From 003acdc36994160ad0adcfb3931352ad17fc200d Mon Sep 17 00:00:00 2001
From: Julian Matschinske <julian@vyze.ai>
Date: Thu, 26 Nov 2020 17:27:40 +0100
Subject: [PATCH] Replace 'host' with 'protein', remove more virus stuff
---
src/app/analysis.service.ts | 12 ++------
.../analysis-panel.component.ts | 14 ++++-----
.../info-tile/info-tile.component.html | 13 +-------
.../query-tile/query-tile.component.html | 8 ++---
.../launch-analysis.component.html | 16 +---------
.../launch-analysis.component.ts | 7 -----
src/app/interfaces.ts | 4 +--
src/app/network-settings.ts | 30 +++++--------------
.../explorer-page.component.html | 12 +++-----
.../explorer-page/explorer-page.component.ts | 4 +--
10 files changed, 28 insertions(+), 92 deletions(-)
diff --git a/src/app/analysis.service.ts b/src/app/analysis.service.ts
index 780307fd..23ce8084 100644
--- a/src/app/analysis.service.ts
+++ b/src/app/analysis.service.ts
@@ -160,7 +160,7 @@ export class AnalysisService {
const newSelection = [];
nodes.forEach((node) => {
const wrapper: Wrapper = node.wrapper;
- if (wrapper.type === 'host' || wrapper.type === 'virus') {
+ if (wrapper.type === 'protein') {
if (!this.inSelection(wrapper)) {
newSelection.push(wrapper);
}
@@ -204,15 +204,7 @@ export class AnalysisService {
}
public removeAllHostProteins() {
- const items: Wrapper[] = Array.from(this.selectedItems.values()).filter(p => p.type === 'host');
- for (const wrapper of items) {
- this.selectedItems.delete(wrapper.nodeId);
- }
- this.selectListSubject.next({items, selected: false});
- }
-
- public removeAllViralProteins() {
- const items: Wrapper[] = Array.from(this.selectedItems.values()).filter(p => p.type === 'virus');
+ const items: Wrapper[] = Array.from(this.selectedItems.values()).filter(p => p.type === 'protein');
for (const wrapper of items) {
this.selectedItems.delete(wrapper.nodeId);
}
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index db253571..ca204933 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -255,7 +255,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const proteinSelection = this.tableSelectedProteins;
const viralProteinSelection = this.tableSelectedViralProteins;
for (const item of items) {
- if (item.type === 'host') {
+ if (item.type === 'protein') {
// TODO: Refactor!
const found = proteinSelection.findIndex((i) => getProteinNodeId(i) === item.nodeId);
const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.nodeId);
@@ -293,7 +293,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const proteinSelection = [];
const viralProteinSelection = [];
for (const item of items) {
- if (item.type === 'host') {
+ if (item.type === 'protein') {
const tableItem = this.tableProteins.find((i) => getProteinNodeId(i) === item.nodeId);
if (tableItem) {
proteinSelection.push(tableItem);
@@ -369,12 +369,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
public inferNodeType(nodeId: string): WrapperType {
- if (nodeId.indexOf('-') !== -1 || nodeId.indexOf('_') !== -1) {
- return 'virus';
- } else if (nodeId.startsWith('DB')) {
+ if (nodeId.startsWith('DB')) {
return 'drug';
}
- return 'host';
+ return 'protein';
}
public createNetwork(result: any): { edges: any[], nodes: any[] } {
@@ -393,7 +391,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const details = attributes.details || {};
const wrappers: { [key: string]: Wrapper } = {};
for (const node of network.nodes) {
- if (nodeTypes[node] === 'host') {
+ if (nodeTypes[node] === 'protein') {
this.proteins.push(details[node]);
wrappers[node] = getWrapperFromProtein(details[node]);
} else if (nodeTypes[node] === 'drug') {
@@ -417,7 +415,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
let wrapper: Wrapper;
let drugType;
let drugInTrial;
- if (nodeType === 'host') {
+ if (nodeType === 'protein') {
const protein = details as Protein;
wrapper = getWrapperFromProtein(protein);
nodeLabel = protein.name;
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index 26cbec22..9d64bd44 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -1,5 +1,5 @@
<div *ngIf="wrapper">
- <div *ngIf="wrapper.type === 'host'">
+ <div *ngIf="wrapper.type === 'protein'">
<p>
<b><span>Gene Name: </span></b>
{{ wrapper.data.name }}
@@ -20,17 +20,6 @@
{{ wrapper.data.expressionLevel|number }}
</p>
</div>
- <div *ngIf="wrapper.type === 'virus'">
- <p>
- <b><span>Virus:</span></b>
- {{ wrapper.data.virusName.replace('V', 'V-') }}
- <span class="icon is-small"><i class="fas fa-virus"></i></span>
- </p>
- <p>
- <b><span>Effect: </span></b>
- {{ wrapper.data.effectName }}
- </p>
- </div>
<div *ngIf="wrapper.type === 'drug'">
<p>
<b><span>Name: </span></b>
diff --git a/src/app/components/query-tile/query-tile.component.html b/src/app/components/query-tile/query-tile.component.html
index 93bdd628..b053d67c 100644
--- a/src/app/components/query-tile/query-tile.component.html
+++ b/src/app/components/query-tile/query-tile.component.html
@@ -2,11 +2,9 @@
<ng-select [items]="queryItems" bindLabel="backendId" bindValue="data" [virtualScroll]="true" class="custom"
placeholder="Search..." [hideSelected]="true" [searchFn]="querySearch" (change)="select($event)" data-tooltip="Find proteins in the network.">
<ng-template ng-option-tmp let-item="item">
- <b *ngIf="item.type == 'host'"> {{item.data.name}}</b>
- <b *ngIf="item.type == 'virus'"> {{item.data.effectName}}</b> <br/>
- <span><small *ngIf="item.type === 'virus'">Viral Protein</small><small *ngIf="item.type === 'host'">Host Protein</small> | </span>
- <span *ngIf="item.type == 'host'"><small>AC: <b>{{item.data.proteinAc}}</b></small> </span>
- <span *ngIf="item.type == 'virus'"><small><b>{{item.data.virusName.replace('V', 'V-')}}</b></small></span>
+ <b *ngIf="item.type == 'protein'"> {{item.data.name}}</b>
+ <span><small *ngIf="item.type === 'protein'">Host Protein</small> | </span>
+ <span *ngIf="item.type == 'protein'"><small>AC: <b>{{item.data.proteinAc}}</b></small> </span>
</ng-template>
</ng-select>
</div>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.html b/src/app/dialogs/launch-analysis/launch-analysis.component.html
index 3fee026f..e2ec0268 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.html
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.html
@@ -13,13 +13,6 @@
<button (click)="close()" class="delete" aria-label="close"></button>
</header>
<section class="modal-card-body">
- <div *ngIf="target === 'drug' && hasBaits">
- <div class="notification is-warning warning">
- You have selected <i class="fa fa-virus"></i> viral proteins.
- When finding drugs, make sure you have selected <i class="fa fa-dna"></i> host proteins only.
- </div>
- </div>
-
<div *ngIf="!analysis.canLaunchTask()">
<div class="notification is-warning warning">
You can only run {{maxTasks}} tasks at once. Please wait for one of them to finish or delete it from the task
@@ -381,13 +374,6 @@
</div>
<div *ngIf="algorithm==='keypathwayminer'">
- <div *ngIf="hasBaits">
- <div class="notification is-warning warning">
- You have selected <i class="fa fa-virus"></i> viral proteins.
- If you want to use KeyPathwayMiner, please remove them because it cannot process them.
- </div>
- </div>
-
<div class="field">
<label class="label" for="keypathwayminer-k">Additional proteins</label>
<div class="control">
@@ -511,7 +497,7 @@
<footer class="modal-card-foot">
<button (click)="startTask(); close()" class="button is-success is-rounded has-tooltip"
data-tooltip="Run the analysis."
- [disabled]="(target === 'drug' && hasBaits) || !analysis.canLaunchTask() || (algorithm === 'keypathwayminer' && hasBaits)">
+ [disabled]="!analysis.canLaunchTask()">
<span class="icon">
<i class="fa fa-rocket"></i>
</span>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 077516b7..6e42901d 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -9,7 +9,6 @@ import {
QuickAlgorithmType,
TRUSTRANK
} from '../../analysis.service';
-import {Dataset} from '../../interfaces';
@Component({
selector: 'app-launch-analysis',
@@ -74,15 +73,9 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public multisteinerMaxDeg = 0;
public multisteinerHubPenalty = 0.0;
- public hasBaits;
-
public maxTasks = MAX_TASKS;
constructor(public analysis: AnalysisService) {
- this.hasBaits = !!analysis.getSelection().find((i) => i.type === 'virus');
- analysis.subscribeList(() => {
- this.hasBaits = !!analysis.getSelection().find((i) => i.type === 'virus');
- });
}
ngOnInit(): void {
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 3e5bcc41..230bb223 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -92,7 +92,7 @@ export function getWrapperFromProtein(protein: Protein): Wrapper {
return {
backendId: getProteinBackendId(protein),
nodeId: getProteinNodeId(protein),
- type: 'host',
+ type: 'protein',
data: protein,
};
}
@@ -106,7 +106,7 @@ export function getWrapperFromDrug(drug: Drug): Wrapper {
};
}
-export type WrapperType = 'host' | 'virus' | 'drug';
+export type WrapperType = 'protein' | 'drug';
export interface Wrapper {
backendId: string;
diff --git a/src/app/network-settings.ts b/src/app/network-settings.ts
index e74902c2..83a622c3 100644
--- a/src/app/network-settings.ts
+++ b/src/app/network-settings.ts
@@ -80,20 +80,16 @@ export class NetworkSettings {
private static drugInTrialShape = 'triangle';
static getNodeSize(wrapperType: WrapperType) {
- if (wrapperType === 'host') {
+ if (wrapperType === 'protein') {
return this.hostSize;
- } else if (wrapperType === 'virus') {
- return this.virusSize;
} else if (wrapperType === 'drug') {
return this.drugSize;
}
}
static getNodeShape(wrapperType: WrapperType, drugInTrial?: boolean) {
- if (wrapperType === 'host') {
+ if (wrapperType === 'protein') {
return this.hostShape;
- } else if (wrapperType === 'virus') {
- return this.virusShape;
} else if (wrapperType === 'drug') {
if (drugInTrial) {
return this.drugInTrialShape;
@@ -125,13 +121,11 @@ export class NetworkSettings {
}
}
- static getColor(color: 'host' | 'virus' | 'approvedDrug' | 'unapprovedDrug' | 'hostFont' | 'virusFont' | 'drugFont' |
+ static getColor(color: 'protein' | 'approvedDrug' | 'unapprovedDrug' | 'hostFont' | 'virusFont' | 'drugFont' |
'nonSeedHost' | 'nonSeedVirus' | 'selectedForAnalysis' | 'selectedForAnalysisText' |
'edgeHostVirus' | 'edgeHostVirusHighlight' | 'edgeHostDrug' | 'edgeHostDrugHighlight') {
- if (color === 'host') {
+ if (color === 'protein') {
return this.hostColor;
- } else if (color === 'virus') {
- return this.virusColor;
} else if (color === 'approvedDrug') {
return this.approvedDrugColor;
} else if (color === 'unapprovedDrug') {
@@ -158,10 +152,8 @@ export class NetworkSettings {
}
static getFont(wrapperType: WrapperType, drugInTrial?: boolean) {
- if (wrapperType === 'host') {
+ if (wrapperType === 'protein') {
return {color: this.hostFontColor, size: this.hostFontSize};
- } else if (wrapperType === 'virus') {
- return {color: this.virusFontColor, size: this.virusFontSize};
} else if (wrapperType === 'drug') {
if (!drugInTrial) {
return {color: this.drugFontColor, size: this.drugFontSize};
@@ -188,20 +180,12 @@ export class NetworkSettings {
nodeShape = NetworkSettings.getNodeShape(nodeType);
nodeSize = NetworkSettings.getNodeSize(nodeType);
nodeFont = NetworkSettings.getFont(nodeType);
- if (nodeType === 'host') {
+ if (nodeType === 'protein') {
nodeColor = NetworkSettings.getColor(nodeType);
- nodeFont = NetworkSettings.getFont('host');
+ nodeFont = NetworkSettings.getFont('protein');
if (!isSeed) {
nodeColor = NetworkSettings.getColor('nonSeedHost');
}
- } else if (nodeType === 'virus') {
- nodeColor = NetworkSettings.getColor(nodeType);
- if (nodeType === 'virus') {
- nodeFont = NetworkSettings.getFont('virus');
- if (!isSeed) {
- nodeColor = NetworkSettings.getColor('nonSeedVirus');
- }
- }
} else if (nodeType === 'drug') {
if (drugType === 'approved') {
nodeColor = NetworkSettings.getColor('approvedDrug');
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 7dd2fdc8..9130e3e1 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -171,15 +171,13 @@
<p class="card-header-title">
<span class="icon">
<i *ngIf="!selectedWrapper" class="fas fa-info" aria-hidden="true"></i>
- <i *ngIf="selectedWrapper && selectedWrapper.type === 'host'" class="fas fa-dna" aria-hidden="true"></i>
- <i *ngIf="selectedWrapper && selectedWrapper.type === 'virus'" class="fas fa-virus" aria-hidden="true"></i>
+ <i *ngIf="selectedWrapper && selectedWrapper.type === 'protein'" class="fas fa-dna" aria-hidden="true"></i>
<i *ngIf="selectedWrapper && selectedWrapper.type === 'drug'" class="fas fa-capsules"
aria-hidden="true"></i>
</span>
<span *ngIf="!selectedWrapper">No item selected</span>
<span *ngIf="selectedWrapper">
- <span *ngIf="selectedWrapper.type === 'host'">Host Protein</span>
- <span *ngIf="selectedWrapper.type === 'virus'">Viral Protein</span>
+ <span *ngIf="selectedWrapper.type === 'protein'">Host Protein</span>
<span *ngIf="selectedWrapper.type === 'drug'">Drug</span>
</span>
</p>
@@ -408,12 +406,10 @@
<tr *ngFor="let p of analysis.getSelection()">
<td>
<span class="icon">
- <i class="fa fa-dna" *ngIf="p.type == 'host'"></i>
- <i class="fa fa-virus" *ngIf="p.type =='virus'"></i>
+ <i class="fa fa-dna" *ngIf="p.type == 'protein'"></i>
</span>
</td>
- <td *ngIf="p.type == 'virus'">{{p.data.effectName}}</td>
- <td *ngIf="p.type == 'host'">{{p.data.name}}</td>
+ <td *ngIf="p.type == 'protein'">{{p.data.name}}</td>
<td>
<button (click)="analysis.removeItems([p])" class="button is-small is-danger is-outlined has-tooltip"
data-tooltip="Remove from selection.">
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index d42cf733..b8a20738 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -299,7 +299,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
private mapHostProteinToNode(hostProtein: Protein): any {
const wrapper = getWrapperFromProtein(hostProtein);
- const node = NetworkSettings.getNodeStyle('host', true, this.analysis.inSelection(wrapper));
+ const node = NetworkSettings.getNodeStyle('protein', true, this.analysis.inSelection(wrapper));
let nodeLabel = hostProtein.name;
if (hostProtein.name.length === 0) {
nodeLabel = hostProtein.proteinAc;
@@ -365,7 +365,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
gProfilerLink(): string {
const queryString = this.analysis.getSelection()
- .filter(wrapper => wrapper.type === 'host')
+ .filter(wrapper => wrapper.type === 'protein')
.map(wrapper => wrapper.data.proteinAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
--
GitLab