Move stuff around

cmdcolin · cmdcolin · commit d8050797e02d · 2025-06-04T21:17:53.000-04:00
diff --git a/src/LinearMafDisplay/components/GetSequenceDialog/index.tsx b/src/LinearMafDisplay/components/GetSequenceDialog/index.tsx
@@ -71,6 +71,7 @@ const SequenceDialog = observer(function ({
           {
             sessionId,
             adapterConfig: model.adapterConfig,
+            samples,
             regions: [
               {
                 refName,
@@ -79,7 +80,6 @@ const SequenceDialog = observer(function ({
                 assemblyName,
               },
             ],
-            bpPerPx: view.bpPerPx,
           },
         )
 
diff --git a/src/LinearMafDisplay/components/LinearMafDisplayComponent.tsx b/src/LinearMafDisplay/components/LinearMafDisplayComponent.tsx
@@ -6,9 +6,9 @@ import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 
 import Crosshairs from './Crosshairs'
+import SequenceDialog from './GetSequenceDialog/index'
 import MAFTooltip from './MAFTooltip'
-import SequenceDialog from './SequenceDialog/index'
-import YScaleBars from './YScaleBars'
+import YScaleBars from './Sidebar/YScaleBars'
 
 import type { LinearMafDisplayModel } from '../stateModel'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
diff --git a/src/LinearMafDisplay/components/SetRowHeightDialog/SetRowHeightDialog.tsx b/src/LinearMafDisplay/components/SetRowHeightDialog/SetRowHeightDialog.tsx
diff --git a/src/LinearMafDisplay/components/Sidebar/ColorLegend.tsx b/src/LinearMafDisplay/components/Sidebar/ColorLegend.tsx
@@ -5,7 +5,7 @@ import { observer } from 'mobx-react'
 import RectBg from './RectBg'
 import Tree from './Tree'
 
-import type { LinearMafDisplayModel } from '../stateModel'
+import type { LinearMafDisplayModel } from '../../stateModel'
 
 const ColorLegend = observer(function ({
   model,
diff --git a/src/LinearMafDisplay/components/Sidebar/RectBg.tsx b/src/LinearMafDisplay/components/Sidebar/RectBg.tsx
diff --git a/src/LinearMafDisplay/components/Sidebar/SvgWrapper.tsx b/src/LinearMafDisplay/components/Sidebar/SvgWrapper.tsx
@@ -3,7 +3,7 @@ import React from 'react'
 import { getContainingView } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
-import type { LinearMafDisplayModel } from '../stateModel'
+import type { LinearMafDisplayModel } from '../../stateModel'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 const SvgWrapper = observer(function ({
diff --git a/src/LinearMafDisplay/components/Sidebar/Tree.tsx b/src/LinearMafDisplay/components/Sidebar/Tree.tsx
@@ -2,7 +2,7 @@ import React from 'react'
 
 import { observer } from 'mobx-react'
 
-import type { LinearMafDisplayModel } from '../stateModel'
+import type { LinearMafDisplayModel } from '../../stateModel'
 
 const Tree = observer(function ({ model }: { model: LinearMafDisplayModel }) {
   const {
diff --git a/src/LinearMafDisplay/components/Sidebar/YScaleBars.tsx b/src/LinearMafDisplay/components/Sidebar/YScaleBars.tsx
@@ -5,7 +5,7 @@ import { observer } from 'mobx-react'
 import ColorLegend from './ColorLegend'
 import SvgWrapper from './SvgWrapper'
 
-import type { LinearMafDisplayModel } from '../stateModel'
+import type { LinearMafDisplayModel } from '../../stateModel'
 
 export const YScaleBars = observer(function (props: {
   model: LinearMafDisplayModel
diff --git a/src/LinearMafDisplay/renderSvg.tsx b/src/LinearMafDisplay/renderSvg.tsx
@@ -2,7 +2,7 @@ import React from 'react'
 
 import { getContainingView } from '@jbrowse/core/util'
 
-import YScaleBars from './components/YScaleBars'
+import YScaleBars from './components/Sidebar/YScaleBars'
 
 import type { LinearMafDisplayModel } from './stateModel'
 import type {
diff --git a/src/LinearMafDisplay/stateModel.ts b/src/LinearMafDisplay/stateModel.ts
@@ -22,7 +22,9 @@ import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view
 import type { HierarchyNode } from 'd3-hierarchy'
 import type { Instance } from 'mobx-state-tree'
 
-const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog'))
+const SetRowHeightDialog = lazy(
+  () => import('./components/SetRowHeightDialog/SetRowHeightDialog'),
+)
 
 /**
  * #stateModel LinearMafDisplay
diff --git a/src/LinearMafDisplay/types.ts b/src/LinearMafDisplay/types.ts
@@ -16,6 +16,6 @@ export interface NodeWithIdsAndLength {
 
 export interface Sample {
   id: string
-  label: string
+  label?: string
   color?: string
 }
diff --git a/src/LinearMafRenderer/makeImageData.ts b/src/LinearMafRenderer/makeImageData.ts
@@ -62,15 +62,16 @@ export function makeImageData({
   const hp2 = h / 2
   const offset = (rowHeight - h) / 2
 
+  // sample as alignments
   ctx.font = 'bold 10px Courier New,monospace'
 
   for (const feature of features.values()) {
     const [leftPx] = featureSpanPx(feature, region, bpPerPx)
-    const vals = feature.get('alignments') as Record<string, { data: string }>
+    const vals = feature.get('alignments') as Record<string, { seq: string }>
     const seq = feature.get('seq').toLowerCase()
     const r = Object.entries(vals)
     for (const [sample, val] of r) {
-      const origAlignment = val.data
+      const origAlignment = val.seq
       const alignment = origAlignment.toLowerCase()
 
       const row = sampleToRowMap.get(sample)
@@ -180,11 +181,11 @@ export function makeImageData({
   // insertions are always 'on top' of the other features
   for (const feature of features.values()) {
     const [leftPx] = featureSpanPx(feature, region, bpPerPx)
-    const vals = feature.get('alignments') as Record<string, { data: string }>
+    const vals = feature.get('alignments') as Record<string, { seq: string }>
     const seq = feature.get('seq').toLowerCase()
 
     for (const [sample, val] of Object.entries(vals)) {
-      const origAlignment = val.data
+      const origAlignment = val.seq
       const alignment = origAlignment.toLowerCase()
       const row = sampleToRowMap.get(sample)
       if (row === undefined) {
diff --git a/src/MafGetSamples/MafGetSamples.ts b/src/MafGetSamples/MafGetSamples.ts
@@ -2,6 +2,7 @@ import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions'
 
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
+import type { Region } from '@jbrowse/core/util'
 
 export default class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
   name = 'MafGetSamples'
diff --git a/src/MafGetSequences/MafGetSequences.ts b/src/MafGetSequences/MafGetSequences.ts
@@ -4,18 +4,18 @@ import { firstValueFrom, toArray } from 'rxjs'
 
 import { processFeaturesToFasta } from '../util/fastaUtils'
 
+import type { Sample } from '../LinearMafDisplay/types'
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import type { Region } from '@jbrowse/core/util'
 
-
-
 export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRegions {
   name = 'MafGetSequences'
 
   async execute(
     args: {
       adapterConfig: AnyConfigurationModel
+      samples: Sample[]
       stopToken?: string
       sessionId: string
       headers?: Record<string, string>
@@ -28,7 +28,7 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
       args,
       rpcDriverClassName,
     )
-    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { samples, regions, adapterConfig, sessionId } = deserializedArgs
     const { dataAdapter } = await getAdapter(
       this.pluginManager,
       sessionId,
@@ -42,9 +42,11 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
     const featuresObservable = (
       dataAdapter as BaseFeatureDataAdapter
     ).getFeatures(regions[0]!, deserializedArgs)
-    return processFeaturesToFasta(
-      await firstValueFrom(featuresObservable.pipe(toArray())),
-      regions[0],
-    )
+    const features = await firstValueFrom(featuresObservable.pipe(toArray()))
+    return processFeaturesToFasta({
+      features: new Map(features.map(f => [f.id(), f])),
+      samples,
+      regions,
+    })
   }
 }
diff --git a/src/MafTabixAdapter/MafTabixAdapter.ts b/src/MafTabixAdapter/MafTabixAdapter.ts
@@ -22,7 +22,7 @@ interface OrganismRecord {
   srcSize: number
   strand: number
   unknown: number
-  data: string
+  seq: string
 }
 
 export default class MafTabixAdapter extends BaseFeatureDataAdapter {
@@ -113,7 +113,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                 srcSize: +ad[2]!,
                 strand: ad[3] === '-' ? -1 : 1,
                 unknown: +ad[4]!,
-                data: seq,
+                seq,
               }
             }
           }
@@ -129,8 +129,8 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                 score: feature.get('score'),
                 alignments,
                 seq:
-                  alignments[refAssemblyName || query.assemblyName]?.data ||
-                  alignments[firstAssemblyNameFound]?.data,
+                  alignments[refAssemblyName || query.assemblyName]?.seq ||
+                  alignments[firstAssemblyNameFound]?.seq,
               },
             }),
           )
diff --git a/src/util/__snapshots__/fastaUtils.test.ts.snap b/src/util/__snapshots__/fastaUtils.test.ts.snap
@@ -2,20 +2,21 @@
 
 exports[`gap in assembly1 1`] = `
 [
-  ">assembly1.chr1:100:+",
-  "AC-TAC",
-  ">assembly2.chr2:200:+",
-  "ACTTC",
-  "",
+  ".....",
+  "...T.",
 ]
 `;
 
-exports[`processes a feature with a selected region 1`] = `
+exports[`no showAllLetters 1`] = `
+[
+  ".....",
+  "..-.T",
+]
+`;
+
+exports[`showAllLetters 1`] = `
 [
-  ">assembly1.chr1:100:+",
   "ACGTA",
-  ">assembly2.chr2:200:+",
   "AC-TT",
-  "",
 ]
 `;
diff --git a/src/util/fastaUtils.test.ts b/src/util/fastaUtils.test.ts
@@ -1,41 +1,63 @@
-import { SimpleFeature } from '@jbrowse/core/util'
+import { Feature, SimpleFeature } from '@jbrowse/core/util'
 import { expect, test } from 'vitest'
 
 import { processFeaturesToFasta } from './fastaUtils'
 
-test('processes a feature with a selected region', () => {
-  const mockFeature = new SimpleFeature({
-    uniqueId: '123',
-    refName: 'abc',
-    start: 100,
-    end: 110,
-    alignments: {
-      assembly1: {
-        chr: 'chr1',
+function makeMap(features: Feature[]) {
+  return new Map(features.map(f => [f.id(), f]))
+}
+const mockFeature = new SimpleFeature({
+  uniqueId: '123',
+  refName: 'abc',
+  start: 100,
+  end: 110,
+  seq: 'ACGTACGTAC',
+  alignments: {
+    assembly1: {
+      chr: 'chr1',
+      start: 100,
+      data: 'ACGTACGTAC',
+      strand: 1,
+    },
+    assembly2: {
+      chr: 'chr2',
+      start: 200,
+      data: 'AC-TTCGTAC',
+      strand: 1,
+    },
+  },
+})
+test('no showAllLetters', () => {
+  const result = processFeaturesToFasta({
+    features: makeMap([mockFeature]),
+    samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+    regions: [
+      {
+        refName: 'chr1',
         start: 100,
-        data: 'ACGTACGTAC',
-        strand: 1,
-      },
-      assembly2: {
-        chr: 'chr2',
-        start: 200,
-        data: 'AC-TTCGTAC',
-        strand: 1,
+        end: 105,
+        assemblyName: 'assembly1',
       },
-    },
+    ],
   })
+  expect(result).toMatchSnapshot()
+})
 
-  const result = processFeaturesToFasta([mockFeature], {
-    refName: 'chr1',
-    start: 100,
-    end: 105,
-    assemblyName: 'assembly1',
-  }).split('\n')
+test('showAllLetters', () => {
+  const result = processFeaturesToFasta({
+    features: makeMap([mockFeature]),
+    samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+    showAllLetters: true,
+    regions: [
+      {
+        refName: 'chr1',
+        start: 100,
+        end: 105,
+        assemblyName: 'assembly1',
+      },
+    ],
+  })
   expect(result).toMatchSnapshot()
-  expect(result[0]).toContain('>assembly1.chr1:100:+')
-  expect(result[1]).toContain('ACGTA')
-  expect(result[2]).toContain('>assembly2.chr2:200:+')
-  expect(result[3]).toContain('AC-TT')
 })
 
 test('gap in assembly1', () => {
@@ -44,6 +66,7 @@ test('gap in assembly1', () => {
     refName: 'abc',
     start: 100,
     end: 110,
+    seq: 'AC-TACGTAC',
     alignments: {
       assembly1: {
         chr: 'chr1',
@@ -60,18 +83,17 @@ test('gap in assembly1', () => {
     },
   })
 
-  const result = processFeaturesToFasta([mockFeature], {
-    refName: 'chr1',
-    start: 100,
-    end: 105,
-    assemblyName: 'assembly1',
-  }).split('\n')
+  const result = processFeaturesToFasta({
+    features: makeMap([mockFeature]),
+    samples: [{ id: 'assembly1' }, { id: 'assembly2' }],
+    regions: [
+      {
+        refName: 'chr1',
+        start: 100,
+        end: 105,
+        assemblyName: 'assembly1',
+      },
+    ],
+  })
   expect(result).toMatchSnapshot()
-  expect(result[0]).toContain('>assembly1.chr1:100:+')
-  expect(result[1]).toContain('AC-TAC')
-  expect(result[2]).toContain('>assembly2.chr2:200:+')
-  // When there's a gap in the reference assembly (assembly1), those positions should be skipped
-  // in all other alignments as well. In this case, the third character in assembly1 is a gap,
-  // so we should skip the corresponding position (G) in assembly2.
-  expect(result[3]).toContain('ACTTC')
 })
diff --git a/src/util/fastaUtils.ts b/src/util/fastaUtils.ts
diff --git a/src/util/fastaUtilsAdvanced.test.ts b/src/util/fastaUtilsAdvanced.test.ts

Original file line number	Diff line number	Diff line change
`@@ -71,6 +71,7 @@ const SequenceDialog = observer(function ({`
`71`	`71`	`{`
`72`	`72`	`sessionId,`
`73`	`73`	`adapterConfig: model.adapterConfig,`
	`74`	`+ samples,`
`74`	`75`	`regions: [`
`75`	`76`	`{`
`76`	`77`	`refName,`
`@@ -79,7 +80,6 @@ const SequenceDialog = observer(function ({`
`79`	`80`	`assemblyName,`
`80`	`81`	`},`
`81`	`82`	`],`
`82`		`- bpPerPx: view.bpPerPx,`
`83`	`83`	`},`
`84`	`84`	`)`
`85`	`85`