Class BAMTrack

Hierarchy (View Summary)

Constructors

constructor

Properties

alignmentTrack bigwig_track bottom color color_function config coverageTrack display_alignments draw_bigwig feature_source filterOption pairsSupported sortDirection sortOption top viewAsPairs visibilityWindow custom_tracks filters

Methods

_setFeatureSource addExtraControls altClick computePixelHeight drawFeatures drawMessage drawScale getConfig getFeatureAt getFeatures getSettings paintAxis popupData popupMenuItems setColorFunction setConfig setConfigAttribute calculateLabel getTrack getTypeFromURL parseConfig

Constructors

constructor

Properties

alignmentTrack

alignmentTrack: undefined | AlignmentTrack

bigwig_track

bigwig_track: undefined | MLVWigTrack

bottom

bottom: any

color

color: any

color_function

color_function: any

config

config: any

coverageTrack

coverageTrack: undefined | CoverageTrack

display_alignments

display_alignments: boolean

draw_bigwig

draw_bigwig: undefined | boolean

feature_source

feature_source: undefined | BamSource

filterOption

filterOption: any

pairsSupported

pairsSupported: boolean

sortDirection

sortDirection: boolean

sortOption

sortOption: any

top

top: any

viewAsPairs

viewAsPairs: boolean

visibilityWindow

visibilityWindow: any

Staticcustom_tracks

custom_tracks: {}

Staticfilters

filters: {
    mappingQuality: (lower: any, upper: any) => (alignment: any) => boolean;
    noop: () => (alignment: any) => boolean;
    strand: (strand: any) => (alignment: any) => boolean;
}

Methods

_setFeatureSource

addExtraControls

altClick

computePixelHeight

  • computePixelHeight(alignmentContainer: any): number

  • Optional method to compute pixel height to accomodate the list of features. The implementation below has side effects (modifiying the samples hash). This is unfortunate, but harmless.

    Parameters

    • alignmentContainer: any

    Returns number

drawFeatures

drawMessage

drawScale

getConfig

getFeatureAt

getFeatures

  • getFeatures(chr: any, bpStart: any, bpEnd: any, force: any, data: any): any

  • Retrieves the features requested, the default is just to get the features from the feature source

    Parameters

    • chr: any

      The chromosome

    • bpStart: any

      The start of the range from which to obtain features

    • bpEnd: any

      The end of the range from which to obtain features

    • force: any

      If true then cached features should not be used but fresh features retrieved

    • data: any

      contains bp ber pixel and width of the canvas

    Returns any

getSettings

  • getSettings(
        panel: any,
    ): (
        | {
            current_value: any;
            func: (x: any) => void;
            label: string;
            max?: undefined;
            min?: undefined;
            type: string;
        }
        | {
            current_value: any;
            func: (x: any) => void;
            label: string;
            max: number;
            min: number;
            type: string;
        }
        | {
            current_value?: undefined;
            func: () => void;
            label: string;
            max?: undefined;
            min?: undefined;
            type: string;
        }
    )[]

  • Parameters

    • panel: any

    Returns (
        | {
            current_value: any;
            func: (x: any) => void;
            label: string;
            max?: undefined;
            min?: undefined;
            type: string;
        }
        | {
            current_value: any;
            func: (x: any) => void;
            label: string;
            max: number;
            min: number;
            type: string;
        }
        | {
            current_value?: undefined;
            func: () => void;
            label: string;
            max?: undefined;
            min?: undefined;
            type: string;
        }
    )[]

paintAxis

  • paintAxis(ctx: any, pixelWidth: any, pixelHeight: any): void

  • Parameters

    • ctx: any
    • pixelWidth: any
    • pixelHeight: any

    Returns void

popupData

  • popupData(genomicLocation: any, xOffset: any, yOffset: any): any

  • Parameters

    • genomicLocation: any
    • xOffset: any
    • yOffset: any

    Returns any

popupMenuItems

setColorFunction

setConfig

setConfigAttribute

StaticcalculateLabel

StaticgetTrack

StaticgetTypeFromURL

StaticparseConfig

Settings

Member Visibility

On This Page

Constructors
Properties
Methods