Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fmenus%2Falwview.html;h=cb3870816a13d7b5eab42c3b3a5f57a65972d8c3;hb=d305e02d8b425bb501141ad32142aeb8572adc57;hp=28ad82e33bc1140b4485c68a5fbf3208a4f61c4c;hpb=cd08c68e4ed1605a42ebdccb0add217e74ec9fb0;p=jalview.git diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 28ad82e..cb38708 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -1,71 +1,104 @@ - -Alignment Window Menus - - -

Alignment Window View Menu

Font
- Change the font of the display from the "Choose Font" - dialog box, which is shown when this item is selected.
Smooth Fonts
- If selected, the alignment will be drawn with anti-aliasing on which looks - better, but performace is reduced.
Show (all Columns / Sequences)
- All hidden Columns / Sequences will be revealed.
Hide (all Columns / Sequences)
- Hides the all the currently selected Columns / Sequences
Wrap
- When ticked, the alignment display is "wrapped" - to the width of the alignment window. This is useful if your alignment has - only a few sequences to view its full width at once.
- Options are available to show the residue numbering at the start and/or end - of an alignment as well as showing the alignment position above each sequence - row.
- NOTE: When in wrapped alignment view, the alignment cannot - be edited or have regions selected on it.
Show Full Sequence ID
- If this box is selected the sequence name will have the start - and end position of the sequence appended to the name, in the format NAME/START-END
Boxes
- If this is selected the background of a residue will be coloured using the - selected background colour. Useful if used in conjunction with "Colour - Text."
Text
- If this is selected the residues will be displayed using the - standard 1 character amino acid alphabet.
Colour Text
- If this is selected the residues will be coloured according to - the background colour associated with that residue. The colour is slightly - darker than background so the amino acid symbol remains visible.
Show Gaps
- When this is selected, gap characters will be displayed as "." - or "-". If unselected, then gap characters will appear as blank - spaces.
- You may set the default gap character in preferences.
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.
Fetch Sequence Features
- If the sequence names are Swissprot entries Jalview will use - the names to retrieve sequence features - from the EBI. Features which are 1 residue in length are coloured red, sequences - longer than 1 residue are coloured blue. Move the mouse over a coloured feature - to display the details of the feature.
- Note: The retrieved information will update the sequence start and end labels - if they are incorrect.
Show Sequence Features
- Show or hide sequence features on this alignment.
Seqence Feature Settings...
- Control the colour and display of sequence features on the alignment. - See Sequence Feature Settings.
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.
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 All Annotations
+ Show all available annotations on the alignment. You can selectively hide these from the Popup + or Annotation menus. (Since Jalview 2.8.2)
Hide All Annotations
+ Hide all annotations on the alignment. (Since Jalview 2.8.2)
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.
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.

+ +