X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=e55a7f71e8fafe885ac00f595b9568dcfc22df49;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=e58d4c24163d669e1e673e2a32a018cce02e4ace;hpb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;p=jalview.git
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index e58d4c2..e55a7f7 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,41 +1,67 @@
-
-
-Alignment Window Menus
-
-
-
-Alignment Window View Menu
-
- - New View (Control T)
- Creates a new view from the current alignment view.
- - Expand Views (X)
- Display each view associated with the alignment in its own alignment
- window, allowing several views to be displayed simultaneously.
- - Gather Views (G)
- Each view associated with the alignment will be displayed within its
- own tab on the current alignment window.
- - Show→(all Columns / Sequences)
- All hidden Columns / Sequences will be revealed.
- - Hide→(all Columns / Sequences)
- Hides the all the currently selected Columns / Sequences
- - Show Annotations
- If this is selected the "Annotation Panel" will be
- displayed below the alignment. The default setting is to display the
- conservation calculation, quality calculation and consensus values as
- bar charts.
- - Show Sequence Features
- Show or hide sequence features on this alignment.
- - Seqence Feature Settings...
- Opens the Sequence
- Feature Settings dialog box to control the colour and display of
- sequence features on the alignment, and configure and retrieve features
- from DAS annotation servers.
- - Overview
- Window
- A scaled version of the alignment will be displayed in a small
- window. A red box will indicate the currently visible area of the
- alignment. Move the visible region using the mouse.
-
-
-
-
+
+
+
+Alignment Window Menus
+
+
+
+Alignment Window View Menu
+
+ - New View (Control T)
+ Creates a new view from the current alignment view.
+ - Expand Views (X)
+ Display each view associated with the alignment in its own alignment window,
+ allowing several views to be displayed simultaneously.
+ - Gather Views (G)
+ Each view associated with the alignment will be displayed within its own tab
+ on the current alignment window.
+ - Show→(all Columns / Sequences / Sequences and Columns )
+ All hidden Columns / Sequences / Sequences and Columns will be revealed.
+ - Hide→(all Columns / Sequences / Selected Region / All but Selected Region)
+ Hides the currently selected Columns / Sequences / Region or everything but the selected Region.
+ - Automatic Scrolling
+ When selected, the view will automatically scroll to display the
+ highlighted sequence position corresponding to the position under the mouse
+ pointer in a linked alignment or structure view.
+
+ - Show Sequence Features
+ Show or hide sequence features on this alignment.
+ - Sequence Feature Settings...
+ Opens the Sequence Feature Settings dialog box to control the colour and display
+ of sequence features on the alignment, and configure and retrieve features
+ from DAS annotation servers.
+ - Sequence ID Tooltip (application only)
+
This submenu's options allow the inclusion or exclusion of
+ non-positional sequence features or database cross references
+ from the tooltip shown when the mouse hovers over the sequence ID panel.
+ - Alignment Properties...
+ Displays some simple statistics computed for the
+ current alignment view and any named properties defined on the
+ whole alignment.
+ - Overview Window
+ A scaled version of the alignment will be displayed in a small
+ window. A red box will indicate the currently visible area of the alignment.
+ Move the visible region using the mouse.
+
+
+
+