CGView - XML - featureSlot element

XML - featureSlot element
The featureSlot element represents a slot of space on the sequence map. When the map is drawn, the featureSlots form concentric rings around the backbone circle. Individual features, which are described using feature elements, are drawn in the featureSlots. featureSlots are allocated space in the order that they are encountered, such that those encountered first receive space closest to the backbone circle. The featureSlot element can contain any number of feature elements. The featureSlot element is a child of the cgview element.

The following sample CGView document shows how featureSlot elements are used to reserve space for sequence features:

<?xml version="1.0" encoding="ISO-8859-1"?> <cgview backboneRadius="160" sequenceLength="1000" height="600" width="600"> <featureSlot strand="direct"> <feature color="red" decoration="clockwise-arrow" label="feature A"> <featureRange start="463" stop="493" /> </feature> <feature color="blue" decoration="clockwise-arrow" label="feature B"> <featureRange start="800" stop="830" /> </feature> </featureSlot> <featureSlot strand="direct"> <feature color="black" decoration="arc" label="feature C"> <featureRange start="500" stop="900" /> </feature> </featureSlot> <featureSlot strand="reverse"> <feature color="purple" decoration="counterclockwise-arrow" label="feature D"> <featureRange start="850" stop="100" /> </feature> </featureSlot> </cgview>

This is the map generated by the above document:

output of above document

Required featureSlot attributes

Attribute	Description	Values
strand	Specifies whether this featureSlot corresponds to the direct DNA strand or the reverse DNA strand. Direct-strand featureSlots are drawn on the outside of the backbone circle, while reverse-strand featureSlots are drawn on the inside of the backbone circle.	direct - this is a direct-strand featureSlot. reverse - this is a reverse-strand featureSlot.

Optional featureSlot attributes

Attribute	Description	Values	Default value
featureThickness	Sets the maximum thickness of the arcs used when drawing features in this featureSlot. This setting overrides the featureThickness value of the parent cgview element. The widths of individual features can be varied using the proportionOfThickness attribute in the feature element.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	Inherited from the featureThickness value of the parent cgview element.
minimumFeatureLength	When very small features are drawn they are artificially increased in length to the minimumFeatureLength, to ensure that they are visible.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	Inherited from the minimumFeatureLength value of the parent cgview element.
showShading	Specifies whether or not the features in this featureSlot should be drawn with shading. This setting overrides the showShading value of the parent cgview element. feature elements can override this value using their own showShading attribute.	true - shading should be used. false - shading should not be used.	Inherited from the showShading value of the parent cgview element.

color = the color name (black for example), or the RGB values for the color (rgb(0,255,0) for example). The following color names are supported: aqua, black, blue, fuchsia, gray (and grey), green, lime, maroon, navy, olive, orange, purple, red, silver, teal, white, and yellow.

font = the name of the font, followed by the style, and then the size. An example font is Monospaced, bold, 50. Valid font names are: Default, Dialog, DialogInput, Monospaced, Serif, and SansSerif. Valid styles are: plain, bold, italic, and bold-italic.

integer = a whole number between -2,147,483,648 and +2,147,483,647.

real = a real number between 1.4e-45 and 3.4e+38.

Citing CGView:

Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.