X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Ffeatureschemes.html;h=63dd0e59ac54feb4a39f8909245f90152004023b;hb=56ce5cb6fd0b54f831cf35859886cd69a7f522a3;hp=37243d2ed58626adc2345d29d41799527a16bc3e;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git diff --git a/help/help/html/features/featureschemes.html b/help/help/html/features/featureschemes.html index 37243d2..63dd0e5 100644 --- a/help/help/html/features/featureschemes.html +++ b/help/help/html/features/featureschemes.html @@ -25,82 +25,111 @@
- 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). + Visualisation of Sequence Features
+Jalview can visualize sequence features - the positional + annotation present on parts of a sequence, as colours overlaid on + corresponding positions in the alignment. Features may be coloured + either according to their type, or for a particular type, according to + each feature's associated label, score, or other attributes.
++ The Feature Settings dialog box + controls the order and display of each feature type, and + also allows filters and colour schemes to be configured. +
-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. - | -
The Feature Display Settings has the following controls: +
Colour
+
+ Filters
Any number of filter
+ conditions may be specified to select features based on one or more
+ attributes. The join condition specifies whether all
+ filters must apply (And) or whether any one
+ filter must apply (Or) for a feature to be
+ selected.
+
The filters available depend on the type of attribute:
++ The filters and colour schemes active for a particular feature type + are shown in the Colour and Configuration columns in + the feature settings dialog. Styles and filters can be saved as a + Jalview Feature Colours file, and are also exported and imported via Jalview Feature files. + +
+ Icon styles for feature rendering styles
+
+
+ When a graduated colour scheme is applied to a feature according to
+ the value of a particular attribute, 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 (or other attribute) | ++ |
Graduated colour thresholded (greater than) by + feature Score (or other attribute) | ++ |
Colour by Feature Label | ++ |
The + current threshold and attribute is shown in the icon's tooltip. + | +