AI coded rolling average

Author: cmdcolin

plugins/gccontent/src/GCContentAdapter/GCContentAdapter.ts

@@ -61,8 +61,31 @@ export default class GCContentAdapter extends BaseFeatureDataAdapter {
       )
       const residues = feats[0]?.get('seq') || ''
 
-      let start = performance.now()
       await updateStatus('Calculating GC', statusCallback, () => {
+        // Initialize the first window
+        let nc = 0
+        let ng = 0
+        let len = 0
+        let start = performance.now()
+
+        // Calculate initial window
+        const startIdx = halfWindowSize
+        for (
+          let j = startIdx - halfWindowSize;
+          j < startIdx + halfWindowSize;
+          j++
+        ) {
+          const letter = residues[j]
+          if (letter === 'c' || letter === 'C') {
+            nc++
+          } else if (letter === 'g' || letter === 'G') {
+            ng++
+          }
+          if (letter !== 'N') {
+            len++
+          }
+        }
+
         for (
           let i = halfWindowSize;
           i < residues.length - halfWindowSize;
@@ -72,22 +95,52 @@ export default class GCContentAdapter extends BaseFeatureDataAdapter {
             checkStopToken(stopToken)
             start = performance.now()
           }
-          const r = isWindowSizeOneBp
-            ? residues[i]
-            : residues.slice(i - halfWindowSize, i + halfWindowSize)
-          let nc = 0
-          let ng = 0
-          let len = 0
-          for (const letter of r) {
-            if (letter === 'c' || letter === 'C') {
-              nc++
-            } else if (letter === 'g' || letter === 'G') {
-              ng++
+
+          // For windowSize === 1, just get the single character
+          if (isWindowSizeOneBp) {
+            const letter = residues[i]
+            nc = letter === 'c' || letter === 'C' ? 1 : 0
+            ng = letter === 'g' || letter === 'G' ? 1 : 0
+            len = letter !== 'N' ? 1 : 0
+          } else if (i > halfWindowSize) {
+            // Rolling window: remove characters that are no longer in window
+            // and add new characters that entered the window
+            const prevStart = i - windowDelta - halfWindowSize
+            const prevEnd = i - windowDelta + halfWindowSize
+            const currStart = i - halfWindowSize
+            const currEnd = i + halfWindowSize
+
+            // Remove old characters
+            for (let j = prevStart; j < Math.min(prevEnd, currStart); j++) {
+              if (j >= 0 && j < residues.length) {
+                const letter = residues[j]
+                if (letter === 'c' || letter === 'C') {
+                  nc--
+                } else if (letter === 'g' || letter === 'G') {
+                  ng--
+                }
+                if (letter !== 'N') {
+                  len--
+                }
+              }
             }
-            if (letter !== 'N') {
-              len++
+
+            // Add new characters
+            for (let j = Math.max(prevEnd, currStart); j < currEnd; j++) {
+              if (j >= 0 && j < residues.length) {
+                const letter = residues[j]
+                if (letter === 'c' || letter === 'C') {
+                  nc++
+                } else if (letter === 'g' || letter === 'G') {
+                  ng++
+                }
+                if (letter !== 'N') {
+                  len++
+                }
+              }
             }
           }
+
           const pos = qs
           const score =
             this.gcMode === 'content'
@@ -111,10 +164,4 @@ export default class GCContentAdapter extends BaseFeatureDataAdapter {
       observer.complete()
     })
   }
-
-  /**
-   * called to provide a hint that data tied to a certain region
-   * will not be needed for the foreseeable future and can be purged
-   * from caches, etc
-   */
 }