X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Ffeatureschemes.html;h=76bc154f39da4105367d9e0b45c857f6065639c0;hb=74e0948bc8efef9a573f037e8c037c46fade0c6f;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/featureschemes.html b/help/html/features/featureschemes.html index e18e273..76bc154 100644 --- a/help/html/features/featureschemes.html +++ b/help/html/features/featureschemes.html @@ -1,6 +1,6 @@ +
+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).
+ +The Graduated Feature Colour dialog box has the following +controls: +
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. + + |