Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;fp=help%2Fhtml%2Fmenus%2Falwview.html;h=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hp=b252ff54e5f53216db257ea0aeafe0fdac678395;hpb=247b4f59aad27b654fb55268b55645dc6496f12e;p=jalview.git diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index b252ff5..e18e273 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -15,77 +15,4 @@ * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . ---!> - -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 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. -
-
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.

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