CGView - XML - map element

XML - cgview element
The cgview element is the root element of the XML document that is used to describe CGView maps. Its attributes specify the overall appearance of the map (width, height, background color, etc). The cgview element contains featureSlot and legend elements, which describe the contents of the map.

The following sample CGView document shows the relationship of the cgview element to the other elements:

<?xml version="1.0" encoding="ISO-8859-1"?> <cgview backboneRadius="160" sequenceLength="10000" backboneColor="green" height="600" width="600"> <featureSlot strand="direct"> <feature color="red" decoration="clockwise-arrow" label="feature X"> <featureRange start="4630" stop="4700" /> </feature> </featureSlot> <legend position="upper-center" font="SansSerif,bold-italic,40"> <legendItem text="Example map" textAlignment="center" /> </legend> </cgview>

This is the map generated by the above document:

output of above document

Required cgview attributes

Attribute	Description	Values
sequenceLength	Specifies the length of the DNA molecule being mapped, in base pairs.	integer between 1 and 10,000,000.

Optional cgview attributes

Attribute	Description	Values	Default value
arrowheadLength	Sets the length of the arrowhead used for features that are drawn as arrows.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
backboneColor	Sets the color of the circle used to represent the sequence backbone.	color	gray
backboneRadius	Sets the radius of the circle (in pixels) used to represent the sequence backbone. Generally the radius should be about 0.4 times the imageWidth or imageHeight (the smaller of the two). You may want to decrease the backboneRadius value to provide more space for feature labels and legends.	real between 10.0 and 12000.0.	190.0
backboneThickness	Sets the thickness of the line used to draw the circle that represents the sequence backbone.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
backgroundColor	Sets the color of the map canvas.	color	white
borderColor	Sets the color of the map border.	color	black
featureSlotSpacing	Sets the amount of blank space placed between the concentric feature rings (featureSlots).	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
featureThickness	Sets the maximum thickness of the arcs used when drawing features. featureSlot elements can override this value using their own featureThickness attribute. 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	medium
giveFeaturePositions	Specifies whether or not feature position information (the base pair position of the start and stop of the feature) should be added to feature labels that are drawn.	true - feature position information should be added. false - feature position information should not be added. auto - feature position information should only be added when a zoomed map is drawn.	false
globalLabel	Specifies whether or not feature labels should be drawn on this map. When set to false this value overrides the showLabel attributes in all child elements and prevents labels from being drawn. When set to true the showLabel attributes in child elements are used to determine whether or not labels are drawn. When set to auto labels are only drawn when a zoomed map is drawn and when the showLabel attributes in child elements are set to true.	true - feature labels should be drawn. false - feature labels should not be drawn. auto - feature labels should be drawn only when a zoomed map is drawn.	true
globalLabelColor	By default, labels are colored to match the color of the feature they represent. If globalLabelColor is defined all labels are colored according to the globalLabelColor value.	color	-
height	Sets the height of this map in pixels.	integer between 100 and 30,000.	700
isLinear	Specifies whether or not the map is representing a linear molecule. When set to true the map is drawn with a divider line and sequence end labels to indicate the molecule is linear. However, the map is still drawn as a circle.	true - this is a linear molecule. false - this is not a linear molecule.	false
labelFont	Sets the font used for feature labels. feature elements can override this setting using their font attribute.	font	SansSerif, plain, 10
labelLineLength	Sets the initial length of the line that is drawn to connect features to their labels.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
labelLineThickness	The thickness of the line that is drawn to connect features to their labels.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
labelPlacementQuality	Alters the placement of feature labels. Higher quality settings lead to better label placement but slower program execution.	good better best	better
labelsToKeep	Before CGView attempts to place labels, labels are randomly discarded if there are more labels than the labelsToKeep value.	integer	1000
longTickColor	Sets the color of the long tick marks in the sequence ruler.	color	black
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	xxx-small
moveInnerLabelsToOuter	Specifies whether or not inner labels should be moved from the inside of the backbone circle to the outside of the backbone circle when there is insufficient room on the inside on the backbone circle.	true - inner labels should be moved. false - inner labels should not be moved.	true
origin	Sets the clock position of the sequence beginning on the circular map backbone.	integer between 1 and 12.	12
rulerFont	Sets the font used for the sequence ruler.	font	SansSerif, plain, 8
rulerFontColor	Sets the color of the text used for the sequence ruler.	color	black
rulerPadding	Sets the spacing between the inner tickmarks and the sequence ruler labels. Increase this value when the sequence ruler numbers are overlapping the tickmarks.	real	10.0
rulerUnits	Sets the units used for the sequence ruler.	bases - base pair units. centisomes - centisome units.	bases
shortTickColor	Sets the color of the short tick marks in the sequence ruler.	color	black
shortTickThickness	Sets the thickness of the short tick marks in the sequence ruler.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
showBorder	Specifies whether or not a border should be drawn around the map.	true - a border should be drawn. false - a border should not be drawn.	true
showShading	Specifies whether or not map items should be drawn with shading. featureSlot elements can override this value using their own showShading attribute.	true - shading should be used. false - shading should not be used.	true
showWarning	Specifies whether or not CGView should add certain warning messages to the lower left of this map.	true - warning messages should be added. false - warning messages should not be added.	false
tickDensity	Adjusts the density of the tick marks in the sequence ruler.	real between 0.0 and 1.0.	1.0
tickLength	Sets the length of the tick marks in the sequence ruler.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
tickThickness	Sets the thickness of the tick marks in the sequence ruler.	xxx-small xx-small x-small small medium large x-large xx-large xxx-large or real	medium
title	Specifies a title for this map. The title will appear in the center of the backbone circle when an unzoomed map is drawn.	text	-
titleFontColor	Sets the color of the text used for the map title.	color	black
titleFont	Sets the font used for the map title.	font	SansSerif, plain, 12
useColoredLabelBackgrounds	Specifies whether or not a colored rectangle should be drawn around each feature label.	true - a colored rectangle should be drawn. false - a colored rectangle should not be drawn.	false
useInnerLabels	Specifies whether or not reverse-strand feature labels (labels drawn for features in reverse-strand featureSlots) should be drawn on the inside of the backbone circle, i.e. whether or not inner labels should be used. When inner labels are not used, all labels are drawn on the outside of the backbone circle.	true - reverse-strand labels should be drawn on the inside. false - reverse-strand labels should not be drawn on the inside. auto - reverse-strand labels should be drawn on the inside only when a zoomed map is drawn.	auto
warningFont	Sets the font used for the warnings drawn when the showWarning attribute is set to true.	font	SansSerif, plain, 8
warningFontColor	Sets the color of the text used for the warnings drawn when the showWarning attribute is set to true.	color	black
width	Sets the width of this map in pixels.	integer between 100 and 30,000.	700
zeroTickColor	Sets the color of the tick mark drawn at the boundary between the sequence start and end.	color	black

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.