ctlab · AxisAlexNT · Jun 13, 2026 · Jun 10, 2026 · Jun 12, 2026 · Jun 13, 2026
diff --git a/assets/icon.ico b/assets/icon.ico
diff --git a/assets/icon.png b/assets/icon.png
diff --git a/index.html b/index.html
@@ -24,7 +24,10 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
-    <link rel="icon" href="/favicon.ico" />
+    <link rel="icon" href="/favicon.ico" sizes="any" />
+    <link rel="icon" type="image/png" sizes="192x192" href="/hict-icon-192.png" />
+    <link rel="icon" type="image/png" sizes="256x256" href="/hict-icon-256.png" />
+    <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>HiCT</title>
     <style>

diff --git a/package.json b/package.json
@@ -24,6 +24,8 @@
     "tauri:payload": "node scripts/build-tauri-browser-payload.mjs",
     "tauri:payload:linux": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform linux_x86_64",
     "tauri:payload:windows": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform windows_x86_64",
+    "tauri:payload:darwin-arm64": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform darwin_arm64",
+    "tauri:payload:darwin-x86_64": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform darwin_x86_64",
     "app:dev": "npm run electron:compile && concurrently vite \"electron . http://localhost:8080/\" \"npm run watch\"",
     "app:build": "npm run build && electron-builder",
     "app:multibuild": "npm run build && electron-builder -wl --ia-32 --x64 --publish never",
@@ -128,6 +130,7 @@
       "buildResources": "assets",
       "output": "release/${version}"
     },
+    "icon": "assets/icon",
     "win": {
       "target": [
         {

diff --git a/public/apple-touch-icon.png b/public/apple-touch-icon.png
diff --git a/public/favicon.ico b/public/favicon.ico
diff --git a/public/hict-icon-192.png b/public/hict-icon-192.png
diff --git a/public/hict-icon-256.png b/public/hict-icon-256.png
diff --git a/public/hict-logo-512.png b/public/hict-logo-512.png
diff --git a/scripts/build-tauri-browser-payload.mjs b/scripts/build-tauri-browser-payload.mjs
@@ -41,7 +41,7 @@ const generatedIconPngBase64 = [
   "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"
 ].join("");
 
-if (!["linux_x86_64", "windows_x86_64"].includes(platform)) {
+if (!["linux_x86_64", "windows_x86_64", "darwin_arm64", "darwin_x86_64"].includes(platform)) {
   throw new Error(`Unsupported Tauri browser payload platform: ${platform}`);
 }
 if (!existsSync(resolve(repoDir, "dist", "index.html"))) {
@@ -63,7 +63,7 @@ mkdirSync(join(outputDir, "licenses"), { recursive: true });
 
 const command = platform === "windows_x86_64" ? "bin/hict-tauri-browser.exe" : "bin/hict-tauri-browser";
 cpSync(builtExecutable, join(outputDir, command));
-if (platform === "linux_x86_64") {
+if (platform !== "windows_x86_64") {
   chmodExecutable(join(outputDir, command));
 }
 
@@ -75,7 +75,8 @@ writeFileSync(
     "",
     "This payload contains a small Rust/Tauri wrapper written by the HiCT team.",
     "It does not bundle Chromium. It uses the operating system WebView runtime:",
-    "Microsoft Edge WebView2 on Windows and WebKitGTK on Linux.",
+    "Microsoft Edge WebView2 on Windows, WebKitGTK on Linux, and WKWebView",
+    "from macOS.",
     "",
     "Tauri, WRY, TAO and their Rust dependencies are redistributed as compiled",
     "Rust code under their upstream licenses. See cargo-metadata.json for the",
@@ -115,6 +116,10 @@ const manifest = {
     windows: {
       runtime: "Microsoft Edge WebView2 Runtime",
       detection: "EdgeUpdate Clients {F3017226-FE2A-4295-8BDF-00C3A9A7E4C5} pv registry value or standard Microsoft/EdgeWebView installation directory"
+    },
+    macos: {
+      runtime: "WKWebView",
+      detection: "Built into macOS; no separate browser runtime is bundled or required."
     }
   },
   sizeBytes: directorySize(outputDir),
@@ -154,6 +159,9 @@ function detectPlatform() {
   if (process.platform === "linux") {
     return "linux_x86_64";
   }
+  if (process.platform === "darwin") {
+    return process.arch === "arm64" ? "darwin_arm64" : "darwin_x86_64";
+  }
   throw new Error(`Unsupported platform for HiCT Tauri browser payload: ${process.platform}`);
 }
 
@@ -171,14 +179,19 @@ function ensureTauriConventionalIcons() {
   const iconsDir = resolve(tauriDir, "icons");
   const pngPath = resolve(iconsDir, "icon.png");
   const icoPath = resolve(iconsDir, "icon.ico");
+  const sourcePngPath = resolve(repoDir, "public", "hict-logo-512.png");
   const faviconPath = resolve(repoDir, "public", "favicon.ico");
-  const pngBuffer = Buffer.from(generatedIconPngBase64, "base64");
 
   mkdirSync(iconsDir, { recursive: true });
-  writeFileSync(pngPath, pngBuffer);
+  if (existsSync(sourcePngPath)) {
+    cpSync(sourcePngPath, pngPath);
+  } else {
+    writeFileSync(pngPath, Buffer.from(generatedIconPngBase64, "base64"));
+  }
   if (existsSync(faviconPath)) {
     cpSync(faviconPath, icoPath);
   } else {
+    const pngBuffer = readFileSync(pngPath);
     writeFileSync(icoPath, icoBufferFromPng(pngBuffer));
   }
 }

diff --git a/src/ContigMouseWheelZoom.js b/src/ContigMouseWheelZoom.js
@@ -119,6 +119,7 @@ export default class ContigMouseWheelZoom extends MouseWheelZoom {
 
     if (this.useAnchor_) {
       this.lastMouseCoord = mapBrowserEvent.coordinate;
+      this.lastAnchor_ = mapBrowserEvent.coordinate;
       this.lastMousePixel = mapBrowserEvent.pixel;
       this.lastCenterPixel = [
         Math.round(map.getSize()[0] / 2),
@@ -293,22 +294,12 @@ export default class ContigMouseWheelZoom extends MouseWheelZoom {
     } catch (error) {
       console.warn("Unable to derive zoom target guidance resolution", error);
     }
-    const guidanceResolutionChanged =
-      oldGuidanceDescriptor &&
-      newGuidanceDescriptor &&
-      (oldGuidanceDescriptor.bpResolution !==
-        newGuidanceDescriptor.bpResolution ||
-        oldGuidanceDescriptor.pixelResolution !==
-          newGuidanceDescriptor.pixelResolution ||
-        oldGuidanceDescriptor.sourceName !== newGuidanceDescriptor.sourceName);
-
     if (
       this.lastMouseBps &&
       this.lastCenterPixel &&
       this.lastMousePixel &&
       this.lastMouseCoord &&
-      !isNaN(this.lastMouseCoord[0]) &&
-      guidanceResolutionChanged
+      !isNaN(this.lastMouseCoord[0])
     ) {
       if (newGuidanceDescriptor) {
         const dimensionHolder = this.getDimensionHolderForDescriptor(

diff --git a/src/app/core/net/api/RequestManager.ts b/src/app/core/net/api/RequestManager.ts
@@ -77,11 +77,13 @@ import {
   StartConversionJobRequest,
   StartDotplotJobsRequest,
   ListDotplotJobsRequest,
+  StopDotplotJobRequest,
   ListConversionJobsRequest,
   GetConversionJobRequest,
   GetConversionToolchainStatusRequest,
   SetDotplotAlignerPreferenceRequest,
   ConvertAssemblyToAgpRequest,
+  ApplyJuiceboxAssemblyRequest,
   StopConversionJobRequest,
   RenameContigRequest,
   RenameScaffoldRequest,
@@ -913,6 +915,14 @@ class RequestManager {
     );
   }
 
+  public async stopDotplotJob(
+    jobId: string
+  ): Promise<{ status: string; jobId: string }> {
+    return this.sendRequest(new StopDotplotJobRequest(jobId)).then(
+      (response) => response.data
+    );
+  }
+
   public async listConversionJobs(): Promise<ConversionJobResponse[]> {
     return this.sendRequest(new ListConversionJobsRequest()).then((response) =>
       (response.data as Record<string, unknown>[]).map((job) =>
@@ -1094,6 +1104,25 @@ class RequestManager {
       });
   }
 
+  public async applyJuiceboxAssembly(request: ApplyJuiceboxAssemblyRequest): Promise<AssemblyInfo> {
+    return this.sendRequest(request)
+      .then((response) => response.data)
+      .then((json) => new AssemblyInfoDTO(json).toEntity())
+      .then((asmInfo) => {
+        this.networkManager.mapManager?.contigDimensionHolder.updateContigData(
+          asmInfo.contigDescriptors
+        );
+        this.networkManager.mapManager?.scaffoldHolder.updateScaffoldData(
+          asmInfo.scaffoldDescriptors
+        );
+        this.networkManager.mapManager?.reloadVisuals();
+        return asmInfo;
+      })
+      .catch((err) => {
+        throw new Error("Cannot apply Juicebox assembly: " + err);
+      });
+  }
+
   public async getFASTAForAssembly(
     request: GetFastaForAssemblyRequest
   ): Promise<unknown> {

diff --git a/src/app/core/net/api/request.ts b/src/app/core/net/api/request.ts
@@ -285,6 +285,13 @@ class ListDotplotJobsRequest implements HiCTAPIRequest {
   requestPath = "/dotplot/jobs/list";
 }
 
+class StopDotplotJobRequest implements HiCTAPIRequest {
+  public requestPath: string;
+  public constructor(public readonly jobId: string) {
+    this.requestPath = `/dotplot/jobs/${jobId}/stop`;
+  }
+}
+
 class SetContrastRangeRequest implements HiCTAPIRequest {
   requestPath = "/set_contrast_range";
 
@@ -403,6 +410,18 @@ class LoadAGPRequest implements HiCTAPIRequest {
   ) {}
 }
 
+class ApplyJuiceboxAssemblyRequest implements HiCTAPIRequest {
+  requestPath = "/apply_juicebox_assembly";
+
+  public constructor(
+    public readonly options: {
+      readonly assemblyFilename: string;
+      readonly fastaFilename?: string;
+      readonly source?: "PRIMARY" | "SECONDARY";
+    }
+  ) {}
+}
+
 class OpenProgressRequest implements HiCTAPIRequest {
   requestPath = "/open_progress";
   public constructor() {}
@@ -690,6 +709,7 @@ export {
   SetDotplotAlignerPreferenceRequest,
   StartDotplotJobsRequest,
   ListDotplotJobsRequest,
+  StopDotplotJobRequest,
   RenameContigRequest,
   RenameScaffoldRequest,
   ExportNameMappingRequest,
@@ -708,6 +728,7 @@ export {
   MoveSelectionRangeRequest,
   ListAGPFilesRequest,
   LoadAGPRequest,
+  ApplyJuiceboxAssemblyRequest,
   OpenProgressRequest,
   OpenSecondarySourceRequest,
   CloseSecondarySourceRequest,

diff --git a/src/app/core/net/dto/requestDTO.ts b/src/app/core/net/dto/requestDTO.ts
@@ -35,6 +35,7 @@ import {
   MoveSelectionRangeRequest,
   ListAGPFilesRequest,
   LoadAGPRequest,
+  ApplyJuiceboxAssemblyRequest,
   OpenProgressRequest,
   OpenSecondarySourceRequest,
   CloseSecondarySourceRequest,
@@ -76,6 +77,7 @@ import {
   SetDotplotAlignerPreferenceRequest,
   ConvertAssemblyToAgpRequest,
   ListDotplotJobsRequest,
+  StopDotplotJobRequest,
   ListConversionJobsRequest,
   GetConversionJobRequest,
   StopConversionJobRequest,
@@ -144,6 +146,8 @@ abstract class HiCTAPIRequestDTO<
         );
       case entity instanceof ListDotplotJobsRequest:
         return new ListDotplotJobsRequestDTO(entity as ListDotplotJobsRequest);
+      case entity instanceof StopDotplotJobRequest:
+        return new StopDotplotJobRequestDTO(entity as StopDotplotJobRequest);
       case entity instanceof UngroupContigsFromScaffoldRequest:
         return new UngroupContigsFromScaffoldRequestDTO(
           entity as UngroupContigsFromScaffoldRequest
@@ -240,6 +244,10 @@ abstract class HiCTAPIRequestDTO<
         return new ListAGPFilesRequestDTO(entity);
       case entity instanceof LoadAGPRequest:
         return new LoadAGPRequestDTO(entity as LoadAGPRequest);
+      case entity instanceof ApplyJuiceboxAssemblyRequest:
+        return new ApplyJuiceboxAssemblyRequestDTO(
+          entity as ApplyJuiceboxAssemblyRequest
+        );
       case entity instanceof OpenProgressRequest:
         return new OpenProgressRequestDTO(entity);
       case entity instanceof OpenSecondarySourceRequest:
@@ -569,6 +577,12 @@ class ListDotplotJobsRequestDTO extends HiCTAPIRequestDTO<ListDotplotJobsRequest
   }
 }
 
+class StopDotplotJobRequestDTO extends HiCTAPIRequestDTO<StopDotplotJobRequest> {
+  toDTO(): Record<string, unknown> {
+    return {};
+  }
+}
+
 class ListConversionJobsRequestDTO extends HiCTAPIRequestDTO<ListConversionJobsRequest> {
   toDTO(): Record<string, unknown> {
     return {};
@@ -680,6 +694,16 @@ class LoadAGPRequestDTO extends HiCTAPIRequestDTO<LoadAGPRequest> {
   }
 }
 
+class ApplyJuiceboxAssemblyRequestDTO extends HiCTAPIRequestDTO<ApplyJuiceboxAssemblyRequest> {
+  toDTO(): Record<string, unknown> {
+    return {
+      assemblyFilename: this.entity.options.assemblyFilename,
+      fastaFilename: this.entity.options.fastaFilename,
+      source: this.entity.options.source,
+    };
+  }
+}
+
 class GroupContigsIntoScaffoldRequestDTO extends HiCTAPIRequestDTO<GroupContigsIntoScaffoldRequest> {
   toDTO(): Record<string, unknown> {
     return {
@@ -1005,6 +1029,7 @@ export {
   StartDotplotJobsRequestDTO,
   SetDotplotAlignerPreferenceRequestDTO,
   ListDotplotJobsRequestDTO,
+  StopDotplotJobRequestDTO,
   ListConversionJobsRequestDTO,
   GetConversionJobRequestDTO,
   StopConversionJobRequestDTO,