X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=c433e1f7a429c8cd4e8ffb97e66d85cce4b0729c;hb=496a78f25054b4003f6115c7194a2a466c44197f;hp=7c4840d781bc27437736100c6a8c828bc8ddc4a7;hpb=8e068512cd4573dc4388dfca63072c95f294ef84;p=jalview.git diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 7c4840d..c433e1f 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,4 +1,24 @@ +
The top section of the dialog box lists all the sequence feature groups, along with a tickbox for each that controls whether its features are displayed. The table in the middle lists all the features in the -currently selected groups, along with their display colour and whether +currently selected groups, along with their display style and whether they are currently being displayed (only the ticked features and groups -are displayed). You can change the colour used -for a feature in the associated alignment by clicking on its colour box.
-Feature settings pop-up menu
+are displayed). You can change the colour or
+shading style used for a feature in the associated alignment by clicking
+on its colour box.
+ Selecting
+ alignment columns by feature
Double-clicking
+ a feature type in the Feature
+ Settings dialog allows you to select columns in the
+ alignment that contain (or do not contain) features of that type. If a
+ region of the alignment is currently selected, then only features in
+ the current selection will be searched. The following keys affect the
+ way in which selections are made:
Feature settings pop-up menu
Right-click on a feature to open a pop-up menu that
allows you to sort the alignment or current selection using that feature
-type (see below), or create a feature colourscheme based on either the
+type (see below), or toggle the type of colouring used for the feature.
+Features may be highlighted with either a single colour or a feature colourscheme based on either the
scores associated with that feature or from the feature's description
(e.g. to distinguish different names associated with a DOMAIN feature).
Ordering alignment by features
-The 'Order by Score' and 'Order by Density' buttons will order the
+The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the
alignment based on the average score or total number of currently active
-features and groups on each sequence.
-Feature sorting and colour feature by score and description was
-introduced in jalview 2.4.1
Transparency and Feature Ordering
It is important to realise that sequence features are often not @@ -37,7 +85,7 @@ distinct and often overlap (for example, a metal binding site feature may be attached to one position along a stretch of sequence marked with a secondary structure feature).
The ordering of the sequence features in the dialog box list is
-the order used by jalview for rendering sequence features. A feature at
+the order used by Jalview for rendering sequence features. A feature at
the bottom of the list is rendered below a feature higher up in
the list.
You can change the order of a feature by