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40 changes: 40 additions & 0 deletions
40
packages/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| import RpcMethodType from './RpcMethodType' | ||
| import { renameRegionsIfNeeded } from '../util' | ||
| import SerializableFilterChain from './renderers/util/serializableFilterChain' | ||
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| import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods' | ||
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| export default abstract class RpcMethodTypeWithFiltersAndRenameRegions extends RpcMethodType { | ||
| async deserializeArguments(args: any, rpcDriverClassName: string) { | ||
| const l = await super.deserializeArguments(args, rpcDriverClassName) | ||
| return { | ||
| ...l, | ||
| filters: args.filters | ||
| ? new SerializableFilterChain({ | ||
| filters: args.filters, | ||
| }) | ||
| : undefined, | ||
| } | ||
| } | ||
|
|
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| async serializeArguments( | ||
| args: RenderArgs & { | ||
| stopToken?: string | ||
| statusCallback?: (arg: string) => void | ||
| }, | ||
| rpcDriverClassName: string, | ||
| ) { | ||
| const pm = this.pluginManager | ||
| const assemblyManager = pm.rootModel?.session?.assemblyManager | ||
| if (!assemblyManager) { | ||
| throw new Error('no assembly manager') | ||
| } | ||
|
|
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| const renamedArgs = await renameRegionsIfNeeded(assemblyManager, { | ||
| ...args, | ||
| filters: args.filters?.toJSON().filters, | ||
| }) | ||
|
|
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| return super.serializeArguments(renamedArgs, rpcDriverClassName) | ||
| } | ||
| } |
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47 changes: 47 additions & 0 deletions
47
plugins/linear-genome-view/src/BaseLinearDisplay/components/BlockError.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| import React from 'react' | ||
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| import ErrorMessageStackTraceDialog from '@jbrowse/core/ui/ErrorMessageStackTraceDialog' | ||
| import { getSession } from '@jbrowse/core/util' | ||
| import RefreshIcon from '@mui/icons-material/Refresh' | ||
| import ReportIcon from '@mui/icons-material/Report' | ||
| import { IconButton, Tooltip } from '@mui/material' | ||
| import { observer } from 'mobx-react' | ||
|
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| import BlockMsg from './BlockMsg' | ||
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| const BlockError = observer(function ({ model }: { model: any }) { | ||
| return ( | ||
| <BlockMsg | ||
| message={`${model.error}`} | ||
| severity="error" | ||
| action={ | ||
| <> | ||
| <Tooltip title="Reload track"> | ||
| <IconButton | ||
| data-testid="reload_button" | ||
| onClick={() => { | ||
| model.reload() | ||
| }} | ||
| > | ||
| <RefreshIcon /> | ||
| </IconButton> | ||
| </Tooltip> | ||
| <Tooltip title="Show stack trace"> | ||
| <IconButton | ||
| onClick={() => { | ||
| getSession(model).queueDialog(onClose => [ | ||
| ErrorMessageStackTraceDialog, | ||
| { onClose, error: model.error as Error }, | ||
| ]) | ||
| }} | ||
| > | ||
| <ReportIcon /> | ||
| </IconButton> | ||
| </Tooltip> | ||
| </> | ||
| } | ||
| /> | ||
| ) | ||
| }) | ||
|
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| export default BlockError |
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86 changes: 86 additions & 0 deletions
86
...src/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| import React from 'react' | ||
|
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| import { getContainingView, getSession } from '@jbrowse/core/util' | ||
| import { observer } from 'mobx-react' | ||
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| import type { MultiLinearVariantMatrixDisplayModel } from '../model' | ||
| import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' | ||
|
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| const Wrapper = observer(function ({ | ||
| children, | ||
| model, | ||
| exportSVG, | ||
| }: { | ||
| model: MultiLinearVariantMatrixDisplayModel | ||
| children: React.ReactNode | ||
| exportSVG?: boolean | ||
| }) { | ||
| const { height } = model | ||
| return exportSVG ? ( | ||
| <g | ||
| transform={`translate(${Math.max( | ||
| 0, | ||
| -(getContainingView(model) as LinearGenomeViewModel).offsetPx, | ||
| )})`} | ||
| > | ||
| {children} | ||
| </g> | ||
| ) : ( | ||
| <svg | ||
| style={{ | ||
| position: 'absolute', | ||
| top: 0, | ||
| left: Math.max( | ||
| 0, | ||
| -(getContainingView(model) as LinearGenomeViewModel).offsetPx, | ||
| ), | ||
| pointerEvents: 'none', | ||
| height, | ||
| width: getContainingView(model).width, | ||
| }} | ||
| > | ||
| {children} | ||
| </svg> | ||
| ) | ||
| }) | ||
|
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| const LinesConnectingMatrixToGenomicPosition = observer(function ({ | ||
| model, | ||
| exportSVG, | ||
| }: { | ||
| model: MultiLinearVariantMatrixDisplayModel | ||
| exportSVG?: boolean | ||
| }) { | ||
| const { assemblyManager } = getSession(model) | ||
| const view = getContainingView(model) as LinearGenomeViewModel | ||
| const { featuresVolatile } = model | ||
| const { offsetPx, assemblyNames } = view | ||
| const assembly = assemblyManager.get(assemblyNames[0]!) | ||
| const b0 = view.dynamicBlocks.contentBlocks[0]?.widthPx || 0 | ||
| const w = b0 / (featuresVolatile?.length || 1) | ||
| return assembly && featuresVolatile ? ( | ||
| <Wrapper exportSVG={exportSVG} model={model}> | ||
| {featuresVolatile.map((f, i) => { | ||
| const c = | ||
| (view.bpToPx({ | ||
| refName: | ||
| assembly.getCanonicalRefName(f.get('refName')) || | ||
| f.get('refName'), | ||
| coord: f.get('start'), | ||
| })?.offsetPx || 0) - Math.max(offsetPx, 0) | ||
| return ( | ||
| <line | ||
| stroke="black" | ||
| key={f.id()} | ||
| x1={i * w + w / 2} | ||
| x2={c} | ||
| y1={20} | ||
| y2={0} | ||
| /> | ||
| ) | ||
| })} | ||
| </Wrapper> | ||
| ) : null | ||
| }) | ||
|
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| export default LinesConnectingMatrixToGenomicPosition |
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