rename maxCachesize, remove comments and refactor to simplify

examples/src/Viewer.tsx

@@ -1041,7 +1041,7 @@ class Viewer extends React.Component<InputParams, ViewerState> {
                         backgroundColor={[0, 0, 0]}
                         lockedCamera={false}
                         disableCache={false}
-                        // maxCacheLength={2000} // linked list to do test cache trimming
+                        // maxCacheSize={2000} // in bytes, 1MB = 1000000, 1GB = 1000000000
                     />
                 </div>
             </div>

src/controller/index.ts

@@ -380,7 +380,6 @@ export default class SimulariumController {
         }
 
         // start the simulation paused and get first frame
-        // linked list to do, confused here, it says "start sim paused" but this.start() sets isPaused to false
         if (this.simulator) {
             return this.start()
                 .then(() => {

src/simularium/VisData.ts

@@ -48,7 +48,6 @@ class VisData {
             new URL("../visGeometry/workers/visDataWorker", import.meta.url),
             { type: "module" }
         );
-        // linked list to do make sure event is of type CachedData
         this.webWorker.onmessage = (event) => {
             this.linkedListCache.addFrame(event.data);
         };
@@ -60,8 +59,14 @@ class VisData {
             this.setupWebWorker();
         }
         this.currentFrameNumber = -1;
+        /**
+         * if cache is not enabled only one current frame is ever stored
+         * if cache is enabled and maxSize is -1, unlimited frames are stored
+         * if cache is enabled and maxSize is set above -1, cache will be trimmed to below setting before adding frames
+         * if a maxCacheSize prop has been provided, it will override this value
+         */
         this.enableCache = true;
-        // this.maxCacheSize = 10000000; // todo define defaults / constants for different browser environments
+        // this.maxCacheSize = 10000000;
         this.maxCacheSize = -1;
         this.linkedListCache = new LinkedListCache(
             this.maxCacheSize,
@@ -140,7 +145,6 @@ class VisData {
         return frame;
     }
 
-    // linked list to do is this sufficient?
     public gotoNextFrame(): void {
         if (!this.atLatestFrame()) {
             this.currentFrameNumber += 1;
@@ -155,7 +159,7 @@ class VisData {
         this.lockedForFrame = true;
     }
 
-    public setMaxCacheLength(cacheLength: number | undefined): void {
+    public setMaxCacheSize(cacheLength: number | undefined): void {
         if (cacheLength === undefined || cacheLength < 0) {
             this.maxCacheSize = -1;
             return;
@@ -164,7 +168,6 @@ class VisData {
         this.maxCacheSize = cacheLength > 0 ? cacheLength : 1;
     }
 
-    // linked list to do make sure we are still covering all these bases when we "clear"
     public clearCache(): void {
         this.linkedListCache.clear();
         this.currentFrameNumber = -1;
@@ -223,7 +226,6 @@ class VisData {
         ) {
             this.webWorker.postMessage(visDataMsg);
         } else {
-            // to do linked list can this be more than one frame?
             const frame = parseVisDataMessage(visDataMsg);
             this.linkedListCache.addFrame(frame);
         }
@@ -232,20 +234,13 @@ class VisData {
     public parseAgentsFromFrameData(msg: VisDataMessage | ArrayBuffer): void {
         if (msg instanceof ArrayBuffer) {
             const frame = VisData.parseOneBinaryFrame(msg);
-            if (
-                // linked list to do
-                // this isn't actually the same check as before, its asking if there is agent dat awhich we maybe shuoldnt do
-                // frame.agentData.length > 0 &&
-                // this is asking if the first frame in the new data is frame 0
-                frame.frameNumber === 0
-            ) {
+            if (frame.frameNumber === 0) {
                 this.clearCache(); // new data has arrived
             }
             this.linkedListCache.addFrame(frame);
             return;
         }
 
-        // linked list to do: handle VisDataMessage properly
         this.parseAgentsFromVisDataMessage(msg);
     }
 
@@ -268,14 +263,12 @@ class VisData {
     // // for use w/ a drag-and-drop trajectory file
     // //  save a file for playback
     // // will be caught by controller.changeFile(...).catch()
-    // linked list to do confirm this is still used and working
     public cacheJSON(visDataMsg: VisDataMessage): void {
         if (!this.linkedListCache.isEmpty()) {
             throw new Error(
                 "cache not cleared before cacheing a new drag-and-drop file"
             );
         }
-        // linked list to do can this be more than one frame?
         const frame = parseVisDataMessage(visDataMsg);
         this.linkedListCache.addFrame(frame);
     }
@@ -306,7 +299,6 @@ class VisData {
     }
 
     // will be caught by controller.changeFile(...).catch()
-    // linked list to do TODO: check if this code is still used
     public checkTypeMapping(typeMappingFromFile: EncodedTypeMapping): number[] {
         if (!typeMappingFromFile) {
             throw new Error(

src/simularium/VisDataCache.ts

@@ -93,16 +93,12 @@ class LinkedListCache {
         return this.tail ? this.tail.data : null;
     }
 
-    // linked list to do check if this is working well
     public getLastFrameNumber(): number {
-        if (this.tail && this.tail.data) {
-            return this.tail.data.frameNumber;
-        }
-        return -1;
+        return this.tail?.data.frameNumber || -1;
     }
 
     public getLastFrameTime(): number {
-        return this.tail ? this.tail.data.time : -1;
+        return this.tail?.data.time || -1;
     }
 
     public addFrame(data: CachedFrame): void {
@@ -128,7 +124,7 @@ class LinkedListCache {
             this.tail = newNode;
         }
         this.numFrames++;
-        // linked list to do: trim cache if necessary
+
         this.size += data.size;
         if (this.cacheSizeLimited && this.size > this.maxSize) {
             this.trimCache();
@@ -149,7 +145,7 @@ class LinkedListCache {
             this.head = newNode;
         }
         this.numFrames++;
-        // linked list to do: trim cache if necessary
+
         this.size += data.size;
         if (this.cacheSizeLimited && this.size > this.maxSize) {
             this.trimCache();

src/simularium/VisDataParse.ts

@@ -119,7 +119,7 @@ import { FrontEndError, ErrorLevel } from "./FrontEndError";
 //     "nSubPoints",
 // ];
 const HEADER_SIZE = 3; // frameNumber, time, agentCount
-const AGENT_HEADER_SIZE = AGENT_OBJECT_KEYS.length;
+const FRAME_DATA_SIZE = AGENT_OBJECT_KEYS.length;
 
 function parseVisDataMessage(visDataMsg: VisDataMessage): CachedFrame {
     // Assuming visDataMsg.bundleData has only one frame for simplicity
@@ -136,14 +136,14 @@ function parseVisDataMessage(visDataMsg: VisDataMessage): CachedFrame {
     // Write header data
     view[0] = frame.frameNumber;
     view[1] = frame.time;
-    view[2] = frame.data.length / (AGENT_HEADER_SIZE + 1); // Estimating agent count
+    view[2] = frame.data.length / (FRAME_DATA_SIZE + 1); // Estimating agent count
 
     let writeIndex = HEADER_SIZE;
     let readIndex = 0;
 
     while (readIndex < frame.data.length) {
         // Copy agent data
-        for (let i = 0; i < AGENT_HEADER_SIZE; i++) {
+        for (let i = 0; i < FRAME_DATA_SIZE; i++) {
             view[writeIndex++] = frame.data[readIndex++];
         }
 
@@ -182,10 +182,10 @@ function calculateBufferSize(data: number[]): number {
     let index = 0;
 
     while (index < data.length) {
-        size += AGENT_HEADER_SIZE * 4; // Agent header size in bytes
-        const nSubPoints = data[index + AGENT_HEADER_SIZE - 1];
+        size += FRAME_DATA_SIZE * 4; // Agent header size in bytes
+        const nSubPoints = data[index + FRAME_DATA_SIZE - 1];
         size += nSubPoints * 4; // Subpoints size in bytes
-        index += AGENT_HEADER_SIZE + nSubPoints;
+        index += FRAME_DATA_SIZE + nSubPoints;
     }
 
     return size;

src/viewport/index.tsx

@@ -47,7 +47,7 @@ type ViewportProps = {
     onRecordedMovie?: (blob: Blob) => void; // providing this callback enables movie recording
     disableCache?: boolean;
     onFollowObjectChanged?: (agentData: AgentData) => void; // passes agent data about the followed agent to the front end
-    maxCacheLength?: number;
+    maxCacheSize?: number;
 } & Partial<DefaultProps>;
 
 const defaultProps = {
@@ -127,8 +127,8 @@ class Viewport extends React.Component<
         this.handleTimeChange = this.handleTimeChange.bind(this);
 
         this.visGeometry = new VisGeometry(loggerLevel);
-        this.props.simulariumController.visData.setMaxCacheLength(
-            this.props.maxCacheLength
+        this.props.simulariumController.visData.setMaxCacheSize(
+            this.props.maxCacheSize
         );
         this.props.simulariumController.visData.clearCache();
         this.props.simulariumController.visData.setCacheEnabled(

src/visGeometry/index.ts

@@ -1562,7 +1562,7 @@ class VisGeometry {
         for (let i = 0; i < MAX_MESHES && i < this.visAgents.length; i++) {
             this.visAgents[i].hideAndDeactivate();
         }
-        // to do this is a naming conflict
+
         let offset = AGENT_HEADER_SIZE;
         const newVisAgentInstances = new Map<number, VisAgent>();
         for (let i = 0; i < agentCount; i++) {

src/visGeometry/workers/visDataWorker.ts

@@ -1,6 +1,5 @@
 import { parseVisDataMessage } from "../../simularium/VisDataParse";
 
-//linked list to do make sure this actually works
 self.addEventListener(
     "message",
     (e: MessageEvent) => {