From 830c0a7586bca1ed77e4aa04feae213a91a1b01d Mon Sep 17 00:00:00 2001
From: = <=>
Date: Thu, 2 Oct 2025 21:56:39 +0000
Subject: [PATCH] update wfa.js, reduce clobbering of global namespaces

---
 index.html |  10 ++---
 main.go    |   4 +-
 wfa.js     | 107 +++++++++++++++++++++++++++++++----------------------
 3 files changed, 70 insertions(+), 51 deletions(-)
diff --git a/index.html b/index.html
index 0c2d337..cf240f3 100644
--- a/index.html
+++ b/index.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
 <html>
     <head>
-        <script src="dist/wfa.js" type="module"></script>
+        <script src="wfa.js" type="module"></script>
         <script type="module">
-            import wfaInit from "./dist/wfa.js";
+            import wfaInit from "./wfa.js";
+            wfaInit("dist/wfa.wasm");
             window.addEventListener("DOMContentLoaded", () => {
-                wfaInit("dist/wfa.wasm");
                 document.querySelector("#submit").addEventListener("click", () => {
                     a = document.querySelector("#a").value
                     b = document.querySelector("#b").value
@@ -15,8 +15,8 @@
                         o: 0,
                         e: 1
                     };
-                    const { score, CIGAR } = global.wfAlign(a, b, penalties, true);
-                    const alignment = global.DecodeCIGAR(CIGAR);
+                    const { score, CIGAR } = global.wfa.wfAlign(a, b, penalties, true);
+                    const alignment = global.wfa.DecodeCIGAR(CIGAR);
                     document.querySelector("#result").innerText = `${score}, ${CIGAR}, ${alignment}`;
                 })
             });            
diff --git a/main.go b/main.go
index 94d62e2..2771326 100644
--- a/main.go
+++ b/main.go
@@ -7,8 +7,8 @@ import (
 
 func main() {
 	c := make(chan bool)
-	js.Global().Set("wfAlign", js.FuncOf(wfAlign))
-	js.Global().Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR))
+	js.Global().Get("wfa").Set("wfAlign", js.FuncOf(wfAlign))
+	js.Global().Get("wfa").Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR))
 	<-c
 }
 
diff --git a/wfa.js b/wfa.js
index d785298..f99b95d 100644
--- a/wfa.js
+++ b/wfa.js
@@ -1,5 +1,3 @@
-// wasm_exec.js from tinygo
-
 // Copyright 2018 The Go Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style
 // license that can be found in the LICENSE file.
@@ -134,6 +132,7 @@
 	const decoder = new TextDecoder("utf-8");
 	let reinterpretBuf = new DataView(new ArrayBuffer(8));
 	var logLine = [];
+	const wasmExit = {}; // thrown to exit via proc_exit (not an error)
 
 	global.Go = class {
 		constructor() {
@@ -272,14 +271,11 @@
 					fd_close: () => 0,      // dummy
 					fd_fdstat_get: () => 0, // dummy
 					fd_seek: () => 0,       // dummy
-					"proc_exit": (code) => {
-						if (global.process) {
-							// Node.js
-							process.exit(code);
-						} else {
-							// Can't exit in a browser.
-							throw 'trying to exit with code ' + code;
-						}
+					proc_exit: (code) => {
+						this.exited = true;
+						this.exitCode = code;
+						this._resolveExitPromise();
+						throw wasmExit;
 					},
 					random_get: (bufPtr, bufLen) => {
 						crypto.getRandomValues(loadSlice(bufPtr, bufLen));
@@ -287,31 +283,45 @@
 					},
 				},
 				gojs: {
-					// func ticks() float64
+					// func ticks() int64
 					"runtime.ticks": () => {
-						return timeOrigin + performance.now();
+						return BigInt((timeOrigin + performance.now()) * 1e6);
 					},
 
-					// func sleepTicks(timeout float64)
+					// func sleepTicks(timeout int64)
 					"runtime.sleepTicks": (timeout) => {
 						// Do not sleep, only reactivate scheduler after the given timeout.
-						setTimeout(this._inst.exports.go_scheduler, timeout);
+						setTimeout(() => {
+							if (this.exited) return;
+							try {
+								this._inst.exports.go_scheduler();
+							} catch (e) {
+								if (e !== wasmExit) throw e;
+							}
+						}, Number(timeout)/1e6);
 					},
 
 					// func finalizeRef(v ref)
 					"syscall/js.finalizeRef": (v_ref) => {
-						const id = mem().getUint32(unboxValue(v_ref), true);
-						this._goRefCounts[id]--;
-						if (this._goRefCounts[id] === 0) {
-							const v = this._values[id];
-							this._values[id] = null;
-							this._ids.delete(v);
-							this._idPool.push(id);
+						// Note: TinyGo does not support finalizers so this is only called
+						// for one specific case, by js.go:jsString. and can/might leak memory.
+						const id = v_ref & 0xffffffffn;
+						if (this._goRefCounts?.[id] !== undefined) {
+							this._goRefCounts[id]--;
+							if (this._goRefCounts[id] === 0) {
+								const v = this._values[id];
+								this._values[id] = null;
+								this._ids.delete(v);
+								this._idPool.push(id);
+							}
+						} else {
+							console.error("syscall/js.finalizeRef: unknown id", id);
 						}
 					},
 
 					// func stringVal(value string) ref
 					"syscall/js.stringVal": (value_ptr, value_len) => {
+						value_ptr >>>= 0;
 						const s = loadString(value_ptr, value_len);
 						return boxValue(s);
 					},
@@ -472,21 +482,25 @@
 			this._ids = new Map();  // mapping from JS values to reference ids
 			this._idPool = [];      // unused ids that have been garbage collected
 			this.exited = false;    // whether the Go program has exited
+			this.exitCode = 0;
 
-			while (true) {
-				const callbackPromise = new Promise((resolve) => {
-					this._resolveCallbackPromise = () => {
-						if (this.exited) {
-							throw new Error("bad callback: Go program has already exited");
-						}
-						setTimeout(resolve, 0); // make sure it is asynchronous
-					};
+			if (this._inst.exports._start) {
+				let exitPromise = new Promise((resolve, reject) => {
+					this._resolveExitPromise = resolve;
 				});
-				this._inst.exports._start();
-				if (this.exited) {
-					break;
+
+				// Run program, but catch the wasmExit exception that's thrown
+				// to return back here.
+				try {
+					this._inst.exports._start();
+				} catch (e) {
+					if (e !== wasmExit) throw e;
 				}
-				await callbackPromise;
+
+				await exitPromise;
+				return this.exitCode;
+			} else {
+				this._inst.exports._initialize();
 			}
 		}
 
@@ -494,7 +508,11 @@
 			if (this.exited) {
 				throw new Error("Go program has already exited");
 			}
-			this._inst.exports.resume();
+			try {
+				this._inst.exports.resume();
+			} catch (e) {
+				if (e !== wasmExit) throw e;
+			}
 			if (this.exited) {
 				this._resolveExitPromise();
 			}
@@ -524,8 +542,9 @@
 		}
 
 		const go = new Go();
-		WebAssembly.instantiate(fs.readFileSync(process.argv[2]), go.importObject).then((result) => {
-			return go.run(result.instance);
+		WebAssembly.instantiate(fs.readFileSync(process.argv[2]), go.importObject).then(async (result) => {
+			let exitCode = await go.run(result.instance);
+			process.exit(exitCode);
 		}).catch((err) => {
 			console.error(err);
 			process.exit(1);
@@ -537,22 +556,22 @@
 export default function init (path) {
 	return new Promise ((res) => {
 		const go = new Go();
-		var wasm;
-		
+		const run = (obj) => {
+			const wasm = obj.instance;
+			global.wfa = wasm
+			go.run(wasm);
+			res()
+		}
 		if ('instantiateStreaming' in WebAssembly) {
 			WebAssembly.instantiateStreaming(fetch(path), go.importObject).then(function (obj) {
-				wasm = obj.instance;
-				go.run(wasm);
-				res()
+				run(obj)				
 			})
 		} else {
 			fetch(path).then(resp =>
 				resp.arrayBuffer()
 			).then(bytes =>
 				WebAssembly.instantiate(bytes, go.importObject).then(function (obj) {
-					wasm = obj.instance;
-					go.run(wasm);
-					res()
+					run(obj)	
 				})
 			)
 		}
