diff --git a/packages/core/assemblyManager/assemblyManager.ts b/packages/core/assemblyManager/assemblyManager.ts index 72e071e868..45ee3928e5 100644 --- a/packages/core/assemblyManager/assemblyManager.ts +++ b/packages/core/assemblyManager/assemblyManager.ts @@ -1,13 +1,14 @@ import { addDisposer, - cast, getParent, types, Instance, IAnyType, } from 'mobx-state-tree' -import { when } from '../util' import { reaction } from 'mobx' + +// locals +import { when } from '../util' import { readConfObject, AnyConfigurationModel } from '../configuration' import assemblyFactory, { Assembly } from './assembly' import PluginManager from '../PluginManager' @@ -167,20 +168,17 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) { reaction( () => self.assemblyList, assemblyConfs => { - self.assemblies.forEach(asm => { + for (const asm of self.assemblies) { if (!asm.configuration) { this.removeAssembly(asm) } - }) - assemblyConfs.forEach(conf => { - if ( - !self.assemblies.some( - a => a.name === readConfObject(conf, 'name'), - ) - ) { + } + for (const conf of assemblyConfs) { + const name = readConfObject(conf, 'name') + if (!self.assemblies.some(a => a.name === name)) { this.addAssembly(conf) } - }) + } }, { fireImmediately: true, name: 'assemblyManagerAfterAttach' }, ), @@ -210,16 +208,6 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) { addAssembly(configuration: Conf) { self.assemblies.push({ configuration }) }, - - /** - * #action - * private: you would generally want to add to manipulate - * jbrowse.assemblies, session.sessionAssemblies, or - * session.temporaryAssemblies instead of using this directly - */ - replaceAssembly(idx: number, configuration: Conf) { - self.assemblies[idx] = cast({ configuration }) - }, })) } diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.tsx index 0cdabed361..f757f3f00e 100644 --- a/plugins/breakpoint-split-view/src/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.tsx +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.tsx @@ -87,15 +87,16 @@ export async function renderToSvg(model: BSV, opts: ExportSvgOptions) { - + + + @@ -105,15 +106,16 @@ export async function renderToSvg(model: BSV, opts: ExportSvgOptions) { - + + + diff --git a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts index ebea237900..ae028e8633 100644 --- a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts +++ b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts @@ -73,14 +73,31 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { } async hasDataForRefName() { - // determining this properly is basically a call to getFeatures - // so is not really that important, and has to be true or else - // getFeatures is never called (BaseFeatureDataAdapter filters it out) + // determining this properly is basically a call to getFeatures so is not + // really that important, and has to be true or else getFeatures is never + // called (BaseFeatureDataAdapter filters it out) return true } - async getRefNames() { - // we cannot determine this accurately + getAssemblyNames() { + const assemblyNames = this.getConf('assemblyNames') as string[] + return assemblyNames + } + + async getRefNames(opts: BaseOptions = {}) { + // @ts-expect-error + const r1 = opts.regions?.[0].assemblyName + const { feats } = await this.setup(opts) + + const idx = this.getAssemblyNames().indexOf(r1) + if (idx !== -1) { + const set = new Set() + for (const feat of feats) { + set.add(idx === 0 ? feat[0].refName : feat[1].refName) + } + return [...set] + } + console.warn('Unable to do ref renaming on adapter') return [] } diff --git a/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts b/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts index 26e6ffdf93..7f8a22ed5f 100644 --- a/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts +++ b/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts @@ -93,8 +93,31 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { return true } - async getRefNames() { - // we cannot determine this accurately + getAssemblyNames() { + const assemblyNames = this.getConf('assemblyNames') as string[] + return assemblyNames + } + + async getRefNames(opts: BaseOptions = {}) { + // @ts-expect-error + const r1 = opts.regions?.[0].assemblyName + const { feats } = await this.setup(opts) + + const idx = this.getAssemblyNames().indexOf(r1) + if (idx !== -1) { + const set = new Set() + for (const feat of feats) { + if (idx === 0) { + set.add(feat[0].refName) + set.add(feat[1].refName) + } else { + set.add(feat[2].refName) + set.add(feat[3].refName) + } + } + return [...set] + } + console.warn('Unable to do ref renaming on adapter') return [] } diff --git a/plugins/config/src/index.ts b/plugins/config/src/index.ts index 0a1fa9909e..4da311a0c8 100644 --- a/plugins/config/src/index.ts +++ b/plugins/config/src/index.ts @@ -23,6 +23,4 @@ export default class ConfigurationPlugin extends Plugin { } } -export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor' - export { LazyConfigurationEditorComponent as ConfigurationEditor } diff --git a/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts b/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts index b85c5ed101..6c28b3b0b9 100644 --- a/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts +++ b/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts @@ -3,7 +3,7 @@ import { ConfigurationReference, AnyConfigurationSchemaType, } from '@jbrowse/core/configuration' -import { types, getSnapshot, Instance } from 'mobx-state-tree' +import { types, getSnapshot, Instance, getParent } from 'mobx-state-tree' import { dedupe, Feature, @@ -34,10 +34,6 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { * #property */ configuration: ConfigurationReference(configSchema), - /** - * #property - */ - height: 100, }), ) .volatile((/* self */) => ({ @@ -165,20 +161,22 @@ function renderBlockData(self: LinearComparativeDisplay) { const { rpcManager } = getSession(self) const display = self - // Alternative to readConfObject(config) is below used because renderProps is - // something under our control. Compare to serverSideRenderedBlock + // Alternative to readConfObject(config) is below used because + // renderProps is something under our control. Compare to + // serverSideRenderedBlock readConfObject(self.configuration) const { adapterConfig } = self const parent = getContainingView(self) as LinearComparativeViewModel const sessionId = getRpcSessionId(self) getSnapshot(parent) - return parent.initialized ? { rpcManager, renderProps: { ...display.renderProps(), + // @ts-expect-error + level: getParent(self, 4).level as number, view: parent, adapterConfig, sessionId, @@ -195,11 +193,10 @@ async function renderBlockEffect(props: ReturnType) { } const { rpcManager, renderProps } = props - const { adapterConfig } = renderProps - const view0 = renderProps.view.views[0] - + const { adapterConfig, level } = renderProps + const view = renderProps.view.views[level] const features = (await rpcManager.call('getFeats', 'CoreGetFeatures', { - regions: view0.staticBlocks.contentBlocks, + regions: view.staticBlocks.contentBlocks, sessionId: 'getFeats', adapterConfig, })) as Feature[] diff --git a/plugins/linear-comparative-view/src/LinearComparativeView/components/Header.tsx b/plugins/linear-comparative-view/src/LinearComparativeView/components/Header.tsx index fda03a343a..0bb095cc82 100644 --- a/plugins/linear-comparative-view/src/LinearComparativeView/components/Header.tsx +++ b/plugins/linear-comparative-view/src/LinearComparativeView/components/Header.tsx @@ -1,9 +1,9 @@ import React, { useState } from 'react' -import { IconButton, Typography } from '@mui/material' +import { Typography } from '@mui/material' import { makeStyles } from 'tss-react/mui' import { SearchBox } from '@jbrowse/plugin-linear-genome-view' import { observer } from 'mobx-react' -import { Menu } from '@jbrowse/core/ui' +import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton' // icons import MoreVertIcon from '@mui/icons-material/MoreVert' @@ -11,9 +11,6 @@ import MoreVertIcon from '@mui/icons-material/MoreVert' // locals import { LinearComparativeViewModel } from '../model' import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons' -import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton' - -type LCV = LinearComparativeViewModel const useStyles = makeStyles()(() => ({ headerBar: { @@ -39,7 +36,11 @@ const useStyles = makeStyles()(() => ({ }, })) -const TrackSelector = observer(({ model }: { model: LCV }) => { +const TrackSelector = observer(function ({ + model, +}: { + model: LinearComparativeViewModel +}) { return ( { ) }) -const Header = observer(function ({ model }: { model: LCV }) { +const Header = observer(function ({ + model, +}: { + model: LinearComparativeViewModel +}) { const { classes } = useStyles() - const [menuAnchorEl, setMenuAnchorEl] = useState() - const anyShowHeaders = model.views.some(view => !view.hideHeader) + const { views } = model + const [showSearchBoxes, setShowSearchBoxes] = useState(false) return (
- - setMenuAnchorEl(event.currentTarget)} + setShowSearchBoxes(!showSearchBoxes), + type: 'checkbox', + }, + ]} > - - {!anyShowHeaders - ? model.views.map(view => ( + + + {showSearchBoxes ? ( +
+ {views.map(view => (
-
- - {Math.round(view.coarseTotalBp).toLocaleString('en-US')} bp - -
+ + {view.assemblyNames.join(',')}{' '} + {Math.round(view.coarseTotalBp).toLocaleString('en-US')} bp +
- )) - : null} + ))} +
+ ) : null}
- - {menuAnchorEl ? ( - { - callback() - setMenuAnchorEl(undefined) - }} - menuItems={model.headerMenuItems()} - onClose={() => setMenuAnchorEl(undefined)} - /> - ) : null}
) }) diff --git a/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeRenderArea.tsx b/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeRenderArea.tsx new file mode 100644 index 0000000000..1a4399468a --- /dev/null +++ b/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeRenderArea.tsx @@ -0,0 +1,90 @@ +import React from 'react' +import { makeStyles } from 'tss-react/mui' +import { observer } from 'mobx-react' +import { getEnv } from '@jbrowse/core/util' +import { ResizeHandle } from '@jbrowse/core/ui' + +// locals +import { LinearComparativeViewModel } from '../model' +import { getConf } from '@jbrowse/core/configuration' +import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' + +const useStyles = makeStyles()({ + container: { + display: 'grid', + }, + overlay: { + zIndex: 100, + gridArea: '1/1', + }, + resizeHandle: { + height: 4, + background: '#ccc', + }, +}) + +function View({ view }: { view: LinearGenomeViewModel }) { + const { pluginManager } = getEnv(view) + const { ReactComponent } = pluginManager.getViewType(view.type) + return +} + +const LinearComparativeRenderArea = observer(function ({ + model, +}: { + model: LinearComparativeViewModel +}) { + const { classes } = useStyles() + const { views, levels } = model + const RenderList = [ + , + ] as React.ReactNode[] + for (let i = 1; i < views.length; i++) { + RenderList.push( + +
+ +
+ levels[i - 1].setHeight(levels[i - 1].height + n)} + className={classes.resizeHandle} + /> + + , + ) + } + return
{RenderList}
+}) + +const Overlays = observer(function ({ + model, + level, +}: { + model: LinearComparativeViewModel + level: number +}) { + const { classes } = useStyles() + return ( + <> + {model.levels[level]?.tracks.map(track => { + const [display] = track.displays + const { RenderingComponent } = display + const trackId = getConf(track, 'trackId') + return RenderingComponent ? ( +
+ +
+ ) : null + })} + + ) +}) + +export default LinearComparativeRenderArea diff --git a/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeView.tsx b/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeView.tsx index e6a84eee2f..0ba322ee09 100644 --- a/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeView.tsx +++ b/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeView.tsx @@ -1,34 +1,14 @@ import React from 'react' import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' -import { getConf, AnyConfigurationModel } from '@jbrowse/core/configuration' -import { getEnv } from '@jbrowse/core/util' -import { ResizeHandle } from '@jbrowse/core/ui' // locals import { LinearComparativeViewModel } from '../model' import Rubberband from './Rubberband' import Header from './Header' +import LinearComparativeRenderArea from './LinearComparativeRenderArea' const useStyles = makeStyles()(theme => ({ - container: { - display: 'grid', - }, - overlay: { - zIndex: 100, - gridArea: '1/1', - }, - content: { - gridArea: '1/1', - position: 'relative', - }, - grid: { - display: 'grid', - }, - relative: { - position: 'relative', - }, - // this helps keep the vertical guide inside the parent view container, // similar style exists in the single LGV's trackscontainer rubberbandContainer: { @@ -46,39 +26,12 @@ const useStyles = makeStyles()(theme => ({ }, })) -type LCV = LinearComparativeViewModel - -const Overlays = observer(({ model }: { model: LCV }) => { - const { classes } = useStyles() - return ( - <> - {model.tracks.map(track => { - const [display] = track.displays - const { RenderingComponent } = display - const trackId = getConf(track, 'trackId') - return RenderingComponent ? ( -
- -
- ) : null - })} - - ) -}) - -// The comparative is in the middle of the views -const MiddleComparativeView = observer(({ model }: { model: LCV }) => { +const LinearComparativeView = observer(function ({ + model, +}: { + model: LinearComparativeViewModel +}) { const { classes } = useStyles() - const { views } = model - const { pluginManager } = getEnv(model) - const { ReactComponent } = pluginManager.getViewType(views[0].type) return (
@@ -87,68 +40,9 @@ const MiddleComparativeView = observer(({ model }: { model: LCV }) => { model={model} ControlComponent={
} /> -
- -
- -
- - model.setMiddleComparativeHeight(model.middleComparativeHeight + n) - } - style={{ - height: 4, - background: '#ccc', - }} - /> - -
+
) }) -const OverlayComparativeView = observer(({ model }: { model: LCV }) => { - const { classes } = useStyles() - const { views } = model - const { pluginManager } = getEnv(model) - return ( -
-
- } - /> - -
-
-
- {views.map(view => { - const { ReactComponent } = pluginManager.getViewType(view.type) - return - })} -
- -
-
-
- ) -}) - -const LinearComparativeView = observer(function (props: { - ExtraButtons?: React.ReactNode - model: LCV -}) { - const { model } = props - - const middle = model.tracks.some(({ displays }) => - displays.some((d: { configuration: AnyConfigurationModel }) => - getConf(d, 'middle'), - ), - ) - return middle ? ( - - ) : ( - - ) -}) export default LinearComparativeView diff --git a/plugins/linear-comparative-view/src/LinearComparativeView/model.ts b/plugins/linear-comparative-view/src/LinearComparativeView/model.ts index e7e77fcaab..1da1e96936 100644 --- a/plugins/linear-comparative-view/src/LinearComparativeView/model.ts +++ b/plugins/linear-comparative-view/src/LinearComparativeView/model.ts @@ -64,15 +64,24 @@ function stateModelFactory(pluginManager: PluginManager) { * #property */ interactToggled: false, + /** * #property */ - middleComparativeHeight: 100, - /** - * #property - */ - tracks: types.array( - pluginManager.pluggableMstType('track', 'stateModel'), + levels: types.array( + types + .model({ + tracks: types.array( + pluginManager.pluggableMstType('track', 'stateModel'), + ), + height: 100, + level: types.number, + }) + .actions(self => ({ + setHeight(n: number) { + self.height = n + }, + })), ), /** * #property @@ -101,12 +110,6 @@ function stateModelFactory(pluginManager: PluginManager) { width: undefined as number | undefined, })) .views(self => ({ - /** - * #getter - */ - get highResolutionScaling() { - return 2 - }, /** * #getter */ @@ -188,9 +191,9 @@ function stateModelFactory(pluginManager: PluginManager) { /** * #action */ - setMiddleComparativeHeight(n: number) { - self.middleComparativeHeight = n - return self.middleComparativeHeight + setLevelHeight(n: number, level = 0) { + self.levels[level].setHeight(n) + return self.levels[level].height }, /** @@ -216,10 +219,10 @@ function stateModelFactory(pluginManager: PluginManager) { /** * #action */ - toggleTrack(trackId: string) { - const hiddenCount = this.hideTrack(trackId) + toggleTrack(trackId: string, level = 0) { + const hiddenCount = this.hideTrack(trackId, level) if (!hiddenCount) { - this.showTrack(trackId) + this.showTrack(trackId, level) return true } return false @@ -228,7 +231,7 @@ function stateModelFactory(pluginManager: PluginManager) { /** * #action */ - showTrack(trackId: string, initialSnapshot = {}) { + showTrack(trackId: string, level = 0, initialSnapshot = {}) { const schema = pluginManager.pluggableConfigSchemaType('track') const configuration = resolveIdentifier(schema, getRoot(self), trackId) if (!configuration) { @@ -250,12 +253,20 @@ function stateModelFactory(pluginManager: PluginManager) { `could not find a compatible display for view type ${self.type}`, ) } - self.tracks.push( + if (!self.levels[level]) { + self.levels[level] = cast({ level }) + } + self.levels[level].tracks.push( trackType.stateModel.create({ ...initialSnapshot, type: configuration.type, configuration, - displays: [{ type: displayConf.type, configuration: displayConf }], + displays: [ + { + type: displayConf.type, + configuration: displayConf, + }, + ], }), ) }, @@ -263,11 +274,15 @@ function stateModelFactory(pluginManager: PluginManager) { /** * #action */ - hideTrack(trackId: string) { + hideTrack(trackId: string, level = 0) { const schema = pluginManager.pluggableConfigSchemaType('track') const config = resolveIdentifier(schema, getRoot(self), trackId) - const shownTracks = self.tracks.filter(t => t.configuration === config) - transaction(() => shownTracks.forEach(t => self.tracks.remove(t))) + const shownTracks = self.levels[level].tracks.filter( + t => t.configuration === config, + ) + transaction(() => + shownTracks.forEach(t => self.levels[level].tracks.remove(t)), + ) return shownTracks.length }, /** @@ -289,7 +304,7 @@ function stateModelFactory(pluginManager: PluginManager) { */ clearView() { self.views = cast([]) - self.tracks = cast([]) + self.levels = cast([]) }, })) .views(() => ({ @@ -360,6 +375,14 @@ function stateModelFactory(pluginManager: PluginManager) { ) }, })) + .preProcessSnapshot(snap => { + // @ts-expect-error + const { tracks, levels = [{ tracks, level: 0 }], ...rest } = snap || {} + return { + ...rest, + levels, + } + }) } export type LinearComparativeViewStateModel = ReturnType< diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts index fb2ff77554..02deabd0d8 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts @@ -1,4 +1,4 @@ -import { addDisposer, getSnapshot } from 'mobx-state-tree' +import { addDisposer, getParent, getSnapshot } from 'mobx-state-tree' import { Feature, getContainingView, getSession } from '@jbrowse/core/util' import { bpToPx } from '@jbrowse/core/util/Base1DUtils' @@ -39,7 +39,7 @@ export function doAfterAttach(self: LinearSyntenyDisplayModel) { return } - const height = view.middleComparativeHeight + const height = self.height const width = view.width ctx1.clearRect(0, 0, width, height) ctx3.clearRect(0, 0, width, height) @@ -86,6 +86,8 @@ export function doAfterAttach(self: LinearSyntenyDisplayModel) { } const { assemblyManager } = getSession(self) const view = getContainingView(self) as LSV + // @ts-expect-error + const level = getParent(self, 4).level const viewSnaps = view.views.map(view => ({ ...getSnapshot(view), width: view.width, @@ -113,8 +115,8 @@ export function doAfterAttach(self: LinearSyntenyDisplayModel) { const r2 = mate.refName const ref1 = a1?.getCanonicalRefName(r1) || r1 const ref2 = a2?.getCanonicalRefName(r2) || r2 - const v1 = viewSnaps[0] - const v2 = viewSnaps[1] + const v1 = viewSnaps[level] + const v2 = viewSnaps[level + 1] const p11 = bpToPx({ self: v1, refName: ref1, coord: f1s }) const p12 = bpToPx({ self: v1, refName: ref1, coord: f1e }) const p21 = bpToPx({ self: v2, refName: ref2, coord: f2s }) diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx index 9f66fbd506..014dbd593e 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx @@ -24,12 +24,13 @@ const useStyles = makeStyles()({ rel: { position: 'relative', }, - abs: { + mouseoverCanvas: { position: 'absolute', - }, - none: { pointEvents: 'none', }, + mainCanvas: { + position: 'absolute', + }, }) const LinearSyntenyRendering = observer(function ({ @@ -37,11 +38,10 @@ const LinearSyntenyRendering = observer(function ({ }: { model: LinearSyntenyDisplayModel }) { - const { classes, cx } = useStyles() + const { classes } = useStyles() const xOffset = useRef(0) const currScrollFrame = useRef() const view = getContainingView(model) as LinearSyntenyViewModel - const height = view.middleComparativeHeight const width = view.width const delta = useRef(0) const timeout = useRef() @@ -51,7 +51,7 @@ const LinearSyntenyRendering = observer(function ({ const [mouseCurrDownX, setMouseCurrDownX] = useState() const [mouseInitialDownX, setMouseInitialDownX] = useState() const [currY, setCurrY] = useState() - const { mouseoverId } = model + const { mouseoverId, height } = model // these useCallbacks avoid new refs from being created on any mouseover, etc. const k1 = useCallback( @@ -63,8 +63,8 @@ const LinearSyntenyRendering = observer(function ({ (ref: HTMLCanvasElement) => { model.setMainCanvasRef(ref) function onWheel(event: WheelEvent) { - event.preventDefault() if (event.ctrlKey === true) { + event.preventDefault() delta.current += event.deltaY / 500 for (const v of view.views) { v.setScaleFactor( @@ -88,6 +88,7 @@ const LinearSyntenyRendering = observer(function ({ }, 300) } else { if (Math.abs(event.deltaY) < Math.abs(event.deltaX)) { + event.preventDefault() xOffset.current += event.deltaX / 2 } if (currScrollFrame.current === undefined) { @@ -106,12 +107,10 @@ const LinearSyntenyRendering = observer(function ({ if (ref) { ref.addEventListener('wheel', onWheel) - // this is a react 19-ism to have a cleanup in the ref callback + // there is a react 19-ism to have a cleanup in the ref callback // https://react.dev/blog/2024/04/25/react-19#cleanup-functions-for-refs // note: it warns in earlier versions of react - return () => ref.removeEventListener('wheel', onWheel) } - return () => {} }, // eslint-disable-next-line react-hooks/exhaustive-deps [model, height, width], @@ -133,7 +132,7 @@ const LinearSyntenyRendering = observer(function ({ ref={k1} width={width} height={height} - className={cx(classes.abs, classes.none)} + className={classes.mouseoverCanvas} /> onSynContextClick(evt, model, setAnchorEl)} data-testid="synteny_canvas" - className={classes.abs} + className={classes.mainCanvas} width={width} height={height} /> diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx index 2c3a0077fd..6e44465f68 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx @@ -5,6 +5,7 @@ import { Menu } from '@jbrowse/core/ui' // locals import { LinearSyntenyDisplayModel } from '../model' import { LinearSyntenyViewModel } from '../../LinearSyntenyView/model' +import { getParent } from 'mobx-state-tree' interface ClickCoord { clientX: number @@ -54,22 +55,27 @@ export default function SyntenyContextMenu({ label: 'Center on feature', onClick: () => { const { f } = feature + const track = getParent<{ level: number }>(model, 4) const start = f.get('start') const end = f.get('end') const refName = f.get('refName') const mate = f.get('mate') - view.views[0] - .navToLocString(`${refName}:${start}-${end}`) - .catch(e => { - console.error(e) - getSession(model).notifyError(`${e}`, e) - }) - view.views[1] - .navToLocString(`${mate.refName}:${mate.start}-${mate.end}`) - .catch(e => { - console.error(e) - getSession(model).notifyError(`${e}`, e) - }) + + const l1 = view.views[track.level] + const l2 = view.views[track.level + 1] + l1.navToLocString(`${refName}:${start}-${end}`).catch(e => { + const err = `${l1.assemblyNames[0]}:${e}` + console.error(err) + getSession(model).notifyError(err, e) + }) + + l2.navToLocString( + `${mate.refName}:${mate.start}-${mate.end}`, + ).catch(e => { + const err = `${l2.assemblyNames[0]}:${e}` + console.error(err) + getSession(model).notifyError(err, e) + }) }, }, ]} diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts index 8d8b6b296c..4c16225e1c 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts @@ -34,6 +34,7 @@ export function drawMatchSimple({ feature, ctx, offsets, + level, cb, height, drawCurves, @@ -44,6 +45,7 @@ export function drawMatchSimple({ feature: FeatPos ctx: CanvasRenderingContext2D offsets: number[] + level: number oobLimit: number viewWidth: number cb: (ctx: CanvasRenderingContext2D) => void @@ -53,10 +55,10 @@ export function drawMatchSimple({ }) { const { p11, p12, p21, p22 } = feature - const x11 = p11.offsetPx - offsets[0] - const x12 = p12.offsetPx - offsets[0] - const x21 = p21.offsetPx - offsets[1] - const x22 = p22.offsetPx - offsets[1] + const x11 = p11.offsetPx - offsets[level] + const x12 = p12.offsetPx - offsets[level] + const x21 = p21.offsetPx - offsets[level + 1] + const x22 = p22.offsetPx - offsets[level + 1] const l1 = Math.abs(x12 - x11) const l2 = Math.abs(x22 - x21) diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts index 3ad6f44d14..9f3a564967 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts @@ -3,6 +3,7 @@ import { doesIntersect2, getContainingView } from '@jbrowse/core/util' import { LinearSyntenyViewModel } from '../LinearSyntenyView/model' import { LinearSyntenyDisplayModel } from './model' import { draw, drawMatchSimple } from './components/util' +import { getParent } from 'mobx-state-tree' export const MAX_COLOR_RANGE = 255 * 255 * 255 // max color range @@ -36,9 +37,11 @@ export function drawRef( ctx3?: CanvasRenderingContext2D, ) { const view = getContainingView(model) as LinearSyntenyViewModel + // @ts-expect-error + const level = getParent(model, 4).level const drawCurves = view.drawCurves const drawCIGAR = view.drawCIGAR - const height = view.middleComparativeHeight + const { height, featPositions } = model const width = view.width const bpPerPxs = view.views.map(v => v.bpPerPx) @@ -47,20 +50,18 @@ export function drawRef( } ctx1.beginPath() - const featPos = model.featPositions const offsets = view.views.map(v => v.offsetPx) - - const unitMultiplier = Math.floor(MAX_COLOR_RANGE / featPos.length) + const unitMultiplier = Math.floor(MAX_COLOR_RANGE / featPositions.length) // this loop is optimized to draw many thin lines with a single ctx.stroke // call, a separate loop below draws larger boxes ctx1.fillStyle = colorMap.M ctx1.strokeStyle = colorMap.M - for (const { p11, p12, p21, p22 } of featPos) { - const x11 = p11.offsetPx - offsets[0] - const x12 = p12.offsetPx - offsets[0] - const x21 = p21.offsetPx - offsets[1] - const x22 = p22.offsetPx - offsets[1] + for (const { p11, p12, p21, p22 } of featPositions) { + const x11 = p11.offsetPx - offsets[level] + const x12 = p12.offsetPx - offsets[level] + const x21 = p21.offsetPx - offsets[level + 1] + const x22 = p22.offsetPx - offsets[level + 1] const l1 = Math.abs(x12 - x11) const l2 = Math.abs(x22 - x21) const y1 = 0 @@ -89,11 +90,11 @@ export function drawRef( // ctx.stroke once is much more efficient than calling stroke() many times ctx1.fillStyle = colorMap.M ctx1.strokeStyle = colorMap.M - for (const { p11, p12, p21, p22, f, cigar } of featPos) { - const x11 = p11.offsetPx - offsets[0] - const x12 = p12.offsetPx - offsets[0] - const x21 = p21.offsetPx - offsets[1] - const x22 = p22.offsetPx - offsets[1] + for (const { p11, p12, p21, p22, f, cigar } of featPositions) { + const x11 = p11.offsetPx - offsets[level] + const x12 = p12.offsetPx - offsets[level] + const x21 = p21.offsetPx - offsets[level + 1] + const x22 = p22.offsetPx - offsets[level + 1] const l1 = Math.abs(x12 - x11) const l2 = Math.abs(x22 - x21) const minX = Math.min(x21, x22) @@ -137,8 +138,8 @@ export function drawRef( px2 = cx2 } - const d1 = len / bpPerPxs[0] - const d2 = len / bpPerPxs[1] + const d1 = len / bpPerPxs[level] + const d2 = len / bpPerPxs[level + 1] if (op === 'M' || op === '=' || op === 'X') { cx1 += d1 * rev1 @@ -149,17 +150,17 @@ export function drawRef( cx2 += d2 * rev2 } - // check that we are even drawing in view here, e.g. that all - // points are not all less than 0 or greater than width + // check that we are even drawing in view here, e.g. that + // all points are not all less than 0 or greater than width if ( !( Math.max(px1, px2, cx1, cx2) < 0 || Math.min(px1, px2, cx1, cx2) > width ) ) { - // if it is a small feature and not the last element of the - // CIGAR (which could skip rendering it entire if we did turn - // it on), then turn on continuing flag + // if it is a small feature and not the last element of + // the CIGAR (which could skip rendering it entire if we + // did turn it on), then turn on continuing flag const isNotLast = j < cigar.length - 2 if ( Math.abs(cx1 - px1) <= 1 && @@ -197,8 +198,8 @@ export function drawRef( } ctx2.imageSmoothingEnabled = false ctx2.clearRect(0, 0, width, height) - for (let i = 0; i < featPos.length; i++) { - const feature = featPos[i] + for (let i = 0; i < featPositions.length; i++) { + const feature = featPositions[i] const idx = i * unitMultiplier + 1 ctx2.fillStyle = makeColor(idx) @@ -208,6 +209,7 @@ export function drawRef( feature, ctx: ctx2, drawCurves, + level, offsets, oobLimit, viewWidth: view.width, @@ -222,10 +224,12 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { const highResolutionScaling = 1 const view = getContainingView(model) as LinearSyntenyViewModel const drawCurves = view.drawCurves - const height = view.middleComparativeHeight + const height = model.height const width = view.width const ctx = model.mouseoverCanvas?.getContext('2d') const offsets = view.views.map(v => v.offsetPx) + // @ts-expect-error + const level = getParent(model, 4).level if (!ctx) { return @@ -239,6 +243,7 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { drawMatchSimple({ cb: ctx => ctx.fill(), feature: feature1, + level, ctx, oobLimit, viewWidth: view.width, @@ -255,6 +260,7 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { cb: ctx => ctx.stroke(), feature: feature2, ctx, + level, oobLimit, viewWidth: view.width, drawCurves, diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts index 3efaa999de..a95d5fdc8c 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts @@ -1,4 +1,4 @@ -import { types, Instance } from 'mobx-state-tree' +import { types, Instance, getParent } from 'mobx-state-tree' import { getConf, ConfigurationReference, @@ -143,6 +143,13 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { get trackIds() { return getConf(self, 'trackIds') as string[] }, + /** + * #getter + */ + get height() { + // @ts-expect-error + return getParent(self, 4).height as number + }, /** * #getter */ diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx index 063b252e42..7e184aec53 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx @@ -82,164 +82,162 @@ function getAdapter({ type Conf = SnapshotIn -const OpenTrack = observer( - ({ - assembly1, - assembly2, - setSessionTrackData, - }: { - sessionTrackData: Conf - assembly1: string - assembly2: string - setSessionTrackData: (arg: Conf) => void - }) => { - const [bed2Location, setBed2Location] = useState() - const [bed1Location, setBed1Location] = useState() - const [fileLocation, setFileLocation] = useState() - const [value, setValue] = useState('') - const [error, setError] = useState() - const fileName = getName(fileLocation) +const ImportCustomTrack = observer(function ({ + assembly1, + assembly2, + setSessionTrackData, +}: { + sessionTrackData: Conf + assembly1: string + assembly2: string + setSessionTrackData: (arg: Conf) => void +}) { + const [bed2Location, setBed2Location] = useState() + const [bed1Location, setBed1Location] = useState() + const [fileLocation, setFileLocation] = useState() + const [value, setValue] = useState('') + const [error, setError] = useState() + const fileName = getName(fileLocation) - const radioOption = value || (fileName ? extName(stripGz(fileName)) : '') + const radioOption = value || (fileName ? extName(stripGz(fileName)) : '') - useEffect(() => { - try { - if (fileLocation) { - const fn = fileName ? basename(fileName) : 'MyTrack' - const trackId = `${fn}-${Date.now()}` - setError(undefined) + useEffect(() => { + try { + if (fileLocation) { + const fn = fileName ? basename(fileName) : 'MyTrack' + const trackId = `${fn}-${Date.now()}` + setError(undefined) - setSessionTrackData({ - trackId, - name: fn, - assemblyNames: [assembly2, assembly1], - type: 'SyntenyTrack', - adapter: getAdapter({ - radioOption, - assembly1, - assembly2, - fileLocation, - bed1Location, - bed2Location, - }), - }) - } - } catch (e) { - console.error(e) - setError(e) + setSessionTrackData({ + trackId, + name: fn, + assemblyNames: [assembly2, assembly1], + type: 'SyntenyTrack', + adapter: getAdapter({ + radioOption, + assembly1, + assembly2, + fileLocation, + bed1Location, + bed2Location, + }), + }) } - }, [ - fileName, - assembly1, - assembly2, - bed1Location, - bed2Location, - fileLocation, - radioOption, - setSessionTrackData, - ]) - return ( - - {error ? : null} - - Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or - .anchors.simple (MCScan) file to view in the dotplot. These file types - can also be gzipped. The first assembly should be the query sequence - (e.g. left column of the PAF) and the second assembly should be the - target sequence (e.g. right column of the PAF) - - setValue(event.target.value)} - > - - - } label=".paf" /> - - - } label=".out" /> - - - } - label=".delta" - /> - - - } - label=".chain" - /> - - - } - label=".anchors" - /> - - - } - label=".anchors.simple" - /> - - - + } catch (e) { + console.error(e) + setError(e) + } + }, [ + fileName, + assembly1, + assembly2, + bed1Location, + bed2Location, + fileLocation, + radioOption, + setSessionTrackData, + ]) + return ( + + {error ? : null} + + Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or + .anchors.simple (MCScan) file to view in the dotplot. These file types + can also be gzipped. The first assembly should be the query sequence + (e.g. left column of the PAF) and the second assembly should be the + target sequence (e.g. right column of the PAF) + + setValue(event.target.value)} + > - {value === '.anchors' || value === '.anchors.simple' ? ( -
-
- Open the {value} and .bed files for both genome assemblies - from the MCScan (Python version) pipeline{' '} - - (more info) - + } label=".paf" /> + + + } label=".out" /> + + + } + label=".delta" + /> + + + } + label=".chain" + /> + + + } + label=".anchors" + /> + + + } + label=".anchors.simple" + /> + + + + + + {value === '.anchors' || value === '.anchors.simple' ? ( +
+
+ Open the {value} and .bed files for both genome assemblies from + the MCScan (Python version) pipeline{' '} + + (more info) + +
+
+
+ setFileLocation(loc)} + /> +
+
+ setBed1Location(loc)} + />
-
-
- setFileLocation(loc)} - /> -
-
- setBed1Location(loc)} - /> -
-
- setBed2Location(loc)} - /> -
+
+ setBed2Location(loc)} + />
- ) : ( - setFileLocation(loc)} - /> - )} - +
+ ) : ( + setFileLocation(loc)} + /> + )} - - ) - }, -) + + + ) +}) -export default OpenTrack +export default ImportCustomTrack diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelector.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelector.tsx index f99cf18715..f2e0c81e77 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelector.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelector.tsx @@ -12,71 +12,58 @@ import { observer } from 'mobx-react' // locals import { LinearSyntenyViewModel } from '../../model' -function f(track: AnyConfigurationModel, assembly1: string, assembly2: string) { - const assemblyNames = readConfObject(track, 'assemblyNames') - return ( - assemblyNames.includes(assembly1) && - assemblyNames.includes(assembly2) && - track.type.includes('Synteny') - ) -} - -const Selector = observer( - ({ - model, - assembly1, - assembly2, - setShowTrackId, - }: { - model: LinearSyntenyViewModel - assembly1: string - assembly2: string - setShowTrackId: (arg: string) => void - }) => { - const session = getSession(model) - const { tracks = [], sessionTracks = [] } = session - const allTracks = [...tracks, ...sessionTracks] as AnyConfigurationModel[] - const filteredTracks = allTracks.filter(t => f(t, assembly2, assembly1)) - const resetTrack = filteredTracks[0]?.trackId || '' - const [value, setValue] = useState(resetTrack) - useEffect(() => { - // if assembly1/assembly2 changes, then we will want to use this effect to - // change the state of the useState because it otherwise gets locked to a - // stale value - setValue(resetTrack) - }, [resetTrack]) - - useEffect(() => { - // sets track data in a useEffect because the initial load is needed as well - // as onChange's to the select box - setShowTrackId(value) - }, [value, setShowTrackId]) +const ImportSyntenyTrackSelector = observer(function ({ + model, + assembly1, + assembly2, + setShowTrackId, +}: { + model: LinearSyntenyViewModel + assembly1: string + assembly2: string + setShowTrackId: (arg: string) => void +}) { + const session = getSession(model) + const { tracks = [], sessionTracks = [] } = session + const allTracks = [...tracks, ...sessionTracks] as AnyConfigurationModel[] + const filteredTracks = allTracks.filter(track => { + const assemblyNames = readConfObject(track, 'assemblyNames') return ( - - - Select a track from the select box below, the track will be shown when - you hit "Launch". - - - {filteredTracks.length ? ( - - ) : ( - - )} - + assemblyNames.includes(assembly1) && + assemblyNames.includes(assembly2) && + track.type.includes('Synteny') ) - }, -) + }) + const resetTrack = filteredTracks[0]?.trackId || '' + const [value, setValue] = useState(resetTrack) + + useEffect(() => { + // sets track data in a useEffect because the initial load is needed as well + // as onChange's to the select box + setShowTrackId(value) + }, [value, setShowTrackId]) + return ( + + + Select a track from the select box below, the track will be shown when + you hit "Launch". + + + {filteredTracks.length ? ( + + ) : ( + + )} + + ) +}) -export default Selector +export default ImportSyntenyTrackSelector diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorUtil.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorUtil.tsx new file mode 100644 index 0000000000..6f9f76cd78 --- /dev/null +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorUtil.tsx @@ -0,0 +1,89 @@ +import React, { useState, useEffect } from 'react' +import { + FormControl, + FormLabel, + FormControlLabel, + Radio, + RadioGroup, +} from '@mui/material' +import { SnapshotIn } from 'mobx-state-tree' +import { AnyConfigurationModel } from '@jbrowse/core/configuration' + +// locals +import { LinearSyntenyViewModel } from '../../model' +import ImportCustomTrack from './ImportCustomTrack' +import ImportSyntenyTrackSelector from './ImportSyntenyTrackSelector' + +type Conf = SnapshotIn + +export default function TrackSelector({ + setSessionTrackData, + setShowTrackId, + sessionTrackData, + assembly1, + assembly2, + model, + idx, +}: { + sessionTrackData: Conf + setSessionTrackData: (arg: Conf) => void + setShowTrackId: (arg?: string) => void + model: LinearSyntenyViewModel + assembly1: string + assembly2: string + idx: number +}) { + const [choice, setChoice] = useState('tracklist') + + useEffect(() => { + if (choice === 'none') { + setSessionTrackData(undefined) + setShowTrackId(undefined) + } + }, [choice, setSessionTrackData, setShowTrackId]) + return ( + <> + + + (Optional) Select or add a synteny track between row {idx} and{' '} + {idx + 1} + + setChoice(event.target.value)} + aria-labelledby="group-label" + > + } label="None" /> + } + label="Existing track" + /> + } + label="New track" + /> + + + {choice === 'custom' ? ( + + ) : null} + {choice === 'tracklist' ? ( + + ) : null} + + ) +} diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/index.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/index.tsx index 3df3a68512..11daec95e6 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/index.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/index.tsx @@ -1,14 +1,11 @@ -import React, { useState, useEffect } from 'react' +import React, { useState } from 'react' import { Button, Container, FormControl, - FormLabel, - FormControlLabel, Grid, + IconButton, Paper, - Radio, - RadioGroup, } from '@mui/material' import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' @@ -16,11 +13,12 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration' import { SnapshotIn } from 'mobx-state-tree' import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util' import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui' - +// icons +import ArrowForward from '@mui/icons-material/ArrowForward' +import ArrowBack from '@mui/icons-material/ArrowBack' // locals import { LinearSyntenyViewModel } from '../../model' -import ImportCustomTrack from './ImportCustomTrack' -import ImportSyntenyTrackSelector from './ImportSyntenyTrackSelector' +import TrackSelector from './ImportSyntenyTrackSelectorUtil' const useStyles = makeStyles()(theme => ({ importFormContainer: { @@ -35,74 +33,6 @@ const useStyles = makeStyles()(theme => ({ type Conf = SnapshotIn -function TrackSelector({ - setSessionTrackData, - setShowTrackId, - sessionTrackData, - assembly1, - assembly2, - model, -}: { - sessionTrackData: Conf - setSessionTrackData: (arg: Conf) => void - setShowTrackId: (arg?: string) => void - model: LinearSyntenyViewModel - assembly1: string - assembly2: string -}) { - const [choice, setChoice] = useState('tracklist') - - useEffect(() => { - if (choice === 'none') { - setSessionTrackData(undefined) - setShowTrackId(undefined) - } - }, [choice, setSessionTrackData, setShowTrackId]) - return ( - <> - - - (Optional) Select or add a synteny track - - setChoice(event.target.value)} - aria-labelledby="group-label" - > - } label="None" /> - } - label="Existing track" - /> - } - label="New track" - /> - - - {choice === 'custom' ? ( - - ) : null} - {choice === 'tracklist' ? ( - - ) : null} - - ) -} - const LinearSyntenyViewImportForm = observer(function ({ model, }: { @@ -111,51 +41,16 @@ const LinearSyntenyViewImportForm = observer(function ({ const { classes } = useStyles() const session = getSession(model) const { assemblyNames } = session - const [assembly2, setAssembly2] = useState(assemblyNames[0] || '') - const [assembly1, setAssembly1] = useState(assemblyNames[0] || '') + const [currIdx, setCurrIdx] = useState(0) + const [assemblies, setAssemblies] = useState([ + assemblyNames[0] || '', + assemblyNames[0] || '', + ]) const [error, setError] = useState() - const [sessionTrackData, setSessionTrackData] = useState() - const [showTrackId, setShowTrackId] = useState() - - async function onOpenClick() { - try { - if (!isSessionWithAddTracks(session)) { - return - } - setError(undefined) - - const { assemblyManager } = session - const assemblies = [assembly1, assembly2] - model.setViews( - await Promise.all( - assemblies.map(async sel => { - const asm = await assemblyManager.waitForAssembly(sel) - if (!asm) { - throw new Error(`Assembly ${sel} failed to load`) - } - return { - type: 'LinearGenomeView' as const, - bpPerPx: 1, - offsetPx: 0, - hideHeader: true, - displayedRegions: asm.regions, - } - }), - ), - ) - model.views.forEach(view => view.setWidth(model.width)) - model.views.forEach(view => view.showAllRegions()) - if (sessionTrackData) { - session.addTrackConf(sessionTrackData) - model.toggleTrack(sessionTrackData.trackId) - } else if (showTrackId) { - model.showTrack(showTrackId) - } - } catch (e) { - console.error(e) - setError(e) - } - } + const [sessionTrackData, setSessionTrackData] = useState< + (Conf | undefined)[] + >([]) + const [showTrackId, setShowTrackId] = useState<(string | undefined)[]>([]) // this is a combination of any displayed error message we have const displayError = error @@ -174,45 +69,117 @@ const LinearSyntenyViewImportForm = observer(function ({

Select assemblies for linear synteny view

- - - setAssembly1(val)} - session={session} - /> - - - setAssembly2(val)} - session={session} - /> - - + <> + {assemblies.map((assembly, idx) => ( +
+ Row {idx + 1}: + + setAssemblies( + assemblies.map((value, index) => + index === idx ? newValue : value, + ), + ) + } + session={session} + /> +
+ ))} + +
- - +
+ + setCurrIdx(currIdx - 1)} + > + + + = assemblies.length - 2} + onClick={() => setCurrIdx(currIdx + 1)} + > + + { + const clone = [...showTrackId] + clone[currIdx] = arg + setShowTrackId(clone) + }} + assembly1={assemblies[currIdx]} + assembly2={assemblies[currIdx + 1]} + setSessionTrackData={arg => { + const clone = [...sessionTrackData] + clone[currIdx] = arg + setSessionTrackData(clone) + }} + sessionTrackData={sessionTrackData[currIdx]} model={model} /> diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/components/LinearSyntenyView.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/components/LinearSyntenyView.tsx index b7145c4907..b9662b7c4e 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/components/LinearSyntenyView.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/LinearSyntenyView.tsx @@ -9,7 +9,7 @@ const ImportForm = lazy(() => import('./ImportForm')) type LSV = LinearSyntenyViewModel -const LinearSyntenyView = observer(({ model }: { model: LSV }) => { +const LinearSyntenyView = observer(function ({ model }: { model: LSV }) { return !model.initialized ? ( ) : ( diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/model.test.ts b/plugins/linear-comparative-view/src/LinearSyntenyView/model.test.ts deleted file mode 100644 index 5761fb9989..0000000000 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/model.test.ts +++ /dev/null @@ -1,1605 +0,0 @@ -import PluginManager from '@jbrowse/core/PluginManager' -import LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view' -import SequencePlugin from '@jbrowse/plugin-sequence' -import stateModelFactory from './model' - -test('creation', () => { - const pluginManager = new PluginManager([ - new LinearGenomeViewPlugin(), - new SequencePlugin(), - ]) - .createPluggableElements() - .configure() - const model = stateModelFactory(pluginManager) - model.create({ - // @ts-expect-error - type: 'LinearSyntenyView', - views: [ - { - type: 'LinearGenomeView', - displayedRegions: [ - { - refName: 'Pp01', - start: 0, - end: 47851208, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'Pp02', - start: 0, - end: 30405870, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'Pp03', - start: 0, - end: 27368013, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'Pp04', - start: 0, - end: 25843236, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'Pp05', - start: 0, - end: 18496696, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'Pp06', - start: 0, - end: 30767194, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'Pp07', - start: 0, - end: 22388614, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'Pp08', - start: 0, - end: 22573980, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_12', - start: 0, - end: 167479, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_15', - start: 0, - end: 72028, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_13', - start: 0, - end: 69962, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_16', - start: 0, - end: 38727, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_18', - start: 0, - end: 32503, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_19', - start: 0, - end: 32043, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_20', - start: 0, - end: 30119, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_21', - start: 0, - end: 28663, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_23', - start: 0, - end: 27846, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_24', - start: 0, - end: 25707, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_26', - start: 0, - end: 23005, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_32', - start: 0, - end: 22324, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_28', - start: 0, - end: 21453, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_40', - start: 0, - end: 18616, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_30', - start: 0, - end: 18507, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_38', - start: 0, - end: 18477, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_34', - start: 0, - end: 18055, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_33', - start: 0, - end: 17159, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_35', - start: 0, - end: 16788, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_37', - start: 0, - end: 16633, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_39', - start: 0, - end: 15657, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_101', - start: 0, - end: 15118, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_42', - start: 0, - end: 14945, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_58', - start: 0, - end: 14802, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_57', - start: 0, - end: 13972, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_199', - start: 0, - end: 13173, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_51', - start: 0, - end: 12576, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_295', - start: 0, - end: 12535, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_69', - start: 0, - end: 12322, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_53', - start: 0, - end: 12283, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_54', - start: 0, - end: 12175, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 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'scaffold_284', - start: 0, - end: 2907, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_311', - start: 0, - end: 2890, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_347', - start: 0, - end: 2805, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_321', - start: 0, - end: 2536, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_308', - start: 0, - end: 2380, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_313', - start: 0, - end: 2374, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_312', - start: 0, - end: 2068, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_334', - start: 0, - end: 1821, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_327', - start: 0, - end: 1589, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_331', - start: 0, - end: 1501, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_333', - start: 0, - end: 1452, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_338', - start: 0, - end: 1306, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_343', - start: 0, - end: 1164, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_344', - start: 0, - end: 1163, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_345', - start: 0, - end: 1145, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_349', - start: 0, - end: 1099, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_350', - start: 0, - end: 1092, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_351', - start: 0, - end: 1071, - reversed: false, - assemblyName: 'peach', - }, - { - refName: 'scaffold_352', - start: 0, - end: 1061, - reversed: false, - assemblyName: 'peach', - }, - ], - bpPerPx: 19914.295609223023, - offsetPx: 3973, - tracks: [], - }, - { - type: 'LinearGenomeView', - displayedRegions: [ - { - refName: 'chr1', - start: 0, - end: 23037639, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr10', - start: 0, - end: 18140952, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr10_random', - start: 0, - end: 789605, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr11', - start: 0, - end: 19818926, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr11_random', - start: 0, - end: 282498, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr12', - start: 0, - end: 22702307, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr12_random', - start: 0, - end: 1566225, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr13', - start: 0, - end: 24396255, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr13_random', - start: 0, - end: 3268264, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr14', - start: 0, - end: 30274277, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr15', - start: 0, - end: 20304914, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr16', - start: 0, - end: 22053297, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr16_random', - start: 0, - end: 740079, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr17', - start: 0, - end: 17126926, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr17_random', - start: 0, - end: 829735, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr18', - start: 0, - end: 29360087, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr18_random', - start: 0, - end: 5170003, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr19', - start: 0, - end: 24021853, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr1_random', - start: 0, - end: 568933, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr2', - start: 0, - end: 18779844, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr3', - start: 0, - end: 19341862, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr3_random', - start: 0, - end: 1220746, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr4', - start: 0, - end: 23867706, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr4_random', - start: 0, - end: 76237, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr5', - start: 0, - end: 25021643, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr5_random', - start: 0, - end: 421237, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr6', - start: 0, - end: 21508407, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr7', - start: 0, - end: 21026613, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr7_random', - start: 0, - end: 1447032, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr8', - start: 0, - end: 22385789, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr9', - start: 0, - end: 23006712, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chr9_random', - start: 0, - end: 487831, - reversed: false, - assemblyName: 'grape', - }, - { - refName: 'chrUn', - start: 0, - end: 43154196, - reversed: false, - assemblyName: 'grape', - }, - ], - bpPerPx: 67300.98485738254, - offsetPx: 5893, - tracks: [], - }, - ], - displayName: 'A vs B', - }) -}) diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.tsx new file mode 100644 index 0000000000..760749e503 --- /dev/null +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.tsx @@ -0,0 +1,55 @@ +import React from 'react' +import { useTheme } from '@mui/material' +import { getFillProps } from '@jbrowse/core/util' +import { + SVGTracks, + SVGRuler, + LinearGenomeViewModel, +} from '@jbrowse/plugin-linear-genome-view' + +export default function SVGLinearGenomeView({ + trackLabelOffset, + fontSize, + textHeight, + trackLabels, + view, + displayResults, + rulerHeight, + shift, +}: { + textHeight: number + trackLabels: string + trackLabelOffset: number + fontSize: number + view: LinearGenomeViewModel + // eslint-disable-next-line @typescript-eslint/no-explicit-any + displayResults: any + rulerHeight: number + shift: number +}) { + const theme = useTheme() + return ( + + + + {view.assemblyNames.join(', ')} + + + + + + + + ) +} diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.tsx index 2a19d9581a..1ffe1e0f10 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.tsx @@ -11,29 +11,25 @@ import { renderToAbstractCanvas, renderToStaticMarkup, sum, - getFillProps, } from '@jbrowse/core/util' import { getTrackName } from '@jbrowse/core/util/tracks' import { createJBrowseTheme } from '@jbrowse/core/ui' -import { - SVGTracks, - SVGRuler, - totalHeight, -} from '@jbrowse/plugin-linear-genome-view' +import { totalHeight } from '@jbrowse/plugin-linear-genome-view' // locals import SVGBackground from './SVGBackground' +import SVGLinearGenomeView from './SVGLinearGenomeView' import { ExportSvgOptions, LinearSyntenyViewModel } from '../model' import { drawRef } from '../../LinearSyntenyDisplay/drawSynteny' -type LSV = LinearSyntenyViewModel - // render LGV to SVG -export async function renderToSvg(model: LSV, opts: ExportSvgOptions) { +export async function renderToSvg( + model: LinearSyntenyViewModel, + opts: ExportSvgOptions, +) { await when(() => model.initialized) const { textHeight = 18, - headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', @@ -42,15 +38,16 @@ export async function renderToSvg(model: LSV, opts: ExportSvgOptions) { } = opts const session = getSession(model) const themeVar = session.allThemes?.()[themeName] - const { width, views, middleComparativeHeight: synH, tracks } = model + const { width, views, levels } = model const shift = 50 - const offset = headerHeight + rulerHeight + const offset = rulerHeight // eslint-disable-next-line @typescript-eslint/no-explicit-any const { createRootFn } = getRoot(model) const heights = views.map( v => totalHeight(v.tracks, textHeight, trackLabels) + offset, ) - const totalHeightSvg = sum(heights) + synH + 100 + const totalHeightSvg = sum(heights) + sum(levels.map(l => l.height)) + 100 + const displayResults = await Promise.all( views.map( async view => @@ -71,37 +68,42 @@ export async function renderToSvg(model: LSV, opts: ExportSvgOptions) { ) const renderings = await Promise.all( - tracks.map(async track => { - const d = track.displays[0] - await when(() => (d.ready !== undefined ? d.ready : true)) - const r = await renderToAbstractCanvas( - width, - synH, - { exportSVG: opts }, - ctx => drawRef(d, ctx), - ) + levels.map( + async level => + await Promise.all( + level.tracks.map(async track => { + const d = track.displays[0] + await when(() => (d.ready !== undefined ? d.ready : true)) + const r = await renderToAbstractCanvas( + width, + level.height, + { exportSVG: opts }, + ctx => drawRef(d, ctx), + ) - if ('imageData' in r) { - throw new Error('found a canvas in svg export, probably a bug') - } else if ('canvasRecordedData' in r) { - return { - html: await getSerializedSvg({ - ...r, - width, - height: synH, + if ('imageData' in r) { + throw new Error('found a canvas in svg export, probably a bug') + } else if ('canvasRecordedData' in r) { + return { + html: await getSerializedSvg({ + ...r, + width, + height: level.height, + }), + } + } else { + return r + } }), - } - } else { - return r - } - }), + ), + ), ) const trackLabelMaxLen = max( views.flatMap(view => - view.tracks.map(t => - measureText(getTrackName(t.configuration, session), fontSize), + view.tracks.map(track => + measureText(getTrackName(track.configuration, session), fontSize), ), ), 0, @@ -109,6 +111,53 @@ export async function renderToSvg(model: LSV, opts: ExportSvgOptions) { const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0 const w = width + trackLabelOffset const theme = createJBrowseTheme(themeVar) + const RenderList = [ + , + ] as React.ReactNode[] + let currOffset = heights[0] + fontSize + rulerHeight + for (let i = 1; i < views.length; i++) { + RenderList.push( + + + + + + + + {renderings[i - 1].map((r, i) => ( + + ))} + + + + + , + ) + currOffset += heights[i] + levels[i - 1].height + fontSize + rulerHeight + } // the xlink namespace is used for rendering tag return renderToStaticMarkup( @@ -122,65 +171,7 @@ export async function renderToSvg(model: LSV, opts: ExportSvgOptions) { viewBox={[0, 0, w + shift * 2, totalHeightSvg].toString()} > - - - - {views[0].assemblyNames.join(', ')} - - - - - - - - - - - - - - {renderings.map((r, i) => ( - - ))} - - - - - {views[1].assemblyNames.join(', ')} - - - - - + {RenderList} , diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/Scalebar.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/Scalebar.tsx index d92ffde8b4..75432e2c66 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/Scalebar.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/Scalebar.tsx @@ -103,7 +103,7 @@ const RenderedRefNameLabels = observer(function ({ model }: { model: LGV }) { ) }) -const RenderedBlockTicks = function ({ +const RenderedBlockTickLabels = function ({ block, bpPerPx, }: { @@ -145,7 +145,9 @@ const RenderedScalebarLabels = observer(function ({ model }: { model: LGV }) { const { key, widthPx } = block const k = `${key}-${idx}` if (block.type === 'ContentBlock') { - return + return ( + + ) } else if (block.type === 'ElidedBlock') { return } else if (block.type === 'InterRegionPaddingBlock') { diff --git a/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx b/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx index 374c4f474e..513797a135 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx @@ -82,15 +82,16 @@ export async function renderToSvg(model: LGV, opts: ExportSvgOptions) { cytobandHeight={cytobandHeight} /> - + + + diff --git a/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGTracks.tsx b/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGTracks.tsx index 961570c42d..2de1a83ea7 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGTracks.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/svgcomponents/SVGTracks.tsx @@ -21,7 +21,6 @@ interface DisplayResult { export default function SVGTracks({ displayResults, model, - offset, textHeight, fontSize, trackLabels = 'offset', @@ -29,7 +28,6 @@ export default function SVGTracks({ }: { displayResults: DisplayResult[] model: LGV - offset: number textHeight: number fontSize: number trackLabels?: string @@ -37,6 +35,7 @@ export default function SVGTracks({ }) { const session = getSession(model) const textOffset = trackLabels === 'offset' ? textHeight : 0 + let offset = 0 return ( <> {displayResults.map(({ track, result }) => { diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg b/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg index 4c62a82fcd..65d47b62b8 100644 --- a/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg +++ b/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg @@ -1 +1 @@ -hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds \ No newline at end of file +hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds \ No newline at end of file diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/lgv_snapshot.svg b/products/jbrowse-web/src/tests/__image_snapshots__/lgv_snapshot.svg index 772d0c130a..6563442670 100644 --- a/products/jbrowse-web/src/tests/__image_snapshots__/lgv_snapshot.svg +++ b/products/jbrowse-web/src/tests/__image_snapshots__/lgv_snapshot.svg @@ -1 +1 @@ -volvox80bpctgA020406080001111GTACAGAGTGACGCTCAAAGCvolvox-sorted.bam (ctgA, canvas) \ No newline at end of file +volvox80bpctgA020406080001111GTACAGAGTGACGCTCAAAGCvolvox-sorted.bam (ctgA, canvas) \ No newline at end of file diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/synteny_snapshot.svg b/products/jbrowse-web/src/tests/__image_snapshots__/synteny_snapshot.svg index 8b6b61590c..d6a4525239 100644 --- a/products/jbrowse-web/src/tests/__image_snapshots__/synteny_snapshot.svg +++ b/products/jbrowse-web/src/tests/__image_snapshots__/synteny_snapshot.svg @@ -1 +1 @@ -volvoxctgA1,8001,9002,0002,100333619537636283334354210515volvox_inv_indelsvolvox_random_invctgA1,8001,9002,0002,1003345844231067567193728415volvox_inv_indels \ No newline at end of file +volvoxctgA1,8001,9002,0002,100333619537636283334354210515volvox_inv_indelsvolvox_random_invctgA1,8001,9002,0002,1003345844231067567193728415volvox_inv_indels \ No newline at end of file diff --git a/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap b/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap index 2cbd14b784..19a09e82fd 100644 --- a/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap +++ b/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap @@ -4,6 +4,6 @@ exports[`export svg of circular 1`] = `"ctgA16,00018,00020,00022,00024,000volvoxctgA13,00014,00015,00016,00017,00018,00019,00020,000volvox_random_inv"`; -exports[`export svg of lgv 1`] = `"volvox80bpctgA020406080001111GTACAGAGTGACGCTCAAAGCvolvox-sorted.bam (ctgA, canvas)"`; +exports[`export svg of lgv 1`] = `"volvox80bpctgA020406080001111GTACAGAGTGACGCTCAAAGCvolvox-sorted.bam (ctgA, canvas)"`; -exports[`export svg of synteny 1`] = `"volvoxctgA1,8001,9002,0002,100333619537636283334354210515volvox_inv_indelsvolvox_random_invctgA1,8001,9002,0002,1003345844231067567193728415volvox_inv_indels"`; +exports[`export svg of synteny 1`] = `"volvoxctgA1,8001,9002,0002,100333619537636283334354210515volvox_inv_indelsvolvox_random_invctgA1,8001,9002,0002,1003345844231067567193728415volvox_inv_indels"`; diff --git a/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap b/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap index 678bcf503d..a2b2980663 100644 --- a/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap +++ b/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap @@ -1,3 +1,3 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`export svg of breakpoint split view 1`] = `"hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds"`; +exports[`export svg of breakpoint split view 1`] = `"hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds"`; diff --git a/test_data/config_demo.json b/test_data/config_demo.json index b723b05a04..ac59c1bbc2 100644 --- a/test_data/config_demo.json +++ b/test_data/config_demo.json @@ -4326,6 +4326,26 @@ }, "assemblyNames": ["chm13v2.0"] }, + { + "type": "FeatureTrack", + "trackId": "hprc-v1.0-minigraph-grch38.bb.bed", + "name": "hprc-v1.0-minigraph-grch38.bb.bed", + "adapter": { + "type": "BedTabixAdapter", + "bedGzLocation": { + "uri": "hprc-v1.0-minigraph-grch38.bb.bed.gz", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "hprc-v1.0-minigraph-grch38.bb.bed.gz.tbi", + "locationType": "UriLocation" + }, + "indexType": "TBI" + } + }, + "assemblyNames": ["hg38"] + }, { "type": "VariantTrack", "trackId": "NA12878_LINE1", diff --git a/website/yarn.lock b/website/yarn.lock index 788c192bd9..062a9a4060 100644 --- a/website/yarn.lock +++ b/website/yarn.lock @@ -2,13 +2,13 @@ # yarn lockfile v1 -"@algolia/autocomplete-core@1.17.4": - version "1.17.4" - resolved "https://registry.yarnpkg.com/@algolia/autocomplete-core/-/autocomplete-core-1.17.4.tgz#43b6160b67cff853e05769c5f15b91ced5eff7c4" - integrity sha512-H1CAzj43RDeC4Vq9FW2JLtRDNxhjRG/aPX69nbNrKbYzX9P0YohxrEj3kJ9G+e20y0L0pYboAOeU6wgbKJ6gOA== +"@algolia/autocomplete-core@1.17.2": + version "1.17.2" + resolved "https://registry.yarnpkg.com/@algolia/autocomplete-core/-/autocomplete-core-1.17.2.tgz#dbdd0a57597b05f38d20d4de381ba446cc609001" + integrity sha512-Fi5cPV5pzEmJgTJ/KTcccJoR/v94OkBwJFyLTsmAx9jbBg5rlgoumRXQM41cgwzY1s/eBLNduUMak2KnZYofcA== dependencies: - "@algolia/autocomplete-plugin-algolia-insights" "1.17.4" - "@algolia/autocomplete-shared" "1.17.4" + "@algolia/autocomplete-plugin-algolia-insights" "1.17.2" + "@algolia/autocomplete-shared" "1.17.2" "@algolia/autocomplete-core@1.9.3": version "1.9.3" @@ -19,22 +19,22 @@ "@algolia/autocomplete-shared" "1.9.3" "@algolia/autocomplete-js@^1.8.2": - version "1.17.4" - resolved "https://registry.yarnpkg.com/@algolia/autocomplete-js/-/autocomplete-js-1.17.4.tgz#5bb3990b38123a64568430f3a85e1e92806dc5c3" - integrity sha512-ANhINMwusKmsW/xHhgiKvUSLis/Lll9OilueBR9h/lxBlgEJ/hHIOTnZupzksyna1OtGZaW5keAu04E19+CW1w== + version "1.17.2" + resolved "https://registry.yarnpkg.com/@algolia/autocomplete-js/-/autocomplete-js-1.17.2.tgz#d3affab63094bf28a1bea9050cfdeb382b694a52" + integrity sha512-2UP5ZMEAtIJvnJ3qLiz3AzFjJD66n4UWsAf6mFGFXSYA/UU0LuaC8Bzrfj4CnK1d/AZyPLe+rgZXr6mQtBI8jg== dependencies: - "@algolia/autocomplete-core" "1.17.4" - "@algolia/autocomplete-preset-algolia" "1.17.4" - "@algolia/autocomplete-shared" "1.17.4" + "@algolia/autocomplete-core" "1.17.2" + "@algolia/autocomplete-preset-algolia" "1.17.2" + "@algolia/autocomplete-shared" "1.17.2" htm "^3.1.1" preact "^10.13.2" -"@algolia/autocomplete-plugin-algolia-insights@1.17.4": - version "1.17.4" - resolved "https://registry.yarnpkg.com/@algolia/autocomplete-plugin-algolia-insights/-/autocomplete-plugin-algolia-insights-1.17.4.tgz#b88e2e54a226da0de47984022f43f8e329607819" - integrity sha512-fPABTwZtfD83qAzwnMYjJQ6ohCK7XE2l2++H+dOtV76cCIsAYYAC1bO5DnCbIi6Ma+OkNOgB1jCPI5EYOEsSpg== +"@algolia/autocomplete-plugin-algolia-insights@1.17.2": + version "1.17.2" + resolved "https://registry.yarnpkg.com/@algolia/autocomplete-plugin-algolia-insights/-/autocomplete-plugin-algolia-insights-1.17.2.tgz#af431f36d559ffdeb4bbcb6132d21ba63501bdc1" + integrity sha512-bgVuThYaY9NSQMHOE/GMvlEzQxFzqDH3Lbls7fWuei8iIfcBWGtRUH01m/w5LY1mAw1wv8SyZ9xwuvfdXt8XkA== dependencies: - "@algolia/autocomplete-shared" "1.17.4" + "@algolia/autocomplete-shared" "1.17.2" "@algolia/autocomplete-plugin-algolia-insights@1.9.3": version "1.9.3" @@ -43,12 +43,12 @@ dependencies: "@algolia/autocomplete-shared" "1.9.3" -"@algolia/autocomplete-preset-algolia@1.17.4": - version "1.17.4" - resolved "https://registry.yarnpkg.com/@algolia/autocomplete-preset-algolia/-/autocomplete-preset-algolia-1.17.4.tgz#ca4dd2308615858d932ff2b2546e77c7873d4983" - integrity sha512-ijYn6hAGr3luVBVYDubaX600KXolVJH6yZlpeWZ9CNCEewgKIQ9ok3eNGha9EEJ0s9REYbp1TmDQ3T1I1aqcBA== +"@algolia/autocomplete-preset-algolia@1.17.2": + version "1.17.2" + resolved "https://registry.yarnpkg.com/@algolia/autocomplete-preset-algolia/-/autocomplete-preset-algolia-1.17.2.tgz#65387d60c2d8fc8485caea6591bf5e5c5210cc46" + integrity sha512-pXOD059R1giNJkcFpPEWI20XdQevHlmuTxPisKk/XkqjOCFnMmyNq2O7AWJylkcOeb62o2Ord166tJ90vNTSvw== dependencies: - "@algolia/autocomplete-shared" "1.17.4" + "@algolia/autocomplete-shared" "1.17.2" "@algolia/autocomplete-preset-algolia@1.9.3": version "1.9.3" @@ -57,10 +57,10 @@ dependencies: "@algolia/autocomplete-shared" "1.9.3" -"@algolia/autocomplete-shared@1.17.4": - version "1.17.4" - resolved "https://registry.yarnpkg.com/@algolia/autocomplete-shared/-/autocomplete-shared-1.17.4.tgz#446e8b8f1a72d4b9b7cc68f55729d14a8260f6f7" - integrity sha512-AM7KntpKinDZGVYfZ4j8zt5ymgYBRXOZg0CFEeHLmViqu5BvQzzoc1aoNHQx6lBjViGckBYP9szA+t2QzRXy3A== +"@algolia/autocomplete-shared@1.17.2": + version "1.17.2" + resolved "https://registry.yarnpkg.com/@algolia/autocomplete-shared/-/autocomplete-shared-1.17.2.tgz#62d91594eb6077a47a0709fd9410150d1eb3394f" + integrity sha512-L9gmDgv2J6cXXefV4tg/xlfomd+jjbzKmoc6kcvtS2USkxowoLNvqkLRNQP8bHvX+RXXGNLJBwJj+Ul7JIpv8A== "@algolia/autocomplete-shared@1.9.3": version "1.9.3" @@ -68,135 +68,135 @@ integrity sha512-Wnm9E4Ye6Rl6sTTqjoymD+l8DjSTHsHboVRYrKgEt8Q7UHm9nYbqhN/i0fhUYA3OAEH7WA8x3jfpnmJm3rKvaQ== "@algolia/autocomplete-theme-classic@^1.8.2": - version "1.17.4" - resolved 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+ "@babel/plugin-transform-modules-commonjs" "^7.24.7" "@babel/plugin-transform-modules-systemjs" "^7.24.7" "@babel/plugin-transform-modules-umd" "^7.24.7" "@babel/plugin-transform-named-capturing-groups-regex" "^7.24.7" @@ -1152,7 +1152,7 @@ "@babel/plugin-transform-object-rest-spread" "^7.24.7" "@babel/plugin-transform-object-super" "^7.24.7" "@babel/plugin-transform-optional-catch-binding" "^7.24.7" - "@babel/plugin-transform-optional-chaining" "^7.24.8" + "@babel/plugin-transform-optional-chaining" "^7.24.7" "@babel/plugin-transform-parameters" "^7.24.7" "@babel/plugin-transform-private-methods" "^7.24.7" "@babel/plugin-transform-private-property-in-object" "^7.24.7" @@ -1163,7 +1163,7 @@ "@babel/plugin-transform-spread" "^7.24.7" "@babel/plugin-transform-sticky-regex" "^7.24.7" "@babel/plugin-transform-template-literals" "^7.24.7" - "@babel/plugin-transform-typeof-symbol" "^7.24.8" + "@babel/plugin-transform-typeof-symbol" "^7.24.7" "@babel/plugin-transform-unicode-escapes" 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"^2.0.0" is-decimal@^2.0.0: version "2.0.1" @@ -5876,9 +5886,9 @@ micromark-core-commonmark@^2.0.0: micromark-util-types "^2.0.0" micromark-extension-directive@^3.0.0: - version "3.0.1" - resolved "https://registry.yarnpkg.com/micromark-extension-directive/-/micromark-extension-directive-3.0.1.tgz#67b3985bb991a69dbcae52664c57ee54b22f635a" - integrity sha512-VGV2uxUzhEZmaP7NSFo2vtq7M2nUD+WfmYQD+d8i/1nHbzE+rMy9uzTvUybBbNiVbrhOZibg3gbyoARGqgDWyg== + version "3.0.0" + resolved "https://registry.yarnpkg.com/micromark-extension-directive/-/micromark-extension-directive-3.0.0.tgz#527869de497a6de9024138479091bc885dae076b" + integrity sha512-61OI07qpQrERc+0wEysLHMvoiO3s2R56x5u7glHq2Yqq6EHbH4dW25G9GfDdGCDYqA21KE6DWgNSzxSwHc2hSg== dependencies: devlop "^1.0.0" micromark-factory-space "^2.0.0" @@ -5899,9 +5909,9 @@ micromark-extension-frontmatter@^2.0.0: micromark-util-types "^2.0.0" micromark-extension-gfm-autolink-literal@^2.0.0: - version "2.1.0" - resolved 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sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w== webpack@^5.88.1: - version "5.93.0" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.93.0.tgz#2e89ec7035579bdfba9760d26c63ac5c3462a5e5" - integrity sha512-Y0m5oEY1LRuwly578VqluorkXbvXKh7U3rLoQCEO04M97ScRr44afGVkI0FQFsXzysk5OgFAxjZAb9rsGQVihA== + version "5.92.1" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.92.1.tgz#eca5c1725b9e189cffbd86e8b6c3c7400efc5788" + integrity sha512-JECQ7IwJb+7fgUFBlrJzbyu3GEuNBcdqr1LD7IbSzwkSmIevTm8PF+wej3Oxuz/JFBUZ6O1o43zsPkwm1C4TmA== dependencies: "@types/eslint-scope" "^3.7.3" "@types/estree" "^1.0.5" @@ -8740,9 +8745,9 @@ ws@^7.3.1: integrity sha512-+dbF1tHwZpXcbOJdVOkzLDxZP1ailvSxM6ZweXTegylPny803bFhA+vqBYw4s31NSAk4S2Qz+AKXK9a4wkdjcQ== ws@^8.13.0: - version "8.18.0" - resolved "https://registry.yarnpkg.com/ws/-/ws-8.18.0.tgz#0d7505a6eafe2b0e712d232b42279f53bc289bbc" - integrity 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