diff --git a/src/app/app.module.ts b/src/app/app.module.ts index c57f5f284c0877f639bd0a887a5ec5a0e8eec221..ed0291588b7b6a66abfd8b71d7a35c9a4f78125f 100644 --- a/src/app/app.module.ts +++ b/src/app/app.module.ts @@ -1,16 +1,15 @@ -import { BrowserModule } from '@angular/platform-browser'; -import { NgModule } from '@angular/core'; +import {BrowserModule} from '@angular/platform-browser'; +import {NgModule} from '@angular/core'; -import { CommonModule } from '@angular/common'; -import { FormsModule } from '@angular/forms'; +import {CommonModule} from '@angular/common'; +import {FormsModule} from '@angular/forms'; -import { AppRoutingModule } from './app-routing.module'; -import { AppComponent } from './app.component'; +import {AppRoutingModule} from './app-routing.module'; +import {AppComponent} from './app.component'; import {ExplorerPageComponent} from './pages/explorer-page/explorer-page.component'; import {AboutPageComponent} from './pages/about-page/about-page.component'; import {HomePageComponent} from './pages/home-page/home-page.component'; -import { HttpClientModule } from '@angular/common/http'; - +import {HttpClientModule} from '@angular/common/http'; @NgModule({ declarations: [ @@ -24,10 +23,11 @@ import { HttpClientModule } from '@angular/common/http'; AppRoutingModule, FormsModule, CommonModule, - HttpClientModule + HttpClientModule, ], providers: [], bootstrap: [AppComponent] }) -export class AppModule { } +export class AppModule { +} diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html index c55281178bd5445c9eea13aa15269f4d241ca8fb..cd02afdbcdf97436b16ab5d5f16e1d6510fc1fc5 100644 --- a/src/app/pages/explorer-page/explorer-page.component.html +++ b/src/app/pages/explorer-page/explorer-page.component.html @@ -81,6 +81,24 @@ </button> </footer> </div> + + <div class="card bar"> + <header class="card-header"> + <p class="card-header-title"> + <span class="icon"> + <i class="fas fa-cog" aria-hidden="true"></i> + </span> Settings + </p> + </header> + <div class="card-content"> + <div class="content"> + <label class="checkbox"> + <input type="checkbox" class="checkbox" [(ngModel)]="physicsEnabled" (ngModelChange)="physicsEnabled = $event; updatePhysicsEnabled()"> + Physics enabled + </label> + </div> + </div> + </div> </div> <div class="content bar-right"> diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts index af49fd37572b8a60d92d019cac5c40989444eddd..30ffde5a1e235ae1a4b74bc414b870d760674a26 100644 --- a/src/app/pages/explorer-page/explorer-page.component.ts +++ b/src/app/pages/explorer-page/explorer-page.component.ts @@ -1,9 +1,8 @@ import {AfterViewInit, Component, ElementRef, OnInit, ViewChild} from '@angular/core'; import {ActivatedRoute, Router} from '@angular/router'; -import { HttpClient } from '@angular/common/http'; -import { environment } from '../../../environments/environment'; import {Effect, ProteinNetwork} from '../protein-network'; -import { ApiService } from '../../api.service'; +import {HttpClient} from '@angular/common/http'; +import {ApiService} from '../../api.service'; declare var vis: any; @@ -37,9 +36,12 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { private seed = 1; // TODO: Remove this + private dumpPositions = false; + public physicsEnabled = false; + @ViewChild('network', {static: false}) networkEl: ElementRef; - constructor(private route: ActivatedRoute, private router: Router, private api: ApiService) { + constructor(private http: HttpClient, private route: ActivatedRoute, private router: Router, private api: ApiService) { this.groupId = 'IFI16'; this.geneNames.push('IFI16'); this.proteinNames.push('Gamma-interface-inducible protein 16'); @@ -51,6 +53,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { this.baitNames.push('Bait Protein 5'); this.route.queryParams.subscribe(async (params) => { + this.dumpPositions = params.dumpPositions; + this.physicsEnabled = !!this.dumpPositions; + const proteinGroup = params.proteinGroup; if (!proteinGroup) { // In this case, the URL is just `/explorer` @@ -80,7 +85,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { } - async ngAfterViewInit() { if (!this.network) { await this.createNetwork(); @@ -94,7 +98,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { this.edges = data.edges; } - public reset(event) { + public reset(event) { const checked = event.target.checked; this.baitProteins.forEach(item => item.checked = checked); this.filterNodes(); @@ -125,7 +129,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { private async createNetwork() { await this.getNetwork(); this.proteinData = new ProteinNetwork(this.proteinGroups, this.effects, this.edges); - this.proteinData.loadPositions(); + if (!this.dumpPositions) { + await this.proteinData.loadPositions(this.http); + } this.proteinData.linkNodes(); // Populate baits @@ -150,6 +156,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { smooth: false, }, physics: { + enabled: this.physicsEnabled, stabilization: { enabled: false, }, @@ -167,9 +174,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { } }); - if (!localStorage.getItem('positions')) { + if (this.dumpPositions) { this.network.on('stabilizationIterationsDone', () => { - localStorage.setItem('positions', JSON.stringify(this.network.getPositions())); + console.log(JSON.stringify(this.network.getPositions())); }); this.network.stabilize(); } @@ -191,7 +198,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { const connectedProteinGroupIds = new Set<number>(); this.baitProteins.forEach((bait) => { - const nodeId = `eff${bait.data.id}`; + const nodeId = `eff_${bait.data.name}`; const found = visibleIds.has(nodeId); if ((bait.checked || showAll) && !found) { const node = this.mapEffectToNode(bait.data); @@ -208,7 +215,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { } }); for (const proteinGroup of this.proteinData.proteinGroups) { - const nodeId = `pg${proteinGroup.id}`; + const nodeId = `pg_${proteinGroup.groupId}`; const contains = connectedProteinGroupIds.has(proteinGroup.id); const found = visibleIds.has(nodeId); if (contains && !found) { @@ -226,11 +233,17 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { } + public updatePhysicsEnabled() { + this.network.setOptions({ + physics: {enabled: this.physicsEnabled}, + }); + } + private mapProteinGroupToNode(proteinGroup: any): any { return { - id: `pg${proteinGroup.id}`, - label: `pg${proteinGroup.id}`, - size: 5, color: '#ADADAD', shape: 'square', shadow: true, + id: `pg_${proteinGroup.groupId}`, + label: `${proteinGroup.name}`, + size: 10, font: '5px', color: '#e2b600', shape: 'ellipse', shadow: false, x: proteinGroup.x, y: proteinGroup.y }; @@ -238,16 +251,16 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit { private mapEffectToNode(effect: any): any { return { - id: `eff${effect.id}`, - label: `eff${effect.id}`, - size: 10, color: '#118AB2', shape: 'circle', shadow: true, + id: `eff_${effect.name}`, + label: `${effect.name}`, + size: 10, color: '#118AB2', shape: 'box', shadow: true, font: {color: '#FFFFFF'}, x: effect.x, y: effect.y }; } private mapEdge(edge: any): any { - return {from: `pg${edge.proteinGroupId}`, to: `eff${edge.effectId}`}; + return {from: `pg_${edge.groupId}`, to: `eff_${edge.effectName}`, color: { color: '#afafaf', highlight: '#854141' }}; } private mapDataToNodes(data: ProteinNetwork): { nodes: any[], edges: any[] } { diff --git a/src/app/pages/protein-network.ts b/src/app/pages/protein-network.ts index 2398b9f2d05209a3924756680a48802dc04738e8..34f536c0f38977e49252a2c8b2ca6df060589d02 100644 --- a/src/app/pages/protein-network.ts +++ b/src/app/pages/protein-network.ts @@ -1,6 +1,9 @@ +import {HttpClient} from '@angular/common/http'; + export interface ProteinGroup { id: number; name: string; + groupId: number; effects?: Effect[]; x?: number; y?: number; @@ -15,8 +18,8 @@ export interface Effect { } export interface Edge { - proteinGroupId: number; - effectId: number; + groupId: number; + effectName: string; } export class ProteinNetwork { @@ -24,21 +27,17 @@ export class ProteinNetwork { constructor(public proteinGroups: ProteinGroup[], public effects: Effect[], public edges: Edge[]) { } - public loadPositions() { - const savedPositions = localStorage.getItem('positions'); - if (!savedPositions) { - return; - } - const nodePositions = JSON.parse(savedPositions); + public async loadPositions(http: HttpClient) { + const nodePositions = await http.get(`assets/positions/network.json`).toPromise(); this.proteinGroups.forEach((node) => { - const nodePosition = nodePositions[`pg${node.id}`]; + const nodePosition = nodePositions[`pg_${node.groupId}`]; if (nodePosition) { node.x = nodePosition.x; node.y = nodePosition.y; } }); this.effects.forEach((node) => { - const nodePosition = nodePositions[`eff${node.id}`]; + const nodePosition = nodePositions[`eff_${node.name}`]; if (nodePosition) { node.x = nodePosition.x; node.y = nodePosition.y; @@ -47,11 +46,11 @@ export class ProteinNetwork { } public getProteinGroup(id: number): ProteinGroup { - return this.proteinGroups.find((pg) => pg.id === id); + return this.proteinGroups.find((pg) => pg.groupId === id); } - public getEffect(id: number): Effect { - return this.effects.find((eff) => eff.id === id); + public getEffect(name: string): Effect { + return this.effects.find((eff) => eff.name === name); } public linkNodes() { @@ -62,8 +61,8 @@ export class ProteinNetwork { eff.proteinGroups = []; }); this.edges.forEach((edge) => { - const proteinGroup = this.getProteinGroup(edge.proteinGroupId); - const effect = this.getEffect(edge.effectId); + const 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