diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index a616c00fca744b42d1394ff7e80d20afe84b5591..ef9ccbac12ee5fc857e8f7baa7abe204b0ab168d 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -9,12 +9,9 @@ import {
Output,
SimpleChanges,
ViewChild,
-} from "@angular/core";
-import { HttpClient } from "@angular/common/http";
-import {
- algorithmNames,
- AnalysisService,
-} from "../../services/analysis/analysis.service";
+} from '@angular/core';
+import { HttpClient } from '@angular/common/http';
+import { algorithmNames, AnalysisService } from '../../services/analysis/analysis.service';
import {
Drug,
NodeAttributeMap,
@@ -26,26 +23,23 @@ import {
Tissue,
Wrapper,
NodeInteraction,
-} from "../../interfaces";
-import { NetworkSettings } from "../../network-settings";
-import { NetexControllerService } from "src/app/services/netex-controller/netex-controller.service";
-import {
- mapCustomEdge,
- mapNetexEdge,
- ProteinNetwork,
-} from "src/app/main-network";
-import { DrugstoneConfigService } from "src/app/services/drugstone-config/drugstone-config.service";
-import { NetworkHandlerService } from "src/app/services/network-handler/network-handler.service";
-import { LegendService } from "src/app/services/legend-service/legend-service.service";
-import { LoadingScreenService } from "src/app/services/loading-screen/loading-screen.service";
-import { version } from "../../../version";
-import { downloadCSV } from "src/app/utils";
+} from '../../interfaces';
+import { NetworkSettings } from '../../network-settings';
+import { NetexControllerService } from 'src/app/services/netex-controller/netex-controller.service';
+import { mapCustomEdge, mapNetexEdge, ProteinNetwork } from 'src/app/main-network';
+import { DrugstoneConfigService } from 'src/app/services/drugstone-config/drugstone-config.service';
+import { NetworkHandlerService } from 'src/app/services/network-handler/network-handler.service';
+import { LegendService } from 'src/app/services/legend-service/legend-service.service';
+import { LoadingScreenService } from 'src/app/services/loading-screen/loading-screen.service';
+import { version } from '../../../version';
+import { downloadCSV } from 'src/app/utils';
+import { Observable } from 'rxjs';
declare var vis: any;
interface Scored {
- score: number; // Normalized or unnormalized (whichever user selects, will be displayed in the table)
- rawScore: number; // Unnormalized (kept to restore unnormalized value)
+ score: number; // Normalized or unnormalized (whichever user selects, will be displayed in the table)
+ rawScore: number; // Unnormalized (kept to restore unnormalized value)
rank: number;
}
@@ -53,25 +47,23 @@ interface Seeded {
isSeed: boolean;
}
+
@Component({
- selector: "app-analysis-panel",
- templateUrl: "./analysis-panel.component.html",
- styleUrls: ["./analysis-panel.component.scss"],
+ selector: 'app-analysis-panel',
+ templateUrl: './analysis-panel.component.html',
+ styleUrls: ['./analysis-panel.component.scss'],
})
-export class AnalysisPanelComponent
- implements OnInit, OnChanges, AfterViewInit
-{
- @ViewChild("networkWithLegend", { static: false })
- networkWithLegendEl: ElementRef;
+export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit {
+
+ @ViewChild('networkWithLegend', { static: false }) networkWithLegendEl: ElementRef;
@Input() token: string | null = null;
@Input() tokenType: string | null = null;
+
@Output() tokenChange = new EventEmitter<string | null>();
@Output() showDetailsChange = new EventEmitter<Wrapper>();
@Output() setInputNetwork = new EventEmitter<any>();
- @Output() visibleItems = new EventEmitter<
- [any[], [Node[], Tissue], NodeInteraction[]]
- >();
+ @Output() visibleItems = new EventEmitter<[any[], [Node[], Tissue], NodeInteraction[]]>();
public task: Task | null = null;
public result: any = null;
@@ -80,10 +72,10 @@ export class AnalysisPanelComponent
public algorithmDefault = undefined;
public network: any;
- public nodeData: { nodes: any; edges: any } = { nodes: null, edges: null };
+ public nodeData: { nodes: any, edges: any } = { nodes: null, edges: null };
// private drugNodes: any[] = [];
// private drugEdges: any[] = [];
- public tab: "meta" | "network" | "table" = "network";
+ public tab: 'meta' | 'network' | 'table' = 'network';
private proteins: any;
public effects: any;
@@ -94,15 +86,15 @@ export class AnalysisPanelComponent
public tableNormalize = false;
public tableHasScores = false;
- public LegendContext: LegendContext = "drugTarget";
+ public LegendContext: LegendContext = 'drugTarget';
public expressionExpanded = false;
public selectedTissue: Tissue | null = null;
public algorithmNames = algorithmNames;
- public tableDrugScoreTooltip = "";
- public tableProteinScoreTooltip = "";
+ public tableDrugScoreTooltip = '';
+ public tableProteinScoreTooltip = '';
public versionString = undefined;
@@ -110,24 +102,23 @@ export class AnalysisPanelComponent
public loading = false;
- constructor(
- public legendService: LegendService,
- public networkHandler: NetworkHandlerService,
- public drugstoneConfig: DrugstoneConfigService,
- private http: HttpClient,
- public analysis: AnalysisService,
- public netex: NetexControllerService,
- public loadingScreen: LoadingScreenService
- ) {
+
+ constructor(public legendService: LegendService, public networkHandler: NetworkHandlerService, public drugstoneConfig: DrugstoneConfigService, private http: HttpClient, public analysis: AnalysisService, public netex: NetexControllerService, public loadingScreen: LoadingScreenService) {
try {
this.versionString = version;
- } catch (e) {}
+ } catch (e) {
+ }
}
- async ngOnInit() {}
+ async ngOnInit() {
+ }
ngAfterViewInit() {
- this.networkHandler.setActiveNetwork("analysis");
+ this.networkHandler.setActiveNetwork('analysis');
+ this.networkHandler.activeNetwork.subscribeSelection(() => {
+ this.refresh();
+ }
+ );
}
async ngOnChanges(changes: SimpleChanges) {
@@ -143,69 +134,52 @@ export class AnalysisPanelComponent
}
private setNetworkListeners() {
- this.networkHandler.activeNetwork.networkInternal.on(
- "dragEnd",
- (properties) => {
- const node_ids =
- this.networkHandler.activeNetwork.networkInternal.getSelectedNodes();
- if (node_ids.length === 0 || !this.networkHandler.shiftDown) {
+ this.networkHandler.activeNetwork.networkInternal.on('dragEnd', (properties) => {
+ const node_ids = this.networkHandler.activeNetwork.networkInternal.getSelectedNodes();
+ if (node_ids.length === 0 || !this.networkHandler.shiftDown) {
+ return;
+ }
+ this.analysis.addNodesByIdsToSelection(node_ids);
+ this.networkHandler.activeNetwork.networkInternal.unselectAll();
+ });
+ this.networkHandler.activeNetwork.networkInternal.on('deselectNode', (properties) => {
+ this.showDetailsChange.emit(null);
+ });
+ this.networkHandler.activeNetwork.networkInternal.on('doubleClick', (properties) => {
+ const nodeIds: Array<string> = properties.nodes;
+ if (nodeIds.length > 0) {
+ const nodeId = nodeIds[0];
+ const node = this.nodeData.nodes.get(nodeId);
+ if (node.drugstoneId === undefined || node.nodeType === 'drug' || node.drugstoneType !== 'protein') {
+ this.analysis.unmappedNodeToast();
return;
}
- this.analysis.addNodesByIdsToSelection(node_ids);
- this.networkHandler.activeNetwork.networkInternal.unselectAll();
- }
- );
- this.networkHandler.activeNetwork.networkInternal.on(
- "deselectNode",
- (properties) => {
- this.showDetailsChange.emit(null);
- }
- );
- this.networkHandler.activeNetwork.networkInternal.on(
- "doubleClick",
- (properties) => {
- const nodeIds: Array<string> = properties.nodes;
- if (nodeIds.length > 0) {
- const nodeId = nodeIds[0];
- const node = this.nodeData.nodes.get(nodeId);
- if (
- node.drugstoneId === undefined ||
- node.nodeType === "drug" ||
- node.drugstoneType !== "protein"
- ) {
- this.analysis.unmappedNodeToast();
- return;
- }
- const wrapper = getWrapperFromNode(node);
- if (this.analysis.inSelection(wrapper)) {
- this.analysis.removeItems([wrapper]);
- this.analysis.getCount();
- } else {
- this.analysis.addItems([wrapper]);
- this.analysis.getCount();
- }
+ const wrapper = getWrapperFromNode(node);
+ if (this.analysis.inSelection(wrapper)) {
+ this.analysis.removeItems([wrapper]);
+ this.analysis.getCount();
+ } else {
+ this.analysis.addItems([wrapper]);
+ this.analysis.getCount();
}
}
- );
+ });
- this.networkHandler.activeNetwork.networkInternal.on(
- "click",
- (properties) => {
- if (properties.nodes.length === 0 && properties.edges.length === 1) {
- // clicked on one edge
- const edgeId = properties.edges[0];
- this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
+ this.networkHandler.activeNetwork.networkInternal.on('click', (properties) => {
+ if (properties.nodes.length === 0 && properties.edges.length === 1) {
+ // clicked on one edge
+ const edgeId = properties.edges[0];
+ this.networkHandler.activeNetwork.openEdgeSummary(edgeId);
+ } else {
+ this.networkHandler.activeNetwork.activeEdge = null;
+ const selectedNodes = this.nodeData.nodes.get(properties.nodes);
+ if (selectedNodes.length > 0) {
+ this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
} else {
- this.networkHandler.activeNetwork.activeEdge = null;
- const selectedNodes = this.nodeData.nodes.get(properties.nodes);
- if (selectedNodes.length > 0) {
- this.showDetailsChange.emit(getWrapperFromNode(selectedNodes[0]));
- } else {
- this.showDetailsChange.emit(null);
- }
+ this.showDetailsChange.emit(null);
}
}
- );
+ });
this.analysis.subscribeList((items, selected) => {
// return if analysis panel is closed or no nodes are loaded
if (!this.token) {
@@ -219,15 +193,10 @@ export class AnalysisPanelComponent
if (!node) {
continue;
}
- const pos =
- this.networkHandler.activeNetwork.networkInternal.getPositions([
- item.id,
- ]);
+ const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([item.id]);
node.x = pos[item.id].x;
node.y = pos[item.id].y;
- const isSeed = this.networkHandler.activeNetwork.highlightSeeds
- ? this.networkHandler.activeNetwork.seedMap[node.id]
- : false;
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
const nodeStyled = NetworkSettings.getNodeStyle(
node,
this.drugstoneConfig.currentConfig(),
@@ -243,12 +212,8 @@ export class AnalysisPanelComponent
const proteinSelection = this.tableSelectedProteins;
for (const item of items) {
// TODO: Refactor!
- const found = proteinSelection.findIndex(
- (i) => getProteinNodeId(i) === item.id
- );
- const tableItem = this.tableProteins.find(
- (i) => getProteinNodeId(i) === item.id
- );
+ const found = proteinSelection.findIndex((i) => getProteinNodeId(i) === item.id);
+ const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
if (selected && found === -1 && tableItem) {
proteinSelection.push(tableItem);
}
@@ -261,9 +226,7 @@ export class AnalysisPanelComponent
// else: selected is null
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
- const isSeed = this.networkHandler.activeNetwork.highlightSeeds
- ? this.networkHandler.activeNetwork.seedMap[node.id]
- : false;
+ const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
if (!isSeed) {
return;
}
@@ -281,9 +244,7 @@ export class AnalysisPanelComponent
const proteinSelection = [];
for (const item of items) {
- const tableItem = this.tableProteins.find(
- (i) => getProteinNodeId(i) === item.id
- );
+ const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.id);
if (tableItem) {
proteinSelection.push(tableItem);
}
@@ -293,9 +254,7 @@ export class AnalysisPanelComponent
});
}
- private rankTable(
- table: Array<Drug & Scored> | Array<Node & Scored & Seeded>
- ) {
+ private rankTable(table: Array<Drug & Scored> | Array<Node & Scored & Seeded>) {
let lastRank = 1;
for (let idx = 0; idx < table.length; idx++) {
if (idx === 0) {
@@ -312,13 +271,14 @@ export class AnalysisPanelComponent
private async refreshView() {
this.loading = true;
this.loadingScreen.stateUpdate(true);
- this.getView(this.token).then(async (view) => {
+ this.getView(this.token).then(async view => {
this.task = view;
this.result = view;
this.drugstoneConfig.set_analysisConfig(view.config);
this.analysis.switchSelection(this.token);
this.loadingScreen.stateUpdate(false);
+
// Reset
this.nodeData = { nodes: null, edges: null };
// this.networkHandler.activeNetwork.networkEl.nativeElement.innerHTML = '';
@@ -330,56 +290,34 @@ export class AnalysisPanelComponent
if (this.drugstoneConfig.config.autofillEdges && nodes.length) {
const node_map = {};
- nodes
- .filter((n) => n.drugstoneType === "protein")
- .forEach((node) => {
- if (typeof node.drugstoneId === "string") {
- if (node_map[node.drugstoneId]) {
- node_map[node.drugstoneId].push(node.id);
- } else {
- node_map[node.drugstoneId] = [node.id];
- }
+ nodes.filter(n => n.drugstoneType === 'protein').forEach(node => {
+ if (typeof node.drugstoneId === 'string') {
+ if (node_map[node.drugstoneId]) {
+ node_map[node.drugstoneId].push(node.id);
} else {
- node.drugstoneId.forEach((n) => {
- if (node_map[n]) {
- node_map[n].push(node.id);
- } else {
- node_map[n] = [node.id];
- }
- });
+ node_map[node.drugstoneId] = [node.id];
}
- });
- const netexEdges = await this.netex.fetchEdges(
- nodes,
- this.drugstoneConfig.config.interactionProteinProtein,
- this.drugstoneConfig.config.licensedDatasets
- );
- edges.push(
- ...netexEdges
- .map((netexEdge) =>
- mapNetexEdge(
- netexEdge,
- this.drugstoneConfig.currentConfig(),
- node_map
- )
- )
- .flatMap((e) => e)
- );
+ } else {
+ node.drugstoneId.forEach(n => {
+ if (node_map[n]) {
+ node_map[n].push(node.id);
+ } else {
+ node_map[n] = [node.id];
+ }
+ });
+ }
+ });
+ const netexEdges = await this.netex.fetchEdges(nodes, this.drugstoneConfig.config.interactionProteinProtein, this.drugstoneConfig.config.licensedDatasets);
+ edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.drugstoneConfig.currentConfig(), node_map)).flatMap(e => e));
}
const edge_map = {};
- edges = edges.filter((edge) => {
- if (
- edge_map[edge.to] &&
- edge_map[edge.to].indexOf(edge.from) !== -1
- ) {
+ edges = edges.filter(edge => {
+ if (edge_map[edge.to] && edge_map[edge.to].indexOf(edge.from) !== -1) {
return false;
}
- if (
- edge_map[edge.from] &&
- edge_map[edge.from].indexOf(edge.to) !== -1
- ) {
+ if (edge_map[edge.from] && edge_map[edge.from].indexOf(edge.to) !== -1) {
return false;
}
if (!edge_map[edge.from]) {
@@ -392,22 +330,15 @@ export class AnalysisPanelComponent
// @ts-ignore
if (!this.drugstoneConfig.selfReferences) {
- edges = edges.filter((el) => el.from !== el.to);
+ edges = edges.filter(el => el.from !== el.to);
}
- this.networkHandler.activeNetwork.inputNetwork = {
- nodes: nodes,
- edges: edges,
- };
+ this.networkHandler.activeNetwork.inputNetwork = { nodes: nodes, edges: edges };
this.nodeData.nodes = new vis.DataSet(nodes);
this.nodeData.edges = new vis.DataSet(edges);
- const container =
- this.networkHandler.activeNetwork.networkEl.nativeElement;
+ const container = this.networkHandler.activeNetwork.networkEl.nativeElement;
const isBig = nodes.length > 100 || edges.length > 100;
- const options = NetworkSettings.getOptions(
- isBig ? "analysis-big" : "analysis",
- this.drugstoneConfig.currentConfig()
- );
+ const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.drugstoneConfig.currentConfig());
// @ts-ignore
options.groups = this.drugstoneConfig.currentConfig().nodeGroups;
// @ts-ignore
@@ -418,31 +349,19 @@ export class AnalysisPanelComponent
if (this.drugstoneConfig.config.physicsOn) {
this.drugstoneConfig.config.physicsOn = !isBig;
}
- this.networkHandler.activeNetwork.networkInternal = new vis.Network(
- container,
- this.nodeData,
- options
- );
+ this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
if (isBig) {
resolve(nodes);
}
- this.networkHandler.activeNetwork.networkInternal.once(
- "stabilizationIterationsDone",
- async () => {
- if (
- !this.drugstoneConfig.config.physicsOn ||
- this.networkHandler.activeNetwork.isBig()
- ) {
- this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
- }
- this.networkHandler
- .updateAdjacentNodes(this.networkHandler.activeNetwork.isBig())
- .then(() => {
- resolve(nodes);
- });
+ this.networkHandler.activeNetwork.networkInternal.once('stabilizationIterationsDone', async () => {
+ if (!this.drugstoneConfig.config.physicsOn || this.networkHandler.activeNetwork.isBig()) {
+ this.networkHandler.activeNetwork.updatePhysicsEnabled(false);
}
- );
+ this.networkHandler.updateAdjacentNodes(this.networkHandler.activeNetwork.isBig()).then(() => {
+ resolve(nodes);
+ });
+ });
}).then(() => {
this.setNetworkListeners();
this.emitVisibleItems(true);
@@ -450,71 +369,69 @@ export class AnalysisPanelComponent
});
}
+
private async refreshTask() {
this.loadingScreen.stateUpdate(true);
this.task = await this.getTask(this.token);
this.analysis.switchSelection(this.token);
- if (this.task.info.algorithm === "degree") {
+ if (this.task.info.algorithm === 'degree') {
this.tableDrugScoreTooltip =
- "Normalized number of direct interactions of the drug with the seeds. " +
- "The higher the score, the more relevant the drug.";
+ 'Normalized number of direct interactions of the drug with the seeds. ' +
+ 'The higher the score, the more relevant the drug.';
this.tableProteinScoreTooltip =
- "Normalized number of direct interactions of the protein with the seeds. " +
- "The higher the score, the more relevant the protein.";
- } else if (
- this.task.info.algorithm === "closeness" ||
- this.task.info.algorithm === "quick" ||
- this.task.info.algorithm === "super"
- ) {
+ 'Normalized number of direct interactions of the protein with the seeds. ' +
+ 'The higher the score, the more relevant the protein.';
+ } else if (this.task.info.algorithm === 'closeness' || this.task.info.algorithm === 'quick' || this.task.info.algorithm === 'super') {
this.tableDrugScoreTooltip =
- "Normalized inverse mean distance of the drug to the seeds. " +
- "The higher the score, the more relevant the drug.";
+ 'Normalized inverse mean distance of the drug to the seeds. ' +
+ 'The higher the score, the more relevant the drug.';
this.tableProteinScoreTooltip =
- "Normalized inverse mean distance of the protein to the seeds. " +
- "The higher the score, the more relevant the protein.";
- } else if (this.task.info.algorithm === "trustrank") {
+ 'Normalized inverse mean distance of the protein to the seeds. ' +
+ 'The higher the score, the more relevant the protein.';
+ } else if (this.task.info.algorithm === 'trustrank') {
this.tableDrugScoreTooltip =
- "Amount of ‘trust’ on the drug at termination of the algorithm. " +
- "The higher the score, the more relevant the drug.";
+ 'Amount of ‘trust’ on the drug at termination of the algorithm. ' +
+ 'The higher the score, the more relevant the drug.';
this.tableProteinScoreTooltip =
- "Amount of ‘trust’ on the protein at termination of the algorithm. " +
- "The higher the score, the more relevant the protein.";
- } else if (this.task.info.algorithm === "proximity") {
+ 'Amount of ‘trust’ on the protein at termination of the algorithm. ' +
+ 'The higher the score, the more relevant the protein.';
+ } else if (this.task.info.algorithm === 'proximity') {
this.tableDrugScoreTooltip =
- "Empirical z-score of mean minimum distance between the drug’s targets and the seeds. " +
- "The lower the score, the more relevant the drug.";
+ 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
+ 'The lower the score, the more relevant the drug.';
this.tableProteinScoreTooltip =
- "Empirical z-score of mean minimum distance between the drug’s targets and the seeds. " +
- "The lower the score, the more relevant the drug.";
+ 'Empirical z-score of mean minimum distance between the drug’s targets and the seeds. ' +
+ 'The lower the score, the more relevant the drug.';
}
if (this.task && this.task.info && this.task.info.done) {
+
this.loading = true;
- this.netex.getTaskResult(this.token).then(async (result) => {
- if (this.networkHandler.activeNetwork.networkType !== "analysis") {
+ this.netex.getTaskResult(this.token).then(async result => {
+ if (this.networkHandler.activeNetwork.networkType !== 'analysis') {
return;
}
this.drugstoneConfig.set_analysisConfig(result.parameters.config);
this.analysis.switchSelection(this.token);
this.result = result;
- if (this.result.parameters.target === "drug") {
- this.legendService.add_to_context("drug");
+ if (this.result.parameters.target === 'drug') {
+ this.legendService.add_to_context('drug');
} else {
- this.legendService.add_to_context("drugTarget");
+ this.legendService.add_to_context('drugTarget');
}
const nodeAttributes = this.result.nodeAttributes || {};
- const analysisNetwork = this.networkHandler.networks["analysis"];
+ const analysisNetwork = this.networkHandler.networks['analysis'];
analysisNetwork.seedMap = nodeAttributes.isSeed || {};
// Reset
this.nodeData = { nodes: null, edges: null };
- analysisNetwork.networkEl.nativeElement.innerHTML = "";
+ analysisNetwork.networkEl.nativeElement.innerHTML = '';
analysisNetwork.networkInternal = null;
// Create
- await this.createNetwork(this.result).then((nw) => {
+ await this.createNetwork(this.result).then(nw => {
return new Promise<any>((resolve, reject) => {
- if (this.networkHandler.activeNetwork.networkType !== "analysis") {
+ if (this.networkHandler.activeNetwork.networkType !== 'analysis') {
return;
}
const nodes = nw.nodes;
@@ -524,10 +441,7 @@ export class AnalysisPanelComponent
this.nodeData.edges = new vis.DataSet(edges);
const container = analysisNetwork.networkEl.nativeElement;
const isBig = nodes.length > 100 || edges.length > 100;
- const options = NetworkSettings.getOptions(
- isBig ? "analysis-big" : "analysis",
- this.drugstoneConfig.currentConfig()
- );
+ const options = NetworkSettings.getOptions(isBig ? 'analysis-big' : 'analysis', this.drugstoneConfig.currentConfig());
// @ts-ignore
options.groups = this.drugstoneConfig.currentConfig().nodeGroups;
// @ts-ignore
@@ -538,103 +452,68 @@ export class AnalysisPanelComponent
if (this.drugstoneConfig.config.physicsOn) {
this.drugstoneConfig.config.physicsOn = !isBig;
}
- analysisNetwork.networkInternal = new vis.Network(
- container,
- this.nodeData,
- options
- );
+ analysisNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
if (isBig) {
resolve(nodes);
}
- analysisNetwork.networkInternal.once(
- "stabilizationIterationsDone",
- async () => {
- if (
- !this.drugstoneConfig.config.physicsOn ||
- analysisNetwork.isBig()
- ) {
- analysisNetwork.updatePhysicsEnabled(false);
- }
- this.networkHandler
- .updateAdjacentNodes(analysisNetwork.isBig())
- .then(() => {
- resolve(nodes);
- });
+ analysisNetwork.networkInternal.once('stabilizationIterationsDone', async () => {
+ if (!this.drugstoneConfig.config.physicsOn || analysisNetwork.isBig()) {
+ analysisNetwork.updatePhysicsEnabled(false);
}
- );
- })
- .then((nodes) => {
- this.tableDrugs = nodes.filter(
- (e) => e.drugstoneId && e.drugstoneType === "drug"
- );
- this.tableDrugs.forEach((r) => {
- r.rawScore = r.score;
- });
- // @ts-ignore
- this.tableDrugs.sort((a, b) => b.score - a.score);
- this.rankTable(this.tableDrugs);
- this.tableProteins = nodes.filter(
- (e) => e.drugstoneId && e.drugstoneType === "protein"
- );
- this.tableSelectedProteins = [];
- this.tableProteins.forEach((r) => {
- r.rawScore = r.score;
- r.isSeed = analysisNetwork.seedMap[r.id];
- const wrapper = getWrapperFromNode(r);
- if (this.analysis.inSelection(wrapper)) {
- this.tableSelectedProteins.push(r);
- }
- });
- this.tableProteins.sort((a, b) => b.score - a.score);
- this.rankTable(this.tableProteins);
-
- this.tableHasScores =
- [
- "trustrank",
- "closeness",
- "degree",
- "betweenness",
- "quick",
- "super",
- ].indexOf(this.task.info.algorithm) !== -1;
- if (this.tableHasScores) {
- this.toggleNormalization(true);
- }
- analysisNetwork.networkInternal.setData({
- nodes: undefined,
- edge: undefined,
+ this.networkHandler.updateAdjacentNodes(analysisNetwork.isBig()).then(() => {
+ resolve(nodes);
});
- setTimeout(() => {
- analysisNetwork.networkInternal.setData(this.nodeData);
- }, 1000);
- this.setNetworkListeners();
- this.emitVisibleItems(true);
- })
- .then(() => {
- if (
- !["quick", "super", "connect", "connectSelected"].includes(
- this.task.info.algorithm
- )
- ) {
- return;
+ });
+ }).then(nodes => {
+ this.tableDrugs = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'drug');
+ this.tableDrugs.forEach((r) => {
+ r.rawScore = r.score;
+ });
+ // @ts-ignore
+ this.tableDrugs.sort((a, b) => b.score - a.score);
+ this.rankTable(this.tableDrugs);
+ this.tableProteins = nodes.filter(e => e.drugstoneId && e.drugstoneType === 'protein');
+ this.tableSelectedProteins = [];
+ this.tableProteins.forEach((r) => {
+ r.rawScore = r.score;
+ r.isSeed = analysisNetwork.seedMap[r.id];
+ const wrapper = getWrapperFromNode(r);
+ if (this.analysis.inSelection(wrapper)) {
+ this.tableSelectedProteins.push(r);
}
- this.netex
- .getAlgorithmDefaults(this.task.info.algorithm)
- .then((response) => {
- this.algorithmDefault = response;
- });
- })
- .catch(console.error);
+ });
+ this.tableProteins.sort((a, b) => b.score - a.score);
+ this.rankTable(this.tableProteins);
+
+ this.tableHasScores = ['trustrank', 'closeness', 'degree', 'betweenness', 'quick', 'super']
+ .indexOf(this.task.info.algorithm) !== -1;
+ if (this.tableHasScores) {
+ this.toggleNormalization(true);
+ }
+ analysisNetwork.networkInternal.setData({ nodes: undefined, edge: undefined });
+ setTimeout(() => {
+ analysisNetwork.networkInternal.setData(this.nodeData);
+ }, 1000);
+ this.setNetworkListeners();
+ this.emitVisibleItems(true);
+ }).then(() => {
+ this.loadingScreen.stateUpdate(false);
+ if (!['quick', 'super', 'connect', 'connectSelected'].includes(this.task.info.algorithm)) {
+ return;
+ }
+ this.netex.getAlgorithmDefaults(this.task.info.algorithm).then(response => {
+ this.algorithmDefault = response;
+ });
+ }).catch(console.error);
});
- this.loadingScreen.stateUpdate(false);
});
}
}
private async refresh() {
if (this.token) {
- if (this.tokenType === "view") {
+ if (this.tokenType === 'view') {
this.networkHandler.showSeedsButton = false;
await this.refreshView();
} else {
@@ -642,47 +521,39 @@ export class AnalysisPanelComponent
await this.refreshTask();
}
}
+
}
public emitVisibleItems(on: boolean) {
if (on) {
- this.visibleItems.emit([
- this.nodeData.nodes,
- [this.proteins, this.selectedTissue],
- this.nodeData.edges,
- ]);
+ this.visibleItems.emit([this.nodeData.nodes, [this.proteins, this.selectedTissue], this.nodeData.edges]);
} else {
this.visibleItems.emit(null);
}
}
private async getView(token: string): Promise<any> {
- return await this.http
- .get(`${this.netex.getBackend()}view/?token=${token}`)
- .toPromise();
+ return await this.http.get(`${this.netex.getBackend()}view/?token=${token}`).toPromise();
}
private async getTask(token: string): Promise<any> {
- return await this.http
- .get(`${this.netex.getBackend()}task/?token=${token}`)
- .toPromise();
+ return await this.http.get(`${this.netex.getBackend()}task/?token=${token}`).toPromise();
}
close() {
- const analysisNetwork = this.networkHandler.networks["analysis"];
+ const analysisNetwork = this.networkHandler.networks['analysis'];
analysisNetwork.gradientMap = {};
this.drugstoneConfig.remove_analysisConfig();
this.expressionExpanded = false;
this.expressionMap = undefined;
analysisNetwork.seedMap = {};
analysisNetwork.highlightSeeds = false;
- this.legendService.networkHasConnector = false;
- this.analysis.switchSelection("main");
+ this.analysis.switchSelection('main');
// this.analysis.resetSelection();
this.token = null;
this.tokenChange.emit(this.token);
- this.legendService.remove_from_context("drug");
- this.legendService.remove_from_context("drugTarget");
+ this.legendService.remove_from_context('drug');
+ this.legendService.remove_from_context('drugTarget');
this.emitVisibleItems(false);
}
@@ -691,30 +562,30 @@ export class AnalysisPanelComponent
const normalizeFn = (table) => {
let max = 0;
- table.forEach((i) => {
+ table.forEach(i => {
if (i.rawScore > max) {
max = i.rawScore;
}
});
- table.forEach((i) => {
+ table.forEach(i => {
i.score = i.rawScore / max;
});
};
const unnormalizeFn = (table) => {
- table.forEach((i) => {
+ table.forEach(i => {
i.score = i.rawScore;
});
};
if (normalize) {
normalizeFn(this.tableProteins);
- if (this.task.info.target === "drug") {
+ if (this.task.info.target === 'drug') {
normalizeFn(this.tableDrugs);
}
} else {
unnormalizeFn(this.tableProteins);
- if (this.task.info.target === "drug") {
+ if (this.task.info.target === 'drug') {
unnormalizeFn(this.tableDrugs);
}
}
@@ -729,22 +600,11 @@ export class AnalysisPanelComponent
}
});
- if ("score" in data[0]) {
- data = data.sort((a, b) => b["score"] - a["score"]);
+ if ('score' in data[0]) {
+ data = data.sort((a, b) => b['score'] - a['score']);
}
- const columns = [
- "label",
- "symbol",
- "uniprot",
- "ensg",
- "entrez",
- "proteinName",
- "isSeed",
- "score",
- "rank",
- "status",
- ];
+ const columns = ['label', 'symbol', 'uniprot', 'ensg', 'entrez', 'proteinName', 'isSeed', 'score', 'rank', 'status'];
downloadCSV(data, columns, `drugstone_${view}`);
}
@@ -754,14 +614,12 @@ export class AnalysisPanelComponent
* @param result
* @returns
*/
- public async createNetwork(
- result: any
- ): Promise<{ edges: any[]; nodes: any[] }> {
+ public async createNetwork(result: any): Promise<{ edges: any[]; nodes: any[]; }> {
const identifier = this.drugstoneConfig.currentConfig().identifier;
// add drugGroup and foundNodesGroup for added nodes
// these groups can be overwritten by the user
- const nodes = [];
+ let nodes = [];
let edges = [];
const attributes = result.nodeAttributes || {};
@@ -772,84 +630,68 @@ export class AnalysisPanelComponent
network.nodes = [...new Set<string>(network.nodes)];
const details = attributes.details || {};
const nodeIdMap = {};
- Object.entries(details)
// @ts-ignore
- .filter((e) => e[1].drugstoneType === "protein")
- .forEach((e) => {
- // @ts-ignore
- e[1].drugstoneId.forEach((id) => {
- nodeIdMap[id] = e[1][identifier][0];
- });
+ Object.entries(details).filter(e => e[1].drugstoneType === 'protein').forEach(e => {
+ // @ts-ignore
+ e[1].drugstoneId.forEach(id => {
+ nodeIdMap[id] = e[1][identifier][0];
});
+ });
for (const nodeId of network.nodes) {
if (details[nodeId]) {
const nodeDetails = details[nodeId];
- nodeDetails.id = nodeDetails.id
- ? nodeDetails.id
- : typeof nodeDetails.drugstoneId === "string"
- ? nodeDetails.drugstoneId
- : nodeDetails.drugstoneId[0];
- if (
- nodeDetails.drugstoneId &&
- nodeDetails.drugstoneType === "protein"
- ) {
+ nodeDetails.id = nodeDetails.id ? nodeDetails.id : (typeof nodeDetails.drugstoneId === 'string' ? nodeDetails.drugstoneId : nodeDetails.drugstoneId[0]);
+ if (nodeDetails.drugstoneId && nodeDetails.drugstoneType === 'protein') {
// node is protein from database, has been mapped on init to backend protein from backend
// or was found during analysis
// FIXME connectorNodes are not visualized correctly
- nodeDetails.group =
- result.targetNodes && result.targetNodes.indexOf(nodeId) !== -1
- ? "foundNode"
- : nodeDetails.group
- ? nodeDetails.group
- : "connectorNode";
- nodeDetails.label = nodeDetails.label
- ? nodeDetails.label
- : nodeDetails[identifier];
- nodeDetails.id = nodeDetails[identifier][0]
- ? nodeDetails[identifier][0]
- : nodeDetails.id;
+ nodeDetails.group = result.targetNodes && result.targetNodes.indexOf(nodeId) !== -1 ? 'foundNode' : (nodeDetails.group ? nodeDetails.group : 'connectorNode');
+ nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
+ nodeDetails.id = nodeDetails[identifier][0] ? nodeDetails[identifier][0] : nodeDetails.id;
this.proteins.push(nodeDetails);
- } else if (
- nodeDetails.drugstoneId &&
- nodeDetails.drugstoneType === "drug"
- ) {
+ } else if (nodeDetails.drugstoneId && nodeDetails.drugstoneType === 'drug') {
// node is drug, was found during analysis
- nodeDetails.type = "Drug";
- nodeDetails.group = "foundDrug";
+ nodeDetails.type = 'Drug';
+ nodeDetails.group = 'foundDrug';
+
} else {
// node is custom input from user, could not be mapped to backend protein
- nodeDetails.group = nodeDetails.group ? nodeDetails.group : "default";
- nodeDetails.label = nodeDetails.label
- ? nodeDetails.label
- : nodeDetails[identifier];
+ nodeDetails.group = nodeDetails.group ? nodeDetails.group : 'default';
+ nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
}
// further analysis and the button function can be used to highlight seeds
// option to use scores[node] as gradient, but sccores are very small
- nodes.push(
- NetworkSettings.getNodeStyle(
- nodeDetails as Node,
- this.drugstoneConfig.currentConfig(),
- false,
- false,
- 1,
- this.networkHandler.activeNetwork.nodeRenderer
- )
- );
+ nodes.push(NetworkSettings.getNodeStyle(nodeDetails as Node, this.drugstoneConfig.currentConfig(), false, false, 1, this.networkHandler.activeNetwork.nodeRenderer));
} else {
- console.log("Missing details for " + nodeId);
+ console.log('Missing details for ' + nodeId);
}
}
const uniqEdges = [];
+ const skippedDrugIds = new Set<string>();
+ const drugEdgeTypes = new Set<string>();
for (const edge of network.edges) {
- const e = mapCustomEdge(
- edge,
- this.drugstoneConfig.currentConfig(),
- this.drugstoneConfig
- );
- e.from =
- e.from[0] === "p" && nodeIdMap[e.from] ? nodeIdMap[e.from] : e.from;
- e.to = e.to[0] === "p" && nodeIdMap[e.to] ? nodeIdMap[e.to] : e.to;
- const hash = e.from + "_" + e.to;
+ const e = mapCustomEdge(edge, this.drugstoneConfig.currentConfig(), this.drugstoneConfig);
+ const isDrugEdge = e.to[0] === 'd' && e.to[1] === 'r';
+ e.from = e.from[0] === 'p' && nodeIdMap[e.from] ? nodeIdMap[e.from] : e.from;
+ e.to = e.to[0] === 'p' && nodeIdMap[e.to] ? nodeIdMap[e.to] : e.to;
+ if (isDrugEdge) {
+ skippedDrugIds.add(e.to);
+ if (edge.actions) {
+ edge.actions.forEach(a => drugEdgeTypes.add(a));
+ }
+ if (edge.actions && this.networkHandler.activeNetwork.getSelectedDrugTargetType() && !edge.actions.includes(this.networkHandler.activeNetwork.getSelectedDrugTargetType())) {
+ continue;
+ }
+ const label = edge.actions && edge.actions.length > 0 ? edge.actions.join(',') : undefined;
+ skippedDrugIds.delete(e.to);
+ if (label) {
+ e.label = label;
+ }
+ }
+
+ this.networkHandler.activeNetwork.setDrugTargetTypes(Array.from(drugEdgeTypes));
+
+ const hash = e.from + '_' + e.to;
if (uniqEdges.indexOf(hash) === -1) {
uniqEdges.push(hash);
edges.push(e);
@@ -857,35 +699,30 @@ export class AnalysisPanelComponent
}
// remove self-edges/loops
if (!this.drugstoneConfig.currentConfig().selfReferences) {
- edges = edges.filter((el) => el.from !== el.to);
+ edges = edges.filter(el => el.from !== el.to);
}
+ nodes = nodes.filter(n => !(n.drugstoneId && skippedDrugIds.has(n.drugstoneId)));
+ // if (this.networkHandler.activeNetwork.selectedDrugTargetType) {
+ // }
+
+ this.legendService.networkHasConnector = nodes.filter(node => node.group === 'connectorNode').length > 0;
- this.legendService.networkHasConnector =
- nodes.filter((node) => node.group === "connectorNode").length > 0;
-
- return {
+ return {
nodes,
edges,
};
}
getResultNodes() {
- if (this.nodeData && this.nodeData["nodes"]) {
- return this.nodeData["nodes"].get();
+ if (this.nodeData && this.nodeData['nodes']) {
+ return this.nodeData['nodes'].get();
}
return [];
}
getResultEdges() {
- if (this.nodeData && this.nodeData["edges"]) {
- return this.nodeData["edges"]
- .get()
- .filter(
- (e) =>
- !e.id ||
- !e.groupName ||
- (typeof e.from === "string" && typeof e.to === "string")
- );
+ if (this.nodeData && this.nodeData['edges']) {
+ return this.nodeData['edges'].get().filter(e => !e.id || !e.groupName || (typeof e.from === 'string' && typeof e.to === 'string'));
}
return [];
}
@@ -923,4 +760,5 @@ export class AnalysisPanelComponent
public openBugreport() {
this.drugstoneConfig.showBugreport = true;
}
+
}
diff --git a/src/app/components/network/network-menu/network-menu.component.html b/src/app/components/network/network-menu/network-menu.component.html
index cf04a2a70b9f986f6e026d37e6353c7ec5adaa3a..1568447f2f0b71fdf56c2faad713136eb887708b 100644
--- a/src/app/components/network/network-menu/network-menu.component.html
+++ b/src/app/components/network/network-menu/network-menu.component.html
@@ -61,7 +61,7 @@
[ngClass]="{
'text-normal': drugstoneConfig.smallStyle
}"
- >Screenshot</span
+ >Screenshot</span
>
</button>
</div>
@@ -112,14 +112,14 @@
[ngClass]="{
'text-small': drugstoneConfig.smallStyle
}"
- >Tissue</span
+ >Tissue</span
>
<span
*ngIf="networkHandler.activeNetwork.selectedTissue"
[ngClass]="{
'text-small': drugstoneConfig.smallStyle
}"
- >{{ networkHandler.activeNetwork.selectedTissue.name }}</span
+ >{{ networkHandler.activeNetwork.selectedTissue.name }}</span
>
<app-fa-solid-icon
icon="angle-down"
@@ -182,7 +182,93 @@
networkHandler.activeNetwork.updateAdjacentDrugs($event, true)
"
></app-toggle-inplace>
+<!-- <div class="row is-full m-1" *ngIf="networkHandler.activeNetwork.showsAdjacentDrugs() || networkHandler.activeNetwork.hasDrugsLoaded()">-->
+<!-- <div-->
+<!-- class="dropdown network-footer-toolbar-element"-->
+<!-- [class.is-active]="networkHandler.activeNetwork.drugTargetSelectionExpanded"-->
+<!-- [ngClass]="{-->
+<!-- 'inner-dropdown': !networkHandler.networkSidebarOpen-->
+<!-- }"-->
+<!-- >-->
+<!-- <div class="dropdown-trigger">-->
+<!-- <button-->
+<!-- (click)="-->
+<!-- networkHandler.activeNetwork.drugTargetSelectionExpanded =-->
+<!-- !networkHandler.activeNetwork.drugTargetSelectionExpanded-->
+<!-- "-->
+<!-- class="button is-rounded"-->
+<!-- [disabled]="networkHandler.activeNetwork.getDrugTargetTypes().length === 0"-->
+<!-- [class.is-primary]="networkHandler.activeNetwork.getSelectedDrugTargetType()"-->
+<!-- aria-haspopup="true"-->
+<!-- aria-controls="dropdown-menu"-->
+<!-- pTooltip="Filter drug-target edges by drug action annotation."-->
+<!-- [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-left'"-->
+<!-- tooltipPosition="left"-->
+<!-- [ngClass]="{-->
+<!-- 'is-small': drugstoneConfig.smallStyle-->
+<!-- }"-->
+<!-- >-->
+<!-- <app-fa-solid-icon icon="crosshairs"></app-fa-solid-icon>-->
+
+<!-- <span-->
+<!-- *ngIf="!networkHandler.activeNetwork.getSelectedDrugTargetType()"-->
+<!-- [ngClass]="{-->
+<!-- 'text-small': drugstoneConfig.smallStyle-->
+<!-- }"-->
+<!-- >Actions</span-->
+<!-- >-->
+<!-- <span-->
+<!-- *ngIf="networkHandler.activeNetwork.getSelectedDrugTargetType()"-->
+<!-- [ngClass]="{-->
+<!-- 'text-small': drugstoneConfig.smallStyle-->
+<!-- }"-->
+<!-- >{{ networkHandler.activeNetwork.getSelectedDrugTargetType() }}</span-->
+<!-- >-->
+<!-- <app-fa-solid-icon-->
+<!-- icon="angle-down"-->
+<!-- classString="is-small last-item-in-button"-->
+<!-- *ngIf="networkHandler.activeNetwork.drugTargetSelectionExpanded"-->
+<!-- ></app-fa-solid-icon>-->
+<!-- <app-fa-solid-icon-->
+<!-- icon="angle-left"-->
+<!-- classString="is-small last-item-in-button"-->
+<!-- *ngIf="!networkHandler.activeNetwork.drugTargetSelectionExpanded"-->
+<!-- ></app-fa-solid-icon>-->
+<!-- </button>-->
+<!-- </div>-->
+<!-- <div class="dropdown-menu" id="drug-dropdown-menu" role="menu">-->
+<!-- <div class="dropdown-content tissue-dropdown">-->
+<!-- <div class="scroll-area">-->
+<!-- <a-->
+<!-- (click)="networkHandler.activeNetwork.updateAdjacentDrugSelection(null,true)"-->
+<!-- [class.is-active]="-->
+<!-- !networkHandler.activeNetwork.getSelectedDrugTargetType()-->
+<!-- "-->
+<!-- [ngClass]="{'text-small': drugstoneConfig.smallStyle}"-->
+<!-- class="dropdown-item"-->
+<!-- >-->
+<!-- None-->
+<!-- </a>-->
+<!-- <a-->
+<!-- *ngFor="-->
+<!-- let drugTargetType of networkHandler.activeNetwork.getDrugTargetTypes()-->
+<!-- "-->
+<!-- (click)="networkHandler.activeNetwork.updateAdjacentDrugSelection(drugTargetType, true)"-->
+<!-- [class.is-active]="-->
+<!-- networkHandler.activeNetwork.getSelectedDrugTargetType() && networkHandler.activeNetwork.getSelectedDrugTargetType() === drugTargetType-->
+<!-- "-->
+<!-- [ngClass]="{'text-small': drugstoneConfig.smallStyle}"-->
+<!-- class="dropdown-item"-->
+<!-- >-->
+<!-- {{ drugTargetType }}-->
+<!-- </a>-->
+<!-- </div>-->
+<!-- </div>-->
+<!-- </div>-->
+<!-- </div>-->
+<!-- </div>-->
</div>
+
<div
class="row is-full m-1"
*ngIf="
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 66c2bbe61aea7a12ba2335f489d00f48cc3a4975..3f2d8264fffd09aec2ce3e651860302f1894e2e6 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -23,6 +23,7 @@ import {NetworkHandlerService} from 'src/app/services/network-handler/network-ha
import {LegendService} from 'src/app/services/legend-service/legend-service.service';
import {LoadingScreenService} from 'src/app/services/loading-screen/loading-screen.service';
import {version} from '../../../version';
+import {Subject} from 'rxjs';
@Component({
selector: 'app-network',
@@ -60,6 +61,12 @@ export class NetworkComponent implements OnInit {
public adjacentDrugs = false;
+ public selectedDrugTargetType = new Subject<string | null>();
+ public selectedDrugTargetTypeLast: string | null = null;
+ public selectedDrugTargetType$ = this.selectedDrugTargetType.asObservable();
+ public drugTargetTypes: string[] = [];
+ public drugTargetTypesWithoutAdj: string[] = [];
+
public adjacentDisordersProtein = false;
public adjacentDisordersDrug = false;
public adjacentDrugList: Node[] = [];
@@ -77,8 +84,10 @@ export class NetworkComponent implements OnInit {
public currentViewEdges: NodeInteraction[];
public expressionExpanded = false;
+ public drugTargetSelectionExpanded = false;
public selectedTissue: Tissue | null = null;
+
// change this to true to have sidebar open per default
// public networkSidebarOpen = false;
@@ -130,6 +139,37 @@ export class NetworkComponent implements OnInit {
return {edges: this.inputNetwork.edges, nodes};
}
+ public getDrugTargetTypes() {
+ return this.drugTargetTypes;
+ }
+
+ public subscribeSelection(callback) {
+ this.selectedDrugTargetType$.subscribe(() => {
+ callback();
+ });
+ }
+
+ public setDrugTargetTypes(drugTargetTypes: string[], adj = false) {
+ if (adj) {
+ this.drugTargetTypesWithoutAdj = [...drugTargetTypes];
+ drugTargetTypes.filter(type => !this.drugTargetTypes.includes(type)).forEach((type) => {
+ this.drugTargetTypes.push(type);
+ });
+ } else {
+ this.drugTargetTypes = drugTargetTypes;
+ }
+ }
+
+ // TODO create method to get selected drug target type as string instead of subject or observable
+ public setSelectedDrugTargetType(value: string | null) {
+ this.selectedDrugTargetTypeLast = value;
+ this.selectedDrugTargetType.next(value);
+ }
+
+ public getSelectedDrugTargetType() {
+ return this.selectedDrugTargetTypeLast;
+ }
+
resetInputNetwork() {
const nodes = this.inputNetwork.nodes;
nodes.forEach(n => {
@@ -333,6 +373,38 @@ export class NetworkComponent implements OnInit {
});
}
+ public updateAdjacentDrugSelection(event, stabil: boolean) {
+ this.networkHandler.activeNetwork.drugTargetSelectionExpanded = false;
+ if (event === this.getSelectedDrugTargetType()) {
+ return;
+ }
+ this.setSelectedDrugTargetType(event);
+ if (this.networkHandler.activeNetwork.showsAdjacentDrugs()) {
+ this.updateAdjacentDrugs(false, false).then(() => {
+ // if (this.networkHandler.activeNetwork.hasDrugsLoaded()) {
+ // this.updateFoundDrugs(stabil).then(() => {
+ this.updateAdjacentDrugs(true, stabil);
+ // });
+ // } else {
+ // this.updateAdjacentDrugs(true, stabil);
+ // }
+ });
+ }
+ // else {
+ // this.updateFoundDrugs(stabil);
+ // }
+ }
+
+ public showsAdjacentDrugs(): boolean {
+ return this.adjacentDrugs;
+ }
+
+ public updateFoundDrugs(stabl: boolean): Promise<any> {
+ return new Promise<boolean>(async (resolve, reject) => {
+
+ });
+ }
+
public updateAdjacentDrugs(bool: boolean, stabl: boolean): Promise<any> {
return new Promise<boolean>(async (resolve, reject) => {
this.loadingScreen.stateUpdate(true);
@@ -345,12 +417,21 @@ export class NetworkComponent implements OnInit {
const proteinMap = this.getProteinMap();
this.netex.adjacentDrugs(this.drugstoneConfig.config.interactionDrugProtein, this.drugstoneConfig.config.licensedDatasets, this.nodeData.nodes.get()).then(response => {
const existingDrugIDs = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'drug').map(n => n.drugstoneId);
+ const availableDrugTargetTypes = new Set<string>();
for (const interaction of response.pdis) {
+ if (interaction.actions) {
+ for (const action of interaction.actions) {
+ availableDrugTargetTypes.add(action);
+ }
+ }
+ if (this.networkHandler.activeNetwork.getSelectedDrugTargetType() && interaction.actions && !interaction.actions.includes(this.networkHandler.activeNetwork.getSelectedDrugTargetType())) {
+ continue;
+ }
+ const label = interaction.actions && interaction.actions.length > 0 ? interaction.actions.join(',') : undefined;
const edge = mapCustomEdge({
from: interaction.protein,
to: interaction.drug
}, this.drugstoneConfig.currentConfig(), this.drugstoneConfig);
-
if (proteinMap[edge.from]) {
proteinMap[edge.from].forEach(from => {
if (addedEdge[from] && addedEdge[from].indexOf(edge.to) !== -1) {
@@ -359,6 +440,9 @@ export class NetworkComponent implements OnInit {
const e = JSON.parse(JSON.stringify(edge));
e.from = from;
e.to = edge.to;
+ if (label) {
+ e.label = label;
+ }
this.adjacentDrugEdgesList.push(e);
if (!addedEdge[from]) {
addedEdge[from] = [edge.to];
@@ -367,11 +451,16 @@ export class NetworkComponent implements OnInit {
}
});
}
+ this.networkHandler.activeNetwork.setDrugTargetTypes(Array.from(availableDrugTargetTypes), true);
}
+ const addedDrugs = new Set<string>();
+ Object.values(addedEdge).forEach(targets => { // @ts-ignore
+ targets.forEach(t => addedDrugs.add(t));
+ });
for (const drug of response.drugs) {
drug.group = 'foundDrug';
drug.id = getDrugNodeId(drug);
- if (!existingDrugIDs.includes(drug.drugstoneId)) {
+ if (!existingDrugIDs.includes(drug.drugstoneId) && addedDrugs.has(drug.drugstoneId)) {
existingDrugIDs.push(drug.drugstoneId);
this.adjacentDrugList.push(mapCustomNode(drug, this.drugstoneConfig.currentConfig(), this.drugstoneConfig));
}
@@ -633,7 +722,7 @@ export class NetworkComponent implements OnInit {
public hasDrugsLoaded(): boolean {
if (this.nodeData && this.nodeData.nodes) {
for (const node of this.nodeData.nodes.get()) {
- if (node.drugstoneType && node.drugstoneId === 'drug') {
+ if (node.drugstoneType && node.drugstoneType === 'drug') {
return true;
}
}