diff --git a/packages/core/assemblyManager/assemblyManager.ts b/packages/core/assemblyManager/assemblyManager.ts index 0534f9072b..11a04830a0 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' @@ -164,20 +165,17 @@ 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' }, ), @@ -207,16 +205,6 @@ 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 6a836a061f..16707c3fb5 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 f6da0a47fa..197dcf3640 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 00903fb828..0e3d884557 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 040b774122..3023c9bb75 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 e26fbbdecd..ac753e815b 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..3d7444fdf4 --- /dev/null +++ b/plugins/linear-comparative-view/src/LinearComparativeView/components/LinearComparativeRenderArea.tsx @@ -0,0 +1,92 @@ +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++) { + const view = views[i]! + const level = levels[i - 1]! + RenderList.push( + +
+ +
+ level.setHeight(level.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 048576c12b..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 edc9b796ad..d66a8921e0 100644 --- a/plugins/linear-comparative-view/src/LinearComparativeView/model.ts +++ b/plugins/linear-comparative-view/src/LinearComparativeView/model.ts @@ -66,12 +66,21 @@ function stateModelFactory(pluginManager: PluginManager) { /** * #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 + return self.height + }, + })), ), /** * #property @@ -100,12 +109,6 @@ function stateModelFactory(pluginManager: PluginManager) { width: undefined as number | undefined, })) .views(self => ({ - /** - * #getter - */ - get highResolutionScaling() { - return 2 - }, /** * #getter */ @@ -178,9 +181,9 @@ 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 }, /** @@ -206,10 +209,10 @@ 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 @@ -218,7 +221,7 @@ 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) { @@ -240,12 +243,20 @@ 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, + }, + ], }), ) }, @@ -253,12 +264,16 @@ 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) + const shownTracks = self.levels[level]!.tracks.filter( + t => t.configuration === config, + ) transaction(() => { - shownTracks.forEach(t => self.tracks.remove(t)) + shownTracks.forEach(t => { + self.levels[level]!.tracks.remove(t) + }) }) return shownTracks.length }, @@ -281,7 +296,7 @@ function stateModelFactory(pluginManager: PluginManager) { */ clearView() { self.views = cast([]) - self.tracks = cast([]) + self.levels = cast([]) }, })) .views(() => ({ @@ -353,6 +368,15 @@ function stateModelFactory(pluginManager: PluginManager) { ) }, })) + .preProcessSnapshot(snap => { + // @ts-expect-error + // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition + 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 dfc44ec240..d41449edc8 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 a5abb847e5..496578edeb 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 xOffset = useRef(0) + 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. @@ -143,7 +143,7 @@ const LinearSyntenyRendering = observer(function ({ ref={k1} width={width} height={height} - className={cx(classes.abs, classes.none)} + className={classes.mouseoverCanvas} /> diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx index b578580b94..9df93e7adf 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx @@ -1,6 +1,7 @@ import React from 'react' import { getContainingView, getSession, Feature } from '@jbrowse/core/util' import { Menu } from '@jbrowse/core/ui' +import { getParent } from 'mobx-state-tree' // locals import { LinearSyntenyDisplayModel } from '../model' @@ -54,21 +55,28 @@ 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( + + const l1 = view.views[track.level]! + const l2 = view.views[track.level + 1]! + l1.navToLocString(`${refName}:${start}-${end}`).catch( (e: unknown) => { - console.error(e) - getSession(model).notifyError(`${e}`, e) + const err = `${l1.assemblyNames[0]}:${e}` + console.error(err) + getSession(model).notifyError(err, e) }, ) - view.views[1]!.navToLocString( + + l2.navToLocString( `${mate.refName}:${mate.start}-${mate.end}`, ).catch((e: unknown) => { - console.error(e) - getSession(model).notifyError(`${e}`, 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 9ba5ee2904..58a9880d1e 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 0dbfa0ebfa..759896da7c 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 @@ -170,9 +171,9 @@ export function drawRef( ) { continuingFlag = true } else { - // allow rendering the dominant color when using continuing flag - // if the last element of continuing was a large feature, else - // just use match + // allow rendering the dominant color when using continuing + // flag if the last element of continuing was a large + // feature, else just use match ctx1.fillStyle = colorMap[(continuingFlag && d1 > 1) || d2 > 1 ? op : 'M'] continuingFlag = false @@ -198,8 +199,8 @@ 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) @@ -211,6 +212,7 @@ export function drawRef( feature, ctx: ctx2, drawCurves, + level, offsets, oobLimit, viewWidth: view.width, @@ -218,7 +220,6 @@ export function drawRef( height, }) } - return undefined } export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { @@ -226,10 +227,12 @@ 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 @@ -245,6 +248,7 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { ctx.fill() }, feature: feature1, + level, ctx, oobLimit, viewWidth: view.width, @@ -263,6 +267,7 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { }, 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 a17f83d529..3bf2a8066b 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx @@ -82,174 +82,172 @@ 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 7a8941e003..6305f6096f 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelector.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelector.tsx @@ -12,73 +12,63 @@ 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..3da632d3dc --- /dev/null +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorUtil.tsx @@ -0,0 +1,91 @@ +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 04ed6a4001..f7a56da23c 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: { @@ -35,76 +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, }: { @@ -113,55 +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 @@ -180,49 +69,125 @@ 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: 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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..9023db2a8e --- /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 + + 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 32f6a68444..6aabb90f9b 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 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 => @@ -71,40 +68,45 @@ 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) - return undefined - }, - ) + 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) + return undefined + }, + ) - if ('imageData' in r) { - throw new Error('found a canvas in svg export, probably a bug') - } - 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 + } }), - } - } - 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, @@ -112,6 +114,58 @@ 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++) { + const view = views[i]! + const level = levels[i - 1]! + const rendering = renderings[i - 1]! + const height = heights[i]! + RenderList.push( + + + + + + + + {rendering.map((r, i) => ( + /* biome-ignore lint/suspicious/noArrayIndexKey: */ + + ))} + + + + + , + ) + currOffset += height + level.height + fontSize + rulerHeight + } // the xlink namespace is used for rendering tag return renderToStaticMarkup( @@ -125,66 +179,7 @@ export async function renderToSvg(model: LSV, opts: ExportSvgOptions) { viewBox={[0, 0, w + shift * 2, totalHeightSvg].toString()} > - - - - {views[0]!.assemblyNames.join(', ')} - - - - - - - - - - - - - - {renderings.map((r, i) => ( - /* biome-ignore lint/suspicious/noArrayIndexKey: */ - - ))} - - - - - {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 2811a898dd..32a934f1a3 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 8664632bbc..68328121c8 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 877eea01a6..4a058eca08 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 4e67079201..788c192bd9 100644 --- a/website/yarn.lock +++ b/website/yarn.lock @@ -214,38 +214,38 @@ "@babel/highlight" "^7.24.7" picocolors "^1.0.0" -"@babel/compat-data@^7.22.6", "@babel/compat-data@^7.25.2": - version "7.25.2" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.25.2.tgz#e41928bd33475305c586f6acbbb7e3ade7a6f7f5" - integrity sha512-bYcppcpKBvX4znYaPEeFau03bp89ShqNMLs+rmdptMw+heSZh9+z84d2YG+K7cYLbWwzdjtDoW/uqZmPjulClQ== +"@babel/compat-data@^7.22.6", "@babel/compat-data@^7.24.8": + version "7.24.9" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.24.9.tgz#53eee4e68f1c1d0282aa0eb05ddb02d033fc43a0" + integrity sha512-e701mcfApCJqMMueQI0Fb68Amflj83+dvAvHawoBpAz+GDjCIyGHzNwnefjsWJ3xiYAqqiQFoWbspGYBdb2/ng== "@babel/core@^7.21.3", 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+"@babel/helper-create-regexp-features-plugin@^7.18.6", "@babel/helper-create-regexp-features-plugin@^7.24.7": + version "7.24.7" + resolved "https://registry.yarnpkg.com/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.24.7.tgz#be4f435a80dc2b053c76eeb4b7d16dd22cfc89da" + integrity sha512-03TCmXy2FtXJEZfbXDTSqq1fRJArk7lX9DOFC/47VthYcxyIOx+eXQmdo6DOQvrbpIix+KfXwvuXdFDZHxt+rA== dependencies: "@babel/helper-annotate-as-pure" "^7.24.7" regexpu-core "^5.3.1" semver "^6.3.1" -"@babel/helper-define-polyfill-provider@^0.6.2": +"@babel/helper-define-polyfill-provider@^0.6.1", "@babel/helper-define-polyfill-provider@^0.6.2": version "0.6.2" resolved "https://registry.yarnpkg.com/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.6.2.tgz#18594f789c3594acb24cfdb4a7f7b7d2e8bd912d" integrity sha512-LV76g+C502biUK6AyZ3LK10vDpDyCzZnhZFXkH1L75zHPj68+qc8Zfpx2th+gzwA2MzyK+1g/3EPl62yFnVttQ== @@ -309,7 +311,29 @@ lodash.debounce "^4.0.8" resolve "^1.14.2" -"@babel/helper-member-expression-to-functions@^7.24.8": +"@babel/helper-environment-visitor@^7.24.7": + version "7.24.7" + resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.24.7.tgz#4b31ba9551d1f90781ba83491dd59cf9b269f7d9" + integrity sha512-DoiN84+4Gnd0ncbBOM9AZENV4a5ZiL39HYMyZJGZ/AZEykHYdJw0wW3kdcsh9/Kn+BRXHLkkklZ51ecPKmI1CQ== + dependencies: + "@babel/types" "^7.24.7" + +"@babel/helper-function-name@^7.24.7": + version "7.24.7" + resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.24.7.tgz#75f1e1725742f39ac6584ee0b16d94513da38dd2" + integrity sha512-FyoJTsj/PEUWu1/TYRiXTIHc8lbw+TDYkZuoE43opPS5TrI7MyONBE1oNvfguEXAD9yhQRrVBnXdXzSLQl9XnA== + dependencies: + "@babel/template" "^7.24.7" + "@babel/types" "^7.24.7" + +"@babel/helper-hoist-variables@^7.24.7": + version "7.24.7" + resolved 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"^7.24.7" "@babel/plugin-transform-json-strings@^7.24.7": version "7.24.7" @@ -771,12 +789,12 @@ "@babel/helper-plugin-utils" "^7.24.7" "@babel/plugin-syntax-json-strings" "^7.8.3" -"@babel/plugin-transform-literals@^7.25.2": - version "7.25.2" - resolved "https://registry.yarnpkg.com/@babel/plugin-transform-literals/-/plugin-transform-literals-7.25.2.tgz#deb1ad14fc5490b9a65ed830e025bca849d8b5f3" - integrity sha512-HQI+HcTbm9ur3Z2DkO+jgESMAMcYLuN/A7NRw9juzxAezN9AvqvUTnpKP/9kkYANz6u7dFlAyOu44ejuGySlfw== +"@babel/plugin-transform-literals@^7.24.7": + version "7.24.7" + resolved "https://registry.yarnpkg.com/@babel/plugin-transform-literals/-/plugin-transform-literals-7.24.7.tgz#36b505c1e655151a9d7607799a9988fc5467d06c" + integrity sha512-vcwCbb4HDH+hWi8Pqenwnjy+UiklO4Kt1vfspcQYFhJdpthSnW8XvWGyDZWKNVrVbVViI/S7K9PDJZiUmP2fYQ== dependencies: - "@babel/helper-plugin-utils" "^7.24.8" + "@babel/helper-plugin-utils" "^7.24.7" "@babel/plugin-transform-logical-assignment-operators@^7.24.7": 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dependencies: nanoid "^3.3.7" picocolors "^1.0.1" source-map-js "^1.2.0" preact@^10.13.2: - version "10.23.1" - resolved "https://registry.yarnpkg.com/preact/-/preact-10.23.1.tgz#d400107289bc979881c5212cb5f5cd22cd1dc38c" - integrity sha512-O5UdRsNh4vdZaTieWe3XOgSpdMAmkIYBCT3VhQDlKrzyCm8lUYsk0fmVEvoQQifoOjFRTaHZO69ylrzTW2BH+A== + version "10.22.1" + resolved "https://registry.yarnpkg.com/preact/-/preact-10.22.1.tgz#6a3589973fe0c6e53211091607d31f4b7b27334d" + integrity sha512-jRYbDDgMpIb5LHq3hkI0bbl+l/TQ9UnkdQ0ww+lp+4MMOdqaUYdFc5qeyP+IV8FAd/2Em7drVPeKdQxsiWCf/A== pretty-error@^4.0.0: version "4.0.0" @@ -7626,9 +7643,9 @@ rtl-detect@^1.0.4: integrity sha512-PGMBq03+TTG/p/cRB7HCLKJ1MgDIi07+QU1faSjiYRfmY5UsAttV9Hs08jDAHVwcOwmVLcSJkpwyfXszVjWfIQ== rtlcss@^4.1.0: - version "4.2.0" - resolved "https://registry.yarnpkg.com/rtlcss/-/rtlcss-4.2.0.tgz#627b08806bd6851adb4d0670b63919fb6a3ea038" - integrity 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version "5.5.3" + resolved "https://registry.yarnpkg.com/typescript/-/typescript-5.5.3.tgz#e1b0a3c394190838a0b168e771b0ad56a0af0faa" + integrity sha512-/hreyEujaB0w76zKo6717l3L0o/qEUtRgdvUBvlkhoWeOVMjMuHNHk0BRBzikzuGDqNmPQbg5ifMEqsHLiIUcQ== + +undici-types@~5.26.4: + version "5.26.5" + resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-5.26.5.tgz#bcd539893d00b56e964fd2657a4866b221a65617" + integrity sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA== unicode-canonical-property-names-ecmascript@^2.0.0: version "2.0.0"