X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=3d7c944b864b78c32f40afa078e26db841489b10;hb=806c9dc4a3d841fe36e7d17ab45d783a9fc95f26;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ 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. +
+ +