X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=c0fbf32bd6163e6ce1b513e9cac704032a5e18ec;hb=a16c37a5983e3c581dc3d3030e1439e8fb3239f1;hp=05d1a5142b206b5366748901c36cafe57a41c0a7;hpb=e2f0c0750cedc538bbe04fdc291ae799b9cb4b7a;p=jalview.git diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 05d1a51..c0fbf32 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,4 +1,21 @@ + Sequence Feature Settings Dialog Box @@ -8,22 +25,34 @@ 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.

+are displayed). You can change the colour or +shading style used for a feature in the associated alignment by clicking +on its colour box.

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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. +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
-Right click on a feature type to order the alignment by either the -feature's score, or the number of features of that type. The 'Order by -Score' and 'Order by Density' buttons will order the alignnment based on -the average score or total number of currently active features and -groups on each sequence. (Experimental - added in jalview 2.4.1)

+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. 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

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Transparency and Feature Ordering

It is important to realise that sequence features are often not distinct and often overlap (for example, a metal binding site feature @@ -44,10 +73,6 @@ visibility of features rendered below other features. Reducing the transparency will mean that features at the top of the list can obscure features lower down, and increasing it allows the user to 'see through' the upper layers of a set of features.

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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, or create a graduated feature colourscheme based on the -scores associated with that feature.

You can save all features, with their current colours and visibility in a Jalview format file.