From f7e7a0f5674fc2d185ea814ba620eae52b5dba3f Mon Sep 17 00:00:00 2001
From: Julian Matschinske <ge93nar@mytum.de>
Date: Thu, 4 Jun 2020 19:40:09 +0200
Subject: [PATCH] Fix betweenness
---
.../info-tile/info-tile.component.html | 2 +-
.../launch-analysis.component.html | 30 +++++++++++++++++++
.../launch-analysis.component.ts | 8 +++++
3 files changed, 39 insertions(+), 1 deletion(-)
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index abc58f66..26cbec22 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -51,7 +51,7 @@
<p *ngIf="wrapper.data.inTrial">
<b>In trial(s) </b> <span class="icon is-small"><i class="fas fa-check"></i></span>
</p>
- <div *ngIf="wrapper.data.trialLinks.length > 0" class="list">
+ <div *ngIf="wrapper.data.inTrial && wrapper.data.trialLinks.length > 0" class="list">
<div *ngFor="let link of wrapper.data.trialLinks" class="list-item">
<a [href]="link" target="_blank">{{beautify(link)}}</a>
</div>
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.html b/src/app/dialogs/launch-analysis/launch-analysis.component.html
index 04521325..3fee026f 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.html
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.html
@@ -331,6 +331,36 @@
</div>
</div>
+ <div class="field">
+ <label class="label" for="betweenness-md">Maximum degree</label>
+ <div class="control">
+ <input [(ngModel)]="betweennessMaxDeg" id="betweenness-md" class="input" type="number"
+ placeholder="Maximum degree" min="0" max="1" required>
+ </div>
+ <p class="help">
+ All nodes with degree greater than this value will be ignored. Disabled if equal to 0.
+ </p>
+ </div>
+
+ <div class="field">
+ <label class="label" for="betweenness-hp">Hub penalty</label>
+ <div class="control">
+ <input [(ngModel)]="betweennessHubPenalty" id="betweenness-hp" class="input" type="number"
+ placeholder="Maximum degree" min="0" max="1" required>
+ </div>
+ <p class="help">
+ Penalty parameter for hubs.
+ </p>
+ </div>
+
+ <div class="field">
+ <label class="label">Include non-seed viral proteins</label>
+ <app-toggle textOn="Include" textOff="Ignore"
+ tooltipOn="Include viral proteins that are not seeds."
+ tooltipOff="Exclude viral proteins that are not seeds."
+ [(value)]="betweennessIncludeViralNonSeeds"></app-toggle>
+ </div>
+
<div class="box">
<article class="media">
<div class="media-left">
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 640fc909..8fe85ae8 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -61,6 +61,9 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public proximityResultSize = 20;
// Betweenness Parameters
+ public betweennessIncludeViralNonSeeds = true;
+ public betweennessMaxDeg = 0;
+ public betweennessHubPenalty = 0.0;
public betweennessResultSize = 20;
// Keypathwayminer Parameters
@@ -144,6 +147,11 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
parameters.hub_penalty = this.proximityHubPenalty;
parameters.result_size = this.proximityResultSize;
} else if (this.algorithm === 'betweenness') {
+ parameters.ignore_non_seed_baits = !this.betweennessIncludeViralNonSeeds;
+ if (this.betweennessMaxDeg && this.betweennessMaxDeg > 0) {
+ parameters.max_deg = this.betweennessMaxDeg;
+ }
+ parameters.hub_penalty = this.betweennessHubPenalty;
parameters.result_size = this.betweennessResultSize;
} else if (this.algorithm === 'keypathwayminer') {
parameters.k = this.keypathwayminerK;
--
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