react-msaview 5.10.0 → 6.1.0

package/src/sequenceLogo.test.ts

@@ -0,0 +1,88 @@
+import { expect, test } from 'vitest'
+
+import { columnCountsFromColumns } from './columnCounts.ts'
+import { columnLogoStack, maxBitsFor } from './sequenceLogo.ts'
+
+const dnaBits = maxBitsFor('dna')
+const aminoBits = maxBitsFor('amino')
+
+function stackOf(column: string, maxBits = dnaBits) {
+  return columnLogoStack(columnCountsFromColumns([column]), 0, maxBits)
+}
+
+test('maxBits is log2 of the alphabet', () => {
+  expect(maxBitsFor('dna')).toBe(2)
+  expect(maxBitsFor('rna')).toBe(2)
+  expect(maxBitsFor('amino')).toBeCloseTo(4.3219, 4)
+})
+
+test('a fully conserved column is one letter at the full height', () => {
+  const stack = stackOf('AAAA')
+  expect(stack).toHaveLength(1)
+  expect(stack[0]!.letter).toBe('A')
+  expect(stack[0]!.bits).toBeCloseTo(2, 10)
+})
+
+test('an even four-way column carries no information', () => {
+  expect(stackOf('ACGT')).toEqual([])
+})
+
+test('a two-way split is half the height, shared evenly', () => {
+  const stack = stackOf('AACC')
+  expect(stack.map(s => s.letter)).toEqual(['A', 'C'])
+  // entropy 1 bit, so information content is 2 - 1 = 1, split evenly
+  expect(stack[0]!.bits).toBeCloseTo(0.5, 10)
+  expect(stack[1]!.bits).toBeCloseTo(0.5, 10)
+})
+
+test('letters are ordered ascending so the tallest draws last, on top', () => {
+  const stack = stackOf('AAAC')
+  expect(stack.map(s => s.letter)).toEqual(['C', 'A'])
+  expect(stack[0]!.bits).toBeLessThan(stack[1]!.bits)
+})
+
+test('ties break on letter so redraws are stable', () => {
+  expect(stackOf('GGCC').map(s => s.letter)).toEqual(['C', 'G'])
+  expect(stackOf('CCGG').map(s => s.letter)).toEqual(['C', 'G'])
+})
+
+test('gaps scale the stack down without skewing the frequencies', () => {
+  // 'A' is the only residue, so it takes the whole stack either way; the height
+  // is what the gaps change
+  const clean = stackOf('AAAA')
+  const gappy = stackOf('AA--')
+  expect(gappy[0]!.letter).toBe('A')
+  expect(gappy[0]!.bits).toBeCloseTo(clean[0]!.bits / 2, 10)
+})
+
+test('gaps do not make a two-residue column look like a four-way one', () => {
+  // frequencies come from the two real residues, so this is a 1-bit choice
+  // scaled by the half-gap occupancy, not a 4-way split
+  const stack = stackOf('AC--')
+  expect(stack.map(s => s.letter)).toEqual(['A', 'C'])
+  expect(stack[0]!.bits + stack[1]!.bits).toBeCloseTo(0.5, 10)
+})
+
+test('an all-gap column has no stack', () => {
+  expect(stackOf('----')).toEqual([])
+  expect(stackOf('....')).toEqual([])
+})
+
+test('the protein ceiling is higher than the nucleotide one', () => {
+  const protein = stackOf('WWWW', aminoBits)
+  expect(protein[0]!.bits).toBeCloseTo(aminoBits, 10)
+  expect(protein[0]!.bits).toBeGreaterThan(stackOf('AAAA')[0]!.bits)
+})
+
+test('stack height never exceeds the ceiling', () => {
+  const columns = ['AAAA', 'AACG', 'A-C-', 'ACGT', 'AAAT']
+  for (const column of columns) {
+    const total = stackOf(column).reduce((a, b) => a + b.bits, 0)
+    expect(total).toBeLessThanOrEqual(dnaBits + 1e-9)
+  }
+})
+
+test('a column past the end of a ragged alignment is empty, not a crash', () => {
+  const counts = columnCountsFromColumns(['AC'])
+  expect(columnLogoStack(counts, 5, dnaBits)).toEqual([])
+})

package/src/sequenceLogo.ts

@@ -0,0 +1,63 @@
+import { letterOfResidueSlot } from './columnCounts.ts'
+
+import type { ColumnCounts } from './columnCounts.ts'
+
+export interface LogoLetter {
+  letter: string
+  /** height of this letter's slice of the stack, in bits */
+  bits: number
+}
+
+/** the y-axis ceiling of a logo: the information content of a fully conserved
+ * column, log2 of the alphabet size */
+export function maxBitsFor(sequenceType: 'dna' | 'rna' | 'amino') {
+  return Math.log2(sequenceType === 'amino' ? 20 : 4)
+}
+
+/**
+ * One column of a sequence logo, tallest letter last so a caller can draw the
+ * stack bottom-up in array order.
+ *
+ * Heights follow Schneider & Stephens: the column's information content is
+ * `log2(alphabet) - H` bits, and each residue takes the share of that its own
+ * frequency earns. Frequencies come from the non-gap residues only, so a column
+ * of two residues and eight gaps is read as a two-way choice rather than a
+ * ten-way one -- otherwise every gappy column would look uninformative for the
+ * wrong reason.
+ *
+ * The whole stack is then scaled by the non-gap fraction, which plain WebLogo
+ * does not do. Here it earns its place: the track sits directly under an
+ * alignment where the gaps are visible, and a column that is 90% gap drawing a
+ * full-height stack off its one remaining pair of residues reads as a conserved
+ * site. Scaling makes stack height mean "how much this column tells you about
+ * the family", matching what the conservation track above it already plots.
+ */
+export function columnLogoStack(
+  colStats: ColumnCounts,
+  col: number,
+  maxBits: number,
+): LogoLetter[] {
+  const total = colStats.total(col)
+  const nonGapTotal = total - colStats.gapCount(col)
+  if (nonGapTotal === 0) {
+    return []
+  }
+
+  const informationContent =
+    Math.max(0, maxBits - colStats.entropy(col)) * (nonGapTotal / total)
+  if (informationContent === 0) {
+    return []
+  }
+
+  const stack: LogoLetter[] = []
+  colStats.forEachResidue(col, (slot, count) => {
+    stack.push({
+      letter: letterOfResidueSlot(slot),
+      bits: (count / nonGapTotal) * informationContent,
+    })
+  })
+  // ascending, so drawing in order stacks the tallest letter on top. Ties break
+  // on letter to keep the stack order stable between redraws.
+  stack.sort((a, b) => a.bits - b.bits || a.letter.localeCompare(b.letter))
+  return stack
+}

package/src/types.ts

@@ -1,13 +1,21 @@
+import type { Annotation } from 'msa-parsers'
+
 export interface Accession {
   accession: string
   name: string
   description: string
 }
+// which renderer draws a track's content. Every track kind draws into the same
+// per-column coordinate space, so the kind picks the draw function rather than
+// the geometry -- see drawTracks.ts, which dispatches on it.
+export type TrackKind = 'text' | 'bar' | 'logo'
+
 export interface BasicTrackModel {
   id: string
   name: string
   associatedRowName?: string
   height: number
+  kind: TrackKind
 }
 
 export interface TextTrackModel extends BasicTrackModel {
@@ -16,7 +24,7 @@ export interface TextTrackModel extends BasicTrackModel {
 }
 
 // a track that draws a per-column bar chart (conservation, property
-// conservation). `barColor` doubles as the marker that a track is a bar track.
+// conservation)
 export interface BarTrackModel extends BasicTrackModel {
   barColor?: string
 }
@@ -26,24 +34,17 @@ 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 = '6.1.0'

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/ConservationTrack.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../model.ts';
-import type { BasicTrack } from '../types.ts';
-declare const ConservationTrack: ({ model, track, }: {
-    model: MsaViewModel;
-    track: BasicTrack;
-}) => React.JSX.Element;
-export default ConservationTrack;

package/dist/components/ConservationTrack.js

@@ -1,49 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import { useCanvasAutorun } from '../useCanvasAutorun.js';
-import { ConservationTrackResizeHandle } from './ResizeHandles.js';
-import { barTrackValues, drawConservationBars, } from './tracks/renderTracksSvg.js';
-const ConservationBlock = observer(function ({ model, track, offsetX, trackHeight, }) {
-    const { blockSize, scrollX, highResScaleFactor } = model;
-    const ref = useCanvasAutorun({
-        draw: ctx => {
-            const { colWidth } = model;
-            ctx.resetTransform();
-            ctx.scale(highResScaleFactor, highResScaleFactor);
-            ctx.clearRect(0, 0, blockSize, trackHeight);
-            ctx.translate(-offsetX, 0);
-            drawConservationBars({
-                ctx,
-                values: barTrackValues(model, track.model.id),
-                color: track.model.barColor ?? 'gray',
-                colWidth,
-                trackHeight,
-                offsetX,
-                blockSize,
-            });
-        },
-        width: blockSize * highResScaleFactor,
-        height: trackHeight * highResScaleFactor,
-        deps: [model, track, offsetX, trackHeight],
-    });
-    return (React.createElement("canvas", { ref: ref, height: trackHeight * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-            position: 'absolute',
-            left: scrollX + offsetX,
-            width: blockSize,
-            height: trackHeight,
-        } }));
-});
-const ConservationTrack = observer(function ({ model, track, }) {
-    const { blocksX, msaAreaWidth } = model;
-    const trackHeight = track.model.height;
-    return (React.createElement("div", { style: {
-            position: 'relative',
-            height: trackHeight,
-            width: msaAreaWidth,
-            overflow: 'hidden',
-        } },
-        blocksX.map(bx => (React.createElement(ConservationBlock, { key: bx, model: model, track: track, offsetX: bx, trackHeight: trackHeight }))),
-        React.createElement(ConservationTrackResizeHandle, { model: model })));
-});
-export default ConservationTrack;
-//# sourceMappingURL=ConservationTrack.js.map

package/dist/components/ConservationTrack.js.map

@@ -1 +0,0 @@
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package/dist/components/TextTrack.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../model.ts';
-import type { BasicTrack } from '../types.ts';
-declare const AnnotationTrack: ({ track, model, }: {
-    track: BasicTrack;
-    model: MsaViewModel;
-}) => React.JSX.Element | null;
-export default AnnotationTrack;

package/dist/components/TextTrack.js

@@ -1,58 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import { setFontSize } from '../setFontSize.js';
-import { useCanvasAutorun } from '../useCanvasAutorun.js';
-import { useColorContrast } from '../useColorContrast.js';
-import { drawTextTrackContent } from './tracks/renderTracksSvg.js';
-const AnnotationBlock = observer(function ({ track, model, offsetX, }) {
-    const { blockSize, scrollX, colorScheme: modelColorScheme, rowHeight, highResScaleFactor, } = model;
-    const { model: { customColorScheme, data }, } = track;
-    const colorScheme = customColorScheme ?? modelColorScheme;
-    const { theme, contrastScheme } = useColorContrast(colorScheme);
-    const ref = useCanvasAutorun({
-        draw: ctx => {
-            const { bgColor, colWidth, fontSize } = model;
-            ctx.resetTransform();
-            ctx.scale(highResScaleFactor, highResScaleFactor);
-            ctx.clearRect(0, 0, blockSize, rowHeight);
-            ctx.translate(-offsetX, 0);
-            ctx.textAlign = 'center';
-            setFontSize(ctx, fontSize);
-            drawTextTrackContent({
-                ctx,
-                data,
-                colorScheme,
-                contrastScheme,
-                bgColor,
-                textColor: theme.palette.text.primary,
-                colWidth,
-                rowHeight,
-                offsetX,
-                blockSize,
-            });
-        },
-        width: blockSize * highResScaleFactor,
-        height: rowHeight * highResScaleFactor,
-        deps: [model, offsetX, theme, contrastScheme, colorScheme, data],
-    });
-    return (React.createElement("canvas", { ref: ref, height: rowHeight * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-            position: 'absolute',
-            left: scrollX + offsetX,
-            width: blockSize,
-            height: rowHeight,
-        } }));
-});
-const AnnotationTrack = observer(function ({ track, model, }) {
-    const { blocksX, msaAreaWidth, rowHeight } = model;
-    if (!track.model.data) {
-        return null;
-    }
-    return (React.createElement("div", { style: {
-            position: 'relative',
-            height: rowHeight,
-            width: msaAreaWidth,
-            overflow: 'hidden',
-        } }, blocksX.map(bx => (React.createElement(AnnotationBlock, { key: bx, track: track, model: model, offsetX: bx })))));
-});
-export default AnnotationTrack;
-//# sourceMappingURL=TextTrack.js.map

package/dist/components/TextTrack.js.map

@@ -1 +0,0 @@
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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

@@ -1 +0,0 @@
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package/dist/components/dialogs/UserProvidedDomainsDialog.js.map

@@ -1 +0,0 @@
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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

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

@@ -1 +0,0 @@
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package/dist/components/header/getDomainsMenu.js.map

@@ -1 +0,0 @@
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package/dist/components/msa/DomainLegend.js.map

@@ -1 +0,0 @@
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