From: jprocter Date: Thu, 15 Sep 2011 13:19:06 +0000 (+0100) Subject: documentation for new preferences (JAL-234 and web services from 2.6.x) X-Git-Tag: Release_2_7~40 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ffe5ef44f4431b1fcf87a55e17edcd77b5e1da38;hp=0e6634756268f473daa6dc76ddd21890baa88820;p=jalview.git documentation for new preferences (JAL-234 and web services from 2.6.x) --- diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 03b4993..014de2e 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -22,11 +22,14 @@

Preferences

There are four tabs in the Preferences dialog box: +

There are six tabs in the Preferences dialog box:

The "Visual" Preferences tab allows you to configure the default display for a new alignment window.
The "Colours" + Preferences tab allows you to configure default colourschemes for a new + alignment window.
The "Connections" Preferences tab allows you to change the links made from Jalview to your default web browser.
The "DAS Settings" Preferences tab allows you to select which DAS sources to use when fetching DAS Features.
The "Web Service" Preferences tab allows you to configure the JABAWS servers that Jalview uses, and change the layout of the alignment's Web Services menu.

Visual Preferences tab

@@ -78,16 +82,25 @@ rendering of the alignment.

windows in wrapped mode or not.

Gap Symbol - The default gap symbol may be set to either "-" or "."

Colour - The default colour scheme for a new alignment -window. If the chosen option is "User Defined" then the last -User Defined Colour loaded or saved via the User Defined Colours panel -will be loaded.

Sort by - When the alignment is loaded in, it will can be sorted by Id or pairwise identity.

Open file - If this is selected then the default alignment file will be opened when Jalview is started. You can change the default file by clicking on file name and either typing in the file path or selecting it from the file chooser window.

"Colours" Preferences tab

Alignment Colour - The default colour scheme for a new alignment +window. If the chosen option is "User Defined" then the last +User Defined Colour loaded or saved via the User Defined Colours panel +will be loaded.

+ Annotation Shading Default - set the default minimum + and maximum colours used when Colour by + Annotation .. is selected from the alignment window's colours menu. +

+
+

"Connections" Preferences tab

URL Link From Sequence ID