diff --git a/src/app/analysis.service.ts b/src/app/analysis.service.ts
index a1a2b97dbe0328636e028324ddd19cf155aefd6c..780307fdced4f8c610a95acc253f7656aa13922c 100644
--- a/src/app/analysis.service.ts
+++ b/src/app/analysis.service.ts
@@ -1,4 +1,4 @@
-import {Wrapper, Task, getWrapperFromProtein, getWrapperFromViralProtein, Protein, ViralProtein, Dataset, Tissue} from './interfaces';
+import {Wrapper, Task, getWrapperFromProtein, Protein, Dataset, Tissue} from './interfaces';
import {Subject} from 'rxjs';
import {HttpClient} from '@angular/common/http';
import {environment} from '../environments/environment';
@@ -203,21 +203,6 @@ export class AnalysisService {
return items.length;
}
- public addVisibleViralProteins(nodes, viralProteins: ViralProtein[]): number {
- const items: Wrapper[] = [];
- const visibleIds = new Set<string>(nodes.getIds());
- for (const viralProtein of viralProteins) {
- const wrapper = getWrapperFromViralProtein(viralProtein);
- const found = visibleIds.has(wrapper.nodeId);
- if (found && !this.inSelection(wrapper)) {
- items.push(wrapper);
- this.selectedItems.set(wrapper.nodeId, wrapper);
- }
- }
- this.selectListSubject.next({items, selected: true});
- return items.length;
- }
-
public removeAllHostProteins() {
const items: Wrapper[] = Array.from(this.selectedItems.values()).filter(p => p.type === 'host');
for (const wrapper of items) {
@@ -251,10 +236,6 @@ export class AnalysisService {
return this.inSelection(getWrapperFromProtein(protein));
}
- viralProteinInSelection(viralProtein: ViralProtein): boolean {
- return this.inSelection(getWrapperFromViralProtein(viralProtein));
- }
-
getSelection(): Wrapper[] {
return Array.from(this.selectedItems.values());
}
diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index 81afb3e1bb484ee3ac9f57fcf76bb4d4806ebdb1..e5dd42fb96387cfe095cf42914a9da1c97105367 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -416,63 +416,6 @@
</tr>
</ng-template>
</p-table>
-
- <div *ngIf="tableViralProteins.length > 0" class="table-header">
- <h4 class="is-4">
- <span class="icon"><i class="fa fa-virus"></i></span>
- <span>Viral Proteins</span>
- </h4>
- <a [href]="downloadLink('viral_proteins')" class="button is-primary is-outlined is-pulled-right is-small">
- <span class="icon"><i class="fa fa-download"></i></span>
- <span>Download</span>
- </a>
- </div>
- <p-table *ngIf="tableViralProteins.length > 0" selectionMode="multiple"
- [value]="tableViralProteins" [selection]="tableSelectedViralProteins" dataKey="effectId"
- (selectionChange)="tableViralProteinSelection($event)">
- <ng-template pTemplate="header">
- <tr>
- <th class="checkbox-col">
- <p-tableHeaderCheckbox></p-tableHeaderCheckbox>
- </th>
- <th [pSortableColumn]="'effectName'">
- Name
- <p-sortIcon [field]="'effectName'"></p-sortIcon>
- </th>
- <th [pSortableColumn]="'virusName'">
- Virus Strain
- <p-sortIcon [field]="'virusName'"></p-sortIcon>
- </th>
- <th *ngIf="tableHasScores" [pSortableColumn]="'score'">
- Score
- <p-sortIcon [field]="'score'"></p-sortIcon>
- </th>
- <th [pSortableColumn]="'isSeed'">
- Seed
- <p-sortIcon [field]="'isSeed'"></p-sortIcon>
- </th>
- </tr>
- </ng-template>
- <ng-template pTemplate="body" let-e>
- <tr>
- <td>
- <p-tableCheckbox [value]="e"></p-tableCheckbox>
- </td>
- <td>{{e.effectName}}</td>
- <td>{{e.virusName}}</td>
- <td *ngIf="tableHasScores">{{e.score | number}}</td>
- <td>
- <span *ngIf="e.isSeed">
- <i class="fa fa-asterisk has-text-primary"></i>
- Seed
- </span>
- <span *ngIf="!e.isSeed">
- <i class="fa fa-times"></i>
- </span>
- </td>
- </tr>
- </ng-template>
- </p-table>
</div>
</div>
</div>
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 34df030f21fc11ddbcc2020c670db34091738c76..db25357172167037310a3b4d0ce5255ec855e1a5 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -15,16 +15,13 @@ import {AnalysisService, algorithmNames} from '../../analysis.service';
import {
Protein,
Task,
- ViralProtein,
Drug,
Wrapper,
WrapperType,
getWrapperFromProtein,
getWrapperFromDrug,
- getWrapperFromViralProtein,
getNodeIdsFromPDI,
getNodeIdsFromPPI,
- getViralProteinNodeId,
getProteinNodeId, Tissue
} from '../../interfaces';
import html2canvas from 'html2canvas';
@@ -60,7 +57,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
@Output() tokenChange = new EventEmitter<string | null>();
@Output() showDetailsChange = new EventEmitter<Wrapper>();
- @Output() visibleItems = new EventEmitter<[any[], [Protein[], ViralProtein[], Tissue]]>();
+ @Output() visibleItems = new EventEmitter<[any[], [Protein[], Tissue]]>();
public task: Task | null = null;
@@ -78,8 +75,8 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
public tableDrugs: Array<Drug & Scored & Baited> = [];
public tableProteins: Array<Protein & Scored & Seeded & Baited> = [];
public tableSelectedProteins: Array<Protein & Scored & Seeded & Baited> = [];
- public tableViralProteins: Array<ViralProtein & Scored & Seeded> = [];
- public tableSelectedViralProteins: Array<ViralProtein & Scored & Seeded> = [];
+ public tableViralProteins: Array<Scored & Seeded> = [];
+ public tableSelectedViralProteins: Array<Scored & Seeded> = [];
public tableNormalize = false;
public tableHasScores = false;
@@ -181,14 +178,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
});
}));
- promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=viral_proteins`).toPromise()
- .then((table) => {
- this.tableViralProteins = table;
- this.tableViralProteins.forEach((r) => {
- r.rawScore = r.score;
- r.isSeed = isSeed[r.effectId];
- });
- }));
await Promise.all(promises);
this.tableHasScores = ['trustrank', 'closeness', 'degree', 'proximity', 'betweenness', 'quick', 'super']
@@ -276,16 +265,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
if (!selected && found !== -1 && tableItem) {
proteinSelection.splice(found, 1);
}
- } else if (item.type === 'virus') {
- // TODO: Refactor!
- const found = viralProteinSelection.findIndex((i) => getViralProteinNodeId(i) === item.nodeId);
- const tableItem = this.tableViralProteins.find((i) => getViralProteinNodeId(i) === item.nodeId);
- if (selected && found === -1 && tableItem) {
- viralProteinSelection.push(tableItem);
- }
- if (!selected && found !== -1 && tableItem) {
- viralProteinSelection.splice(found, 1);
- }
}
}
this.tableSelectedProteins = [...proteinSelection];
@@ -319,11 +298,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
if (tableItem) {
proteinSelection.push(tableItem);
}
- } else if (item.type === 'virus') {
- const tableItem = this.tableViralProteins.find((i) => getViralProteinNodeId(i) === item.nodeId);
- if (tableItem) {
- viralProteinSelection.push(tableItem);
- }
}
}
this.tableSelectedProteins = [...proteinSelection];
@@ -337,7 +311,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
public emitVisibleItems(on: boolean) {
if (on) {
- this.visibleItems.emit([this.nodeData.nodes, [this.proteins, this.effects, this.selectedTissue]]);
+ this.visibleItems.emit([this.nodeData.nodes, [this.proteins, this.selectedTissue]]);
} else {
this.visibleItems.emit(null);
}
@@ -422,9 +396,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
if (nodeTypes[node] === 'host') {
this.proteins.push(details[node]);
wrappers[node] = getWrapperFromProtein(details[node]);
- } else if (nodeTypes[node] === 'virus') {
- this.effects.push(details[node]);
- wrappers[node] = getWrapperFromViralProtein(details[node]);
} else if (nodeTypes[node] === 'drug') {
wrappers[node] = getWrapperFromDrug(details[node]);
}
@@ -441,7 +412,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
};
}
- private mapNode(nodeType: WrapperType, details: Protein | ViralProtein | Drug, isSeed?: boolean, score?: number): any {
+ private mapNode(nodeType: WrapperType, details: Protein | Drug, isSeed?: boolean, score?: number): any {
let nodeLabel;
let wrapper: Wrapper;
let drugType;
@@ -463,10 +434,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
} else {
nodeLabel = drug.drugId;
}
- } else if (nodeType === 'virus') {
- const viralProtein = details as ViralProtein;
- wrapper = getWrapperFromViralProtein(viralProtein);
- nodeLabel = viralProtein.effectName;
}
const node = NetworkSettings.getNodeStyle(nodeType, isSeed, this.analysis.inSelection(wrapper), drugType, drugInTrial);
@@ -599,27 +566,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.analysis.removeItems(removeItems);
}
- public tableViralProteinSelection(e) {
- const oldSelection = [...this.tableSelectedViralProteins];
- this.tableSelectedViralProteins = e;
- const addItems = [];
- const removeItems = [];
- for (const i of this.tableSelectedViralProteins) {
- const wrapper = getWrapperFromViralProtein(i);
- if (oldSelection.indexOf(i) === -1) {
- addItems.push(wrapper);
- }
- }
- for (const i of oldSelection) {
- const wrapper = getWrapperFromViralProtein(i);
- if (this.tableSelectedViralProteins.indexOf(i) === -1) {
- removeItems.push(wrapper);
- }
- }
- this.analysis.addItems(addItems);
- this.analysis.removeItems(removeItems);
- }
-
public previewStringArray(arr: string[], count: number): string {
if (arr.length < count) {
return arr.join(', ');
diff --git a/src/app/components/query-tile/query-tile.component.ts b/src/app/components/query-tile/query-tile.component.ts
index 62f952f34ba3046a2290c91975575a63627b5480..63997a24984901c9a0c6757117be5c612be0996d 100644
--- a/src/app/components/query-tile/query-tile.component.ts
+++ b/src/app/components/query-tile/query-tile.component.ts
@@ -1,5 +1,5 @@
import {Component, Input, Output, EventEmitter} from '@angular/core';
-import {Protein, Wrapper, ViralProtein} from '../../interfaces';
+import {Protein, Wrapper} from '../../interfaces';
@Component({
selector: 'app-query-tile-component',
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index bcd16bfa72345c336977a9d0a8359b81d21b3803..3e5bcc41c8cf6792d983f324d79456e72fb995f2 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -4,7 +4,7 @@ export interface Protein {
name: string;
proteinAc: string;
proteinName: string;
- effects?: ViralProtein[];
+ interactions?: Protein[];
x?: number;
y?: number;
expressionLevel?: number;
@@ -15,21 +15,9 @@ export interface Tissue {
name: string;
}
-export interface ViralProtein {
- effectId: string;
- effectName: string;
- virusName: string;
- datasetName: string;
- proteins?: Protein[];
- x?: number;
- y?: number;
-}
-
-export interface ProteinViralInteraction {
- effectName: string;
- virusName: string;
- datasetName: string;
- proteinAc: string;
+export interface ProteinProteinInteraction {
+ from: string;
+ to: string;
}
export interface NetworkEdge {
@@ -71,14 +59,10 @@ export function getProteinBackendId(protein: Protein) {
return protein.proteinAc;
}
-export function getViralProteinNodeId(viralProtein: ViralProtein) {
- return `v_${viralProtein.effectName}_${viralProtein.virusName}`;
-}
-
-export function getNodeIdsFromPVI(pvi: ProteinViralInteraction) {
+export function getNodeIdsFromI(pvi: ProteinProteinInteraction) {
return {
- from: `p_${pvi.proteinAc}`,
- to: `v_${pvi.effectName}_${pvi.virusName}`,
+ from: `p_${pvi.from}`,
+ to: `p_${pvi.to}`,
};
}
@@ -96,10 +80,6 @@ export function getNodeIdsFromPDI(edge: NetworkEdge) {
};
}
-export function getViralProteinBackendId(viralProtein: ViralProtein) {
- return viralProtein.effectId;
-}
-
export function getDrugNodeId(drug: Drug) {
return `d_${drug.drugId}`;
}
@@ -117,15 +97,6 @@ export function getWrapperFromProtein(protein: Protein): Wrapper {
};
}
-export function getWrapperFromViralProtein(viralProtein: ViralProtein): Wrapper {
- return {
- backendId: getViralProteinBackendId(viralProtein),
- nodeId: getViralProteinNodeId(viralProtein),
- type: 'virus',
- data: viralProtein,
- };
-}
-
export function getWrapperFromDrug(drug: Drug): Wrapper {
return {
backendId: getDrugBackendId(drug),
diff --git a/src/app/main-network.ts b/src/app/main-network.ts
index 76acc1f64ba083e928eab5caff8e6f5b82c5e2de..2217f357dedd41e734e5ab41af434aa4d2a55298 100644
--- a/src/app/main-network.ts
+++ b/src/app/main-network.ts
@@ -1,5 +1,5 @@
import {HttpClient} from '@angular/common/http';
-import {ProteinViralInteraction, ViralProtein, Protein, getProteinNodeId, getViralProteinNodeId} from './interfaces';
+import {ProteinProteinInteraction, Protein, getProteinNodeId} from './interfaces';
export function getDatasetFilename(dataset: Array<[string, string]>): string {
return `network-${JSON.stringify(dataset).replace(/[\[\]\",]/g, '')}.json`;
@@ -7,7 +7,7 @@ export function getDatasetFilename(dataset: Array<[string, string]>): string {
export class ProteinNetwork {
- constructor(public proteins: Protein[], public effects: ViralProtein[], public edges: ProteinViralInteraction[]) {
+ constructor(public proteins: Protein[], public edges: ProteinProteinInteraction[]) {
}
public async loadPositions(http: HttpClient, dataset: Array<[string, string]>) {
@@ -19,36 +19,22 @@ export class ProteinNetwork {
node.y = nodePosition.y;
}
});
- this.effects.forEach((node) => {
- const nodePosition = nodePositions[getViralProteinNodeId(node)];
- if (nodePosition) {
- node.x = nodePosition.x;
- node.y = nodePosition.y;
- }
- });
}
public getProtein(ac: string): Protein | undefined {
return this.proteins.find((p) => p.proteinAc === ac);
}
- public getEffect(name: string, virus: string, dataset: string): ViralProtein | undefined {
- return this.effects.find((eff) => eff.effectName === name && eff.virusName === virus && eff.datasetName === dataset);
- }
-
public linkNodes() {
this.proteins.forEach((pg) => {
- pg.effects = [];
- });
- this.effects.forEach((eff) => {
- eff.proteins = [];
+ pg.interactions = [];
});
this.edges.forEach((edge) => {
- const proteinGroup = this.getProtein(edge.proteinAc);
- const effect = this.getEffect(edge.effectName, edge.virusName, edge.datasetName);
- if (proteinGroup && effect) {
- proteinGroup.effects.push(effect);
- effect.proteins.push(proteinGroup);
+ const protein1 = this.getProtein(edge.from);
+ const protein2 = this.getProtein(edge.to);
+ if (protein1 && protein2) {
+ protein1.interactions.push(protein2);
+ protein2.interactions.push(protein1);
}
});
}
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 659a682fde6fbd92400da1764e5672c3d2a1a2dd..7dd2fdc8f8cbe4f4a1f42fc5174869b481d2af97 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -88,44 +88,6 @@
</div>
</div>
</div>
-
- <div *ngIf="myConfig.showFilter" class="card bar-large">
- <header class="card-header">
- <p class="card-header-title">
- <span class="icon">
- <i class="fas fa-filter" aria-hidden="true"></i>
- </span> Filter Proteins
- </p>
- <a (click)="collapseBaitFilter = !collapseBaitFilter" data-action="collapse"
- class="card-header-icon is-hidden-fullscreen" aria-label="more options">
- <span class="icon">
- <i *ngIf="collapseBaitFilter" class="fas fa-angle-down" aria-hidden="true"></i>
- <i *ngIf="!collapseBaitFilter" class="fas fa-angle-left" aria-hidden="true"></i>
- </span>
- </a>
- </header>
- <div *ngIf="collapseBaitFilter">
- <div class="card-content overflow">
- <div *ngFor="let bait of viralProteinCheckboxes">
- <label class="checkbox">
- <input type="checkbox" class="checkbox" [ngModel]="bait.checked"
- (ngModelChange)="bait.checked = $event; filterNodes()">
- {{ bait.data["effectName"] }}
- </label>
- </div>
- </div>
- <footer class="card-footer">
- <a (click)="reset($event);" class="card-footer-item has-text-danger" data-tooltip="Remove filter and show all proteins.">
- <span class="icon">
- <i class="fa fa-broom"></i>
- </span>
- <span>
- Reset
- </span>
- </a>
- </footer>
- </div>
- </div>
</div>
<div class="covex network">
@@ -487,27 +449,6 @@
</a>
</footer>
- <footer class="card-footer">
- <a (click)="analysis.addVisibleViralProteins(currentViewNodes, currentViewViralProteins)"
- class="card-footer-item has-text-success" data-tooltip="Add all visible viral proteins.">
- <span class="icon">
- <i class="fa fa-plus"></i>
- </span>
- <span>
- Add viral proteins
- </span>
- </a>
- <a (click)="analysis.removeAllViralProteins()"
- class="card-footer-item has-text-danger" data-tooltip="Remove all viral proteins.">
- <span class="icon">
- <i class="fa fa-minus"></i>
- </span>
- <span>
- Remove viral proteins
- </span>
- </a>
- </footer>
-
<footer class="card-footer" *ngIf="selectedAnalysisToken">
<a (click)="analysis.addSeeds(currentViewNodes)"
class="card-footer-item has-text-success" data-tooltip="Add all visible seeds.">
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 1d41f1c30d7e6b0a67f279912538e9ace5b84422..d42cf73363857a219f66f76adcddd40d255a11fe 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -6,25 +6,18 @@ import {
ViewChild
} from '@angular/core';
import {
- ProteinViralInteraction,
- ViralProtein,
+ ProteinProteinInteraction,
Protein,
Wrapper,
- getWrapperFromViralProtein,
getWrapperFromProtein,
- getNodeIdsFromPVI,
- getViralProteinNodeId,
- getProteinNodeId,
- Dataset,
- Tissue
+ Tissue, getNodeIdsFromI
} from '../../interfaces';
-import {ProteinNetwork, getDatasetFilename} from '../../main-network';
-import {HttpClient, HttpParams} from '@angular/common/http';
+import {ProteinNetwork} from '../../main-network';
+import {HttpClient} from '@angular/common/http';
import {AnalysisService} from '../../analysis.service';
import html2canvas from 'html2canvas';
-import {environment} from '../../../environments/environment';
import {NetworkSettings} from '../../network-settings';
-import {defaultConfig, IConfig} from "../../config";
+import {defaultConfig, IConfig} from '../../config';
declare var vis: any;
@@ -83,12 +76,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public collapseData = true;
public collapseOverview = true;
- public viralProteinCheckboxes: Array<{ checked: boolean; data: ViralProtein }> = [];
-
public proteinData: ProteinNetwork;
public proteins: any;
- public effects: any;
public edges: any;
private networkInternal: any;
@@ -109,7 +99,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public currentDataset = [];
public currentViewProteins: Protein[];
- public currentViewViralProteins: ViralProtein[];
public currentViewSelectedTissue: Tissue | null = null;
public currentViewNodes: any[];
@@ -188,16 +177,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
const network = JSON.parse(this.networkJSON);
this.proteins = network.nodes;
- this.effects = [];
this.edges = network.edges;
}
- public reset(event) {
- const checked = event.target.checked;
- this.viralProteinCheckboxes.forEach(item => item.checked = checked);
- this.filterNodes();
- }
-
private zoomToNode(id: string) {
this.nodeData.nodes.getIds();
const coords = this.networkInternal.getPositions(id)[id];
@@ -234,25 +216,11 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.analysis.resetSelection();
this.selectedWrapper = null;
this.getNetwork();
- this.proteinData = new ProteinNetwork(this.proteins, this.effects, this.edges);
+ this.proteinData = new ProteinNetwork(this.proteins, this.edges);
this.proteinData.linkNodes();
// Populate baits
const effectNames = [];
- this.proteinData.effects.sort((a, b) => {
- return a.effectName.localeCompare(b.effectName);
- });
- this.viralProteinCheckboxes = [];
- this.proteinData.effects.forEach((effect) => {
- const effectName = effect.effectName;
- if (effectNames.indexOf(effectName) === -1) {
- effectNames.push(effectName);
- this.viralProteinCheckboxes.push({
- checked: false,
- data: effect,
- });
- }
- });
const {nodes, edges} = this.mapDataToNodes(this.proteinData);
this.nodeData.nodes = new vis.DataSet(nodes);
@@ -295,83 +263,20 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
this.queryItems = [];
- this.fillQueryItems(this.proteins, this.effects);
+ this.fillQueryItems(this.proteins);
if (this.selectedWrapper) {
this.networkInternal.selectNodes([this.selectedWrapper.nodeId]);
}
}
- fillQueryItems(hostProteins: Protein[], viralProteins: ViralProtein[]) {
+ fillQueryItems(hostProteins: Protein[]) {
this.queryItems = [];
hostProteins.forEach((protein) => {
this.queryItems.push(getWrapperFromProtein(protein));
});
- viralProteins.forEach((viralProtein) => {
- this.queryItems.push(getWrapperFromViralProtein(viralProtein));
- });
-
this.currentViewNodes = this.nodeData.nodes;
this.currentViewProteins = this.proteins;
- this.currentViewViralProteins = this.effects;
- }
-
- public async filterNodes() {
- const visibleIds = new Set<string>(this.nodeData.nodes.getIds());
-
- const removeIds = new Set<string>();
- const addNodes = new Map<string, Node>();
-
- const showAll = !this.viralProteinCheckboxes.find((eff) => eff.checked);
- const connectedProteinAcs = new Set<string>();
-
- const filteredViralProteins = [];
- this.viralProteinCheckboxes.forEach((cb) => {
- const viralProteins: Array<ViralProtein> = [];
- this.proteinData.effects.forEach((effect) => {
- if (effect.effectName === cb.data.effectName) {
- viralProteins.push(effect);
- }
- });
- viralProteins.forEach((effect) => {
- const nodeId = getViralProteinNodeId(effect);
- const found = visibleIds.has(nodeId);
- if ((cb.checked || showAll) && !found) {
- const node = this.mapViralProteinToNode(effect);
- // this.nodeData.nodes.add(node);
- addNodes.set(node.id, node);
- } else if ((!showAll && !cb.checked) && found) {
- // this.nodeData.nodes.remove(nodeId);
- removeIds.add(nodeId);
- }
- if (cb.checked || showAll) {
- filteredViralProteins.push(effect);
- effect.proteins.forEach((pg) => {
- connectedProteinAcs.add(pg.proteinAc);
- });
- }
- });
- });
- const filteredProteins = [];
- for (const protein of this.proteinData.proteins) {
- const nodeId = getProteinNodeId(protein);
- const contains = connectedProteinAcs.has(protein.proteinAc);
- const found = visibleIds.has(nodeId);
- if (contains) {
- filteredProteins.push(protein);
-
- if (!found) {
- const node = this.mapHostProteinToNode(protein);
- addNodes.set(node.id, node);
- }
- } else if (found) {
- removeIds.add(nodeId);
- }
- }
-
- this.nodeData.nodes.remove(Array.from(removeIds.values()));
- this.nodeData.nodes.add(Array.from(addNodes.values()));
- this.fillQueryItems(filteredProteins, filteredViralProteins);
}
public queryAction(item: any) {
@@ -407,20 +312,8 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
return node;
}
- private mapViralProteinToNode(viralProtein: ViralProtein): any {
- const wrapper = getWrapperFromViralProtein(viralProtein);
- const node = NetworkSettings.getNodeStyle('virus', true, this.analysis.inSelection(wrapper));
- node.id = wrapper.nodeId;
- node.label = viralProtein.effectName;
- node.id = wrapper.nodeId;
- node.x = viralProtein.x;
- node.y = viralProtein.y;
- node.wrapper = wrapper;
- return node;
- }
-
- private mapEdge(edge: ProteinViralInteraction): any {
- const {from, to} = getNodeIdsFromPVI(edge);
+ private mapEdge(edge: ProteinProteinInteraction): any {
+ const {from, to} = getNodeIdsFromI(edge);
return {
from, to,
color: {
@@ -438,10 +331,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
nodes.push(this.mapHostProteinToNode(protein));
}
- for (const effect of data.effects) {
- nodes.push(this.mapViralProteinToNode(effect));
- }
-
for (const edge of data.edges) {
edges.push(this.mapEdge(edge));
}
@@ -462,16 +351,14 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
});
}
- analysisWindowChanged($event: [any[], [Protein[], ViralProtein[], Tissue]]) {
+ analysisWindowChanged($event: [any[], [Protein[], Tissue]]) {
if ($event) {
this.currentViewNodes = $event[0];
this.currentViewProteins = $event[1][0];
- this.currentViewViralProteins = $event[1][1];
- this.currentViewSelectedTissue = $event[1][2];
+ this.currentViewSelectedTissue = $event[1][1];
} else {
this.currentViewNodes = this.nodeData.nodes;
this.currentViewProteins = this.proteins;
- this.currentViewViralProteins = this.effects;
this.currentViewSelectedTissue = this.selectedTissue;
}
}
diff --git a/src/environments/environment.prod.ts b/src/environments/environment.prod.ts
index c46256ea57bccaf21afe4c8ba5a5a08296574489..2dec8afe762c3bba69754df1325f56ba1b89d934 100644
--- a/src/environments/environment.prod.ts
+++ b/src/environments/environment.prod.ts
@@ -1,4 +1,4 @@
export const environment = {
production: true,
- backend: 'https://exbio.wzw.tum.de/covex/api/',
+ backend: 'https://exbio.wzw.tum.de/drugstone/api/',
};
diff --git a/src/environments/environment.ts b/src/environments/environment.ts
index bb4892770cb650bf8f867689a7ed6f886098e911..2516ae63c61a0bc2ac8839acdd8fcddd073ff3c6 100644
--- a/src/environments/environment.ts
+++ b/src/environments/environment.ts
@@ -4,7 +4,7 @@
export const environment = {
production: false,
- backend: 'https://exbio.wzw.tum.de/netex_dev/api/',
+ backend: 'https://exbio.wzw.tum.de/drugstone/api/',
};
/*
diff --git a/src/index.html b/src/index.html
index d2831825101c723d2ef1b42c0c3b12dcb16b2e4e..2083606c17722e21deac36498c00ca99750a9e2e 100644
--- a/src/index.html
+++ b/src/index.html
@@ -82,7 +82,16 @@
proteinName: "Ras GTPase-activating protein-binding protein 2"
}
],
- edges: []
+ edges: [
+ {
+ from: 'Q9NXA8',
+ to: 'Q9Y3U8',
+ },
+ {
+ from: 'Q9Y3U8',
+ to: 'Q9UN86',
+ }
+ ]
}));
}
</script>