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Commit 5a40f957 authored by Julian Matschinske's avatar Julian Matschinske
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Extend frontend with option to exclude viral non seed baits

parent 176d24f7
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...@@ -59,6 +59,13 @@ ...@@ -59,6 +59,13 @@
<i *ngIf="!task.info.parameters.includeNonApprovedDrugs" class="fa fa-times"></i> <i *ngIf="!task.info.parameters.includeNonApprovedDrugs" class="fa fa-times"></i>
</td> </td>
</tr> </tr>
<tr *ngIf="task.info.parameters.ignoreNonSeedBaits !== undefined && task.info.target === 'drug-target'">
<td>Include non-seed viral proteins</td>
<td>
<i *ngIf="!task.info.parameters.ignoreNonSeedBaits" class="fa fa-check"></i>
<i *ngIf="task.info.parameters.ignoreNonSeedBaits" class="fa fa-times"></i>
</td>
</tr>
<tr *ngIf="task.info.parameters.resultSize"> <tr *ngIf="task.info.parameters.resultSize">
<td>Result Size</td> <td>Result Size</td>
<td>{{task.info.parameters.resultSize}}</td> <td>{{task.info.parameters.resultSize}}</td>
......
...@@ -70,6 +70,13 @@ ...@@ -70,6 +70,13 @@
required> required>
</div> </div>
</div> </div>
<div class="field" *ngIf="target === 'drug-target'">
<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)]="trustrankIncludeViralNonSeeds"></app-toggle>
</div>
<div class="field"> <div class="field">
<label class="label" for="trustrank-rs">Result Size</label> <label class="label" for="trustrank-rs">Result Size</label>
<div class="control"> <div class="control">
...@@ -97,6 +104,13 @@ ...@@ -97,6 +104,13 @@
tooltipOff="Exclude non-approved drugs from the result." tooltipOff="Exclude non-approved drugs from the result."
[(value)]="closenessIncludeNonApprovedDrugs"></app-toggle> [(value)]="closenessIncludeNonApprovedDrugs"></app-toggle>
</div> </div>
<div class="field" *ngIf="target === 'drug-target'">
<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)]="closenessIncludeViralNonSeeds"></app-toggle>
</div>
<div class="field"> <div class="field">
<label class="label" for="closeness-rs">Result Size</label> <label class="label" for="closeness-rs">Result Size</label>
<div class="control"> <div class="control">
...@@ -118,6 +132,13 @@ ...@@ -118,6 +132,13 @@
tooltipOff="Exclude non-approved drugs from the result." tooltipOff="Exclude non-approved drugs from the result."
[(value)]="degreeIncludeNonApprovedDrugs"></app-toggle> [(value)]="degreeIncludeNonApprovedDrugs"></app-toggle>
</div> </div>
<div class="field" *ngIf="target === 'drug-target'">
<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)]="degreeIncludeViralNonSeeds"></app-toggle>
</div>
<div class="field"> <div class="field">
<label class="label" for="degree-rs">Result Size</label> <label class="label" for="degree-rs">Result Size</label>
<div class="control"> <div class="control">
...@@ -190,6 +211,13 @@ ...@@ -190,6 +211,13 @@
</div> </div>
</div> </div>
</div> </div>
<div class="field" *ngIf="target === 'drug-target'">
<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)]="multisteinerIncludeViralNonSeeds"></app-toggle>
</div>
</div> </div>
</section> </section>
......
...@@ -33,16 +33,19 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges { ...@@ -33,16 +33,19 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
// Trustrank Parameters // Trustrank Parameters
public trustrankIncludeIndirectDrugs = false; public trustrankIncludeIndirectDrugs = false;
public trustrankIncludeNonApprovedDrugs = false; public trustrankIncludeNonApprovedDrugs = false;
public trustrankIncludeViralNonSeeds = true;
public trustrankDampingFactor = 0.85; public trustrankDampingFactor = 0.85;
public trustrankResultSize = 20; public trustrankResultSize = 20;
// Closeness Parameters // Closeness Parameters
public closenessIncludeIndirectDrugs = false; public closenessIncludeIndirectDrugs = false;
public closenessIncludeNonApprovedDrugs = false; public closenessIncludeNonApprovedDrugs = false;
public closenessIncludeViralNonSeeds = true;
public closenessResultSize = 20; public closenessResultSize = 20;
// Degree Parameters // Degree Parameters
public degreeIncludeNonApprovedDrugs = false; public degreeIncludeNonApprovedDrugs = false;
public degreeIncludeViralNonSeeds = true;
public degreeResultSize = 20; public degreeResultSize = 20;
// Keypathwayminer Parameters // Keypathwayminer Parameters
...@@ -51,6 +54,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges { ...@@ -51,6 +54,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
// Multisteiner Parameters // Multisteiner Parameters
public multisteinerNumTrees = 5; public multisteinerNumTrees = 5;
public multisteinerTolerance = 10; public multisteinerTolerance = 10;
public multisteinerIncludeViralNonSeeds = true;
public hasBaits; public hasBaits;
...@@ -91,16 +95,18 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges { ...@@ -91,16 +95,18 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
parameters.damping_factor = this.trustrankDampingFactor; parameters.damping_factor = this.trustrankDampingFactor;
parameters.include_indirect_drugs = this.trustrankIncludeIndirectDrugs; parameters.include_indirect_drugs = this.trustrankIncludeIndirectDrugs;
parameters.include_non_approved_drugs = this.trustrankIncludeNonApprovedDrugs; parameters.include_non_approved_drugs = this.trustrankIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.trustrankIncludeViralNonSeeds;
parameters.result_size = this.trustrankResultSize; parameters.result_size = this.trustrankResultSize;
} else if (this.algorithm === 'closeness') { } else if (this.algorithm === 'closeness') {
parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset; parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs; parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs;
parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs; parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.closenessIncludeViralNonSeeds;
parameters.result_size = this.closenessResultSize; parameters.result_size = this.closenessResultSize;
} else if (this.algorithm === 'degree') { } else if (this.algorithm === 'degree') {
parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset; parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs; parameters.include_non_approved_drugs = this.degreeIncludeNonApprovedDrugs;
parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs; parameters.ignore_non_seed_baits = !this.degreeIncludeViralNonSeeds;
parameters.result_size = this.closenessResultSize; parameters.result_size = this.closenessResultSize;
} else if (this.algorithm === 'keypathwayminer') { } else if (this.algorithm === 'keypathwayminer') {
parameters.k = this.keypathwayminerK; parameters.k = this.keypathwayminerK;
...@@ -108,6 +114,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges { ...@@ -108,6 +114,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
parameters.strain_or_drugs = this.dataset; parameters.strain_or_drugs = this.dataset;
parameters.num_trees = this.multisteinerNumTrees; parameters.num_trees = this.multisteinerNumTrees;
parameters.tolerance = this.multisteinerTolerance; parameters.tolerance = this.multisteinerTolerance;
parameters.ignore_non_seed_baits = !this.multisteinerIncludeViralNonSeeds;
} }
await this.analysis.startAnalysis(this.algorithm, this.target, parameters); await this.analysis.startAnalysis(this.algorithm, this.target, parameters);
......
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