X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=3d7c944b864b78c32f40afa078e26db841489b10;hb=4e60a6952c6b85e10335b3feb5fef6c81bba79a4;hp=05d1a5142b206b5366748901c36cafe57a41c0a7;hpb=e2f0c0750cedc538bbe04fdc291ae799b9cb4b7a;p=jalview.git diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 05d1a51..3d7c944 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,54 +1,132 @@ +
Sequence Feature Settings Dialog Box
-Select View→Feature Settings... menu entry -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.
-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 -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.
-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)
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 -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 bottom of the list is rendered below a feature higher up in
-the list.
-You can change the order of a feature by
-dragging it up and down the list with the mouse.
The Optimise order button (currently -only available in the application) will re-order the feature render -ordering based on the average length of each feature type.
-The transparency slider setting -(currently only available in the application version) controls the -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.
-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.
++ Sequence Feature Settings Dialog Box +
++ Select View→Feature Settings... menu entry 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. +
++ 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 + style and whether 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-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
+
+ 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 '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 were
+ introduced in Jalview 2.5
+
+ 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 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 bottom of the list is rendered below a feature higher
+ up in the list.
You can change
+ the order of a feature by dragging it up and down the list with
+ the mouse (not applet).
+
+ The Optimise order button (currently only + available in the application) will re-order the feature render + ordering based on the average length of each feature type. +
++ The transparency slider setting controls + the 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. +
++ You can save all features, with their + current colours and visibility in a Jalview format file. +