X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=8156e9347b7d7918ccca1735eb72f09462602eda;hb=cb4b4b590add93fb0fb5c5ecd1d0532f1456ecc2;hp=d2ca48190c5e066a94100e4e009f8f34e7896cfc;hpb=c554d41a4effc6719895bda6b3abc04c032715a8;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d2ca481..8156e93 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,4 +1,21 @@
+
Alignment Window Menus
@@ -193,6 +210,12 @@
Undefine Groups (Control U)
The alignment will be reset with no defined groups.
WARNING: This cannot be undone.
+ Make Groups
+ The currently selected groups of the alignment will be
+ subdivided according to the contents of the currently selected region.
+
Use this to subdivide an alignment based on the
+ different combinations of residues observed at specific
+ positions. (new in jalview 2.5)
View
@@ -205,22 +228,58 @@
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→(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 all 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 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
+ Autocalculated Annotation
Settings for the display of autocalculated annotation.
+ -
+ Apply to all groups
+ When ticked, any modification to the current settings will be applied to all autocalculated annotation.
+
+ -
+ Show Consensus Histogram
+ Enable or disable the display of the histogram above the consensus sequence.
+
+ -
+ Show Consensus Profile
+ Enable or disable the display of the sequence logo above the consensus sequence.
+
+ -
+ Group Conservation
+ When ticked, display a conservation row for all groups (only available for protein alignments).
+
+ -
+ Apply to all groups
+ When ticked, display a consensus row for all groups.
+
+
+
+ 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.
+ 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
@@ -283,6 +342,10 @@
Centre Annotation Labels
Select this to center labels along an annotation row
relative to their associated column (default is off, i.e. left-justified).
+ Show Unconserved
+ When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
+
+
Colour
@@ -333,7 +396,10 @@
- by ID
This will sort the sequences according to sequence name. If the sort
is repeated, the order of the sorted sequences will be inverted.
- - by Group
+ - by Length
+ This will sort the sequences according to their length (excluding gap characters). If the sort is
+ repeated, the order of the sorted sequences will be inverted.
+ - by Group
This will sort the sequences according to sequence name. If
the sort is repeated, the order of the sorted sequences will be
inverted.