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Michael Hartung authoredMichael Hartung authored
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explorer-page.component.html 24.32 KiB
<div id="appWindow" [style.color]="textColor" (window:resize)="onResize($event)">
<div class="is-hidden-mobile fullheight">
<app-launch-analysis [(show)]="showAnalysisDialog"
[target]="analysisDialogTarget"
[config]="myConfig"
[inputNetwork]="{nodes:proteins, edges:edges}">
</app-launch-analysis>
<app-custom-proteins [(show)]="showCustomProteinsDialog" [visibleNodes]="currentViewNodes">
</app-custom-proteins>
<app-add-expressed-proteins [(show)]="showThresholdDialog"
[selectedTissue]="currentViewSelectedTissue"
[visibleNodes]="currentViewNodes"
[currentViewProteins]="currentViewProteins"
[expressionMap]="expressionMap"
>
</app-add-expressed-proteins>
<!-- Start explorer -->
<div class="covex explorer">
<!-- Start left sidebar -->
<div *ngIf="myConfig.showLeftSidebar" class="covex sidebar bar-left">
<div *ngIf="myConfig.showOverview" class="card bar-large" [ngClass]="{'b-text-small':smallStyle}">
<header class="card-header">
<p class="card-header-title">
<span class="icon">
<i class="fas fa-info" aria-hidden="true"></i>
</span> Network Overview
</p>
<a (click)="collapseOverview= !collapseOverview" data-action="collapse"
class="card-header-icon is-hidden-fullscreen" aria-label="more options">
<span *ngIf="collapseOverview" class="icon">
<i class="fas fa-angle-down" aria-hidden="true"></i>
</span>
<span *ngIf="!collapseOverview" class="icon">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</a>
</header>
<div *ngIf="collapseOverview">
<div class="card-content">
<nav class="level" *ngIf="proteinData">
<!-- TO DO : CHANGE THIS LATER
<div class="level-item has-text-centered">
<div>
<p class="heading">Viral<br>Proteins</p>
<p class="title"> {{ proteinData.effects.length }}</p>
</div>
</div>
-->
<div class="level-item has-text-centered">
<div>
<p class="heading">Proteins</p>
<p class="title">{{ proteinData.proteins.length }}</p>
</div>
</div>
<div class="level-item has-text-centered">
<div>
<p class="heading">Interactions</p>
<p class="title">{{ proteinData.edges.length }}</p>
</div>
</div>
</nav>
</div> </div>
</div>
<div *ngIf="myConfig.showQuery" class="card bar-large" [ngClass]="{'b-text-small':smallStyle}">
<header class="card-header">
<p class="card-header-title">
<span class="icon">
<i class="fas fa-search" aria-hidden="true"></i>
</span> Query Protein/Gene
</p>
<a (click)="collapseQuery = !collapseQuery" data-action="collapse"
class="card-header-icon is-hidden-fullscreen" aria-label="more options">
<span class="icon">
<span *ngIf="collapseQuery" class="icon">
<i class="fas fa-angle-down" aria-hidden="true"></i>
</span>
<span *ngIf="!collapseQuery" class="icon">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</span>
</a>
</header>
<div *ngIf="collapseQuery">
<div class="card-content">
<div class="field">
<div class="control">
<app-query-tile-component (selectItem)="queryAction($event)"
[queryItems]="queryItems"></app-query-tile-component>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Start network block -->
<div class="covex network center-panel" id="main-column">
<div class="analysis-view" *ngIf="selectedAnalysisToken">
<app-analysis-panel [(token)]="selectedAnalysisToken"
(showDetailsChange)="selectedWrapper = $event"
(visibleItems)="analysisWindowChanged($event)" [config]="myConfig"
[smallStyle]="smallStyle"></app-analysis-panel>
</div>
<div class="card network">
<header class="card-header network-header">
<p class="card-header-title">
{{myConfig.title}}
</p>
</header>
<div class="card-content explorer-network-view-settings">
<div class="card-image canvas-content" #networkWithLegend>
<div *ngIf="myConfig.showLegend">
<app-network-legend [config]="myConfig" [context]="legendContext"></app-network-legend>
</div>
<div class="center image1 fullheight" #network>
<button class="button is-loading center" alt="loading...">Loading</button>
</div>
</div>
<footer *ngIf="myConfig.showFooter" class="card-footer toolbar network-footer-toolbar">
<div class="network-footer-toolbar-inner-container">
<ng-container *ngIf="myConfig.showFooterButtonScreenshot">
<button (click)="toImage()"
class="button is-primary is-rounded has-tooltip network-footer-toolbar-element"
pTooltip="Take a screenshot of the current network." tooltipPosition="top"> <span class="icon">
<i class="fas fa-camera" aria-hidden="true"></i>
</span>
<span [ngClass]="{'text-normal':smallStyle}">Screenshot</span>
</button>
</ng-container>
<ng-container *ngIf="myConfig.showFooterButtonExpression">
<div class="footer-buttons dropdown is-up network-footer-toolbar-element"
[class.is-active]="expressionExpanded">
<div class="dropdown-trigger">
<button (click)="expressionExpanded=!expressionExpanded"
class="button is-rounded is-primary" [class.is-outlined]="!selectedTissue"
aria-haspopup="true" aria-controls="dropdown-menu"
pTooltip="Tissue expression data is provided by the GTEx project." tooltipPosition="top"
[ngClass]="{'button-small':smallStyle}">
<span *ngIf="!selectedTissue" [ngClass]="{'text-small':smallStyle}">Tissue</span>
<span *ngIf="selectedTissue">{{selectedTissue.name}}</span>
<span *ngIf="expressionExpanded" class="icon is-small">
<i class="fas fa-angle-up" aria-hidden="true"></i>
</span>
<span *ngIf="!expressionExpanded" class="icon is-small">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</button>
</div>
<div class="dropdown-menu" id="dropdown-menu" role="menu">
<div class="dropdown-content tissue-dropdown">
<div class="scroll-area">
<a (click)="selectTissue(null)"
[class.is-active]="!selectedTissue"
class="dropdown-item">
None
</a>
<a *ngFor="let tissue of analysis.getTissues()"
(click)="selectTissue(tissue)"
[class.is-active]="selectedTissue && tissue.netexId === selectedTissue.netexId"
class="dropdown-item">
{{tissue.name}}
</a>
</div>
</div>
</div>
</div>
</ng-container>
<app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Drugs" textOff="Off"
tooltipOn="Display adjacent drugs ON."
tooltipOff="Display adjacent drugs OFF."
[smallStyle]="smallStyle"
[value]="adjacentDrugs" (valueChange)="updateAdjacentDrugs($event)"></app-toggle>
<app-toggle class="footer-buttons network-footer-toolbar-element" textOn="Animation On" textOff="Off"
tooltipOn="Enable the network animation."
tooltipOff="Disable the network animation and freeze nodes."
[smallStyle]="smallStyle"
[value]="physicsEnabled" (valueChange)="updatePhysicsEnabled($event)"></app-toggle>
</div>
</footer>
</div>
</div>
</div>
<!-- End network block -->
<div *ngIf="myConfig.showRightSidebar" class="covex sidebar bar-right">
<div *ngIf="myConfig.showItemSelector" class="card bar-large">
<header class="card-header" [ngClass]="{'b-text-small':smallStyle}">
<p class="card-header-title"> <span *ngIf="!selectedWrapper" class="icon">
<i class="fas fa-info" aria-hidden="true"></i>
</span>
<!-- <i *ngIf="selectedWrapper && selectedWrapper.data.netexId && selectedWrapper.data.netexId.startsWith('p')" class="fas fa-dna" aria-hidden="true"></i>
<i *ngIf="selectedWrapper && selectedWrapper.data.netexId && selectedWrapper.data.netexId.startsWith('d')" class="fas fa-capsules"
aria-hidden="true"></i> -->
<span *ngIf="!selectedWrapper">No item selected</span>
<span *ngIf="selectedWrapper">
<span>{{ selectedWrapper.data.type }}</span>
</span>
</p>
<a (click)="collapseDetails = !collapseDetails" data-action="collapse"
class="card-header-icon is-hidden-fullscreen" aria-label="more options">
<span *ngIf="collapseDetails" class="icon">
<i class="fas fa-angle-down" aria-hidden="true"></i>
</span>
<span *ngIf="!collapseDetails" class="icon">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</a>
</header>
<div *ngIf="collapseDetails">
<div class="card-content">
<app-info-tile [wrapper]="selectedWrapper" [smallStyle]="smallStyle"></app-info-tile>
</div>
</div>
</div>
<div *ngIf="myConfig.showSimpleAnalysis" class="card bar-large">
<header class="card-header" [ngClass]="{'b-text-small':smallStyle}">
<p class="card-header-title">
<span class="icon">
<i class="fas fa-flask" aria-hidden="true"></i>
</span>
Simple Analysis
</p>
<a (click)="collapseAnalysisQuick = !collapseAnalysisQuick" data-action="collapse"
class="card-header-icon is-hidden-fullscreen" aria-label="more options">
<span *ngIf="collapseAnalysisQuick" class="icon">
<i class="fas fa-angle-down" aria-hidden="true"></i>
</span>
<span *ngIf="!collapseAnalysisQuick" class="icon">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</a>
</header>
<div *ngIf="collapseAnalysisQuick">
<div class="card-content quick-find">
<div class="field">
<div class="control">
<div class="tile notification is-danger">
<div class="align-vmiddle">
<div class="digit"><i class="fa fa-fast-forward"></i></div>
<button (click)="analysis.startQuickAnalysis(true, null)"
[disabled]="analysis.isLaunchingQuick()"
class="button is-white is-rounded has-tooltip" pTooltip="Find drugs for all proteins."
tooltipPosition="top">
<span class="icon">
<i class="fa fa-capsules" *ngIf="!analysis.isLaunchingQuick()"></i>
<i class="fa fa-spin fa-spinner" *ngIf="analysis.isLaunchingQuick()"></i>
</span>
<span [ngClass]="{'text-normal':smallStyle}">
Quick Start
</span>
</button>
</div>
</div>
<div class="divisor-rapid">
— or —
</div> <div class="tile notification is-info">
<div class="align-vmiddle">
<div class="digit" *ngIf="analysis.getCount() == 0">1</div>
<div class="digit" *ngIf="analysis.getCount() > 0"><i class="fa fa-check"></i></div>
<div>
<span [ngClass]="{'text-normal':smallStyle}">Select Proteins</span>
</div>
</div>
</div>
<div class="tile notification is-info">
<div class="align-vmiddle">
<div class="digit">2</div>
<button (click)="analysis.startQuickAnalysis(false, null)"
[disabled]="analysis.getCount() === 0 || analysis.isLaunchingQuick()"
class="button is-white is-rounded has-tooltip"
pTooltip="Find drugs for the selected proteins." tooltipPosition="top">
<span class="icon">
<i class="fa fa-capsules" *ngIf="!analysis.isLaunchingQuick()"></i>
<i class="fa fa-spin fa-spinner" *ngIf="analysis.isLaunchingQuick()"></i>
</span>
<span [ngClass]="{'text-normal':smallStyle}">
{{ myConfig.taskName }}
</span>
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div *ngIf="myConfig.showAdvAnalysis" class="card bar-large">
<header class="card-header" [ngClass]="{'b-text-small':smallStyle}">
<p class="card-header-title">
<span class="icon">
<i class="fas fa-flask" aria-hidden="true"></i>
</span>
Analysis
</p>
<a (click)="collapseAnalysis = !collapseAnalysis" data-action="collapse"
class="card-header-icon is-hidden-fullscreen" aria-label="more options">
<span *ngIf="collapseAnalysis" class="icon">
<i class="fas fa-angle-down" aria-hidden="true"></i>
</span>
<span *ngIf="!collapseAnalysis" class="icon">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</a>
</header>
<div *ngIf="collapseAnalysis">
<div class="card-content">
<div class="field">
<div class="control" pTooltip="Find drug targets for the selected proteins." tooltipPosition="top">
<button (click)="analysisDialogTarget = 'drug-target'; showAnalysisDialog = true;"
class="button is-primary is-fullwidth is-rounded has-tooltip"
[disabled]="analysis.getCount() === 0" [ngClass]="{'text-small':smallStyle}">
<span class="icon">
<i class="fa fa-crosshairs"></i>
</span>
<span>
Find Drug Targets
</span>
</button>
</div>
</div>
<div class="field">
<div class="control" pTooltip="Find drugs for the selected proteins." tooltipPosition="top">
<button (click)="analysisDialogTarget = 'drug'; showAnalysisDialog = true;"
class="button is-primary is-fullwidth is-rounded has-tooltip" [disabled]="analysis.getCount() === 0" [ngClass]="{'text-small':smallStyle}">
<span class="icon">
<i class="fa fa-capsules"></i>
</span>
<span>
{{myConfig.taskName}}
</span>
</button>
</div>
</div>
<div class="field">
<div class="control">
<a *ngIf="analysis.getCount() > 0" [href]="gProfilerLink()" target="_blank"
class="button is-primary is-fullwidth is-rounded has-tooltip"
pTooltip="Use enrichment analysis via g:Profiler (external)." tooltipPosition="top">
<span class="icon">
<i class="fa fa-external-link-alt"></i>
</span>
<span [ngClass]="{'text-small':smallStyle}">
Enrichment Analysis
</span>
</a>
<a *ngIf="analysis.getCount() === 0" disabled
class="button is-primary is-fullwidth is-rounded has-tooltip"
pTooltip="Use enrichment analysis via g:Profiler (external)." tooltipPosition="top">
<span class="icon">
<i class="fa fa-external-link-alt"></i>
</span>
<span [ngClass]="{'text-small':smallStyle}">
Enrichment Analysis
</span>
</a>
</div>
</div>
</div>
</div>
</div>
<div *ngIf="myConfig.showTasks" class="card bar-large">
<header class="card-header" [ngClass]="{'b-text-small':smallStyle}">
<p class="card-header-title">
<span class="icon">
<i class="fas fa-tasks" aria-hidden="true"></i>
</span>
Tasks ({{analysis.tasks.length}})
</p>
<a (click)="collapseTask = !collapseTask" data-action="collapse"
class="card-header-icon is-hidden-fullscreen"
aria-label="more options">
<span *ngIf="collapseTask" class="icon">
<i class="fas fa-angle-down" aria-hidden="true"></i>
</span>
<span *ngIf="!collapseTask" class="icon">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</a>
</header>
<div *ngIf="collapseTask">
<div class="card-content overflow task-list-container" *ngIf="analysis.tasks && analysis.tasks.length > 0">
<app-task-list [(token)]="selectedAnalysisToken"></app-task-list>
</div>
<footer class="card-footer">
<a *ngIf="analysis.tasks && analysis.tasks.length > 0"
(click)="analysis.removeAllTasks(); selectedAnalysisToken = null;"
class="card-footer-item text-danger" pTooltip="Delete all tasks." tooltipPosition="top">
<span class="icon">
<i class="fa fa-trash"></i>
</span>
<span>
Delete all </span>
</a>
</footer>
</div>
</div>
<div *ngIf="myConfig.showSelection" class="card bar-large">
<header class="card-header" [ngClass]="{'b-text-small':smallStyle}">
<p class="card-header-title">
<span class="icon">
<i class="fas fa-filter" aria-hidden="true"></i>
</span> Selection ({{analysis.getCount()}})
</p>
<a (click)="collapseSelection = !collapseSelection" data-action="collapse"
class="card-header-icon is-hidden-fullscreen" aria-label="more options">
<span *ngIf="collapseSelection" class="icon">
<i class="fas fa-angle-down" aria-hidden="true"></i>
</span>
<span *ngIf="!collapseSelection" class="icon">
<i class="fas fa-angle-left" aria-hidden="true"></i>
</span>
</a>
</header>
<div *ngIf="collapseSelection" class="seed-selection" [ngClass]="{'text-normal':smallStyle}">
<!-- <div class="card-content overflow">
<table class="table selection-table" *ngIf="analysis.getCount() > 0">
<thead>
<tr>
<td>Label</td>
<td>Actions</td>
</tr>
</thead>
<tbody>
<tr *ngFor="let p of analysis.getSelection()">
<td><p class="is-capitalized">{{p.data.label}}</p></td>
<td>
<button (click)="analysis.removeItems([p])" class="button is-small is-danger is-outlined has-tooltip"
tooltipPosition="top" pTooltip="Remove from selection.">
<i class="fa fa-trash"></i>
</button>
</td>
</tr>
</tbody>
</table>
<i *ngIf="analysis.getCount() === 0">
Double-click on a protein to select it for the analysis.
</i>
</div>
<footer class="card-footer" *ngIf="selectedAnalysisToken">
<a (click)="analysis.addSeeds(currentViewNodes)"
class="card-footer-item has-text-success" tooltipPosition="top" pTooltip="Add all visible seeds.">
<span class="icon">
<i class="fa fa-plus"></i>
</span>
<span>
Add seeds
</span>
</a>
<a (click)="analysis.removeSeeds(currentViewNodes)"
class="card-footer-item text-danger" tooltipPosition="top" pTooltip="Remove all seeds.">
<span class="icon">
<i class="fa fa-minus"></i>
</span>
<span>
Remove seeds
</span>
</a> </footer>
<footer class="card-footer">
<a (click)="showCustomProteinsDialog = true"
class="card-footer-item text-primary"
tooltipPosition="top" pTooltip="Add a custom list of proteins.">
<span class="icon">
<i class="fa fa-upload"></i>
</span>
<span>
Custom proteins
</span>
</a>
<a (click)="showThresholdDialog = true"
class="card-footer-item text-primary"
pTooltip="Add proteins expressed in the tissue." tooltipPosition="top">
<span class="icon">
<i class="fas fa-angle-double-up"></i>
</span>
<span>
Tissue proteins
</span>
</a>
</footer> -->
<!-- <footer class="card-footer">
<a (click)="analysis.invertSelection(currentViewNodes)" class="card-footer-item text-primary"
tooltipPosition="top" pTooltip="Invert the current selection.">
<span class="icon">
<i class="fa fa-sync"></i>
</span>
<span>
Invert
</span>
</a>
<a (click)="analysis.resetSelection()" class="card-footer-item text-danger"
tooltipPosition="top" pTooltip="Remove all entries from the selection.">
<span class="icon">
<i class="fa fa-broom"></i>
</span>
<span>
Reset
</span>
</a>
</footer> -->
</div>
</div>
</div>
</div>
</div>
<div class="is-hidden-tablet mobile-fallback">
Sorry, CoVex is not available for mobile phones.
To find information about CoVex, please check the <a routerLink="/about">About</a> page or visit this page
with another device with a larger screen.
</div>
</div>