Sequence feature colour schemes

Jalview can visualize annotation present on parts of a sequence by overlaying colours according to the annotation present at each position. It allows features to be colored either according to type, or for a particular type, according to an individual feature's associated label or score. The Feature Settings dialog box controls the order and display of each sequence annotation type, and also allows the colour scheme used for the the feature to be changed via the 'Graduated Colour' option in the sequence feature pop-up menu (obtained by right-clicking on a sequence feature).

Graduated feature colour scheme settings dialog box

The Graduated Feature Colour dialog box has the following controls:

- Colour by Label - when checked this derives a colour for each feature based on the label text.
- Min and Max Color boxes - Click on these boxes to set the minimum and maximum colours used to shade features by their associated score.
- Threshold type combo box - Allows features to be hidden features if their score is below or above a given threshold.
  Set the threshold using the slider or type it in to the text box. The threshold cannot be set outside the available range of feature scores.
- Threshold is Min/Max - When checked, the threshold will be used as the upper or lower limit when shading the features according to their score using the Min and Max colour.

Icon styles for graduated feature styles

When a graduated colourscheme is applied to a feature, it is indicated in the feature settings or amend feature dialog box by the following types of icon:

Type of Colouring | Icon
Graduated colour by Feature Score |
Graduated colour thresholded (less than) by feature Score |
Graduated colour thresholded (greater than) by feature Score |
Colour by Feature Label (may also be thresholded) |
The current threshold is given in the icon's tooltip.

Graduated feature colours were introduced in Jalview 2.5