.values(nodesGroupCycle).map(node=>node.id); + const linksGroupCycle=getLinksForListNodes(subgraphNetwork.network.value,nodesGroupCycleName); + return {nodes:nodesGroupCycle,links:linksGroupCycle}; +} + +/** + * Retrieves an object for node and a list for links for a specific cycle group. + * + * @param subgraphNetwork - The subgraph network object. + * @param groupCycleName - The name of the cycle group. + * + * @returns An object containing the list of nodes and links for the cycle group. + */ +export function getListNodeLinksForCycleGroupAsObject(subgraphNetwork:SubgraphNetwork,groupCycleName:string) +:{nodes:{[key:string]:{ x:number,y:number }},links:{source:string,target:string}[]}{ + const nodesGroupCycle=getNodesPlacedInGroupCycleAsObject(subgraphNetwork,groupCycleName); + const nodesGroupCycleName=Object.keys(nodesGroupCycle); + const linksGroupCycle=getLinksForListNodes(subgraphNetwork.network.value,nodesGroupCycleName); + return {nodes:nodesGroupCycle,links:linksGroupCycle}; +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________3. Get relation cycle __________________________________________________________________________ + + + +/** + * Return the name of the parent cycle of the cycle, if not, return the name of the cycle + * @param cycleName + * @param subgraphNetwork + * @returns the name of the parent cycle of the cycle, if not, return the name of the cycle + */ +export function parentCycle(cycleName:string,subgraphNetwork:SubgraphNetwork):string{ + if (subgraphNetwork[TypeSubgraph.CYCLE][cycleName].parentSubgraph && subgraphNetwork[TypeSubgraph.CYCLE][cycleName].parentSubgraph.type==TypeSubgraph.CYCLE){ + return subgraphNetwork[TypeSubgraph.CYCLE][cycleName].parentSubgraph.name; + }else{ + return cycleName; + } +} + + + + +// function getLinkParent2GroupCycle(subgraphNetwork:SubgraphNetwork,parentId:string,groupCycle:string){ +// return Object.values(subgraphNetwork.network.value.links).filter((link) => { +// return link.source.id === parentId && link.target.metadata && TypeSubgraph.CYCLEGROUP in link.target.metadata && link.target.metadata[TypeSubgraph.CYCLEGROUP] === groupCycle; +// }); +// } + +// function listOfCycles(cycleList:string[],subgraphNetwork:SubgraphNetwork):string[]{ +// const newCyclesList=[]; +// cycleList.forEach(cycle=>{ +// // if cycle is a 'child' of another cycle : no new metanode, it is considered as the parent cycle metanode (else it is the cycle) +// const biggerCycle=inBiggerCycle(cycle,subgraphNetwork); +// if (!newCyclesList.includes(biggerCycle)){ +// newCyclesList.push(biggerCycle); +// } +// }); +// return newCyclesList; +// } diff --git a/src/composables/CalculateSize.ts b/src/composables/CalculateSize.ts new file mode 100644 index 0000000..4a8f814 --- /dev/null +++ b/src/composables/CalculateSize.ts @@ -0,0 +1,427 @@ +// Type imports +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { Node } from "@metabohub/viz-core/src/types/Node"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Subgraph, TypeSubgraph } from "../types/Subgraph"; +import { Coordinate, Size } from "../types/CoordinatesSize"; + +// Composable imports +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; +import { inCycle, isSideCompound } from "./GetSetAttributsNodes"; + +// General imports +import { e } from "vitest/dist/reporters-1evA5lom"; + + + +/** + * This file contains functions to calculate the size of nodes, edges and subgraphs. Anf function to shift coordinates depending on node size. + * + * ********************************* + * 0. Nodes + * + * -> pixelsToInches : + * Converts pixels to inches based on the given DPI (dots per inch). + * + * -> inchesToPixels : + * Converts inches to pixels based on the given DPI (dots per inch). + * + * -> getSizeNodePixel : + * Calculates the size of a node in pixels based on its style properties. + * + * -> getMeanNodesSizePixel : + * Calculates the mean size of nodes in pixels. + * + * -> getSepAttributesInches : + * Calculate the rank separation and node separation in inches depending on node size. + * + * -> getSepAttributesPixel : + * Calculate the rank separation and node separation in pixels depending on node size. + * + * + * ********************************* + * 1. Edges + * + * -> minEdgeLength : + * Calculates the minimum edge length between nodes in a network. + * + * -> medianLengthDistance : + * Calculates the median edge length between nodes in a network. + * + * + * ********************************* + * 2. Subgraphs + * + * -> rectangleSize : + * Calculates the size and center coordinates of a rectangle based on a list of coordinates. + * + * -> getSizeAllGroupCycles : + * Calculates the size of all group cycles. + * + * -> getSizeGroupCycles : + * Calculates the size of a group cycle. + * + * + * ********************************* + * 3. Shift coordinates depending on size + * + * -> shiftAllToGetTopLeftCoord : + * Shifts all nodes in the network to get the top left coordinate based on the given style. + * + * -> getTopLeftCoordFromCenter : +* Calculates the top left coordinate of a node based on its center coordinate and size. + * + * -> getCenterCoordFromTopLeft : + * Calculates the center coordinates of a node based on its top-left coordinates and size. + * + */ + + +/*******************************************************************************************************************************************************/ +//___________________________________________________0. Nodes __________________________________________________________________________ + + +const defaultHeightNode = 25; +const defaultWidthNode = 25; + + +/** + * Converts pixels to inches based on the given DPI (dots per inch). + * @param pixels - The number of pixels to convert. + * @param dpi - The DPI value to use for the conversion. Defaults to 96 DPI. + * @returns The converted value in inches. + */ +export function pixelsToInches(pixels: number, dpi: number = 72): number { + if (!pixels) throw new Error("No pixels to convert to inches"); + return parseFloat((pixels / dpi).toFixed(2)); +} + +/** + * Converts inches to pixels based on the given DPI (dots per inch). + * @param inches - The number of inches to convert. + * @param dpi - The DPI value to use for the conversion. Defaults to 72 DPI. + * @returns The converted value in pixels. + */ +export function inchesToPixels(inches: number, dpi: number = 72): number { + if (!inches) throw new Error("No inches to convert to pixels"); + return parseFloat((inches * dpi).toFixed(2)); +} + +/** + * Calculates the size of a node in pixels based on its style properties. + * @param node - The node for which to calculate the size. + * @param styleNetwork - The style properties of the graph. + * @returns An object containing the height and width of the node in pixels. + */ +export function getSizeNodePixel(node:Node,styleNetwork:GraphStyleProperties):Size{ + let height:number; + let width:number; + if (node.classes && styleNetwork.nodeStyles){ + node.classes.forEach((classe)=>{ + if (classe in styleNetwork.nodeStyles){; + const style=styleNetwork.nodeStyles[classe]; + height = style.height? style.height:height; + width = style.width? style.width:width; + } + }); + } + if (!height){ + height = defaultHeightNode; + } + if (!width){ + width = defaultWidthNode; + } + + return {height:height,width:width}; +} + +/** + * Calculates the mean size of nodes in pixels. + * + * @param nodes - An array of nodes. + * @param styleNetwork - The style properties of the graph. + * @returns An object containing the mean height and width of the nodes in pixels. + */ +export async function getMeanNodesSizePixel(nodes:Node[],styleNetwork:GraphStyleProperties,includeSideCompounds:boolean=true):Promise<Size>{ + let height:number = 0; + let width:number = 0; + let n:number = 0; + nodes.forEach((node)=>{ + if (includeSideCompounds || !isSideCompound(node) ){ + let size = getSizeNodePixel(node,styleNetwork); + height += size.height; + width += size.width; + n+=1; + } + }); + + if (n===0){ + return {height:defaultHeightNode,width:defaultWidthNode}; + } + + return {height:height/n,width:width/n}; +} + + +/** + * Calculate the rank separation and node separation in inches depending on node size : + * rank separation = mean height node * factor + * node separation = mean width node * factor + * @param network contains nodes + * @param styleNetwork contains informations of nodes size + * @param factor number of mean size node for the sep attributes + * @returns rank separation and node separation in inches + */ +export async function getSepAttributesInches(network:Network,styleNetwork:GraphStyleProperties,factor:number=1):Promise<{rankSep:number,nodeSep:number}>{ + const meanSizeNode= await getMeanNodesSizePixel(Object.values(network.nodes),styleNetwork); + const rankSep = pixelsToInches(meanSizeNode.height * factor); + const nodeSep = pixelsToInches(meanSizeNode.width * factor); + return { rankSep, nodeSep }; +} + +/** + * Calculate the rank separation and node separation in pixels depending on node size : + * rank separation = mean height node * factor + * node separation = mean width node * factor + * @param network contains nodes + * @param styleNetwork contains informations of nodes size + * @param factor number of mean size node for the sep attributes + * @returns rank separation and node separation in pixels + */ +export async function getSepAttributesPixel(network:Network,styleNetwork:GraphStyleProperties,factor:number=1):Promise<{rankSep:number,nodeSep:number}>{ + const meanSizeNode= await getMeanNodesSizePixel(Object.values(network.nodes),styleNetwork); + const rankSep = meanSizeNode.height * factor; + const nodeSep = meanSizeNode.width *factor; + return { rankSep, nodeSep }; +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________1. Edges __________________________________________________________________________ + + +const defaultMinEdgeLength = 25; + + +/** + * Calculates the minimum edge length between nodes in a network. + * + * @param network - The network object containing nodes. + * @returns The minimum edge length between nodes. + */ +export function minEdgeLength(network: Network,cycleInclude:boolean=true): number { + let minDistance = Infinity; + network.links.forEach((link) => { + if (cycleInclude || (!inCycle(network,link.target.id) || !inCycle(network,link.source.id)) ){ + const dx = link.source.x - link.target.x; + const dy = link.source.y - link.target.y; + const distance = Math.sqrt(dx * dx + dy * dy); + if (distance !==null && distance !== undefined && !isNaN(distance)){ + minDistance = Math.min(minDistance, distance); + } + } + }); + minDistance= parseFloat(minDistance.toFixed(2)); + if(!isFinite(minDistance)){ + return NaN; + } + return minDistance; +} + +/** + * Calculates the median edge length between nodes in a network. + * + * @param network - The network object containing nodes. + * @param cycleInclude - Flag to include or exclude links in cycles. + * @returns The median length distance between nodes. + */ +export function medianEdgeLength(network: Network, cycleInclude: boolean = true): number { + const distances: number[] = []; + network.links.forEach((link) => { + if (cycleInclude || (!inCycle(network, link.target.id) || !inCycle(network, link.source.id))) { + const dx = link.source.x - link.target.x; + const dy = link.source.y - link.target.y; + const distance = Math.sqrt(dx * dx + dy * dy); + distances.push(distance); + } + }); + + distances.sort((a, b) => a - b); + + if (distances.length === 0) return 0; // Handle case with no distances + + const mid = Math.floor(distances.length / 2); + + // If even number of distances, median is average of two middle numbers + if (distances.length % 2 === 0) { + return parseFloat(((distances[mid - 1] + distances[mid]) / 2).toFixed(2)); + } + + // If odd number of distances, median is middle number + return parseFloat(distances[mid].toFixed(2)); +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________2. Subgraphs __________________________________________________________________________ + + +/** + * Calculates the size and center coordinates of a rectangle based on a list of coordinates. + * @param listCoordinates - The list of coordinates in the rectangle. + * @returns An object containing the width, height, and center coordinates of the rectangle. + */ +export function rectangleSize(listCoordinates:Coordinate[],listID?:string[],subgraphNetwork?:SubgraphNetwork):{width:number,height:number,center:Coordinate}{ + + // get the x and y coordinates + const xCoordinates=listCoordinates.map(coord=>coord.x); + const yCoordinates=listCoordinates.map(coord=>coord.y); + + // get the min and max of x and y coordinates + let minX = Math.min(...xCoordinates); + const minXIndex = xCoordinates.indexOf(minX); + + let maxX = Math.max(...xCoordinates); + const maxXIndex = xCoordinates.indexOf(maxX); + + let minY = Math.min(...yCoordinates); + const minYIndex = yCoordinates.indexOf(minY); + + let maxY = Math.max(...yCoordinates); + const maxYIndex = yCoordinates.indexOf(maxY); + + // if nodes ID : take into account its size + if (listID && subgraphNetwork){ + + // min x + if (minXIndex === -1){ + minX = -defaultWidthNode/2; + } else { + const minXNode = listID[minXIndex]; + const sizeMinXNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[minXNode],subgraphNetwork.networkStyle.value); + minX = minX - sizeMinXNode.width/2; + } + + // max x + if (maxXIndex === -1){ + maxX = defaultWidthNode/2; + }else { + const maxXNode = listID[maxXIndex]; + const sizeMaxXNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[maxXNode],subgraphNetwork.networkStyle.value); + maxX = maxX + sizeMaxXNode.width/2; + } + + // min y + if (minYIndex === -1){ + minY = -defaultHeightNode/2; + } else { + const minYNode = listID[minYIndex]; + const sizeMinYNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[minYNode],subgraphNetwork.networkStyle.value); + minY = minY - sizeMinYNode.height/2; + } + + // max y + if (maxYIndex === -1){ + maxY = defaultHeightNode/2; + } else { + const maxYNode = listID[maxYIndex]; + const sizeMaxYNode = getSizeNodePixel(subgraphNetwork.network.value.nodes[maxYNode],subgraphNetwork.networkStyle.value); + maxY = maxY + sizeMaxYNode.height/2; + } + } + + return { + width: maxX - minX, + height: maxY - minY, + center: { + x: (minX + maxX) / 2, + y: (minY + maxY) / 2 + } + }; +} + + + +/** + * Calculates the size of all group cycles + * + * @param subgraphNetwork - The subgraph network to calculate the size for. + * @returns The subgraphNetwork with the size of all group cycles calculated. + */ +export function getSizeAllGroupCycles(subgraphNetwork:SubgraphNetwork):SubgraphNetwork{ + Object.values(subgraphNetwork[TypeSubgraph.CYCLEGROUP]).forEach(groupCycle => { + subgraphNetwork=getSizeGroupCycles(subgraphNetwork,groupCycle); + }); + + return subgraphNetwork; +} + +/** + * Calculates the size of a group cycle. + * + * @param subgraphNetwork - The subgraph network to calculate the size for. + * @param groupCycle - The group cycle to calculate the size for. + * @returns The subgraphNetwork with the size of the group cycle calculated. + */ +function getSizeGroupCycles(subgraphNetwork:SubgraphNetwork,groupCycle:Subgraph):SubgraphNetwork{ + if (groupCycle.metadata){ + // get all nodes with x and y coordinates + console.warn('modifier getSizeGroupCycle avec nouveau attribut position'); + const listNodesMetadata = Object.entries(groupCycle.metadata) + .filter(([_,item]) => item["x"] !== undefined && item["y"] !== undefined); + const listCoordinates = listNodesMetadata.map(([_,item]) => {return {x:item["x"],y:item["y"]}}); + const listID = listNodesMetadata.map(([id,_]) => {return id}); + // get the size of the rectangle + const {width,height,center}=rectangleSize(listCoordinates,listID,subgraphNetwork); + groupCycle.width=width; + groupCycle.height=height; + groupCycle.originalPosition=center; + } + return subgraphNetwork; +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________3. Shift coordinates depending on size ____________________________________________________________ + + +/** + * Shifts all nodes in the network to get the top left coordinate based on the given style. + * + * @param network - The network object containing the nodes. + * @param style - The style properties used to calculate the top left coordinate. + * @param moveCycleToo - Optional parameter indicating whether to move nodes in cycles as well. Defaults to true. + */ +export function shiftAllToGetTopLeftCoord(network:Network,style:GraphStyleProperties,moveCycleToo:boolean=true) { + Object.values(network.nodes).forEach(node=>{ + if( moveCycleToo || !inCycle(network,node.id)){ + const {x,y}=getTopLeftCoordFromCenter(node,style); + node.x=x; + node.y=y; + } + }) +} + +/** + * Calculates the top left coordinate of a node based on its center coordinate and size. + * + * @param node - The node for which to calculate the top left coordinate. + * @param style - The style properties of the node. + * @returns The top left coordinate of the node. + */ +export function getTopLeftCoordFromCenter(node:Node,style:GraphStyleProperties):Coordinate{ + const size = getSizeNodePixel(node,style); + return {x:node.x-size.width/2,y:node.y-size.height/2} +} + +/** + * Calculates the center coordinates of a node based on its top-left coordinates and size. + * + * @param node - The node for which to calculate the center coordinates. + * @param style - The style properties of the node. + * @returns The center coordinates of the node. + */ +export function getCenterCoordFromTopLeft(node:Node,style:GraphStyleProperties):Coordinate{ + const size = getSizeNodePixel(node,style); + return {x:node.x+size.width/2,y:node.y+size.height/2} +} \ No newline at end of file diff --git a/src/composables/CalculateStartNodes.ts b/src/composables/CalculateStartNodes.ts new file mode 100644 index 0000000..e46dd26 --- /dev/null +++ b/src/composables/CalculateStartNodes.ts @@ -0,0 +1,195 @@ +// Types imports +import { StartNodesType } from "../types/EnumArgs"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { NodeLayout } from "../types/NetworkLayout"; + +// Composable imports +import { networkToGDSGraph } from "./ConvertFromNetwork"; + + +/** + * This file contains the functions to calculate the start nodes of a network for graph traversal. + * + * -> assignRankOrder : + * assign rank and order to nodes of a network + * + * -> getStartNodes : + * get the start nodes of a network for graph traversal + * + * -> concatSources : + * concatenate two arrays of strings and remove duplicates + * + * -> hasRank0 : + * check if a node has rank 0 in metadata + * + * -> needRank : + * check if the rank information is needed for the sourcetype + * + * -> needSource : + * check if the topological source information is needed for the sourcetype + * + * -> needAll : + * check if all nodes are needed for the sourcetype + * + * -> concatSources : + * concatenate two arrays of strings and remove duplicates + * + */ + +/** + * Take network and all the unique y coordinate. Add the rank (y position : first, second...; not coordinate) and order ( x position in the rank: first, second,....) to metadata of network. + * @param {Network} Network object + * @param unique_y array of all unique y for node position + */ +export function assignRankOrder(network: Network, unique_y: Array<number>):void { + + // sort the y to know the associated rank for a y coordinate + unique_y.sort((a:number, b:number) => a - b); + + // get the rank for each node + const xNodeByRank: number[][] = Array.from({ length: unique_y.length }, () => []); + Object.values(network.nodes).forEach((node) => { + const rank = unique_y.indexOf(node.y); + if(rank >-1){ + node.metadata = node.metadata || {}; + node.metadata.rank = rank; + xNodeByRank[rank].push(node.x); + }else{ + node.metadata.rank = undefined; + } + }); + + // sort the y by rank + xNodeByRank.forEach(sublist => { + sublist.sort((a, b) => a - b); + }); + + // get the order for each node + Object.values(network.nodes).forEach((node) => { + if (node.metadata && Object.keys(node.metadata).includes("rank") && node.metadata.rank !== undefined){ + const rank = node.metadata.rank; + if (typeof rank === 'number') { + const order = xNodeByRank[rank].indexOf(node.x); + node.metadata.order = order; + } else { + console.error("Le rang n'est pas un nombre"); + node.metadata.order = undefined; + } + }else{ + node.metadata.order = undefined; + } + }); +} + + +/** + * Get a list of nodes to use as start node for graph traversal (DFS for example) + * @param network + * @param typeSource type of sources to get, with a certain order if several types + * RANK_ONLY : sources are nodes of rank 0 + * SOURCE_ONLY : sources are topological sources of the network (nul indegree) + * RANK_SOURCE : sources are node of rank 0, then source nodes + * ALL : sources are all nodes + * SOURCE_ALL : sources are topological sources, then all the others nodes + * RANK_SOURCE_ALL : sources are node of rank 0, then topological sources, then all the other nodes + * @returns the id of the sources + */ +export async function getStartNodes(network:Network, typeSource:StartNodesType):Promise<Array<string>>{ + + // if all nodes as source + if (typeSource==StartNodesType.ALL){ + return Object.keys(network.nodes).sort(); + } + + const start_rank=[]; + const start_source=[]; + const start_all=[]; + + // get object for data-graph-structure if indegree information needed (when source nodes needed) + let graph:{[key:string]:Function}; + if(needSource(typeSource)){ + graph= await networkToGDSGraph(network); + } + + // adding node depending on sourcetype : Order is important !! + // always rank, then source, then all + Object.entries(network.nodes).sort(([keyA], [keyB]) => keyA.localeCompare(keyB)) + .map(([, value]) => value) + .forEach(node =>{ + if(needRank(typeSource) && hasRank0(node)){ + start_rank.push(node.id); + } else if (needSource(typeSource) && graph.indegree(node.id)===0){ + start_source.push(node.id); + } else if (needAll(typeSource)) { + start_all.push(node.id); + } + }); + + return start_rank.concat(start_source, start_all); + +} + + +// function getSourcesParam(network:Network,sourceType:SourceType):string[]{ +// let sources:string[]=[]; +// if(onlyUserSources){ +// sources=userSources; +// }else{ +// sources = concatSources(userSources as string[],getSources(network,sourceType)); +// } +// return sources; +// } + + +/** + * Node has rank 0 in metadata ? + * @param node Node + * @returns boolean + */ +function hasRank0(node:NodeLayout):boolean{ + console.warn('change rank attr'); + return (node.metadata && Object.keys(node.metadata).includes("rank") && node.metadata.rank===0); +} + +/** + * Depending on the sourcetype, does the information of rank is needed ? + * @param sourcetype + * @returns boolean + */ +function needRank(sourcetype:StartNodesType):boolean{ + return [StartNodesType.RANK_ONLY,StartNodesType.RANK_SOURCE,StartNodesType.RANK_SOURCE_ALL].includes(sourcetype); +} + +/** + * Depending on the sourcetype, does the information of topological source is needed ? + * @param sourcetype + * @returns boolean + */ +function needSource(sourcetype:StartNodesType):boolean{ + return [StartNodesType.SOURCE_ONLY,StartNodesType.SOURCE_ALL,StartNodesType.RANK_SOURCE,StartNodesType.RANK_SOURCE_ALL].includes(sourcetype); +} + +/** + * Depending on the sourcetype, does all the nodes are needed ? + * @param sourcetype + * @returns boolean + */ +function needAll(sourcetype:StartNodesType):boolean{ + return [StartNodesType.ALL,StartNodesType.SOURCE_ALL,StartNodesType.RANK_SOURCE_ALL].includes(sourcetype); +} + +/** + * Concatenates two source arrays of strings and removes duplicates. The result is the first array, then the second (order is preserved). + * @param firstSources - The first array of strings. + * @param secondSources - The second array of strings. + * @returns A new array containing the unique elements from both input arrays. + */ +export function concatSources(firstSources: string[], secondSources: string[]): string[] { + const result = [...firstSources]; + secondSources.forEach(item => { + if (!result.includes(item)) { + result.push(item); + } + }); + return result; +} \ No newline at end of file diff --git a/src/composables/ConvertFromNetwork.ts b/src/composables/ConvertFromNetwork.ts new file mode 100644 index 0000000..90240fc --- /dev/null +++ b/src/composables/ConvertFromNetwork.ts @@ -0,0 +1,482 @@ +// Type imports +import { Network } from '@metabohub/viz-core/src/types/Network'; +import { Subgraph, TypeSubgraph } from '../types/Subgraph'; +import { SubgraphNetwork } from '../types/SubgraphNetwork'; +import { Node } from '@metabohub/viz-core/src/types/Node'; +import { LinkLayout, NetworkLayout, NodeLayout } from '../types/NetworkLayout'; +import { Ordering } from '../types/EnumArgs'; + +// Composable imports +import { addMainChainClusterViz,addClusterDot } from './useSubgraphs'; +import { getSizeNodePixel, pixelsToInches } from './CalculateSize'; +import { inCycle } from './GetSetAttributsNodes'; +import { cycleMetanodeLink, sortLinksWithAllGroupCycle } from './CalculateRelationCycle'; + + +// General imports +import dagre from 'dagrejs/dist/dagre.js'; +import { Graph } from "@viz-js/viz"; +import * as GDS from 'graph-data-structure'; +import { h } from 'vue'; +import { link } from 'fs'; +import { s } from 'vitest/dist/reporters-1evA5lom'; +import { get } from 'http'; +import cytoscape, { ElementDefinition,Stylesheet } from 'cytoscape'; +import { layout } from 'dagrejs'; +import { dot } from 'node:test/reporters'; + + +/** + * This file contains functions to convert a network object into different formats. + * + * ********************************* + * 0. Graph + * + * -> networktoNetworkLayout + * convert a network object into a network layout object (network with information to calculate layout) + * + * -> networkToSerialized + * take a network object and return a serialized object for graph-data-strucutre lib containing the same nodes and edge + * + * -> networkToGDSGraph + * take a network object and return a graph object for graph-data-structure + * + * -> networkToAdjacentObject + * convert a network into an adjacency object. + * + * ********************************* + * 1. Layout library + * + * -> networkToDagre + * take a network object and return a dagre.graphlib.Graph object containing the same nodes and edge + * + * -> networkToCytoscape + * take a network object and return a cytoscape object containing the same nodes and edge + * + * -> networkToDOT + * take a network object and return a DOT string representation + * + * -> networkToViz + * take a network object and return a graph object for viz containing the same nodes and edge + * + * -> graphVizToDot + * converts a viz graph to a DOT string representation. + * + * -> customStringify + * converts an object into a custom string representation (used in graphVizToDot) + * + * + */ + + +/*******************************************************************************************************************************************************/ +//___________________________________________________0. Graph __________________________________________________________________________ + + + +/** + * Convert a network object into a network layout object (network with information to calculate layout) + * @param network the network object to convert + * @returns the new network layout object + */ +export function networktoNetworkLayout(network: Network): NetworkLayout { + + // Convert nodes + const nodes: { [key: string]: NodeLayout } = Object.keys(network.nodes).reduce( + (acc, key) => { + const node = network.nodes[key]; + acc[key] = { + ...node, + metadataLayout: {} + }; + return acc; + }, + {} as { [key: string]: NodeLayout } + ); + + // Convert links + const links: Array<LinkLayout> = network.links.map(link => ({ + ...link, + source: nodes[link.source.id], // update of pointer + target: nodes[link.target.id], // update of pointer + metadataLayout: {} + })); + + // Convert network to network layout + const networkLayout: NetworkLayout = { + ...network, + nodes, + links, + } as NetworkLayout; + + return networkLayout; + } + + + /** + * Take a network object and return a serialized object for graph-data-strucutre lib containing the same nodes and edge + * @param {Network} Network object + * @returns {Serialized} Return serialized object for graph-data-strucutre + */ +export function networkToSerialized(network: Network): GDS.Serialized { + const serializedNodes = Object.values(network.nodes).map(node => ({ id: node.id })); + const serializedLinks = network.links.map(link => ({ + source: link.source.id, + target: link.target.id, + weight: 1 + })); + return { nodes: serializedNodes, links: serializedLinks }; +} + + +/** + * Take a network object and return a graph for graph-data-structure + * @param network + * @returns Graph object as {[key:string]:Function} + */ +export async function networkToGDSGraph(network: Network):Promise<{[key:string]:Function}>{ + const graph = GDS.Graph(); + const networkSerialized: GDS.Serialized = networkToSerialized(network); + graph.deserialize(networkSerialized); + return graph; +} + + +/** + * Convert a network into an adjacency object. + * @param network The network to convert. + * @returns An adjacency object representing the network : an object with nodes as key, and children of node as values + */ +export function networkToAdjacentObject(network:Network):{[key : string]:string[]}{ + const adjacence:{[key : string]:string[]}={}; + Object.keys(network.nodes).forEach(node=>{ + if (!(node in Object.keys(adjacence))){ + adjacence[node]=[]; + } + }) + network.links.forEach(link=>{ + const source=link.source.id; + const target=link.target.id; + adjacence[source].push(target); + }); + return adjacence; +} + +/*******************************************************************************************************************************************************/ +//___________________________________________________1. Layout library __________________________________________________________________________ + + + +/** + * Take a network object and return a dagre.graphlib.Graph object containing the same nodes and edge + * @param {Network} Network object + * @param graphAttributes for dagre layout (see https://github.com/dagrejs/dagre/wiki) + * @returns {dagre.graphlib.Graph} Return dagre.graphlib.Graph object + */ +export function networkToDagre(network: Network,graphAttributes={}): dagre.graphlib.Graph{ + + // initialisation dagre graph + var g = new dagre.graphlib.Graph(); + g.setGraph(graphAttributes); + g.setDefaultEdgeLabel(() => ({})); + + // insert nodes into graph + Object.values(network.nodes).forEach((node) => { + const { id, label, x, y } = node; + g.setNode(id, { label, width: 100, height: 100, x, y }); + }); + + // insert edges into graph + network.links.forEach((link) => { + const { source, target } = link; + g.setEdge(source.id, target.id); + }); + + return g; + +} + + + +/** + * Converts a network object to a Cytoscape object. + * + * @param network - The network object to convert. + * @param initialPosition - Optional. Specifies whether to initialize the position of the nodes. Default is false. + * @returns The converted Cytoscape object. + */ +export function networkToCytoscape(network: Network, initialPosition:boolean=false): cytoscape.Core { + + // Convert nodes + const nodes: ElementDefinition[] = Object.values(network.nodes).map(node => ({ + data: { + id: node.id, + }, + position: { + x: node.x, + y: node.y, + }, + })); + + // Convert links + const edges: ElementDefinition[] = []; + network.links.forEach(link => { + edges.push({ + data: { + id: link.id, + source: link.source.id, + target: link.target.id, + } + }); + }); + + + if (initialPosition){ + return cytoscape({ + container: undefined, + elements: {nodes:nodes, edges:edges}, + layout: { + name: 'preset', // to initialize the position of the nodes + }, + }); + }else{ + return cytoscape({ + container: undefined, + elements: {nodes:nodes, edges:edges}, + }); + } +} + + +/** + * Converts a SubgraphNetwork object to a DOT string representation. + * + * @param subgraphNetwork - The SubgraphNetwork object to convert. + * @param cycle - Optional. Specifies whether to include cycles in the DOT string. Default is true. + * @param addNodes - Optional. Specifies whether to include nodes in the DOT string. Default is true. + * @param groupOrCluster - Optional. Specifies whether to use "group" or "cluster" for grouping nodes. Default is "cluster". + * @param orderChange - Optional. Specifies whether to change the order of links in the DOT string. Default is false. + * @returns The DOT string representation of the SubgraphNetwork. + */ +export function networkToDOT(subgraphNetwork:SubgraphNetwork,cycle:boolean=true, addNodes:boolean=true,groupOrCluster:"group"|"cluster"="cluster",orderChange:boolean=false): string{ + const graphViz=networkToViz(subgraphNetwork,cycle,addNodes,groupOrCluster,orderChange); + const dotString=graphVizToDot(graphViz); + return dotString; +} + +/** + * Take a network object and return a graph object for viz containing the same nodes and edge + * @param {Network} Network object + * @param graphAttributes for viz dot layout (see https://graphviz.org/docs/layouts/dot/) + * @param clusters clusters for viz + * @returns {Graph} Return graph object for viz + */ +export function networkToViz(subgraphNetwork:SubgraphNetwork,cycle:boolean=true, addNodes:boolean=true,groupOrCluster:"group"|"cluster"="cluster",orderChange:boolean=false): Graph{ + + if (groupOrCluster==="group" && !addNodes){ + console.warn('Group without nodes in the file not taken into account'); + }else if (groupOrCluster==="cluster" && orderChange){ + console.warn('When ordering and cluster : cluster is prioritized over ordering'); + } + + // initialisation viz graph + let graphViz: Graph ={ + graphAttributes: subgraphNetwork.attributs, + directed: true, + edges: [], + nodes: [], + subgraphs:[] + } + + // insert nodes + if (addNodes){ + Object.entries(subgraphNetwork.network.value.nodes) + .sort(([keyA], [keyB]) => keyA.localeCompare(keyB)) + .forEach(([key, node])=> { + const nodeViz=nodeForViz(subgraphNetwork,node,cycle,groupOrCluster); + if (nodeViz && !graphViz.nodes.some(node => node.name === nodeViz.name)){ + graphViz.nodes.push(nodeViz); + } + }); + } + + // insert link (but with cycle metanode if cycle is true) + let links:LinkLayout[]=[]; + const resultOrdering=sortLinksWithAllGroupCycle(subgraphNetwork,orderChange); // order of link changed for cycle group + links=resultOrdering.linksOrdered; + subgraphNetwork=resultOrdering.subgraphNetwork; // BEWARE: do this before adding cycle metanode (because of attribut ordering) + links.forEach((link)=>{ + // get tail and head (take into account cycle metanode) + const {tail,head}=cycleMetanodeLink(link,cycle); + if (tail!==head && !graphViz.edges.some(edge => edge.tail === tail && edge.head === head)){ + graphViz.edges.push({ + tail: tail, + head: head, + }); + } + }); + + + // insert mainChain cluster + if (groupOrCluster==="cluster" && Object.keys(subgraphNetwork).includes(TypeSubgraph.MAIN_CHAIN)){ + Object.keys(subgraphNetwork[TypeSubgraph.MAIN_CHAIN]).sort((a, b) => subgraphNetwork[TypeSubgraph.MAIN_CHAIN][b].nodes.length - subgraphNetwork[TypeSubgraph.MAIN_CHAIN][a].nodes.length) // sort depending on size : bigger first + .forEach((nameMainChain) => { + graphViz=addMainChainClusterViz(graphViz,nameMainChain,subgraphNetwork,cycle); + }); + } + + // insert cycle metanode + if (cycle && subgraphNetwork[TypeSubgraph.CYCLEGROUP]){ + Object.values(subgraphNetwork[TypeSubgraph.CYCLEGROUP]).sort((a, b) => { // sort depending on size : bigger first + const areaB = b.width * b.height; + const areaA = a.width * a.height; + return areaB - areaA; + }) + .forEach((cycleGroup) => { + const height=pixelsToInches(cycleGroup.height); + const width=pixelsToInches(cycleGroup.width); + let ordering=Ordering.DEFAULT; + if(orderChange){ + ordering=cycleGroup.ordering; + } + graphViz.nodes.push({name:cycleGroup.name, attributes:{height:height,width:width,ordering:ordering,fixedsize:true}}); + }); + } + return graphViz; +} + +/** + * Converts a node from the subgraph network to a format suitable for the Viz library. + * + * @param subgraphNetwork - The subgraph network. + * @param node - The node + * @param cycle - Indicates whether cycle is taken into account : no node if in a metanode cycle + * @param groupOrCluster - Specifies whether the node belongs to a group or cluster. + * @returns An object containing the name and attributes of the converted node. + */ +function nodeForViz(subgraphNetwork:SubgraphNetwork,node:NodeLayout,cycle:boolean,groupOrCluster:"group"|"cluster"):{name:string,attributes:AttributesViz}{ + // if cycle not taken into account or not in cycle + if (!cycle || !inCycle(subgraphNetwork.network.value,node.id)){ + const attributes:AttributesViz={}; + // size of node in inches + const sizeNode= getSizeNodePixel(node,subgraphNetwork.networkStyle.value); + attributes.height=pixelsToInches(sizeNode.height); + attributes.width=pixelsToInches(sizeNode.width); + attributes.fixedsize=true; + // if main chain : add group attribut + if (groupOrCluster==="group"){ + if (node.metadataLayout && node.metadataLayout[TypeSubgraph.MAIN_CHAIN]){ + const mainChain=node.metadataLayout[TypeSubgraph.MAIN_CHAIN]; + if (mainChain.length!==0){ + attributes.group=mainChain[0]; // can't be in several main chain + } + } + } + return {name:node.id,attributes:attributes}; + }else{ + return undefined; + } +} + + + +/** + * Converts a viz graph to a DOT string representation. + * + * @param vizGraph - The network graph to convert. + * @param subgraphFirst - Determines whether subgraphs should be placed before nodes and edges. Default is true. + * @returns The DOT string representation of the network graph. + */ +export function graphVizToDot(vizGraph:Graph, subgraphFirst:boolean=true):string{ + // initialisation viz graph with graph attributs + let dotString="strict digraph G {\n graph "+customStringify(vizGraph.graphAttributes)+"\n"; + + if (subgraphFirst){ + // clusters + vizGraph.subgraphs.forEach((subgraph) => { + dotString+=addClusterDot(subgraph as SubgraphViz); + }); + + // nodes + vizGraph.nodes.forEach((node) => { + const nodeAttributes= customStringify(node.attributes); + dotString+=`${node.name} ${nodeAttributes};\n`; + }); + + // edges + vizGraph.edges.forEach((edge) => { + dotString+=`${edge.tail} -> ${edge.head};\n`; + }); + } else { + + // nodes + vizGraph.nodes.forEach((node) => { + const nodeAttributes= customStringify(node.attributes); + dotString+=`${node.name} ${nodeAttributes};\n`; + }); + // edges + vizGraph.edges.forEach((edge) => { + dotString+=`${edge.tail} -> ${edge.head};\n`; + }); + + // clusters + vizGraph.subgraphs.forEach((subgraph) => { + dotString+=addClusterDot(subgraph as SubgraphViz); + }); + } + + return dotString+"}"; +} + + +/** + * Converts an object into a custom string representation. + * + * @param obj - The object to be converted. + * @returns The custom string representation of the object. + */ +function customStringify(obj) { + if (Object.keys(obj).length === 0) { + return ""; + } + let str = '['; + for (let key in obj) { + str += `${key}="${obj[key]}", `; + } + str = str.slice(0, -2); // remove trailing comma and space + str += ']'; + return str; +} + + + + + +// /** +// * Return a copy of the network +// * @param network +// * @returns a copy of the network +// */ +// export function networkCopy(network: Network): Network { +// const newNetwork: Network = { +// id: network.id, +// label: network.label, +// nodes: {}, +// links: [] +// }; + +// Object.keys(network.nodes).forEach(key=>{ +// newNetwork.nodes[key] = Object.assign({}, network.nodes[key]); +// }) + +// network.links.forEach(item=>{ +// //get all info from links +// const newlink=Object.assign({}, item); +// // update the node to have a pointeur +// newlink.source=newNetwork.nodes[item.source.id]; +// newlink.target=newNetwork.nodes[item.target.id]; +// newNetwork.links.push(newlink); +// }); +// return newNetwork; +// } + diff --git a/src/composables/ConvertToNetwork.ts b/src/composables/ConvertToNetwork.ts new file mode 100644 index 0000000..2367645 --- /dev/null +++ b/src/composables/ConvertToNetwork.ts @@ -0,0 +1,154 @@ +// Type imports +import { JsonViz } from '../types/FormatJsonViz'; +import { Coordinate } from '../types/CoordinatesSize'; +import { Network } from '@metabohub/viz-core/src/types/Network'; +import type { Node } from "@metabohub/viz-core/src/types/Node"; +import { NetworkLayout } from '../types/NetworkLayout'; +import { SubgraphNetwork } from '../types/SubgraphNetwork'; + +// Composable imports +import { assignRankOrder } from './CalculateStartNodes'; +import { getSizeNodePixel } from './CalculateSize'; + +// General imports +import cytoscape, { ElementDefinition } from 'cytoscape'; +import dagre from 'dagrejs/dist/dagre.js'; +import { type } from 'os'; +import { TypeSubgraph } from '../types/Subgraph'; + +/** + * This file contains functions to get or update a network from another format. + * + * -> networkLayoutToNetwork : + * Convert a network layout object (network with information to calculate layout) into a network object + * + * -> changeNetworkFromDagre : + * Take dagre.graphlib.Graph object and the network associated (with the graph) : change the position and metadata (rank and order) of network's node by the one of the graph. + * + * -> changeNetworkFromViz : + * Take a json of a viz graph and the network associated (with the json) : change the position and metadata (rank and order) of network's node by the one of the json. + * + * -> changeNetworkFromCytoscape : + * Updates the positions of nodes in the network based on the provided Cytoscape JSON. + */ + + + +/** + * Convert a network layout object (network with information to calculate layout) into a network object + * @param networkLayout the network layout object + * @returns the new network object + */ +export function networkLayoutToNetwork(networkLayout: NetworkLayout): Network { + + Object.values(networkLayout.nodes).forEach((nodeLayout) => { + delete nodeLayout.metadataLayout; + }); + + networkLayout.links.forEach((linkLayout) => { + delete linkLayout.metadataLayout; + }); + + return networkLayout as Network; +} + + +/** + * Take dagre.graphlib.Graph object and the network associated (with the graph) : change the position and metadata (rank and order) of network's node by the one of the graph. + * The graph and network need to have the same nodes ! + * @param {dagre.graphlib.Graph} dagre.graphlib.Graph object + * @param {Network} Network object (value of pointer) + */ +export async function changeNetworkFromDagre(graph: dagre.graphlib.Graph,network: NetworkLayout): Promise<void>{ + Object.entries(graph["_nodes"]).forEach(([node, nodeData]:[string, dagre.graphlib.Node]) => { + if (!network.nodes[node].metadataLayout) { + network.nodes[node].metadataLayout = {}; + } + const { x, y, _order,_rank } = nodeData; + // if there is some position x and y : network is updated + if (x !== undefined && y !== undefined){ + if (network.nodes[node]) { + network.nodes[node].x = x; + network.nodes[node].y = y; + } else { + throw new Error(`Node '${node}' not found in the network.`); + } + network.nodes[node].metadataLayout.order = _order; + network.nodes[node].metadataLayout.rank = _rank / 2; // because rank 0 is 0, and the next is 2, 4, ... + } + }); +} + + +/** + * Take a json of a viz graph and the network associated (with the json) : change the position and metadata (rank and order) of network's node by the one of the json. + * The json and network need to have the same nodes ! + * @param {object} object return by render method from viz (renderJSON) + * @param {Network} Network object (value of pointer) + * @param assignRank boolean that indicates if rank and order need to be infered and assigned to nodes + */ +export async function changeNetworkFromViz(json: JsonViz, subgraphNetwork: SubgraphNetwork, assignRank:boolean=false): Promise<SubgraphNetwork> { + const network=subgraphNetwork.network.value; + const unique_y:Array<number> =[]; + json["objects"].forEach((node) => { + + const nodeId = node.name; + + // if node is a 'classic' node + if (nodeId in network.nodes && 'pos' in node){ + const pos = node.pos.split(','); + let x = parseFloat(pos[0]); + let y = parseFloat(pos[1]); + + network.nodes[nodeId].x = x; + network.nodes[nodeId].y = y; + + if( !unique_y.includes(y)){ + unique_y.push(y); + } + + }else if (subgraphNetwork[TypeSubgraph.CYCLEGROUP] && nodeId in subgraphNetwork[TypeSubgraph.CYCLEGROUP] && 'pos' in node){ + + //if node is a cycle metanode + const pos = node.pos.split(','); + const x = parseFloat(pos[0]); + const y = parseFloat(pos[1]); + // if (!subgraphNetwork[TypeSubgraph.CYCLEGROUP][nodeId].metadata){ + // subgraphNetwork[TypeSubgraph.CYCLEGROUP][nodeId].metadata={}; + // } + subgraphNetwork[TypeSubgraph.CYCLEGROUP][nodeId].position={x:x,y:y}; + + }else{ + throw new Error(`Node ou group cycle '${nodeId}' not found in the network.`); + } + }); + + if(assignRank){ + assignRankOrder(network,unique_y); // the information of rank isn't in the result, unlike dagre + } + + return subgraphNetwork; +} + + +/** + * Updates the positions of nodes in the network based on the provided Cytoscape JSON. + * + * @param jsonCytoscape - The Cytoscape JSON containing the elements and their positions. + * @param network - The network to update. + */ +export function changeNetworkFromCytoscape(jsonCytoscape: {elements: { nodes:ElementDefinition[] } }, network:Network) : void { + + jsonCytoscape.elements.nodes.forEach((node: any) => { + const idNode= node.data.id; + if (Object.keys(network.nodes).includes(idNode)) { + network.nodes[idNode].x = node.position.x; + network.nodes[idNode].y = node.position.y; + }else{ + throw new Error(`Node '${idNode}' not found in the network.`); + } + }); +} + + + diff --git a/src/composables/GetSetAttributsNodes.ts b/src/composables/GetSetAttributsNodes.ts new file mode 100644 index 0000000..5da8874 --- /dev/null +++ b/src/composables/GetSetAttributsNodes.ts @@ -0,0 +1,260 @@ +// Type imports +import { TypeSubgraph } from "../types/Subgraph"; +import { Node } from "@metabohub/viz-core/src/types/Node"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { Link } from "@metabohub/viz-core/src/types/Link"; +import { NetworkLayout } from "../types/NetworkLayout"; + +/** + * This file contains functions to check if a node has a specific attribute + * + * ********************************* + * 0. Side Compounds + * + * -> isSideCompound : + * Return if the node is declare as side compound + * + * -> getAttributSideCompounds : + * Returns the attribut for side compound nodes. + * + * -> setAsSideCompound : + * Set the node as side compound + * + * + * ********************************* + * 1. Duplicate + * + * -> isDuplicate : + * Checks if a node in the network is a duplicate. + * + * -> getClassDuplicate : + * Returns the class name for duplicated nodes. + * + * ********************************* + * 2. Reversible + * + * -> addMetadataReversibleWithClass : + * Adds the reversible attribute to the given node in the network. + * + * -> addReversibleNetwork : + * Adds the reversible attribute to the given node in the network. + * + * -> addReversible : + * Adds the reversible attribute to the given node. + * + * -> addLinkClassReversible : + * Adds a class to the given node's classes array in a reversible manner. + * + * -> pushUniqueString : + * Adds a unique string value to an array if it does not already exist. + * + * -> isReversible : + * Checks if a node in the network is reversible. + * + * -> isReaction : + * Checks if a given node is a reaction. + * + * + * ********************************* + * 3. Cycle + * + * + */ + + +/*******************************************************************************************************************************************************/ +//___________________________________________________0. Side Compounds __________________________________________________________________________ + + + +const sideCompoundAttribute="isSideCompound"; + +/** + * Return if the node is declare as side compound + * @param network + * @param nodeID id of the node + * @returns node is a side compound ? + */ +export function isSideCompound(node:Node):boolean{ + return Boolean(node.metadata && node.metadata[sideCompoundAttribute]); +} + +/** + * Returns the attribut for side compound nodes. + * @returns the attribut for side compound nodes + */ +export function getAttributSideCompounds():string{ + return sideCompoundAttribute; +} + +/** + * Set the node as side compound + * @param network + * @param nodeID id of the node + */ +export function setAsSideCompound(network:Network,nodeID:string):void{ + if(!network.nodes[nodeID]) throw new Error("Node not found"); + if(!network.nodes[nodeID].metadata) network.nodes[nodeID].metadata={}; + network.nodes[nodeID].metadata[sideCompoundAttribute]=true; +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________1. Duplicate __________________________________________________________________________ + + + +const classDuplicate="duplicate"; + +/** + * Checks if a node in the network is a duplicate. + * @param network - The network object. + * @param nodeID - The ID of the node to check. + * @returns A boolean indicating whether the node is a duplicate. + */ +export function isDuplicate(network:Network,nodeID:string):boolean{ + if(!network.nodes[nodeID]) throw new Error("Node not found"); + return Boolean(network.nodes[nodeID].classes && network.nodes[nodeID].classes.includes(classDuplicate)); +} + +/** + * Returns the class name for duplicated nodes. + * @returns the class name for duplicate nodes + */ +export function getClassDuplicate():string{ + return classDuplicate; +} + + + +/*******************************************************************************************************************************************************/ +//___________________________________________________2. Reversible __________________________________________________________________________ + +const classReversible="reversible"; +const reversibleAttribute="reversible"; +const reactionClass="reaction"; + +/** + * Checks if a node in the network is reversible by checking its classes. + * => done for my type of file, not necessaty if reversible information already in the metadata + * @param network - The network object. + */ +export async function addMetadataReversibleWithClass(network:Network):Promise<void>{ + Object.values(network.nodes).forEach((node) => { + if(node.classes && node.classes.includes(classReversible)){ + addReversibleNetwork(network,node.id); + } + }); + } + + +/** + * Adds the reversible attribute to the given node in the network. + * + * @param network - The network object. + * @param node - The node to add the reversible attribute to. + */ +export function addReversibleNetwork(network:Network,nodeID:string):void{ + if (!network.nodes[nodeID]){ + throw new Error("Node not found to set as reversible "); + } + if(!network.nodes[nodeID].metadata){ + network.nodes[nodeID].metadata={}; + } + network.nodes[nodeID].metadata[reversibleAttribute]=true; +} + +/** + * Adds the reversible attribute to the given node. + * + * @param node - The node to add the reversible attribute to. + * @returns The modified node with the reversible attribute added. + */ +export function addReversible(node:Node):Node{ + if(!node.metadata){ + node.metadata={}; + } + node.metadata[reversibleAttribute]=true; + return node; +} + +/** + * Adds a class to the given node's classes array in a reversible manner. + * If the node does not have a classes array, it creates one. + * @param node - The node to add the class to. + * @returns The modified node with the added class. + */ +export function addLinkClassReversible(link:Link):Link{ + if(!link.classes){ + link.classes=[]; + } + link.classes=pushUniqueString(link.classes,classReversible); + return link; +} + +/** + * Adds a unique string value to an array if it does not already exist. + * + * @param object - The array to add the value to. + * @param value - The string value to add. + * @returns The updated array with the added value, if it was not already present. + */ +export function pushUniqueString(object:Array<string>, value: string): Array<string> { + if (!object.includes(value)) { + object.push(value); + } + return object; + } + + +/** + * Checks if a node in the network is reversible. + * + * @param {Network} network - The network object. + * @param {string} nodeID - The ID of the node to check. + * @returns {boolean} - Returns true if the node is reversible, otherwise false. + * @throws {Error} - Throws an error if the node is not found. + */ +export function isReversible(network:Network,nodeID:string):boolean{ + if (!network.nodes[nodeID]){ + throw new Error("Node not found to check if reversible"); + } + return Boolean(network.nodes[nodeID].metadata && network.nodes[nodeID].metadata[reversibleAttribute]); +} + +/** + * Checks if a given node is a reaction. + * + * @param node - The node to check. + * @returns A boolean indicating whether the node is a reaction. + */ +export function isReaction(node:Node):boolean{ + return Boolean(node.classes && node.classes.includes(reactionClass)); +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________3. Cycle __________________________________________________________________________ + + + +/** + * Checks if a node is part of a cycle in the network. + * @param network - The network object. + * @param idNode - The ID of the node to check. + * @returns A boolean indicating whether the node is in a cycle or not. + */ +export function inCycle(network: NetworkLayout, idNode: string): boolean { + if (!(idNode in network.nodes)) { + throw new Error("Node not found in network"); + } + // no metadata or no cycle metadata or empty cycle metadata : that is, not in a cycle + console.warn("change matadatlayout inCycle"); + let inCycle:boolean=false; + if ( network.nodes[idNode].metadataLayout && TypeSubgraph.CYCLE in network.nodes[idNode].metadataLayout){ + const cycles=network.nodes[idNode].metadataLayout[TypeSubgraph.CYCLE]; + if (cycles.length>0) inCycle=true; + } + return inCycle; +} + diff --git a/src/composables/LayoutDrawCycle.ts b/src/composables/LayoutDrawCycle.ts new file mode 100644 index 0000000..7d55213 --- /dev/null +++ b/src/composables/LayoutDrawCycle.ts @@ -0,0 +1,1377 @@ +// Type imports +import { Subgraph, TypeSubgraph } from "../types/Subgraph"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; +import { Link } from "@metabohub/viz-core/src/types/Link"; +import { Node } from "@metabohub/viz-core/src/types/Node"; + +// Composable imports +import { getMeanNodesSizePixel, medianEdgeLength, rectangleSize } from "./CalculateSize"; +import { isIntersectionGraph, isOverlapNodes, isOverlapNodesEdges } from "./countIntersections"; +import { inCycle } from "./GetSetAttributsNodes"; + + +// General imports +import { group } from "console"; +import { start } from "repl"; +import { a } from "vitest/dist/suite-ghspeorC"; +import * as d3 from 'd3'; +import { link } from "fs"; +import { emit } from "process"; +import { childNodeNotInCycle, getListNodeLinksForCycleGroup, getListNodeLinksForCycleGroupAsObject, parentNodeNotInCycle } from "./CalculateRelationCycle"; + + + +//------------------------------------------------------------------------------------------------------------ +//__________________________________Calculate coordinates for nodes in cycles______________________________________________________ +//------------------------------------------------------------------------------------------------------------ + + + +/** + * give coordinates for all cycles in the subgraph network. + * @param subgraphNetwork - The subgraph network containing cycles. + * @param allowInterncircle - Whether to allow internal circles within cycles. Default is false. + * @param radiusFactor - The factor to determine the radius of the cycles. Default is 15. + * @returns The updated subgraph network with coordinated cycles. + */ + +export async function coordinateAllCycles(subgraphNetwork:SubgraphNetwork,allowInterncircle:boolean=false):Promise<SubgraphNetwork> { + const network = subgraphNetwork.network.value; + const cycles = subgraphNetwork.cycles? Object.values(subgraphNetwork.cycles):undefined; + let i=0 + let newGroup=true; + if (cycles && cycles.length > 0) { + // creation first cycle group + let group=0; + let groupName=cycleGroupName(String(group)); + subgraphNetwork=addNewCycleGroup(subgraphNetwork,groupName); + + // Find the first cycle to draw : it shouldn't have a 'forgraph' of type cycle as it should be a parent ------------------- + const parentCycles = cycles.filter(cycle => !cycle.parentSubgraph || cycle.parentSubgraph.type !== TypeSubgraph.CYCLE); + if (parentCycles.length === 0) { + console.error("No cycle found without a forSubgraph of type cycle"); + return; + } + parentCycles.sort((a, b) => sortingCycleForDrawing(subgraphNetwork,a,b,true)); + const largestParentCycle = parentCycles[0]; // get largest cycle + subgraphNetwork.cyclesGroup[groupName].nodes.push(largestParentCycle.name); // add it to the current group of cycle + coordinateCycle(subgraphNetwork, largestParentCycle.name,groupName); // give coordinate for largest cycle + + // Drawing the others : -------------------------------------------------------------------------------------------- + + // Remove the drawn cycle from the list + const remainingCycles = cycles.filter(cycle => cycle.name !== largestParentCycle.name); + + // If group of connected cycle is drawn : update group cycle + const updateGroupCycle=await updateGroupCycles(remainingCycles,subgraphNetwork,group,groupName); + subgraphNetwork=updateGroupCycle.subgraphNetwork; + if(updateGroupCycle.group!==group){ + group=updateGroupCycle.group; + groupName=cycleGroupName(String(group)); + newGroup=true; + }else{ + newGroup=false; + } + + // Draw the remaining cycles, starting with the one with the most fixed nodes (and if equal number : the largest one) + while (remainingCycles.length > 0 ) { + + // sort cycles by number of fixed node (and then by size) + remainingCycles.sort((a, b) => sortingCycleForDrawing(subgraphNetwork,a,b,newGroup)); + + const cycleToDraw = remainingCycles[0]; // the cycle with the most fixed nodes + // if groupcycle do not exist : add one + if (!(groupName in subgraphNetwork.cyclesGroup)){ + subgraphNetwork=addNewCycleGroup(subgraphNetwork,groupName); + } + // add the cycle to the current group of cycle + subgraphNetwork.cyclesGroup[groupName].nodes.push(cycleToDraw.name); + // give coordinate to cycle node + coordinateCycle(subgraphNetwork, cycleToDraw.name,groupName,allowInterncircle); + // remove cycle from the list of cycle to process + remainingCycles.shift(); + + // If group of connected cycle is processed : update cycle group + const updateGroupCycle=await updateGroupCycles(remainingCycles,subgraphNetwork,group,groupName); + subgraphNetwork=updateGroupCycle.subgraphNetwork; + if(updateGroupCycle.group!==group){ + group=updateGroupCycle.group; + groupName=cycleGroupName(String(group)); + newGroup=true; + }else{ + newGroup=false; + } + + } + } + return subgraphNetwork; +} + +/** + * Returns the cycle group name by appending the given name with a prefix. + * + * @param name - The name to be appended with the prefix. + * @returns The cycle group name. + */ +function cycleGroupName(name:string):string{ + return "cycle_group_"+name; +} +/** + * Adds a new cycle group to the subgraph network. + * + * @param subgraphNetwork - The subgraph network to add the cycle group to. + * @param groupName - The name of the cycle group. + * @returns The updated subgraph network with the added cycle group. + */ +function addNewCycleGroup(subgraphNetwork:SubgraphNetwork, groupName:string):SubgraphNetwork{ + if(!subgraphNetwork.cyclesGroup){ + subgraphNetwork.cyclesGroup={}; + } + subgraphNetwork.cyclesGroup[groupName]={name:groupName,nodes:[],metadata:{}}; + return subgraphNetwork; +} + +/** + * Sorting function for knowing order of cycle drawing. + * First sort by number of circle fixed nodes (nodes fixed in a circle drawing), then by size, by number of parent nodes (of the cycle), and finally by number of child nodes (of the cycle) . + * @param subgraphNetwork - The subgraph network. + * @param a - The first cycle to compare. + * @param b - The second cycle to compare. + * @returns A number indicating the sorting order. + */ +function sortingCycleForDrawing(subgraphNetwork:SubgraphNetwork,a:Subgraph,b:Subgraph,fullConstraint:boolean=false):number{ + const network=subgraphNetwork.network.value; + + // first sort by number of fixed nodes + const fixedNodesA = a.nodes.filter(node => network.nodes[node].metadata && network.nodes[node].metadata.fixedCycle).length; + const fixedNodesB = b.nodes.filter(node => network.nodes[node].metadata && network.nodes[node].metadata.fixedCycle).length; + if (fixedNodesA !== fixedNodesB){ + return fixedNodesB - fixedNodesA; + }else{ + // sort by size + if ( !fullConstraint || b.nodes.length !== a.nodes.length ){ + return b.nodes.length - a.nodes.length; + }else{ + // then by number of parent nodes + const totalParentNodesA = parentNodeNotInCycle(subgraphNetwork, a.nodes) + .flat().length; + const totalParentNodesB = parentNodeNotInCycle(subgraphNetwork, b.nodes) + .flat().length; + if (totalParentNodesA !== totalParentNodesB){ + return totalParentNodesB - totalParentNodesA; + }else{ + // then by number of child nodes + const totalChildNodesA = childNodeNotInCycle(subgraphNetwork, a.nodes) + .flat().length; + const totalChildNodesB = childNodeNotInCycle(subgraphNetwork, b.nodes) + .flat().length; + + return totalChildNodesB - totalChildNodesA; + } + } + } +} + + + +/** + * Give coordinates for a cycle in a group of cycles. A group of cycle is cycles with common nodes. All the group of cycle are independent (no common nodes) from each other. + * + * @param subgraphNetwork - The subgraph network containing the nodes and cycles. + * @param cycleToDrawID - The ID of the cycle to draw. + * @param groupCycleName - The name of the cycle group that contain the cycle to draw. + * @param radiusFactor - The factor to determine the radius size of the cycle (default: 15). + * @param allowInterncircle - A flag indicating whether to allow internal circles for fixed nodes (default: true). + * + * @returns The updated subgraph network with the nodes placed in the cycle. + */ +async function coordinateCycle(subgraphNetwork:SubgraphNetwork, cycleToDrawID:string,groupCycleName:string,allowInterncircle:boolean=true):Promise<SubgraphNetwork>{ + const network = subgraphNetwork.network.value; + + // Get nodes to place + let cycle:string[]=[]; + if (cycleToDrawID in subgraphNetwork.cycles){ + cycle=subgraphNetwork.cycles[cycleToDrawID].nodes; + subgraphNetwork.cycles[cycleToDrawID].metadata={}; + }else{ + console.log('cycle not in subgraph network'); + } + + + // Check existence of all nodes + const cycleExist = cycle.every(node => node in network.nodes); + + // Nodes with attribute 'fixedCycle' : if a node had been fixed in a line, his position can change, if fixed in a circle , no change + const nodesFixedCircle = cycle.filter(node => + network.nodes[node].metadata && network.nodes[node].metadata.fixedCycle + ); + const nodesFixed = cycle.filter(node => + network.nodes[node].metadata && network.nodes[node].metadata.fixedInCycle + ); + + + // Update node metadata to place them in cycleGroup + cycle.forEach(node=>{ + network.nodes[node].metadata[TypeSubgraph.CYCLEGROUP]=groupCycleName; + }); + + // If cycle exist: place his nodes + if (cycleExist && cycle.length>0){ + if (nodesFixedCircle.length===0){ // if independant cycle (first of a group cycle)---------------------------------------------------------------------------------- + + subgraphNetwork=await independentCycleCoordinates(subgraphNetwork,cycleToDrawID,groupCycleName); + + } else if (nodesFixedCircle.length===1){ // if cycle linked to another cycle by one node ---------------------------------------------------------------------------------- + + const tangentNode=network.nodes[nodesFixedCircle[0]]; + subgraphNetwork=await tangentCycleCoordinates(subgraphNetwork,cycleToDrawID,groupCycleName,tangentNode,nodesFixed,allowInterncircle); + + + } else { // several node in common with other cycle(s) ---------------------------------------------------------------------------------- + + subgraphNetwork=lineCycleCoordinates(subgraphNetwork,cycleToDrawID,groupCycleName); + + } + } + + + return subgraphNetwork; +} + +async function independentCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDrawID:string,groupCycleName:string):Promise<SubgraphNetwork>{ + const network = subgraphNetwork.network.value; + const cycle=subgraphNetwork.cycles[cycleToDrawID].nodes; + + // radius and centroid + const radius = await getRadiusSize(cycle,network,subgraphNetwork.networkStyle.value); + // first cycle centered at 0,0 + const centroidX=0; + const centroidY=0; + subgraphNetwork.cycles[cycleToDrawID].metadata.radius=radius; + subgraphNetwork.cycles[cycleToDrawID].metadata.centroid={x:centroidX,y:centroidY}; + + // Shift cycle + const topIndex = findTopCycleNode(subgraphNetwork,cycle); // first node of list is the top + const cycleCopy= cycle.slice(); + const shiftedCycle = cycleCopy.splice(topIndex).concat(cycleCopy); + + // Give position to each node (no nedd to check if overlap with other cycle, it is the first of the group) + subgraphNetwork=cycleNodesCoordinates(cycleToDrawID,shiftedCycle,centroidX,centroidY,radius,subgraphNetwork,-Math.PI/2,groupCycleName).subgraphNetwork; + return subgraphNetwork; +} + +async function tangentCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDrawID:string,groupCycleName:string,nodeFixed:Node,nodesPlaced:string[],allowInterncircle:boolean=false):Promise<SubgraphNetwork>{ + const network = subgraphNetwork.network.value; + const cycle=subgraphNetwork.cycles[cycleToDrawID].nodes; + + // get fixed node coordinates (in the group cycle) + const groupCycleFixed=nodeFixed.metadata[TypeSubgraph.CYCLEGROUP] as string; + const coordNodeFixed=subgraphNetwork.cyclesGroup[groupCycleFixed].metadata[nodeFixed.id] as {x:number,y:number}; + + // first node of cycle is the one fixed : + const cycleCopy= cycle.slice(); + const firstIndex=cycle.indexOf(nodeFixed.id); + const shiftedCycle = cycleCopy.splice(firstIndex).concat(cycleCopy); + + // radius + const radius = await getRadiusSize(cycle,network,subgraphNetwork.networkStyle.value); + subgraphNetwork.cycles[cycleToDrawID].metadata.radius=radius; + + //centroid depending on fixed cycle + const radiusFixedCycle=subgraphNetwork.cycles[nodeFixed.metadata.fixedCycle as string].metadata.radius as number; + const centroidFixedCycle=subgraphNetwork.cycles[nodeFixed.metadata.fixedCycle as string].metadata.centroid; + const fixedAngle = Math.atan2(coordNodeFixed.y - centroidFixedCycle["y"], coordNodeFixed.x - centroidFixedCycle["x"]); + let centroidX:number; + let centroidY:number; + let d:number; + // if has some node fixed in a line : + if(allowInterncircle && nodesPlaced.length >1){ + d = radiusFixedCycle - radius; // circle draw internally + + }else{ // completely indep of fixed nodes but for the common node + d = radius + radiusFixedCycle; // circle draw externally + } + centroidX = centroidFixedCycle["x"] + d * Math.cos(fixedAngle); + centroidY = centroidFixedCycle["y"] + d * Math.sin(fixedAngle); + subgraphNetwork.cycles[cycleToDrawID].metadata.centroid={x:centroidX,y:centroidY}; + + + // shift of start angle (default:pi/2) : angle of fixed node in the new cycle (with centroid calculted before) + const positionFixedNode=subgraphNetwork.cyclesGroup[groupCycleName].metadata[nodeFixed.id] as {x:number,y:number}; + const shiftAngle = Math.atan2(positionFixedNode.y - centroidY, positionFixedNode.x - centroidX); + + // Give position to each node, and get position before drawing cycle + const cycleCoord=cycleNodesCoordinates(cycleToDrawID,shiftedCycle,centroidX,centroidY,radius,subgraphNetwork,shiftAngle,groupCycleName); + subgraphNetwork=cycleCoord.subgraphNetwork; + const positionBefore=cycleCoord.positionBefore; + subgraphNetwork=undoIfOverlap(subgraphNetwork,groupCycleName,positionBefore); + + return subgraphNetwork; +} + +function lineCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDrawID:string,groupCycleName:string){ + const cycle=subgraphNetwork.cycles[cycleToDrawID].nodes; + + const unfixedInterval=getUnfixedIntervals(cycle,subgraphNetwork); + let cycleAsLine:string[]=[]; + unfixedInterval.forEach(interval=>{ + const startNode=cycle[(interval[0]-1+ cycle.length) % cycle.length]; + const endNode=cycle[(interval[1]+1+ cycle.length) % cycle.length]; + const startNodePosition=subgraphNetwork.cyclesGroup[groupCycleName].metadata[startNode] as {x:number,y:number}; + const endNodePosition=subgraphNetwork.cyclesGroup[groupCycleName].metadata[endNode] as {x:number,y:number}; + if (interval[0]>interval[1]){ + // if begginning of the cycle at the end, and the end at the beginning + cycleAsLine=cycle.slice(interval[0],cycle.length).concat(cycle.slice(0,interval[1]+1)); + }else{ + cycleAsLine=cycle.slice(interval[0],interval[1]+1); + } + // Give position to each node + const lineCoord=lineNodesCoordinates(startNodePosition,endNodePosition,cycleAsLine,subgraphNetwork,groupCycleName); + subgraphNetwork=lineCoord.subgraphNetwork; + const positionBefore=lineCoord.positionBefore; + subgraphNetwork=undoIfOverlap(subgraphNetwork,groupCycleName,positionBefore); + }); + return subgraphNetwork; +} + +/** + * Calculates the radius size based on the length of the cycle array and the radius factor. + * @param cycle - The array of strings representing the cycle. + * @param radiusFactor - The factor to multiply the length of the cycle by to calculate the radius size. Default value is 15. + * @returns The calculated radius size. + */ +async function getRadiusSize(cycle:string[],network:Network,styleNetwork:GraphStyleProperties):Promise<number>{ + const nodes=Object.values(network.nodes).filter(node=>cycle.includes(node.id)); + const meanSize=await getMeanNodesSizePixel(nodes,styleNetwork); + return cycle.length*(meanSize.height+meanSize.width)/2; +} + + +/** + * Calculates and assigns the coordinates for nodes to draw it as a circle. + * + * @param cycleName - The name of the cycle. + * @param cycle - An array of node names in the cycle. + * @param centroidX - The x-coordinate of the centroid. + * @param centroidY - The y-coordinate of the centroid. + * @param radius - The radius of the cycle. + * @param subgraphNetwork - The subgraph network. + * @param shiftAngle - The angle by which to shift the cycle from the first node (optional, default is -Math.PI/2 to put the first node at the top). + * @param groupcycle - The name of the group cycle (optional). + * @returns The updated subgraph network. + */ +function cycleNodesCoordinates(cycleName:string,cycle:string[],centroidX:number,centroidY:number,radius:number,subgraphNetwork:SubgraphNetwork, + shiftAngle:number=-Math.PI/2,groupcycle?:string,):{subgraphNetwork:SubgraphNetwork,positionBefore:{[key:string]:{x:number,y:number}}}{ + + const network=subgraphNetwork.network.value; + let positionBefore:{[key:string]:{x:number,y:number}}={}; + + cycle.forEach((node, i) => { + const nodeNetwork=network.nodes[node]; + // positive shift angle rotate cycle to the right, negative to the left + const x = centroidX + radius * Math.cos(2 * Math.PI * i / cycle.length + shiftAngle ); + const y = centroidY + radius * Math.sin(2 * Math.PI * i / cycle.length + shiftAngle ); + + // Give position if not fixed + if(network.nodes[node].metadata && !network.nodes[node].metadata.fixedCycle){ + if (groupcycle){ + if (groupcycle in subgraphNetwork.cyclesGroup){ + if (!subgraphNetwork.cyclesGroup[groupcycle].metadata[node]){ + subgraphNetwork.cyclesGroup[groupcycle].metadata[node] = {}; + // get position before drawing cycle + positionBefore[node]={x:null,y:null}; + }else{ + // get position before drawing cycle + const xBefore=subgraphNetwork.cyclesGroup[groupcycle].metadata[node]["x"]; + const yBefore=subgraphNetwork.cyclesGroup[groupcycle].metadata[node]["y"]; + positionBefore[node]={x:xBefore,y:yBefore}; + } + // assign new position + subgraphNetwork.cyclesGroup[groupcycle].metadata[node]["x"]=x; + subgraphNetwork.cyclesGroup[groupcycle].metadata[node]["y"]=y; + } else { + console.error("CycleGroup not in subgraphNetwork"); + } + } else if (node in subgraphNetwork.network.value.nodes) { + // get position before drawing cycle + const xBefore=subgraphNetwork.network.value.nodes[node].x; + const yBefore=subgraphNetwork.network.value.nodes[node].x; + positionBefore[node]={x:xBefore,y:yBefore}; + // assign new position + subgraphNetwork.network.value.nodes[node].x=x; + subgraphNetwork.network.value.nodes[node].y=y; + } else{ + console.error("Node not in network or groupcycle not provided") + } + + // Fix the nodes + if (!nodeNetwork.metadata) nodeNetwork.metadata={}; + nodeNetwork.metadata.fixedInCycle= true; + nodeNetwork.metadata.fixedCycle= cycleName; + } + + }); + + return {subgraphNetwork:subgraphNetwork,positionBefore:positionBefore}; +} + + + +function undoIfOverlap(subgraphNetwork:SubgraphNetwork,groupCycleName:string,positionBefore:{[key:string]:{x:number,y:number}}):SubgraphNetwork{ + // is there overlap in the group cycle ? + const isOverlap=isOverlapCycles(subgraphNetwork,groupCycleName); + // if overlap, put back the position before drawing cycle + if(isOverlap){ + Object.entries(positionBefore).forEach(([nodeID,coord])=>{ + const node=subgraphNetwork.cyclesGroup[groupCycleName].metadata[nodeID] as {x:number,y:number}; + node.x = positionBefore[nodeID].x; + node.y = positionBefore[nodeID].y; + }); + } + return subgraphNetwork; +} + +function isOverlapCycles(subgraphNetwork:SubgraphNetwork,groupCycleName:string):boolean{ + const graph =getListNodeLinksForCycleGroupAsObject(subgraphNetwork,groupCycleName); + // intersection of edges : + const intersectionEdges=isIntersectionGraph(graph.nodes ,graph.links,subgraphNetwork.network.value,subgraphNetwork.networkStyle.value); + if (intersectionEdges){ + return true; + }else{ + // overlap of nodes + const nodesOverlap=isOverlapNodes(graph.nodes,subgraphNetwork.network.value,subgraphNetwork.networkStyle.value); + if (nodesOverlap){ + return true; + }else{ + // overlap of node with edges + const edgeNodeOverlap=isOverlapNodesEdges(graph.nodes,graph.links,subgraphNetwork.network.value,subgraphNetwork.networkStyle.value); + if (edgeNodeOverlap){ + return true; + } + } + } + return false; +} + + +/** + * Retrieves the unfixed intervals from a list of nodes. An unfixed interval is a continuous range of nodes that are not fixed in a cycle. + * An unfixed interval is a continuous range of nodes that are not fixed in the cycle. + * + * @param nodes - An array of node IDs. + * @param subgraphNetwork - The subgraph network containing the nodes. + * @returns An array of intervals representing the unfixed intervals. + */ +function getUnfixedIntervals(nodes:string[],subgraphNetwork:SubgraphNetwork) { + let intervals:number[][] = []; + let start = null; + const network=subgraphNetwork.network.value; + nodes.forEach((nodeID,i) => { + const node=network.nodes[nodeID]; + if (node.metadata && !node.metadata.fixedInCycle) { + if (start === null) { + start = i; + } + } else { + if (start !== null) { + intervals.push([start, i - 1]); + start = null; + } + } + }); + + // Handle case where the last node is fixed + if (start !== null) { + intervals.push([start, nodes.length - 1]); + } + + // case first interval and last are linked : combine interval as one long interval + if (intervals.length!==0 && intervals[0][0]===0 && intervals[intervals.length-1][1]===nodes.length-1){ + intervals[0][0]=intervals[intervals.length-1][0]; // change start of first interval + intervals.pop(); // remove last interval + } + + return intervals; +} + + +/** + * Calculates and assigns the coordinates for nodes along a line between two points. + * @param start - The starting point coordinates (x, y). + * @param end - The ending point coordinates (x, y). + * @param nodes - An array of node names to place. + * @param subgraphNetwork - The subgraph network object. + * @param groupCycleName - Optional. The name of the group cycle in witch the line is draw. + * @returns The updated subgraph network object. + */ +function lineNodesCoordinates(start: {x: number, y: number}, end: {x: number, y: number}, nodes: string[], + subgraphNetwork:SubgraphNetwork,groupCycleName?:string):{subgraphNetwork:SubgraphNetwork,positionBefore:{[key:string]:{x:number,y:number}}} { + const network=subgraphNetwork.network.value; + let positionBefore:{[key:string]:{x:number,y:number}}={}; + + // Calculate direction vector + let dx = end.x - start.x; + let dy = end.y - start.y; + + // Calculate distance between start and end + let distance = Math.sqrt(dx * dx + dy * dy); + + // Normalize direction vector to get unit vector + let ux = dx / distance; + let uy = dy / distance; + + // Calculate distance between each node + let nodeDistance = distance / (nodes.length + 1); + + // Place nodes + nodes.forEach((node, i) => { + let d = nodeDistance * (i + 1); + const x= start.x + ux * d; + const y = start.y + uy * d; + + // Give position + if (groupCycleName){ + if (groupCycleName in subgraphNetwork.cyclesGroup){ + if (!subgraphNetwork.cyclesGroup[groupCycleName].metadata[node]){ + subgraphNetwork.cyclesGroup[groupCycleName].metadata[node] = {}; + // get position before drawing cycle + positionBefore[node]={x:null,y:null}; + }else{ + // get position before drawing cycle + const xBefore=subgraphNetwork.cyclesGroup[groupCycleName].metadata[node]["x"]; + const yBefore=subgraphNetwork.cyclesGroup[groupCycleName].metadata[node]["y"]; + positionBefore[node]={x:xBefore,y:yBefore}; + } + // assign new position + subgraphNetwork.cyclesGroup[groupCycleName].metadata[node]["x"]=x; + subgraphNetwork.cyclesGroup[groupCycleName].metadata[node]["y"]=y; + } else { + console.error("CycleGroup not in subgraphNetwork"); + } + } else if (node in subgraphNetwork.network.value.nodes) { + // get position before drawing cycle + const xBefore=subgraphNetwork.network.value.nodes[node].x; + const yBefore=subgraphNetwork.network.value.nodes[node].x; + positionBefore[node]={x:xBefore,y:yBefore}; + // assign new position + subgraphNetwork.network.value.nodes[node].x=x; + subgraphNetwork.network.value.nodes[node].y=y; + } else{ + console.error("Node not in network or groupcycle not provided") + } + + // Fix the nodes + const nodeNetwork=network.nodes[node]; + if (!nodeNetwork.metadata) nodeNetwork.metadata={}; + nodeNetwork.metadata.fixedInCycle= true; + nodeNetwork.metadata.fixedCycle= undefined; + + }); + return {subgraphNetwork:subgraphNetwork,positionBefore:positionBefore}; +} + + +/** + * If the group cycle is drawn : + * - Updates the group cycles in the subgraph network : add its size and center of rectangle. + * - Change the group number. + * + * @param remainingCycles - The remaining cycles to process in the subgraph. + * @param subgraphNetwork - The subgraph network. + * @param group - The current cycle group number. + * @param groupCycleName - The name of the group cycle. + * @returns An object containing the updated subgraph network and group number. + */ +async function updateGroupCycles(remainingCycles: Subgraph[], subgraphNetwork: SubgraphNetwork, group: number, groupCycleName: string): Promise<{subgraphNetwork: SubgraphNetwork, group: number}> { + const network = subgraphNetwork.network.value; + const groupCycleIsDraw = isRemainingCycleIndepOfDrawing(remainingCycles, subgraphNetwork); + + if (groupCycleIsDraw && subgraphNetwork.cyclesGroup[groupCycleName].metadata) { + + + // force algo for node that have null position + subgraphNetwork = await forceGroupCycle(subgraphNetwork, groupCycleName); + + // get size of group and update cycle group information + const listCoord = Object.values(subgraphNetwork.cyclesGroup[groupCycleName].metadata) + .filter(item => item["x"] !== undefined && item["y"] !== undefined); + const {width, height, center} = rectangleSize(listCoord as {x: number, y: number}[]); + subgraphNetwork.cyclesGroup[groupCycleName].width = width; + subgraphNetwork.cyclesGroup[groupCycleName].height = height; + subgraphNetwork.cyclesGroup[groupCycleName].originalPosition = center; + + // change group + group += 1; + } else if (groupCycleIsDraw) { + console.error('No coordinates for group cycle'); + // change group + group += 1; + } + + return {subgraphNetwork: subgraphNetwork, group: group}; +} + + +async function forceGroupCycle(subgraphNetwork:SubgraphNetwork, groupCycleName:string,force:number=-500):Promise<SubgraphNetwork>{ + + if (!subgraphNetwork.cyclesGroup[groupCycleName] || !subgraphNetwork.cyclesGroup[groupCycleName].metadata){ + return subgraphNetwork; + } + + // get subgraph for groupCycle + const graph =getListNodeLinksForCycleGroup(subgraphNetwork,groupCycleName,true); + + // need to apply force ? + const nullNode= graph.nodes.filter(node=>node["fx"]==null || node["fy"]==null); + if (nullNode.length==0){ + return subgraphNetwork; + } + + // get attributes for force layout + const distanceLinks=medianEdgeLength(subgraphNetwork.network.value,false); + const strengthManyBody=-distanceLinks*10; + + // applying force layout + const simulation = d3.forceSimulation(graph.nodes) + .force('link', d3.forceLink().id((d: any) => {return d.id;}).links(graph.links).distance(distanceLinks).strength(0.3)) + .force('charge', d3.forceManyBody().strength(strengthManyBody)) + //.force("collide", d3.forceCollide(distanceLinks/2)) + //.force('center', d3.forceCenter(0,0)) + //.force("radial", d3.forceRadial(0,0)) + .alphaMin(0.4) + .stop(); + + await sendTick(); + + async function sendTick() { + for (let i = simulation.alpha(); i > 0.4; i = simulation.alpha()) { + simulation.tick(); + } + } + + // get the new position of the nodes + graph.nodes.forEach(node => { + subgraphNetwork.cyclesGroup[groupCycleName].metadata[node.id] = { x: node["x"], y: node["y"] }; + }); + + return subgraphNetwork; +} + +/** + * Checks if all nodes in the remaining cycles are unfixed in the subgraph network. + * + * @param remainingCycles - An array of remaining cycles in the subgraph. + * @param subgraphNetwork - The subgraph network containing the nodes. + * @returns A boolean indicating whether all nodes in the remaining cycles are unfixed. + */ +function isRemainingCycleIndepOfDrawing(remainingCycles:Subgraph[], subgraphNetwork:SubgraphNetwork):boolean{ + + const network = subgraphNetwork.network.value; + + if (remainingCycles.every(cycle => + cycle.nodes.every(node => + !network.nodes[node].metadata || !network.nodes[node].metadata.fixedInCycle + ) + )) { + // All nodes in all remaining cycles are unfixed + return true; + } else { + // At least one node in the remaining cycles fixed + return false; + } +} + + + + + + + + + + +//------------------------------------------------------------------------------------------------------------ +//__________________________________ Utility functions______________________________________________________ +//------------------------------------------------------------------------------------------------------------ + + + +/** + * Finds the index of the top cycle node based on the given subgraph network and cycle nodes. + * The top cycle node is determined by the node with the highest parent (smaller y) if it exists. Or the opposite node in the cycle of the node with the lowest child (bigger y). + * If multiple nodes have the highest parent or lowest child, the one with the median x value is chosen. + * If no parent or child nodes are found, the first node in the cycle is chosen. + * + * @param subgraphNetwork - The subgraph network object. + * @param cycleNodes - An array of cycle node names. + * @returns The index of the top cycle node. + */ +function findTopCycleNode(subgraphNetwork: SubgraphNetwork, cycleNodes:string[]):number{ + + // find node with the highest parent (smaller y) + // get parent nodes of the cycle + const cycleNodesParent = parentNodeNotInCycle(subgraphNetwork, cycleNodes); + // get the one with highest parent + const withHighestParent=getNodesAssociatedMinY(subgraphNetwork, cycleNodesParent) + .map(i=>cycleNodes[i]); + if (withHighestParent.length===1){ + return cycleNodes.indexOf(withHighestParent[0]); + + } else if (withHighestParent.length>1){ + // if several : take the one with median x + const nodeMedianName=nodeMedianX(subgraphNetwork, withHighestParent); + return cycleNodes.indexOf(nodeMedianName); + + }else{ + // if no parent : opposite node of the node with lowest child (to put the one with with to the bottom) + let bottomNode:number; + // find node with the lowest child (bigger y) + // get child nodes of the cycle + const cycleNodesChild = childNodeNotInCycle(subgraphNetwork, cycleNodes); + + // get the one with lowest child + const withLowestChild=getNodesAssociatedMaxY(subgraphNetwork, cycleNodesChild) + .map(i=>cycleNodes[i]); + + if (withLowestChild.length>=1){ + if(withLowestChild.length==1){ + bottomNode=cycleNodes.indexOf(withLowestChild[0]); + }else if (withLowestChild.length>1){ + // if several : take the one with median x + const nodeMedianName=nodeMedianX(subgraphNetwork, withLowestChild); + bottomNode=cycleNodes.indexOf(nodeMedianName); + } + // get the opposite node of the first (one as to be chosen) node in the + return (bottomNode+Math.floor(cycleNodes.length/2))%cycleNodes.length; + + }else{ + return 0; + } + } +} + + + +/** + * Returns indices of lists containing minimum y-coordinate nodes. + * + * @param subgraphNetwork - The subgraph network object. + * @param associatedListNodes - The list of list of nodes. + * @returns An array of indices representing lists containing minimum y-coordinate nodes. + */ +function getNodesAssociatedMinY(subgraphNetwork: SubgraphNetwork, associatedListNodes: string[][]): number[] { + const network=subgraphNetwork.network.value; + let minY=Infinity; + let minNodes: number[] = []; + associatedListNodes.forEach((listNodes,i) => { + listNodes.forEach(node => { + if (network.nodes[node] && network.nodes[node].y!==undefined && network.nodes[node].y!==null) { + if (network.nodes[node].y < minY) { + minY = network.nodes[node].y; + minNodes = [i]; + }else if (network.nodes[node].y == minY && !minNodes.includes(i)) { + minNodes.push(i); + } + } + }); + }); + return minNodes; +} + +/** + * Returns indices of lists containing maximum y-coordinate nodes. + * + * @param subgraphNetwork - The subgraph network object. + * @param associatedListNodes - The list of list of nodes. + * @returns An array of indices representing lists containing maximum y-coordinate nodes. + */ +function getNodesAssociatedMaxY(subgraphNetwork: SubgraphNetwork, associatedListNodes: string[][]): number[] { + const network=subgraphNetwork.network.value; + let maxY=-Infinity; + let maxNodes:number[]=[]; + associatedListNodes.forEach((listNodes,i) => { + listNodes.forEach(node => { + if (network.nodes[node] && network.nodes[node].y!==undefined && network.nodes[node].y!==null) { + if (network.nodes[node].y > maxY) { + maxY = network.nodes[node].y; + maxNodes = [i]; + }else if (network.nodes[node].y == maxY && !maxNodes.includes(i)) { + maxNodes.push(i); + } + } + }); + }); + return maxNodes; +} + +/** + * Get the name of the node with the median x-coordinate from a list of nodes. + * + * @param subgraphNetwork - The subgraph network object. + * @param listNodes - An array of node names. + * @returns The name of the node with the median x-coordinate. + */ +function nodeMedianX(subgraphNetwork: SubgraphNetwork, listNodes: string[]): string { + const network=subgraphNetwork.network.value; + let xValues = listNodes.map(node => [node,network.nodes[node].x]); + xValues.sort((a, b) => Number(a[1]) - Number(b[1])); // sort by x + + let midIndex :number; + // if even number of nodes + if (xValues.length % 2 === 0) { + midIndex = (xValues.length / 2)-1; // the lowest x of the two median + } else { // odd number of nodes + midIndex = Math.floor(xValues.length / 2); + } + const nodeNameMedian=xValues[midIndex][0] as string; + return nodeNameMedian; +} + + + + + + + +//------------------------------------------------------------------------------------------------------------ +//________________________________Drawing cycle : shift position and placement in network_______________________________________ +//------------------------------------------------------------------------------------------------------------ + + + +/** + * Draws all cycle groups in the given subgraph network, that is put the precalculated coordinates inside the network + * + * @param subgraphNetwork - The subgraph network containing the cycle groups. + */ +export function drawAllCyclesGroup(subgraphNetwork:SubgraphNetwork) { + + //console.log('drawing cycles group'); + if (TypeSubgraph.CYCLEGROUP in subgraphNetwork){ + const cycleGroups = Object.keys(subgraphNetwork.cyclesGroup); + cycleGroups.forEach(cycleGroup => { + drawCycleGroup(cycleGroup,subgraphNetwork); + }); + } +} + +/** + * Shift the precalculated coordinates nodes in a cycle group to their new positions based on the given metanode position, + * there are put inside the network to be drawn. + * The coordinates of nodes (to be shifted) need to be in the metadata of the cycle group. + * @param cycleGroup - The name of the cycle group. + * @param subgraphNetwork - The subgraph network containing the cycle group and its nodes. + */ +function drawCycleGroup(cycleGroup:string,subgraphNetwork:SubgraphNetwork):void{ + const metanodePosition=subgraphNetwork.cyclesGroup[cycleGroup].position; + const currentCenterPosition=subgraphNetwork.cyclesGroup[cycleGroup].originalPosition; + const dx=metanodePosition.x-currentCenterPosition.x; + const dy=metanodePosition.y-currentCenterPosition.y; + const listNode = Object.entries(subgraphNetwork.cyclesGroup[cycleGroup].metadata) + .filter(([key,item]) => item["x"] !== undefined && item["y"] !== undefined); + listNode.forEach(([nodeID,coord])=>{ + const node=subgraphNetwork.network.value.nodes[nodeID]; + node.x = coord["x"] + dx; + node.y = coord["y"] + dy; + }); +} + + +// ________________________Method 2________________________________________________________ + +// export function coordinateAllCycles(subgraphNetwork:SubgraphNetwork):Promise<SubgraphNetwork>{ +// return new Promise((resolve) => { +// // creation of group cycle and placement of first cycle +// subgraphNetwork=firstStepGroupCycles(subgraphNetwork); +// // if there are group cycle : continue to place the other cycles +// if (subgraphNetwork.cyclesGroup && Object.keys(subgraphNetwork.cyclesGroup).length>0){ +// Promise.all( +// Object.keys(subgraphNetwork.cyclesGroup).map(groupCycleName => { +// forceGroupCycle(subgraphNetwork, groupCycleName) +// }) +// ).then(() => { +// subgraphNetwork=getSizeAllGroupCycles(subgraphNetwork); +// resolve(subgraphNetwork); +// }); +// } +// }); +// } + +// function firstStepGroupCycles(subgraphNetwork:SubgraphNetwork):SubgraphNetwork { +// let cycles = subgraphNetwork.cycles? Object.values(subgraphNetwork.cycles):undefined; +// let i=0; +// let group=-1; +// let groupName:string=""; +// let newGroup=true; + +// while (cycles && cycles.length > 0) { + +// if (newGroup){ +// // if first cycle of a group cycle +// // creation of a new group cycle +// group+=1; +// groupName=cycleGroupName(String(group)); +// subgraphNetwork=addNewCycleGroup(subgraphNetwork,groupName); +// // find biggest cycle, or the one with most constraint +// // cycles that are not subgraph of a cycle +// const parentCycles = cycles.filter(cycle => !cycle.forSubgraph || cycle.forSubgraph.type !== TypeSubgraph.CYCLE); +// if (parentCycles.length === 0) { +// console.error("No cycle found without a forSubgraph of type cycle"); +// return; +// } +// parentCycles.sort((a, b) => sortCycleSizeRelation(subgraphNetwork,a,b,true)); +// const largestParentCycle = parentCycles[0]; + +// // add it to the group cycle and remove it from the list of cycle to process +// subgraphNetwork.cyclesGroup[groupName].nodes.push(largestParentCycle.name); +// cycles = cycles.filter(cycle => cycle.name !== largestParentCycle.name); +// // give it coordinates +// subgraphNetwork=coordinateCycle(subgraphNetwork, largestParentCycle.name,groupName,true); + +// }else{ +// // if not first cycle of a group cycle +// // find all cycles with common nodes (fixed nodes) +// const dependantCyclesList=dependantCycles(cycles,subgraphNetwork); + +// dependantCyclesList.forEach(dependantCycle => { +// // add them to the group cycle +// subgraphNetwork.cyclesGroup[groupName].nodes.push(dependantCycle); +// // fix the nodes (to (0,0)) +// const nodes=subgraphNetwork.cycles[dependantCycle].nodes; +// subgraphNetwork=coordinateCycle(subgraphNetwork, dependantCycle,groupName,false); +// }); + +// // remove them from the list of cycle to process +// cycles = cycles.filter(cycle => !dependantCyclesList.includes(cycle.name)); + +// } + +// // check all cycles of the group cycle are processed +// newGroup=isRemainingCycleIndepOfDrawing(cycles, subgraphNetwork); + +// } + +// return subgraphNetwork; +// } + + + + +// function coordinateCycle(subgraphNetwork:SubgraphNetwork, cycleToDrawID:string,groupCycleName:string,asCircle:boolean=true):SubgraphNetwork{ +// const network = subgraphNetwork.network.value; +// let centroidX :number=0; +// let centroidY :number=0; + +// // Get nodes to place +// let cycle:string[]=[]; +// if (cycleToDrawID in subgraphNetwork.cycles){ +// cycle=subgraphNetwork.cycles[cycleToDrawID].nodes; +// subgraphNetwork.cycles[cycleToDrawID].metadata={}; +// }else{ +// console.log('cycle not in subgraph network'); +// } + +// // Check existence of all nodes +// const cycleExist = cycle.every(node => node in network.nodes); + + +// // If cycle exist: place his nodes +// if (cycleExist && cycle.length>0){ + +// // Update node metadata to place them in cycleGroup +// cycle.forEach(node=>{ +// network.nodes[node].metadata[TypeSubgraph.CYCLEGROUP]=groupCycleName; +// }); + +// // if the cycle has to be drawn as a circle +// if (asCircle){ +// // radius and centroid +// const radius = getRadiusSize(cycle,network,subgraphNetwork.networkStyle.value); +// subgraphNetwork.cycles[cycleToDrawID].metadata.radius=radius; +// subgraphNetwork.cycles[cycleToDrawID].metadata.centroid={x:centroidX,y:centroidY}; + +// // Shift cycle +// const topIndex = findTopCycleNode(subgraphNetwork,cycle); // first node of list is the top +// const cycleCopy= cycle.slice(); +// const shiftedCycle = cycleCopy.splice(topIndex).concat(cycleCopy); + +// // Give position to each node +// subgraphNetwork=cycleNodesCoordinates(cycleToDrawID,shiftedCycle,centroidX,centroidY,radius,subgraphNetwork,-Math.PI/2,groupCycleName); +// } else { +// subgraphNetwork=fixedCycleNodesToOrigin(cycle,subgraphNetwork,groupCycleName); +// } +// } + +// return subgraphNetwork; +// } + + +// function sortCycleSizeRelation(subgraphNetwork:SubgraphNetwork,a:Subgraph,b:Subgraph,byRelation:boolean=false):number{ +// // sort by size +// if ( !byRelation || b.nodes.length !== a.nodes.length ){ +// return b.nodes.length - a.nodes.length; +// }else{ +// // then by number of parent nodes +// const totalParentNodesA = parentNodeNotInCycle(subgraphNetwork, a.nodes) +// .flat().length; +// const totalParentNodesB = parentNodeNotInCycle(subgraphNetwork, b.nodes) +// .flat().length; +// if (totalParentNodesA !== totalParentNodesB){ +// return totalParentNodesB - totalParentNodesA; +// }else{ +// // then by number of child nodes +// const totalChildNodesA = childNodeNotInCycle(subgraphNetwork, a.nodes) +// .flat().length; +// const totalChildNodesB = childNodeNotInCycle(subgraphNetwork, b.nodes) +// .flat().length; + +// return totalChildNodesB - totalChildNodesA; +// } +// } +// } + + + + + + +// function fixedCycleNodesToOrigin(cycle:string[],subgraphNetwork:SubgraphNetwork,groupcycle:string,):SubgraphNetwork{ +// const network=subgraphNetwork.network.value; +// cycle.forEach((node) => { +// const nodeNetwork=network.nodes[node]; +// // Give position if not fixed +// if(network.nodes[node].metadata && !network.nodes[node].metadata.fixedCycle){ +// if (groupcycle in subgraphNetwork.cyclesGroup){ +// if (!subgraphNetwork.cyclesGroup[groupcycle].metadata[node]){ +// subgraphNetwork.cyclesGroup[groupcycle].metadata[node] = {}; +// } +// subgraphNetwork.cyclesGroup[groupcycle].metadata[node]["x"]=0; +// subgraphNetwork.cyclesGroup[groupcycle].metadata[node]["y"]=0; + +// // Fix the nodes +// if (!nodeNetwork.metadata) nodeNetwork.metadata={}; +// nodeNetwork.metadata.fixedInCycle= true; +// } else { +// console.error("CycleGroup not in subgraphNetwork"); +// } +// } +// }); + +// return subgraphNetwork; +// } + + +// function dependantCycles(remainingCycles:Subgraph[], subgraphNetwork:SubgraphNetwork):Array<string>{ + +// const network = subgraphNetwork.network.value; + +// const fixedCycleIds = remainingCycles.filter(cycle => +// cycle.nodes.some(node => +// network.nodes[node].metadata && network.nodes[node].metadata.fixedInCycle +// ) +// ).map(cycle => cycle.name); + +// return fixedCycleIds; +// } + + +// function centroidFromNodes(nodesList:string[],subgraphNetwork:SubgraphNetwork):{x:number,y:number}{ +// if (nodesList.length>0){ +// const network=subgraphNetwork.network.value; +// let centroid={x:0,y:0} +// nodesList.forEach(node=> { +// if ("x" in network.nodes[node] && "y" in network.nodes[node]){ +// centroid.x += network.nodes[node].x; +// centroid.y += network.nodes[node].y; +// } +// }); +// return {x:centroid.x/nodesList.length,y:centroid.y/nodesList.length}; +// } +// return {x:0,y:0}; +// } + + + +// function euclideanDistance(point1: {x: number, y: number}, point2: {x: number, y: number}): number { +// let dx = point2.x - point1.x; +// let dy = point2.y - point1.y; +// return Math.sqrt(dx * dx + dy * dy); +// } + + +// function totalIntervals(startArc: {x: number, y: number}, endArc: {x: number, y: number}, centroidArc: {x: number, y: number}, nodesInArc: number): number { +// // Calculate distances +// let a = euclideanDistance(startArc, endArc); +// let b = euclideanDistance(startArc, centroidArc); +// let c = euclideanDistance(endArc, centroidArc); + +// // Calculate angle of arc using law of cosines +// let angle = Math.acos((b*b + c*c - a*a) / (2 * b * c)); + +// // Calculate total intervals in full circle +// let totalIntervals = Math.round(2 * Math.PI / angle) * nodesInArc; + +// return totalIntervals; +// } + +// function centroidOneFixedCycleNode(subgraphNetwork:SubgraphNetwork,nodeFixedID:string,radius:number):{x:number,y:number}{ +// const nodeFixed=subgraphNetwork.network.value.nodes[nodeFixedID]; +// const radiusFixedCycle=subgraphNetwork.cycles[nodeFixed.metadata.fixedCycle as string].metadata.radius as number; +// const centroidFixedCycle=subgraphNetwork.cycles[nodeFixed.metadata.fixedCycle as string].metadata.centroid; +// const fixedAngle = Math.atan2(nodeFixed.y - centroidFixedCycle["y"], nodeFixed.x - centroidFixedCycle["x"]); +// const d = radius + radiusFixedCycle; +// const centroidX = centroidFixedCycle["x"] + d * Math.cos(fixedAngle); +// const centroidY = centroidFixedCycle["y"] + d * Math.sin(fixedAngle); +// return {x:centroidX,y:centroidY} +// } + + + +// function pushFromIndepGroupCycles(subgraphNetwork:SubgraphNetwork, groupCyclesID:string[],allGroupCycleDrawn:string[][]):void{ + +// console.log('--------------------------------------------------------------------'); +// // nodes in the group of cycle that won't move (others nodes will be pushed deprending on their positions) +// const nodesCycles = groupCyclesID +// .filter(cycleID => cycleID in subgraphNetwork.cycles) // Check if cycleID exists +// .flatMap(cycleID => subgraphNetwork.cycles[cycleID].nodes) // get all nodes from all cycles +// .reduce((unique, item) => unique.includes(item) ? unique : [...unique, item], []); // remove duplicates + +// // centroid of the group +// const centroid = centroidFromNodes(nodesCycles,subgraphNetwork); + +// const radius=subgraphNetwork.cycles[groupCyclesID[0]].metadata.radius as number; // TO CHANGE when several nodes + +// // get list of nodes to push : all but the cycle with its shortcut +// // and group of cycle already draw considered as a node +// const network = subgraphNetwork.network.value; +// const nodesNetwork = Object.keys(network.nodes).filter(node => !nodesCycles.includes(node)); +// const nodesGroupCycleDrawn=allGroupCycleDrawn.flatMap(groupCycle=>groupCycle) +// .flatMap(cycleID=>subgraphNetwork.cycles[cycleID].nodes) // get all nodes from all cycles +// .reduce((unique, item) => unique.includes(item) ? unique : [...unique, item], []); // remove duplicates +// const nodesNotInDrawCycle=nodesNetwork.filter(node => !nodesGroupCycleDrawn.includes(node)); +// let nodeToPush=nodesNotInDrawCycle.filter(node => !nodesGroupCycleDrawn.includes(node)); +// allGroupCycleDrawn.forEach(groupCycle=>{ +// nodeToPush.push(groupCycle[0]); // metanode of cycle group +// }); + + +// // Need to push ? + +// const needPush=nodesInsideMetanode(groupCyclesID,nodesNetwork,subgraphNetwork); +// console.log(needPush); + +// // push nodes + +// if (needPush){ +// nodeToPush.forEach(nodeID =>{ + +// if (nodeID in subgraphNetwork.cycles){ // if in a cycle +// // get connected cycle group +// const fullGroupCycle=allGroupCycleDrawn.filter(groupCycle=> groupCycle.includes(nodeID))[0]; +// const nodesAsMetanode=fullGroupCycle.flatMap(cycleID=>subgraphNetwork.cycles[cycleID].nodes) +// .reduce((unique, item) => unique.includes(item) ? unique : [...unique, item], []); // remove duplicates +// const metanodeCentroid=centroidFromNodes(nodesAsMetanode,subgraphNetwork); + +// const distanceCentroidToMetanode=euclideanDistance(centroid,metanodeCentroid); +// const distanceToMoveCentroid=(distanceCentroidToMetanode/radius+1)*radius; +// pushMetanode(nodesAsMetanode,centroid,distanceToMoveCentroid,subgraphNetwork); + + +// }else if (nodeID in network.nodes){ // if classic node + +// const distanceCentroidToNode=euclideanDistance(centroid,network.nodes[nodeID]); +// const distanceToMove=(distanceCentroidToNode/radius+1)*radius; +// pushMetanode([nodeID],centroid,distanceToMove,subgraphNetwork); + +// } + +// }); +// } + +// } + +// function pushMetanode(metanode:string[],centroidToPushfrom:{x:number,y:number},radius:number=1,subgraphNetwork:SubgraphNetwork):void{ +// const network = subgraphNetwork.network.value; +// if (metanode.length===1){ +// const node=network.nodes[metanode[0]]; +// let dx = node.x - centroidToPushfrom.x; +// let dy = node.y - centroidToPushfrom.y; +// let angle = Math.atan2(dy, dx); +// node.x = centroidToPushfrom.x + radius * Math.cos(angle); +// node.y = centroidToPushfrom.y + radius * Math.sin(angle); +// }else{ + +// // MARCHE PAS + +// // const centroidMetanode=centroidFromNodes(metanode,subgraphNetwork); +// // let dx = centroidMetanode.x - centroidToPushfrom.x; +// // let dy = centroidMetanode.y - centroidToPushfrom.y; +// // let angle = Math.atan2(dy, dx); +// // const newCentroid={x : centroidToPushfrom.x + radius * Math.cos(angle), +// // y : centroidToPushfrom.y + radius * Math.sin(angle)}; + +// // metanode.forEach(nodeID=>{ +// // const node=network.nodes[nodeID]; +// // node.x += newCentroid.x - centroidMetanode.x; +// // node.y += newCentroid.y - centroidMetanode.y; +// // }); +// } +// } + +// function nodesInsideMetanode(groupCyclesID:string[],nodeToCheck:string[],subgraphNetwork:SubgraphNetwork):boolean{ + + +// const cycles=groupCyclesID.filter(cycleID => cycleID in subgraphNetwork.cycles && subgraphNetwork.cycles[cycleID].metadata +// && "radius" in subgraphNetwork.cycles[cycleID].metadata && subgraphNetwork.cycles[cycleID].metadata.radius !== undefined +// && "centroid" in subgraphNetwork.cycles[cycleID].metadata && subgraphNetwork.cycles[cycleID].metadata.centroid +// && subgraphNetwork.cycles[cycleID].metadata.centroid["x"] !== undefined +// && typeof subgraphNetwork.cycles[cycleID].metadata.centroid["y"] !== undefined +// ) + +// let i=0; +// let flag=true; +// while (flag && i<cycles.length){ +// flag=!nodesInsideCircle(cycles[i],nodeToCheck,subgraphNetwork); +// i++; +// } +// return !flag; +// } + +// function nodesInsideCircle(cycleID:string,nodeToCheck:string[],subgraphNetwork:SubgraphNetwork):boolean{ +// const centroid=subgraphNetwork.cycles[cycleID].metadata.centroid as {x:number,y:number}; +// const radius=subgraphNetwork.cycles[cycleID].metadata.radius as number; + + +// let i=-1; +// let flag=true; +// while (flag && i<nodeToCheck.length){ +// i++; +// if( nodeToCheck[i] && Object.keys(subgraphNetwork.network.value.nodes).includes(nodeToCheck[i]) ){ + +// const node=subgraphNetwork.network.value.nodes[nodeToCheck[i]]; +// const distance=euclideanDistance(node,centroid); +// if (distance<=radius){ +// flag=false; +// } + +// }else{ +// //console.log('node '+nodeToCheck[i]+' not in network'); // PROBLEM !!! +// } + + +// } +// return !flag; +// } + + + +// function drawCycle(subgraphNetwork:SubgraphNetwork,cycleToDrawID:string,radius:number|undefined=undefined,radiusFactor:number=15):void { + +// console.log('drawing '+cycleToDrawID); + +// let cycle:string[]=[]; +// let centroidX :number; +// let centroidY :number; +// if (!subgraphNetwork.cycles[cycleToDrawID].metadata) subgraphNetwork.cycles[cycleToDrawID].metadata={}; +// subgraphNetwork.cycles[cycleToDrawID].metadata["radius"]=undefined; +// subgraphNetwork.cycles[cycleToDrawID].metadata["centroid"]=undefined; + + +// if (cycleToDrawID in subgraphNetwork.cycles){ +// cycle=subgraphNetwork.cycles[cycleToDrawID].nodes; +// }else{ +// console.log('argument cycleToDraw invalid'); +// } + +// // Check if the node are present in the graph, and see if position is fixed in another cycle +// const network = subgraphNetwork.network.value; +// let cycleExist = true; +// const nodesFixed:string[]=[]; +// cycle.forEach(node=>{ +// if (!(node in network.nodes)){ +// cycleExist=false; +// } else if (network.nodes[node].metadata && network.nodes[node].metadata.fixedInCycle){ +// nodesFixed.push(node); +// } +// }); + + +// if (cycleExist && cycle.length>0){ + +// if (nodesFixed.length===0){ // if independant cycle ---------------------------------------------------------------------------------- + +// // radius +// if (radius === undefined){ +// radius = getRadiusSize(cycle,radiusFactor); +// } +// subgraphNetwork.cycles[cycleToDrawID].metadata.radius=radius; + +// // centroid +// if (subgraphNetwork.cycles[cycleToDrawID].metadata && subgraphNetwork.cycles[cycleToDrawID].metadata["x"] && subgraphNetwork.cycles[cycleToDrawID].metadata["y"]){ +// centroidX=subgraphNetwork.cycles[cycleToDrawID].metadata["x"] as number; +// centroidY=subgraphNetwork.cycles[cycleToDrawID].metadata["y"] as number; +// }else { +// const centroid=centroidFromNodes(cycle,subgraphNetwork); +// centroidX=centroid.x; +// centroidY=centroid.y; +// } +// subgraphNetwork.cycles[cycleToDrawID].metadata.centroid={x:centroidX,y:centroidY}; + + +// // Shift cycle +// const topIndex = findTopCycleNode(subgraphNetwork,cycle); // first node of list is the top + +// const cycleCopy= cycle.slice(); +// const shiftedCycle = cycleCopy.splice(topIndex).concat(cycleCopy); + +// // Give position to each node +// cycleNodesCoordinates(cycleToDrawID,shiftedCycle,centroidX,centroidY,radius,subgraphNetwork,-Math.PI/2); + +// } else if (nodesFixed.length===1){ // if cycle linked to another cycle by one node ---------------------------------------------------------------------------------- +// const nodeFixed=network.nodes[nodesFixed[0]]; + +// // first node is the one fixed : +// const cycleCopy= cycle.slice(); +// const firstIndex=cycle.indexOf(nodesFixed[0]); +// const shiftedCycle = cycleCopy.splice(firstIndex).concat(cycleCopy); + +// // radius +// if (radius === undefined){ +// radius = getRadiusSize(cycle,radiusFactor); +// } +// subgraphNetwork.cycles[cycleToDrawID].metadata.radius=radius; + +// //centroid depending on fixed cycle +// const radiusFixedCycle=subgraphNetwork.cycles[nodeFixed.metadata.fixedCycle as string].metadata.radius as number; +// const centroidFixedCycle=subgraphNetwork.cycles[nodeFixed.metadata.fixedCycle as string].metadata.centroid; +// const fixedAngle = Math.atan2(nodeFixed.y - centroidFixedCycle["y"], nodeFixed.x - centroidFixedCycle["x"]); +// const d = radius + radiusFixedCycle; +// const centroidX = centroidFixedCycle["x"] + d * Math.cos(fixedAngle); +// const centroidY = centroidFixedCycle["y"] + d * Math.sin(fixedAngle); +// subgraphNetwork.cycles[cycleToDrawID].metadata.centroid={x:centroidX,y:centroidY}; + + +// // shift of start angle (default:pi/2) : angle of fixed node in the new cycle (with centroid calculted before) +// const shiftAngle = Math.atan2(nodeFixed.y - centroidY, nodeFixed.x - centroidX); + +// // drawing : +// cycleNodesCoordinates(cycleToDrawID,shiftedCycle,centroidX,centroidY,radius,subgraphNetwork,shiftAngle); + +// } else { // several node in common with other cycle(s) ---------------------------------------------------------------------------------- + +// const unfixedInterval=getUnfixedIntervals(cycle,subgraphNetwork); +// unfixedInterval.forEach(interval=>{ + +// const startNode=cycle[(interval[0]-1+ cycle.length) % cycle.length]; +// const endNode=cycle[(interval[1]+1+ cycle.length) % cycle.length]; +// lineNodesCoordinates(network.nodes[startNode],network.nodes[endNode],cycle.slice(interval[0],interval[1]+1),subgraphNetwork); + +// }); + +// } +// } + +// } + diff --git a/src/composables/LayoutFindCycle.ts b/src/composables/LayoutFindCycle.ts new file mode 100644 index 0000000..52677f0 --- /dev/null +++ b/src/composables/LayoutFindCycle.ts @@ -0,0 +1,267 @@ +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { addNewSubgraph, createSubgraph, updateNodeMetadataSubgraph } from "./UseSubgraphNetwork"; +import { TypeSubgraph } from "../types/Subgraph"; +import { keepFirstReversibleNode, renameAllIDNode } from "./LayoutReversibleReactions"; + + +export function addDirectedCycleToSubgraphNetwork(subgraphNetwork:SubgraphNetwork,minsize:number=4):SubgraphNetwork{ + //console.log('add cycle'); + if (!subgraphNetwork.cycles){ + subgraphNetwork.cycles={}; + } + let nodeToRename:{[key: string]: string}={}; // to keep track of reversible reaction that have been removed + + // get cycles + const cycles =getJohnsonCycles(subgraphNetwork,true,minsize); + // sort result depending on size : longest cycles first + const sortedCycles = Object.entries(cycles).sort((a, b) => b[1].length - a[1].length); // [1] to get the value of object (not key) + + // adding cycles to subgraph network, and choose appropriate direction for reversible reactions + sortedCycles.forEach(cycle=>{// cycle[0] is the name/id, cycle[1] is the list of nodes + // check if all nodes of cycle still exists (needed because of removal of reversible nodes) + let existingCycle=true; + let i=0; + while (existingCycle && i< cycle[1].length){ + if (!(cycle[1][i] in subgraphNetwork.network.value.nodes)){ + existingCycle=false; + } + i++; + } + + if (existingCycle){ + // update metada node : add cycle information + cycle[1].forEach(node=>{ + updateNodeMetadataSubgraph(subgraphNetwork.network.value,node,cycle[0],TypeSubgraph.CYCLE); + }); + // remove reversible version of node in cycle, to only keep the one in the direction of cycle + const toRename=keepFirstReversibleNode(subgraphNetwork,cycle[1],false) as {[key: string]: string}; + nodeToRename=Object.assign(nodeToRename, toRename); + + + // has common nodes with a cycle in subgraphNetwork ? + let networkCycles = Object.values(subgraphNetwork.cycles); + let i = 0; + let commonNodes = []; + while (i < networkCycles.length) { + commonNodes = cycle[1].filter(node => networkCycles[i].nodes.includes(node)); + if (commonNodes.length > 0) { + break; + } + i++; + } + + const subgraph=createSubgraph(cycle[0],cycle[1],[],TypeSubgraph.CYCLE); + subgraphNetwork=addNewSubgraph(subgraphNetwork,subgraph,TypeSubgraph.CYCLE); + + // if combined cycle (with cycle i) : that is, if there are more than one common nodes + if (commonNodes.length > 1) { + const sizeCycle=cycle[1].length; + const sizeCommonCycle= networkCycles[i].nodes.length; + // add information of 'parent' (bigger cycle) and 'child' (smaller cycle) cycle + if (sizeCycle<=sizeCommonCycle){ // if sorting worked : it is always the case + subgraphNetwork.cycles[cycle[0]].parentSubgraph={name:networkCycles[i].name,type:TypeSubgraph.CYCLE}; + if(! subgraphNetwork.cycles[networkCycles[i].name].childrenSubgraphs){ + subgraphNetwork.cycles[networkCycles[i].name].childrenSubgraphs=[]; + } + subgraphNetwork.cycles[networkCycles[i].name].childrenSubgraphs.push({name:cycle[0],type:TypeSubgraph.CYCLE}); + }else{ + subgraphNetwork.cycles[networkCycles[i].name].parentSubgraph={name:cycle[0],type:TypeSubgraph.CYCLE}; + if(! subgraphNetwork.cycles[cycle[0]].childrenSubgraphs){ + subgraphNetwork.cycles[cycle[0]].childrenSubgraphs=[]; + } + subgraphNetwork.cycles[cycle[0]].childrenSubgraphs.push({name:networkCycles[i].name,type:TypeSubgraph.CYCLE}); + } + } + + } + }); + + // rename reversible reactions (keep the original name) + renameAllIDNode(subgraphNetwork,nodeToRename); + + return subgraphNetwork; +} + +function getJohnsonCycles(subNetwork:SubgraphNetwork,onlyDirectedCycle:boolean=true,minsize:number=4):{[key:string]:string[]} { + // get graph structure for johnson algorithm + const nodes=Object.keys(subNetwork.network.value.nodes).sort(); + const graph=graphForJohnson(subNetwork.network.value,nodes,onlyDirectedCycle); + // apply johnson algorithm : get cycle + return JohnsonAlgorithm(graph,nodes,"All",onlyDirectedCycle,minsize,subNetwork.network.value); +} + + + +function graphForJohnson(network:Network, list_nodes:string[], onlyDirectedCycle:boolean=true):number[][]{ + let graph: number[][] = Array.from({ length: list_nodes.length }, () => []); + network.links.forEach(link=>{ + const sourceIndex=list_nodes.indexOf(link.source.id); + const targetIndex=list_nodes.indexOf(link.target.id); + graph[sourceIndex].push(targetIndex); + if(!onlyDirectedCycle){ + graph[targetIndex].push(sourceIndex); + } + }); + return graph; +} + + +export function JohnsonAlgorithm(graph: number[][], list_nodes:string[],flag: "Single" | "All"="All",onlyDirectedCycle:boolean=true,minsize:number=4,network?:Network): {[key:string]:string[]} { + const nVertices: number = graph.length; + let nbcycle:number=0; + let start: number = 0; + let Ak: number[][] = graph; // Ak is the adjacency list of each node + let B: number[][] = []; // B is the adjacency list of the parent of each node + let blocked: boolean[] = []; // block search of cycle not starting by start node (it will be done later) + for (let i = 0; i < nVertices; i++) { + B.push(Array(nVertices).fill(0)); + blocked[i] = false; + } + let stack: (number | null)[] = []; // stack to store the path of the cycle + for (let i = 0; i < nVertices; i++) { + stack.push(null); + } + let stackTop: number = 0; + const nbNodeToRun: number = (flag === "Single") ? 1 : nVertices; + let result: {[key:string]:string[]} ={}; + + function unblock(u: number): void { // called when a cycle is found : unblock all parent of u (and u) => allow to find other cycle passing by same nodes (but always starting from start) + blocked[u] = false; + // for each parent w of u + for (let wPos = 0; wPos < B[u].length; wPos++) { + let w: number = B[u][wPos]; + + wPos -= removeFromList(B[u], w); // ??? + if (blocked[w]) { + unblock(w); + } + } + } + + function circuit(v: number): boolean { + + let f: boolean = false; + // Push v to the stack and mark it as blocked + stackPush(v); + blocked[v] = true; + + // for each neighbor w of v + for (let wPos = 0; wPos < Ak[v].length; wPos++) { + let w: number = Ak[v][wPos]; + + // If w is less than start, skip the current iteration because already process this node in previous iteration of start + if (w < start) { + continue; + } + // if network : node w not taken into account if reversible version in the stack (cycle with only one of the version) + if(network){ + const wNode=network.nodes[list_nodes[w]]; + if( "metadata" in wNode && "reversibleVersion" in wNode.metadata){ + const stackCopy = stack.slice(0, stackTop); + const reactionRev =wNode.metadata["reversibleVersion"] as string; + const reversibleNumber=list_nodes.indexOf(reactionRev); + if(stackCopy.includes(reversibleNumber)){ + continue; // the reversible reaction is not processed as the original version is already in the stack + } + } + } + + // If w is equal to start, a cycle is found (find only cycle that start from start node) + if (w === start) { + let cycle: number[] = stack.slice(0, stackTop); + + + // If the cycle length is more than 3, add it to the result + if (cycle.length >= minsize) { + const cycleID:string[]=[]; + stack.slice(0, stackTop).forEach(nodeIndex=>{ + cycleID.push(list_nodes[nodeIndex]); + }); + //adding check that not already found in the case of undirected cycle + if (!onlyDirectedCycle && !Object.values(result).some(existingCycle => arePermutations(existingCycle, cycleID))) { + result["cycle_"+String(nbcycle)]=cycleID; + nbcycle+=1; + } + else if (onlyDirectedCycle) { + result["cycle_"+String(nbcycle)]=cycleID; + nbcycle+=1; + } + } + f = true; + } else if (!blocked[w]) { // If w is not blocked, find a cycle starting from w (dfs principle) + if (circuit(w)) { + f = true; + } + } + } + + // If a cycle is found, unblock v and return true + if (f) { + unblock(v); + } else { + // for each neighbor w of v + for (let wPos = 0; wPos < Ak[v].length; wPos++) { + let w: number = Ak[v][wPos]; + if (w < start) { + continue; + } + // Add v to the adjacency list of w in B (parent of w) + if (!B[w].includes(v)) { + B[w].push(v); + } + } + } + v = stackPop(); + return f; + } + + function stackPush(val: number): void { + if (stackTop >= stack.length) { + stack.push(null); + } + stack[stackTop++] = val; // set at index and then stackTop++ + } + + function stackPop(): number | null { + return stack[--stackTop]; // stackTop-- an then get index + } + + function removeFromList(list: number[], val: number): number { + let nOcurrences: number = 0; + let itemIndex: number = 0; + while ((itemIndex = list.indexOf(val, itemIndex)) > -1) { + list.splice(itemIndex, 1); + nOcurrences++; + } + return nOcurrences; + } + + start = 0; + // for (let i = 0; i < nVertices; i++) { + // console.log(String(i)+" "+String(list_nodes[i])); + // } + while (start < nbNodeToRun) { + for (let i = 0; i < nVertices; i++) { + blocked[i] = false; + B[i].length = 0; + } + circuit(start); + start++; + } + return result; +} + +//chatgtp function +function arePermutations(arr1: string[], arr2: string[]): boolean { + if (arr1.length !== arr2.length) return false; + + const sortedArr1 = arr1.slice().sort(); + const sortedArr2 = arr2.slice().sort(); + + for (let i = 0; i < sortedArr1.length; i++) { + if (sortedArr1[i] !== sortedArr2[i]) return false; + } + + return true; +} \ No newline at end of file diff --git a/src/composables/LayoutMain.ts b/src/composables/LayoutMain.ts new file mode 100644 index 0000000..40f012f --- /dev/null +++ b/src/composables/LayoutMain.ts @@ -0,0 +1,232 @@ +// Type imports +import { defaultParameters,Parameters } from "../types/Parameters"; +import { StartNodesType } from "../types/EnumArgs"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { TypeSubgraph } from "../types/Subgraph"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { NetworkLayout } from "../types/NetworkLayout"; +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; + +// Composable imports +import { putDuplicatedSideCompoundAside, reinsertionSideCompounds } from "./LayoutManageSideCompounds"; +import { vizLayout } from "./LayoutSugiyamaForce"; +import { chooseReversibleReaction, duplicateReversibleReactions } from "./LayoutReversibleReactions"; +import { addDirectedCycleToSubgraphNetwork } from "./LayoutFindCycle"; +import { BFSWithSources } from "./AlgorithmBFS"; +import { addMainChainFromSources, addMiniBranchToMainChain } from "./LayoutMainChain"; +import { coordinateAllCycles, drawAllCyclesGroup } from "./LayoutDrawCycle"; +import { shiftAllToGetTopLeftCoord } from "./CalculateSize"; +import { getStartNodes } from "./CalculateStartNodes"; +import { networktoNetworkLayout } from "./ConvertFromNetwork"; +import { networkLayoutToNetwork } from "./ConvertToNetwork"; + +// General imports +import { ref } from "vue"; + + + +/******************************************************************************************************************************************************* + * This file contains the main function of the algorithm (that is to change the coordinates of a network => application of the layout). + * + * -> algorithmOnNetwork : + * change the nodes coordinates of network + * -> allSteps : + * apply all steps of the algorithm to change node coordinates of a network + * *******************************************************************************************************************************************************/ + + +/** + * Executes the layout algorithm on a network with the given network style and parameters. + * + * @param network - The network to apply the algorithm on. + * @param networkStyle - The style properties for the network. + * @param parameters - The optional parameters for the algorithm. + * @returns A promise that resolves to the modified network after applying the algorithm. + * @throws An error if the network or networkStyle is not defined or empty. + */ +export async function algorithmOnNetwork(network:Network,networkStyle:GraphStyleProperties,parameters:Parameters=defaultParameters):Promise<Network>{ + + // check if the network is not empty + if ( !network || Object.keys(network.nodes).length===0){ + console.warn('The network is not defined or has no nodes : the algorithm will not be executed'); + throw new Error('The network is not defined or has no nodes : the algorithm will not be executed'); + } + + // check if the networkStyle is not empty + if ( !networkStyle || Object.keys(networkStyle).length===0){ + console.warn('The networkStyle is not defined or has no properties : the algorithm will not be executed'); + throw new Error('The networkStyle is not defined or has no properties : the algorithm will not be executed'); + } + + // convert network to networkLayout + let networkLayout:NetworkLayout=networktoNetworkLayout(network); + + // initialize the subgraphNetwork object + let subgraphNetwork:SubgraphNetwork={ + network:ref<NetworkLayout>(networkLayout), + networkStyle:ref<GraphStyleProperties>(networkStyle) + } + + + try { + // change coordinates of the network with the algorithm + await allSteps(subgraphNetwork,parameters,true,true); + // convert networkLayout to network + return networkLayoutToNetwork(subgraphNetwork.network.value); + + } catch(err){ + console.log(" Error during execution of algorithm : " + err); + throw err; + } + +} + + +/** + * Apply all steps of the algorithm to change node coordinates of a network. SubgraphNetwork is an object that contains the network to change and all the information needed during the steps. + * @param subgraphNetwork object that contains the network, network style, attributs for viz, subgraph information and side compounds + * @param parameters parameters for the algorithm + * @param shiftCoord change the coordinates to have the one of the top left corner of nodes, if false, the coordinates are the centers + * @param printNameStep print the name of the steps during execution + * @returns a promise of the subgraphNetwork + */ +export async function allSteps(subgraphNetwork: SubgraphNetwork,parameters:Parameters,shiftCoord:boolean=true,printNameStep:boolean=false):Promise<SubgraphNetwork> { + + let network=subgraphNetwork.network.value; + let networkStyle=subgraphNetwork.networkStyle.value; + + if (printNameStep){ + console.log('_____________________________________________'); + console.log('Parameters :'); + console.log(parameters); + console.log('---------------'); + } + + + // duplicate side compounds and put them aside + if (printNameStep) console.log('SideCompound duplication and put aside'); + await putDuplicatedSideCompoundAside(subgraphNetwork,parameters.doDuplicateSideCompounds,parameters.doPutAsideSideCompounds,true,"/sideCompounds.txt").then( + (subgraphNetworkModified)=>{ + subgraphNetwork=subgraphNetworkModified; + } + ).then( + async () => { + if (parameters.doMainChain || parameters.doReactionReversible){ + // get rank 0 with Sugiyama (usefull for main chain and reaction reversible) + if (printNameStep) console.log('First Viz (get ranks)'); + await vizLayout(subgraphNetwork, true,false,parameters.addNodes,parameters.groupOrCluster,false); + } + } + ).then( + async () => { + if (parameters.doReactionReversible){ + // duplicate reactions + if (printNameStep) console.log('Duplicate reversible reactions'); + await duplicateReversibleReactions(network); + } + } + ).then( + () => { + // detect cycles and choose some of the reaction duplicated + if (parameters.doCycle){ + if (printNameStep) console.log('Find directed cycles'); + addDirectedCycleToSubgraphNetwork(subgraphNetwork,3); + } + } + ).then( + () => { + // if no cycle, we don't need to do the cycle step + if (parameters.doCycle && subgraphNetwork[TypeSubgraph.CYCLE] && Object.keys(subgraphNetwork[TypeSubgraph.CYCLE]).length===0){ + parameters.doCycle=false; + console.warn('doCycle is true but no cycle found : doCycle set to false'); + } + } + ).then( + async () => { + if (parameters.doReactionReversible){ + // choose all other reversible reactions + if (printNameStep) console.log('Choose reversible reactions'); + const sources=await getStartNodes(network,StartNodesType.RANK_SOURCE_ALL); + subgraphNetwork=await chooseReversibleReaction(subgraphNetwork,sources,BFSWithSources); + } + } + ).then( + async () => { + // get main chains + if (parameters.doMainChain){ + if (printNameStep) console.log('Find main chain'); + const sources=await getStartNodes(network,parameters.startNodeTypeMainChain); + addMainChainFromSources(subgraphNetwork, sources,parameters.getSubgraph, parameters.merge,parameters.pathType); + } + } + ).then( + () => { + // add minibranch + if(parameters.doMainChain && parameters.doMiniBranch){ + if (printNameStep) console.log('Add minibranch'); + subgraphNetwork= addMiniBranchToMainChain(subgraphNetwork); + }else if ( !parameters.doMainChain && parameters.doMiniBranch){ + console.warn('doMiniBranch is true but doMainChain is false : minibranch will not be added'); + } + } + ).then( + async () => { + // Sugiyama without cycle metanodes (to get top nodes for cycles) + if (printNameStep) console.log('Second Viz (get top nodes if cycles, else final viz)'); + await vizLayout(subgraphNetwork, false,false,parameters.addNodes,parameters.groupOrCluster,false); + } + ).then( + async () => { + // relative coordinates for cycles + if (parameters.doCycle){ + if (printNameStep) console.log('Coordinate directed cycles'); + await coordinateAllCycles(subgraphNetwork,parameters.allowInternalCycles); + } + } + ).then( + async () => { + // Sugiyama with cycle metanodes + if (parameters.doCycle){ + if (printNameStep) console.log('Third Viz (metanodes for directed cycles)'); + await vizLayout(subgraphNetwork, false,true,parameters.addNodes,parameters.groupOrCluster,parameters.ordering,false,parameters.dpi,parameters.numberNodeOnEdge); + } + } + ).then( + () => { + // place the cycles + if (parameters.doCycle){ + if (printNameStep) console.log('Place directed cycles'); + drawAllCyclesGroup(subgraphNetwork); + } + } + ).then( + async () => { + if (parameters.doDuplicateSideCompounds && parameters.doPutAsideSideCompounds){ + // reverse side compounds of reversed reactions, and apply motif to insert side compounds + if (printNameStep) console.log('Insert side compounds'); + subgraphNetwork= await reinsertionSideCompounds(subgraphNetwork,parameters.factorLengthSideCompounds,parameters.doReactionReversible); + }else if (!parameters.doDuplicateSideCompounds && parameters.doPutAsideSideCompounds){ + console.warn('doPutAsideSideCompounds is true but doDuplicateSideCompounds is false : side compounds will not be inserted '); + } + } + ).then( + () => { + // shift coordinates to have top left corner coordinate (because of svg drawing) + if (shiftCoord){ + if (printNameStep) console.log('Shift coordinates nodes to have center at the old coordinates'); + shiftAllToGetTopLeftCoord(network,networkStyle); + } + } + ).then( + () => { + // add color to link (optional : for debug) + //subgraphNetwork = addBoldLinkMainChain(subgraphNetwork); + //subgraphNetwork=addRedLinkcycleGroup(subgraphNetwork); + } + ); + return subgraphNetwork; + +} + + + \ No newline at end of file diff --git a/src/composables/LayoutMainChain.ts b/src/composables/LayoutMainChain.ts new file mode 100644 index 0000000..4ffa31c --- /dev/null +++ b/src/composables/LayoutMainChain.ts @@ -0,0 +1,391 @@ +import { PathType, StartNodesType } from "../types/EnumArgs"; +import { DFSWithSources, DFSsourceDAG } from "./AlgorithmDFS"; +import { networkToGDSGraph } from "./ConvertFromNetwork"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { getStartNodes } from "./CalculateStartNodes"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { BFS } from "./AlgorithmBFS"; +import {TypeSubgraph, type Subgraph} from "../types/Subgraph"; +import { addNewSubgraph, addNodeToSubgraph, createSubgraph, updateNodeMetadataSubgraph } from './UseSubgraphNetwork'; + + +/** + * Add clusters (in ClusterNetwork object) taht are at least of a minimum size. A method is given in the parameters to get the clusters + * @param subgraphNetwork an object with the network and object for clusters + * @param sources array of node ID or a type of method to get sources automatically + * RANK_ONLY : sources are nodes of rank 0 + * SOURCE_ONLY : sources are topological sources of the network (nul indegree) + * RANK_SOURCE : sources are node of rank 0, then source nodes + * ALL : sources are all nodes + * SOURCE_ALL : sources are topological sources, then all the others nodes + * RANK_SOURCE_ALL : sources are node of rank 0, then topological sources, then all the other nodes + * For this function, the advised choice is either RANK_ONLY, SOURCE_ONLY or RANK_SOURCE. + * @param getMainChains function that return the clusters to add + * @param merge if true, merge the path with an existing one if a common node is found, else common nodes in several clusters + * => not taken by all methods of getCluster + * @param pathType the type of path to target node wanted : + * LONGEST : one of the longest path + * ALL_LONGEST : all the longest lenght + * ALL : all path + * => not taken by all methods of getCluster + * @param minHeight minimum size of a cluster to be added + * @returns the clusterNetwork with more cluster + */ +export function addMainChainFromSources(subgraphNetwork:SubgraphNetwork, sources:Array<string> | StartNodesType, + getMainChains:(network: Network, sources: Array<string>,merge?:boolean,pathType?:PathType) => {[key:string]:{nodes:Array<string>, height:number}}=getPathSourcesToTargetNode, + merge:boolean=true, + pathType:PathType=PathType.ALL_LONGEST, + minHeight:number=4 +):SubgraphNetwork{ + + //console.log('create main chain from longest path'); + const network=subgraphNetwork.network.value; + subgraphNetwork[TypeSubgraph.MAIN_CHAIN]={}; + + // get sources + if (!Array.isArray(sources)){ + sources=getStartNodes(network,sources); + } + + // get main chains of paths from sources + const newMainChains=getMainChains(network,sources as string[],merge,pathType); + + // add main chains if length > minsize, and update metadata for nodes + Object.entries(newMainChains).forEach(([mainChainID,mainChain]:[string,{nodes:Array<string>, height:number}])=>{ + if (mainChain.height >= minHeight){ + // create subgraph and add it + const newMainChainId="mainChain__"+mainChainID; + const newMainChain= createSubgraph(newMainChainId, mainChain.nodes,[],TypeSubgraph.MAIN_CHAIN); + subgraphNetwork.mainChains[newMainChainId]=newMainChain; + // add metadata for node in cluster + mainChain.nodes.forEach(nodeID=>{ + updateNodeMetadataSubgraph(network, nodeID, newMainChainId); + }); + } + }); + + return subgraphNetwork; +} + + +/** + * Adds mini branches to the main chain in the cluster network. + * A mini branch is a child of a node in main chain cluster that has no children. + * @param subgraphNetwork - The cluster network to modify. + * @returns The modified cluster network. + */ +export function addMiniBranchToMainChain(subgraphNetwork:SubgraphNetwork):SubgraphNetwork{ + //console.log('add mini branch to main chain'); + const network=subgraphNetwork.network.value; + const graph=networkToGDSGraph(network); + // for each main chain : + Object.entries(subgraphNetwork.mainChains).forEach(([mainChainID,mainChain]:[string,Subgraph]) => { + const nodesToAdd:string[]=[]; + // for each node of the main chain : + mainChain.nodes.forEach(node=>{ + const children=graph.adjacent(node); + children.forEach(child=>{ + // if child is sink : + if (graph.outdegree(child)===0){ + // it's a mini branch, so add it to the list (if not already in the main chain or in the list of nodes to add) + if (!nodesToAdd.includes(child) && !mainChain.nodes.includes(child)) { + nodesToAdd.push(child); + } + } + }); + }); + // add the nodes to a subgraph associated with the main chain + if (nodesToAdd.length>0){ + const subgraph=createSubgraph("minibranch_"+mainChainID,nodesToAdd,[],TypeSubgraph.SECONDARY_CHAIN,{name:mainChainID,type:TypeSubgraph.MAIN_CHAIN}); + subgraphNetwork=addNewSubgraph(subgraphNetwork,subgraph,TypeSubgraph.SECONDARY_CHAIN); + } + }); + return subgraphNetwork; +} + + + + +// ---------------------------------------------------------------------------------------------------------------------------------------------- +// ---------------------------------------------- Method 1 of getCluster for main chains --------------------------------------------------------- +// ---------------------------------------------------------------------------------------------------------------------------------------------- + + +/** + * Get a long path from sources using a DFS. The path isn't the longest if there some undirected cycle. + * @param network + * @param sources to use for DFS + * @returns some node clusters with id + */ +export function getLongPathDFS(network:Network,sources:string[]):{[key:string]:{nodes:Array<string>, height:number}}{ + //console.log('DFS long path'); + // create graph for library from network + const graph=networkToGDSGraph(network); + // DFS + const dfs=DFSWithSources(network, sources); + // get new clusters : 'longest' paths from sources with DFS + return longestPathFromDFS(graph,dfs,sources as string[]); +} + + +/** + * The 'longest' (not the longest if undirected or directed cycle) path associated with each source with the DFS is found. BEWARE : the order of the id can change the result. + * @param graph object for graph-data-structure library + * @param dfs the return string (of nodes id) of a dfs (logically obtained with same sources as the sources for this functions) + * @param sources array of node ID or a type of method to get sources automatically + * RANK_ONLY : sources are nodes of rank 0 + * SOURCE_ONLY : sources are topological sources of the network (nul indegree) + * RANK_SOURCE : sources are node of rank 0, then source nodes + * ALL : sources are all nodes + * SOURCE_ALL : sources are topological sources, then all the others nodes + * RANK_SOURCE_ALL : sources are node of rank 0, then topological sources, then all the other nodes + * For this function, the advised choice is either RANK_ONLY, SOURCE_ONLY or RANK_SOURCE. + * + * @returns an object for the different path, the key is the source of the path + */ +function longestPathFromDFS(graph:{[key:string]:Function},DFSreversed:Array<string>,sources:Array<string>):{[key:string]:{nodes:Array<string>, height:number}}{ + let dfs = Array.from(DFSreversed).reverse(); // the code has been done whith a backward reading of dfs + + let longestPaths:{[key:string]:{nodes:Array<string>, height:number}}={}; + let path:Array<string>; + let source:string=undefined; + let i=dfs.length-1; // index of node in dfs array + let add=false; + + while( i !== -1 ){ // dfs nodes are read backwards + const visitedNode=dfs[i]; + const previousNode: string = (dfs.length - 1 >= i + 1) ? dfs[i + 1] : undefined; + + // if visited node is source + if( sources.includes(visitedNode) ){ + + if (source!==undefined){ + // end the path (of the previous source, if one) + longestPaths=endPath(source,longestPaths,path); + // suppress nodes after the current node (those already analysed in while loop, because backward reading) + dfs.splice(i + 1); + } + + // define new source and add to path + source = visitedNode; + longestPaths[source]={nodes:[source],height:1}; + add=true; + path=[source]; + + // if there is a previous node + } else if (previousNode){ + // if visited node is child of the previous visited node in dfs : add to path + if (nodeIsChildOf(graph,visitedNode,previousNode)){ + add=true; + path.push(visitedNode); + }else{ + // end the path if a node has been added in the last pass of the loop + if (add && source!==undefined){ + longestPaths=endPath(source,longestPaths,path); + } + // remove previous visited node if this node is not the parent of current node + dfs.splice(i+1,1); + path.splice(path.length-1); + i++; // next loop pass will be on the same visited node (because the parent of the visited node wasn't found) + add=false; // no node has been added + } + } + + i--; //backward reading + } + return longestPaths; +} + +/** + * Is the node a child of the parent node ? + * @param graph object that contains function to get children of a node + * @param node is this node a child of the parent? + * @param parentNode the parent node + * @returns boolean + */ +function nodeIsChildOf(graph:{[key:string]:Function},node:string, parentNode:string):boolean{ + return graph.adjacent(parentNode).includes(node); +} + +/** + * Check if the given path is longer than the one in the longest, if it is : update the path to keep the longest of the two + * @param source source of the path (first node) + * @param longestPaths + * @param path the path to check + * @returns the new longest paths + */ +function endPath(source:string, longestPaths:{[key:string]:{nodes:Array<string>, height:number}},path:Array<string>):{[key:string]:{nodes:Array<string>, height:number}}{ + if (source in longestPaths){ + if(longestPaths[source].height < path.length){ + longestPaths[source]={nodes:path.slice(),height:path.length}; + } + }else{ + console.error("source key not in object") + } + return longestPaths; +} + +// ---------------------------------------------------------------------------------------------------------------------------------------------- +// ---------------------------------------------- Method 2 of getCluster for main chains --------------------------------------------------------- +// ---------------------------------------------------------------------------------------------------------------------------------------------- + +/** + * Return the longest paths from source nodes for the source DAG. "Source DAG" doesn't mean the graph is a DAG, but the subraph containing all descendant of the source is a DAG. + * Paths obtained are the longest for the created DAG, not the general graph (because it is NP-hard). + * If several sources have nodes in common in their longest path (from the DAG), then there are merged in one path. + * @param network + * @param sources to use for the paths + * @param merge if true, merge the path with an existing one if a common node is found, else common nodes in several clusters + * @param pathType the type of path to target node wanted : + * LONGEST : one of the longest path + * ALL_LONGEST : all the longest lenght + * ALL : all path + * @returns some node clusters with id + */ +export function getPathSourcesToTargetNode(network:Network, sources:string[],merge:boolean=true,pathType:PathType=PathType.ALL_LONGEST):{[key:string]:{nodes:Array<string>, height:number}}{ + + //console.log('DAG_Dijkstra'); + + let pathsFromSources:{[key:string]:{nodes:Array<string>, height:number}}={}; + + // for each source : do an independant dfs + sources.forEach(source=>{ + // DFS to get a DAG from this source, and get topological sort + const {dfs,graph}=DFSsourceDAG(network,[source]); + // get max distance from source node for all nodes, and by which parent nodes the node had been accessed + const {distances, parents}=DistanceFromSourceDAG(graph,dfs,pathType); + // get the farthest node from source (node with max distance) + const targetNodes=findMaxKeys(distances); + // for each target node : (if several path wanted) + if (pathType==PathType.ALL_LONGEST || pathType==PathType.ALL){ + targetNodes.key.forEach(target => { + // get the parents that goes from source to target node + const nodesBetweenSourceTarget=BFS(parents,target); + // merge with an existing path if node in common + // height is the max distance +1 + pathsFromSources=mergeNewPath(source,{nodes:nodesBetweenSourceTarget, height:targetNodes.max+1},pathsFromSources,merge); + }); + } else if(pathType==PathType.LONGEST){ // if only one path wanted : take the first + // get the parents that goes from source to target node + const nodesBetweenSourceTarget=BFS(parents,targetNodes.key[0]); + // merge with an existing path if node in common + pathsFromSources=mergeNewPath(source,{nodes:nodesBetweenSourceTarget, height:targetNodes.max},pathsFromSources,merge); + } + + }); + return pathsFromSources; +} + +/** + * Dijkstra like algorithm to get longest distance from source node for each node + * @param graph object that contains function to get children of a node, and remove an edge + * @param topologicalOrderFromSource a topological order of node from a source + * @param pathType the parent nodes include for a child node : + * LONGEST : add unique parent from one of the longest path + * ALL_LONGEST : add parents from path from the longest lenght + * ALL : add all parents + * @returns maximal distance to the source and parents nodes for each nodes + */ +function DistanceFromSourceDAG(graph:{[key:string]:Function}, topologicalOrderFromSource:string[],pathType:PathType=PathType.ALL_LONGEST):{distances:{[key:string]:number}, parents:{[key:string]:string[]}} { + + // the source is the first node in the topological order + const source=topologicalOrderFromSource[0]; + + // Initialization + const distanceFromSource:{[key:string]:number} = {}; + const parentsFromSource:{[key:string]:string[]}={}; + topologicalOrderFromSource.forEach(node=> { + distanceFromSource[node] = node === source ? 0 : Number.NEGATIVE_INFINITY; + parentsFromSource[node]=[]; + }); + + // Process node in topological order + topologicalOrderFromSource.forEach(parent=> { + // For each children + graph.adjacent(parent).sort().forEach( child => { + const childDistance= distanceFromSource[child]; + const newDistance=distanceFromSource[parent] + graph.getEdgeWeight(parent,child); + if ( newDistance > childDistance) { + distanceFromSource[child] = newDistance; + + /// If only the parents from the longest path(s) are kept: + if (pathType==PathType.LONGEST || pathType==PathType.ALL_LONGEST ){ + parentsFromSource[child]=[parent]; + } + } + // If all parent from longest path are wanted : (case of already maximum path found, so same distance) + if(pathType==PathType.ALL_LONGEST && newDistance === childDistance){ + if (!parentsFromSource[child].includes(parent)) { + parentsFromSource[child].push(parent); + } + } + if(pathType==PathType.ALL){ + if (!parentsFromSource[child].includes(parent)) { + parentsFromSource[child].push(parent); + } + } + }) + }); + + return {distances:distanceFromSource, parents:parentsFromSource}; +} + +/** + * Find the keys associated with the maximum value in the object. + * @param obj The object containing key-value pairs. + * @returns The keys associated with the maximum value (or undefined if the object is empty) and the max value. + */ +function findMaxKeys(obj: { [key: string]: number }): {key:string[]|undefined,max:number} { + let maxKeys: string[] | undefined; + let maxValue = -Infinity; + Object.entries(obj).sort(([keyA], [keyB]) => keyA.localeCompare(keyB)) + .forEach(([key, value]) => { + if (value > maxValue) { + maxValue = value; + maxKeys = [key]; + } + else if (value == maxValue){ + maxKeys.push(key); + } + }); + + return {key:maxKeys,max:maxValue}; +} + +/** + * Merge a new path in the object with all paths. If a common node is find between the new path and the other : the two paths are merged into one. + * Else the path is added as a new one. + * @param source source node use to get the longest path from a source DAG + * @param newPath path to add in the object with all paths + * @param pathsFromSources object with all paths (array of node id with an path id) + * @param [merge=true] if true, merge the path with an existing one if a common node is found + * @returns all paths including the new one + */ +function mergeNewPath(source:string,newPath:{nodes:Array<string>, height:number},pathsFromSources:{[key:string]:{nodes:Array<string>, height:number}}, merge:boolean=true):{[key:string]:{nodes:Array<string>, height:number}}{ + const keys=Object.keys(pathsFromSources).sort(); + let hasmerged=false; + if (merge) { + keys.forEach(key=>{ + const pathNodes = pathsFromSources[key].nodes; + // Check for common nodes, but target nodes + const commonNodes = pathNodes.find(node => newPath.nodes.includes(node)); + if (commonNodes) { + // Merge paths + const mergedPath = Array.from(new Set(pathNodes.concat(newPath.nodes))); + // Create new key + const newKey = `${key}__${source}`; + // Update pathsFromSources object + const newheight=newPath.height>pathsFromSources[key].height?newPath.height:pathsFromSources[key].height; + pathsFromSources[newKey] = {nodes:mergedPath,height:newheight}; + // Remove old key + delete pathsFromSources[key]; + hasmerged=true; + } + }); + } + // if no merge : added on it's own + if (!hasmerged){ + pathsFromSources[source]=newPath; + } + return pathsFromSources; +} \ No newline at end of file diff --git a/src/composables/LayoutManageSideCompounds.ts b/src/composables/LayoutManageSideCompounds.ts new file mode 100644 index 0000000..95819f7 --- /dev/null +++ b/src/composables/LayoutManageSideCompounds.ts @@ -0,0 +1,839 @@ +// Type imports +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { Node } from "@metabohub/viz-core/src/types/Node"; +import { MetaboliteType, Reaction, ReactionInterval } from "../types/Reaction"; +import { VizArgs } from "../types/EnumArgs"; +import { Coordinate } from "../types/CoordinatesSize"; +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; + +// Composable imports +import { getContentFromURL } from "./importNetwork"; +import { removeAllSelectedNodes , duplicateAllNodesByAttribut} from "@metabohub/viz-core"; +import { getMeanNodesSizePixel, inchesToPixels, minEdgeLength as minEdgeLength, pixelsToInches } from "./CalculateSize"; +import { getAttributSideCompounds, isDuplicate, isReaction, isSideCompound, setAsSideCompound } from "./GetSetAttributsNodes"; + +// General imports +import { e, S } from "vitest/dist/reporters-1evA5lom"; +import { c } from "vite/dist/node/types.d-aGj9QkWt"; +import { resolve } from "path"; +import { error } from "console"; + + + + + +/******************************************************************************************************************************************************* + * + * This file contains the functions to manage side compounds. + * + * ********************************* + * + * 0. Declare side compounds + * + * -> addSideCompoundAttributeFromList : + * add attribute of side compound to all nodes in network from a list + * + * -> getIDSideCompoundsInNetworkFromFile : + * return the list of id of side compounds in the network + * + * -> getIDSideCompoundsFromFile : + * return the list of id of side compounds from a file + * + * + ********************************** + * + * + * 1. Duplicate and remove side compounds + * + * + * -> putDuplicatedSideCompoundAside : + * duplicate and put aside side compounds in the network + * + * -> duplicateSideCompound : + * duplicate the side compounds in the given subgraph network + * + * -> sideCompoundAttributeOnDuplicate : + * adds side compound attribute to nodes in the network that are duplicates + * + * -> removeSideCompoundsFromNetwork : + * removes side compounds from the network, and put them aside in sideCompounds + * + * + * ********************************* + * + * + * 2. Reinsert side compounds + * + * -> reinsertionSideCompounds : + * reinsert side compounds in the network + * + * -> minEdgeLengthDefault : + * calculates the default minimum edge length based on the given subgraph network and a factor + * + * -> updateSideCompoundsReversibleReaction : + * updates side compounds for reversed reactions + * + * -> motifStampSideCompound : + * applies a motif stamp to place side compound for a reaction + * + * -> initializeReactionSideCompounds : + * initializes a reaction for side compounds motif + * + * -> getMetaboliteFromReaction : + * retrieves the metabolites associated with a given reaction in a subgraph network + * + * -> angleRadianSegment : + * calculates the angle in radians between two points + * + * -> addSideCompoundsIntervals : + * finds the cofactor intervals for a given reaction + * + * -> addIntervalsBetweenMetabolites : + * finds intervals between metabolites in a reaction + * + * -> addInterval : + * creates a reaction interval based on the given parameters + * + * -> biggestInterval : + * finds the biggest interval (between two metabolites) in all intervals of a reaction + * + * -> sizeInterval : + * calculates the size of an interval (between two metabolites) in a reaction + * + * -> findSpacingSideCompounds : + * finds spacing between side compounds + * + * -> giveCoordAllSideCompounds : + * calculates the coordinates for all side compounds in a subgraph network + * + * -> calculateDistance : + * calculates the distance between two points + * + * -> placeSideCompounds : + * places a type of side compounds (reactants or products) around a reaction + * + * -> determineDirection : + * determines the direction of the angle of the side compound + * + * -> giveCoordSideCompound : + * calculates the coordinates for a side compound + * + * -> insertAllSideCompoundsInNetwork : + * inserts all side compounds in the network + * + * -> insertSideCompoundInNetwork : + * inserts a side compound in the network + * + * + * + * + * *******************************************************************************************************************************************************/ + + + + + +/*******************************************************************************************************************************************************/ +//___________________________________________________0. Declare side compounds__________________________________________________________________________ + + + + +/** + * Add attribute of side compound to all nodes in network from a list + * @param network + * @param pathListSideCompounds path to the list of id of side compounds + */ +export async function addSideCompoundAttributeFromList(subgraphNetwork:SubgraphNetwork, pathListSideCompounds):Promise<void>{ + const listIDSideCompounds = await getIDSideCompoundsInNetworkFromFile(subgraphNetwork,pathListSideCompounds); + listIDSideCompounds.forEach((sideCompoundID) => { + setAsSideCompound(subgraphNetwork.network.value,sideCompoundID); + }); +} + +/** + * Return the list of id of side compounds in the network + * @param subgraphNetwork + * @param pathListSideCompounds path to the list of id of side compounds + * @returns list of id of side compounds in the network + */ +async function getIDSideCompoundsInNetworkFromFile(subgraphNetwork:SubgraphNetwork,pathListSideCompounds:string):Promise<string[]>{ + let listIDSideCompounds:string[]; + const network = subgraphNetwork.network.value; + try { + listIDSideCompounds = await getIDSideCompoundsFromFile(pathListSideCompounds); + const sideCompoundInNetwork = Object.keys(network.nodes).filter(id => listIDSideCompounds.includes(id)); + return sideCompoundInNetwork; + } catch (error) { + throw error; + } +} + +/** + * Return the list of id of side compounds from a file + * @param pathListSideCompounds path to the list of id of side compounds + * @returns list of id of side compounds + */ +async function getIDSideCompoundsFromFile(pathListSideCompounds:string):Promise<string[]>{ + try { + const sideCompoundsFile=pathListSideCompounds; + const sideCompoundsString = await getContentFromURL(sideCompoundsFile); + const lines = sideCompoundsString.split('\n'); + const listId: Array<string> = []; + lines.forEach((line: string) => { + listId.push(line.split('\t')[0]); + }) + return listId; + }catch (error) { + throw error; + } +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________1. Duplicate and remove side compounds__________________________________________________________________________ + + + +/** + * Duplicate and put aside side compounds in the network + * @param subgraphNetwork contains network with sideCompounds + * @param doDuplicateSideCompounds do duplication ? + * @param doPutAsideSideCompounds put aside ? + * @param addSideCompoundAttribute add attribut of side compound with a list? + * @param pathListSideCompounds path to the list of id of side compounds + * @returns subgraphNetwork with updated network and sideCompounds + */ +export async function putDuplicatedSideCompoundAside(subgraphNetwork:SubgraphNetwork, doDuplicateSideCompounds:boolean,doPutAsideSideCompounds:boolean, addSideCompoundAttribute:boolean=true, pathListSideCompounds:string):Promise<SubgraphNetwork>{ + try { + // finding side compounds in network + if (addSideCompoundAttribute){ + await addSideCompoundAttributeFromList(subgraphNetwork,pathListSideCompounds); + } + // duplication of side compounds + if (doDuplicateSideCompounds){ + await duplicateSideCompound(subgraphNetwork); + } + // remove side compounds from network, they are keeped aside in subgraphNetwork.sideCompounds + if (doPutAsideSideCompounds){ + return removeSideCompoundsFromNetwork(subgraphNetwork); + } + return subgraphNetwork; + } catch (error) { + throw error; + } +} + + + +/** + * Duplicates the side compounds in the given subgraph network. + * + * @param subgraphNetwork - The subgraph network containing the side compounds to be duplicated. + * @returns void + */ +export async function duplicateSideCompound(subgraphNetwork:SubgraphNetwork):Promise<void>{ + const network = subgraphNetwork.network.value; + const networkStyle = subgraphNetwork.networkStyle.value; + // duplication of side compounds + duplicateAllNodesByAttribut(network, networkStyle, getAttributSideCompounds()); + // add attributes to side compounds duplicates + sideCompoundAttributeOnDuplicate(subgraphNetwork); +} + +/** + * Adds side compound attribute to nodes in the network that are duplicates. + * + * @param subgraphNetwork - The subgraph network containing the nodes. + * @returns void + */ +function sideCompoundAttributeOnDuplicate(subgraphNetwork:SubgraphNetwork):void{ + const network = subgraphNetwork.network.value; + Object.keys(network.nodes).forEach((nodeID)=>{ + if(isDuplicate(network,nodeID)){ + setAsSideCompound(subgraphNetwork.network.value,nodeID); + } + }); +} + + + +/** + * Removes side compounds from the network, and put them aside in sideCompounds. + * + * @param subgraphNetwork - The subgraph network from which side compounds will be removed. + * @returns The updated subgraph network with side compounds removed. + */ +function removeSideCompoundsFromNetwork(subgraphNetwork:SubgraphNetwork): SubgraphNetwork{ + + const network = subgraphNetwork.network.value; + subgraphNetwork.sideCompounds={}; + const listIDCoftactors:string[]=[]; + + // for each link, see if the source or target is in the list of side compounds : add information in subgraphNetwork.sideCompounds + network.links.forEach((link) => { + // if source is side compound + if (isSideCompound(link.source)) { + if(!(link.target.id in subgraphNetwork.sideCompounds)){ + subgraphNetwork.sideCompounds[link.target.id]={reactants:[],products:[]}; + } + subgraphNetwork.sideCompounds[link.target.id].reactants.push(link.source); + listIDCoftactors.push(link.source.id); + } + // if target is side compound + if (isSideCompound(link.target)) { + if(!(link.source.id in subgraphNetwork.sideCompounds)){ + subgraphNetwork.sideCompounds[link.source.id]={reactants:[],products:[]}; + } + subgraphNetwork.sideCompounds[link.source.id].products.push(link.target); + listIDCoftactors.push(link.target.id); + } + }); + + // remove side compounds from network + removeAllSelectedNodes(listIDCoftactors,network); + + return subgraphNetwork; +} + +/*******************************************************************************************************************************************************/ +//___________________________________________________2. Reinsert side compounds__________________________________________________________________________ + + +/** + * Reinsert side compounds in the network + * @param subgraphNetwork + * @param factorMinEdgeLength factor of the minimal length of edge to calculate side compounds edge length + * @param doReactionReversible do reaction reversible ? + * @returns subgraphNetwork with updated network and sideCompounds + */ +export async function reinsertionSideCompounds(subgraphNetwork:SubgraphNetwork,factorMinEdgeLength:number=1/2,doReactionReversible:boolean):Promise<SubgraphNetwork>{ + if(subgraphNetwork.sideCompounds){ + // get information for length of edge for side compounds : + // get the min length of edge in the network (if not, use default value) + let minLength=minEdgeLength(subgraphNetwork.network.value,false); + // get the default value : min lenght if there is no link in the network (when side compounds are removed) : + if (isNaN(minLength)){ + console.warn('Minimal edge length by default'); + minLength=await minEdgeLengthDefault(subgraphNetwork,factorMinEdgeLength); + } + // add information in subgraphNetwork.stats + if (!subgraphNetwork.stats) subgraphNetwork.stats={}; + subgraphNetwork.stats.minEdgeLengthPixel=minLength; + + // update side compounds for reversed reactions + if (doReactionReversible){ + subgraphNetwork= await updateSideCompoundsReversibleReaction(subgraphNetwork); + } + + // for each reaction, apply motif stamp + Object.keys(subgraphNetwork.sideCompounds).forEach( async (reactionID)=>{ + subgraphNetwork= await motifStampSideCompound(subgraphNetwork,reactionID,factorMinEdgeLength); + }); + } + return subgraphNetwork; + +} + +/** + * Calculates the default minimum edge length based on the given subgraph network and a factor. + * + * @param subgraphNetwork - The subgraph network object. + * @param factorMinEdgeLength - The factor to multiply the calculated minimum edge length by. + * @returns The calculated minimum edge length. + */ +async function minEdgeLengthDefault(subgraphNetwork:SubgraphNetwork,factorMinEdgeLength:number):Promise<number>{ + const network = subgraphNetwork.network.value; + const networkStyle = subgraphNetwork.networkStyle.value; + const meanSize=await getMeanNodesSizePixel(Object.values(network.nodes),networkStyle, false); + const defaultSep=(meanSize.height+meanSize.width)/2; + const rankSep=subgraphNetwork.attributs[VizArgs.RANKSEP]?inchesToPixels(subgraphNetwork.attributs[VizArgs.RANKSEP] as number):defaultSep; + const nodeSep=subgraphNetwork.attributs[VizArgs.NODESEP]?inchesToPixels(subgraphNetwork.attributs[VizArgs.NODESEP] as number):defaultSep; + //const invFactor=factorMinEdgeLength===0?1:1/factorMinEdgeLength; + return (nodeSep+rankSep)/2*factorMinEdgeLength; +} + +/** + * Inverse product and reactant for reaction that are the duplicated version of the original reaction : they have been reversed. + * @param subgraphNetwork + * @returns subgraphNetwork updated + */ +async function updateSideCompoundsReversibleReaction(subgraphNetwork:SubgraphNetwork):Promise<SubgraphNetwork>{ + const network = subgraphNetwork.network.value; + Object.keys(subgraphNetwork.sideCompounds).forEach((reactionID)=>{ + if (!(reactionID in network.nodes)) throw new Error("Reaction not in subgraphNetwork") + // if reaction has been reversed : exchange products and reactants + if(network.nodes[reactionID].metadataLayout && network.nodes[reactionID].metadataLayout.isReversedVersion){ + const products=subgraphNetwork.sideCompounds[reactionID].products; + const reactants=subgraphNetwork.sideCompounds[reactionID].reactants; + subgraphNetwork.sideCompounds[reactionID].products=reactants; + subgraphNetwork.sideCompounds[reactionID].reactants=products; + } + }); + return subgraphNetwork; +} + + +/** + * Applies a motif stamp to place side compound for a reaction. + * + * @param subgraphNetwork + * @param reactionID - The ID of the reaction. + * @param factorMinEdgeLength - The factor length for the side compounds. Default value is 1/2. + * @returns The subgraphNetwork with the motif stamp applied for the reaction. + */ +async function motifStampSideCompound(subgraphNetwork:SubgraphNetwork,reactionID:string,factorMinEdgeLength:number=1/2):Promise<SubgraphNetwork>{ + //try { + // initialize reaction stamp + let reaction= await initializeReactionSideCompounds(subgraphNetwork,reactionID); + // find intervals between reactants and products + reaction = await addSideCompoundsIntervals(reaction); + // find the biggest interval + const biggest= await biggestInterval(reaction); + reaction.intervalsAvailables=[biggest.interval]; + // find spacing between side compounds + const spacing= await findSpacingSideCompounds(reaction,biggest.size); + reaction.angleSpacingReactant=spacing.reactant; + reaction.angleSpacingProduct=spacing.product; + // give coordinates to all side compounds + subgraphNetwork= await giveCoordAllSideCompounds(subgraphNetwork,reaction,factorMinEdgeLength); + // insert side compounds in network + insertAllSideCompoundsInNetwork(subgraphNetwork,reaction); + // } catch (error) { + // throw new Error("Error in motifStampSideCompound, reaction : "+ reactionID+ "\n"+error); + // } + return subgraphNetwork; +} + + +/***********************************************************************/ +//______________2.1 Stamp motif : initialization + + +/** + * Initializes a reaction for side compounds motif + * + * @param subgraphNetwork - The subgraph network containing the reaction and side compounds. + * @param idReaction - The ID of the reaction. + * @returns The initialized Reaction object with side compounds and metabolite angles. + * @throws Error if the reaction is not found in the network. + */ +async function initializeReactionSideCompounds(subgraphNetwork:SubgraphNetwork,idReaction:string):Promise<Reaction>{ + const network = subgraphNetwork.network.value; + if (network.nodes[idReaction] && subgraphNetwork.sideCompounds && subgraphNetwork.sideCompounds[idReaction]){ + try { + // position of reaction + const x=network.nodes[idReaction].x; + const y=network.nodes[idReaction].y; + // reactant side compounds + const reactantSideCompounds=subgraphNetwork.sideCompounds[idReaction].reactants.map((node)=>node.id); + // product side compounds + const productSideCompounds=subgraphNetwork.sideCompounds[idReaction].products.map((node)=>node.id); + // angle metabolites (but side compounds) associated with the reaction + const angleMetabolites:{[key:string]:{angle:number,type:MetaboliteType}}={}; + const metabolitesReaction= await getMetaboliteFromReaction(subgraphNetwork,idReaction); + metabolitesReaction.forEach((metabolite)=>{ + const xMetabolite=network.nodes[metabolite.id].x; + const yMetabolite=network.nodes[metabolite.id].y; + const angle= angleRadianSegment(x,y,xMetabolite,yMetabolite); + angleMetabolites[metabolite.id]={angle:angle,type:metabolite.type}; + }); + return { + id:idReaction, + sideCompoundsReactants:reactantSideCompounds, + sideCompoundsProducts:productSideCompounds, + metabolitesAngles:angleMetabolites, + }; + } catch (error) { + throw error; + } + }else if (!network.nodes[idReaction]){ + throw new Error("Reaction not found"); + } +} + +/** + * Retrieves the metabolites associated with a given reaction in a subgraph network. + * + * @param subgraphNetwork - The subgraph network containing the reaction and metabolites. + * @param idReaction - The ID of the reaction. + * @returns An array of objects representing the metabolites, each containing an ID and a type. + */ +async function getMetaboliteFromReaction(subgraphNetwork: SubgraphNetwork, idReaction: string): Promise<{ id: string; type: MetaboliteType }[]> { + const network = subgraphNetwork.network.value; + return network.links + .filter((link) => link.source.id === idReaction || link.target.id === idReaction) + .map((link) => ({ + id: link.source.id === idReaction ? link.target.id : link.source.id, + type: link.source.id === idReaction ? MetaboliteType.PRODUCT : MetaboliteType.REACTANT, + })); +} + +/** + * Calculates the angle in radians between two points. + * + * @param x1 The x-coordinate of the first point. + * @param y1 The y-coordinate of the first point. + * @param x2 The x-coordinate of the second point. + * @param y2 The y-coordinate of the second point. + * @param clockwise Determines whether the angle should be calculated in the clockwise direction. Default is true. + * @returns The angle in radians between the two points. + */ +function angleRadianSegment(x1:number,y1:number,x2:number,y2:number,clockwise:boolean=true):number{ + if (!isFinite(x1) || !isFinite(y1) || !isFinite(x2) || !isFinite(y2)) { + //console.error("Invalid coordinates for angle : one or more coordinates are not finite numbers."); + throw new Error("Invalid coordinates for angle : one or more coordinates are not finite numbers."); + } + + const angle = Math.atan2(y2 - y1, x2 - x1); + if (isNaN(angle)) { + console.error("Calculation angle resulted in NaN."); + return NaN; + } + + // angle in the anti-clockwise direction from the positive x-axis to the line segment from (x1,y1) to (x2,y2) : + if (!clockwise) { + return 2 * Math.PI - (angle + 2 * Math.PI) % (2 * Math.PI); + } + // angle in the clockwise direction from the positive x-axis to the line segment from (x1,y1) to (x2,y2) : + else { + return (angle + 2 * Math.PI) % (2 * Math.PI); + } +} + +/***********************************************************************/ +//______________2.2 Stamp motif : find intervals + + + +/** + * Finds the cofactor intervals for a given reaction. If possible, the intervals are found between reactants and products. + * + * @param reaction - The reaction object. + * @returns An array of ReactionInterval objects representing the cofactor intervals. + */ +async function addSideCompoundsIntervals(reaction: Reaction):Promise<Reaction> { + + try { + // Sort metabolites by angle + const sortedMetabolites = Object.entries(reaction.metabolitesAngles) + .map(([id, {angle, type}]) => ({id, angle, type})) + .sort((a, b) => { + if (isNaN(a.angle)) return 1; // Place `a` after `b` if `a.angle` is `NaN` + if (isNaN(b.angle)) return -1; // Place `b` after `a` if `b.angle` is `NaN` + return a.angle - b.angle; // Normal comparison if both angles are numbers + }); + + // Initialisation + if (!sortedMetabolites || sortedMetabolites.length === 0) { + throw new Error("No sorted metabolite for side compounds insertion"); + } + + const lastIndex = sortedMetabolites.length - 1; + let previousType = sortedMetabolites[lastIndex]?.type; + let previousId = sortedMetabolites[lastIndex]?.id; + + // Process sorted metabolites to find intervals between reactants and products + reaction = await addIntervalsBetweenMetabolites(reaction,sortedMetabolites, previousId, previousType,true); + + // If no interval between reactants and products + if (!reaction.intervalsAvailables || reaction.intervalsAvailables.length === 0) { + reaction = await addIntervalsBetweenMetabolites(reaction,sortedMetabolites, previousId, previousType,false); + } + + // If still no intervals, add a default interval + if (!reaction.intervalsAvailables || reaction.intervalsAvailables.length === 0) { + reaction.intervalsAvailables =[{ + typeInterval: 0, + reactant: null, + product: null, + }]; + } + + return reaction; + } catch(error){ + throw error; + } +} + + +/** + * Finds intervals between metabolites in a reaction. + * + * @param reaction - The reaction to add intervals to. + * @param sortedMetabolites - An array of sorted metabolites. + * @param firstPreviousID - The ID of the first previous metabolite. + * @param firstPreviousType - The type of the first previous metabolite. + * @param checkChangeType - Optional. Specifies whether to ask for a change in metabolite type to be considered as an interval. Defaults to true. + * @returns The reaction with added intervals. + */ +async function addIntervalsBetweenMetabolites(reaction:Reaction,sortedMetabolites: {id: string, angle: number, type: MetaboliteType}[], firstPreviousID: string, firstPreviousType: MetaboliteType, checkChangeType: boolean = true):Promise<Reaction> { + let firstInterval = false; + sortedMetabolites.forEach((currentMetabolite, i) => { + if ( !checkChangeType || (currentMetabolite.type !== firstPreviousType)) { + firstInterval = (i === 0); + reaction = addInterval(reaction, firstPreviousID, firstPreviousType, currentMetabolite.id, firstInterval); + } + firstPreviousType = currentMetabolite.type; + firstPreviousID = currentMetabolite.id; + }); + return reaction; +} + +/** + * Creates a reaction interval based on the given parameters. + * Type of interval is 1 if reactant then product, 0 if product then reactant, + * or special case if the x-axis is between the two metabolites : 3 if reactant is the smaller angle, 2 if product is the smaller angle. + * + * @param reaction - The reaction object. + * @param id1 - The first metabolite ID. + * @param type1 - The type of the first metabolite. + * @param id2 - The second metabolite ID. + * @param firstInterval - Optional. Indicates if it's the first interval. Defaults to false. + * @returns The created reaction interval. + */ +function addInterval(reaction:Reaction,id1:string,type1:MetaboliteType,id2:string,firstInterval:boolean=false):Reaction{ + let typeInterval:number; + const angles=reaction.metabolitesAngles; + const reactant= type1 === MetaboliteType.REACTANT ? id1 : id2; + const product= type1 === MetaboliteType.REACTANT ? id2 : id1; + + if (angles[reactant].angle<angles[product].angle){ + // 1 if not special case , else 3 + typeInterval=1+2*Number(firstInterval); + }else{ + // 0 if not special case , else 2 + typeInterval=0+2*Number(firstInterval); + } + + // add interval in reaction + if(!reaction.intervalsAvailables) reaction.intervalsAvailables=[]; + reaction.intervalsAvailables.push({typeInterval: typeInterval, reactant: reactant, product: product}); + return reaction; +} + +/** + * Find the biggest interval (between two metabolites) in all intervals of a reaction. + * @param reaction + * @returns the biggest interval and its size + */ +async function biggestInterval(reaction: Reaction): Promise<{interval:ReactionInterval,size:number}> { + try { + const intervals = reaction.intervalsAvailables; + if (intervals.length === 0) { + throw new Error("Empty intervals"); + }else if (intervals.length === 1) { + return {interval:intervals[0],size:sizeInterval(reaction,0)}; + } + // size of intervals + const sizes = intervals.map((_, index) => sizeInterval(reaction, index)); + // find biggest size + const maxValue = Math.max(...sizes); + // Return interval associated + const maxIndex = sizes.indexOf(maxValue); + if(maxIndex===-1) throw new Error("No interval of max size found"); + return {interval:intervals[maxIndex],size:maxValue}; + }catch(error){ + throw error; + } +} + + +/** + * Calculates the size of an interval (between two metabolites) in a reaction, depending on the type of interval. + * Type of interval is 1 if reactant then product, 0 if product then reactant, + * or special case if the x-axis is between the two metabolites : 3 if reactant is the smaller angle, 2 if product is the smaller angle. + * + * @param reaction - The reaction object. + * @param intervalIndex - The index of the interval to process, in all the intervals of the reaction . + * @returns The size of the interval in radians. + * @throws {Error} If the angles or interval are undefined. + */ +function sizeInterval(reaction:Reaction,intervalIndex:number):number{ + const angles=reaction.metabolitesAngles; + if (angles===undefined) throw new Error("No angles"); + const interval=reaction.intervalsAvailables[intervalIndex]; + if (interval===undefined) throw new Error("No interval"); + // if reactant or product null : return 2*PI + if (!interval.reactant || !interval.product) return Math.PI*2; + if (interval.typeInterval===0 || interval.typeInterval===1){ + // |angle1-angle2| + return Math.abs(angles[interval.product].angle-angles[interval.reactant].angle); + }else{ + // special case where we want the complementary angle + return 2*Math.PI-Math.abs(angles[interval.product].angle-angles[interval.reactant].angle); + } +} + +/***********************************************************************/ +//______________2.3 Stamp motif : find spacing + + +async function findSpacingSideCompounds(reaction:Reaction,sizeInterval:number):Promise<{reactant:number,product:number}>{ + const reactantNumber=reaction.sideCompoundsReactants.length; + const productNumber=reaction.sideCompoundsProducts.length; + return { + reactant: reactantNumber === 0 ? undefined : sizeInterval / (2 * (reactantNumber+1)), + product: productNumber === 0 ? undefined : sizeInterval / (2 * (productNumber+1)) + }; +} + +/***********************************************************************/ +//______________2.4 Stamp motif : give coordinates + + +/** + * Calculates the coordinates for all side compounds in a subgraph network. + * + * @param subgraphNetwork - The subgraph network containing the side compounds. + * @param reaction - The reaction for which the side compounds are being calculated. + * @param factorLength - The factor length used for edge length of side compounds. Default value is 1/2. + * @returns The updated subgraph network with the calculated coordinates for the side compounds. + */ +async function giveCoordAllSideCompounds(subgraphNetwork:SubgraphNetwork,reaction:Reaction,factorLength:number=1/2):Promise<SubgraphNetwork>{ + const distance=calculateDistance(subgraphNetwork, factorLength); + const sideCompounds=subgraphNetwork.sideCompounds[reaction.id]; + const reactionCoord=subgraphNetwork.network.value.nodes[reaction.id]; + // Reactants Placement + if (sideCompounds.reactants && sideCompounds.reactants.length>0){ + await placeSideCompounds(sideCompounds.reactants, reaction, reactionCoord, distance, true); + } + // Products Placement + if (sideCompounds.products && sideCompounds.products.length>0){ + await placeSideCompounds(sideCompounds.products, reaction, reactionCoord, distance, false); + } + + return subgraphNetwork; +} + +/** + * Calculates the distance based on the given subgraph network and factor length. + * If the minimum edge length of the graph is available in the statistics, + * it uses that value : minimum edge length * factor . Otherwise, it uses a default value of 1 inch * factor. + * + * @param subgraphNetwork - The subgraph network to calculate the distance for. + * @param factorLength - The factor length to multiply the base length by. + * @returns The calculated distance. + */ +function calculateDistance(subgraphNetwork: SubgraphNetwork, factorLength: number): number { + let baseLengthPixel: number; + if (subgraphNetwork.stats.minEdgeLengthPixel) { + baseLengthPixel = subgraphNetwork.stats.minEdgeLengthPixel; + } else { + console.error("stats minEdgeLengthPixel not found, use default value 1 inch"); + baseLengthPixel = pixelsToInches(1); + } + return baseLengthPixel * factorLength; +} + + +/** + * Places a type of side compounds (reactants or products) around a reaction. + * + * @param sideCompounds - An array of side compounds (node) to be placed. + * @param reaction - The reaction object. + * @param reactionCoord - The coordinates of the reaction. + * @param distance - The distance from the reaction to place the side compounds. + * @param placeReactants - A boolean indicating whether to place reactants or products. + */ +async function placeSideCompounds(sideCompounds: Array<Node>, reaction: Reaction, reactionCoord: Coordinate, distance: number, placeReactants: boolean): Promise<void> { + const startSideCompound = placeReactants ? reaction.intervalsAvailables[0].reactant : reaction.intervalsAvailables[0].product; + if (!startSideCompound) { + console.error("No start side compound found"); + return; + } + let startAngle = startSideCompound ? reaction.metabolitesAngles[startSideCompound].angle : 0; + const angleSpacing = placeReactants ? reaction.angleSpacingReactant : reaction.angleSpacingProduct; + if (!isFinite(angleSpacing)) { + console.error("No angle spacing found"); + return; + } + + sideCompounds.forEach((sideCompoundNode, i) => { + const direction = determineDirection(reaction.intervalsAvailables[0].typeInterval, placeReactants); + const angle = startAngle + direction * (i + 1) * angleSpacing; + sideCompoundNode = giveCoordSideCompound(sideCompoundNode, angle, reactionCoord, distance); + }); +} + +/** + * Determines the direction based on the type interval and whether to place reactants. + * Type of interval is 1 if reactant then product, 0 if product then reactant, + * or special case if the x-axis is between the two metabolites : 3 if reactant is the smaller angle, 2 if product is the smaller angle. + * + * @param typeInterval - The type interval value. + * @param placeReactants - A boolean indicating whether to place reactants. + * @returns The direction value (-1 or 1). + */ +function determineDirection(typeInterval: number, placeReactants: boolean): number { + if (placeReactants) { + return (typeInterval === 0 || typeInterval === 3) ? -1 : 1; + } else { + return (typeInterval === 0 || typeInterval === 3) ? 1 : -1; + } +} + +/** + * Calculates the coordinates of a side compound from a reaction based on the given parameters. + * A reaction node is considered the center of the circle where the side compound is added. + * + * @param sideCompound - The side compound node. + * @param angle - The angle in radians to place side compound in the circle. + * @param center - The center of the circle (coordinates of reaction). + * @param distance - The distance from the center. + * @returns The side compound node with updated coordinates. + */ +function giveCoordSideCompound(sideCompound:Node,angle:number,center:{x:number,y:number},distance:number):Node{ + sideCompound.x = center.x + distance * Math.cos(angle); + sideCompound.y = center.y + distance * Math.sin(angle); + return sideCompound; +} + + +/***********************************************************************/ +//______________2.4 Stamp motif : insertion in network + + +/** + * Inserts all side compounds of a reaction into the network. + * + * @param subgraphNetwork - The subgraph network to insert the side compounds into. + * @param reaction - The reaction containing the side compounds. + * @returns void + */ +function insertAllSideCompoundsInNetwork(subgraphNetwork:SubgraphNetwork,reaction:Reaction):void{ + const sideCompounds=subgraphNetwork.sideCompounds[reaction.id]; + // Reactants + Object.keys(reaction.sideCompoundsReactants).forEach((reactant)=>{ + insertSideCompoundInNetwork(subgraphNetwork,reaction.id,sideCompounds.reactants[reactant],MetaboliteType.REACTANT); + }); + // Products + Object.keys(reaction.sideCompoundsProducts).forEach((product)=>{ + insertSideCompoundInNetwork(subgraphNetwork,reaction.id,sideCompounds.products[product],MetaboliteType.PRODUCT); + }); +} + +/** + * Inserts a side compound into the network. + * + * @param subgraphNetwork - The subgraph network to insert the side compound into. + * @param reactionID - The ID of the reaction. + * @param sideCompound - Node : The side compound to insert. + * @param typeSideCompound - The type of the side compound (reactant or product). + */ +function insertSideCompoundInNetwork(subgraphNetwork:SubgraphNetwork,reactionID:string,sideCompound:Node,typeSideCompound:MetaboliteType):void{ + const network = subgraphNetwork.network.value; + // insert node + network.nodes[sideCompound.id]=sideCompound; + // insert link + if (typeSideCompound===MetaboliteType.REACTANT){ + const idLink=sideCompound.id+"--"+reactionID; + network.links.push({id:idLink,source:network.nodes[sideCompound.id],target:network.nodes[reactionID]}); + }else{ + const idLink=reactionID+"--"+sideCompound.id; + network.links.push({id:idLink,source:network.nodes[reactionID],target:network.nodes[sideCompound.id]}); + } +} + + diff --git a/src/composables/LayoutReversibleReactions.ts b/src/composables/LayoutReversibleReactions.ts new file mode 100644 index 0000000..d2faf2c --- /dev/null +++ b/src/composables/LayoutReversibleReactions.ts @@ -0,0 +1,458 @@ +// Type imports +import { Link } from "@metabohub/viz-core/src/types/Link"; +import { Node } from "@metabohub/viz-core/src/types/Node"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { TypeSubgraph } from "../types/Subgraph"; +import { StartNodesType } from "../types/EnumArgs"; +import { NetworkLayout, NodeLayout } from "../types/NetworkLayout"; + +// Composable imports +import { removeAllSelectedNodes } from "@metabohub/viz-core"; +import { BFSWithSources } from "./AlgorithmBFS"; +import { addLinkClassReversible, addMetadataReversibleWithClass, isReaction, isReversible } from "./GetSetAttributsNodes"; + +// General imports +import { e } from "vitest/dist/reporters-1evA5lom"; +import { l } from "vite/dist/node/types.d-aGj9QkWt"; + + + +/** + * This file contains the functions to duplicate reversible reactions in a network and choose one of the duplicated reactions to keep. + * + * ********************************* + * + * 0. Duplicate reaction + * + * -> duplicateReversibleReactions : + * Take a network and add a duplicated node of reversible reactions, and add links to this reaction + * + * -> linkIsReversible : + * Determines if a link is reversible in a network by checking if the source or target is a reversible reaction. + * + * -> duplicateNodeReactionReversible : + * Duplicates a node reaction and makes it reversible. + * + * -> reversibleNodeReaction : + * Reverses the given node layout by appending a suffix to its ID and updating its metadataLayout. + * + * -> reversibleLink : + * Links two nodes in a network with a reversible link. + * + * + * ********************************* + * + * 1. Choose reaction + * + * -> chooseReversibleReaction : + * Take a network with duplicated nodes (a node is duplicated if the id of the duplicated version is in metadata.reversibleVersion of a node), + * + * -> keepFirstReversibleNode : + * Keeps the first reversible node in the given node order, removing all others and their corresponding reversible versions from the network. + * + * -> renameAllIDNode : + * Renames the nodes and edges in a subgraph network based on the provided mapping. + * + * -> renameInSubgraph : + * Renames all nodes in a subgraph based on a given mapping. + * + * + */ + + + +/*******************************************************************************************************************************************************/ +//___________________________________________________0. Duplicate reaction __________________________________________________________________________ + + + + +/** + * Take a network and add a duplicated node of reversible reactions, and add links to this reaction + * @param {Network} Network object + * @param suffix to put at the end of id of the original reaction : can't be "" ! + */ +export async function duplicateReversibleReactions(networkLayout:NetworkLayout):Promise<void> { + + try { + // add metadata "reversible" to nodes + console.warn("add metadata reversible if in the class. Not necessary if file with correct format (done bcs of the file I have) => to remove ?"); + await addMetadataReversibleWithClass(networkLayout); + + const newLinks: Array<Link> = []; //links associated with new reactions nodes + + console.warn("metadata en double pr old et new attr") + + await Promise.all(networkLayout.links.map(async (link) => { + // If the link is reversible: get the reaction node and duplicate it + const linkReversible = linkIsReversible(networkLayout, link); + + if (linkReversible.isReversible) { + // Duplication of the reaction node + let nodeToDuplicate: NodeLayout; + const reactionIsSource: boolean = linkReversible.sourceIsReversible; + + if (reactionIsSource) { + nodeToDuplicate = link.source; + } else { + nodeToDuplicate = link.target; + } + + await duplicateNodeReactionReversible(networkLayout, nodeToDuplicate).then((newReactionNode) => { + // Add the new reaction node if it is not already present + + if (newReactionNode && !networkLayout.nodes[newReactionNode.id]) { + networkLayout.nodes[newReactionNode.id] = newReactionNode; + } + // Adding the link to the new reaction node in the opposite direction (the target becomes the source and the source becomes the target) + if (reactionIsSource) { + const target = link.target; + newLinks.push(reversibleLink(networkLayout, link, newReactionNode.id, target.id)); + } else { + const source = link.source; + newLinks.push(reversibleLink(networkLayout, link, source.id, newReactionNode.id)); + } + }); + } + })); + + newLinks.forEach((link) => { + networkLayout.links.push(link); + }); + + } catch (error) { + throw error; + } +} + +/** + * Determines if a link is reversible in a network by checking if the source or target is a reversible reaction. + * + * @param network - The network object. + * @param link - The link object. + * @returns An object containing the reversibility information: + * - `isReversible` - A boolean indicating if the link is reversible. + * - `sourceIsReversible` - A boolean indicating if it's the source of the link that is reversible. + */ +function linkIsReversible(network:Network,link: Link): {isReversible:boolean,sourceIsReversible:boolean}{ + if (isReaction(link.source) && isReversible(network,link.source.id)){ + return {isReversible:true,sourceIsReversible:true}; + } else if (isReaction(link.target) && isReversible(network,link.target.id)){ + return {isReversible:true,sourceIsReversible:false}; + } else{ + return {isReversible:false,sourceIsReversible:undefined}; + } +} + +/** + * Duplicates a node reaction and makes it reversible. + * + * @param networkLayout - The network layout. + * @param nodeReaction - The node reaction to duplicate. + * @returns The duplicated node reaction with reversible metadata. + */ +async function duplicateNodeReactionReversible(networkLayout: NetworkLayout, nodeReaction: Node): Promise<Node> { + return new Promise(async (resolve, reject) => { + try { + // Duplicate target node + const newReactionNode = await reversibleNodeReaction(nodeReaction); + const newId = newReactionNode.id; + + // Add attribute reversible to original reaction + if (!networkLayout.nodes[nodeReaction.id]) { + throw new Error("Node not found to set as reversible"); + } + + if (!networkLayout.nodes[nodeReaction.id].metadataLayout) { + networkLayout.nodes[nodeReaction.id].metadataLayout = {}; + } + networkLayout.nodes[nodeReaction.id].metadataLayout.reversibleNodeVersion = newId; + + resolve(newReactionNode); + } catch (error) { + reject(error); + } + }); +} + + +/** + * Reverses the given node layout by appending a suffix to its ID and updating its metadataLayout. + * + * @param node - The original node layout to be reversed. + * @param suffix - The suffix to be appended to the ID of the reversed node. Default value is "_rev". + * @returns The reversed node layout. + */ +async function reversibleNodeReaction(node: NodeLayout, suffix: string = "_rev"): Promise<Node> { + const id = node.id; + const newId = id.endsWith(suffix) ? id.slice(0, -suffix.length) : id + suffix; + let newNodeReversed:boolean; + // if original node is a reversed version : + if (node.metadataLayout && node.metadataLayout.isReversedVersion){ + newNodeReversed=false; // the new node is the original one + }else{ + newNodeReversed=true; + } + + //const newLabel = label.endsWith(suffix) ? label.slice(0, -suffix.length) : label + suffix; + + //const newClasses: string[] = []; + // add classes of original reaction, + // and add class reversibleVersion if not present, removed if present + // classes.forEach(item =>{ + // newClasses.push(item) + // }); + // const revIndex = newClasses.indexOf("reversibleVersion"); + // if (revIndex !== -1) { + // newClasses.splice(revIndex, 1); + // }else{ + // newClasses.push("reversibleVersion"); + // } + + const newNode: NodeLayout = { + ...node, + id: newId, + //metadata: {...node.metadata, reversibleVersion: id}, // to remove : doest work + metadataLayout: {reversibleNodeVersion:id,isReversedVersion:newNodeReversed}, + }; + return newNode; +} + +/** + * Links two nodes in a network with a reversible link. + * + * @param network - The network object. + * @param link - The link to be made reversible. + * @param sourceID - The ID of the source node. + * @param targetID - The ID of the target node. + * @returns The new reversible link. + * @throws Error if either the source node or the target node is not found in the network. + */ +function reversibleLink(network:Network,link:Link,sourceID:string,targetID:string):Link{ + if (!network.nodes[sourceID] || !network.nodes[targetID]){ + throw new Error("Node not found to set as reversible "); + } + let newLink:Link={ + ...link, + id: `${targetID}--${sourceID}`, + source: network.nodes[targetID], + target: network.nodes[sourceID], + } + newLink= addLinkClassReversible(newLink); + return newLink; +} + + +/*******************************************************************************************************************************************************/ +//___________________________________________________1. Choose reaction __________________________________________________________________________ + + + + +/** + * Take a network with duplicated nodes (a node is duplicated if the id of the duplicated version is in metadata.reversibleVersion of a node), + * and remove one of the duplication. A method in argument (nodeOrderFunction) is used for the choice, the source nodes for the method are in parameter of the function. The node that is keeped + * is the first in the returned array. + * BEWARE : the method with not all sources might miss some duplicated nodes + * @param subgraphNetwork + * @param sources sources nodes (id) to use, if type source : + * RANK_ONLY : sources are nodes of rank 0 + * SOURCE_ONLY : sources are topological sources of the network (nul indegree) + * RANK_SOURCE : sources are node of rank 0, then source nodes + * ALL : sources are all nodes + * SOURCE_ALL : sources are topological sources, then all the others nodes + * RANK_SOURCE_ALL : sources are node of rank 0, then topological sources, then all the other nodes + * For this method, a source type with "all" is advised, to not miss any duplicated reaction. + * @param nodeOrderFunction the method that return an array of nodes order (a same node can be present several time!), with sources as input + */ +export async function chooseReversibleReaction( + subgraphNetwork:SubgraphNetwork, + sources: Array<string> | StartNodesType, + nodeOrderFunction: (network: Network, sources: Array<string> | StartNodesType) => Promise<string[]> = BFSWithSources +): Promise<SubgraphNetwork> { + let nodeOrder: string[] = []; + const network = subgraphNetwork.network.value; + // get node order + nodeOrder = await nodeOrderFunction(network,sources); + // keep the first node seen only, for duplicated nodes + subgraphNetwork=keepFirstReversibleNode(subgraphNetwork, nodeOrder) as SubgraphNetwork; + + return subgraphNetwork; +} + + +/** + * Keeps the first reversible node in the given node order, removing all others and their corresponding reversible versions from the network. + * @param subgraphNetwork + * @param nodeOrder The order of nodes to consider for keeping the first reversible node. + */ +export function keepFirstReversibleNode(subgraphNetwork:SubgraphNetwork,nodeOrder:string[],doRename:boolean=true):SubgraphNetwork |{[key: string]: string}{ + const network = subgraphNetwork.network.value; + const reactionToRemove:Array<string>=[]; + const nodeToRename:{[key: string]: string}={}; + + for(let i=0;i<nodeOrder.length;i++){ + const nodeID=nodeOrder[i]; + // if there is a reversible version of the current node: + if(network.nodes[nodeID].metadataLayout && network.nodes[nodeID].metadataLayout.reversibleNodeVersion){ + const reversibleNodeID=network.nodes[nodeID].metadataLayout.reversibleNodeVersion; + if (!(reversibleNodeID in network.nodes)) throw new Error("Error : the reversible version of the node "+nodeID+" is not found in the network."); + + // add the reversible reaction to the list of nodes to remove + reactionToRemove.push(reversibleNodeID); + + // Put on list renaming of id if necessary : + if(network.nodes[nodeID].metadataLayout.isReversedVersion){ + // the duplicated version is the one keeped, its id have to be renamed by the original id + nodeToRename[nodeID]=reversibleNodeID; + }else if (!network.nodes[reversibleNodeID].metadataLayout.isReversedVersion){ + throw new Error("One duplication of node lack attribut isReversedVersion"); + } + + // remove metadata information about reversible node for current node and its reversible version + delete network.nodes[nodeID].metadataLayout.reversibleNodeVersion; + if(network.nodes[reversibleNodeID].metadataLayout && network.nodes[reversibleNodeID].metadataLayout.reversibleNodeVersion){ + delete network.nodes[reversibleNodeID].metadataLayout.reversibleNodeVersion; + } + } + } + // remove one version of the reaction + removeAllSelectedNodes(reactionToRemove,network); + // rename the other if it was the reversible version that is keeped + console.warn("need to check if subgraph still exist ?") + if(doRename){ + const subgraphNetworkRename=renameAllIDNode(subgraphNetwork,nodeToRename); + return subgraphNetworkRename// return object renamed + } + return nodeToRename; // if doRename is false, return the list of node to rename to do it later +} + +/** + * Renames the nodes and edges in a subgraph network based on the provided mapping. + * + * @param subgraphNetwork - The subgraph network to modify. + * @param nodesToRename - An object containing the mapping of old node IDs to new node IDs. + * @returns The modified subgraph network. + */ +export function renameAllIDNode(subgraphNetwork:SubgraphNetwork,nodesToRename:{[key: string]: string}):SubgraphNetwork{ + const network = subgraphNetwork.network.value; + + // Modify nodes + Object.keys(network.nodes).forEach(ID => { + if (nodesToRename[ID]) { + // then change the name of the node : + const oldName=ID; + const newName=nodesToRename[ID]; + // insert new node with new name + network.nodes[newName]=network.nodes[oldName]; + network.nodes[newName].id=newName; + // delete old node + delete network.nodes[oldName]; + } + }); + + // Modify edges + network.links.forEach(link => { + if (nodesToRename[link.source.id]) { + link.source = network.nodes[nodesToRename[link.source.id]]; + } + if (nodesToRename[link.target.id]) { + link.target = network.nodes[nodesToRename[link.target.id]]; + } + }); + + // Modify subgraphs + // in cycles + renameAllInSubgraph(subgraphNetwork,TypeSubgraph.CYCLE,nodesToRename); + // in main chains + renameAllInSubgraph(subgraphNetwork,TypeSubgraph.MAIN_CHAIN,nodesToRename); + // in secondary chains + renameAllInSubgraph(subgraphNetwork,TypeSubgraph.SECONDARY_CHAIN,nodesToRename); + + return subgraphNetwork; +} + + + +/** + * Renames all nodes in a subgraph based on a given mapping. + * + * @param subgraphNetwork - The subgraph network object. + * @param typeSubgraph - The type of subgraph. + * @param nodesToRename - The mapping of nodes to their new names. + */ +function renameAllInSubgraph(subgraphNetwork:SubgraphNetwork, typeSubgraph:TypeSubgraph, nodesToRename:{[key: string]: string}){ + const subgraphs = subgraphNetwork[typeSubgraph] ? subgraphNetwork[typeSubgraph] : {}; + Object.entries(subgraphs).forEach(([ID, subgraph]) => { + subgraph.nodes = subgraph.nodes.map(node => { + if(nodesToRename[node]){ + // change metadata of node to know in which subgraph it is + //console.warn("pk fonction ici ?"); + //updateNodeMetadataSubgraph(subgraphNetwork.network.value, nodesToRename[node], ID, typeSubgraph); + // change the name of the node in the subgraph + return nodesToRename[node]; + } + return node; + }); + }); +} + + + + +// export function renameIDNode(subgraphNetwork:SubgraphNetwork,oldName:string,newName:string):SubgraphNetwork{ +// const network = subgraphNetwork.network.value; +// if(oldName in network.nodes && !(newName in network.nodes)){ + +// // modify node : +// // insert new node with new name +// network.nodes[newName]=network.nodes[oldName]; +// const newNode=network.nodes[newName]; +// newNode.id=newName; +// // delete old node +// delete network.nodes[oldName]; + +// // modify edges : +// // when the node is source +// const linksOldNodeAsSource = Object.values(network.links).filter((link) => { +// return link.source.id === oldName; +// }); +// linksOldNodeAsSource.forEach((link) => { +// link.source = newNode; +// }); +// // when the node is target +// const linksOldNodeAsTarget = Object.values(network.links).filter((link) => { +// return link.target.id === oldName; +// }); +// linksOldNodeAsTarget.forEach((link) => { +// link.target = newNode; +// }); + +// // modify subgraphs : +// // in cycles +// renameInSubgraph(subgraphNetwork,TypeSubgraph.CYCLE,oldName,newName); +// // in main chains +// renameInSubgraph(subgraphNetwork,TypeSubgraph.MAIN_CHAIN,oldName,newName); +// // in secondary chains +// renameInSubgraph(subgraphNetwork,TypeSubgraph.SECONDARY_CHAIN,oldName,newName); + +// return subgraphNetwork; + +// }else{ +// console.log("Error : impossible to rename node "+oldName+" to "+newName+", node already exist or not found in network."); +// } +// } + +// function renameInSubgraph(subgraphNetwork:SubgraphNetwork,typeSubgraph:TypeSubgraph,oldName:string,newName:string){ +// const subgraphs = subgraphNetwork[typeSubgraph]? subgraphNetwork[typeSubgraph]:{}; +// Object.entries(subgraphs).forEach(([ID,subgraph])=>{ +// if(subgraph.nodes.includes(oldName)){ +// // change the name of the node in the subgraph +// subgraph.nodes = subgraph.nodes.map(node => node === oldName ? newName : node); +// // change metadata of node to know in which subgraph it is +// updateNodeMetadataSubgraph(subgraphNetwork.network.value, newName, ID,typeSubgraph); //newName because the node has been renamed +// } +// }); +// } + diff --git a/src/composables/LayoutSugiyamaForce.ts b/src/composables/LayoutSugiyamaForce.ts new file mode 100644 index 0000000..99147e7 --- /dev/null +++ b/src/composables/LayoutSugiyamaForce.ts @@ -0,0 +1,225 @@ +// Type imports +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; +import { JsonViz } from "../types/FormatJsonViz"; +import { Subgraph } from "../types/Subgraph"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Network } from "@metabohub/viz-core/src/types/Network"; + +// Composable imports +import { getMeanNodesSizePixel } from "./CalculateSize"; +import { getSepAttributesInches, shiftAllToGetTopLeftCoord } from "./CalculateSize"; +import { networkToCytoscape, networkToDagre, graphVizToDot, networkToViz, networkToDOT } from './ConvertFromNetwork'; +import { changeNetworkFromCytoscape, changeNetworkFromDagre, changeNetworkFromViz } from './ConvertToNetwork'; + +// General imports +import * as d3 from 'd3'; +import { reactive } from "vue"; +import cytoscape from 'cytoscape'; +import fcose from 'cytoscape-fcose'; +import cosebilkent from 'cytoscape-cose-bilkent'; +import dagre from 'dagrejs'; +import { Graph, instance } from "@viz-js/viz"; + + +/** + * This file contains functions to apply layout algorithms to a network. + * + * -> dagreLayout : + * Take a network object and change the (x,y) position of the node with dagre lib + * + * -> vizLayout : + * Take a network object and change the (x,y) position of the node with viz lib + * + * -> forceLayout : + * Applies the force-directed layout algorithm to the given network. + */ + + + + +/** + * Take a network object and change the (x,y) position of the node with dagre lib + * @param {Network} Network object + * @param graphAttributes for dagre layout (see https://github.com/dagrejs/dagre/wiki) + * @param [callbackFunction=() => {}] function to do after the layout is done + */ +export function dagreLayout(network: Network,graphAttributes={},callbackFunction = () => {}):void { + + setTimeout(async function() { + let graphDagre = networkToDagre(network,graphAttributes); + dagre.layout(graphDagre); + changeNetworkFromDagre(graphDagre, network).then(() => { + callbackFunction(); + }); + }, 1); + +} + + +/** + * Take a network object and change the (x,y) position of the node with viz lib + * @param {Network} Network object + * @param mainChains clusters for viz (type version for quick search) + * @param graphAttributes for viz dot layout (see https://graphviz.org/docs/layouts/dot/) + * @param assignRank indicates if rank and order need to be infered after layout is applied + * @param [callbackFunction=() => {}] function to do after the layout is done + */ +export async function vizLayout(subgraphNetwork:SubgraphNetwork,assignRank:boolean=false, cycle:boolean=true,addNodes:boolean=true, + groupOrCluster:"group"|"cluster"="cluster",orderChange:boolean=false,printDot:boolean=false,dpi:number=72,factorLenghtEdge:number=3,callbackFunction = () => {}): Promise<SubgraphNetwork> { + + await instance().then( async viz => { + // attributes for viz + const sep =await getSepAttributesInches(subgraphNetwork.network.value,subgraphNetwork.networkStyle.value,factorLenghtEdge); + console.log('sep',sep); + subgraphNetwork.attributs={rankdir: "BT" , newrank:true, compound:true,splines:false,ranksep:sep.rankSep,nodesep:sep.nodeSep,dpi:dpi}; + const dot=networkToDOT(subgraphNetwork,cycle,addNodes,groupOrCluster,orderChange); + if(printDot) console.log(dot); + const json=viz.renderJSON(dot) as JsonViz; + subgraphNetwork= await changeNetworkFromViz(json,subgraphNetwork,assignRank); + callbackFunction(); + }); + return subgraphNetwork; +} + + + +/** + * Applies the force-directed layout algorithm to the given network. + * Use cytoscapes' cose-bilkent layout. + * + * @param network - The network to apply the layout to. + * @param networkStyle - The style properties of the network. + * @param shiftCoord - Optional. Specifies whether to shift the coordinates of the nodes to the top-left corner. Defaults to false. + * @returns A Promise that resolves to the updated network after applying the layout. + */ +export async function forceLayout(network: Network, networkStyle:GraphStyleProperties, shiftCoord: boolean = false): Promise<Network> { + + //cytoscape.use(fcose); + cytoscape.use(cosebilkent); + + const size=await getMeanNodesSizePixel(Object.values(network.nodes), networkStyle,false); + const edgeFactor=3; + const edgeLength = Math.max(size.height, size.width) * edgeFactor; + + const layout ={ + name:"cose-bilkent", //fcose + animate: false, + randomize: false, + idealEdgeLength: edgeLength, + nodeRepulsion: 70000, // high number if randomize = false + gravity : 0.001, + numIter: 3000 + + } + + let cyto = networkToCytoscape(network,true); + + await new Promise<void>((resolve) => { + cyto.ready(function () { + setTimeout(function () { + cyto.elements().layout(layout).run(); + resolve(); + }, 5000); + }); + }); + + if (shiftCoord) { + shiftAllToGetTopLeftCoord(network, networkStyle); + } + + const json = cyto.json(); + changeNetworkFromCytoscape(json, network); + + return network; +} + + + + +// /** +// * Take a network and apply a d3 force layout algorithm on WITHOUT simulation +// * @param network Network object +// * @returns {Network} Network object with d3 force layout apply on +// */ +// export async function forceLayout3(network: Network, autoRescale: Boolean = false): Promise<Network> { +// const seuil = 0.04; +// const maxiter = 1000; +// const minMovement = 0.01; +// const listNodesID=Object.keys(network.nodes); +// let svgHeight = screen.height; +// let svgWidth = screen.width; + +// const simulation = d3.forceSimulation(Object.values(network.nodes)) +// .force('link', d3.forceLink() +// .id((d: any) => d.id) +// .links(network.links) +// ) +// .force('charge', d3.forceManyBody()) +// .velocityDecay(0.1) +// .force('center', d3.forceCenter(svgWidth / 2, svgHeight / 2)) +// .stop(); + +// await sendTick(); + +// async function sendTick() { +// let iter=0; +// let lastPositions = new Map(Object.values(network.nodes).map(node => [node.id, { x: node.x, y: node.y }])); +// while (iter < maxiter) { +// iter++; +// simulation.tick(); + +// let maxMovement = 0; +// for (let nodeID of listNodesID) { +// const node=network.nodes[nodeID]; +// const lastPos = lastPositions.get(nodeID); +// const dx = node.x - lastPos.x; +// const dy = node.y - lastPos.y; +// const distance = Math.sqrt(dx * dx + dy * dy); + +// if (distance > maxMovement) { +// maxMovement = distance; +// } + +// lastPositions.set(node.id, { x: node.x, y: node.y }); +// } + +// if (maxMovement < minMovement) { +// console.log('Force layout converged after ' + iter + ' iterations'); +// break; +// }else{ +// console.log(iter); +// } +// } +// } + +// return network; +// } + + +// export async function forceLayout2(network: Network, autoRescale: Boolean = false): Promise<Network> { +// let svgHeight = screen.height; +// let svgWidth = screen.width; + +// const simulation = d3.forceSimulation(Object.values(network.nodes)) +// .force('link', d3.forceLink() +// .id((d: any) => { +// return d.id; +// }) +// .links(network.links) +// ) +// .force('charge', d3.forceManyBody()) +// .force('center', d3.forceCenter(svgWidth / 2, svgHeight / 2)) +// .alphaMin(0.4) +// .stop(); + +// await sendTick(); + +// async function sendTick() { +// for (let i = simulation.alpha(); i > 0.4; i = simulation.alpha()) { +// simulation.tick(); +// } +// } + +// return network; + +// } diff --git a/src/composables/MetricsApplication.ts b/src/composables/MetricsApplication.ts new file mode 100644 index 0000000..6fa8868 --- /dev/null +++ b/src/composables/MetricsApplication.ts @@ -0,0 +1,329 @@ +import { ref } from "vue"; +import { getContentFromURL, importNetworkFromURL } from "./importNetwork"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { addSideCompoundAttributeFromList, duplicateSideCompound, putDuplicatedSideCompoundAside } from "./LayoutManageSideCompounds"; +import { createStaticForceLayout } from "@metabohub/viz-core"; +import { Parameters,defaultParameters } from "../types/Parameters"; +import { forceLayout, vizLayout } from "./LayoutSugiyamaForce"; +import { Algo, PathType } from "../types/EnumArgs"; +import { countIntersectionEdgeNetwork, countOverlapNodeNetwork, countOverlapNodeEdgeNetwork, countDifferentCoordinatesNodeNetwork, countNodes, countEdges, coefficientOfVariationEdgeLength, analyseDirectorVector } from "./MetricsCalculation"; +import { TypeSubgraph } from "../types/Subgraph"; +import { networkToGDSGraph } from "./ConvertFromNetwork"; +import { allSteps } from "./LayoutMain"; + + +export async function analyseAllJSON(pathListJSON: string,algo:Algo=Algo.DEFAULT,metricGraph:boolean=true): Promise<void> { + const jsonFileString = await getContentFromURL(pathListJSON); + const allJson = jsonFileString.split('\n'); + let resultGraphAllJSON: Array<Array<number>> = []; + let resultLayoutAllJSON: Array<Array<number>> = []; + let nameMetrics:{graph:string[],layout:string[]}= {graph:[],layout:[]}; + let nameFile: string[] = []; + + // which layout to apply + let applyLayout: (subgraph: SubgraphNetwork) => Promise<SubgraphNetwork> =defaultApplyLayout; + switch (algo) { + case Algo.FORCE: + console.log('apply Force'); + applyLayout = applyForceLayout; + console.warn('Use of timeout so exec time is not accurate (no comparison possible)'); + break; + case Algo.VIZ: + console.log('apply Viz'); + applyLayout = applyVizLayout; + break; + case Algo.ALGO: + console.log('applyAlgo : default'); + applyLayout = applyAlgo; + break; + case Algo.ALGO_V0: + console.log('applyAlgo_V0: no main chain'); + applyLayout = applyAlgo_V0; + break; + case Algo.ALGO_V1: + console.log('applyAlgo_V1 : longuest'); + applyLayout = applyAlgo_V1; + break; + case Algo.ALGO_V3: + console.log('applyAlgo_V3 : all'); + applyLayout = applyAlgo_V3; + break; + default: + console.log('no change'); + applyLayout = defaultApplyLayout; + break; + } + let firstJSON=true; + for (const json of allJson) { + console.log(json); + const resultJSON= await analyseJSON(json,metricGraph,applyLayout,false); + if (firstJSON){ + nameMetrics.graph=resultJSON.graph.nameMetrics; + nameMetrics.layout=resultJSON.layout.nameMetrics; + firstJSON=false; + } + if (resultJSON.graph !== undefined){ + resultGraphAllJSON.push(resultJSON.graph.result); + } + if (resultJSON.layout !== undefined){ + nameFile.push(json); + resultLayoutAllJSON.push(resultJSON.layout.result); + } + + } + + if (metricGraph){ + print1DArray(nameMetrics.graph); + print2DArray(resultGraphAllJSON); + } + print1DArray(nameMetrics.layout); + print2DArray(resultLayoutAllJSON); + + console.warn("If apply metrics on another layout : refresh the page, else results are the same than last time (idk why)"); + console.warn('Some metrics are calculated without side compounds'); +} + + +async function analyseJSON(json: string, metricGraph:boolean=true, applyLayout: (subgraph: SubgraphNetwork) => Promise<SubgraphNetwork> =defaultApplyLayout,printColumnName:boolean=true): + Promise<{graph:{nameMetrics:string[],result:number[]},layout:{nameMetrics:string[],result:number[]}} | undefined> { + + // initialize objects + const networkForJSON = ref<Network>({ id: '', nodes: {}, links: [] }); + const networkStyleforJSON = ref<GraphStyleProperties>({ + nodeStyles: {}, + linkStyles: {} + }); + let startTime:number; + let endTime:number; + let subgraphNetwork:SubgraphNetwork; + let resultGraph: {nameMetrics:string[],result:number[]}= {nameMetrics:[],result:[]}; + let resultLayout:{nameMetrics:string[],result:number[]}= {nameMetrics:[],result:[]}; + + // import network from JSON, and process it + try { + await new Promise<void>((resolve, reject) => { + try { + importNetworkFromURL(json, networkForJSON, networkStyleforJSON, () => { + //// Callback function (after network imported) : + + // set style (same for all) + changeNodeStyles(networkStyleforJSON.value); + // create subgraphNetwork object + subgraphNetwork={network:networkForJSON,networkStyle:networkStyleforJSON,attributs:{},mainChains:{}}; + // duplicate side compounds + addSideCompoundAttributeFromList(subgraphNetwork,"/sideCompounds.txt").then( + ()=>{ + duplicateSideCompound(subgraphNetwork); + } + ).then( + ()=>{ + // calculate metrics of graph + if (metricGraph) { + const metricsGraph=applyMetricsGraph(subgraphNetwork.network.value,printColumnName); + resultGraph.result=metricsGraph.metrics + resultGraph.nameMetrics=metricsGraph.nameMetrics; + } + } + ).then( + ()=>{ + startTime = performance.now(); + } + ).then( + async ()=>{ + // apply layout + subgraphNetwork=await applyLayout(subgraphNetwork); + } + ).then( + ()=>{ + endTime = performance.now(); + } + ).then( + ()=>{ + // calculate metrics on resulting layout + const metricsLayout=applyMetricsLayout(subgraphNetwork,true,printColumnName); + resultLayout.result= metricsLayout.metrics; + resultLayout.nameMetrics=metricsLayout.nameMetrics; + resolve(); + } + ); + + }); + } catch (error) { + reject(error); + } + }); + } catch (error) { + console.error("error file : " + json + "\n" + error); + return undefined; + } + // add execution time of layout only (not duplication side compounds) + const executionTime = parseFloat((endTime - startTime).toFixed(3)); + if (executionTime) { + resultLayout.result.push(executionTime); + resultLayout.nameMetrics.push('execution time (ms)'); + } + + return {graph:resultGraph,layout:resultLayout}; +} + + +function changeNodeStyles(networkStyle:GraphStyleProperties):void{ + networkStyle.nodeStyles = { + metabolite: { + width: 25, + height: 25, + fill: '#FFFFFF', + shape: 'circle' + }, + sideCompound: { + width: 12, + height: 12, + fill: '#f0e3e0', + shape: 'circle' + }, + reaction: { + width: 15, + height: 15, + fill: "grey", + shape: 'rect' + }, + // reversible : { + // fill : "green", + // shape:"inverseTriangle" + // }, + // reversibleVersion:{ + // fill:"red", + // shape: "triangle" + // } + + } +} + +function print1DArray(data: Array<string|number|boolean>): void { + const stringData = data.join(','); + console.log(stringData); +} + +function print2DArray(data: Array<Array<string|number|boolean>>): void { + const stringData = data.map(row => row.join(',')).join('\n'); + console.log(stringData); +} + + + +const defaultApplyLayout = async (subgraphNetwork: SubgraphNetwork): Promise<SubgraphNetwork> => { + return subgraphNetwork; +}; + +const applyForceLayout = (subgraphNetwork: SubgraphNetwork): Promise<SubgraphNetwork> => { + const network=subgraphNetwork.network.value; + const styleNetwork= subgraphNetwork.networkStyle.value; + const subgraphNetworkPromise = new Promise<SubgraphNetwork>(async (resolve, reject) => { + try { + await forceLayout(network, styleNetwork, false); + resolve(subgraphNetwork); + } catch (error) { + reject(error); + } + }); + return subgraphNetworkPromise; +}; + +const applyVizLayout = async (subgraphNetwork: SubgraphNetwork): Promise<SubgraphNetwork> => { + let parameters: Parameters = defaultParameters; + const subgraphNetworkPromise = new Promise<SubgraphNetwork>((resolve, reject) => { + resolve(vizLayout(subgraphNetwork, false, false, parameters.addNodes, parameters.groupOrCluster, false, false, parameters.dpi, parameters.numberNodeOnEdge)) + }) + return subgraphNetworkPromise; +}; + +const applyAlgo = async (subgraphNetwork: SubgraphNetwork): Promise<SubgraphNetwork> => { + let parameters: Parameters=defaultParameters; + const subgraphNetworkPromise = new Promise<SubgraphNetwork>((resolve, reject) => { + resolve(allSteps(subgraphNetwork,parameters,false)); + }) + return subgraphNetworkPromise; +}; + +const applyAlgo_V0 = async (subgraphNetwork: SubgraphNetwork): Promise<SubgraphNetwork> => { + let parameters: Parameters=defaultParameters; + parameters.doMainChain=false; + const subgraphNetworkPromise = new Promise<SubgraphNetwork>((resolve, reject) => { + resolve(allSteps(subgraphNetwork,parameters,false)); + }) + return subgraphNetworkPromise; +}; + +const applyAlgo_V1 = async (subgraphNetwork: SubgraphNetwork): Promise<SubgraphNetwork> => { + let parameters: Parameters=defaultParameters; + parameters.pathType=PathType.LONGEST; + const subgraphNetworkPromise = new Promise<SubgraphNetwork>((resolve, reject) => { + resolve(allSteps(subgraphNetwork,parameters,false)); + }) + return subgraphNetworkPromise; +}; + +const applyAlgo_V3 = async (subgraphNetwork: SubgraphNetwork): Promise<SubgraphNetwork> => { + let parameters: Parameters=defaultParameters; + parameters.pathType=PathType.ALL; + const subgraphNetworkPromise = new Promise<SubgraphNetwork>((resolve, reject) => { + resolve(allSteps(subgraphNetwork,parameters,false)); + }) + return subgraphNetworkPromise; +}; + + + + +export function applyMetricsGraph(network: Network,printColumnName:boolean=true): {nameMetrics:string[],metrics:number[]} { + const networkGDS=networkToGDSGraph(network); + const result: number[]=[]; + + const nameColumnGraph: string[] = ['nodes', 'node not side compound','edges','edge not side compound', 'hasDirectedCycle' ]; + if (printColumnName) print1DArray(nameColumnGraph); + + // number of nodes + result.push(countNodes(network,true)); + // number of nodes not side compounds + result.push(countNodes(network,false)); + // number of edges + result.push(countEdges(network,true)); + // number of edges not side compounds + result.push(countEdges(network,false)); + // has directed cycle + result.push(Number(networkGDS.hasCycle())); + + return {nameMetrics:nameColumnGraph,metrics:result}; +} + +export function applyMetricsLayout(subgraphNetwork: SubgraphNetwork, coordAreCenter:boolean=true, printColumnName:boolean=true): {nameMetrics:string[],metrics:number[]} { + const network=subgraphNetwork.network.value; + const networkStyle=subgraphNetwork.networkStyle.value; + const networkGDS=networkToGDSGraph(network); + const result: number[]=[]; + + const nameColumnLayout: string[] = ['node overlap', 'edge node overlap', 'different x (not SD)' ,'different y (not SD)','edge intersections','coef var edge length (no SD)','% colineat axis (not SD)', 'coef var vect dir (not SD)']; + if (printColumnName) print1DArray(nameColumnLayout); + + + //number of node overlap + result.push(countOverlapNodeNetwork(network,networkStyle,coordAreCenter)); + // number of edge node overlap + result.push(countOverlapNodeEdgeNetwork(network,networkStyle,coordAreCenter)); + // number of different x and y coordinates (without side compounds) + const countDiffCoord=countDifferentCoordinatesNodeNetwork(network,networkStyle,coordAreCenter,false); + result.push(countDiffCoord.x); + result.push(countDiffCoord.y); + // number of edges intersections + result.push(countIntersectionEdgeNetwork(network,networkStyle,coordAreCenter)); + // variance edge length (without side compounds?) + result.push(coefficientOfVariationEdgeLength(network,networkStyle,coordAreCenter,false)); + // direction edge : % of edge colinear to axis and coef of variaton of angle + const resultDirection=analyseDirectorVector(network,networkStyle,coordAreCenter,true,false); + result.push(resultDirection.colinearAxis) + result.push(resultDirection.coefVariation) + + return {nameMetrics:nameColumnLayout,metrics:result}; +} diff --git a/src/composables/MetricsCalculation.ts b/src/composables/MetricsCalculation.ts new file mode 100644 index 0000000..5843b71 --- /dev/null +++ b/src/composables/MetricsCalculation.ts @@ -0,0 +1,448 @@ +import { Link } from "@metabohub/viz-core/src/types/Link"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { Node } from "@metabohub/viz-core/src/types/Node"; +import { getTopLeftCoordFromCenter, getSizeNodePixel, getCenterCoordFromTopLeft } from "./CalculateSize"; +import { checkIntersection } from "line-intersect"; +import { Coordinate,Size } from "../types/CoordinatesSize"; +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; + +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// +//---------------------------------------------------- Utilitary Functions -----------------------------------------------------------// +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + +export function getCenterNode(node: Node,networkStyle:GraphStyleProperties,coordAreCenter:boolean=false): Coordinate { + let nodeCenter: {x:number,y:number}; + + if (coordAreCenter) { + nodeCenter={x:node.x,y:node.y}; + }else{ + nodeCenter=getCenterCoordFromTopLeft(node,networkStyle); + } + return nodeCenter; +} + + +function commonNodeBetween2Links(link1: Link,link2: Link): boolean { + if (link1.source==link2.source || link1.source==link2.target || link1.target==link2.source || link1.target==link2.target) { + return true; + }else { + return false; + } +} + +export function countNodes(network: Network, countSideCompound: boolean = true): number { + if (countSideCompound) { + return Object.keys(network.nodes).length; + } else { + let nodes = 0; + Object.keys(network.nodes).forEach((nodeID) => { + const node = network.nodes[nodeID]; + if (!(node.metadata && node.metadata["isSideCompound"])) { + nodes += 1; + } + }); + return nodes; + } +} + +export function countEdges(network: Network, countSideCompound: boolean = true): number { + if (countSideCompound) { + return network.links.length; + } else { + let links = 0; + network.links.forEach(link => { + if (!(link.source.metadata && link.source.metadata["isSideCompound"]) && !(link.target.metadata && link.target.metadata["isSideCompound"])) { + links += 1; + } + }); + return links; + } +} + +function getNormalizedDirectorVector(link: Link, style: GraphStyleProperties, coordAreCenter: boolean = false): Coordinate { + + const sourceCenter = getCenterNode(link.source, style, coordAreCenter); + const targetCenter = getCenterNode(link.target, style, coordAreCenter); + + const dx = targetCenter.x - sourceCenter.x; + const dy = targetCenter.y - sourceCenter.y; + + const length = edgeLength(link, style, coordAreCenter); + + if (length === 0) { + return { x: 0, y: 0 }; // Handle case with zero length + } + + return { + x: parseFloat((dx / length).toFixed(2)), + y: parseFloat((dy / length).toFixed(2)) + }; +} + +function linkOfSideCompound(link:Link):boolean{ + return (link.source.metadata && (link.source.metadata["isSideCompound"]) as boolean) || (link.target.metadata && (link.target.metadata["isSideCompound"]) as boolean); +} + + +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// +//-------------------------------------------------------- Node Metrics --------------------------------------------------------------// +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + + +///////////////////////////////////////////////////// +// ------------------------- Node overlap + + +export function countOverlapNodeNetwork(network: Network,networkStyle:GraphStyleProperties,coordAreCenter:boolean=false): number { + let nb=0; + const nodesID=Object.keys(network.nodes); + + for (let i=0 ; i<nodesID.length ; i++) { + for (let j=i+1 ; j<nodesID.length ; j++) { + // node1 + const node1=network.nodes[nodesID[i]]; + const coordNode1=getCenterNode(node1,networkStyle,coordAreCenter); + const sizeNode1=getSizeNodePixel(node1,networkStyle); + // node2 + const node2=network.nodes[nodesID[j]]; + const coordNode2=getCenterNode(node2,networkStyle,coordAreCenter); + const sizeNode2=getSizeNodePixel(node2,networkStyle); + + if (nodesOverlap(coordNode1,sizeNode1,coordNode2,sizeNode2)){ + nb+=1; + } + } + } + return nb; +} + + + +function nodesOverlap(coord1: Coordinate, size1: Size, coord2: Coordinate, size2: Size): boolean { + + // coordinate are center + + if ( !size1.width || !size1.height || !size2.width || !size2.height || !coord1.x || !coord1.y || !coord2.x || !coord2.y) { + // Handle null or undefined inputs appropriately + return false; + } + + // rectangle 1 + const left1 = coord1.x - size1.width / 2; + const right1 = coord1.x + size1.width / 2; + const top1 = coord1.y - size1.height / 2; + const bottom1 = coord1.y + size1.height / 2; + + // rectangle 2 + const left2 = coord2.x - size2.width / 2; + const right2 = coord2.x + size2.width / 2; + const top2 = coord2.y - size2.height / 2; + const bottom2 = coord2.y + size2.height / 2; + + // overlap? + const overlapX = left1 < right2 && right1 > left2; + const overlapY = top1 < bottom2 && bottom1 > top2; + + return overlapX && overlapY; +} + + +///////////////////////////////////////////////////// +// ------------------------- Node on edge + + + +export function countOverlapNodeEdgeNetwork(network: Network,networkStyle:GraphStyleProperties,coordAreCenter:boolean=false): number { + let nb=0; + const nodesID=Object.keys(network.nodes); + nodesID.forEach( (nodeID) =>{ + + const node=network.nodes[nodeID]; + const coordNode1=getCenterNode(node,networkStyle,coordAreCenter); + const sizeNode=getSizeNodePixel(node,networkStyle); + nb += countOverlapEdgeForNode(network,networkStyle,nodeID,coordNode1,sizeNode,coordAreCenter); + + }); + + return nb; +} + +function countOverlapEdgeForNode(network:Network,networkStyle:GraphStyleProperties,nodeID:string,coordNode:Coordinate,sizeNode:Size,coordAreCenter:boolean=false): number { + let nb=0; + + network.links.forEach(link => { + // if node not linked to the edge : check if it is on the edge + if(!(link.source.id==nodeID || link.target.id==nodeID)){ + + let coordSource=getCenterNode(link.source,networkStyle,coordAreCenter); + let coordTarget=getCenterNode(link.target,networkStyle,coordAreCenter); + + if (nodeEdgeOverlap(coordNode,sizeNode,coordSource,coordTarget)){ + nb+=1; + } + } + }); + return nb; +} + + +function nodeEdgeOverlap(centerCoordNode: Coordinate, sizeNode: Size, coordSource: Coordinate, coordTarget: Coordinate): boolean { // CORRIGER !!!!! + + // Treat the node as a rectangle (coordinates are center of node) + const rect = { + left: centerCoordNode.x - sizeNode.width / 2, + right: centerCoordNode.x + sizeNode.width / 2, + top: centerCoordNode.y - sizeNode.height / 2, + bottom: centerCoordNode.y + sizeNode.height / 2 + }; + + // Check if any of the edge's endpoints is inside the rectangle => same as node overlap (to suppress ?) + const isPointInsideRect = (point: Coordinate) => + point.x >= rect.left && point.x <= rect.right && point.y >= rect.top && point.y <= rect.bottom; + + if (isPointInsideRect(coordSource) || isPointInsideRect(coordTarget)) { + return true; // One of the endpoints is inside the rectangle + } + + // Check for overlap between the edge and the sides of the rectangle + // Convert the sides of the rectangle into line segments + const rectangleEdges = [ + { start: { x: rect.left, y: rect.top }, end: { x: rect.right, y: rect.top } }, // Top + { start: { x: rect.right, y: rect.top }, end: { x: rect.right, y: rect.bottom } }, // Right + { start: { x: rect.left, y: rect.bottom }, end: { x: rect.right, y: rect.bottom } }, // Bottom + { start: { x: rect.left, y: rect.top }, end: { x: rect.left, y: rect.bottom } } // Left + ]; + + // Use checkIntersection function to check if two line segments intersect + for (const edge of rectangleEdges) { + const result = checkIntersection(edge.start.x,edge.start.y, edge.end.x,edge.end.y, coordSource.x, coordSource.y,coordTarget.x,coordTarget.y); + if (result.type === "intersecting") { + return true; // There is an overlap + } + } + + return false; // No overlap detected +} + + +///////////////////////////////////////////////////// +// ------------------------- Node different coordinates + +export function countDifferentCoordinatesNodeNetwork(network: Network, networkStyle: GraphStyleProperties, coordAreCenter: boolean = false, countSideCompound:boolean=true,roundAt: number = 2): { x: number, y: number } { + let uniqueX = new Set<number>(); + let uniqueY = new Set<number>(); + + Object.keys(network.nodes).forEach((nodeID) => { + const node = network.nodes[nodeID]; + // Do not count side compounds if countSideCompound is false + if (countSideCompound || !(node.metadata && node.metadata["isSideCompound"])) { + const coordNode = getCenterNode(node, networkStyle, coordAreCenter); + + // Round the coordinates based on roundAt + const roundedX = parseFloat(coordNode.x.toFixed(roundAt)); + const roundedY = parseFloat(coordNode.y.toFixed(roundAt)); + + uniqueX.add(roundedX); + uniqueY.add(roundedY); + } + }); + + return { x: uniqueX.size, y: uniqueY.size }; +} + +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// +//-------------------------------------------------------- Edge Metrics --------------------------------------------------------------// +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + + +///////////////////////////////////////////////////// +// ------------------------- Edge intersection +// (overlap not taken into account) + + +/** + * Counts how many crossings are in a network + * @param network the network + * @returns the number of crossings + */ +export function countIntersectionEdgeNetwork(network: Network,style:GraphStyleProperties,coordAreCenter:boolean=false): number { + let nb: number = 0; + for (let i=0 ; i<network.links.length ; i++) { + for (let j=i+1 ; j<network.links.length ; j++) { + const link1=network.links[i]; + const link2=network.links[j]; + if (edgesIntersect(link1, link2,style,coordAreCenter)){ + nb++; + } + } + } + return nb; +} + +function edgesIntersect(link1: Link, link2: Link,style:GraphStyleProperties,coordAreCenter:boolean=false): boolean { + + // Case of common node + if (commonNodeBetween2Links(link1,link2)) { + return false; + } + + // Get center of node : where the link is attached + const node1Center=getCenterNode(link1.source,style,coordAreCenter); + const node2Center=getCenterNode(link1.target,style,coordAreCenter); + const node3Center=getCenterNode(link2.source,style,coordAreCenter); + const node4Center=getCenterNode(link2.target,style,coordAreCenter); + + + // Check intersection + const result = checkIntersection(node1Center.x, node1Center.y, node2Center.x, node2Center.y, node3Center.x, node3Center.y, node4Center.x, node4Center.y); + if (result.type == "intersecting") { + return true; + } else { + return false; + } + +} + +///////////////////////////////////////////////////// +// ------------------------- Edge length + + +export function coefficientOfVariationEdgeLength(network: Network,style:GraphStyleProperties,coordAreCenter:boolean=false,includeSideCompounds:boolean=true): number { + + let links = network.links; + + if (!includeSideCompounds) { + links = links.filter(link => + !(link.source.metadata && link.source.metadata["isSideCompound"]) && + !(link.target.metadata && link.target.metadata["isSideCompound"]) + ); + } + + if (links.length === 0) { + return 0; // Handle case with no edge + } + + const lengths = links.map(link => edgeLength(link, style, coordAreCenter)); + + const mean = lengths.reduce((a, b) => a + b, 0) / lengths.length; + if (mean === 0) { + return 0; // Handle case with no edge lengths + } + const variance = lengths.reduce((a, b) => a + Math.pow(b - mean, 2), 0) / lengths.length; + const stdDeviation = Math.sqrt(variance); + const coefVariation = stdDeviation / Math.abs(mean); + return parseFloat(coefVariation.toFixed(3)); +} + +function edgeLength(link: Link,style:GraphStyleProperties,coordAreCenter:boolean=false): number { + const sourceCenter=getCenterNode(link.source,style,coordAreCenter); + const targetCenter=getCenterNode(link.target,style,coordAreCenter); + + const dx = sourceCenter.x - targetCenter.x; + const dy = sourceCenter.y - targetCenter.y; + return Math.sqrt(dx * dx + dy * dy); +} + + + +///////////////////////////////////////////////////// +// ------------------------- Edge colinear with axis +// => function used with edge direction + +function calculateNormalizedDirectorVectors(links: Link[], style: GraphStyleProperties, coordAreCenter: boolean = false,includeSideCompounds:boolean=true): Coordinate[] { + const vectors: Coordinate[] = []; + + links.forEach(link => { + if (includeSideCompounds || !linkOfSideCompound(link)){ + const normalizedVector = getNormalizedDirectorVector(link, style, coordAreCenter); + vectors.push(normalizedVector); + } + + }); + + return vectors; +} + +function isColinearAxisNetwork(vector:Coordinate): boolean { + return vector.x === 0 || vector.y === 0; +} + +function countEdgeColinearAxisNetwork(vectors:Coordinate[], pourcentage:boolean=false): number { + + if (vectors.length === 0) { + return 0; + } + + let count = 0; + vectors.forEach(vector => { + if (isColinearAxisNetwork(vector)) { + count += 1; + } + }); + if (pourcentage) { + return parseFloat((count / vectors.length).toFixed(2)); + } + return count; +} + + +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// +//-------------------------------------------------------- Domain Metrics --------------------------------------------------------------// +//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + +// WHEN CLEAN : fonction that said if sidecompound or not + +///////////////////////////////////////////////////// +// ------------------------- Edge direction + +export function analyseDirectorVector(network: Network, style: GraphStyleProperties, coordAreCenter: boolean = false, pourcentageColinearAxis:boolean=false, includeSideCompounds:boolean=true):{colinearAxis:number,coefVariation:number} { + + const result: { colinearAxis: number, coefVariation: number } = { colinearAxis: undefined, coefVariation: undefined }; + + let links = network.links; + + if (!includeSideCompounds) { + links = links.filter(link => + !(link.source.metadata && link.source.metadata["isSideCompound"]) && + !(link.target.metadata && link.target.metadata["isSideCompound"]) + ); + } + + // get all normalized director vectors + const vectors = calculateNormalizedDirectorVectors(links, style, coordAreCenter,includeSideCompounds); + if (vectors.length==0) return { colinearAxis: 0, coefVariation: 0 } + + // count colinear with axis + result.colinearAxis = countEdgeColinearAxisNetwork(vectors,pourcentageColinearAxis); + + // coeficient of variation of angle + + // calculate angles of vectors + const angles = vectors.map(vector => Math.atan2(vector.y, vector.x)); + + // calculate mean of angles + const mean = angles.reduce((a, b) => a + b, 0) / angles.length; + if (mean === 0) { + result.coefVariation = 0; // Handle case with no angles + return result; + } + + // calculate variance of angles + const variance = angles.reduce((a, b) => a + Math.pow(b - mean, 2), 0) / angles.length; + + // calculate standard deviation + const stdDeviation = Math.sqrt(variance); + + // calculate coefficient of variation + const coefVariation = stdDeviation / mean; + result.coefVariation = parseFloat(coefVariation.toFixed(2)); + + return result; + +} + + diff --git a/src/composables/SBMLtoJSON.ts b/src/composables/SBMLtoJSON.ts new file mode 100644 index 0000000..b57bce0 --- /dev/null +++ b/src/composables/SBMLtoJSON.ts @@ -0,0 +1,160 @@ +import { parseString } from 'xml2js'; +import type { JSONGraphFormat, XMLSpecies, XMLReactions } from '../types/JSONGraphFormat'; + +/** + * Return a number between min (inclusive) and max (inclusive) + * @param min + * @param max + * @returns a number + */ +function getRandomInt(min: number, max: number): number { + min = Math.ceil(min); + max = Math.floor(max); + return Math.floor(Math.random() * (max - min + 1)) + min; +} + +/** + * Convert an xml graph into a JSON graph format + * @param sbmlString the xml file as a string + * @returns the graph as a Promise + */ +export async function sbml2json(sbmlString: string): Promise<JSONGraphFormat> { + return new Promise((resolve, reject) => { + parseString(sbmlString, { explicitArray: false }, (err, result) => { + if (err) { + console.log("Error during the parsing of the file"); + console.log(err); + reject(err); + } else { + const model = result.sbml.model; + // graph to return + const graph: JSONGraphFormat = { + graph: { + id: model.$.id, + type: 'metabolic', + metadata: { + style: { + nodeStyles: { + metabolite: { + width: 25, + height: 25, + strokeWidth: 1, + shape: 'circle' + }, + reaction: { + width: 15, + height: 15, + strokeWidth: 0.5, + shape: 'rect', + fill: 'grey' + }, + reversible: { + fill: 'green', + shape: 'inverseTriangle' + }, + reversibleVersion: { + fill: 'red', + shape: 'triangle' + } + } + } + }, + nodes: {}, + edges: [] + } + }; + + // Transform species to nodes + const speciesList = model.listOfSpecies.species; + // add a metabolite node for each species + speciesList.forEach((species: XMLSpecies) => { + graph.graph.nodes[species.$.id] = { + id: species.$.id, + metadata: { + classes: ['metabolite'], + position: { + x: getRandomInt(0, 100), + y: getRandomInt(0, 100) + } + }, + label: species.$.name + }; + }); + + // Transform reactions to nodes and edges + const reactions = model.listOfReactions.reaction; + reactions.forEach((reaction: XMLReactions) => { + const reactionId = reaction.$.id; + + let classReversible :string; + const isReversible=reaction.$.reversible; + if (isReversible==="true"){ + classReversible = "reversible"; + }else{ + classReversible = "irreversible"; + } + + // get the reactants and products for every reaction + const reactants: string[] = []; + if (reaction.listOfReactants.speciesReference != undefined && (reaction.listOfReactants.speciesReference as Partial<XMLSpecies>[]).length != undefined) { + // type : array + (reaction.listOfReactants.speciesReference as Partial<XMLSpecies>[]).forEach((ref: Partial<XMLSpecies>) => { + reactants.push(ref.$.species); + }); + } else if (reaction.listOfReactants.speciesReference != undefined) { + // type : object + reactants.push((reaction.listOfReactants.speciesReference as Partial<XMLSpecies>).$.species); + } + const products: string[] = []; + if (reaction.listOfProducts.speciesReference != undefined && (reaction.listOfProducts.speciesReference as Partial<XMLSpecies>[]).length != undefined) { + // type : array + (reaction.listOfProducts.speciesReference as Partial<XMLSpecies>[]).forEach((ref: Partial<XMLSpecies>) => { + products.push(ref.$.species); + }); + } else if (reaction.listOfProducts.speciesReference != undefined) { + // type : object + products.push((reaction.listOfProducts.speciesReference as Partial<XMLSpecies>).$.species); + } + + // add the reaction as a node + graph.graph.nodes[reactionId] = { + id: reactionId, + metadata: { + classes: ['reaction',classReversible], + position: { + x: getRandomInt(0, 100), + y: getRandomInt(0, 100) + } + }, + label: reaction.$.name + }; + + // add the edges for the reaction and its reactants and products + reactants.forEach((reactant: string) => { + graph.graph.edges.push({ + id: `${reactant}--${reactionId}`, + source: reactant, + target: reactionId, + metadata: { + classes: [classReversible] + } + }); + }); + products.forEach((product: string) => { + graph.graph.edges.push({ + id: `${reactionId}--${product}`, + source: reactionId, + target: product, + metadata: { + classes: [classReversible] + } + }); + }); + }); + + // return the graph object + resolve(graph); + } + }); + }); +} diff --git a/src/composables/UseSubgraphNetwork.ts b/src/composables/UseSubgraphNetwork.ts new file mode 100644 index 0000000..df5097c --- /dev/null +++ b/src/composables/UseSubgraphNetwork.ts @@ -0,0 +1,160 @@ +import { NetworkLayout } from "../types/NetworkLayout"; +import { Subgraph, TypeSubgraph } from "../types/Subgraph"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { Node } from "@metabohub/viz-core/src/types/Node"; + + +/** + * Creates a new subgraph with the specified properties. + * @param name The name of the subgraph. + * @param nodes The array of nodes in the subgraph (defaults to an empty array). + * @param classes The array of classes associated with the subgraph (defaults to an empty array). + * @returns The newly created subgraph. + */ +export function createSubgraph(name: string, nodes: Array<string>, classes: Array<string>, type: TypeSubgraph = TypeSubgraph.MAIN_CHAIN, forSubgraph?: {name:string,type:TypeSubgraph}, associatedSubgraphs?:Array<{name:string,type:TypeSubgraph}>): Subgraph { + return { + name, + classes, + nodes, + type, + parentSubgraph: forSubgraph, + childrenSubgraphs: associatedSubgraphs + }; +} + +export function addNewSubgraph(subgraphNetwork:SubgraphNetwork,subgraph:Subgraph,type:TypeSubgraph=TypeSubgraph.MAIN_CHAIN): SubgraphNetwork { + if (!subgraphNetwork[type]) subgraphNetwork[type]={}; + if(!(subgraph.name in subgraphNetwork[type])){ + // adding subgraph to subgraphNetwork + subgraphNetwork[type][subgraph.name]=subgraph; + // node matadata update + subgraph.nodes.forEach(node=>{ + updateNodeMetadataSubgraph(subgraphNetwork.network.value, node, subgraph.name, type); + }); + // if subgraph associated with another subgraph : add to associatedSubgraphs of the "parent" subgraph + if (subgraph.parentSubgraph){ + subgraphNetwork=updateParentSubgraphOf(subgraphNetwork,subgraph); + } + }else{ + console.error("subgraph already in subgraphNetwork : "+subgraph.name); + } + return subgraphNetwork; + +} + +export function updateParentSubgraphOf(subgraphNetwork:SubgraphNetwork,subgraph:Subgraph):SubgraphNetwork{ + if (subgraph.parentSubgraph){ + const nameParent=subgraph.parentSubgraph.name; + const typeParent=subgraph.parentSubgraph.type; + if (nameParent in subgraphNetwork[typeParent]){ + if (!subgraphNetwork[typeParent][nameParent].childrenSubgraphs){ + subgraphNetwork[typeParent][nameParent].childrenSubgraphs=[]; + } + subgraphNetwork[typeParent][nameParent].childrenSubgraphs.push({name:subgraph.name,type:subgraph.type}); + }else{ + console.error("parent subgraph not in subgraphNetwork"); + } + } + return subgraphNetwork; +} + +/** + * Adds a class to the cluster if it doesn't already exist. + * @param subgraph The cluster to which the class will be added. + * @param newClass The class to be added. + * @returns The updated cluster. + */ +export function addClassSubgraph(subgraph: Subgraph, newClass: string): Subgraph { + if (subgraph.classes && !subgraph.classes.includes(newClass)) { + subgraph.classes.push(newClass); + } + return subgraph; +} + +/** + * Removes a node from the cluster. + * @param subgraph The cluster from which the node will be removed. + * @param name The name of the node to be removed. + * @returns The updated cluster. + */ +export function removeNodeSubgraph(subgraph: Subgraph, name: string): Subgraph { + const index = subgraph.nodes.indexOf(name); + if (index !== -1) { + subgraph.nodes.splice(index, 1); + } + return subgraph; +} + +/** + * Removes a class from the cluster. + * @param subgraph The cluster from which the class will be removed. + * @param className The name of the class to be removed. + * @returns The updated cluster. + */ +export function removeClassSubgraph(subgraph: Subgraph, className: string): Subgraph { + if (subgraph.classes) { + const index = subgraph.classes.indexOf(className); + if (index !== -1) { + subgraph.classes.splice(index, 1); + } + } + return subgraph; +} + + +/** + * Adds a node to a subgraph in the subgraph network, and update the metadata of the node (name of the subgraph to wich it belongs) + * + * @param subgraphNetwork - The subgraph network object. + * @param subgraphID - The ID of the subgraph. + * @param nodeID - The ID of the node to be added. + * @param subgraphType - The type of the subgraph (defaults to MAIN_CHAIN). + * @returns The updated subgraph network object. + */ +export function addNodeToSubgraph(subgraphNetwork:SubgraphNetwork,subgraphID:string,nodeID:string,subgraphType: TypeSubgraph = TypeSubgraph.MAIN_CHAIN):SubgraphNetwork{ + const network=subgraphNetwork.network.value; + + if (subgraphID in subgraphNetwork[subgraphType]){ + // if node not already in subgraph : + if (!subgraphNetwork[subgraphType][subgraphID].nodes.includes(nodeID)){ + // add to subgraph + subgraphNetwork[subgraphType][subgraphID].nodes.push(nodeID); + // update metadata of node + updateNodeMetadataSubgraph(network, nodeID, subgraphID,subgraphType); + } + }else{ + console.error("subgraph not in subgraphNetwork"); + } + return subgraphNetwork; +} + +/** + * Updates the metadata of a node in the network by adding a subgraph ID to its list of subgraph. + * If the metadata does not exist, they will be created. + * + * @param networkLayout - The network object. + * @param nodeID - The ID of the node to update. + * @param subgraphID - The ID of the cluster to add. + */ +export function updateNodeMetadataSubgraph(networkLayout: NetworkLayout, nodeID: string, subgraphID: string, subgraphType: TypeSubgraph = TypeSubgraph.MAIN_CHAIN): void { + if ( ! networkLayout.nodes[nodeID]) throw new Error('Node not found in networkLayout'); + + if ( !(networkLayout.nodes[nodeID].metadataLayout)){ + networkLayout.nodes[nodeID].metadataLayout={}; + } + // if subgraphType is CYCLEGROUP, add the subgraphID to the metadataLayout directly + if (subgraphType == TypeSubgraph.CYCLEGROUP){ + networkLayout.nodes[nodeID].metadataLayout[subgraphType]=subgraphID; + return; + } else { + // if subgraphType is not CYCLEGROUP, add the subgraphID to the metadataLayout[subgraphType] array + if (!(subgraphType in networkLayout.nodes[nodeID].metadataLayout)){ + networkLayout.nodes[nodeID].metadataLayout[subgraphType]=[]; + } + const listSubgraphOfNode=networkLayout.nodes[nodeID].metadataLayout[subgraphType]; + if (!listSubgraphOfNode.includes(subgraphID)){ + listSubgraphOfNode.push(subgraphID); + } + } +} \ No newline at end of file diff --git a/src/composables/__tests__/2_reac_1_metab_4514.xml b/src/composables/__tests__/2_reac_1_metab_4514.xml new file mode 100644 index 0000000..6dd1cba --- /dev/null +++ b/src/composables/__tests__/2_reac_1_metab_4514.xml @@ -0,0 +1,68 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml fbc:required="false" groups:required="false" level="3" version="2" xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> + <model fbc:strict="true" id="_128bceb7_36b8_4227_b83a_11ca91c43b4f" metaid="_128bceb7_36b8_4227_b83a_11ca91c43b4f" name="history_test"> + <fbc:listOfGeneProducts> + <fbc:geneProduct fbc:id="g1" fbc:label="g1" fbc:name="g1"/> + </fbc:listOfGeneProducts> + <groups:listOfGroups> + <groups:group groups:id="pp1" groups:kind="classification" groups:name="pp1"> + <groups:listOfMembers> + <groups:member groups:idRef="r1"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> + <unit exponent="-1" kind="second" multiplier="0.00027778" scale="0"/> + <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> + <unit exponent="1" kind="mole" multiplier="1" scale="0"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <listOfCompartments> + <compartment constant="true" id="tutu" metaid="_97125884-20a5-4aa0-b78a-c3f1115fc57f" name="tutu" spatialDimensions="3"/> + <compartment constant="true" id="c" metaid="_265b6c07-ad95-4aa0-8064-81b050fb5d9d" name="c" spatialDimensions="3"/> + </listOfCompartments> + <listOfSpecies> + <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="m1" initialAmount="1" metaid="f2b12325-eeb5-4dc0-a770-73f199951f8d" name="m1" sboTerm="SBO:0000240"/> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="UPPER_BOUND_9999_0" units="mmol_per_gDW_per_hr" value="9999"/> + <parameter constant="true" id="LOWER_BOUND_0_0" units="mmol_per_gDW_per_hr" value="0"/> + </listOfParameters> + <listOfReactions> + <reaction fbc:lowerFluxBound="LOWER_BOUND_0_0" fbc:upperFluxBound="UPPER_BOUND_9999_0" id="erty" metaid="_6df8d47a-0216-4e17-beb3-8d3e3ec786a9" name="zerty" reversible="false"> + <listOfReactants/> + <listOfProducts/> + </reaction> + <reaction fbc:lowerFluxBound="LOWER_BOUND_0_0" fbc:upperFluxBound="UPPER_BOUND_9999_0" id="r1" metaid="cd8efdf8-c38b-48df-9883-ad09c6748b6d" name="r1" reversible="false"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#cd8efdf8-c38b-48df-9883-ad09c6748b6d"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/ec-code/1.1.1.1"/> + </rdf:Bag> + </bqbiol:is> + <bqbiol:isDescribedBy> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/pubmed/0"/> + </rdf:Bag> + </bqbiol:isDescribedBy> + </rdf:Description> + </rdf:RDF> + </annotation> + <fbc:geneProductAssociation> + <fbc:geneProductRef fbc:geneProduct="g1"/> + </fbc:geneProductAssociation> + <listOfReactants> + <speciesReference constant="true" species="m1" stoichiometry="1"/> + </listOfReactants> + <listOfProducts/> + </reaction> + </listOfReactions> + </model> +</sbml> diff --git a/src/composables/__tests__/SBMLtoJSON.spec.ts b/src/composables/__tests__/SBMLtoJSON.spec.ts new file mode 100644 index 0000000..ac819a1 --- /dev/null +++ b/src/composables/__tests__/SBMLtoJSON.spec.ts @@ -0,0 +1,122 @@ +import { expect, describe, test } from 'vitest'; +import { sbml2json } from '../SBMLtoJSON'; +import type { JSONGraphFormat } from "@/types/JSONGraphFormat"; + +describe('sbml2json.ts', () => { + test('should return a JSON with 3 nodes', async () => { + fetch('2_reac_1_metab.xml') + .then(async (res) => { + // DATA + const sbmlString: string = await res.text(); + + // FUNCTION + const result: JSONGraphFormat = await sbml2json(sbmlString); + const nodes = result.graph.nodes; + + // EXPECT + expect(nodes).toEqual(3); + }) + .catch(() => { + console.log('could not fetch the test data !'); + return false; + }); + }); + test('the nodes should have a position', async () => { + fetch('2_reac_1_metab.xml') + .then(async (res) => { + // DATA + const sbmlString: string = await res.text(); + + // FUNCTION + const result: JSONGraphFormat = await sbml2json(sbmlString); + const nodes = result.graph.nodes; + + // EXPECT + Object.values(nodes).forEach((node) => { + expect(node.metadata.position!.x).toBeDefined(); + expect(node.metadata.position!.y).toBeDefined(); + }); + }) + .catch(() => { + console.log('could not fetch the test data !'); + return false; + }); + }); + test('there should 2 nodes for the reactions', async () => { + fetch('2_reac_1_metab.xml') + .then(async (res) => { + // DATA + const sbmlString: string = await res.text(); + + // FUNCTION + const result: JSONGraphFormat = await sbml2json(sbmlString); + const nodes = result.graph.nodes; + + // EXPECT + expect(nodes['erty']).toBeDefined(); + expect(nodes['erty'].metadata.classes).toContain('reaction'); + expect(nodes['r1']).toBeDefined(); + expect(nodes['r1'].metadata.classes).toContain('reaction'); + }) + .catch(() => { + console.log('could not fetch the test data !'); + return false; + }); + }); + test('there should 1 node for the metabolite', async () => { + fetch('2_reac_1_metab.xml') + .then(async (res) => { + // DATA + const sbmlString: string = await res.text(); + + // FUNCTION + const result: JSONGraphFormat = await sbml2json(sbmlString); + const nodes = result.graph.nodes; + + // EXPECT + expect(nodes['m1']).toBeDefined(); + expect(nodes['m1'].metadata.classes).toContain('metabolite'); + }) + .catch(() => { + console.log('could not fetch the test data !'); + return false; + }); + }); + test('should return a JSON with 1 edge', async () => { + fetch('2_reac_1_metab.xml') + .then(async (res) => { + // DATA + const sbmlString: string = await res.text(); + + // FUNCTION + const result: JSONGraphFormat = await sbml2json(sbmlString); + const edges = result.graph.edges; + + // EXPECT + expect(edges.length).toEqual(1); + }) + .catch(() => { + console.log('could not fetch the test data !'); + return false; + }); + }); + test('the edge should be between "m1" and "r1"', async () => { + fetch('2_reac_1_metab.xml') + .then(async (res) => { + // DATA + const sbmlString: string = await res.text(); + + // FUNCTION + const result: JSONGraphFormat = await sbml2json(sbmlString); + const edge = result.graph.edges[0]; + + // EXPECT + expect(edge.source).toEqual('m1'); + expect(edge.target).toEqual('r1'); + }) + .catch(() => { + console.log('could not fetch the test data !'); + return false; + }); + }); +}); diff --git a/src/composables/__tests__/countIntersection.spec.ts b/src/composables/__tests__/countIntersection.spec.ts new file mode 100644 index 0000000..7b5994c --- /dev/null +++ b/src/composables/__tests__/countIntersection.spec.ts @@ -0,0 +1,33 @@ +import { describe, expect, test } from "vitest"; +import { countIntersection } from "../countIntersections"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import * as fs from 'fs'; +import { readJsonGraph } from "../readJson"; + +function getNetworkFromUrl(url: string): Network { + return (readJsonGraph(fs.readFileSync(url, { encoding: 'utf8', flag: 'r' }))).network; +} + +describe("countIntersections.ts", () => { + test("should return 1 when given a network with one crossing", async () => { + // DATA + const network: Network = getNetworkFromUrl('public/test_intersect/network_one_crossing.json'); + + // TEST + const result = countIntersection(network); + + // EXPECT + expect(result).toEqual(1); + }); + + test("should return 2 when given a network with 2 crossings", () => { + // DATA + const network: Network = getNetworkFromUrl('public/test_intersect/network_two_crossings.json'); + + // TEST + const result = countIntersection(network); + + // EXPECT + expect(result).toEqual(2); + }); +}); diff --git a/src/composables/__tests__/countIsolatedNodes.spec.ts b/src/composables/__tests__/countIsolatedNodes.spec.ts new file mode 100644 index 0000000..fb9634e --- /dev/null +++ b/src/composables/__tests__/countIsolatedNodes.spec.ts @@ -0,0 +1,76 @@ +import { describe, expect, test } from "vitest"; +import { countIsolatedNodes } from "../countIsolatedNodes"; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { Node } from "@metabohub/viz-core/src/types/Node"; + +describe("countIsolatedNodes.ts", () => { + test("should return 0 when all the nodes have >= 1 link", () => { + // DATA + const nodes: { [key: string]: Node } = { + "a": { + id: "a", + x: 0, + y: 0 + }, + "b": { + id: "b", + x: 0, + y: 0 + } + }; + const network: Network = { + id: "test", + nodes: nodes, + links: [ + { + id: "a_b", + source: nodes.a, + target: nodes.b + } + ] + }; + + // FUNCTION + const result = countIsolatedNodes(network); + + // EXPECT + expect(result).toEqual(0); + }); + test("should return 1 when there is an isolated node", () => { + // DATA + const nodes: { [key: string]: Node } = { + "a": { + id: "a", + x: 0, + y: 0 + }, + "b": { + id: "b", + x: 0, + y: 0 + }, + "c": { + id: "c", + x: 0, + y: 0 + } + }; + const network: Network = { + id: "test", + nodes: nodes, + links: [ + { + id: "a_b", + source: nodes.a, + target: nodes.b + } + ] + }; + + // FUNCTION + const result = countIsolatedNodes(network); + + // EXPECT + expect(result).toEqual(1); + }); +}); \ No newline at end of file diff --git a/src/composables/countIntersections.ts b/src/composables/countIntersections.ts new file mode 100644 index 0000000..f833b1a --- /dev/null +++ b/src/composables/countIntersections.ts @@ -0,0 +1,429 @@ +import { Node } from '@metabohub/viz-core/src/types/Node'; +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { checkIntersection } from 'line-intersect'; +import { Link } from '@metabohub/viz-core/src/types/Link'; +import { c } from 'vite/dist/node/types.d-aGj9QkWt'; +import { GraphStyleProperties } from '@metabohub/viz-core/src/types/GraphStyleProperties'; +import { getSizeNodePixel } from './CalculateSize'; +import { link } from 'fs'; +import { Coordinate, Size } from '../types/CoordinatesSize'; + + +// CHNAGE THE CODE : SEE METRICSNETWORK (for end of internship : keep this one) + +/** + * Check if the coordinates (x, y) are the same as the node's coordinates + * @param node the node + * @param x coordinate + * @param y coordinate + * @returns a boolean + */ +function isNodeCoord(node: {x:number,y:number}, x: number, y: number): boolean { + return (node.x == x && node.y == y); +} + + + +//______________________Intersection in the network______________________ +/** + * Check if the 2 edges are crossing. + * Coming from the same node or going to the same node doesn't count as crossing. + * @param link1 an edge + * @param link2 an edge + * @returns a boolean + */ +// function edgesIntersectionLink(link1: Link, link2: Link,style:GraphStyleProperties): boolean { + +// // case of common node +// if (commonNodeBetween2Links(link1,link2)) { +// return false; +// } + +// let x1: Node = link1.source; +// const x1Center=AdjustCoordNodeToCenter(x1,style); +// let x2: Node = link1.target; +// const x2Center=AdjustCoordNodeToCenter(x2,style); +// let x3: Node = link2.source; +// const x3Center=AdjustCoordNodeToCenter(x3,style); +// let x4: Node = link2.target; +// const x4Center=AdjustCoordNodeToCenter(x4,style); + +// const result = checkIntersection(x1Center.x, x1Center.y, x2Center.x, x2Center.y, x3Center.x, x3Center.y, x4Center.x, x4Center.y); +// if (result.type == "intersecting") { +// return true; +// } else { +// return false; +// } + +// } + +// function commonNodeBetween2Links(link1: Link,link2: Link): boolean { +// if (link1.source==link2.source || link1.source==link2.target || link1.target==link2.source || link1.target==link2.target) { +// return true; +// }else { +// return false; +// } +// } + +// function sameAngleBetween2ConnectedLinks(link1: Link,link2: Link,style:GraphStyleProperties): boolean { + +// // get nodes information +// let commonNode: Node; +// let node1: Node; // node from link 1 that is not in link 2 +// let node2: Node; // node from link 2 that is not in link 1 + +// // if link 1 source is the common node : +// if (link1.source==link2.source || link1.source==link2.target){ +// commonNode=link1.source; +// node1=link1.target; +// // if link 1 target is the common node : +// }else if (link1.target==link2.source || link1.target==link2.target){ +// commonNode=link1.target; +// node1=link1.source; +// } +// // get node 2 +// if (link2.source==commonNode){ +// node2=link2.target; +// }else{ +// node2=link2.source; +// } + +// // adjust coord +// const commonNodeCenter=AdjustCoordNodeToCenter(commonNode,style); +// const node1Center=AdjustCoordNodeToCenter(node1,style); +// const node2Center=AdjustCoordNodeToCenter(node2,style); +// // get angle between the 2 edges +// const angle1=adjustAngle(Math.atan2(node1Center.y-commonNodeCenter.y,node1Center.x-commonNodeCenter.x)); +// const angle2=adjustAngle(Math.atan2(node2Center.y-commonNodeCenter.y,node2Center.x-commonNodeCenter.x)); + +// // same angles ? +// return angle1==angle2; + +// } + +// function adjustAngle(angle: number): number { +// return (angle + 2 * Math.PI) % (2 * Math.PI); +// } + +// function AdjustCoordNodeToCenter(node:Node,style:GraphStyleProperties):{x:number,y:number}{ +// const size = getSizeNodePixel(node,style); +// return {x:node.x-size.width/2,y:node.y-size.height/2} +// } + +// /** +// * Counts how many crossings are in a network +// * @param network the network +// * @returns the number of crossings +// */ +// export function countIntersection(network: Network,style:GraphStyleProperties): number { +// let nb: number = 0; +// for (let i=0 ; i<network.links.length ; i++) { +// for (let j=i+1 ; j<network.links.length ; j++) { +// const link1=network.links[i]; +// const link2=network.links[j]; +// if (edgesIntersectionLink(link1, link2,style)){ +// nb++; +// } +// } +// } +// return nb; +// } + + +//______________________Intersection in another format of graph______________________ + +////CLEAN CODE : CHANGE FORMAT TO NETWORK AND USE THE OTHER FUNCTIONS FOR CYCLE + +function AdjustCoordNodeToCenter2(node:Node,nodeCoord:{x:number,y:number},style:GraphStyleProperties):{x:number,y:number}{ + const size = getSizeNodePixel(node,style); + return {x:nodeCoord.x-size.width/2,y:nodeCoord.y-size.height/2} +} + +function edgesIntersection(node1Link1:{x:number,y:number},node2Link1:{x:number,y:number},node1Link2:{x:number,y:number},node2Link2:{x:number,y:number}): boolean { + // case node in common + if (commonNodeBetween2EdgesCoord(node1Link1,node2Link1,node1Link2,node2Link2)) { + return false;//intersection2ConnectedLinks(node1Link1,node2Link1,node1Link2,node2Link2); + } + const result = checkIntersection(node1Link1.x, node1Link1.y, node2Link1.x, node2Link1.y, node1Link2.x, node1Link2.y, node2Link2.x, node2Link2.y); + if (result.type == "intersecting") { + return true; + }else{ + return false; + } +} + + +function commonNodeBetween2EdgesID(link1: {source:string,target:string},link2: {source:string,target:string}): boolean { + if (link1.source==link2.source || link1.source==link2.target || link1.target==link2.source || link1.target==link2.target) { + return true; + }else { + return false; + } +} + +function commonNodeBetween2EdgesCoord(node1Link1:{x:number,y:number},node2Link1:{x:number,y:number},node1Link2:{x:number,y:number},node2Link2:{x:number,y:number}): boolean { + if (sameNode(node1Link1,node1Link2) || sameNode(node1Link1,node2Link2) || sameNode(node2Link1,node1Link2) || sameNode(node2Link1,node2Link2)) { + return true; + }else { + return false; + } +} + +function sameNode(node1: {x:number,y:number},node2: {x:number,y:number}): boolean { + if (!node1 || !node2 || node1.x==null || node1.y==null || node2.x==null || node2.y==null) { + return false; + } + return node1.x===node2.x && node1.y===node2.y; +} + +// function intersection2ConnectedLinks(node1Link1:{x:number,y:number},node2Link1:{x:number,y:number},node1Link2:{x:number,y:number},node2Link2:{x:number,y:number}): boolean { + +// // get nodes information +// let commonNode: {x:number,y:number}; +// let node1: {x:number,y:number}; // node from link 1 that is not in link 2 +// let node2: {x:number,y:number}; // node from link 2 that is not in link 1 + +// // if link 1 node 1 is the common node : +// if (sameNode(node1Link1,node1Link2) || sameNode(node1Link1,node2Link2)){ +// commonNode=node1Link1; +// node1=node2Link1; +// // if link 1 node 2 is the common node : +// }else if (sameNode(node2Link1,node1Link2) || sameNode(node2Link1,node2Link2)){ +// commonNode=node2Link1; +// node1=node1Link1; +// } +// // get node 2 +// if (sameNode(node1Link2,commonNode)){ +// node2=node2Link2; +// }else{ +// node2=node1Link2; +// } + +// // get angle between the 2 edges +// const angle1=adjustAngle(Math.atan2(node1.y-commonNode.y,node1.x-commonNode.x)); +// const angle2=adjustAngle(Math.atan2(node2.y-commonNode.y,node2.x-commonNode.x)); + +// // same angles ? +// return angle1==angle2; + +// } + +export function countIntersectionGraph(nodes: {[key:string]:{x:number,y:number}},links:{source:string,target:string}[],network:Network,style:GraphStyleProperties): number { + let nb: number = 0; + for (let i=0 ; i<links.length ; i++) { + for (let j=i+1 ; j<links.length ; j++) { + const link1=links[i]; + const link2=links[j]; + // check if intersection + let node1Link1=nodes[link1.source]; + //node1Link1=AdjustCoordNodeToCenter2(network.nodes[link1.source],node1Link1,style); + let node2Link1=nodes[link1.target]; + //node2Link1=AdjustCoordNodeToCenter2(network.nodes[link1.target],node2Link1,style); + let node1Link2=nodes[link2.source]; + //node1Link2=AdjustCoordNodeToCenter2(network.nodes[link2.source],node1Link2,style); + let node2Link2=nodes[link2.target]; + //node2Link2=AdjustCoordNodeToCenter2(network.nodes[link2.target],node2Link2,style); + if (edgesIntersection(node1Link1,node2Link1,node1Link2,node2Link2)){ + nb++; + } + } + } + return nb; +} + +export function isIntersectionGraph(nodes: {[key:string]:{x:number,y:number}},links:{source:string,target:string}[],network:Network,style:GraphStyleProperties): boolean { + for (let i=0 ; i<links.length ; i++) { + for (let j=i+1 ; j<links.length ; j++) { + const link1=links[i]; + const link2=links[j]; + // check if intersection + let node1Link1=nodes[link1.source]; + //node1Link1=AdjustCoordNodeToCenter2(network.nodes[link1.source],node1Link1,style); + let node2Link1=nodes[link1.target]; + //node2Link1=AdjustCoordNodeToCenter2(network.nodes[link1.target],node2Link1,style); + let node1Link2=nodes[link2.source]; + //node1Link2=AdjustCoordNodeToCenter2(network.nodes[link2.source],node1Link2,style); + let node2Link2=nodes[link2.target]; + //node2Link2=AdjustCoordNodeToCenter2(network.nodes[link2.target],node2Link2,style); + if (edgesIntersection(node1Link1,node2Link1,node1Link2,node2Link2)){ + return true; + } + } + } + return false; +} + +//______________________Nodes overlap for graph______________________ + +export function countOverlapNodes(nodesPosition: {[key:string]:Coordinate},network:Network,networkStyle:GraphStyleProperties):number{ + let nb=0; + const nodesID=Object.keys(nodesPosition); + for (let i=0 ; i<nodesID.length ; i++) { + for (let j=i+1 ; j<nodesID.length ; j++) { + // info about node1 + const node1=network.nodes[nodesID[i]]; + const posNode1=nodesPosition[nodesID[i]]; + const sizeNode1=getSizeNodePixel(node1,networkStyle); + // info about node2 + const node2=network.nodes[nodesID[j]]; + const posNode2=nodesPosition[nodesID[j]]; + const sizeNode2=getSizeNodePixel(node2,networkStyle); + + if (nodeOverlap(posNode1,sizeNode1,posNode2,sizeNode2)){ + nb+=1; + } + + } + } + return nb; +} + +export function isOverlapNodes(nodesPosition: {[key:string]:Coordinate},network:Network,networkStyle:GraphStyleProperties):boolean{ + const nodesID=Object.keys(nodesPosition); + for (let i=0 ; i<nodesID.length ; i++) { + for (let j=i+1 ; j<nodesID.length ; j++) { + // info about node1 + const node1=network.nodes[nodesID[i]]; + const posNode1=nodesPosition[nodesID[i]]; + const sizeNode1=getSizeNodePixel(node1,networkStyle); + // info about node2 + const node2=network.nodes[nodesID[j]]; + const posNode2=nodesPosition[nodesID[j]]; + const sizeNode2=getSizeNodePixel(node2,networkStyle); + + if (nodeOverlap(posNode1,sizeNode1,posNode2,sizeNode2)){ + return true; + } + + } + } + return false; +} + +function nodeOverlap(coord1: Coordinate, size1: Size, coord2: Coordinate, size2: Size): boolean { + if ( !coord1 || !size1 || !coord2 || !size2 || size1.width == null || size1.height == null || size2.width == null + || size2.height == null || coord1.x == null || coord1.y == null || coord2.x == null || coord2.y == null || + size1.width == undefined || size1.height == undefined || size2.width == undefined || size2.height == undefined || + coord1.x == undefined || coord1.y == undefined || coord2.x == undefined || coord2.y == undefined) { + // Handle null or undefined inputs appropriately + return false; + } + + // rectangle 1 + const left1 = coord1.x - size1.width / 2; + const right1 = coord1.x + size1.width / 2; + const top1 = coord1.y - size1.height / 2; + const bottom1 = coord1.y + size1.height / 2; + + // rectangle 2 + const left2 = coord2.x - size2.width / 2; + const right2 = coord2.x + size2.width / 2; + const top2 = coord2.y - size2.height / 2; + const bottom2 = coord2.y + size2.height / 2; + + // overlap? + const overlapX = left1 < right2 && right1 > left2; + const overlapY = top1 < bottom2 && bottom1 > top2; + + return overlapX && overlapY; +} +//______________________Nodes overlap with edges for graph______________________ + +export function countOverlapNodesEdges(nodesPosition: {[key:string]:{x:number,y:number}},links:{source:string,target:string}[],network:Network,networkStyle:GraphStyleProperties):number{ + let nb=0; + const nodesID=Object.keys(nodesPosition); + for (let i=0 ; i<nodesID.length ; i++) { + // info about node + const node=network.nodes[nodesID[i]]; + const posNode=nodesPosition[nodesID[i]]; + const sizeNode=getSizeNodePixel(node,networkStyle); + + for (let j=0 ; j<links.length ; j++) { + // info about link + const link=links[j]; + // if node is linked to the edge : continue + if(link.source==nodesID[i] || link.target==nodesID[i]){ + continue; + }else{ + let posLink1=nodesPosition[link.source]; + let posLink2=nodesPosition[link.target]; + //posLink1=AdjustCoordNodeToCenter2(network.nodes[link.source],posLink1,networkStyle); + //posLink2=AdjustCoordNodeToCenter2(network.nodes[link.target],posLink2,networkStyle); + if (nodeEdgeOverlap(posNode,sizeNode,posLink1,posLink2)){ + nb+=1; + } + } + + } + } + return nb; +} + +export function isOverlapNodesEdges(nodesPosition: {[key:string]:{x:number,y:number}},links:{source:string,target:string}[],network:Network,networkStyle:GraphStyleProperties):boolean{ + const nodesID=Object.keys(nodesPosition); + for (let i=0 ; i<nodesID.length ; i++) { + // info about node + const node=network.nodes[nodesID[i]]; + const posNode=nodesPosition[nodesID[i]]; + const sizeNode=getSizeNodePixel(node,networkStyle); + + for (let j=0 ; j<links.length ; j++) { + // info about link + const link=links[j]; + // if node is linked to the edge : continue + if(link.source==nodesID[i] || link.target==nodesID[i]){ + continue; + }else{ + let posLink1=nodesPosition[link.source]; + let posLink2=nodesPosition[link.target]; + //posLink1=AdjustCoordNodeToCenter2(network.nodes[link.source],posLink1,networkStyle); + //posLink2=AdjustCoordNodeToCenter2(network.nodes[link.target],posLink2,networkStyle); + if (nodeEdgeOverlap(posNode,sizeNode,posLink1,posLink2)){ + return true; + } + } + + } + } + return false; +} + + + +function nodeEdgeOverlap(centerCoordNode: Coordinate, sizeNode:Size, posLink1: Coordinate, posLink2: Coordinate): boolean { + + // Treat the node as a rectangle + const rect = { + left: centerCoordNode.x - sizeNode.width / 2, + right: centerCoordNode.x + sizeNode.width / 2, + top: centerCoordNode.y - sizeNode.height / 2, + bottom: centerCoordNode.y + sizeNode.height / 2 + }; + + // Check if any of the edge's endpoints is inside the rectangle + const isPointInsideRect = (point: { x: number, y: number }) => + point.x >= rect.left && point.x <= rect.right && point.y >= rect.top && point.y <= rect.bottom; + + if (isPointInsideRect(posLink1) || isPointInsideRect(posLink2)) { + return true; // One of the endpoints is inside the rectangle + } + + // Check for overlap between the edge and the sides of the rectangle + // Convert the sides of the rectangle into line segments + const edges = [ + { start: { x: rect.left, y: rect.top }, end: { x: rect.right, y: rect.top } }, // Top + { start: { x: rect.right, y: rect.top }, end: { x: rect.right, y: rect.bottom } }, // Right + { start: { x: rect.left, y: rect.bottom }, end: { x: rect.right, y: rect.bottom } }, // Bottom + { start: { x: rect.left, y: rect.top }, end: { x: rect.left, y: rect.bottom } } // Left + ]; + + // Use checkIntersection function to check if two line segments intersect + for (const edge of edges) { + const result = checkIntersection(edge.start.x,edge.start.y, edge.end.x,edge.end.y, posLink1.x, posLink1.y,posLink2.x,posLink2.y); + if (result.type == "intersecting") { + return true; // There is an overlap + } + } + + return false; // No overlap detected +} \ No newline at end of file diff --git a/src/composables/countIsolatedNodes.ts b/src/composables/countIsolatedNodes.ts new file mode 100644 index 0000000..e6aec4e --- /dev/null +++ b/src/composables/countIsolatedNodes.ts @@ -0,0 +1,36 @@ +import { Network } from "@metabohub/viz-core/src/types/Network"; + +/** + * Count how many nodes have no edges in the network + * @param network the network + * @returns the number of isolated nodes + */ +export function countIsolatedNodes(network: Network): number { + let nb: number = 0; + const nodesCount: { [x: string]: number} = {}; + Object.keys(network.nodes).forEach(nodeId => { + nodesCount[nodeId] = 0; + }); + + // count number of links for each node + network.links.forEach(link => { + nodesCount[link.source.id] += 1; + nodesCount[link.target.id] += 1; + }); + + /* + // get the nodes + for (const [key, value] of Object.entries(nodesCount)) { + ... + // if value == 0 + // get key + } + */ + Object.values(nodesCount).forEach(count => { + if (count == 0) { + nb += 1; + } + }); + + return nb; +} \ No newline at end of file diff --git a/src/composables/importNetwork.ts b/src/composables/importNetwork.ts new file mode 100644 index 0000000..528dee0 --- /dev/null +++ b/src/composables/importNetwork.ts @@ -0,0 +1,93 @@ +import type { Ref } from "vue"; +import type { Network } from "@metabohub/viz-core/src/types/Network"; +import type { GraphStyleProperties } from "@metabohub/viz-core/src//types/GraphStyleProperties"; + +//import { readJsonGraph } from "./readJson"; +import { readJsonGraph } from "@metabohub/viz-core"; +import { sbml2json } from "./SBMLtoJSON"; + + + +/** + * Import network at JSONGraph format from an URL. + * @param url URL to get network data + * @param network Reference to network object + * @param networkStyle Reference to networkStyle object + * @param callbackFunction Function to call after network load (opt) + */ +export function importNetworkFromURL(url: string, network: Ref<Network>, networkStyle: Ref<GraphStyleProperties>, callbackFunction = () => {}): void { + setTimeout(async function() { + let data:string = await getContentFromURL(url); + // Check if the data is XML + if (data.startsWith('<?xml')) { + // Convert XML to JSON + data = JSON.stringify(await sbml2json(data)); + } + const graphData = readJsonGraph(data); + networkStyle.value = graphData.networkStyle; + loadNetwork(graphData.network, network).then(() => { + callbackFunction(); + }); + }, 1); +} + + +/** + * Import network at JSONGraph format from a file. + * @param file File to get network data + * @param network Reference to network object + * @param networkStyle Reference to networkStyle object + * @param callbackFunction Function to call after network load (opt) + */ + +export function importNetworkFromFile(file: File, network: Ref<Network>, networkStyle: Ref<GraphStyleProperties>, callbackFunction = () => {}): void { + const reader = new FileReader(); + reader.onload = async function () { + let data = reader.result as string; + if (data.startsWith('<?xml')) { + // Convert XML to JSON + data = JSON.stringify(await sbml2json(data)); + } + const networkData = readJsonGraph(data); + networkStyle.value = networkData.networkStyle; + loadNetwork(networkData.network, network).then(() => { + callbackFunction(); + }); + } + + reader.readAsText(file); +} + + +/** + * Make async the step where the data are put in network reference. + * That permit to chain with another function like rescale. + * @param data network data + * @param network Reference to network object + */ +async function loadNetwork(data: Network, network: Ref<Network>): Promise<void> { + network.value = data; + } + + +/** + * Fetch url to return data + * @param url URL to fetch + * @returns Return response + */ +export async function getContentFromURL(url: string): Promise<string> { + try { + const response = await fetch(url); + if (!response.ok) { + throw new Error('La requête a échoué avec le statut ' + response.status); + } + const content = await response.text(); + return content; + } catch (error) { + console.error('Une erreur s\'est produite lors de la récupération du contenu du fichier :', error); + throw error; + } + } + + + diff --git a/src/composables/useSubgraphs.ts b/src/composables/useSubgraphs.ts new file mode 100644 index 0000000..1e7a7d8 --- /dev/null +++ b/src/composables/useSubgraphs.ts @@ -0,0 +1,207 @@ +import { Subgraph, TypeSubgraph } from "../types/Subgraph"; +import { SubgraphNetwork } from "../types/SubgraphNetwork"; +import { Graph } from "@viz-js/viz"; +//import { inBiggerCycle } from "./ConvertFromNetwork"; + +/** + * + */ +export function addMainChainClusterViz(vizGraph: Graph, nameMainChain: string, subgraphNetwork:SubgraphNetwork,cycle:boolean=true,isCluster:boolean=true): Graph { + + // get values from cluster and change nodes format : new cluster format (for viz) + let { name, nodes ,childrenSubgraphs: associatedSubgraphs} = subgraphNetwork.mainChains[nameMainChain]; + if(cycle) { + nodes=changeCycleMetanodes(subgraphNetwork,nodes); + } + + // change format + if (isCluster && !name.startsWith("cluster_")) { + name = "cluster_" + name; + } + const clusterViz: SubgraphViz = { + name: name, + nodes: nodes?.map((name: string) => ({ name:name })) || [] + }; + + //add node of children subgraph !!!!!BEWARE : only one level of children!!!! + if (associatedSubgraphs){ + associatedSubgraphs.forEach(subgraph => { + let nodeToAdd =subgraphNetwork[subgraph.type][subgraph.name].nodes; + if(cycle){ + nodeToAdd=changeCycleMetanodes(subgraphNetwork,nodeToAdd); + } + clusterViz.nodes.push(...nodeToAdd.map((name: string) => ({ name:name }))); // add and change format + }); + } + + + // push cluster for viz + if (!Object.keys(vizGraph).includes("subgraphs")) { + vizGraph.subgraphs = []; + } + vizGraph.subgraphs.push(clusterViz); + + return vizGraph; +} + +function changeCycleMetanodes(subgraphNetwork:SubgraphNetwork,listNodeBefore:string[]):string[]{ + const network=subgraphNetwork.network.value; + const listNodeAfter:string[]=[]; + // for each nodes : + listNodeBefore.forEach(node =>{ + // if node is in cycle metanode : + let cycle:string; + if (network.nodes[node].metadata && network.nodes[node].metadata[TypeSubgraph.CYCLEGROUP]){ + cycle = network.nodes[node].metadata[TypeSubgraph.CYCLEGROUP] as string; + //cycle=inBiggerCycle(cycle,subgraphNetwork) + } + if(cycle!==undefined && !(listNodeAfter.includes(cycle))){ + // push node cycle + listNodeAfter.push(cycle); + } + if (cycle===undefined){ + listNodeAfter.push(node); + } + }) + + return listNodeAfter; +} + +export function addClusterDot(subgraph: SubgraphViz): string { + + + let clusterString = `subgraph ${subgraph.name} {\n`; + // add rank + // if ("rank" in subgraph){ + // clusterString+=`{rank="${subgraph.rank}";`; + // } + + // add nodes + subgraph.nodes.forEach((node) => { + clusterString+=`${node.name};`; + }); + // if ("rank" in subgraph){ + // clusterString+=`}\n`; + // } + return clusterString+"}\n"; + } + + + + +// export function addNoConstraint(subgraphNetwork:SubgraphNetwork):SubgraphNetwork{ +// let network=subgraphNetwork.network.value; +// network.links.forEach(link=>{ +// let clusterSource: string[] = []; +// let clusterTarget: string[] = []; +// if ( Object.keys(link.source).includes("metadata") && Object.keys(link.source.metadata).includes("clusters")){ +// clusterSource= link.source.metadata?.clusters ? link.source.metadata.clusters as string[] : []; +// } + +// if ( Object.keys(link.target).includes("metadata") && Object.keys(link.target.metadata).includes("clusters")){ +// clusterTarget= link.target.metadata?.clusters ? link.target.metadata.clusters as string[] : []; +// } +// let sameClusters=true; +// // if same number of cluster : let's check if there are the same +// if (clusterTarget.length===clusterSource.length){ +// clusterTarget.sort; +// clusterSource.sort; +// for (let i = 0; i < clusterTarget.length; ++i) { +// if (clusterTarget[i] !== clusterSource[i]){ +// sameClusters=false; +// } +// } +// }else{ +// // if not the same number of cluster : the two nodes can't be in the exact same clusters +// sameClusters=false; +// } + +// if (!sameClusters){ +// if(!link.metadata){ +// link.metadata={}; +// } +// link.metadata["constraint"]=false; +// } +// }); + +// return subgraphNetwork; +// } + +// export function addBoldLinkMainChain(subgraphNetwork:SubgraphNetwork):SubgraphNetwork{ +// let network=subgraphNetwork.network.value; +// network.links.forEach(link=>{ +// let mainChainSource: string[] = []; +// let mainChainTarget: string[] = []; +// if ( Object.keys(link.source).includes("metadata") && Object.keys(link.source.metadata).includes(TypeSubgraph.MAIN_CHAIN)){ +// mainChainSource= link.source.metadata.mainChains as string[]; +// } + +// if ( Object.keys(link.target).includes("metadata") && Object.keys(link.target.metadata).includes(TypeSubgraph.MAIN_CHAIN)){ +// mainChainTarget= link.target.metadata.mainChains as string[]; +// } +// // let sameClusters=true; +// // // if same number of cluster, and in a cluster: let's check if there are the same +// // if (clusterTarget.length===clusterSource.length && clusterSource.length!==0){ +// // clusterTarget.sort; +// // clusterSource.sort; +// // for (let i = 0; i < clusterTarget.length; ++i) { +// // if (clusterTarget[i] !== clusterSource[i]){ +// // sameClusters=false; +// // } +// // } +// // }else{ +// // // if not the same number of cluster : the two nodes can't be in the exact same clusters +// // sameClusters=false; +// // } + +// // Check if there is at least one common cluster +// let commonMainChain = mainChainSource.some(mainchain => mainChainTarget.includes(mainchain)); + +// if (commonMainChain){ +// if(!link.classes){ +// link.classes=[]; +// } +// if (!(link.classes.includes(TypeSubgraph.MAIN_CHAIN))){ +// link.classes.push(TypeSubgraph.MAIN_CHAIN); +// } +// }else{ +// if(link.classes){ +// link.classes = link.classes.filter((c) => c !== TypeSubgraph.MAIN_CHAIN); +// } +// } +// }); + +// return subgraphNetwork; +// } + + + +// export function addRedLinkcycleGroup(subgraphNetwork:SubgraphNetwork):SubgraphNetwork{ +// let network=subgraphNetwork.network.value; +// network.links.forEach(link=>{ +// let cycleSource: string; +// let cycleTarget: string; +// if ( Object.keys(link.source).includes("metadata") && Object.keys(link.source.metadata).includes(TypeSubgraph.CYCLEGROUP)){ +// cycleSource=link.source.metadata[TypeSubgraph.CYCLEGROUP] as string; +// } + +// if ( Object.keys(link.target).includes("metadata") && Object.keys(link.target.metadata).includes(TypeSubgraph.CYCLEGROUP)){ +// cycleTarget= link.target.metadata[TypeSubgraph.CYCLEGROUP] as string; +// } +// if (cycleSource && cycleSource===cycleTarget){ +// if(!link.classes){ +// link.classes=[]; +// } +// if (!(link.classes.includes(TypeSubgraph.CYCLEGROUP))){ +// link.classes.push(TypeSubgraph.CYCLEGROUP); +// } +// }else{ +// if(link.classes){ +// link.classes = link.classes.filter((c) => c !== TypeSubgraph.CYCLEGROUP); +// } +// } +// }); + +// return subgraphNetwork; +// } + diff --git a/src/index.ts b/src/index.ts index 946a4b8..525ff2d 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,3 +1,3 @@ -export function add(a: number, b: number): number { - return a + b; -} \ No newline at end of file +import {algorithmOnNetwork} from "./composables/LayoutMain"; + +export {algorithmOnNetwork}; \ No newline at end of file diff --git a/src/types/CoordinatesSize.ts b/src/types/CoordinatesSize.ts new file mode 100644 index 0000000..b7f674b --- /dev/null +++ b/src/types/CoordinatesSize.ts @@ -0,0 +1,11 @@ + +export interface Coordinate { + x: number; + y: number; +} + + +export interface Size { + width: number; + height: number; +} \ No newline at end of file diff --git a/src/types/DFS.ts b/src/types/DFS.ts new file mode 100644 index 0000000..2a0ae39 --- /dev/null +++ b/src/types/DFS.ts @@ -0,0 +1,6 @@ +interface DFS { + dfsOrder: Array<string> + GDSgraph: {[key:string]:Function} // Graph with a format for lib Graph Data Structure + nodesID:Array<string> + visited:Array<boolean> +} \ No newline at end of file diff --git a/src/types/EnumArgs.ts b/src/types/EnumArgs.ts new file mode 100644 index 0000000..ee693a2 --- /dev/null +++ b/src/types/EnumArgs.ts @@ -0,0 +1,35 @@ +export enum StartNodesType { + SOURCE_ONLY = "source_only", + SOURCE_ALL="source_all", + RANK_ONLY = "rank_only", + RANK_SOURCE = "rank_source", + RANK_SOURCE_ALL="rank_source_all", + ALL = "all", +} + +export enum PathType { + LONGEST='longest', + ALL_LONGEST='all_longest', + ALL='all' +} + +export enum Ordering { + DEFAULT = "", + IN = "in", + OUT = "out" +} + +export enum Algo{ + DEFAULT, + FORCE, + VIZ, + ALGO, // default : main chain with all longest + ALGO_V0, // no main chain + ALGO_V1, // main chain with longest + ALGO_V3 // main chain with all paths +} + +export enum VizArgs{ + RANKSEP="ranksep", + NODESEP="nodesep", +} \ No newline at end of file diff --git a/src/types/FormatJSONGraphXML.ts b/src/types/FormatJSONGraphXML.ts new file mode 100644 index 0000000..7587a32 --- /dev/null +++ b/src/types/FormatJSONGraphXML.ts @@ -0,0 +1,58 @@ +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; + +export interface JSONGraphFormat { + graph: { + id: any; + type: string; + metadata: { + style:GraphStyleProperties; + }; + nodes: { + [x: string]: { + id: string; + metadata: { + classes?: string[]; + position?: { + x: number; + y: number; + + }; + }; + label: string; + }; + }; + edges: { + id: string; + source: string; + target: string; + metadata: { + classes?: string[]; + }; + }[]; + }; +} + +export interface XMLSpecies { + $: { + compartment: string; + id: string; + name: string; + species: string + } +} + +export interface XMLReactions { + $: { + id: string; + name: string; + reversible:string; + }, + listOfReactants: { + speciesReference: any[]|{} + }, + listOfProducts: { + speciesReference: Partial<XMLSpecies>[]|Partial<XMLSpecies> + } +} + + diff --git a/src/types/FormatJsonStyle.ts b/src/types/FormatJsonStyle.ts new file mode 100644 index 0000000..9d54eb7 --- /dev/null +++ b/src/types/FormatJsonStyle.ts @@ -0,0 +1,8 @@ + +export interface JsonStyle { + biosource?: {[key:string]:string|number}, + generalStyle?:{[key:string]:string|number|boolean}, + linkStyle?:{[key:string]:string|number|boolean}, + metaboliteStyle?:{[key:string]:string|number|boolean}, + reactionStyle?:{[key:string]:string|number|boolean}, +} diff --git a/src/types/FormatJsonViz.ts b/src/types/FormatJsonViz.ts new file mode 100644 index 0000000..4f95bc5 --- /dev/null +++ b/src/types/FormatJsonViz.ts @@ -0,0 +1,17 @@ + +/** + * This file contains the types for the Json object return by the viz API + */ + +export interface JsonViz { + directed?: boolean, + edges:Array<EdgeViz>, + objects:Array<ObjectsViz> +} + +interface ObjectsViz { + name: string, + pos?: string, + bb?: string, + nodes?:Array<number> // the index in the JsonViz.objects for all nodes +} diff --git a/src/types/NetworkLayout.ts b/src/types/NetworkLayout.ts new file mode 100644 index 0000000..ec8bae2 --- /dev/null +++ b/src/types/NetworkLayout.ts @@ -0,0 +1,37 @@ +import { Link } from "@metabohub/viz-core/src/types/Link"; +import { Node } from "@metabohub/viz-core/src/types/Node"; +import type { Network } from "@metabohub/viz-core/src/types/Network"; +import { TypeSubgraph } from "./Subgraph"; + +/** + * This file contains the types for the NetworkLayout object : a network with nodes and links information and metadataLayout for nodes and links. + * MetadataLayout is used to store the information to calculate the layout. + */ + +export interface NetworkLayout extends Network { + nodes: { + [key: string]: NodeLayout; + }; + links: Array<LinkLayout>; + } + + +export interface NodeLayout extends Node { + metadataLayout?: { + rank? : number; + order? : number; + reversibleNodeVersion? : string; // id of the duplicated version of the node (the reversed node) + isReversedVersion? : boolean; // true if is the duplicated version, false if original node + [TypeSubgraph.MAIN_CHAIN]?:string[], + [TypeSubgraph.SECONDARY_CHAIN]?:string[], + [TypeSubgraph.CYCLE]?:string[], + [TypeSubgraph.CYCLEGROUP]?:string, + } +} + + +export interface LinkLayout extends Link { + source: NodeLayout; + target: NodeLayout; + metadataLayout?: {[key: string]: string | number | {[key: string]: string | number} | Array<string> | boolean}; +} \ No newline at end of file diff --git a/src/types/Parameters.ts b/src/types/Parameters.ts new file mode 100644 index 0000000..ee4c1f3 --- /dev/null +++ b/src/types/Parameters.ts @@ -0,0 +1,72 @@ +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { PathType, StartNodesType } from "./EnumArgs"; +import { getPathSourcesToTargetNode } from "../composables/LayoutMainChain"; + +/** + * This file contains the types for the Parameters object : all parameters for the algorithm. + * And an default object for the parameters. + */ + + +export interface Parameters { + + doDuplicateSideCompounds: boolean; // do the step duplicate side compounds ? + doPutAsideSideCompounds: boolean; // do the step put aside side compounds ? + + doReactionReversible: boolean; // do the step duplication and choice of reaction reversible ? + + doMainChain: boolean; // do the step main chain ? + getSubgraph : (network: Network, sources: Array<string>,merge?:boolean,pathType?:PathType) => {[key:string]:{nodes:Array<string>, height:number}}; // function to get subgraph (main chain) + startNodeTypeMainChain: StartNodesType; // for the main chain step : which are the start nodes? + pathType: PathType; // main chain step : longest path , all longest paths or all paths + merge: boolean; // merging main chain ? If not : nodes can be in several clusters + doMiniBranch: boolean; // adding minibranch for main chains ? + groupOrCluster: "group" | "cluster"; //main chain as group or cluster in DOT + + doCycle: boolean; // do the step cycle ? + allowInternalCycles: boolean; // allow internal cycles for tangent one ? + + addNodes: boolean; // adding node at the beginning of the DOT ? + ordering: boolean; // reorder edges in DOT ? (for cycle step) + + dpi: number; // DPI for the image (viz parameter) + + numberNodeOnEdge: number; // space between two rank, with size of a node as unit (mean of all size) + factorLengthSideCompounds: number; // % of the lenght of minimal edge to use as lenght of side compounds edges + + shiftCoord?: boolean; // shift coordinates : center is at the previous coord (because of top left corner) + + //userSources: string[]; + //onlyUserSources: boolean; +} + +export let defaultParameters: Parameters = { + doDuplicateSideCompounds: true, // user can change this parameter + doPutAsideSideCompounds: true, // user can change this parameter + + doReactionReversible: true, // user can change this parameter + + doMainChain: false, // user can change this parameter + getSubgraph : getPathSourcesToTargetNode, + startNodeTypeMainChain: StartNodesType.RANK_SOURCE, // usefull to allow user to change this parameter with RANK_ONLY or SOURCE_ONLY ? (if source-only, put source_all for reaction rev and no first viz) + pathType: PathType.ALL_LONGEST, // user can change this parameter + merge: true, // no choice for now, but when edit of algo, add option where no merge and keep the largest subgraph + doMiniBranch: true, // usefull choice ? run metrix to see if it's usefull + groupOrCluster: "cluster", + + doCycle: false, // user can change this parameter + allowInternalCycles: false, + + addNodes: true, + ordering: true, + + dpi: 72, + + numberNodeOnEdge: 3, // user can change this parameter, but doesn't work for cycle edge length + factorLengthSideCompounds: 1/2, // user can change this parameter + + shiftCoord: true, + + //userSources: [], + //onlyUserSources: false, +}; \ No newline at end of file diff --git a/src/types/Reaction.ts b/src/types/Reaction.ts new file mode 100644 index 0000000..481365f --- /dev/null +++ b/src/types/Reaction.ts @@ -0,0 +1,34 @@ + +/** + * This file contains the types for the Reaction : use to apply side compound motif + */ + +export enum MetaboliteType { + REACTANT='reactant', + PRODUCT='product', +} + +// export enum MinMedianMax { +// MEDIAN='median', +// MIN='min', +// MAX='max' +// } + +export interface Reaction { + id:string + sideCompoundsReactants: Array<string> + sideCompoundsProducts:Array<string> + metabolitesAngles:{[key:string]:{angle:number,type:MetaboliteType}} + //linkMedianMinMaxLength?:{median:number,min:number,max:number} + intervalsAvailables?: ReactionInterval[] + angleSpacingReactant?:number + angleSpacingProduct?:number +} + +export interface ReactionInterval { + typeInterval: number; + // 0 if reactant then product, 1 if product then reactant, + // but if the x-axis is between the two (special case) : it is 2 when reactant is the smaller angle, 3 when product is the smaller angle + reactant: string; + product: string; +} \ No newline at end of file diff --git a/src/types/Subgraph.ts b/src/types/Subgraph.ts new file mode 100644 index 0000000..8e185dd --- /dev/null +++ b/src/types/Subgraph.ts @@ -0,0 +1,42 @@ +import { Coordinate } from "./CoordinatesSize"; +import { Ordering } from "./EnumArgs"; + +/** + * This file contains the types for the Subgraph object : main chain, secondary chain, cycle and cycle group. + * A subgraph can be considered as a metanode in the network. Its width and height are the width and height of the rectangle containing the metanode. + * Its position is the center of the rectangle, and the originalPosition is the position of the center of the metanode before the layout (when coordinates precalculated). + */ + +export enum TypeSubgraph { + MAIN_CHAIN = "mainChains", + SECONDARY_CHAIN = "secondaryChains", + CYCLE = "cycles", + CYCLEGROUP="cyclesGroup" +} + +export interface Subgraph { + name: string; + classes?: Array<string>; + nodes: Array<string>; + type?: TypeSubgraph; + + // if subgraph associated with another subgraph (like secondary chain associated with a main chain) : + parentSubgraph?: {name:string,type:TypeSubgraph}; // the "parent" subgraph + childrenSubgraphs?: Array<{name:string,type:TypeSubgraph}>; // the "children" subgraphs + + rank?:string; + ordering?:Ordering; + + width?:number; + height?:number; + position?:Coordinate; + originalPosition?:Coordinate; // if metanode : the metanode center not well positionned (precalulated position) + + precalculatedNodesPosition?: {[key: string]: Coordinate}; // if metanode : the position of the nodes in the metanode + + metadata?: {[key: string]: string | number| boolean | {[key: string]: string | number} | Array<string>}; +} + + + + diff --git a/src/types/SubgraphNetwork.ts b/src/types/SubgraphNetwork.ts new file mode 100644 index 0000000..f774499 --- /dev/null +++ b/src/types/SubgraphNetwork.ts @@ -0,0 +1,37 @@ +import { Network } from "@metabohub/viz-core/src/types/Network"; +import { Node } from "@metabohub/viz-core/src/types/Node"; +import { Subgraph } from "./Subgraph"; +import { Ref } from "vue"; +import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties"; +import { NetworkLayout } from "./NetworkLayout"; + +/** + * This file contains the types for the SubgraphNetwork object : a network with nodes and links information, stats information (minimal length of edge for example), attributs for viz, subgraphs (main chains, secondary chains, cycles and cycle groups) and side compounds. + */ + +export interface SubgraphNetwork { + network: Ref<NetworkLayout>; + networkStyle: Ref<GraphStyleProperties>; + + stats?:{minEdgeLengthPixel?:number}; + + attributs?: AttributesViz; + + mainChains?: { + [key: string]: Subgraph + } + secondaryChains?:{ + [key: string]: Subgraph + } + cycles?:{ + [key:string]:Subgraph + } + // The cycle metanode : + cyclesGroup?:{ + [key:string]:Subgraph + } + + sideCompounds?:{ + [key:string]:{reactants:Array<Node>,products:Array<Node>} + } +} \ No newline at end of file diff --git a/src/types/VizType.ts b/src/types/VizType.ts new file mode 100644 index 0000000..7f13d30 --- /dev/null +++ b/src/types/VizType.ts @@ -0,0 +1,37 @@ +// Graph already accessible (see the format below, but implemented in library), but the other interface can't be exported so there are duplicated here +// export interface Graph { +// name?: string +// strict?: boolean +// directed?: boolean +// graphAttributes?: Attributes +// nodeAttributes?: Attributes +// edgeAttributes?: Attributes +// nodes?: Node[] +// edges?: Edge[] +// subgraphs?: Subgraph[] +// } + +interface AttributesViz { + [name: string]: string | number | boolean + } + +interface NodeViz { +name: string +attributes?: AttributesViz +} + +interface EdgeViz { +tail: string +head: string +attributes?: AttributesViz +} + +interface SubgraphViz { +name?: string +graphAttributes?: AttributesViz +nodeAttributes?: AttributesViz +edgeAttributes?: AttributesViz +nodes?: NodeViz[] +edges?: EdgeViz[] +subgraphs?: SubgraphViz[] +} -- GitLab From 831b899ed3ff174949617757b73e60295d3309f0 Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 10 Sep 2024 11:56:41 +0200 Subject: [PATCH 7/8] name package --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 7436292..9638aad 100644 --- a/package.json +++ b/package.json @@ -1,5 +1,5 @@ { - "name": "@metabohub/ts-package-name", + "name": "@metabohub/metabolic-layout", "version": "0.0.0", "private": false, "scripts": { -- GitLab From dc08ce2f838a9c3e4ea15622ccad6e029bc248b4 Mon Sep 17 00:00:00 2001 From: Elora-V <elora95.vigo@gmail.com> Date: Tue, 10 Sep 2024 14:37:29 +0200 Subject: [PATCH 8/8] template test file --- src/__tests__/add.test.ts | 6 - .../__tests__/2_reac_1_metab_4514.xml | 68 ---------- .../__tests__/GetSetAttributsNodes.spec.ts | 16 +++ src/composables/__tests__/SBMLtoJSON.spec.ts | 122 ------------------ .../__tests__/countIntersection.spec.ts | 33 ----- .../__tests__/countIsolatedNodes.spec.ts | 76 ----------- 6 files changed, 16 insertions(+), 305 deletions(-) delete mode 100644 src/__tests__/add.test.ts delete mode 100644 src/composables/__tests__/2_reac_1_metab_4514.xml create mode 100644 src/composables/__tests__/GetSetAttributsNodes.spec.ts delete mode 100644 src/composables/__tests__/SBMLtoJSON.spec.ts delete mode 100644 src/composables/__tests__/countIntersection.spec.ts delete mode 100644 src/composables/__tests__/countIsolatedNodes.spec.ts diff --git a/src/__tests__/add.test.ts b/src/__tests__/add.test.ts deleted file mode 100644 index 6ba006f..0000000 --- a/src/__tests__/add.test.ts +++ /dev/null @@ -1,6 +0,0 @@ -import { add } from '../'; - -test('adds two numbers correctly', () => { - const result = add(2, 3); - expect(result).toBe(5); -}); \ No newline at end of file diff --git a/src/composables/__tests__/2_reac_1_metab_4514.xml b/src/composables/__tests__/2_reac_1_metab_4514.xml deleted file mode 100644 index 6dd1cba..0000000 --- a/src/composables/__tests__/2_reac_1_metab_4514.xml +++ /dev/null @@ -1,68 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<sbml fbc:required="false" groups:required="false" level="3" version="2" xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model fbc:strict="true" id="_128bceb7_36b8_4227_b83a_11ca91c43b4f" metaid="_128bceb7_36b8_4227_b83a_11ca91c43b4f" name="history_test"> - <fbc:listOfGeneProducts> - <fbc:geneProduct fbc:id="g1" fbc:label="g1" fbc:name="g1"/> - </fbc:listOfGeneProducts> - <groups:listOfGroups> - <groups:group groups:id="pp1" groups:kind="classification" groups:name="pp1"> - <groups:listOfMembers> - <groups:member groups:idRef="r1"/> - </groups:listOfMembers> - </groups:group> - </groups:listOfGroups> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> - <unit exponent="-1" kind="second" multiplier="0.00027778" scale="0"/> - <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> - <unit exponent="1" kind="mole" multiplier="1" scale="0"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment constant="true" id="tutu" metaid="_97125884-20a5-4aa0-b78a-c3f1115fc57f" name="tutu" spatialDimensions="3"/> - <compartment constant="true" id="c" metaid="_265b6c07-ad95-4aa0-8064-81b050fb5d9d" name="c" spatialDimensions="3"/> - </listOfCompartments> - <listOfSpecies> - <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="m1" initialAmount="1" metaid="f2b12325-eeb5-4dc0-a770-73f199951f8d" name="m1" sboTerm="SBO:0000240"/> - </listOfSpecies> - <listOfParameters> - <parameter constant="true" id="UPPER_BOUND_9999_0" units="mmol_per_gDW_per_hr" value="9999"/> - <parameter constant="true" id="LOWER_BOUND_0_0" units="mmol_per_gDW_per_hr" value="0"/> - </listOfParameters> - <listOfReactions> - <reaction fbc:lowerFluxBound="LOWER_BOUND_0_0" fbc:upperFluxBound="UPPER_BOUND_9999_0" id="erty" metaid="_6df8d47a-0216-4e17-beb3-8d3e3ec786a9" name="zerty" reversible="false"> - <listOfReactants/> - <listOfProducts/> - </reaction> - <reaction fbc:lowerFluxBound="LOWER_BOUND_0_0" fbc:upperFluxBound="UPPER_BOUND_9999_0" id="r1" metaid="cd8efdf8-c38b-48df-9883-ad09c6748b6d" name="r1" reversible="false"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#cd8efdf8-c38b-48df-9883-ad09c6748b6d"> - <bqbiol:is> - <rdf:Bag> - <rdf:li rdf:resource="https://identifiers.org/ec-code/1.1.1.1"/> - </rdf:Bag> - </bqbiol:is> - <bqbiol:isDescribedBy> - <rdf:Bag> - <rdf:li rdf:resource="https://identifiers.org/pubmed/0"/> - </rdf:Bag> - </bqbiol:isDescribedBy> - </rdf:Description> - </rdf:RDF> - </annotation> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="g1"/> - </fbc:geneProductAssociation> - <listOfReactants> - <speciesReference constant="true" species="m1" stoichiometry="1"/> - </listOfReactants> - <listOfProducts/> - </reaction> - </listOfReactions> - </model> -</sbml> diff --git a/src/composables/__tests__/GetSetAttributsNodes.spec.ts b/src/composables/__tests__/GetSetAttributsNodes.spec.ts new file mode 100644 index 0000000..99eb479 --- /dev/null +++ b/src/composables/__tests__/GetSetAttributsNodes.spec.ts @@ -0,0 +1,16 @@ +import "../GetSetAttributsNodes"; + +describe('GetSetAttributsNodes', () => { + test("name test", () => { + // DATA + + // TEST + + // EXPECT + expect(false).toEqual(true); + }); + + it('should return true', () => { + expect(false).toEqual(true); + }); +}); diff --git a/src/composables/__tests__/SBMLtoJSON.spec.ts b/src/composables/__tests__/SBMLtoJSON.spec.ts deleted file mode 100644 index ac819a1..0000000 --- a/src/composables/__tests__/SBMLtoJSON.spec.ts +++ /dev/null @@ -1,122 +0,0 @@ -import { expect, describe, test } from 'vitest'; -import { sbml2json } from '../SBMLtoJSON'; -import type { JSONGraphFormat } from "@/types/JSONGraphFormat"; - -describe('sbml2json.ts', () => { - test('should return a JSON with 3 nodes', async () => { - fetch('2_reac_1_metab.xml') - .then(async (res) => { - // DATA - const sbmlString: string = await res.text(); - - // FUNCTION - const result: JSONGraphFormat = await sbml2json(sbmlString); - const nodes = result.graph.nodes; - - // EXPECT - expect(nodes).toEqual(3); - }) - .catch(() => { - console.log('could not fetch the test data !'); - return false; - }); - }); - test('the nodes should have a position', async () => { - fetch('2_reac_1_metab.xml') - .then(async (res) => { - // DATA - const sbmlString: string = await res.text(); - - // FUNCTION - const result: JSONGraphFormat = await sbml2json(sbmlString); - const nodes = result.graph.nodes; - - // EXPECT - Object.values(nodes).forEach((node) => { - expect(node.metadata.position!.x).toBeDefined(); - expect(node.metadata.position!.y).toBeDefined(); - }); - }) - .catch(() => { - console.log('could not fetch the test data !'); - return false; - }); - }); - test('there should 2 nodes for the reactions', async () => { - fetch('2_reac_1_metab.xml') - .then(async (res) => { - // DATA - const sbmlString: string = await res.text(); - - // FUNCTION - const result: JSONGraphFormat = await sbml2json(sbmlString); - const nodes = result.graph.nodes; - - // EXPECT - expect(nodes['erty']).toBeDefined(); - expect(nodes['erty'].metadata.classes).toContain('reaction'); - expect(nodes['r1']).toBeDefined(); - expect(nodes['r1'].metadata.classes).toContain('reaction'); - }) - .catch(() => { - console.log('could not fetch the test data !'); - return false; - }); - }); - test('there should 1 node for the metabolite', async () => { - fetch('2_reac_1_metab.xml') - .then(async (res) => { - // DATA - const sbmlString: string = await res.text(); - - // FUNCTION - const result: JSONGraphFormat = await sbml2json(sbmlString); - const nodes = result.graph.nodes; - - // EXPECT - expect(nodes['m1']).toBeDefined(); - expect(nodes['m1'].metadata.classes).toContain('metabolite'); - }) - .catch(() => { - console.log('could not fetch the test data !'); - return false; - }); - }); - test('should return a JSON with 1 edge', async () => { - fetch('2_reac_1_metab.xml') - .then(async (res) => { - // DATA - const sbmlString: string = await res.text(); - - // FUNCTION - const result: JSONGraphFormat = await sbml2json(sbmlString); - const edges = result.graph.edges; - - // EXPECT - expect(edges.length).toEqual(1); - }) - .catch(() => { - console.log('could not fetch the test data !'); - return false; - }); - }); - test('the edge should be between "m1" and "r1"', async () => { - fetch('2_reac_1_metab.xml') - .then(async (res) => { - // DATA - const sbmlString: string = await res.text(); - - // FUNCTION - const result: JSONGraphFormat = await sbml2json(sbmlString); - const edge = result.graph.edges[0]; - - // EXPECT - expect(edge.source).toEqual('m1'); - expect(edge.target).toEqual('r1'); - }) - .catch(() => { - console.log('could not fetch the test data !'); - return false; - }); - }); -}); diff --git a/src/composables/__tests__/countIntersection.spec.ts b/src/composables/__tests__/countIntersection.spec.ts deleted file mode 100644 index 7b5994c..0000000 --- a/src/composables/__tests__/countIntersection.spec.ts +++ /dev/null @@ -1,33 +0,0 @@ -import { describe, expect, test } from "vitest"; -import { countIntersection } from "../countIntersections"; -import { Network } from "@metabohub/viz-core/src/types/Network"; -import * as fs from 'fs'; -import { readJsonGraph } from "../readJson"; - -function getNetworkFromUrl(url: string): Network { - return (readJsonGraph(fs.readFileSync(url, { encoding: 'utf8', flag: 'r' }))).network; -} - -describe("countIntersections.ts", () => { - test("should return 1 when given a network with one crossing", async () => { - // DATA - const network: Network = getNetworkFromUrl('public/test_intersect/network_one_crossing.json'); - - // TEST - const result = countIntersection(network); - - // EXPECT - expect(result).toEqual(1); - }); - - test("should return 2 when given a network with 2 crossings", () => { - // DATA - const network: Network = getNetworkFromUrl('public/test_intersect/network_two_crossings.json'); - - // TEST - const result = countIntersection(network); - - // EXPECT - expect(result).toEqual(2); - }); -}); diff --git a/src/composables/__tests__/countIsolatedNodes.spec.ts b/src/composables/__tests__/countIsolatedNodes.spec.ts deleted file mode 100644 index fb9634e..0000000 --- a/src/composables/__tests__/countIsolatedNodes.spec.ts +++ /dev/null @@ -1,76 +0,0 @@ -import { describe, expect, test } from "vitest"; -import { countIsolatedNodes } from "../countIsolatedNodes"; -import { Network } from "@metabohub/viz-core/src/types/Network"; -import { Node } from "@metabohub/viz-core/src/types/Node"; - -describe("countIsolatedNodes.ts", () => { - test("should return 0 when all the nodes have >= 1 link", () => { - // DATA - const nodes: { [key: string]: Node } = { - "a": { - id: "a", - x: 0, - y: 0 - }, - "b": { - id: "b", - x: 0, - y: 0 - } - }; - const network: Network = { - id: "test", - nodes: nodes, - links: [ - { - id: "a_b", - source: nodes.a, - target: nodes.b - } - ] - }; - - // FUNCTION - const result = countIsolatedNodes(network); - - // EXPECT - expect(result).toEqual(0); - }); - test("should return 1 when there is an isolated node", () => { - // DATA - const nodes: { [key: string]: Node } = { - "a": { - id: "a", - x: 0, - y: 0 - }, - "b": { - id: "b", - x: 0, - y: 0 - }, - "c": { - id: "c", - x: 0, - y: 0 - } - }; - const network: Network = { - id: "test", - nodes: nodes, - links: [ - { - id: "a_b", - source: nodes.a, - target: nodes.b - } - ] - }; - - // FUNCTION - const result = countIsolatedNodes(network); - - // EXPECT - expect(result).toEqual(1); - }); -}); \ No newline at end of file -- GitLab