From ad83306cfc6424c4c4f2a3adf1b852ba4f2153ca Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 14 Mar 2024 18:07:36 -0400 Subject: [PATCH] Clear selection --- src/ProteinView/clearSelection.ts | 5 + src/ProteinView/components/Header.tsx | 63 ++++ src/ProteinView/components/HelpButton.tsx | 34 +- .../components/ProteinAlignment.tsx | 7 +- src/ProteinView/components/ProteinView.tsx | 41 ++- .../components/ProteinViewHeader.tsx | 48 --- src/ProteinView/components/SplitString.tsx | 5 +- src/ProteinView/model.ts | 20 ++ src/ProteinView/proteinToGenomeMapping.ts | 17 +- yarn.lock | 292 +++++++++--------- 10 files changed, 304 insertions(+), 228 deletions(-) create mode 100644 src/ProteinView/clearSelection.ts create mode 100644 src/ProteinView/components/Header.tsx delete mode 100644 src/ProteinView/components/ProteinViewHeader.tsx diff --git a/src/ProteinView/clearSelection.ts b/src/ProteinView/clearSelection.ts new file mode 100644 index 0000000..1876d24 --- /dev/null +++ b/src/ProteinView/clearSelection.ts @@ -0,0 +1,5 @@ +import { PluginContext } from 'molstar/lib/mol-plugin/context' + +export default function clearSelection({ plugin }: { plugin: PluginContext }) { + plugin?.managers.interactivity.lociSelects.deselectAll() +} diff --git a/src/ProteinView/components/Header.tsx b/src/ProteinView/components/Header.tsx new file mode 100644 index 0000000..b46c299 --- /dev/null +++ b/src/ProteinView/components/Header.tsx @@ -0,0 +1,63 @@ +import React, { useState } from 'react' +import { observer } from 'mobx-react' +import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton' + +// icons +import MenuIcon from '@mui/icons-material/Menu' + +// locals +import { JBrowsePluginProteinViewModel } from '../model' +import ProteinAlignment from './ProteinAlignment' +import { Visibility } from '@mui/icons-material' + +const ProteinViewHeader = observer(function ({ + model, +}: { + model: JBrowsePluginProteinViewModel +}) { + const { clickString, hoverString, showHighlight, zoomToBaseLevel } = model + const [show, setShow] = useState(true) + return ( +
+
+ + {[ + clickString ? `Click: ${clickString}` : '', + hoverString ? `Hover: ${hoverString}` : '', + ].join(' ')} + + + setShow(!show), + }, + { + label: 'Show highlight', + type: 'checkbox', + checked: showHighlight, + icon: Visibility, + onClick: () => model.setShowHighlight(!showHighlight), + }, + { + label: 'Zoom to base level on click', + type: 'checkbox', + checked: zoomToBaseLevel, + icon: Visibility, + onClick: () => model.setZoomToBaseLevel(!zoomToBaseLevel), + }, + ]} + > + + +
+
{show ? : null}
+
+ ) +}) + +export default ProteinViewHeader diff --git a/src/ProteinView/components/HelpButton.tsx b/src/ProteinView/components/HelpButton.tsx index 46132b4..4bda7fa 100644 --- a/src/ProteinView/components/HelpButton.tsx +++ b/src/ProteinView/components/HelpButton.tsx @@ -1,23 +1,31 @@ -import React, { Suspense, lazy, useState } from 'react' +import React, { lazy } from 'react' import { IconButton } from '@mui/material' +import { getSession } from '@jbrowse/core/util' // locals +import { JBrowsePluginProteinViewModel } from '../model' + +// icons import Help from '@mui/icons-material/Help' const HelpDialog = lazy(() => import('./HelpDialog')) -export default function HelpButton() { - const [open, setOpen] = useState(false) +export default function HelpButton({ + model, +}: { + model: JBrowsePluginProteinViewModel +}) { return ( - <> - setOpen(true)}> - - - {open ? ( - - setOpen(false)} /> - - ) : null} - + + getSession(model).queueDialog(handleClose => [ + HelpDialog, + { handleClose }, + ]) + } + > + + ) } diff --git a/src/ProteinView/components/ProteinAlignment.tsx b/src/ProteinView/components/ProteinAlignment.tsx index ac70dbc..14936e8 100644 --- a/src/ProteinView/components/ProteinAlignment.tsx +++ b/src/ProteinView/components/ProteinAlignment.tsx @@ -21,6 +21,7 @@ const ProteinAlignment = observer(function ({ alignment, structurePositionToAlignmentMap, alignmentToStructurePosition, + showHighlight, } = model const a0 = alignment!.alns[0].seq as string const a1 = alignment!.alns[1].seq as string @@ -52,7 +53,8 @@ const ProteinAlignment = observer(function ({ } return (
- + + Alignment of the protein structure file's sequence with the selected transcript's sequence. Green is the aligned portion @@ -78,6 +80,7 @@ const ProteinAlignment = observer(function ({         - ) : ( + ) : alignment ? ( + ) : ( + ) }) @@ -62,6 +68,7 @@ const ProteinViewContainer = observer(function ({ structureSeqToTranscriptSeqPosition, seq2, structureSeqHoverPos, + showHighlight, } = model const { error } = useProteinViewClickBehavior({ plugin, model }) @@ -78,14 +85,18 @@ const ProteinViewContainer = observer(function ({ if (!plugin || !structureSeqToTranscriptSeqPosition || !structure) { return } - for (const coord of Object.keys(structureSeqToTranscriptSeqPosition)) { - selectResidue({ - structure, - plugin, - selectedResidue: +coord + 1, - }) + if (showHighlight) { + for (const coord of Object.keys(structureSeqToTranscriptSeqPosition)) { + selectResidue({ + structure, + plugin, + selectedResidue: +coord + 1, + }) + } + } else { + clearSelection({ plugin }) } - }, [plugin, structure, structureSeqToTranscriptSeqPosition]) + }, [plugin, structure, showHighlight, structureSeqToTranscriptSeqPosition]) useEffect(() => { if (!plugin || !structure || structureSeqHoverPos === undefined) { @@ -105,7 +116,7 @@ const ProteinViewContainer = observer(function ({ return (
{error ? : null} - +
-
- - {[ - clickString ? `Click: ${clickString}` : '', - hoverString ? `Hover: ${hoverString}` : '', - ].join(' ')} - - - {alignment ? ( - - ) : null} -
-
- {!alignment ? ( -
Loading pairwise alignment...
- ) : ( -
{show ? : null}
- )} -
-
- ) -}) - -export default ProteinViewHeader diff --git a/src/ProteinView/components/SplitString.tsx b/src/ProteinView/components/SplitString.tsx index 2d1b320..bac1d6c 100644 --- a/src/ProteinView/components/SplitString.tsx +++ b/src/ProteinView/components/SplitString.tsx @@ -1,16 +1,19 @@ import React from 'react' + export default function SplitString({ str, col, set, onMouseOver, onClick, + showHighlight, }: { str: string col?: number set?: Set onMouseOver?: (arg: number) => void onClick?: (arg: number) => void + showHighlight: boolean }) { return str.split('').map((d, i) => ( ({ @@ -206,6 +214,18 @@ function stateModelFactory() { setAlignment(r?: ReturnType) { self.alignment = r }, + /** + * #action + */ + setShowHighlight(arg: boolean) { + self.showHighlight = arg + }, + /** + * #action + */ + setZoomToBaseLevel(arg: boolean) { + self.zoomToBaseLevel = arg + }, })) .views(self => ({ /** diff --git a/src/ProteinView/proteinToGenomeMapping.ts b/src/ProteinView/proteinToGenomeMapping.ts index c06fed2..a97a2fb 100644 --- a/src/ProteinView/proteinToGenomeMapping.ts +++ b/src/ProteinView/proteinToGenomeMapping.ts @@ -42,7 +42,8 @@ export async function clickProteinToGenome({ }) { const session = getSession(model) const result = proteinToGenomeMapping({ structureSeqPos, model }) - const { genomeToTranscriptSeqMapping } = model + const { genomeToTranscriptSeqMapping, zoomToBaseLevel } = model + const { assemblyManager } = session if (!genomeToTranscriptSeqMapping || result === undefined) { return undefined } @@ -57,9 +58,17 @@ export async function clickProteinToGenome({ end: s2, }, ]) - await lgv.navToLocString( - `${refName}:${s1}-${s2}${strand === -1 ? '[rev]' : ''}`, - ) + + if (!zoomToBaseLevel) { + const assembly = assemblyManager.get(lgv.assemblyNames[0]) + const r = assembly?.getCanonicalRefName(refName) ?? refName + // @ts-expect-error + lgv.centerAt(s1, r) + } else { + await lgv.navToLocString( + `${refName}:${s1}-${s2}${strand === -1 ? '[rev]' : ''}`, + ) + } } export function hoverProteinToGenome({ diff --git a/yarn.lock b/yarn.lock index 3f8f6e2..33145d5 100644 --- a/yarn.lock +++ b/yarn.lock @@ -368,120 +368,120 @@ resolved "https://registry.yarnpkg.com/@emotion/weak-memoize/-/weak-memoize-0.3.1.tgz#d0fce5d07b0620caa282b5131c297bb60f9d87e6" integrity sha512-EsBwpc7hBUJWAsNPBmJy4hxWx12v6bshQsldrVmjxJoc3isbxhOrF2IcCpaXxfvq03NwkI7sbsOLXbYuqF/8Ww== -"@esbuild/aix-ppc64@0.20.1": - version "0.20.1" - resolved "https://registry.yarnpkg.com/@esbuild/aix-ppc64/-/aix-ppc64-0.20.1.tgz#eafa8775019b3650a77e8310ba4dbd17ca7af6d5" - integrity sha512-m55cpeupQ2DbuRGQMMZDzbv9J9PgVelPjlcmM5kxHnrBdBx6REaEd7LamYV7Dm8N7rCyR/XwU6rVP8ploKtIkA== - -"@esbuild/android-arm64@0.20.1": - version "0.20.1" - resolved "https://registry.yarnpkg.com/@esbuild/android-arm64/-/android-arm64-0.20.1.tgz#68791afa389550736f682c15b963a4f37ec2f5f6" - integrity sha512-hCnXNF0HM6AjowP+Zou0ZJMWWa1VkD77BXe959zERgGJBBxB+sV+J9f/rcjeg2c5bsukD/n17RKWXGFCO5dD5A== - 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