LinearGenomeView
Note: this document is automatically generated from mobx-state-tree objects in our source code. See Core concepts and intro to pluggable elements for more info
Source file
plugins/linear-genome-view/src/LinearGenomeView/model.ts
extends
LinearGenomeView - Properties
property: id
// type signature
IOptionalIType<ISimpleType<string>, [undefined]>
// code
id: ElementId
property: type
this is a string instead of the const literal 'LinearGenomeView' to reduce some typescripting strictness, but you should pass the string 'LinearGenomeView' to the model explicitly
// type signature
string
// code
type: types.literal('LinearGenomeView') as unknown as string
property: offsetPx
corresponds roughly to the horizontal scroll of the LGV
// type signature
number
// code
offsetPx: 0
property: bpPerPx
corresponds roughly to the zoom level, base-pairs per pixel
// type signature
number
// code
bpPerPx: 1
property: displayedRegions
currently displayed regions, can be a single chromosome, arbitrary subsections, or the entire set of chromosomes in the genome, but it not advised to use the entire set of chromosomes if your assembly is very fragmented
// type signature
IArrayType<IModelType<{ refName: ISimpleType<string>; start: ISimpleType<number>; end: ISimpleType<number>; reversed: IOptionalIType<ISimpleType<boolean>, [...]>; } & { ...; }, { ...; }, _NotCustomized, _NotCustomized>>
// code
displayedRegions: types.array(MUIRegion)
property: tracks
array of currently displayed tracks state models instances
// type signature
IArrayType<IAnyType>
// code
tracks: types.array(
pluginManager.pluggableMstType('track', 'stateModel'),
)
property: hideHeader
// type signature
false
// code
hideHeader: false
property: hideHeaderOverview
// type signature
false
// code
hideHeaderOverview: false
property: hideNoTracksActive
// type signature
false
// code
hideNoTracksActive: false
property: trackSelectorType
// type signature
IOptionalIType<ISimpleType<string>, [undefined]>
// code
trackSelectorType: types.optional(
types.enumeration(['hierarchical']),
'hierarchical',
)
property: showCenterLine
show the "center line"
// type signature
IOptionalIType<ISimpleType<boolean>, [undefined]>
// code
showCenterLine: types.optional(types.boolean, () =>
Boolean(
JSON.parse(localStorageGetItem('lgv-showCenterLine') || 'false'),
),
)
property: showCytobandsSetting
show the "cytobands" in the overview scale bar
// type signature
IOptionalIType<ISimpleType<boolean>, [undefined]>
// code
showCytobandsSetting: types.optional(types.boolean, () =>
Boolean(
JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true'),
),
)
property: trackLabels
how to display the track labels, can be "overlapping", "offset", or "hidden", or empty string "" (which results in conf being used). see LinearGenomeViewPlugin https://jbrowse.org/jb2/docs/config/lineargenomeviewplugin/ docs for how conf is used
// type signature
IOptionalIType<ISimpleType<string>, [undefined]>
// code
trackLabels: types.optional(
types.string,
() => localStorageGetItem('lgv-trackLabels') || '',
)
property: showGridlines
show the "gridlines" in the track area
// type signature
true
// code
showGridlines: true
property: highlight
highlights on the LGV from the URL parameters
// type signature
IOptionalIType<IArrayType<IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [...]>
// code
highlight: types.optional(
types.array(types.frozen<Required<ParsedLocString>>()),
[],
)
property: colorByCDS
color by CDS
// type signature
IOptionalIType<ISimpleType<boolean>, [undefined]>
// code
colorByCDS: types.optional(types.boolean, () =>
Boolean(JSON.parse(localStorageGetItem('lgv-colorByCDS') || 'false')),
)
LinearGenomeView - Getters
getter: trackLabelsSetting
this is the effective value of the track labels setting, incorporating both the config and view state. use this instead of view.trackLabels
// type
any
getter: width
// type
number
getter: interRegionPaddingWidth
// type
number
getter: assemblyNames
// type
any[]
getter: assemblyErrors
// type
string
getter: assembliesInitialized
// type
boolean
getter: initialized
// type
any
getter: hasDisplayedRegions
// type
boolean
getter: scaleBarHeight
// type
number
getter: headerHeight
// type
number
getter: trackHeights
// type
number
getter: trackHeightsWithResizeHandles
// type
any
getter: height
// type
any
getter: totalBp
// type
number
getter: maxBpPerPx
// type
number
getter: minBpPerPx
// type
number
getter: error
// type
any
getter: maxOffset
// type
number
getter: minOffset
// type
number
getter: displayedRegionsTotalPx
// type
number
getter: trackTypeActions
// type
Map<string, MenuItem[]>
getter: canShowCytobands
// type
any
getter: showCytobands
// type
boolean
getter: anyCytobandsExist
// type
boolean
getter: cytobandOffset
the cytoband is displayed to the right of the chromosome name, and that offset is calculated manually with this method
// type
number
getter: staticBlocks
static blocks are an important concept jbrowse uses to avoid re-rendering when you scroll to the side. when you horizontally scroll to the right, old blocks to the left may be removed, and new blocks may be instantiated on the right. tracks may use the static blocks to render their data for the region represented by the block
// type
BlockSet
getter: dynamicBlocks
dynamic blocks represent the exact coordinates of the currently visible genome regions on the screen. they are similar to static blocks, but static blocks can go offscreen while dynamic blocks represent exactly what is on screen
// type
BlockSet
getter: roundedDynamicBlocks
rounded dynamic blocks are dynamic blocks without fractions of bp
// type
any
getter: visibleLocStrings
a single "combo-locstring" representing all the regions visible on the screen
// type
string
getter: coarseVisibleLocStrings
same as visibleLocStrings, but only updated every 300ms
// type
string
getter: centerLineInfo
// type
any
LinearGenomeView - Methods
method: MiniControlsComponent
// type signature
MiniControlsComponent: () => React.FC<any>
method: HeaderComponent
// type signature
HeaderComponent: () => React.FC<any>
method: renderProps
// type signature
renderProps: () => any
method: searchScope
// type signature
searchScope: (assemblyName: string) => { assemblyName: string; includeAggregateIndexes: boolean; tracks: IMSTArray<IAnyType> & IStateTreeNode<IArrayType<IAnyType>>; }
method: getTrack
// type signature
getTrack: (id: string) => any
method: rankSearchResults
// type signature
rankSearchResults: (results: BaseResult[]) => BaseResult[]
method: rewriteOnClicks
modifies view menu action onClick to apply to all tracks of same type
// type signature
rewriteOnClicks: (trackType: string, viewMenuActions: MenuItem[]) => void
method: getSelectedRegions
Helper method for the fetchSequence. Retrieves the corresponding regions that were selected by the rubberband
// type signature
getSelectedRegions: (leftOffset?: BpOffset, rightOffset?: BpOffset) => { start: number; end: number; regionNumber?: number; reversed?: boolean; refName: string; assemblyName: string; key: string; offsetPx: number; widthPx: number; variant?: string; isLeftEndOfDisplayedRegion?: boolean; }[]
method: exportSvg
creates an svg export and save using FileSaver
// type signature
exportSvg: (opts?: ExportSvgOptions) => Promise<void>
method: menuItems
return the view menu items
// type signature
menuItems: () => MenuItem[]
method: rubberBandMenuItems
// type signature
rubberBandMenuItems: () => MenuItem[]
method: bpToPx
// type signature
bpToPx: ({ refName, coord, regionNumber, }: { refName: string; coord: number; regionNumber?: number; }) => { index: number; offsetPx: number; }
method: centerAt
scrolls the view to center on the given bp. if that is not in any of the displayed regions, does nothing
// type signature
centerAt: (coord: number, refName: string, regionNumber?: number) => void
method: pxToBp
// type signature
pxToBp: (px: number) => { coord: number; index: number; refName: string; oob: boolean; assemblyName: string; offset: number; start: number; end: number; reversed: boolean; }
LinearGenomeView - Actions
action: setColorByCDS
// type signature
setColorByCDS: (flag: boolean) => void
action: setShowCytobands
// type signature
setShowCytobands: (flag: boolean) => void
action: setWidth
// type signature
setWidth: (newWidth: number) => void
action: setError
// type signature
setError: (error: unknown) => void
action: setHideHeader
// type signature
setHideHeader: (b: boolean) => void
action: setHideHeaderOverview
// type signature
setHideHeaderOverview: (b: boolean) => void
action: setHideNoTracksActive
// type signature
setHideNoTracksActive: (b: boolean) => void
action: setShowGridlines
// type signature
setShowGridlines: (b: boolean) => void
action: addToHighlights
// type signature
addToHighlights: (highlight: Required<ParsedLocString>) => void
action: setHighlight
// type signature
setHighlight: (highlight: Required<ParsedLocString>[]) => void
action: removeHighlight
// type signature
removeHighlight: (highlight: Required<ParsedLocString>) => void
action: scrollTo
// type signature
scrollTo: (offsetPx: number) => number
action: zoomTo
// type signature
zoomTo: (bpPerPx: number, offset?: number, centerAtOffset?: boolean) => number
action: setOffsets
sets offsets of rubberband, used in the get sequence dialog can call view.getSelectedRegions(view.leftOffset,view.rightOffset) to compute the selected regions from the offsets
// type signature
setOffsets: (left?: BpOffset, right?: BpOffset) => void
action: setSearchResults
// type signature
setSearchResults: (searchResults: BaseResult[], searchQuery: string, assemblyName?: string) => void
action: setNewView
// type signature
setNewView: (bpPerPx: number, offsetPx: number) => void
action: horizontallyFlip
// type signature
horizontallyFlip: () => void
action: showTrack
// type signature
showTrack: (trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}) => any
action: hideTrack
// type signature
hideTrack: (trackId: string) => number
action: moveTrackDown
// type signature
moveTrackDown: (id: string) => void
action: moveTrackUp
// type signature
moveTrackUp: (id: string) => void
action: moveTrackToTop
// type signature
moveTrackToTop: (id: string) => void
action: moveTrackToBottom
// type signature
moveTrackToBottom: (id: string) => void
action: moveTrack
// type signature
moveTrack: (movingId: string, targetId: string) => void
action: closeView
// type signature
closeView: () => void
action: toggleTrack
// type signature
toggleTrack: (trackId: string) => boolean
action: setTrackLabels
// type signature
setTrackLabels: (setting: "offset" | "hidden" | "overlapping") => void
action: setShowCenterLine
// type signature
setShowCenterLine: (b: boolean) => void
action: setDisplayedRegions
// type signature
setDisplayedRegions: (regions: Region[]) => void
action: activateTrackSelector
// type signature
activateTrackSelector: () => Widget
action: afterDisplayedRegionsSet
schedule something to be run after the next time displayedRegions is set
// type signature
afterDisplayedRegionsSet: (cb: Function) => void
action: horizontalScroll
// type signature
horizontalScroll: (distance: number) => number
action: center
// type signature
center: () => void
action: showAllRegions
// type signature
showAllRegions: () => void
action: showAllRegionsInAssembly
// type signature
showAllRegionsInAssembly: (assemblyName?: string) => void
action: setDraggingTrackId
// type signature
setDraggingTrackId: (idx?: string) => void
action: setScaleFactor
// type signature
setScaleFactor: (factor: number) => void
action: clearView
this "clears the view" and makes the view return to the import form
// type signature
clearView: () => void
action: slide
perform animated slide
// type signature
slide: (viewWidths: number) => void
action: zoom
perform animated zoom
// type signature
zoom: (targetBpPerPx: number) => void
action: setCoarseDynamicBlocks
// type signature
setCoarseDynamicBlocks: (blocks: BlockSet) => void
action: moveTo
offset is the base-pair-offset in the displayed region, index is the index of the displayed region in the linear genome view
// type signature
moveTo: (start?: BpOffset, end?: BpOffset) => void
action: navToLocString
Navigate to the given locstring, will change displayed regions if needed, and wait for assemblies to be initialized
// type signature
navToLocString: (input: string, optAssemblyName?: string) => Promise<any>
action: navToSearchString
Performs a text index search, and navigates to it immediately if a single result is returned. Will pop up a search dialog if multiple results are returned
// type signature
navToSearchString: ({ input, assembly, }: { input: string; assembly: { configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise<void>; volatileRegions: BasicRegion[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; } & ... 6 more ... & IStateTreeNode<....
action: navToLocations
Similar to navToLocString, but accepts parsed location objects instead of
strings. Will try to perform setDisplayedRegions if changing regions
// type signature
navToLocations: (parsedLocStrings: ParsedLocString[], assemblyName?: string) => Promise<void>
action: navTo
Navigate to a location based on its refName and optionally start, end, and
assemblyName. Will not try to change displayed regions, use navToLocations
instead. Only navigates to a location if it is entirely within a
displayedRegion. Navigates to the first matching location encountered.
Throws an error if navigation was unsuccessful
// type signature
navTo: (query: NavLocation) => void
action: navToMultiple
Navigate to a location based on its refName and optionally start, end, and assemblyName. Will not try to change displayed regions, use navToLocations instead. Only navigates to a location if it is entirely within a displayedRegion. Navigates to the first matching location encountered.
Throws an error if navigation was unsuccessful
// type signature
navToMultiple: (locations: NavLocation[]) => void