X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=d6cd10f678c2667ad389d03c10c7d61ce8d47ce6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=28ad82e33bc1140b4485c68a5fbf3208a4f61c4c;hpb=cd08c68e4ed1605a42ebdccb0add217e74ec9fb0;p=jalview.git
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 28ad82e..d6cd10f 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,71 +1,76 @@
-
-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.
+ - 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.
+
+
+
+