From bec8a38e9ba816dac0196f213e497d17097e266f Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 24 Sep 2021 17:18:26 +0200
Subject: [PATCH] updating query entries; fixed disorder information;
---
.../analysis-panel.component.html | 21 +++
.../analysis-panel.component.ts | 123 +++++++++++++++---
.../info-tile/info-tile.component.html | 29 +++--
.../info-tile/info-tile.component.ts | 11 +-
.../network-legend.component.ts | 2 +
.../query-tile/query-tile.component.ts | 8 --
.../components/toggle/toggle.component.html | 4 +-
src/app/components/toggle/toggle.component.ts | 1 +
src/app/interfaces.ts | 14 +-
.../explorer-page.component.html | 9 +-
.../explorer-page/explorer-page.component.ts | 84 +++++++-----
11 files changed, 229 insertions(+), 77 deletions(-)
diff --git a/src/app/components/analysis-panel/analysis-panel.component.html b/src/app/components/analysis-panel/analysis-panel.component.html
index 61c25530..5a680644 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.html
+++ b/src/app/components/analysis-panel/analysis-panel.component.html
@@ -245,6 +245,27 @@
tooltipOff="Display adjacent drugs OFF."
[smallStyle]="smallStyle"
[value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
+ <app-toggle
+ class="footer-buttons network-footer-toolbar-element"
+ textOn="Disorders (protein)"
+ textOff="Off"
+ tooltipOn="Show disorders adjacent to all currently displayed proteins/genes ON."
+ tooltipOff="Show disorders adjacent to all currently displayed proteins/genes OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDisordersProtein"
+ (valueChange)="updateAdjacentProteinDisorders($event)"
+ ></app-toggle>
+ <app-toggle
+ class="footer-buttons network-footer-toolbar-element"
+ textOn="Disorders (drugs)"
+ textOff="Off"
+ tooltipOn="Show disorders adjacent to all currently displayed drugs ON."
+ tooltipOff="Show disorders adjacent to all currently displayed drugs OFF."
+ [smallStyle]="smallStyle"
+ [value]="adjacentDisordersDrug"
+ [disabled]="!hasDrugsLoaded()"
+ (valueChange)="updateAdjacentDrugDisorders($event)"
+ ></app-toggle>
<app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Animation" textOff="Off"
tooltipOn="Enable the network animation."
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 6840a471..afe093d5 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -73,7 +73,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
@Output() tokenChange = new EventEmitter<string | null>();
@Output() showDetailsChange = new EventEmitter<Wrapper>();
@Output() visibleItems = new EventEmitter<[any[], [Node[], Tissue], NodeInteraction[]]>();
-
public task: Task | null = null;
public result: any = null;
public myConfig: IConfig = JSON.parse(JSON.stringify(defaultConfig));
@@ -90,6 +89,15 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
public adjacentDrugList: Node[] = [];
public adjacentDrugEdgesList: Node[] = [];
+ public adjacentDisordersProtein = false;
+ public adjacentDisordersDrug = false;
+
+ public adjacentProteinDisorderList: Node[] = [];
+ public adjacentProteinDisorderEdgesList: Node[] = [];
+
+ public adjacentDrugDisorderList: Node[] = [];
+ public adjacentDrugDisorderEdgesList: Node[] = [];
+
public highlightSeeds = false;
public seedMap: NodeAttributeMap;
@@ -329,7 +337,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.emitVisibleItems(true);
this.setLegendContext();
-
}
public emitVisibleItems(on: boolean) {
@@ -389,6 +396,80 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
}
+
+ public saveAddNodes(nodeList: Node[]) {
+ const existing = this.nodeData.nodes.get().map(n => n.id);
+ const toAdd = nodeList.filter(n => existing.indexOf(n.id) === -1)
+ this.nodeData.nodes.add(toAdd);
+ }
+
+ public saveRemoveDisorders(nodeList: Node[]) {
+ const other = this.adjacentDrugDisorderList === nodeList ? this.adjacentProteinDisorderList : this.adjacentDrugDisorderList
+ if (other == null)
+ this.nodeData.nodes.remove(nodeList);
+ else {
+ const otherIds = other.map(d => d.id);
+ const rest = nodeList.filter(d => otherIds.indexOf(d.id) === -1)
+ this.nodeData.nodes.remove(rest)
+ }
+ }
+
+ public updateAdjacentProteinDisorders(bool: boolean) {
+ this.adjacentDisordersProtein = bool;
+ if (this.adjacentDisordersProtein) {
+ this.netex.adjacentDisorders(this.nodeData.nodes, 'proteins').subscribe(response => {
+ for (const interaction of response.edges) {
+ const edge = {from: interaction.protein, to: interaction.disorder};
+ this.adjacentProteinDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
+ }
+ for (const disorder of response.disorders) {
+ disorder.group = 'defaultDisorder';
+ disorder.id = disorder.netexId;
+ this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.myConfig))
+ }
+ this.saveAddNodes(this.adjacentProteinDisorderList);
+ this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
+ this.emitVisibleItems(true);
+ });
+ this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
+ } else {
+ this.saveRemoveDisorders(this.adjacentProteinDisorderList);
+ this.nodeData.edges.remove(this.adjacentProteinDisorderEdgesList);
+ this.adjacentProteinDisorderList = [];
+ this.adjacentProteinDisorderEdgesList = [];
+ this.legendContext = this.adjacentDisordersDrug ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
+ this.emitVisibleItems(true);
+ }
+ }
+
+ public updateAdjacentDrugDisorders(bool: boolean) {
+ this.adjacentDisordersDrug = bool;
+ if (this.adjacentDisordersDrug) {
+ this.netex.adjacentDisorders(this.nodeData.nodes, 'drugs').subscribe(response => {
+ for (const interaction of response.edges) {
+ const edge = {from: interaction.drug, to: interaction.disorder};
+ this.adjacentDrugDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
+ }
+ for (const disorder of response.disorders) {
+ disorder.group = 'defaultDisorder';
+ disorder.id = disorder.netexId;
+ this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.myConfig));
+ }
+ this.saveAddNodes(this.adjacentDrugDisorderList);
+ this.nodeData.edges.add(this.adjacentDrugDisorderEdgesList);
+ this.emitVisibleItems(true);
+ });
+ this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
+ } else {
+ this.saveRemoveDisorders(this.adjacentDrugDisorderList);
+ this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
+ this.adjacentDrugDisorderList = [];
+ this.adjacentDrugDisorderEdgesList = [];
+ this.legendContext = this.adjacentDisordersProtein ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
+ this.emitVisibleItems(true);
+ }
+ }
+
public downloadLink(view: string): string {
return `${environment.backend}task_result/?token=${this.token}&view=${view}&fmt=csv`;
}
@@ -558,31 +639,39 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.setLegendContext();
}
+ hasDrugsLoaded(): boolean {
+ if (this.nodeData == null || this.nodeData.nodes == null)
+ return false;
+ return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.netexId.startsWith('dr')).length > 0;
+ }
+
public updateAdjacentDrugs(bool: boolean) {
this.adjacentDrugs = bool;
if (this.adjacentDrugs) {
- this.netex.adjacentDrugs(this.myConfig.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
- for (const interaction of response.pdis) {
- const edge = {from: interaction.protein, to: interaction.drug};
- this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.myConfig));
- }
- for (const drug of response.drugs) {
- drug.group = 'foundDrug';
- drug.id = getDrugNodeId(drug)
- this.adjacentDrugList.push(mapCustomNode(drug, this.myConfig))
- }
- this.nodeData.nodes.add(this.adjacentDrugList);
- this.nodeData.edges.add(this.adjacentDrugEdgesList);
+ this.netex.adjacentDrugs(this.myConfig.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
+ for (const interaction of response.pdis) {
+ const edge = {from: interaction.protein, to: interaction.drug};
+ this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.myConfig));
+ }
+ for (const drug of response.drugs) {
+ drug.group = 'foundDrug';
+ drug.id = getDrugNodeId(drug)
+ this.adjacentDrugList.push(mapCustomNode(drug, this.myConfig))
+ }
+ this.nodeData.nodes.add(this.adjacentDrugList);
+ this.nodeData.edges.add(this.adjacentDrugEdgesList);
+ this.emitVisibleItems(true);
})
+ this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDrugsAndDisorders' : 'adjacentDrugs';
} else {
this.nodeData.nodes.remove(this.adjacentDrugList);
this.nodeData.edges.remove(this.adjacentDrugEdgesList);
this.adjacentDrugList = [];
this.adjacentDrugEdgesList = [];
+
+ this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDisorders' : 'explorer';
+ this.emitVisibleItems(true);
}
- this.setLegendContext()
- // emit data to update sidebar information
- this.emitVisibleItems(true);
}
public updatePhysicsEnabled(bool: boolean) {
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index 0642dc22..f509cfc2 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -1,6 +1,7 @@
<div *ngIf="wrapper">
<div>
- <p *ngIf="!wrapper.data.drugId && wrapper.data.detailShowLabel && wrapper.data.label" [ngClass]="{'text-normal':smallStyle}">
+ <p *ngIf="!wrapper.data.drugId && wrapper.data.detailShowLabel && wrapper.data.label"
+ [ngClass]="{'text-normal':smallStyle}">
<b><span>Label:</span></b>
<span class="is-capitalized"> {{ wrapper.data.label }}</span>
</p>
@@ -12,16 +13,26 @@
<b><span>Symbol:</span></b>
<span class="is-capitalized"> {{ wrapper.data.symbol }}</span>
</p>
- <p *ngIf="wrapper.data.drugId" [ngClass]="{'text-normal':smallStyle}">
+ <p *ngIf="wrapper.data.drugId || wrapper.data.disorderId" [ngClass]="{'text-normal':smallStyle}">
<b><span>Name:</span></b>
<span class="is-capitalized"> {{ wrapper.data.label }}</span>
</p>
+ <p *ngIf="wrapper.data.icd10" [ngClass]="{'text-normal': smallStyle}">
+ <b><span>ICD10:</span></b>
+ <span class="is-capitalized"> {{wrapper.data.icd10.length===0 || (wrapper.data.icd10.length ===1 && wrapper.data.icd10[0].length===0) ? '-' : wrapper.data.icd10}}</span>
+ </p>
<p *ngIf="wrapper.data.drugId" [ngClass]="{'text-normal':smallStyle}">
<b><span>DrugBank:</span></b>
<a href="https://go.drugbank.com/drugs/{{ wrapper.data.drugId }}" target="_blank">
<span class="is-capitalized"> {{ wrapper.data.drugId }}</span>
</a>
</p>
+ <p *ngIf="wrapper.data.disorderId" [ngClass]="{'text-normal':smallStyle}">
+ <b><span>Mondo:</span></b>
+ <a href="https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_{{writeZeros(7-(''+wrapper.data.disorderId).length)}}{{ wrapper.data.disorderId }}" target="_blank">
+ <span class="is-capitalized"> MONDO:{{ wrapper.data.disorderId }}</span>
+ </a>
+ </p>
<p *ngIf="wrapper.data.groupName" [ngClass]="{'text-normal':smallStyle}">
<b><span>Group:</span></b>
<span class="is-capitalized"> {{ wrapper.data.groupName }}</span>
@@ -34,7 +45,7 @@
</p>
<p *ngIf="wrapper.data.ensg" [ngClass]="{'text-normal':smallStyle}">
<b><span>Ensembl:</span></b>
- <a
+ <a
*ngFor="let ensg of wrapper.data.ensg"
href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?g={{ ensg }}" target="_blank">
<span class="is-capitalized"> {{ ensg }}</span>
@@ -43,12 +54,12 @@
</div>
- <app-toggle
- *ngIf="wrapper.data.netexId && wrapper.data.netexId.startsWith('p')"
- [value]="analysis.inSelection(wrapper)" [smallStyle]="smallStyle"
- (valueChange)="$event ? analysis.addItems([wrapper]) : analysis.removeItems([wrapper])" textOn="Seed"
- textOff="Off" tooltipOn="Add protein to selection." tooltipOff="Remove protein from selection."></app-toggle>
+ <app-toggle
+ *ngIf="wrapper.data.netexId && wrapper.data.netexId.startsWith('p')"
+ [value]="analysis.inSelection(wrapper)" [smallStyle]="smallStyle"
+ (valueChange)="$event ? analysis.addItems([wrapper]) : analysis.removeItems([wrapper])" textOn="Seed"
+ textOff="Off" tooltipOn="Add protein to selection." tooltipOff="Remove protein from selection."></app-toggle>
</div>
-<div *ngIf="!wrapper" [ngClass]="{'text-normal':smallStyle}" >
+<div *ngIf="!wrapper" [ngClass]="{'text-normal':smallStyle}">
Please select a node for further information.
</div>
diff --git a/src/app/components/info-tile/info-tile.component.ts b/src/app/components/info-tile/info-tile.component.ts
index 44bd205e..514b0f72 100644
--- a/src/app/components/info-tile/info-tile.component.ts
+++ b/src/app/components/info-tile/info-tile.component.ts
@@ -13,7 +13,8 @@ export class InfoTileComponent implements OnInit {
@Input() public wrapper: Wrapper;
@Input() smallStyle: boolean;
- constructor(public analysis: AnalysisService) { }
+ constructor(public analysis: AnalysisService) {
+ }
ngOnInit(): void {
}
@@ -31,4 +32,12 @@ export class InfoTileComponent implements OnInit {
return url;
}
+ writeZeros(n: number) {
+ let out = '';
+ while (n > 0) {
+ out += '0';
+ n--;
+ }
+ return out;
+ }
}
diff --git a/src/app/components/network-legend/network-legend.component.ts b/src/app/components/network-legend/network-legend.component.ts
index 79c83120..142c0e07 100644
--- a/src/app/components/network-legend/network-legend.component.ts
+++ b/src/app/components/network-legend/network-legend.component.ts
@@ -16,6 +16,7 @@ export class NetworkLegendComponent implements OnInit {
'explorer': ['foundNode', 'foundDrug', 'seedNode', 'default', 'defaultDisorder'],
'adjacentDrugs': ['foundNode', 'seedNode', 'default', 'defaultDisorder'],
'adjacentDisorders': ['foundDrug', 'foundNode', 'seedNode', 'default'],
+ 'adjacentDrugsAndDisorders': ['foundNode', 'seedNode', 'default'],
'drugTarget': ['foundDrug', 'seedNode', 'default', 'defaultDisorder'],
'drug': ['seedNode', 'default', 'defaultDisorder'],
'drugTargetAndSeeds': ['foundDrug', 'default', 'defaultDisorder'],
@@ -26,6 +27,7 @@ export class NetworkLegendComponent implements OnInit {
'explorer': ['default'],
'adjacentDrugs': ['default'],
'adjacentDisorders': ['default'],
+ 'adjacentDrugsAndDisorders' :['default'],
'drugTarget': ['default'],
'drug': ['default'],
'drugTargetAndSeeds': ['default'],
diff --git a/src/app/components/query-tile/query-tile.component.ts b/src/app/components/query-tile/query-tile.component.ts
index 2ffa2b7a..79741256 100644
--- a/src/app/components/query-tile/query-tile.component.ts
+++ b/src/app/components/query-tile/query-tile.component.ts
@@ -30,32 +30,24 @@ export class QueryTileComponent {
if (data.ensg === undefined) {
data.ensg = []
}
- ;
if (data.groupName === undefined) {
data.groupName = ''
}
- ;
if (data.type === undefined) {
data.type = ''
}
- ;
if (data.symbol === undefined) {
data.symbol = ''
}
- ;
if (data.proteinName === undefined) {
data.proteinName = ''
}
- ;
if (data.uniprotAc === undefined) {
data.uniprotAc = ''
}
- ;
if (data.drugId === undefined) {
data.drugId = ''
}
- ;
-
return data.symbol.toLowerCase().indexOf(term) > -1 || data.uniprotAc.toLowerCase().indexOf(term) > -1 ||
data.label.toLowerCase().indexOf(term) > -1 || this.listStartsWith(data.ensg, term) || data.id.toLowerCase().indexOf(term) > -1
|| data.proteinName.toLowerCase().indexOf(term) > -1 || data.type.toLowerCase().indexOf(term) > -1 ||
diff --git a/src/app/components/toggle/toggle.component.html b/src/app/components/toggle/toggle.component.html
index cab8b7a9..1ba8d66e 100644
--- a/src/app/components/toggle/toggle.component.html
+++ b/src/app/components/toggle/toggle.component.html
@@ -1,6 +1,6 @@
<div class="field has-addons">
<p class="control has-tooltip">
- <button class="button is-rounded has-tooltip" [pTooltip]="tooltipOn" [tooltipStyleClass]="'drgstn drgstn-tooltip'" tooltipPosition="top" [class.is-primary]="value" (click)="toggle(true)" [ngClass]="{'switch-small':smallStyle}">
+ <button class="button is-rounded has-tooltip" [pTooltip]="tooltipOn" [disabled]="disabled" [tooltipStyleClass]="'drgstn drgstn-tooltip'" tooltipPosition="top" [class.is-primary]="value" (click)="toggle(true)" [ngClass]="{'switch-small':smallStyle}">
<span class="icon is-small">
<i class="fa {{iconOn}}"></i>
</span>
@@ -8,7 +8,7 @@
</button>
</p>
<p class="control">
- <button class="button is-rounded has-tooltip" [pTooltip]="tooltipOff" [tooltipStyleClass]="'drgstn drgstn-tooltip'" tooltipPosition="top" [class.is-primary]="!value" (click)="toggle(false)" [ngClass]="{'switch-small':smallStyle}">
+ <button class="button is-rounded has-tooltip" [pTooltip]="tooltipOff" [disabled]="disabled" [tooltipStyleClass]="'drgstn drgstn-tooltip'" tooltipPosition="top" [class.is-primary]="!value" (click)="toggle(false)" [ngClass]="{'switch-small':smallStyle}">
<span [ngClass]="{'text-small':smallStyle}">{{textOff}}</span>
<span *ngIf="iconOff" class="icon is-small">
<i class="fa {{iconOff}}"></i>
diff --git a/src/app/components/toggle/toggle.component.ts b/src/app/components/toggle/toggle.component.ts
index 6b396763..a0f7617a 100644
--- a/src/app/components/toggle/toggle.component.ts
+++ b/src/app/components/toggle/toggle.component.ts
@@ -14,6 +14,7 @@ export class ToggleComponent implements OnInit {
@Input() textOff = 'Off';
@Input() tooltipOn: string;
@Input() tooltipOff: string;
+ @Input() disabled = false;
@Input() smallStyle: boolean;
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 3bebde46..32ab10f6 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -33,7 +33,7 @@ export interface Tissue {
}
export type legendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' |
-'drugTargetAndSeeds' | 'drugAndSeeds' | 'adjacentDisorders';
+'drugTargetAndSeeds' | 'drugAndSeeds' | 'adjacentDisorders' | 'adjacentDrugsAndDisorders';
/// netexId to expressionlvl
export type NodeAttributeMap = { string: number } | {};
@@ -153,16 +153,16 @@ export function getId(gene: Node) {
return `${gene.id}`;
}
-export function getWrapperFromNode(gene: Node): Wrapper {
+export function getWrapperFromNode(node: Node): Wrapper {
/**
* Constructs wrapper interface for gene
*/
// if node does not have property group, it was custom node from user
- gene.group = gene.group ? gene.group : 'default';
- gene.label = gene.label ? gene.label : gene.id
+ node.group = node.group ? node.group : 'default';
+ node.label = node.label ? node.label : node.id
return {
- id: gene.id,
- data: gene,
+ id: node.id,
+ data: node,
};
}
@@ -189,6 +189,8 @@ export interface Wrapper {
x?: number;
y?: number;
drugId?: string;
+ disorderId?: string;
+ icd10?: string[];
status?: 'approved' | 'investigational';
inTrial?: boolean;
inLiterature?: boolean;
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index dc5e1158..fa896d6c 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -303,8 +303,8 @@
class="footer-buttons network-footer-toolbar-element"
textOn="Disorders (protein)"
textOff="Off"
- tooltipOn="Display adjacent disorders ON."
- tooltipOff="Display adjacent disorders OFF."
+ tooltipOn="Show disorders adjacent to all currently displayed proteins/genes ON."
+ tooltipOff="Show disorders adjacent to all currently displayed proteins/genes OFF."
[smallStyle]="smallStyle"
[value]="adjacentDisordersProtein"
(valueChange)="updateAdjacentProteinDisorders($event)"
@@ -313,10 +313,11 @@
class="footer-buttons network-footer-toolbar-element"
textOn="Disorders (drugs)"
textOff="Off"
- tooltipOn="Display adjacent disorders ON."
- tooltipOff="Display adjacent disorders OFF."
+ tooltipOn="Show disorders adjacent to all currently displayed drugs ON."
+ tooltipOff="Show disorders adjacent to all currently displayed drugs OFF."
[smallStyle]="smallStyle"
[value]="adjacentDisordersDrug"
+ [disabled]="!hasDrugsLoaded()"
(valueChange)="updateAdjacentDrugDisorders($event)"
></app-toggle>
<app-toggle
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index 6662d944..ecdf4817 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -152,11 +152,13 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
private dumpPositions = false;
public physicsEnabled = false;
public adjacentDrugs = false;
- public adjacentDisordersProtein = false;
- public adjacentDisordersDrug = false;
+
public adjacentDrugList: Node[] = [];
public adjacentDrugEdgesList: Node[] = [];
+ public adjacentDisordersProtein = false;
+ public adjacentDisordersDrug = false;
+
public adjacentProteinDisorderList: Node[] = [];
public adjacentProteinDisorderEdgesList: Node[] = [];
@@ -458,22 +460,31 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.currentViewEdges = this.nodeData.edges;
this.queryItems = [];
- this.fillQueryItems(this.currentViewNodes);
+ this.updateQueryItems();
+ this.currentViewProteins = this.proteins;
+ // this.fillQueryItems(this.currentViewNodes);
if (this.selectedWrapper) {
this.networkInternal.selectNodes([this.selectedWrapper.id]);
}
}
- fillQueryItems(hostProteins: Node[]) {
+ updateQueryItems() {
this.queryItems = [];
- hostProteins.forEach((protein) => {
+ this.currentViewNodes.forEach((protein) => {
this.queryItems.push(getWrapperFromNode(protein));
});
-
-
- this.currentViewProteins = this.proteins;
}
+ // fillQueryItems(hostProteins: Node[]) {
+ // this.queryItems = [];
+ // hostProteins.forEach((protein) => {
+ // this.queryItems.push(getWrapperFromNode(protein));
+ // });
+ //
+ //
+ // this.currentViewProteins = this.proteins;
+ // }
+
public queryAction(item: any) {
if (item) {
this.openSummary(item, true);
@@ -492,9 +503,9 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
});
}
- public updateAdjacentProteinDisorders(bool: boolean){
+ public updateAdjacentProteinDisorders(bool: boolean) {
this.adjacentDisordersProtein = bool;
- if (this.adjacentDisordersProtein){
+ if (this.adjacentDisordersProtein) {
this.netex.adjacentDisorders(this.nodeData.nodes, 'proteins').subscribe(response => {
for (const interaction of response.edges) {
const edge = {from: interaction.protein, to: interaction.disorder};
@@ -507,20 +518,22 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
this.saveAddNodes(this.adjacentProteinDisorderList);
this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
+ this.updateQueryItems();
});
- this.legendContext = 'adjacentDisorders';
- }else {
+ this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
+ } else {
this.saveRemoveDisorders(this.adjacentProteinDisorderList);
this.nodeData.edges.remove(this.adjacentProteinDisorderEdgesList);
this.adjacentProteinDisorderList = [];
this.adjacentProteinDisorderEdgesList = [];
- this.legendContext = 'explorer';
+ this.legendContext = this.adjacentDisordersDrug ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
+ this.updateQueryItems();
}
}
- public updateAdjacentDrugDisorders(bool: boolean){
+ public updateAdjacentDrugDisorders(bool: boolean) {
this.adjacentDisordersDrug = bool;
- if (this.adjacentDisordersDrug){
+ if (this.adjacentDisordersDrug) {
this.netex.adjacentDisorders(this.nodeData.nodes, 'drugs').subscribe(response => {
for (const interaction of response.edges) {
const edge = {from: interaction.drug, to: interaction.disorder};
@@ -533,33 +546,34 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
this.saveAddNodes(this.adjacentDrugDisorderList);
this.nodeData.edges.add(this.adjacentDrugDisorderEdgesList);
+ this.updateQueryItems();
});
- this.legendContext = 'adjacentDisorders';
- }else {
+ this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
+ } else {
this.saveRemoveDisorders(this.adjacentDrugDisorderList);
this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
this.adjacentDrugDisorderList = [];
this.adjacentDrugDisorderEdgesList = [];
- this.legendContext = 'explorer';
+ this.legendContext = this.adjacentDisordersProtein ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
+ this.updateQueryItems();
}
}
- public saveAddNodes(nodeList: Node[]){
- const existing = this.nodeData.nodes.get().map(n=>n.id);
- const toAdd = nodeList.filter(n=>existing.indexOf(n.id)===-1)
+ public saveAddNodes(nodeList: Node[]) {
+ const existing = this.nodeData.nodes.get().map(n => n.id);
+ const toAdd = nodeList.filter(n => existing.indexOf(n.id) === -1)
this.nodeData.nodes.add(toAdd);
}
- public saveRemoveDisorders(nodeList: Node[]){
+ public saveRemoveDisorders(nodeList: Node[]) {
const other = this.adjacentDrugDisorderList === nodeList ? this.adjacentProteinDisorderList : this.adjacentDrugDisorderList
- if(other==null)
+ if (other == null)
this.nodeData.nodes.remove(nodeList);
- else{
- const otherIds = other.map(d=>d.id);
- const rest = nodeList.filter(d=>otherIds.indexOf(d.id)===-1)
+ else {
+ const otherIds = other.map(d => d.id);
+ const rest = nodeList.filter(d => otherIds.indexOf(d.id) === -1)
this.nodeData.nodes.remove(rest)
}
-
}
public updateAdjacentDrugs(bool: boolean) {
@@ -577,15 +591,17 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
this.nodeData.nodes.add(this.adjacentDrugList);
this.nodeData.edges.add(this.adjacentDrugEdgesList);
+ this.updateQueryItems();
})
- this.legendContext = 'adjacentDrugs'
+ this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDrugsAndDisorders' : 'adjacentDrugs';
} else {
this.nodeData.nodes.remove(this.adjacentDrugList);
this.nodeData.edges.remove(this.adjacentDrugEdgesList);
this.adjacentDrugList = [];
this.adjacentDrugEdgesList = [];
- this.legendContext = 'explorer'
+ this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDisorders' : 'explorer';
+ this.updateQueryItems();
}
}
@@ -706,7 +722,8 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
// changes for either way (analysis open and close)
this.selectedWrapper = null;
- this.fillQueryItems(this.currentViewNodes);
+ this.updateQueryItems();
+ // this.fillQueryItems(this.currentViewNodes);
}
gProfilerLink(): string {
@@ -810,7 +827,14 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.currentViewSelectedTissue = this.selectedTissue;
}
+
emitTaskEvent(eventObject: object) {
this.taskEvent.emit(eventObject);
}
+
+ hasDrugsLoaded(): boolean {
+ if (this.nodeData == null || this.nodeData.nodes == null)
+ return false;
+ return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.netexId.startsWith('dr')).length > 0;
+ }
}
--
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