react-msaview 5.10.0 → 6.0.0

package/src/rowCoordinateCalculations.ts

@@ -18,6 +18,25 @@ import { isBlank } from './util.ts'
  *    Each row can have different seqPos values for the same globalCol due to gaps.
  */
 
+/**
+ * Index of the first element in `[0, len)` for which `pred` holds, over a range
+ * where `pred` is false up to some point and true from there on. Both
+ * conversions below are that shape, since `blanks` is sorted ascending.
+ */
+function partitionPoint(len: number, pred: (i: number) => boolean) {
+  let left = 0
+  let right = len
+  while (left < right) {
+    const mid = (left + right) >>> 1
+    if (pred(mid)) {
+      right = mid
+    } else {
+      left = mid + 1
+    }
+  }
+  return left
+}
+
 /**
  * Convert a visible column index to a global column index.
  * This is used when translating mouse/screen coordinates to MSA coordinates.
@@ -27,32 +46,12 @@ import { isBlank } from './util.ts'
  * @returns The corresponding global column index in the full MSA
  */
 export function visibleColToGlobalCol(blanks: number[], visibleCol: number) {
-  let currentVisibleCol = 0
-  let blankArrayIndex = 0
-  let globalCol = 0
-  const blanksLen = blanks.length
-
-  // Skip any leading blank columns (blanks at the very beginning)
-  while (blankArrayIndex < blanksLen && blanks[blankArrayIndex] === globalCol) {
-    blankArrayIndex++
-    globalCol++
-  }
-
-  while (currentVisibleCol < visibleCol) {
-    currentVisibleCol++
-    globalCol++
-
-    // Skip any blank columns after incrementing
-    while (
-      blankArrayIndex < blanksLen &&
-      blanks[blankArrayIndex] === globalCol
-    ) {
-      blankArrayIndex++
-      globalCol++
-    }
-  }
-
-  return globalCol
+  // `blanks[i] - i` counts the visible columns before the i-th blank, so the
+  // first blank with more than visibleCol of them in front of it is the first
+  // one sitting past this column. Its index is how many blanks shift it right.
+  return (
+    visibleCol + partitionPoint(blanks.length, i => blanks[i]! - i > visibleCol)
+  )
 }
 
 /**
@@ -67,25 +66,30 @@ export function globalColToVisibleCol(
   blanks: number[],
   globalCol: number,
 ): number | undefined {
-  // Check if this column is hidden
-  // Use binary search since blanks is sorted
-  let left = 0
-  let right = blanks.length - 1
-  while (left <= right) {
-    const mid = Math.floor((left + right) / 2)
-    if (blanks[mid] === globalCol) {
-      return undefined // Column is hidden
-    }
-    if (blanks[mid]! < globalCol) {
-      left = mid + 1
-    } else {
-      right = mid - 1
-    }
-  }
+  const blanksBefore = countBlanksBefore(blanks, globalCol)
+  return blanks[blanksBefore] === globalCol
+    ? undefined // Column is hidden
+    : globalCol - blanksBefore
+}
 
-  // Count blanks before this column (left is now the insertion point)
-  const blanksBefore = left
-  return globalCol - blanksBefore
+function countBlanksBefore(blanks: number[], globalCol: number) {
+  return partitionPoint(blanks.length, i => blanks[i]! >= globalCol)
+}
+
+/**
+ * How many visible columns come before a global column. For a visible column
+ * that is its own visible index; for a hidden one it is the index of the next
+ * visible column, i.e. where the hidden column collapses to.
+ *
+ * That total answer is what spans want: resolving both ends of a span through
+ * globalColToVisibleCol instead loses the whole span whenever either end lands
+ * in a hidden column.
+ *
+ * @param blanks - Sorted array of global column indices that are hidden
+ * @param globalCol - The global column index in the full MSA
+ */
+export function visibleColsBefore(blanks: number[], globalCol: number) {
+  return globalCol - countBlanksBefore(blanks, globalCol)
 }
 
 /**

package/src/types.ts

@@ -1,3 +1,5 @@
+import type { Annotation } from 'msa-parsers'
+
 export interface Accession {
   accession: string
   name: string
@@ -26,24 +28,17 @@ export interface BasicTrack {
   model: TextTrackModel & BarTrackModel
 }
 
-// one InterProScan/GFF annotation location flattened onto a single row, as
-// produced by the model's tidyInterProAnnotations
-export interface TidyDomainAnnotation {
-  id: string
-  name: string
-  accession: string
-  description: string
-  featureType?: string
-  start: number
-  end: number
-  strand?: number
-}
+// the overlay annotation itself lives in msa-parsers, alongside the adapters
+// that build it. TidyDomainAnnotation is its former name, kept because
+// downstream plugins name it in their emitted declarations.
+export type { Annotation }
+export type TidyDomainAnnotation = Annotation
 
-// a tidy annotation resolved to the visible column span it is drawn across.
-// stackIndex is its position within its row's annotation list, which the
+// an annotation resolved to the visible column span it is drawn across.
+// stackIndex is its position among the bands its row actually draws, which the
 // sub-row layout uses to stack boxes.
 export interface DomainBand {
-  annotation: TidyDomainAnnotation
+  annotation: Annotation
   startCol: number
   endCol: number
   stackIndex: number

package/src/version.ts

@@ -1 +1 @@
-export const version = '5.10.0'
+export const version = '6.0.0'

package/src/viewChrome.test.tsx

@@ -0,0 +1,134 @@
+// @vitest-environment jsdom
+//
+// The chrome around the alignment -- the tree/height resize handles, the
+// minimap and the vertical scrollbar -- is all built from the same
+// mousedown-then-drag hook, and none of it is exercised by the render tests.
+// This mounts the real view and drives one handle of each kind.
+import React, { act } from 'react'
+
+import { createRoot } from 'react-dom/client'
+import { afterEach, beforeAll, beforeEach, expect, test } from 'vitest'
+
+import MSAView from './components/Loading.tsx'
+import MSAModelF from './model.ts'
+
+import type { MsaViewModel } from './model.ts'
+import type { Root } from 'react-dom/client'
+
+Reflect.set(globalThis, 'IS_REACT_ACT_ENVIRONMENT', true)
+
+beforeAll(() => {
+  HTMLCanvasElement.prototype.getContext = function (this: HTMLCanvasElement) {
+    return {
+      canvas: this,
+      font: '12px sans-serif',
+      measureText: (t: string) => ({ width: t.length * 7 }),
+      arc() {},
+      beginPath() {},
+      clearRect() {},
+      closePath() {},
+      fill() {},
+      fillRect() {},
+      fillText() {},
+      lineTo() {},
+      moveTo() {},
+      resetTransform() {},
+      scale() {},
+      setLineDash() {},
+      stroke() {},
+      strokeRect() {},
+      translate() {},
+    } as unknown as CanvasRenderingContext2D
+  } as unknown as typeof HTMLCanvasElement.prototype.getContext
+})
+
+// tall and wide enough that both scrollbars are on screen
+const names = Array.from({ length: 20 }, (_, i) => `seq${i}`)
+const msa = names.map(name => `>${name}\n${'ACGT'.repeat(25)}`).join('\n')
+const tree = `(${names.map(n => `${n}:0.1`).join(',')});`
+
+let container: HTMLDivElement
+let root: Root
+let model: MsaViewModel
+
+beforeEach(() => {
+  container = document.createElement('div')
+  document.body.append(container)
+  root = createRoot(container)
+  model = MSAModelF().create({
+    type: 'MsaView',
+    msaFormat: 'fasta',
+    height: 200,
+    data: { msa, tree },
+  })
+  model.setWidth(800)
+  act(() => {
+    root.render(<MSAView model={model} />)
+  })
+})
+
+afterEach(() => {
+  act(() => {
+    root.unmount()
+  })
+  container.remove()
+})
+
+function byCursor(cursor: string) {
+  return [...container.querySelectorAll<HTMLElement>('div')].filter(
+    el => el.style.cursor === cursor,
+  )
+}
+
+// useDragScroll defers each move to an animation frame, so a drag needs one
+// flushed frame before the model has moved
+async function drag(el: HTMLElement, { x = 0, y = 0 }) {
+  await act(async () => {
+    el.dispatchEvent(
+      new MouseEvent('mousedown', { bubbles: true, clientX: 0, clientY: 0 }),
+    )
+  })
+  await act(async () => {
+    document.dispatchEvent(
+      new MouseEvent('mousemove', { bubbles: true, clientX: x, clientY: y }),
+    )
+    await new Promise(resolve => {
+      requestAnimationFrame(resolve)
+    })
+  })
+  await act(async () => {
+    document.dispatchEvent(new MouseEvent('mouseup', { bubbles: true }))
+  })
+}
+
+test('the view mounts with both scrollbars', () => {
+  expect(container.querySelector('[data-testid="msa_canvas"]')).toBeTruthy()
+  expect(model.showVerticalScrollbar).toBe(true)
+  expect(model.showHorizontalScrollbar).toBe(true)
+  // one horizontal divider (tree/msa), two vertical (view height, and the
+  // conservation track's own)
+  expect(byCursor('ew-resize')).toHaveLength(1)
+  expect(byCursor('ns-resize')).toHaveLength(2)
+})
+
+test('dragging the tree divider widens the tree area', async () => {
+  const before = model.treeAreaWidth
+  await drag(byCursor('ew-resize')[0]!, { x: 60 })
+  expect(model.treeAreaWidth).toBe(before + 60)
+})
+
+test('dragging the view divider grows the view', async () => {
+  const before = model.height
+  // the last ns-resize handle is the one below the whole view
+  await drag(byCursor('ns-resize').at(-1)!, { y: 50 })
+  expect(model.height).toBe(before + 50)
+})
+
+test('dragging the scrollbar thumb scrolls the alignment', async () => {
+  const thumb = container.querySelector<HTMLElement>(
+    'div[style*="cursor: pointer"]',
+  )!
+  expect(model.scrollX).toBe(0)
+  await drag(thumb, { x: 40 })
+  expect(model.scrollX).toBeLessThan(0)
+})

package/dist/components/dialogs/DomainDialog.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../../model.ts';
-export default function LaunchDomainViewDialog({ handleClose, model, }: {
-    handleClose: () => void;
-    model: MsaViewModel;
-}): React.JSX.Element;

package/dist/components/dialogs/DomainDialog.js

@@ -1,19 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { Tab, Tabs } from '@mui/material';
-import InterProScanPanel from './InterProScanDialog.js';
-import UserProvidedResultPanel from './UserProvidedDomainsDialog.js';
-export default function LaunchDomainViewDialog({ handleClose, model, }) {
-    const [choice, setChoice] = useState(0);
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", onClose: () => {
-            handleClose();
-        }, open: true },
-        React.createElement(Tabs, { value: choice, onChange: (_, val) => {
-                setChoice(val);
-            } },
-            React.createElement(Tab, { value: 0, label: "Automatic lookup" }),
-            React.createElement(Tab, { value: 1, label: "Manual" })),
-        choice === 0 ? (React.createElement(InterProScanPanel, { model: model, handleClose: handleClose })) : null,
-        choice === 1 ? (React.createElement(UserProvidedResultPanel, { model: model, handleClose: handleClose })) : null));
-}
-//# sourceMappingURL=DomainDialog.js.map

package/dist/components/dialogs/DomainDialog.js.map

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package/dist/components/dialogs/UserProvidedDomainsDialog.js.map

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package/dist/components/header/SettingsMenu.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../../model.ts';
-declare const SettingsMenu: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default SettingsMenu;

package/dist/components/header/SettingsMenu.js

@@ -1,40 +0,0 @@
-import React from 'react';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import AccountTree from '@mui/icons-material/AccountTree';
-import Palette from '@mui/icons-material/Palette';
-import Settings from '@mui/icons-material/Settings';
-import { observer } from 'mobx-react';
-import colorSchemes from '../../colorSchemes.js';
-import { msaSettingsMenuItems, treeSettingsMenuItems, } from './settingsMenuItems.js';
-const SettingsMenu = observer(function ({ model }) {
-    const { colorSchemeName } = model;
-    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, menuItems: [
-            {
-                label: 'Color scheme',
-                icon: Palette,
-                type: 'subMenu',
-                subMenu: Object.keys(colorSchemes).map(option => ({
-                    label: option,
-                    type: 'radio',
-                    checked: colorSchemeName === option,
-                    onClick: () => {
-                        model.setColorSchemeName(option);
-                    },
-                })),
-            },
-            {
-                label: 'MSA settings',
-                type: 'subMenu',
-                subMenu: msaSettingsMenuItems(model),
-            },
-            {
-                label: 'Tree settings',
-                type: 'subMenu',
-                icon: AccountTree,
-                subMenu: treeSettingsMenuItems(model),
-            },
-        ] },
-        React.createElement(Settings, null)));
-});
-export default SettingsMenu;
-//# sourceMappingURL=SettingsMenu.js.map

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package/dist/components/header/getDomainsMenu.js.map

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package/dist/components/msa/DomainLegend.js.map

@@ -1 +0,0 @@
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package/src/components/dialogs/DomainDialog.tsx

@@ -1,45 +0,0 @@
-import React, { useState } from 'react'
-
-import { Dialog } from '@jbrowse/core/ui'
-import { Tab, Tabs } from '@mui/material'
-
-import InterProScanPanel from './InterProScanDialog.tsx'
-import UserProvidedResultPanel from './UserProvidedDomainsDialog.tsx'
-
-import type { MsaViewModel } from '../../model.ts'
-
-export default function LaunchDomainViewDialog({
-  handleClose,
-  model,
-}: {
-  handleClose: () => void
-  model: MsaViewModel
-}) {
-  const [choice, setChoice] = useState(0)
-  return (
-    <Dialog
-      maxWidth="xl"
-      title="Launch protein view"
-      onClose={() => {
-        handleClose()
-      }}
-      open
-    >
-      <Tabs
-        value={choice}
-        onChange={(_, val) => {
-          setChoice(val)
-        }}
-      >
-        <Tab value={0} label="Automatic lookup" />
-        <Tab value={1} label="Manual" />
-      </Tabs>
-      {choice === 0 ? (
-        <InterProScanPanel model={model} handleClose={handleClose} />
-      ) : null}
-      {choice === 1 ? (
-        <UserProvidedResultPanel model={model} handleClose={handleClose} />
-      ) : null}
-    </Dialog>
-  )
-}

package/src/components/header/SettingsMenu.tsx

@@ -1,57 +0,0 @@
-import React from 'react'
-
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
-import AccountTree from '@mui/icons-material/AccountTree'
-import Palette from '@mui/icons-material/Palette'
-import Settings from '@mui/icons-material/Settings'
-import { observer } from 'mobx-react'
-
-import colorSchemes from '../../colorSchemes.ts'
-import {
-  msaSettingsMenuItems,
-  treeSettingsMenuItems,
-} from './settingsMenuItems.ts'
-
-import type { MsaViewModel } from '../../model.ts'
-
-const SettingsMenu = observer(function ({ model }: { model: MsaViewModel }) {
-  const { colorSchemeName } = model
-  return (
-    <CascadingMenuButton
-      closeAfterItemClick={false}
-      menuItems={[
-        {
-          label: 'Color scheme',
-          icon: Palette,
-          type: 'subMenu',
-          subMenu: Object.keys(colorSchemes).map(
-            option =>
-              ({
-                label: option,
-                type: 'radio',
-                checked: colorSchemeName === option,
-                onClick: () => {
-                  model.setColorSchemeName(option)
-                },
-              }) as const,
-          ),
-        },
-        {
-          label: 'MSA settings',
-          type: 'subMenu',
-          subMenu: msaSettingsMenuItems(model),
-        },
-        {
-          label: 'Tree settings',
-          type: 'subMenu',
-          icon: AccountTree,
-          subMenu: treeSettingsMenuItems(model),
-        },
-      ]}
-    >
-      <Settings />
-    </CascadingMenuButton>
-  )
-})
-
-export default SettingsMenu