diff --git a/env.d.ts b/env.d.ts
index c1321fe6fef0779b5ceac3f592597fd8bd27f19c..e955ccfb3b567884184daede71782b4770d72ad9 100644
--- a/env.d.ts
+++ b/env.d.ts
@@ -1,6 +1 @@
-declare module '@metabohub/viz-core';
-declare module 'dagrejs';
-declare module '@metabohub/viz-context-menu';
declare module 'line-intersect';
-// declare module 'dagrejs/dist/dagre.js';
-// declare module 'cytoscape';
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index 6b1f97e7c1506dd17b54de46c40169fe76f6d51b..e720393f253a2addf25b10b924ff93142c586526 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,13 +10,9 @@
"license": "Apache-2.0",
"dependencies": {
"@mdi/font": "^7.4.47",
- "@metabohub/viz-context-menu": "^0.0.2",
- "@metabohub/viz-core": "^0.6.1",
"@types/d3": "^7.4.3",
- "cytoscape": "^3.30.2",
"d3": "^7.9.0",
- "line-intersect": "^3.0.0",
- "xml2js": "^0.6.2"
+ "line-intersect": "^3.0.0"
},
"devDependencies": {
"@eslint/js": "^9.10.0",
@@ -24,12 +20,7 @@
"@types/jest": "^29.5.12",
"@types/jsdom": "^21.1.6",
"@types/node": "^20.11.14",
- "@types/xml2js": "^0.4.14",
"@viz-js/viz": "^3.4.0",
- "cytoscape": "^3.30.2",
- "cytoscape-cose-bilkent": "^3.0.0",
- "cytoscape-fcose": "^2.2.0",
- "dagrejs": "^0.2.1",
"eslint": "^9.10.0",
"graph-data-structure": "^3.5.0",
"jest": "^29.7.0",
@@ -205,6 +196,7 @@
"version": "7.24.8",
"resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.24.8.tgz",
"integrity": "sha512-pO9KhhRcuUyGnJWwyEgnRJTSIZHiT+vMD0kPeD+so0l7mxkMT19g3pjY9GTnHySck/hDzq+dtW/4VgnMkippsQ==",
+ "dev": true,
"engines": {
"node": ">=6.9.0"
}
@@ -213,6 +205,7 @@
"version": "7.24.7",
"resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.24.7.tgz",
"integrity": "sha512-rR+PBcQ1SMQDDyF6X0wxtG8QyLCgUB0eRAGguqRLfkCA87l7yAP7ehq8SNj96OOGTO8OBV70KhuFYcIkHXOg0w==",
+ "dev": true,
"engines": {
"node": ">=6.9.0"
}
@@ -330,6 +323,7 @@
"version": "7.25.6",
"resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.25.6.tgz",
"integrity": "sha512-trGdfBdbD0l1ZPmcJ83eNxB9rbEax4ALFTF7fN386TMYbeCQbyme5cOEXQhbGXKebwGaB/J52w1mrklMcbgy6Q==",
+ "dev": true,
"dependencies": {
"@babel/types": "^7.25.6"
},
@@ -553,6 +547,7 @@
"version": "7.25.6",
"resolved": "https://registry.npmjs.org/@babel/types/-/types-7.25.6.tgz",
"integrity": "sha512-/l42B1qxpG6RdfYf343Uw1vmDjeNhneUXtzhojE7pDgfpEypmRhI6j1kr17XCVv4Cgl9HdAiQY2x0GwKm7rWCw==",
+ "dev": true,
"dependencies": {
"@babel/helper-string-parser": "^7.24.8",
"@babel/helper-validator-identifier": "^7.24.7",
@@ -1569,7 +1564,7 @@
"version": "0.3.5",
"resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.5.tgz",
"integrity": "sha512-IzL8ZoEDIBRWEzlCcRhOaCupYyN5gdIK+Q6fbFdPDg6HqX6jpkItn7DFIpW9LQzXG6Df9sA7+OKnq0qlz/GaQg==",
- "devOptional": true,
+ "dev": true,
"dependencies": {
"@jridgewell/set-array": "^1.2.1",
"@jridgewell/sourcemap-codec": "^1.4.10",
@@ -1583,7 +1578,7 @@
"version": "3.1.2",
"resolved": "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.2.tgz",
"integrity": "sha512-bRISgCIjP20/tbWSPWMEi54QVPRZExkuD9lJL+UIxUKtwVJA8wW1Trb1jMs1RFXo1CBTNZ/5hpC9QvmKWdopKw==",
- "devOptional": true,
+ "dev": true,
"engines": {
"node": ">=6.0.0"
}
@@ -1592,32 +1587,22 @@
"version": "1.2.1",
"resolved": "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.2.1.tgz",
"integrity": "sha512-R8gLRTZeyp03ymzP/6Lil/28tGeGEzhx1q2k703KGWRAI1VdvPIXdG70VJc2pAMw3NA6JKL5hhFu1sJX0Mnn/A==",
- "devOptional": true,
+ "dev": true,
"engines": {
"node": ">=6.0.0"
}
},
- "node_modules/@jridgewell/source-map": {
- "version": "0.3.6",
- "resolved": "https://registry.npmjs.org/@jridgewell/source-map/-/source-map-0.3.6.tgz",
- "integrity": "sha512-1ZJTZebgqllO79ue2bm3rIGud/bOe0pP5BjSRCRxxYkEZS8STV7zN84UBbiYu7jy+eCKSnVIUgoWWE/tt+shMQ==",
- "optional": true,
- "peer": true,
- "dependencies": {
- "@jridgewell/gen-mapping": "^0.3.5",
- "@jridgewell/trace-mapping": "^0.3.25"
- }
- },
"node_modules/@jridgewell/sourcemap-codec": {
"version": "1.5.0",
"resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.5.0.tgz",
- "integrity": "sha512-gv3ZRaISU3fjPAgNsriBRqGWQL6quFx04YMPW/zD8XMLsU32mhCCbfbO6KZFLjvYpCZ8zyDEgqsgf+PwPaM7GQ=="
+ "integrity": "sha512-gv3ZRaISU3fjPAgNsriBRqGWQL6quFx04YMPW/zD8XMLsU32mhCCbfbO6KZFLjvYpCZ8zyDEgqsgf+PwPaM7GQ==",
+ "dev": true
},
"node_modules/@jridgewell/trace-mapping": {
"version": "0.3.25",
"resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.25.tgz",
"integrity": "sha512-vNk6aEwybGtawWmy/PzwnGDOjCkLWSD2wqvjGGAgOAwCGWySYXfYoxt00IJkTF+8Lb57DwOb3Aa0o9CApepiYQ==",
- "devOptional": true,
+ "dev": true,
"dependencies": {
"@jridgewell/resolve-uri": "^3.1.0",
"@jridgewell/sourcemap-codec": "^1.4.14"
@@ -1628,30 +1613,6 @@
"resolved": "https://registry.npmjs.org/@mdi/font/-/font-7.4.47.tgz",
"integrity": "sha512-43MtGpd585SNzHZPcYowu/84Vz2a2g31TvPMTm9uTiCSWzaheQySUcSyUH/46fPnuPQWof2yd0pGBtzee/IQWw=="
},
- "node_modules/@metabohub/viz-context-menu": {
- "version": "0.0.2",
- "resolved": "https://forgemia.inra.fr/api/v4/projects/11129/packages/npm/@metabohub/viz-context-menu/-/@metabohub/viz-context-menu-0.0.2.tgz",
- "integrity": "sha1-851aHxYa7Y9LimYhpJEgXdatdkQ=",
- "dependencies": {
- "@mdi/font": "^7.4.47",
- "roboto-fontface": "*",
- "vue": "^3.4.15",
- "vuetify": "^3.5.2",
- "webfontloader": "^1.6.28"
- }
- },
- "node_modules/@metabohub/viz-core": {
- "version": "0.6.1",
- "resolved": "https://forgemia.inra.fr/api/v4/projects/8209/packages/npm/@metabohub/viz-core/-/@metabohub/viz-core-0.6.1.tgz",
- "integrity": "sha1-OtkeLt1AEBpOMOIT8gszu3tftyQ=",
- "dependencies": {
- "@vueuse/core": "^10.7.0",
- "d3": "^7.8.5",
- "lodash-es": "^4.17.21",
- "uuid": "^9.0.1",
- "vue": "^3.3.4"
- }
- },
"node_modules/@microsoft/api-extractor": {
"version": "7.43.0",
"resolved": "https://registry.npmjs.org/@microsoft/api-extractor/-/api-extractor-7.43.0.tgz",
@@ -2578,7 +2539,7 @@
"version": "1.0.5",
"resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.5.tgz",
"integrity": "sha512-/kYRxGDLWzHOB7q+wtSUQlFrtcdUccpfy+X+9iMBpHK8QLLhx2wIPYuS5DYtR9Wa/YlZAbIovy7qVdB1Aq6Lyw==",
- "devOptional": true
+ "dev": true
},
"node_modules/@types/geojson": {
"version": "7946.0.14",
@@ -2649,7 +2610,7 @@
"version": "20.12.12",
"resolved": "https://registry.npmjs.org/@types/node/-/node-20.12.12.tgz",
"integrity": "sha512-eWLDGF/FOSPtAvEqeRAQ4C8LSA7M1I7i0ky1I8U7kD1J5ITyW3AsRhQrKVoWf5pFKZ2kILsEGJhsI9r93PYnOw==",
- "devOptional": true,
+ "dev": true,
"dependencies": {
"undici-types": "~5.26.4"
}
@@ -2666,20 +2627,6 @@
"integrity": "sha512-/Ad8+nIOV7Rl++6f1BdKxFSMgmoqEoYbHRpPcx3JEfv8VRsQe9Z4mCXeJBzxs7mbHY/XOZZuXlRNfhpVPbs6ZA==",
"dev": true
},
- "node_modules/@types/web-bluetooth": {
- "version": "0.0.20",
- "resolved": "https://registry.npmjs.org/@types/web-bluetooth/-/web-bluetooth-0.0.20.tgz",
- "integrity": "sha512-g9gZnnXVq7gM7v3tJCWV/qw7w+KeOlSHAhgF9RytFyifW6AF61hdT2ucrYhPq9hLs5JIryeupHV3qGk95dH9ow=="
- },
- "node_modules/@types/xml2js": {
- "version": "0.4.14",
- "resolved": "https://registry.npmjs.org/@types/xml2js/-/xml2js-0.4.14.tgz",
- "integrity": "sha512-4YnrRemBShWRO2QjvUin8ESA41rH+9nQGLUGZV/1IDhi3SL9OhdpNC/MrulTWuptXKwhx/aDxE7toV0f/ypIXQ==",
- "dev": true,
- "dependencies": {
- "@types/node": "*"
- }
- },
"node_modules/@types/yargs": {
"version": "17.0.32",
"resolved": "https://registry.npmjs.org/@types/yargs/-/yargs-17.0.32.tgz",
@@ -2907,209 +2854,11 @@
"integrity": "sha512-xbqbRanQCG06yfpnv2hsgX43G26q0JCSjcYSpvmUlx1VRCzA0ngi7zsPn0jW9K2ITchpjQiC1tyO6+zFgS/IyA==",
"dev": true
},
- "node_modules/@vue/compiler-core": {
- "version": "3.5.4",
- "resolved": "https://registry.npmjs.org/@vue/compiler-core/-/compiler-core-3.5.4.tgz",
- "integrity": "sha512-oNwn+BAt3n9dK9uAYvI+XGlutwuTq/wfj4xCBaZCqwwVIGtD7D6ViihEbyYZrDHIHTDE3Q6oL3/hqmAyFEy9DQ==",
- "dependencies": {
- "@babel/parser": "^7.25.3",
- "@vue/shared": "3.5.4",
- "entities": "^4.5.0",
- "estree-walker": "^2.0.2",
- "source-map-js": "^1.2.0"
- }
- },
- "node_modules/@vue/compiler-core/node_modules/estree-walker": {
- "version": "2.0.2",
- "resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-2.0.2.tgz",
- "integrity": "sha512-Rfkk/Mp/DL7JVje3u18FxFujQlTNR2q6QfMSMB7AvCBx91NGj/ba3kCfza0f6dVDbw7YlRf/nDrn7pQrCCyQ/w=="
- },
- "node_modules/@vue/compiler-dom": {
- "version": "3.5.4",
- "resolved": "https://registry.npmjs.org/@vue/compiler-dom/-/compiler-dom-3.5.4.tgz",
- "integrity": "sha512-yP9RRs4BDLOLfldn6ah+AGCNovGjMbL9uHvhDHf5wan4dAHLnFGOkqtfE7PPe4HTXIqE7l/NILdYw53bo1C8jw==",
- "dependencies": {
- "@vue/compiler-core": "3.5.4",
- "@vue/shared": "3.5.4"
- }
- },
- "node_modules/@vue/compiler-sfc": {
- "version": "3.5.4",
- "resolved": "https://registry.npmjs.org/@vue/compiler-sfc/-/compiler-sfc-3.5.4.tgz",
- "integrity": "sha512-P+yiPhL+NYH7m0ZgCq7AQR2q7OIE+mpAEgtkqEeH9oHSdIRvUO+4X6MPvblJIWcoe4YC5a2Gdf/RsoyP8FFiPQ==",
- "dependencies": {
- "@babel/parser": "^7.25.3",
- "@vue/compiler-core": "3.5.4",
- "@vue/compiler-dom": "3.5.4",
- "@vue/compiler-ssr": "3.5.4",
- "@vue/shared": "3.5.4",
- "estree-walker": "^2.0.2",
- "magic-string": "^0.30.11",
- "postcss": "^8.4.44",
- "source-map-js": "^1.2.0"
- }
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- "node_modules/@vue/compiler-sfc/node_modules/estree-walker": {
- "version": "2.0.2",
- "resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-2.0.2.tgz",
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- "dependencies": {
- "@vue/compiler-dom": "3.5.4",
- "@vue/shared": "3.5.4"
- }
- },
- "node_modules/@vue/reactivity": {
- "version": "3.5.4",
- "resolved": "https://registry.npmjs.org/@vue/reactivity/-/reactivity-3.5.4.tgz",
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- }
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- "version": "3.5.4",
- "resolved": "https://registry.npmjs.org/@vue/runtime-core/-/runtime-core-3.5.4.tgz",
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- "peer": true,
- "dependencies": {
- "upath": "^2.0.1"
- },
- "peerDependencies": {
- "vue": "^3.0.0",
- "vuetify": "^3.0.0"
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- },
- "funding": {
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- "bin": {
- "vue-demi-fix": "bin/vue-demi-fix.js",
- "vue-demi-switch": "bin/vue-demi-switch.js"
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- "funding": {
- "url": "https://github.com/sponsors/antfu"
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- },
- "peerDependenciesMeta": {
- "@vue/composition-api": {
- "optional": true
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- "funding": {
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- "hasInstallScript": true,
- "bin": {
- "vue-demi-fix": "bin/vue-demi-fix.js",
- "vue-demi-switch": "bin/vue-demi-switch.js"
- },
- "engines": {
- "node": ">=12"
- },
- "funding": {
- "url": "https://github.com/sponsors/antfu"
- },
- "peerDependencies": {
- "@vue/composition-api": "^1.0.0-rc.1",
- "vue": "^3.0.0-0 || ^2.6.0"
- },
- "peerDependenciesMeta": {
- "@vue/composition-api": {
- "optional": true
- }
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"node_modules/acorn": {
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"resolved": "https://registry.npmjs.org/acorn/-/acorn-8.12.1.tgz",
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- "devOptional": true,
+ "dev": true,
"bin": {
"acorn": "bin/acorn"
},
@@ -3454,7 +3203,7 @@
"version": "1.1.2",
"resolved": "https://registry.npmjs.org/buffer-from/-/buffer-from-1.1.2.tgz",
"integrity": "sha512-E+XQCRwSbaaiChtv6k6Dwgc+bx+Bs6vuKJHHl5kox/BaKbhiXzqQOwK4cO22yElGp2OCmjwVhT3HmxgyPGnJfQ==",
- "devOptional": true
+ "dev": true
},
"node_modules/bundle-require": {
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- "node_modules/vuetify": {
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- "engines": {
- "node": "^12.20 || >=14.13"
- },
- "funding": {
- "type": "github",
- "url": "https://github.com/sponsors/johnleider"
- },
- "peerDependencies": {
- "typescript": ">=4.7",
- "vite-plugin-vuetify": ">=1.0.0",
- "vue": "^3.3.0",
- "webpack-plugin-vuetify": ">=2.0.0"
- },
- "peerDependenciesMeta": {
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- },
- "vite-plugin-vuetify": {
- "optional": true
- },
- "webpack-plugin-vuetify": {
- "optional": true
- }
- }
- },
- "node_modules/w3c-xmlserializer": {
- "version": "5.0.0",
- "resolved": "https://registry.npmjs.org/w3c-xmlserializer/-/w3c-xmlserializer-5.0.0.tgz",
- "integrity": "sha512-o8qghlI8NZHU1lLPrpi2+Uq7abh4GGPpYANlalzWxyWteJOCsr/P+oPBA49TOLu5FTZO4d3F9MnWJfiMo4BkmA==",
- "dev": true,
- "dependencies": {
- "xml-name-validator": "^5.0.0"
+ "xml-name-validator": "^5.0.0"
},
"engines": {
"node": ">=18"
@@ -8760,11 +7823,6 @@
"makeerror": "1.0.12"
}
},
- "node_modules/webfontloader": {
- "version": "1.6.28",
- "resolved": "https://registry.npmjs.org/webfontloader/-/webfontloader-1.6.28.tgz",
- "integrity": "sha512-Egb0oFEga6f+nSgasH3E0M405Pzn6y3/9tOVanv/DLfa1YBIgcv90L18YyWnvXkRbIM17v5Kv6IT2N6g1x5tvQ=="
- },
"node_modules/webidl-conversions": {
"version": "4.0.2",
"resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-4.0.2.tgz",
@@ -8982,26 +8040,6 @@
"xml-js": "bin/cli.js"
}
},
- "node_modules/xml2js": {
- "version": "0.6.2",
- "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.6.2.tgz",
- "integrity": "sha512-T4rieHaC1EXcES0Kxxj4JWgaUQHDk+qwHcYOCFHfiwKz7tOVPLq7Hjq9dM1WCMhylqMEfP7hMcOIChvotiZegA==",
- "dependencies": {
- "sax": ">=0.6.0",
- "xmlbuilder": "~11.0.0"
- },
- "engines": {
- "node": ">=4.0.0"
- }
- },
- "node_modules/xmlbuilder": {
- "version": "11.0.1",
- "resolved": "https://registry.npmjs.org/xmlbuilder/-/xmlbuilder-11.0.1.tgz",
- "integrity": "sha512-fDlsI/kFEx7gLvbecc0/ohLG50fugQp8ryHzMTuW9vSa1GJ0XYWKnhsUx7oie3G98+r56aTQIUB4kht42R3JvA==",
- "engines": {
- "node": ">=4.0"
- }
- },
"node_modules/xmlchars": {
"version": "2.2.0",
"resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz",
diff --git a/package.json b/package.json
index 4e94f435278eac9ab6452f5580adc89887bcb52d..852486561b6b4a7b9542cf5598dc27da704ba42b 100644
--- a/package.json
+++ b/package.json
@@ -8,13 +8,9 @@
},
"dependencies": {
"@mdi/font": "^7.4.47",
- "@metabohub/viz-context-menu": "^0.0.2",
- "@metabohub/viz-core": "^0.6.1",
"@types/d3": "^7.4.3",
- "cytoscape": "^3.30.2",
"d3": "^7.9.0",
- "line-intersect": "^3.0.0",
- "xml2js": "^0.6.2"
+ "line-intersect": "^3.0.0"
},
"devDependencies": {
"@eslint/js": "^9.10.0",
@@ -22,12 +18,7 @@
"@types/jest": "^29.5.12",
"@types/jsdom": "^21.1.6",
"@types/node": "^20.11.14",
- "@types/xml2js": "^0.4.14",
"@viz-js/viz": "^3.4.0",
- "cytoscape": "^3.30.2",
- "cytoscape-cose-bilkent": "^3.0.0",
- "cytoscape-fcose": "^2.2.0",
- "dagrejs": "^0.2.1",
"eslint": "^9.10.0",
"graph-data-structure": "^3.5.0",
"jest": "^29.7.0",
diff --git a/src/composables/AlgorithmDFS.ts b/src/composables/AlgorithmDFS.ts
index 04fb29f65fbf0789e4fa3909276a2be0eaf72f6d..1748b83d6ac29af7db9c01cf437a2ac3e511e31b 100644
--- a/src/composables/AlgorithmDFS.ts
+++ b/src/composables/AlgorithmDFS.ts
@@ -66,18 +66,19 @@ export async function DFSWithSources(network:Network, sources:Array<string>|Star
* @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 async function DFSsourceDAG(network:Network, sources:Array<string>):Promise<{dfs:Array<string>, graph:{[key:string]:Function} }> {
+export async function DFSsourceDAG(network:Network, sources:Array<string>):Promise<{dfs:Array<string>, graph:{[key:string]:Function}}> {
let DFS:DFS=await createGraphForDFS(network);
- sources.forEach(async sourceID =>{
- const nodesID:string[]=DFS.nodesID;
- if (nodesID.length===0) return; // no nodes
+ const nodesID:string[]=DFS.nodesID;
+ if (nodesID.length===0) return { dfs:[],graph:DFS.GDSgraph }; // no nodes
+
+ for (const sourceID of sources){
const sourceIndex=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= await nodeDagDFS(DFS,sourceIndex,[]);
}
- });
+ };
return { dfs:DFS.dfsOrder.reverse(),graph:DFS.GDSgraph };
}
@@ -115,8 +116,8 @@ async function nodeDagDFS(DFS:DFS,nodeIndex:number,currentPath:number[]):Promise
path.push(nodeIndex)
// loop through the children of the node
- DFS.GDSgraph.adjacent(DFS.nodesID[nodeIndex]).sort().forEach(async (childID:string) => {
-
+ const childrenOfNode=DFS.GDSgraph.adjacent(DFS.nodesID[nodeIndex]).sort();
+ for (const childID of childrenOfNode){
// get the index of the child
const childIndex = DFS.nodesID.indexOf(childID);
if(childIndex!==-1){
@@ -136,7 +137,7 @@ async function nodeDagDFS(DFS:DFS,nodeIndex:number,currentPath:number[]):Promise
}
}
- });
+ };
// add the node to the dfs order
DFS.dfsOrder.push(DFS.nodesID[nodeIndex]);
diff --git a/src/composables/CalculateOverlaps.ts b/src/composables/CalculateOverlaps.ts
index f7e09f05b02929a51f32b62f7ffa3efe42a439fc..973b7348b835c37a3790390b0a901fc7f564a9bd 100644
--- a/src/composables/CalculateOverlaps.ts
+++ b/src/composables/CalculateOverlaps.ts
@@ -318,259 +318,3 @@ function nodeEdgeOverlap(centerCoordNode: Coordinate, sizeNode:Size, posLink1: C
function isPointInsideRect(point: Coordinate, rectangle:{left:number,right:number,top:number,bottom:number}):boolean{
return point.x >= rectangle.left && point.x <= rectangle.right && point.y >= rectangle.top && point.y <= rectangle.bottom;
}
-
-
-
-// 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 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 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;
-// }
-
-//______________________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;
-// }
-
-//______________________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;
-// }
diff --git a/src/composables/CalculateRelationCycle.ts b/src/composables/CalculateRelationCycle.ts
index 99f9167467de99a642dceb5f3d99932cd085bcdf..805295cfd63bd5a7404986d075172e8e60322912 100644
--- a/src/composables/CalculateRelationCycle.ts
+++ b/src/composables/CalculateRelationCycle.ts
@@ -252,7 +252,6 @@ export function getNodesPlacedInGroupCycleAsArray(subgraphNetwork:SubgraphNetwor
* 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]:Coordinate}{
- console.log(JSON.stringify(subgraphNetwork));
if (subgraphNetwork[TypeSubgraph.CYCLEGROUP] && groupCycleID in subgraphNetwork[TypeSubgraph.CYCLEGROUP]){
const groupCycle =subgraphNetwork[TypeSubgraph.CYCLEGROUP][groupCycleID];
if (groupCycle.precalculatedNodesPosition){
@@ -333,7 +332,8 @@ export async function sortLinksWithAllGroupCycle(subgraphNetwork:SubgraphNetwork
// change ordre with group cycle
if (orderChange && subgraphNetwork[TypeSubgraph.CYCLEGROUP]){
// adding edge in right order for each group cycle
- for (const groupCycle of Object.keys(subgraphNetwork[TypeSubgraph.CYCLEGROUP])) {
+ const allGroupCycle=Object.keys(subgraphNetwork[TypeSubgraph.CYCLEGROUP]);
+ for (const groupCycle of allGroupCycle) {
const resultSorting = await sortLinksWithGroupCycle(subgraphNetwork, groupCycle);
subgraphNetwork = resultSorting.subgraphNetwork;
links = links.concat(resultSorting.linksOrdered);
@@ -385,7 +385,7 @@ async function sortLinksWithGroupCycle(subgraphNetwork:SubgraphNetwork,groupCycl
}
// get links between the parent (or children) and the group cycle in the right order
- nodeOrder.forEach(async (nodeId) => {
+ for (const nodeId of nodeOrder){
// get links for each node
const newLinksOrder = await getLinksNodeGroupCycle(subgraphNetwork,nodeId,groupCycle,source);
// add links
@@ -393,7 +393,7 @@ async function sortLinksWithGroupCycle(subgraphNetwork:SubgraphNetwork,groupCycl
links.push(newLink);
});
- });
+ };
return { subgraphNetwork:subgraphNetwork,linksOrdered:links };
}else{
return { subgraphNetwork:subgraphNetwork,linksOrdered:[] };
diff --git a/src/composables/CalculateSize.ts b/src/composables/CalculateSize.ts
index 742e8c2a1f61fe4b8203cc7e847ea8b456418540..5ecd8154ed53a603cf93b99f82a853b42eca5612 100644
--- a/src/composables/CalculateSize.ts
+++ b/src/composables/CalculateSize.ts
@@ -7,9 +7,6 @@ import { Coordinate, Size } from "../types/CoordinatesSize";
// Composable imports
import { inCycle, isSideCompound } from "./GetSetAttributsNodes";
-// General imports
-
-
/**
* This file contains functions to calculate the size of nodes, edges and subgraphs. Anf function to shift coordinates depending on node size.
@@ -386,7 +383,7 @@ function getSizeGroupCycles(subgraphNetwork:SubgraphNetwork,groupCycle:Subgraph)
* @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) {
+export function shiftAllToGetTopLeftCoord(network:Network,style:GraphStyleProperties,moveCycleToo:boolean=true):void {
Object.values(network.nodes).forEach(node=>{
if( moveCycleToo || !inCycle(network,node.id)){
const {x,y}=getTopLeftCoordFromCenter(node,style);
diff --git a/src/composables/ConvertFromNetwork.ts b/src/composables/ConvertFromNetwork.ts
index c50043c4d1a3a50412132a3747515438fea4b221..861e6448369075b490f239412f29aaaa123165d7 100644
--- a/src/composables/ConvertFromNetwork.ts
+++ b/src/composables/ConvertFromNetwork.ts
@@ -40,12 +40,6 @@ import * as GDS from 'graph-data-structure';
* *********************************
* 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
*
@@ -160,88 +154,6 @@ export function networkToAdjacentObject(network:Network):{[key : string]:string[
//___________________________________________________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.
*
@@ -464,7 +376,7 @@ export function graphVizToDot(vizGraph:Graph, subgraphFirst:boolean=true):string
* @param obj - The object to convert.
* @returns A string representation of the object with attribute-value pairs.
*/
-function customStringify(obj:AttributesViz|undefined) {
+function customStringify(obj:AttributesViz|undefined):string{
if (!obj || Object.keys(obj).length === 0) {
return "[]";
}
diff --git a/src/composables/ConvertToNetwork.ts b/src/composables/ConvertToNetwork.ts
index 79e679a60cbc1c4048bd048238765097a3b5e5d8..995f66dd03fc03463bda6a7604764c560aae9f7c 100644
--- a/src/composables/ConvertToNetwork.ts
+++ b/src/composables/ConvertToNetwork.ts
@@ -17,9 +17,6 @@ import { assignRankOrder } from './CalculateStartNodes';
* -> 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.
*
@@ -48,33 +45,6 @@ export function networkLayoutToNetwork(networkLayout: NetworkLayout): 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 '${node}' not found in the network.`);
-// }
-// network.nodes[node].metadataLayout.order = _order;
-// network.nodes[node].metadataLayout.rank = _rank / 2; // because rank 0 is 0, and the next is 2, 4, ...
-// }
-// });
-// }
-
-
/**
* Take a json of a viz graph and the network associated (with the json) : change the position and metadata (rank and order) of network's node by the one of the json.
* The json and network need to have the same nodes !
@@ -124,24 +94,5 @@ export async function changeNetworkFromViz(json: JsonViz, subgraphNetwork: Subgr
}
-// /**
-// * Updates the positions of nodes in the network based on the provided Cytoscape JSON.
-// *
-// * @param jsonCytoscape - The Cytoscape JSON containing the elements and their positions.
-// * @param network - The network to update.
-// */
-// export function changeNetworkFromCytoscape(jsonCytoscape: {elements: { nodes:ElementDefinition[] } }, network:Network) : void {
-
-// jsonCytoscape.elements.nodes.forEach((node: any) => {
-// const idNode= node.data.id;
-// if (Object.keys(network.nodes).includes(idNode)) {
-// network.nodes[idNode].x = node.position.x;
-// network.nodes[idNode].y = node.position.y;
-// }else{
-// throw new Error(`Node '${idNode}' not found in the network.`);
-// }
-// });
-// }
-
diff --git a/src/composables/GetSetAttributsNodes.ts b/src/composables/GetSetAttributsNodes.ts
index 70387517162a8efebf2b407bf026742155df6a4a..2861b941461e4cf70d8c7af6f5303df60bf17881 100644
--- a/src/composables/GetSetAttributsNodes.ts
+++ b/src/composables/GetSetAttributsNodes.ts
@@ -26,9 +26,6 @@ import { NetworkLayout } from "../types/NetworkLayout";
* *********************************
* 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.
*
@@ -51,6 +48,8 @@ import { NetworkLayout } from "../types/NetworkLayout";
* *********************************
* 3. Cycle
*
+ * -> inCycle :
+ * Checks if a node is part of a cycle in the network.
*
*/
@@ -112,19 +111,6 @@ export const classReversible="reversible";
export const reversibleAttribute="reversible";
export 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.
diff --git a/src/composables/LayoutDrawCycle.ts b/src/composables/LayoutDrawCycle.ts
index 6351d3c29e8a2b06a6bfa11c8297f877b0a29d2b..958977730ddc2bc18b981de473a17929d730eb75 100644
--- a/src/composables/LayoutDrawCycle.ts
+++ b/src/composables/LayoutDrawCycle.ts
@@ -398,7 +398,7 @@ async function lineCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDrawI
let cycleAsLine:string[]=[];
- unfixedInterval.forEach(async interval=>{
+ for (const interval of unfixedInterval){
const startNode=cycleNodes[(interval[0]-1+ cycleNodes.length) % cycleNodes.length];
const endNode=cycleNodes[(interval[1]+1+ cycleNodes.length) % cycleNodes.length];
@@ -420,7 +420,7 @@ async function lineCycleCoordinates(subgraphNetwork:SubgraphNetwork,cycleToDrawI
subgraphNetwork=lineCoord.subgraphNetwork;
const positionBefore=lineCoord.positionBefore;
subgraphNetwork=undoIfCreateOverlap(subgraphNetwork,groupCycleName,positionBefore);
- });
+ };
return subgraphNetwork;
}
@@ -556,9 +556,6 @@ async function forceGroupCycle(subgraphNetwork:SubgraphNetwork, groupCycleName:s
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();
@@ -1162,500 +1159,3 @@ function drawCycleGroup(cycleGroup:string,subgraphNetwork:SubgraphNetwork):void{
}
}
-
-// ________________________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
index 646b378fb22c519c4e61872ed3aafada93b30c8e..8159995846ab2d370e92e11e61f3491db77999b6 100644
--- a/src/composables/LayoutFindCycle.ts
+++ b/src/composables/LayoutFindCycle.ts
@@ -101,17 +101,9 @@ export function addDirectedCycleToSubgraphNetwork(subgraphNetwork:SubgraphNetwor
if (sizeCycle<=sizeCommonCycle){ // if sorting worked : it is supposed to always be the case
subgraphNetwork[TypeSubgraph.CYCLE][cycle[0]].parentSubgraph={name:networkCycles[i].name,type:TypeSubgraph.CYCLE};
updateParentSubgraphOf(subgraphNetwork,subgraphNetwork[TypeSubgraph.CYCLE][cycle[0]]);
- // if(! subgraphNetwork[TypeSubgraph.CYCLE][networkCycles[i].name].childrenSubgraphs){
- // subgraphNetwork[TypeSubgraph.CYCLE][networkCycles[i].name].childrenSubgraphs=[];
- // }
- // subgraphNetwork[TypeSubgraph.CYCLE][networkCycles[i].name].childrenSubgraphs.push({name:cycle[0],type:TypeSubgraph.CYCLE});
}else{
subgraphNetwork[TypeSubgraph.CYCLE][networkCycles[i].name].parentSubgraph={name:cycle[0],type:TypeSubgraph.CYCLE};
updateParentSubgraphOf(subgraphNetwork,subgraphNetwork[TypeSubgraph.CYCLE][networkCycles[i].name]);
- // if(! subgraphNetwork[TypeSubgraph.CYCLE] [cycle[0]].childrenSubgraphs){
- // subgraphNetwork[TypeSubgraph.CYCLE] [cycle[0]].childrenSubgraphs=[];
- // }
- // subgraphNetwork[TypeSubgraph.CYCLE] [cycle[0]].childrenSubgraphs.push({name:networkCycles[i].name,type:TypeSubgraph.CYCLE});
}
}
}
@@ -311,9 +303,7 @@ function JohnsonAlgorithm(graph: number[][], list_nodes:string[],flag: "Single"
}
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;
diff --git a/src/composables/LayoutMain.ts b/src/composables/LayoutMain.ts
index f1decc2ac50e601acb7a8e02abd9dd5bbb8ed763..879a4d79796c6b5c35f21bdd93fe69218fa1326e 100644
--- a/src/composables/LayoutMain.ts
+++ b/src/composables/LayoutMain.ts
@@ -215,13 +215,8 @@ export async function allSteps(subgraphNetwork: SubgraphNetwork,parameters:Param
shiftAllToGetTopLeftCoord(network,networkStyle);
}
}
- ).then(
- () => {
- // add color to link (optional : for debug)
- //subgraphNetwork = addBoldLinkMainChain(subgraphNetwork);
- //subgraphNetwork=addRedLinkcycleGroup(subgraphNetwork);
- }
);
+
return subgraphNetwork;
}
diff --git a/src/composables/LayoutMainChain.ts b/src/composables/LayoutMainChain.ts
index 491995d0200354655a6c96a4fd470e1c47b3675f..f0b06da29112eeeb377bed7f16d362d08d9c4156 100644
--- a/src/composables/LayoutMainChain.ts
+++ b/src/composables/LayoutMainChain.ts
@@ -5,12 +5,12 @@ import {TypeSubgraph, type Subgraph} from "../types/Subgraph";
import { Network } from "../types/TypeVizCore";
// Composable imports
-import { DFSWithSources, DFSsourceDAG } from "./AlgorithmDFS";
+import { DFSsourceDAG } from "./AlgorithmDFS";
import { networkToGDSGraph } from "./ConvertFromNetwork";
import { getStartNodes } from "./CalculateStartNodes";
import { BFS } from "./AlgorithmBFS";
import { addSubgraphToNetwork, createSubgraph } from './SubgraphForSubgraphNetwork';
-import { path } from "d3";
+
/**
* This file contains functions find and add main chains and mini-branch (form main chain) in a subgraphNetwork.
@@ -168,20 +168,16 @@ export async function getPathSourcesToTargetNode(network:Network, sources:string
const {dfs,graph}=await 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}=await DistanceFromSourceDAG(graph,dfs,pathType);
- console.log('distances',distances);
// 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){
for (const target of targetNodes.key){
// get the parents that goes from source to target node
- console.log('parents',parents);
- console.log('target',target);
const nodesBetweenSourceTarget=BFS(parents,target);
// merge with an existing path if node in common
// height is the max distance +1
pathsFromSources=await mergeNewPath(source,{nodes:nodesBetweenSourceTarget, height:targetNodes.max+1},pathsFromSources,merge);
- console.log('pathsFromSources',pathsFromSources);
};
} else if(pathType==PathType.LONGEST){ // if only one path wanted : take the first
// get the parents that goes from source to target node
@@ -290,16 +286,12 @@ async function mergeNewPath(source:string,newPath:{nodes:Array<string>, height:n
// for each path in the object
keys.forEach(key=>{
const pathNodes = pathsFromSources[key].nodes;
- console.log('pathNodes',pathNodes);
// Check for common nodes
const commonNodes = pathNodes.find(node => newPath.nodes.includes(node));
- console.log('commonNodes',commonNodes);
if (commonNodes && commonNodes.length>0){
- console.log('commonNodes',commonNodes);
if(merge){
// Merge paths
const mergedPath = Array.from(new Set(pathNodes.concat(newPath.nodes)));
- console.log('mergedPath',mergedPath);
// Create new key if necessary
let newKey:string = key;
const sourceAlreadyInKey=key.split('__').includes(source);
@@ -330,123 +322,3 @@ async function mergeNewPath(source:string,newPath:{nodes:Array<string>, height:n
return pathsFromSources;
}
-
-
-// // ----------------------------------------------------------------------------------------------------------------------------------------------
-// // ---------------------------------------------- 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;
-// }
diff --git a/src/composables/LayoutManageSideCompounds.ts b/src/composables/LayoutManageSideCompounds.ts
index 5b51fde891450e47d478cbb5554dbe8a61722ba2..680cdbb1b19cb654f64ba373ea5a1ec406bc33f1 100644
--- a/src/composables/LayoutManageSideCompounds.ts
+++ b/src/composables/LayoutManageSideCompounds.ts
@@ -13,33 +13,14 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
-
-
/*******************************************************************************************************************************************************
*
* 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
- *
- * -> getContentFromURL :
- * fetch url to return data
- *
- *
+ *
**********************************
*
*
- * 1. Duplicate and remove side compounds
+ * 0. Duplicate and remove side compounds
*
*
* -> putDuplicatedSideCompoundAside :
@@ -58,7 +39,7 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
* *********************************
*
*
- * 2. Reinsert side compounds
+ * 1. Reinsert side compounds
*
* -> reinsertionSideCompounds :
* reinsert side compounds in the network
@@ -72,6 +53,8 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
* -> motifStampSideCompound :
* applies a motif stamp to place side compound for a reaction
*
+ ****** 1.0 Stamp motif : initialization
+ *
* -> initializeReactionSideCompounds :
* initializes a reaction for side compounds motif
*
@@ -81,6 +64,8 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
* -> angleRadianSegment :
* calculates the angle in radians between two points
*
+ * ***** 1.1 Stamp motif : find intervals
+ *
* -> addSideCompoundsIntervals :
* finds the cofactor intervals for a given reaction
*
@@ -96,9 +81,13 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
* -> sizeInterval :
* calculates the size of an interval (between two metabolites) in a reaction
*
+ * ***** 1.2 Stamp motif : find spacing
+ *
* -> findSpacingSideCompounds :
* finds spacing between side compounds
*
+ * ***** 1.3 Stamp motif : give coordinates
+ *
* -> giveCoordAllSideCompounds :
* calculates the coordinates for all side compounds in a subgraph network
*
@@ -114,6 +103,7 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
* -> giveCoordSideCompound :
* calculates the coordinates for a side compound
*
+ * ***** 1.4 Stamp motif : insert side compounds
* -> insertAllSideCompoundsInNetwork :
* inserts all side compounds in the network
*
@@ -121,93 +111,13 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
* 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:string):Promise<void>{
-// const listIDSideCompounds = await getIDSideCompoundsInNetworkFromFile(subgraphNetwork,pathListSideCompounds);
-// listIDSideCompounds.forEach((sideCompoundID) => {
-// setAsSideCompound(subgraphNetwork.network,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;
-// 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;
-// }
-// }
-
-// /**
-// * 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;
-// }
-// }
-
-
-
/*******************************************************************************************************************************************************/
-//___________________________________________________1. Duplicate and remove side compounds__________________________________________________________________________
+//___________________________________________________0. Duplicate and remove side compounds__________________________________________________________________________
@@ -222,10 +132,6 @@ import { sideCompoundAttribute,isDuplicate, isSideCompound, setAsSideCompound }
*/
export async function putDuplicatedSideCompoundAside(subgraphNetwork:SubgraphNetwork, doDuplicateSideCompounds:boolean,doPutAsideSideCompounds:boolean):Promise<SubgraphNetwork>{
try {
- // finding side compounds in network
- // if (addSideCompoundAttribute){
- // await addSideCompoundAttributeFromList(subgraphNetwork,pathListSideCompounds);
- // }
// duplication of side compounds
if (doDuplicateSideCompounds){
await duplicateSideCompound(subgraphNetwork);
@@ -315,7 +221,7 @@ function removeSideCompoundsFromNetwork(subgraphNetwork:SubgraphNetwork): Subgra
}
/*******************************************************************************************************************************************************/
-//___________________________________________________2. Reinsert side compounds__________________________________________________________________________
+//___________________________________________________1. Reinsert side compounds__________________________________________________________________________
/**
@@ -435,7 +341,7 @@ async function motifStampSideCompound(subgraphNetwork:SubgraphNetwork,reactionID
/***********************************************************************/
-//______________2.1 Stamp motif : initialization
+//______________1.0 Stamp motif : initialization
/**
@@ -531,7 +437,7 @@ function angleRadianSegment(x1:number,y1:number,x2:number,y2:number,clockwise:bo
}
/***********************************************************************/
-//______________2.2 Stamp motif : find intervals
+//______________1.1 Stamp motif : find intervals
@@ -708,7 +614,7 @@ function sizeInterval(reaction:Reaction,intervalIndex:number):number{
}
/***********************************************************************/
-//______________2.3 Stamp motif : find spacing
+//______________1.2 Stamp motif : find spacing
async function findSpacingSideCompounds(reaction:Reaction,sizeInterval:number):Promise<{reactant:number|undefined,product:number|undefined}>{
@@ -722,7 +628,7 @@ async function findSpacingSideCompounds(reaction:Reaction,sizeInterval:number):P
}
/***********************************************************************/
-//______________2.4 Stamp motif : give coordinates
+//______________1.3 Stamp motif : give coordinates
/**
@@ -838,7 +744,7 @@ function giveCoordSideCompound(sideCompound:Node,angle:number,center:{x:number,y
/***********************************************************************/
-//______________2.4 Stamp motif : insertion in network
+//______________1.4 Stamp motif : insertion in network
/**
diff --git a/src/composables/LayoutReversibleReactions.ts b/src/composables/LayoutReversibleReactions.ts
index f801da831e58a7b3ae565d05e2b86bbef9ba864e..cc326725ede5fff81d54773965e117514b5bc114 100644
--- a/src/composables/LayoutReversibleReactions.ts
+++ b/src/composables/LayoutReversibleReactions.ts
@@ -8,8 +8,7 @@ import { NetworkLayout, NodeLayout } from "../types/NetworkLayout";
// Composable imports
import { removeAllSelectedNodes } from "./VizCoreFunctions";
import { BFSWithSources } from "./AlgorithmBFS";
-import { addLinkClassReversible, addMetadataReversibleWithClass, isReaction, isReversible } from "./GetSetAttributsNodes";
-
+import { addLinkClassReversible, isReaction, isReversible } from "./GetSetAttributsNodes";
@@ -72,9 +71,6 @@ import { addLinkClassReversible, addMetadataReversibleWithClass, isReaction, isR
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
@@ -191,25 +187,9 @@ async function reversibleNodeReaction(node: NodeLayout, suffix: string = "_rev")
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;
@@ -321,7 +301,7 @@ export function keepFirstReversibleNode(subgraphNetwork:SubgraphNetwork,nodeOrde
// 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
@@ -353,16 +333,6 @@ export function renameAllIDNode(subgraphNetwork:SubgraphNetwork,nodesToRename:{[
}
});
- // Modify edges -> not necessary because pointer for links (not id of node)
- // 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);
@@ -383,77 +353,15 @@ export function renameAllIDNode(subgraphNetwork:SubgraphNetwork,nodesToRename:{[
* @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}){
+function renameAllInSubgraph(subgraphNetwork:SubgraphNetwork, typeSubgraph:TypeSubgraph, nodesToRename:{[key: string]: string}):void{
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
-// }
-// });
-// }
-
+}
\ No newline at end of file
diff --git a/src/composables/LayoutSugiyama.ts b/src/composables/LayoutSugiyama.ts
index 117ff68305d1f7247f11602eece3fada55daa481..ca42c17508feb9dc650e3a0ed9a7830ec2509764 100644
--- a/src/composables/LayoutSugiyama.ts
+++ b/src/composables/LayoutSugiyama.ts
@@ -14,9 +14,6 @@ import { 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
*
@@ -26,26 +23,6 @@ import { instance } from "@viz-js/viz";
-
-/**
- * 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
@@ -69,146 +46,3 @@ export async function vizLayout(subgraphNetwork:SubgraphNetwork,assignRank:boole
});
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
deleted file mode 100644
index 7a6b41be71e258815596a333117dcd2e4b367701..0000000000000000000000000000000000000000
--- a/src/composables/MetricsApplication.ts
+++ /dev/null
@@ -1,329 +0,0 @@
-// 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
deleted file mode 100644
index 522a6d35cd721be8544dae2f33c46497d2a712d7..0000000000000000000000000000000000000000
--- a/src/composables/MetricsCalculation.ts
+++ /dev/null
@@ -1,448 +0,0 @@
-// 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
deleted file mode 100644
index 4a16b9f44e1b8c9f6b7aef8516e35d670a040e66..0000000000000000000000000000000000000000
--- a/src/composables/SBMLtoJSON.ts
+++ /dev/null
@@ -1,160 +0,0 @@
-// 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/SubgraphForViz.ts b/src/composables/SubgraphForViz.ts
index d2d19e53a4bb232c832ce21826fd268f52c7a039..b479d2ac771c0c2042c6252f28eff6ddb3567f0b 100644
--- a/src/composables/SubgraphForViz.ts
+++ b/src/composables/SubgraphForViz.ts
@@ -97,7 +97,6 @@ function changeCycleMetanodes(subgraphNetwork:SubgraphNetwork,listNodeBefore:str
let cycle:string;
if (network.nodes[node].metadataLayout && network.nodes[node].metadataLayout[TypeSubgraph.CYCLEGROUP]){
cycle = network.nodes[node].metadataLayout[TypeSubgraph.CYCLEGROUP];
- //cycle=inBiggerCycle(cycle,subgraphNetwork)
if(!(listNodeAfter.includes(cycle))){
// push node cycle
listNodeAfter.push(cycle);
diff --git a/src/composables/__tests__/AlgorithmDFS.test.ts b/src/composables/__tests__/AlgorithmDFS.test.ts
index 232c795106e4fe3a2ee1de92756462f29cbc2070..203d358715ef6aa7517affa104ea8af3cf4edd2c 100644
--- a/src/composables/__tests__/AlgorithmDFS.test.ts
+++ b/src/composables/__tests__/AlgorithmDFS.test.ts
@@ -100,6 +100,7 @@ describe('AlgorithmDFS', () => {
it('should return a DFS order, when no directed cycle', async () => {
// MOCK
+ const removeEdgeMock = jest.fn();
const networkToGDSGraphMock = jest.spyOn(ConvertFromNetwork, 'networkToGDSGraph');
networkToGDSGraphMock.mockImplementation(async () => {
return Promise.resolve({
@@ -124,7 +125,7 @@ describe('AlgorithmDFS', () => {
return [];
}
}),
- removeEdge: jest.fn()
+ removeEdge: removeEdgeMock
});
});
@@ -147,9 +148,7 @@ describe('AlgorithmDFS', () => {
// EXPECT
expect(result.dfs).toEqual([ 'A', 'C', 'E', 'B', 'D' ]);
- //expect(true).toBe(false); // need to check if no edge removed
- console.warn('need to check if edge removed : modify test');
-
+ expect(removeEdgeMock).not.toHaveBeenCalled();
});
diff --git a/src/composables/__tests__/CalculateRelationCycle.test.ts b/src/composables/__tests__/CalculateRelationCycle.test.ts
index 8c633ee17fee6583dda6f3718bcf749d1b96f99b..6ad6e6ead41a2aec7608c0a18b2165ec4b72b628 100644
--- a/src/composables/__tests__/CalculateRelationCycle.test.ts
+++ b/src/composables/__tests__/CalculateRelationCycle.test.ts
@@ -525,7 +525,6 @@ describe('CalculateRelationCycle', () => {
// TEST
const result=await CalculateRelationCycle.sortLinksWithAllGroupCycle(subgraphNetwork,true);
- //console.log(result.linksOrdered);
// EXPECT
expect(result.subgraphNetwork).toEqual(expectedSubgraphNetwork);
@@ -579,7 +578,6 @@ describe('CalculateRelationCycle', () => {
// TEST
const result=await CalculateRelationCycle.sortLinksWithAllGroupCycle(subgraphNetwork,true);
- //console.log(result.linksOrdered);
// EXPECT
expect(result.subgraphNetwork).toEqual(expectedSubgraphNetwork);
diff --git a/src/composables/__tests__/GetSetAttributsNodes.test.ts b/src/composables/__tests__/GetSetAttributsNodes.test.ts
index c871d470294dbbdc8e1e529d1873c1f2458b2b74..a0ec06ab11ccfa5071e0d042d713c5525771264b 100644
--- a/src/composables/__tests__/GetSetAttributsNodes.test.ts
+++ b/src/composables/__tests__/GetSetAttributsNodes.test.ts
@@ -291,81 +291,6 @@ describe('Duplicate', () => {
// 2. Reversible *****************************************************************
describe('Reversible', () => {
- test("addMetadataReversibleWithClass", async () => {
-
- const addReversibleNetworkMock = jest.spyOn(GetSetAttributsNodes, 'addReversibleNetwork');
- // DATA
-
- let network:Network = {
- id:"networkTest",
- nodes: {
- node1 :{
- id: "node1",
- x: 10,
- y: 10,
- },
- node2: {
- id: "node2",
- x: 20,
- y: 20,
- classes: [GetSetAttributsNodes.classReversible+"_test"]
- },
- node3: {
- id: "node3",
- x: 30,
- y: 30,
- classes: [GetSetAttributsNodes.classReversible]
- },
- node4: {
- id: "node4",
- x: 40,
- y: 40,
- classes: [GetSetAttributsNodes.classReversible+"_test",GetSetAttributsNodes.classReversible]
- }
- },
- links: []
- };
-
- let networkExpected:Network = {
- id:"networkTest",
- nodes: {
- node1 :{
- id: "node1",
- x: 10,
- y: 10,
- },
- node2: {
- id: "node2",
- x: 20,
- y: 20,
- classes: [GetSetAttributsNodes.classReversible+"_test"]
- },
- node3: {
- id: "node3",
- x: 30,
- y: 30,
- classes: [GetSetAttributsNodes.classReversible],
- metadata: {[GetSetAttributsNodes.reversibleAttribute]:true}
- },
- node4: {
- id: "node4",
- x: 40,
- y: 40,
- classes: [GetSetAttributsNodes.classReversible+"_test",GetSetAttributsNodes.classReversible],
- metadata: {[GetSetAttributsNodes.reversibleAttribute]:true}
- }
- },
- links: []
- };
-
- // TEST
- await GetSetAttributsNodes.addMetadataReversibleWithClass(network);
-
- // EXPECT
- //expect(addReversibleNetworkMock).toHaveBeenCalled();
- expect(network).toEqual(networkExpected);
-
- });
test("addReversibleNetwork", () => {
// DATA
diff --git a/src/composables/__tests__/LayoutReversibleReactions.test.ts b/src/composables/__tests__/LayoutReversibleReactions.test.ts
index 00fd0ecf404b1ee208892dd08c30e62d4208bf06..aa65c0f3e4246b1d357d89a92af31fe7b25eb55b 100644
--- a/src/composables/__tests__/LayoutReversibleReactions.test.ts
+++ b/src/composables/__tests__/LayoutReversibleReactions.test.ts
@@ -34,7 +34,7 @@ describe('LayoutReversibleReactions', () => {
nodeA: {id:"nodeA", x:0, y:0, classes:["metabolite"]},
nodeB: {id:"nodeB", x:0, y:0, classes:["reaction"]},
nodeC: {id:"nodeC", x:0, y:0, classes:["metabolite"]},
- nodeD: {id:"nodeD", x:0, y:0, classes:["reaction"]},
+ nodeD: {id:"nodeD", x:0, y:0, classes:["reaction"],"metadata": {"reversible": true}},
nodeE: {id:"nodeE", x:0, y:0, classes:["metabolite"]},
nodeF: {id:"nodeF", x:0, y:0, classes:["metabolite"]},
}
@@ -80,14 +80,6 @@ describe('LayoutReversibleReactions', () => {
}
// MOCK
- addMetadataReversibleWithClassMock = jest.spyOn(GetSetAttributsNodes, 'addMetadataReversibleWithClass');
- addMetadataReversibleWithClassMock.mockImplementation(
- async (network) =>{
- network.nodes.nodeD.metadata={};
- network.nodes.nodeD.metadata[reversibleAttribute]=true;
- }
- )
-
addLinkClassReversibleMock = jest.spyOn(GetSetAttributsNodes, 'addLinkClassReversible');
addLinkClassReversibleMock.mockImplementation( (link:Link) => {
link.classes=[classReversible];
diff --git a/src/composables/importNetwork.ts b/src/composables/importNetwork.ts
deleted file mode 100644
index ec7117c21656f862a1216c080419a47bf3c10444..0000000000000000000000000000000000000000
--- a/src/composables/importNetwork.ts
+++ /dev/null
@@ -1,93 +0,0 @@
-// 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/types/FormatJSONGraphXML.ts b/src/types/FormatJSONGraphXML.ts
deleted file mode 100644
index 3b279426c36d032d4f6ca1b72aa8b6914b6345cb..0000000000000000000000000000000000000000
--- a/src/types/FormatJSONGraphXML.ts
+++ /dev/null
@@ -1,58 +0,0 @@
-import { GraphStyleProperties } from "../types/TypeVizCore";
-
-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
deleted file mode 100644
index 9d54eb7d7e56d76ff968af38f4f422f94b98a86a..0000000000000000000000000000000000000000
--- a/src/types/FormatJsonStyle.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-
-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/Parameters.ts b/src/types/Parameters.ts
index fac8eb813e421231b0f2ce530b469d340de7a8a2..cce9be9adbdaee9c87218a97e2aba2768fe66ae3 100644
--- a/src/types/Parameters.ts
+++ b/src/types/Parameters.ts
@@ -35,9 +35,6 @@ export interface Parameters {
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 = {
@@ -66,7 +63,4 @@ export let defaultParameters: Parameters = {
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
index cf90a30e4c2440973be11a73e422105364e7bf56..2688d6d174e957d4ecaefad0f71bb5a06915f90e 100644
--- a/src/types/Reaction.ts
+++ b/src/types/Reaction.ts
@@ -8,18 +8,11 @@ export enum MetaboliteType {
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
diff --git a/src/types/SubgraphNetwork.ts b/src/types/SubgraphNetwork.ts
index 12e9f06a56ebff854bbb856b507bcc59ade052ca..9da2c08757ef7e8ac12645bce23e1a6427e766f1 100644
--- a/src/types/SubgraphNetwork.ts
+++ b/src/types/SubgraphNetwork.ts
@@ -1,9 +1,6 @@
-import { Network } from "@metabohub/viz-core/src/types/Network";
-import { Node } from "@metabohub/viz-core/src/types/Node";
import { Subgraph, TypeSubgraph } from "./Subgraph";
-import { Ref } from "vue";
-import { GraphStyleProperties } from "@metabohub/viz-core/src/types/GraphStyleProperties";
-import { NetworkLayout } from "./NetworkLayout";
+import { GraphStyleProperties } from "../types/TypeVizCore";
+import { NetworkLayout, NodeLayout } from "./NetworkLayout";
import { AttributesViz } from "./TypeViz";
/**
@@ -33,6 +30,6 @@ export interface SubgraphNetwork {
}
sideCompounds?:{
- [key:string]:{reactants:Array<Node>,products:Array<Node>}
+ [key:string]:{reactants:Array<NodeLayout>,products:Array<NodeLayout>}
}
}
\ No newline at end of file
diff --git a/src/types/TypeViz.ts b/src/types/TypeViz.ts
index 72b18ecd732297c2e573c0e686d514583de94fee..9c9532e4eda3b85afd4a90f62a6e2311850ecd1f 100644
--- a/src/types/TypeViz.ts
+++ b/src/types/TypeViz.ts
@@ -1,15 +1,3 @@
-// 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[]
-// }
export interface AttributesViz {
[name: string]: string | number | boolean