react-msaview 5.0.5 → 5.0.7

package/src/components/tree/TreeCanvas.tsx

@@ -14,8 +14,8 @@ const TreeCanvas = observer(function ({ model }: { model: MsaViewModel }) {
   const mouseoverRef = useRef<HTMLCanvasElement>(null)
   const scheduled = useRef(false)
   const deltaY = useRef(0)
-  const prevY = useRef<number>(0)
-  const { treeWidth, height, blocksY, treeAreaWidth, scrollY } = model
+  const prevY = useRef(0)
+  const { treeWidth, height, blocksY, treeAreaWidth } = model
   const [mouseDragging, setMouseDragging] = useState(false)
 
   useEffect(() => {
@@ -37,71 +37,75 @@ const TreeCanvas = observer(function ({ model }: { model: MsaViewModel }) {
       event.preventDefault()
       event.stopPropagation()
     }
-    curr.addEventListener('wheel', onWheel)
+    curr.addEventListener('wheel', onWheel, { passive: false })
     return () => {
       curr.removeEventListener('wheel', onWheel)
     }
   }, [model])
 
   useEffect(() => {
-    let cleanup = () => {}
-
-    function globalMouseMove(event: MouseEvent) {
-      event.preventDefault()
-      const currY = event.clientY
-      const distanceY = currY - prevY.current
-      if (distanceY) {
-        // use rAF to make it so multiple event handlers aren't fired per-frame
-        // see
-        // https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
-        if (!scheduled.current) {
-          scheduled.current = true
-          window.requestAnimationFrame(() => {
-            model.doScrollY(distanceY)
-            scheduled.current = false
-            prevY.current = event.clientY
-          })
+    if (mouseDragging) {
+      function globalMouseMove(event: MouseEvent) {
+        event.preventDefault()
+        const currY = event.clientY
+        const distanceY = currY - prevY.current
+        if (distanceY) {
+          if (!scheduled.current) {
+            scheduled.current = true
+            window.requestAnimationFrame(() => {
+              model.doScrollY(distanceY)
+              scheduled.current = false
+              prevY.current = event.clientY
+            })
+          }
         }
       }
-    }
 
-    function globalMouseUp() {
-      prevY.current = 0
-      if (mouseDragging) {
+      function globalMouseUp() {
+        prevY.current = 0
         setMouseDragging(false)
       }
-    }
 
-    if (mouseDragging) {
       window.addEventListener('mousemove', globalMouseMove, true)
       window.addEventListener('mouseup', globalMouseUp, true)
-      cleanup = () => {
+      return () => {
         window.removeEventListener('mousemove', globalMouseMove, true)
         window.removeEventListener('mouseup', globalMouseUp, true)
       }
     }
-    return cleanup
+    return undefined
   }, [model, mouseDragging])
 
-  // Global tree mouseover effect
+  // Global tree mouseover effect. Only [model] is needed in the dependency
+  // array because autorun internally tracks all accessed observables
+  // (treeAreaWidth, height, scrollY, etc.) and re-runs when they change
   useEffect(() => {
     const ctx = mouseoverRef.current?.getContext('2d')
     return ctx
       ? autorun(() => {
           if (isAlive(model)) {
+            const {
+              relativeTo,
+              leaves,
+              rowHeight,
+              hoveredTreeNode,
+              treeAreaWidth: w,
+              height: h,
+              scrollY: sy,
+              mouseOverRowName,
+            } = model
             ctx.resetTransform()
-            ctx.clearRect(0, 0, treeAreaWidth, height)
+            ctx.clearRect(0, 0, w, h)
 
             // Highlight reference row (relativeTo) persistently
-            const { relativeTo, leaves, rowHeight, hoveredTreeNode } = model
             if (relativeTo) {
               const referenceLeaf = leaves.find(
                 leaf => leaf.data.name === relativeTo,
               )
               if (referenceLeaf) {
-                const y = referenceLeaf.x! + scrollY
+                const y = referenceLeaf.x! + sy
                 ctx.fillStyle = 'rgba(0,128,255,0.3)' // Blue highlight for reference row
-                ctx.fillRect(0, y - rowHeight / 2, treeAreaWidth, rowHeight)
+                ctx.fillRect(0, y - rowHeight / 2, w, rowHeight)
               }
             }
 
@@ -113,33 +117,31 @@ const TreeCanvas = observer(function ({ model }: { model: MsaViewModel }) {
                   leaf => leaf.data.name === descendantName,
                 )
                 if (matchingLeaf) {
-                  const y = matchingLeaf.x! + scrollY
-                  ctx.fillRect(0, y - rowHeight / 2, treeAreaWidth, rowHeight)
+                  const y = matchingLeaf.x! + sy
+                  ctx.fillRect(0, y - rowHeight / 2, w, rowHeight)
                 }
               }
             }
 
             // Highlight single tree row corresponding to MSA mouseover (if not part of multi-row hover)
-            const { mouseOverRowName } = model
             if (
               mouseOverRowName &&
               mouseOverRowName !== relativeTo &&
               !hoveredTreeNode?.descendantNames.includes(mouseOverRowName)
             ) {
-              // Find the leaf node that matches the hovered row
               const matchingLeaf = leaves.find(
                 leaf => leaf.data.name === mouseOverRowName,
               )
               if (matchingLeaf) {
-                const y = matchingLeaf.x! + scrollY
+                const y = matchingLeaf.x! + sy
                 ctx.fillStyle = 'rgba(255,165,0,0.2)' // Orange highlight for MSA sync
-                ctx.fillRect(0, y - rowHeight / 2, treeAreaWidth, rowHeight)
+                ctx.fillRect(0, y - rowHeight / 2, w, rowHeight)
               }
             }
           }
         })
       : undefined
-  }, [model, treeAreaWidth, height, scrollY])
+  }, [model])
 
   function mouseDown(event: React.MouseEvent) {
     // check if clicking a draggable element or a resize handle

package/src/components/tree/TreeCanvasBlock.tsx

@@ -4,6 +4,7 @@ import { useTheme } from '@mui/material'
 import Flatbush from 'flatbush'
 import { autorun } from 'mobx'
 import { observer } from 'mobx-react'
+import { makeStyles } from 'tss-react/mui'
 
 import TreeBranchMenu from './TreeBranchMenu.tsx'
 import TreeNodeMenu from './TreeNodeMenu.tsx'
@@ -11,6 +12,23 @@ import { padding, renderTreeCanvas } from './renderTreeCanvas.ts'
 
 import type { MsaViewModel } from '../../model.ts'
 
+const useStyles = makeStyles()(theme => ({
+  tooltip: {
+    position: 'fixed',
+    pointerEvents: 'none',
+    zIndex: 10000,
+    backgroundColor: theme.palette.grey[700],
+    color: theme.palette.common.white,
+    padding: '4px 8px',
+    borderRadius: 4,
+    fontSize: 12,
+    whiteSpace: 'nowrap',
+    maxWidth: 300,
+    overflow: 'hidden',
+    textOverflow: 'ellipsis',
+  },
+}))
+
 interface TooltipData {
   name: string
   id: string
@@ -75,6 +93,7 @@ const TreeCanvasBlock = observer(function ({
   model: MsaViewModel
   offsetY: number
 }) {
+  const { classes } = useStyles()
   const theme = useTheme()
   const ref = useRef<HTMLCanvasElement>(null)
   const clickMap = useRef(new ClickMapIndex())
@@ -82,6 +101,11 @@ const TreeCanvasBlock = observer(function ({
   const [branchMenu, setBranchMenu] = useState<TooltipData>()
   const [toggleNodeMenu, setToggleNodeMenu] = useState<TooltipData>()
   const [hoverElt, setHoverElt] = useState<ClickEntry>()
+  const [tooltipInfo, setTooltipInfo] = useState<{
+    name: string
+    x: number
+    y: number
+  }>()
 
   const { scrollY, treeAreaWidth, blockSize, highResScaleFactor } = model
 
@@ -217,6 +241,17 @@ const TreeCanvasBlock = observer(function ({
           ref.current.style.cursor = hoveredAny ? 'pointer' : 'default'
           setHoverElt(hoveredLeaf) // Only show direct hover highlight for leaf nodes
 
+          // Set tooltip info
+          if (hoveredAny) {
+            setTooltipInfo({
+              name: hoveredAny.name,
+              x: event.clientX,
+              y: event.clientY,
+            })
+          } else {
+            setTooltipInfo(undefined)
+          }
+
           // Handle tree node hover for multi-row highlighting
           if (hoveredAny) {
             model.setHoveredTreeNode(hoveredAny.id)
@@ -249,6 +284,7 @@ const TreeCanvasBlock = observer(function ({
         }}
         onMouseLeave={() => {
           setHoverElt(undefined)
+          setTooltipInfo(undefined)
           // Clear all highlighting when leaving tree area
           model.setHoveredTreeNode(undefined)
           model.setMousePos(undefined, undefined)
@@ -265,6 +301,14 @@ const TreeCanvasBlock = observer(function ({
         height={height}
         ref={mouseoverRef}
       />
+      {tooltipInfo ? (
+        <div
+          className={classes.tooltip}
+          style={{ left: tooltipInfo.x + 12, top: tooltipInfo.y + 12 }}
+        >
+          {tooltipInfo.name}
+        </div>
+      ) : null}
     </>
   )
 })

package/src/model.ts

@@ -344,6 +344,11 @@ function stateModelFactory() {
        */
       minimapHeight: 56,
 
+      /**
+       * #volatile
+       */
+      conservationTrackHeight: 40,
+
       /**
        * #volatile
        */
@@ -1546,7 +1551,7 @@ function stateModelFactory() {
           model: {
             id: 'conservation',
             name: 'Conservation',
-            height: 40,
+            height: self.conservationTrackHeight,
           },
           ReactComponent: ConservationTrack,
         }
@@ -1671,6 +1676,30 @@ function stateModelFactory() {
     }))
 
     .views(self => ({
+      /**
+       * #getter
+       * Returns information about the currently hovered cell
+       */
+      get hoveredCell() {
+        const { mouseCol, mouseRow } = self
+        if (mouseCol === undefined || mouseRow === undefined) {
+          return undefined
+        }
+        const rowName = self.rowNames[mouseRow]
+        if (!rowName) {
+          return undefined
+        }
+        const seq = self.columns[rowName]
+        const base = seq?.[mouseCol]
+        const seqPos = self.visibleColToSeqPosOneBased(rowName, mouseCol)
+        return {
+          rowName,
+          col: mouseCol,
+          base,
+          seqPos,
+        }
+      },
+
       /**
        * #getter
        * widget width minus the tree area gives the space for the MSA
@@ -1792,6 +1821,12 @@ function stateModelFactory() {
       setHeaderHeight(arg: number) {
         self.headerHeight = arg
       },
+      /**
+       * #action
+       */
+      setConservationTrackHeight(arg: number) {
+        self.conservationTrackHeight = arg
+      },
       /**
        * #action
        */

package/src/neighborJoining.test.ts

@@ -1,3 +1,4 @@
+import { parseNewick } from 'msa-parsers'
 import { describe, expect, test } from 'vitest'
 
 import { calculateNeighborJoiningTree } from './neighborJoining.ts'
@@ -80,17 +81,24 @@ describe('calculateNeighborJoiningTree', () => {
     expect(tree).toContain('seq3')
   })
 
-  test('handles special characters in sequence names', () => {
+  test('names with special characters round-trip through Newick parsing', () => {
     const rows: [string, string][] = [
-      ['seq:1', 'MKAA'],
+      ['EU105457.1|chr09:67680268..67675529_LTR/Copia', 'MKAA'],
       ['seq(2)', 'MKAA'],
     ]
-    const tree = calculateNeighborJoiningTree(rows)
+    const newick = calculateNeighborJoiningTree(rows)
+    const tree = parseNewick(newick)
 
-    expect(tree).toMatch(/;$/)
-    // Special characters should be escaped
-    expect(tree).not.toMatch(/seq:1/)
-    expect(tree).not.toMatch(/seq\(2\)/)
+    function getLeafNames(node: Record<string, unknown>): string[] {
+      const children = node.children as Record<string, unknown>[] | undefined
+      if (!children?.length) {
+        return [node.name as string]
+      }
+      return children.flatMap(c => getLeafNames(c))
+    }
+    const names = getLeafNames(tree)
+    expect(names).toContain('EU105457.1|chr09:67680268..67675529_LTR/Copia')
+    expect(names).toContain('seq(2)')
   })
 
   test('identical sequences have zero distance', () => {

package/src/neighborJoining.ts

@@ -851,11 +851,9 @@ function nodeToNewick(node: NJNode, branchLength?: number): string {
   let result: string
 
   if (node.name !== undefined && !node.left && !node.right) {
-    // Leaf node - escape special characters in name
-    const escapedName = node.name.replace(/[():,;[\]]/g, '_')
-    result = escapedName
+    const quotedName = node.name.replaceAll("'", "''")
+    result = `'${quotedName}'`
   } else {
-    // Internal node
     const leftNewick = node.left ? nodeToNewick(node.left, node.leftLength) : ''
     const rightNewick = node.right
       ? nodeToNewick(node.right, node.rightLength)

package/src/parseAsn1.test.ts

@@ -1,10 +1,10 @@
-import fs from 'fs'
+import { readFileSync } from 'node:fs'
 
 import { expect, test } from 'vitest'
 
 import { parseAsn1 } from './parseAsn1.ts'
 
-const r = fs.readFileSync(require.resolve('../test/data/tree.asn'), 'utf8')
+const r = readFileSync(new URL('../test/data/tree.asn', import.meta.url), 'utf8')
 
 test('real data file', () => {
   expect(parseAsn1(r)).toMatchSnapshot()

package/src/version.ts

@@ -1 +1 @@
-export const version = '5.0.5'
+export const version = '5.0.7'

package/dist/createPaletteMap.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/createPaletteMap.test.js

@@ -1,49 +0,0 @@
-import { expect, test } from 'vitest';
-import { createPaletteMap } from "./createPaletteMap.js";
-import palettes from "./ggplotPalettes.js";
-// Original implementation for comparison
-function originalFillPalette(keys) {
-    let i = 0;
-    const map = {};
-    for (const key of keys) {
-        const k = Math.min(keys.length - 1, palettes.length - 1);
-        map[key] = palettes[k][i];
-        i++;
-    }
-    return map;
-}
-test('createPaletteMap matches original implementation with 1 key', () => {
-    const keys = ['IPR001234'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap matches original implementation with 3 keys', () => {
-    const keys = ['IPR001234', 'IPR005678', 'IPR009012'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap matches original implementation with 8 keys (max palette size)', () => {
-    const keys = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap matches original implementation with more keys than palette colors', () => {
-    const keys = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap returns correct colors for 3 keys', () => {
-    const keys = ['X', 'Y', 'Z'];
-    const result = createPaletteMap(keys);
-    // With 3 keys, uses palette index 2 (0-indexed)
-    expect(result).toEqual({
-        X: '#F8766D',
-        Y: '#00BA38',
-        Z: '#619CFF',
-    });
-});
-test('createPaletteMap returns empty object for empty keys', () => {
-    expect(createPaletteMap([])).toEqual({});
-});
-test('createPaletteMap preserves key order', () => {
-    const keys = ['Z', 'A', 'M'];
-    const result = createPaletteMap(keys);
-    expect(Object.keys(result)).toEqual(['Z', 'A', 'M']);
-});
-//# sourceMappingURL=createPaletteMap.test.js.map

package/dist/createPaletteMap.test.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"createPaletteMap.test.js","sourceRoot":"","sources":["../src/createPaletteMap.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,QAAQ,MAAM,qBAAqB,CAAA;AAE1C,yCAAyC;AACzC,SAAS,mBAAmB,CAAC,IAAc;IACzC,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,MAAM,GAAG,GAAG,EAA4B,CAAA;IACxC,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACxD,GAAG,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,CAAA;QAC3B,CAAC,EAAE,CAAA;IACL,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,IAAI,CAAC,6DAA6D,EAAE,GAAG,EAAE;IACvE,MAAM,IAAI,GAAG,CAAC,WAAW,CAAC,CAAA;IAC1B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC,CAAA;AACnE,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,8DAA8D,EAAE,GAAG,EAAE;IACxE,MAAM,IAAI,GAAG,CAAC,WAAW,EAAE,WAAW,EAAE,WAAW,CAAC,CAAA;IACpD,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC,CAAA;AACnE,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,iFAAiF,EAAE,GAAG,EAAE;IAC3F,MAAM,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IACrD,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC,CAAA;AACnE,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,qFAAqF,EAAE,GAAG,EAAE;IAC/F,MAAM,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IAC/D,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC,CAAA;AACnE,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,oDAAoD,EAAE,GAAG,EAAE;IAC9D,MAAM,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,gDAAgD;IAChD,MAAM,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC;QACrB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,sDAAsD,EAAE,GAAG,EAAE;IAChE,MAAM,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;AAC1C,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;IAChD,MAAM,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;AACtD,CAAC,CAAC,CAAA"}

package/dist/neighborJoining.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/neighborJoining.test.js

@@ -1,110 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { calculateNeighborJoiningTree } from "./neighborJoining.js";
-describe('calculateNeighborJoiningTree', () => {
-    test('generates valid Newick tree for 2 sequences', () => {
-        const rows = [
-            ['seq1', 'MKAA'],
-            ['seq2', 'MKAA'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        expect(tree).toMatch(/;$/);
-        expect(tree).toContain('seq1');
-        expect(tree).toContain('seq2');
-    });
-    test('generates valid Newick tree for 3 sequences', () => {
-        const rows = [
-            ['human', 'MKAAYLSMFG'],
-            ['mouse', 'MKAAYLSMFG'],
-            ['chicken', 'MKAAFLSMFG'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        expect(tree).toMatch(/;$/);
-        expect(tree).toContain('human');
-        expect(tree).toContain('mouse');
-        expect(tree).toContain('chicken');
-        expect(tree).toContain('(');
-        expect(tree).toContain(')');
-    });
-    test('generates valid Newick tree for 4 sequences', () => {
-        const rows = [
-            ['A', 'MKAAYLSMFGKED'],
-            ['B', 'MKAAYLSMFGKED'],
-            ['C', 'MKAAFLSMFGKEE'],
-            ['D', 'MKAAFLSMFGKEE'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        expect(tree).toMatch(/;$/);
-        expect(tree).toContain('A');
-        expect(tree).toContain('B');
-        expect(tree).toContain('C');
-        expect(tree).toContain('D');
-    });
-    test('includes branch lengths in tree', () => {
-        const rows = [
-            ['seq1', 'MKAAYLSMFG'],
-            ['seq2', 'MKAAFLSMFG'],
-            ['seq3', 'MKBBFLSMFG'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        // Branch lengths are formatted as :0.123456
-        expect(tree).toMatch(/:\d+\.\d+/);
-    });
-    test('throws error for less than 2 sequences', () => {
-        const rows = [['seq1', 'MKAA']];
-        expect(() => calculateNeighborJoiningTree(rows)).toThrow('Need at least 2 sequences');
-    });
-    test('handles sequences with gaps', () => {
-        const rows = [
-            ['seq1', 'MK-AYLSMFG'],
-            ['seq2', 'MKAAYLSMFG'],
-            ['seq3', 'MKA-YLSMFG'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        expect(tree).toMatch(/;$/);
-        expect(tree).toContain('seq1');
-        expect(tree).toContain('seq2');
-        expect(tree).toContain('seq3');
-    });
-    test('handles special characters in sequence names', () => {
-        const rows = [
-            ['seq:1', 'MKAA'],
-            ['seq(2)', 'MKAA'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        expect(tree).toMatch(/;$/);
-        // Special characters should be escaped
-        expect(tree).not.toMatch(/seq:1/);
-        expect(tree).not.toMatch(/seq\(2\)/);
-    });
-    test('identical sequences have zero distance', () => {
-        const rows = [
-            ['seq1', 'MKAAYLSMFG'],
-            ['seq2', 'MKAAYLSMFG'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        // Identical sequences should have equal branch lengths
-        const match = tree.match(/:(\d+\.\d+)/g);
-        expect(match).not.toBeNull();
-        if (match) {
-            const lengths = match.map(m => parseFloat(m.slice(1)));
-            // Branch lengths should be small or zero for identical sequences
-            for (const len of lengths) {
-                expect(len).toBeGreaterThanOrEqual(0);
-            }
-        }
-    });
-    test('more divergent sequences have larger distances', () => {
-        const rows = [
-            ['similar1', 'MKAAYLSMFGKED'],
-            ['similar2', 'MKAAYLSMFGKED'],
-            ['different', 'WWWWWWWWWWWWW'],
-        ];
-        const tree = calculateNeighborJoiningTree(rows);
-        expect(tree).toMatch(/;$/);
-        // The tree should be valid even with very different sequences
-        expect(tree).toContain('similar1');
-        expect(tree).toContain('similar2');
-        expect(tree).toContain('different');
-    });
-});
-//# sourceMappingURL=neighborJoining.test.js.map

package/dist/neighborJoining.test.js.map

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package/dist/parseAsn1.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/parseAsn1.test.js

@@ -1,8 +0,0 @@
-import fs from 'fs';
-import { expect, test } from 'vitest';
-import { parseAsn1 } from "./parseAsn1.js";
-const r = fs.readFileSync(require.resolve('../test/data/tree.asn'), 'utf8');
-test('real data file', () => {
-    expect(parseAsn1(r)).toMatchSnapshot();
-});
-//# sourceMappingURL=parseAsn1.test.js.map

package/dist/parseAsn1.test.js.map

@@ -1 +0,0 @@
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package/dist/rowCoordinateCalculations.test.d.ts

@@ -1 +0,0 @@
-export {};