From cd08c68e4ed1605a42ebdccb0add217e74ec9fb0 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 11 Aug 2006 14:20:26 +0000 Subject: [PATCH] 2.1 updates --- help/html/menus/alwview.html | 136 +++++++++++++++++++----------------------- 1 file changed, 62 insertions(+), 74 deletions(-) diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index d83d105..28ad82e 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -4,80 +4,68 @@

Alignment Window View Menu

View
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.

-
-
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.
-
-

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