SecondaryStructureAxis | bioblocks-viz

Class to represent the x and y axis for a secondary structure on a Plotly graph.

export

Hierarchy

AuxiliaryAxis<SECONDARY_STRUCTURE_KEYS>
- SecondaryStructureAxis

Index

Constructors

constructor

Properties

Accessors

Methods

Constructors

constructor

new SecondaryStructureAxis(sections: SECONDARY_STRUCTURE, minimumRequiredResidues?: number, axisIndex?: number, colorMap?: ColorMapper<"C" | "E" | "G" | "H" | "I" | "S" | "T" | "B">, dataTransformFn?: object, filterFn?: (Anonymous function)): SecondaryStructureAxis

Overrides AuxiliaryAxis.constructor
- Defined in src/component/chart/SecondaryStructureAxis.ts:27
Parameters
- sections: SECONDARY_STRUCTURE
- Default value minimumRequiredResidues: number = 3
- Default value axisIndex: number = 2
- Default value colorMap: ColorMapper<"C" | "E" | "G" | "H" | "I" | "S" | "T" | "B"> = new ColorMapper<SECONDARY_STRUCTURE_KEYS>(new Map([['C', 'red'],['E', 'green'],['H', 'blue'],]),'black',)
- Default value dataTransformFn: object = {C: SecondaryStructureAxis.centerSectionPositionFn,E: SecondaryStructureAxis.centerSectionPositionFn,H: (section: SECONDARY_STRUCTURE_SECTION, index: number) => ({main: index,opposite: Math.sin(index),}),}
  - C: centerSectionPositionFn
  - E: centerSectionPositionFn
  - H: function
    - H(section: SECONDARY_STRUCTURE_SECTION, index: number): object
    - Defined in src/component/chart/SecondaryStructureAxis.ts:44
      Parameters
      - section: SECONDARY_STRUCTURE_SECTION
      - index: number
      Returns object
      - main: number
      - opposite: number
- Default value filterFn: (Anonymous function) = (section: SECONDARY_STRUCTURE_SECTION) => section.length <= minimumRequiredResidues
Returns SecondaryStructureAxis

Properties

Protected axes

axes: Map<SECONDARY_STRUCTURE_KEYS, IAxisMapping> = new Map()

axisIndex

axisIndex: number

colorMap

colorMap: ColorMapper<"C" | "E" | "G" | "H" | "I" | "S" | "T" | "B">

dataTransformFn

dataTransformFn: object

Type declaration

C: centerSectionPositionFn
E: centerSectionPositionFn
H: function
- H(section: SECONDARY_STRUCTURE_SECTION, index: number): object
- - Defined in src/component/chart/SecondaryStructureAxis.ts:44
  Parameters
  - section: SECONDARY_STRUCTURE_SECTION
  - index: number
  Returns object
  - main: number
  - opposite: number

filterFn

filterFn: (Anonymous function)

Protected highlightedAxes

highlightedAxes: Map<SECONDARY_STRUCTURE_KEYS, IAxisMapping> = new Map()

minimumRequiredResidues

minimumRequiredResidues: number

sections

sections: SECONDARY_STRUCTURE

Accessors

axis

get axis(): Map<T, IAxisMapping>

Inherited from AuxiliaryAxis.axis
- Defined in src/component/chart/AuxiliaryAxis.ts:31
Get all the axis objects belonging to this Auxiliary Axis.

Returns Map<T, IAxisMapping>

highlightedXAxes

get highlightedXAxes(): object[]

Inherited from AuxiliaryAxis.highlightedXAxes
- Defined in src/component/chart/AuxiliaryAxis.ts:50
Get all the highlighted x-axis objects belonging to this Auxiliary Axis.

Returns object[]

highlightedYAxes

get highlightedYAxes(): object[]

Inherited from AuxiliaryAxis.highlightedYAxes
- Defined in src/component/chart/AuxiliaryAxis.ts:74
Get all the highlighted y-axis objects belonging to this Auxiliary Axis.

Returns object[]

xAxes

get xAxes(): object[]

Inherited from AuxiliaryAxis.xAxes
- Defined in src/component/chart/AuxiliaryAxis.ts:38
Get all the x-axis objects belonging to this Auxiliary Axis.

Returns object[]

yAxes

get yAxes(): object[]

Inherited from AuxiliaryAxis.yAxes
- Defined in src/component/chart/AuxiliaryAxis.ts:62
Get all the y-axis objects belonging to this Auxiliary Axis.

Returns object[]

Methods

Protected auxiliaryAxisDefaults

auxiliaryAxisDefaults(key: SECONDARY_STRUCTURE_KEYS): REQUIRED_BIOBLOCKS_PLOTLY_DATA

Inherited from AuxiliaryAxis.auxiliaryAxisDefaults
- Defined in src/component/chart/AuxiliaryAxis.ts:203
Default plotly data for an axis.

Parameters
- key: SECONDARY_STRUCTURE_KEYS
  
  The label for this piece of data.
Returns REQUIRED_BIOBLOCKS_PLOTLY_DATA

Protected deriveHighlightedPointsInAxis

deriveHighlightedPointsInAxis(section: Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>): object

Inherited from AuxiliaryAxis.deriveHighlightedPointsInAxis
- Defined in src/component/chart/AuxiliaryAxis.ts:262
Parameters
- section: Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>
Returns object
- main: number[]
- opposite: (null | number)[]

Protected derivePointsInAxis

derivePointsInAxis(section: Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>): object

Inherited from AuxiliaryAxis.derivePointsInAxis
- Defined in src/component/chart/AuxiliaryAxis.ts:241
Determines the points that make up the axis for both the main and opposite axis side.

Parameters
- section: Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>
  
  The section of data to derive points for.
Returns object
- main: number[]
- opposite: (null | number)[]

Protected generateBetaSheetStyle

generateBetaSheetStyle(data: Partial<IPlotlyData>, symbols: string[]): Partial<IPlotlyData>

- Defined in src/component/chart/SecondaryStructureAxis.ts:93
Generate the Plotly layout specific to beta sheet representation.

Parameters
- data: Partial<IPlotlyData>
  
  Data for this axis.
- symbols: string[]
  
  The symbols that make up this axis. Should be an array of empty lines with an arrow at the end.
Returns Partial<IPlotlyData>

Plotly layout specific to beta sheet representation.

Protected generateHighlightedXAxisSegment

generateHighlightedXAxisSegment(key: SECONDARY_STRUCTURE_KEYS): BIOBLOCKS_PLOTLY_DATA

Inherited from AuxiliaryAxis.generateHighlightedXAxisSegment
- Defined in src/component/chart/AuxiliaryAxis.ts:167
Plotly data specific for the highlighted x axis.

Parameters
- key: SECONDARY_STRUCTURE_KEYS
  
  The label for this piece of data.
Returns BIOBLOCKS_PLOTLY_DATA

Protected generateHighlightedYAxisSegment

generateHighlightedYAxisSegment(key: SECONDARY_STRUCTURE_KEYS): BIOBLOCKS_PLOTLY_DATA

Inherited from AuxiliaryAxis.generateHighlightedYAxisSegment
- Defined in src/component/chart/AuxiliaryAxis.ts:191
Plotly data specific for the highlighted y axis.

Parameters
- key: SECONDARY_STRUCTURE_KEYS
  
  The label for this piece of data.
Returns BIOBLOCKS_PLOTLY_DATA

Protected generateXAxisSegment

generateXAxisSegment(key: SECONDARY_STRUCTURE_KEYS): BIOBLOCKS_PLOTLY_DATA

Inherited from AuxiliaryAxis.generateXAxisSegment
- Defined in src/component/chart/AuxiliaryAxis.ts:155
Plotly data specific for the x axis.

Parameters
- key: SECONDARY_STRUCTURE_KEYS
  
  The label for this piece of data.
Returns BIOBLOCKS_PLOTLY_DATA

Protected generateYAxisSegment

generateYAxisSegment(key: SECONDARY_STRUCTURE_KEYS): BIOBLOCKS_PLOTLY_DATA

Inherited from AuxiliaryAxis.generateYAxisSegment
- Defined in src/component/chart/AuxiliaryAxis.ts:179
Plotly data specific for the y axis.

Parameters
- key: SECONDARY_STRUCTURE_KEYS
  
  The label for this piece of data.
Returns BIOBLOCKS_PLOTLY_DATA

getAxisById

getAxisById(id: SECONDARY_STRUCTURE_KEYS): undefined | IAxisMapping

Inherited from AuxiliaryAxis.getAxisById
- Defined in src/component/chart/AuxiliaryAxis.ts:104
Parameters
- id: SECONDARY_STRUCTURE_KEYS
Returns undefined | IAxisMapping

Protected highlightedAuxiliaryAxisDefaults

highlightedAuxiliaryAxisDefaults(key: SECONDARY_STRUCTURE_KEYS): BIOBLOCKS_PLOTLY_DATA

Inherited from AuxiliaryAxis.highlightedAuxiliaryAxisDefaults
- Defined in src/component/chart/AuxiliaryAxis.ts:228
Default plotly data for a highlighted axis.

Parameters
- key: SECONDARY_STRUCTURE_KEYS
  
  The label for this piece of data.
Returns BIOBLOCKS_PLOTLY_DATA

Protected setupAuxiliaryAxis

setupAuxiliaryAxis(): void

Overrides AuxiliaryAxis.setupAuxiliaryAxis
- Defined in src/component/chart/SecondaryStructureAxis.ts:54
Returns void

Static Protected centerSectionPositionFn

centerSectionPositionFn(section: SECONDARY_STRUCTURE_SECTION, index: number): object

- Defined in src/component/chart/SecondaryStructureAxis.ts:24
Parameters
- section: SECONDARY_STRUCTURE_SECTION
- index: number
Returns object
- main: number
- opposite: number

Hierarchy

Index

Constructors

Properties

Accessors

Methods

Constructors

constructor

Parameters

sections: SECONDARY_STRUCTURE

Default value minimumRequiredResidues: number = 3

Default value axisIndex: number = 2

Default value colorMap: ColorMapper<"C" | "E" | "G" | "H" | "I" | "S" | "T" | "B"> = new ColorMapper<SECONDARY_STRUCTURE_KEYS>(new Map([['C', 'red'],['E', 'green'],['H', 'blue'],]),'black',)

Default value dataTransformFn: object = {C: SecondaryStructureAxis.centerSectionPositionFn,E: SecondaryStructureAxis.centerSectionPositionFn,H: (section: SECONDARY_STRUCTURE_SECTION, index: number) => ({main: index,opposite: Math.sin(index),}),}

C: centerSectionPositionFn

E: centerSectionPositionFn

H: function

Parameters

section: SECONDARY_STRUCTURE_SECTION

index: number

Returns object

main: number

opposite: number

Default value filterFn: (Anonymous function) = (section: SECONDARY_STRUCTURE_SECTION) => section.length <= minimumRequiredResidues

Returns SecondaryStructureAxis

Properties

Protected axes

axisIndex

colorMap

dataTransformFn

Type declaration

C: centerSectionPositionFn

E: centerSectionPositionFn

H: function

Parameters

section: SECONDARY_STRUCTURE_SECTION

index: number

Returns object

main: number

opposite: number

filterFn

Protected highlightedAxes

minimumRequiredResidues

sections

Accessors

axis

Returns Map<T, IAxisMapping>

highlightedXAxes

Returns object[]

highlightedYAxes

Returns object[]

xAxes

Returns object[]

yAxes

Returns object[]

Methods

Protected auxiliaryAxisDefaults

Parameters

key: SECONDARY_STRUCTURE_KEYS

Returns REQUIRED_BIOBLOCKS_PLOTLY_DATA

Protected deriveHighlightedPointsInAxis

Parameters

section: Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>

Returns object

main: number[]

opposite: (null | number)[]

Protected derivePointsInAxis

Parameters

section: Bioblocks1DSection<SECONDARY_STRUCTURE_KEYS>

Returns object

main: number[]

opposite: (null | number)[]

Protected generateBetaSheetStyle

Parameters

data: Partial<IPlotlyData>

symbols: string[]

Returns Partial<IPlotlyData>

Protected generateHighlightedXAxisSegment

Parameters

key: SECONDARY_STRUCTURE_KEYS