Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=53ae079702193aaf7cf8a4bc1d1d569a02d0d10c;hb=524f1bc53749f18e8217ec14b72d3a2a444c072f;hp=ca8f81b9a4560bdfc7bbe427d1ba831cc451ef55;hpb=96b6991703b70a1bbb0491f9946d397c9fcf5a38;p=jalview.git diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index ca8f81b..53ae079 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -1,4 +1,21 @@ + Alignment Window Menus @@ -6,36 +23,73 @@

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.
- +
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.
+
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.
+
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 Logo
+ Enable or disable the display of the sequence logo above the consensus sequence. +
+
Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height, + making it easier to compare symbol diversity in highly variable + regions.
+ +
+ 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. +
+
+
+
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.
+
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 small + window. A red box will indicate the currently visible area of the alignment. + Move the visible region using the mouse.