X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=9be277572b72e3b32b5a6697b59325b3af4861a2;hb=0118e3685a087b37bb9d38d606f437638c9544d9;hp=66f4284eba7a7584c49e04bb5b8a04e1d27cf224;hpb=f902741a45fba3856958b893e37c74344d397a60;p=jalview.git diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 66f4284..9be2775 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -6,65 +6,74 @@
+
- Font
+
- Change the font of the display from the - "Choose Font" dialog box, which is shown when this - item is selected.
+ 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 + 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.
+ 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 + 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 + 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 + 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 + 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. -
+ 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 + 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.
+ 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.
+- Seqence Settings
+ If features have been added to the alignment then the priority of rendering + the features can be altered so that overlapping features can be displayed + or hidden. See Sequence Features.
- 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. + 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.