From 72e422ac0344ed3ca9c3f3e0b3807878b72ab02c Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Wed, 30 Oct 2024 14:54:14 +1300
Subject: [PATCH] Implement a manual residue selection box

Refs pombase/website#2266
---
 .../transcript-sequence-select.component.css  | 14 ++++
 .../transcript-sequence-select.component.html | 13 +++-
 .../transcript-sequence-select.component.ts   | 70 ++++++++++++++++++-
 3 files changed, 94 insertions(+), 3 deletions(-)

diff --git a/src/app/transcript-sequence-select/transcript-sequence-select.component.css b/src/app/transcript-sequence-select/transcript-sequence-select.component.css
index e3050cc4..e1b17c75 100644
--- a/src/app/transcript-sequence-select/transcript-sequence-select.component.css
+++ b/src/app/transcript-sequence-select/transcript-sequence-select.component.css
@@ -42,6 +42,7 @@
 .selected-range {
   font-size: 120%;
   padding: 0 0.5em;
+  display: flex;
 }
 
 .seq-title {
@@ -183,3 +184,16 @@
 .dropdown-item a {
   text-decoration: none;
 }
+
+.manual-selection {
+  margin-left: auto;
+  font-size: 90%
+}
+
+.manual-selection input {
+  width: 16em;
+}
+
+.manual-selection-error {
+  color: red;
+}
diff --git a/src/app/transcript-sequence-select/transcript-sequence-select.component.html b/src/app/transcript-sequence-select/transcript-sequence-select.component.html
index 47d238e6..08af3858 100644
--- a/src/app/transcript-sequence-select/transcript-sequence-select.component.html
+++ b/src/app/transcript-sequence-select/transcript-sequence-select.component.html
@@ -17,7 +17,7 @@
     </select>
   </div>
 
-  <div (mousemove)="mousemove()">
+  <div (mousemove)="checkSelection()" (mouseup)="checkSelection()">
     <div *ngIf="hasTranscripts">
         <div class="controls">
           <div *ngIf="featureHasProtein()">
@@ -192,7 +192,17 @@
             {{selectedResidueMessage()}}
           </div>
           <div *ngIf="!selectedResidueRange">&nbsp;</div>
+          
+          <div *ngIf="!deployConfigService.productionMode()" class="manual-selection">
+            <a *ngIf="!selectedResidueRange && !manualSelectionVisible" (click)="manualSelectionVisible=true;">Manually select residues</a>
+            <div *ngIf="manualSelectionVisible && !selectedResidueRange && !showNucSequence">
+              Select range: <input [(ngModel)]="manualSelection" (change)="manualSelectionChanged()"
+                                   placeholder="Examples: 10..25 or 15-30 or 40">
+              <span class="manual-selection-error" *ngIf="manualSelectionErrorMessage">error: {{manualSelectionErrorMessage}}</span>
+            </div>
+          </div>
           </div>
+
           <div class="sequence-display">
           <div *ngIf="wrappedSequence || wrappedProteinSequence">
           <div class="header">
@@ -202,6 +212,7 @@
                    title="{{partTitle(part)}}" class="{{partClass(part)}}"
                    #partSpan
                  (mouseenter)="mouseenter(part)" (mouseleave)="mouseleave()"
+                 (mousedown)="clearManualSelection()"
                  [attr.data-part-id]="part.partId">{{part.residues}}</span></div>
           </div>
           <div *ngIf="!wrappedSequence && showNucSequence">
diff --git a/src/app/transcript-sequence-select/transcript-sequence-select.component.ts b/src/app/transcript-sequence-select/transcript-sequence-select.component.ts
index ca40ea9c..2ae4de6b 100644
--- a/src/app/transcript-sequence-select/transcript-sequence-select.component.ts
+++ b/src/app/transcript-sequence-select/transcript-sequence-select.component.ts
@@ -1,4 +1,4 @@
-import { Component, OnChanges, Input, Inject } from '@angular/core';
+import { Component, OnChanges, Input, Inject, ElementRef, ViewChild } from '@angular/core';
 
 import { saveAs } from 'file-saver';
 
@@ -6,6 +6,7 @@ import { GeneDetails, ProteinDetails, PombaseAPIService, Strand } from '../pomba
 import { Util } from '../shared/util';
 import { DisplaySequence, DisplaySequencePart, ResidueRange } from '../display-sequence';
 import { getAppConfig, replaceFieldsInUrl } from '../config';
+import { DeployConfigService } from '../deploy-config.service';
 
 @Component({
   selector: 'app-transcript-sequence-select',
@@ -43,6 +44,12 @@ export class TranscriptSequenceSelectComponent implements OnChanges {
   upstreamBases = 0;
   downstreamBases = 0;
 
+  manualSelection?: string;
+  manualSelectionErrorMessage?: string;
+  manualSelectionVisible = false;
+
+  @ViewChild('partSpan') partSpanElement: ElementRef;
+
   linksInNewWindow = true;
 
   hoverPart?: DisplaySequencePart;
@@ -57,6 +64,7 @@ export class TranscriptSequenceSelectComponent implements OnChanges {
   downloadWithFeaturesURL = getAppConfig().seq_and_features_download_url;
 
   constructor(private apiService: PombaseAPIService,
+              public deployConfigService: DeployConfigService,
               @Inject('Window') private window: Window) { }
 
   updateHeader(sequenceLength: number) {
@@ -132,6 +140,11 @@ export class TranscriptSequenceSelectComponent implements OnChanges {
     return retVal;
   }
 
+  clearManualSelection(): void {
+    this.manualSelection = undefined;
+    this.manualSelectionErrorMessage = undefined;
+  }
+
   mouseenter(part: DisplaySequencePart): void {
     if (this.showNucSequence) {
       this.hoverPart = part;
@@ -142,7 +155,7 @@ export class TranscriptSequenceSelectComponent implements OnChanges {
     this.hoverPart = undefined;
   }
 
-  mousemove(): void {
+  checkSelection(): void {
     this.selectedResidueRange = undefined;
 
     const selection = this.window.getSelection();
@@ -169,6 +182,10 @@ export class TranscriptSequenceSelectComponent implements OnChanges {
               this.selectedResidueRange =
                 displaySequence.rangeFromParts(+startPartId, startOffset,
                   +endPartId, endOffset - 1);
+              if (this.selectedResidueRange) {
+                this.manualSelectionVisible = false;
+                this.manualSelection = undefined;
+              }
             }
           }
         }
@@ -426,6 +443,55 @@ export class TranscriptSequenceSelectComponent implements OnChanges {
     this.updateSequence();
   }
 
+  manualSelectionChanged(): void {
+    this.manualSelectionErrorMessage = undefined;
+    const selection = this.window.getSelection();
+    if (selection) {
+      selection.removeAllRanges();
+    }
+
+    if (this.manualSelection && this.manualSelection.trim().length >= 0) {
+      const parts = /^(\d+)(?:(?:\.\.|--?)(\d+))?$/.exec(this.manualSelection.trim());
+
+      if (parts) {
+        let start = parseInt(parts[1], 10);
+        let end = undefined;
+
+        const endMatch = parts[2];
+
+        if (endMatch) {
+          end = parseInt(endMatch, 10);
+          if (end < start) {
+            this.manualSelectionErrorMessage = 'end position < start';
+            return;
+          }
+        } else {
+          end = start;
+        }
+
+        if (start <= end && selection) {
+          const range = document.createRange();
+          const residuesText = this.partSpanElement.nativeElement.firstChild;
+          if (end >= residuesText.length) {
+            this.manualSelectionErrorMessage = 'end > sequence length';
+            return;
+          }
+          try {
+            range.setStart(residuesText, start-1);
+            range.setEnd(residuesText, end);
+            selection.addRange(range);
+            this.checkSelection();
+          }
+          catch (e) {
+            console.log(e);
+          }
+        }
+      } else {
+        this.manualSelectionErrorMessage = 'invalid range - example "10..20"';
+      }
+    }
+  }
+
   selectedResidueMessage(): string {
     if (!this.selectedResidueRange) {
       return '';