X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwview.html;h=3d2d3beeb3ab0666dbc18b98762025e00c0b4abe;hb=e1cd94839128776e14e51ded3f3be2dcc7e72273;hp=66f4284eba7a7584c49e04bb5b8a04e1d27cf224;hpb=f902741a45fba3856958b893e37c74344d397a60;p=jalview.git
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 66f4284..3d2d3be 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,72 +1,99 @@
-
-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.
-
- - 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.
-
- - 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.
-
- - 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.
+ - 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.
+
+
+
+