Class: Layout

Members

backboneBackbone

Get the Backbone

bbInsideOffsetNumber

Get the distance from the backbone to the inner/bottom edge of the map.

bbOutsideOffsetNumber

Get the distance from the backbone to the outer/top edge of the map.

canvasCanvas

Get the Canvas

centerInsideOffsetNumber

Get the distance from the center of the map to the inner/bottom edge of the map.

centerOutsideOffsetNumber

Get the distance from the center of the map to the outer/top edge of the map.

heightNumber

Get the canvas height

initialMapThicknessProportion

Get or set the initial map thickness as a proportion of a viewer dimension (height for linear maps, minimum dimension for circular maps). The initial map thickness is at a zoomFactor of 1.

maxMapThicknessProportion

Get or set the maximum map thickness as a proportion of a viewer dimension (height for linear maps, minimum dimension for circular maps).

maxSlotThickness

Get or set the max slot thickness.

minSlotThickness

Get or set the min slot thickness.

scaleObject

Return an object that contains the 3 D3 Continuous Scales used by CGView. See Map Scales for details.

Scale	Description
x	Convert between the canvas x position (0 is left side of canvas) and map x position (center of map).
y	Convert between the canvas y position (0 is top side of canvas) and map y position (center of map).
bp - circular	Convert between bp and radians (Top of map is 1 bp and -π/2).
bp - linear	Convert between bp and distance on x-axis

sequenceSequence

Get the Sequence

typeCanvas

Get or set the layout type: linear or circular.

viewerViewer

Get the Viewer

widthNumber

Get the canvas width

Methods

adjustedBackboneCenterOffset(centerOffset){Number}

Layout.js, line 341

Return an the backbone center offset adjusted for the zoom level.

Name	Type	Description
centerOffset	Number	The backbone initial centerOffset.

Returns:

Type	Description
Number	adjustedCenterOffset

bpForPoint(point){Number}

Layout.js, line 219

Returns the basepair corresponding to the given point on the canvas.

Name	Type	Description
point	Point	Point on the canvas.

Returns:

Type	Description
Number	The basepair.

centerOffsetForPoint(point){Number}

Layout.js, line 231

Returns the Center Offset for the given point on the canvas. Center offset is the distance from the center of the map. For a circular map, this is the radius, while for a linear map, it's the distance from the backbone.

Name	Type	Description
point	Point	Point on the canvas.

Returns:

Type	Description
Number	Center Offset

clockPositionForBp(bp, invers){Number}

Layout.js, line 298

Returns the clock position (1-12) for the supplied bp. For example, the top of the map would be 12, the bottom would be 6 and the right side of a circular map will be 3.

Name	Type	Description
bp	Number	Basepair position on the map.
invers	Boolean	When true, give the opposite clock position (e.g. 6 instead of 12).

Returns:

Type	Description
Number	An integer between 1 and 12.

domainsFor(bp, zoomFactor){Array}

Layout.js, line 242

Returns the X and Y scale domains for the given bp and zoomFactor.

Name	Type	Default	Description
bp	Number		Basepair
zoomFactor	Number	Current viewer zoom factor	optional The zoom factor used to calculate the domains

Returns:

Type	Description
Array	The X and Y scale domains in the form of [[X1, X2], [Y1, Y2]].

path(layer, centerOffset, startBp, stopBp, anticlockwise, startType)

Layout.js, line 360

Adds a lineTo path to the given layer. Path does not draw. It only adds lineTo and optionally moveTo commands to the context for the given layer.

Name	Type	Default	Description
layer	String		The name of the canvas layer to add the path.
centerOffset	Number		This distance from the center of the Map.
startBp	Number		The start position in basepairs.
stopBp	Number		The stop position in basepairs.
anticlockwise	Boolean	false	optional For circular maps the default direction is clockwise. Set this to true to draw arcs, anticlockwise.
startType	String	'moveTo'	optional How the path should be started. Allowed values: moveTo: moveTo start; lineTo stop lineTo: lineTo start; lineTo stop noMoveTo: ingore start; lineTo stop

pixelsPerBp(centerOffset){Number}

Layout.js, line 285

The number of pixels per basepair along the given centerOffset.

Name	Type	Default	Description
centerOffset	Number	Backbone.adjustedCenterOffset	optional Distance from the center of the map. For a circular map, this is the radius, while for a linear map, it's the distance from the backbone.

Returns:

Type	Description
Number	Pixels per basepair.

pointForBp(bp, centerOffset){Point}

Layout.js, line 209

Returns the point on the canvas for the given bp and centerOffset.

Name	Type	Default	Description
bp	Number		Basepair
centerOffset	Number	Backbone.adjustedCenterOffset	optional Distance from the center of the map. For a circular map, this is the radius, while for a linear map, it's the distance from the backbone.

Returns:

Type	Description
Point	The point on the canvas.

visibleRangeForCenterOffset(centerOffset, margin){CGRange}

Layout.js, line 267

Return the CGRange for the sequence visisible at the given centerOffset. The margin is a distance in pixels added on to the Canvas size when calculating the CGRange.

Name	Type	Description
centerOffset	Number	The distance from the center of them map.
margin	Number	An amount (in pixels) added to the Canvas in all dimensions.

Returns:

Type	Description
CGRange	the visible range.