X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=3830302a79132be740fcd233d01c871bc8be105d;hb=2273eba5668e5340354da60fed329c6c716cc439;hp=c8e6bc405168170b2a72ec899c19104a072a2b08;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index c8e6bc4..3830302 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,22 +1,24 @@ + --> Sequence Feature Settings Dialog Box @@ -37,7 +39,30 @@ 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.

-

Feature settings pop-up menu
+

+ 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 toggle the type of colouring used for the feature. @@ -51,8 +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 @@ -60,7 +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