X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=c433e1f7a429c8cd4e8ffb97e66d85cce4b0729c;hb=ad15cff29620f960119f80176f1fd443da9f6763;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 @@ + Sequence Feature Settings Dialog Box @@ -8,28 +28,56 @@ in an alignment window to open the feature settings dialog box, which allows you to precisely control the presence and appearance of sequence features for the current alignment.

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+

Sequence Feature Settings for the Jalview Application

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:

+ Options are also provided in the feature's pop-up menu (see below). +
+ Select columns by feature was added in Jalview 2.8.1 +

+

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

+features and groups on each sequence. To order the alignment using a +specific feature type, use the sort by .. entries in the pop-up +menu for that type.
+Feature sorting and graduated feature colouring were introduced +in Jalview 2.5

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