Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=20283044dbeef3eacb3c7b7fed7c4c1b9979300f;hb=53e232c25d1956fdcc239b0db8d6b18cecc601a4;hp=53ae079702193aaf7cf8a4bc1d1d569a02d0d10c;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 53ae079..2028304 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -1,96 +1,76 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> 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.
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.

+ 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.