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:

The "Visual" Preferences tab allows you to configure the default display for a new @@ -20,7 +20,7 @@
The "Editing" Preferences tab contains settings affecting the export of sequence alignments and EPS files.
The "DAS +
The "DAS Settings" Preferences tab allows you to select which DAS sources to use when fetching DAS Features.

@@ -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

-- 1.7.10.2