X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=c433e1f7a429c8cd4e8ffb97e66d85cce4b0729c;hb=496a78f25054b4003f6115c7194a2a466c44197f;hp=9335d93e7ac4b06352f1f1297c763eebec17d524;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 9335d93..c433e1f 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,22 +1,24 @@ + --> Sequence Feature Settings Dialog Box @@ -37,15 +39,29 @@ they are currently being displayed (only the ticked features and groups 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-click a feature to add all the columns where - that feature is found to the current column selection. Shift+Double-click - will add all the columns where that feature is not - found. You can also find these options in the feature's pop-up menu - (see below).
- Select columns by feature was added in Jalview 2.8.1 -

+

+ 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 @@ -60,8 +76,8 @@ alignment based on the average score or total number of currently active 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 was introduced -in jalview 2.5

+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 @@ -69,7 +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