X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=4248f9a36d6ac5ae1bd287209124338996e3b0dc;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d83d1050ae19f3e079e89395f506108a0de1a6f2;hpb=2e2bc3fbb0231c705e5d019df9cb8e0e600ca12e;p=jalview.git diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index d83d105..4248f9a 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -1,83 +1,97 @@ - -
Alignment Window View Menu
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-- Font
-
- Change the font of the display from the "Choose Font" - dialog box, which is shown when this item is selected. Select a "Monospaced" - font for fast rendering of your alignment. The checkbox labelled "Monospaced" - indicates whether the chosen font uses characters all of the same width.
-- Smooth Fonts
-
- If selected, the alignment will be drawn with anti-aliasing on which looks - better, but performace is reduced.
-- 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 View Menu
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