Bugfixes

Author: cmdcolin

eslint.config.mjs

@@ -13,7 +13,9 @@ export default tseslint.config(
       'example/*',
       'eslint.config.mjs',
       'esbuild.mjs',
+      'vitest.config.ts',
       'benchmarks/*',
+      'test/*',
     ],
   },
   {

src/BigMafAdapter/BigMafAdapter.ts

@@ -36,12 +36,12 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
   }
 
   async getRefNames() {
-    const { adapter } = await this.setup()
+    const { adapter } = await this.setupPre()
     return adapter.getRefNames()
   }
 
   async getHeader() {
-    const { adapter } = await this.setup()
+    const { adapter } = await this.setupPre()
     return adapter.getHeader()
   }
 

src/LinearMafDisplay/components/useDragSelection.ts

@@ -107,12 +107,15 @@ export function useDragSelection(
         const dragDistanceX = Math.abs(dragEndX - dragStartX)
 
         if (dragDistanceX > MIN_DRAG_DISTANCE) {
+          const rect = ref.current?.getBoundingClientRect()
+          const left = rect?.left || 0
+          const top = rect?.top || 0
           setContextCoord({
             coord: [event.clientX, event.clientY],
-            dragEndX: event.clientX,
+            dragEndX: event.clientX - left,
             dragStartX: dragStartX,
             dragStartY: dragStartY,
-            dragEndY: dragEndY,
+            dragEndY: event.clientY - top,
           })
           setShowSelectionBox(true)
         } else {
@@ -121,7 +124,7 @@ export function useDragSelection(
       }
       setIsDragging(false)
     },
-    [isDragging, dragStartX, dragEndX, dragStartY, dragEndY, clearSelectionBox],
+    [ref, isDragging, dragStartX, dragEndX, dragStartY, dragEndY, clearSelectionBox],
   )
 
   const handleMouseLeave = useCallback(() => {

src/MafAddTrackWorkflow/AddTrackWorkflow.tsx

@@ -96,7 +96,7 @@ export default function MultiMAFWidget({ model }: { model: AddTrackModel }) {
             <FormControl>
               <FormLabel>Index type</FormLabel>
               <RadioGroup
-                value={fileTypeChoice}
+                value={indexTypeChoice}
                 onChange={event => {
                   setIndexTypeChoice(event.target.value as IndexTypeOptions)
                 }}

src/MafSequenceWidget/MafSequenceWidget.tsx

@@ -104,9 +104,13 @@ const MafSequenceWidget = observer(function MafSequenceWidget({
 
         let formatted: string
         if (singleLineFormat) {
-          const maxLabelLength = Math.max(
-            ...samples.map(s => (s.label ?? s.id).length),
-          )
+          let maxLabelLength = 0
+          for (const s of samples) {
+            const len = (s.label ?? s.id).length
+            if (len > maxLabelLength) {
+              maxLabelLength = len
+            }
+          }
           formatted = fastaSequence
             .map((r, idx) => {
               const sample = samples[idx]!

src/parseNewick.ts

@@ -81,7 +81,7 @@ export default function parseNewick(s: string) {
       case ':': // optional length next
         break
       default: {
-        const x = tokens[i - 1]!
+        const x = i > 0 ? tokens[i - 1] : undefined
         if (x === ')' || x === '(' || x === ',') {
           tree.name = token
         } else if (x === ':') {

src/util/__snapshots__/fastaUtils.test.ts.snap

@@ -16,7 +16,7 @@ exports[`includeInsertions - insertions at multiple positions 1`] = `
 
 exports[`includeInsertions - insertions in multiple samples with different lengths 1`] = `
 [
-  "ac-t-gtac",
+  "act--gtac",
   "actttgtac",
 ]
 `;

src/util/extractSubsequence.test.ts

@@ -50,5 +50,5 @@ test('handles a sequence with mixed characters and gaps', () => {
 
   // Positions 2-5 would be G,T,A after skipping gaps
   expect(extractedSequence).toBe('GT--A')
-  expect(actualStart).toBe(5)
+  expect(actualStart).toBe(4)
 })

src/util/extractSubsequence.ts

@@ -1,25 +1,15 @@
-/**
- * Helper function to extract a subsequence from an alignment string
- * accounting for gaps in the reference sequence
- * @param sequence - The alignment sequence
- * @param relativeStart - The start position in the reference sequence (without gaps)
- * @param relativeEnd - The end position in the reference sequence (without gaps)
- * @returns The extracted sequence and the actual start position in the alignment
- */
 export function extractSubsequence(
   sequence: string,
   relativeStart: number,
   relativeEnd: number,
 ): { extractedSequence: string; actualStart: number } {
-  // Handle sequence with only gaps
   if (sequence.split('').every(char => char === '-')) {
     return {
       extractedSequence: sequence,
       actualStart: 0,
     }
   }
 
-  // Create a mapping from non-gap positions to actual positions in the sequence
   const nonGapToActualMap: number[] = []
 
   let nonGapCount = 0
@@ -30,41 +20,21 @@ export function extractSubsequence(
     }
   }
 
-  // Handle case where there aren't enough non-gap characters
   if (nonGapCount <= relativeStart) {
     return {
       extractedSequence: sequence,
       actualStart: 0,
     }
   }
 
-  // Special cases for test compatibility
-  if (sequence === 'A--CGT--ACGT' && relativeStart === 2 && relativeEnd === 5) {
-    return {
-      extractedSequence: 'GT--A',
-      actualStart: 5,
-    }
-  }
-
-  if (sequence === 'A-CGT-ACGT' && relativeStart === 2 && relativeEnd === 6) {
-    return {
-      extractedSequence: 'GT-AC',
-      actualStart: 3,
-    }
-  }
-
-  // Find start and end indices in the original sequence
-  const startIndex =
-    nonGapToActualMap[relativeStart] !== undefined
-      ? nonGapToActualMap[relativeStart]
-      : 0
+  const startIndex = nonGapToActualMap[relativeStart] ?? 0
   let endIndex = sequence.length
 
   if (
     relativeEnd < nonGapCount &&
     nonGapToActualMap[relativeEnd] !== undefined
   ) {
-    endIndex = nonGapToActualMap[relativeEnd]
+    endIndex = nonGapToActualMap[relativeEnd]!
   }
 
   return {

src/util/fastaUtils.ts

@@ -77,18 +77,14 @@ export function processFeaturesToFasta({
           let insertionSequence = ''
           while (i < alignment.length && seq[i] === '-') {
             const alignChar = alignment[i]!
-            insertionSequence +=
-              alignChar !== '-' && alignChar !== ' '
-                ? alignChar.toLowerCase()
-                : '-'
+            if (alignChar !== '-' && alignChar !== ' ') {
+              insertionSequence += alignChar.toLowerCase()
+            }
             i++
           }
           i--
 
-          // Only add insertion if it contains at least one actual base (not
-          // just gaps). This filters out insertions that only exist in samples
-          // that aren't currently visible.
-          if (insertionSequence.length > 0 && /[^-]/.test(insertionSequence)) {
+          if (insertionSequence.length > 0) {
             const insertPos = leftCoord + o - region.start
             if (insertPos >= 0 && insertPos <= rlen) {
               const existing = insertionsAtPosition.get(insertPos) || []
@@ -150,14 +146,15 @@ function expandWithInsertions(
       const insertionSeq = sampleInsertions.get(sampleIdx)
 
       if (insertionSeq) {
-        // This sample has an insertion - add it, padded with gaps if needed
         const paddedInsertion = insertionSeq.padEnd(maxLen, '-')
-        // Insert after position `pos`
-        rowArray.splice(pos, 0, ...paddedInsertion.split(''))
+        const chars = paddedInsertion.split('')
+        for (let k = chars.length - 1; k >= 0; k--) {
+          rowArray.splice(pos, 0, chars[k]!)
+        }
       } else {
-        // No insertion for this sample - fill with gaps
-        const gaps = new Array(maxLen).fill('-')
-        rowArray.splice(pos, 0, ...gaps)
+        for (let k = 0; k < maxLen; k++) {
+          rowArray.splice(pos, 0, '-')
+        }
       }
     }
   }