From 582d2986d230f2ba687dd2d5f8425a32e980be83 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 28 Apr 2010 10:21:05 +0000 Subject: [PATCH] group/annotation association, logos, autocalc group annotation and sequence id tooltip --- help/html/features/preferences.html | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 2e1cf43..caa951e 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -6,7 +6,7 @@

Preferences

-

There are four tabs in the Preferences dialog box: +

There are four tabs in the Preferences dialog box:

@@ -35,7 +35,13 @@ for a new alignment window.

will display an annotation panel below the sequences. This annotation panel may have several rows describing the whole alignment. The 3 standard annotations Conservation, Quality and Consensus - may be shown or hidden by default.

+for the alignment may be shown or hidden by default using the checkboxes +below.

+

Show group: Conservation and Consensus controls the +display of per-group automatic annotation.

+

Consensus: Histogram and Logo checkboxes control the +display of the consensus histogram and sequence logo for consensus +annotation rows.

Full Sequence ID - If selected the ID panel will display the name of a sequence plus the start and end residues in the format name/start-end. If not selected, the displayed ID will be the name of @@ -45,6 +51,9 @@ the left-hand edge of the sequence alignment, rather than the left-hand edge of the alignment display window.

Font - The default font name, size and style can be set for a new alignment window.

+

Sequence ID Tooltip: Control the display of Database +References and Non-positional annotation in the tooltip displayed when +the mouse is over a sequence's ID.

Sequence Name Italics - select to apply the italicised vbersion of the font to sequence labels.

Smooth Font - Toggles anti-aliasing on / off for faster @@ -108,8 +117,7 @@ style for EPS export:

Sequence//Start-End Numbering
The output tab also has a group of checkboxes for each file format. If these are ticked, then Jalview will write files with the start and end -sequence positions appended to each sequence id: -

+sequence positions appended to each sequence id: 
   >ID/1-10
   AACDEAAFEA
 
@@ -134,8 +142,6 @@ sequence edit. New alignment windows will have their "Autocalculate Consensus" option set according to this setting.

Pad gaps when editing - New alignment windows will "Pad Gaps" according to this setting.

-

DAS Settings

-

See DAS Settings

 

 

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