X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=3d2d3beeb3ab0666dbc18b98762025e00c0b4abe;hb=e5cbd35e13f46ae1d59a08b0af1086677418141d;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 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.
-- 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 View Menu
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