From de17a37c2ff922ce86ef4fdaee65cae9e6e6a3af Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 17 Aug 2005 09:13:22 +0000 Subject: [PATCH] Advice on proxy servers --- help/html/features/preferences.html | 34 ++++++++++++++++++++++++++++------ 1 file changed, 28 insertions(+), 6 deletions(-) diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index e3dc703..e9ec458 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -4,8 +4,8 @@

Preferences

The "Visual" tab on the preferences window allows you to configure - the default display for a new alignment window.

The "Visual" tab on the preferences window allows + you to configure the default display for a new alignment window.

Maximise Window - If this is selected, a new alignment window will stretch to fit the available space.

Show Annotations - If this is selected the new window will display an annotation @@ -21,9 +21,31 @@

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.

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.

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.

The "Connections" tab allows you to change the links made from Jalview + to your default web browser.

URL Link From Sequence ID
+ Right click a sequence id to see a popup menu with "Link" as one of + the items. By default the item "SRS" is added to this link menu. This + link will show a web page in your default browser with the selected sequence + id as part of the URL.
+ Jalview allows you to add your own custom links to other web pages. Click new + to add a new link. You can name the link, this will be displayed on a new menu + item under the "Link" menu when you right click on a sequence id. +
+ You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen + sequence id when you click on it.

Default Browser (Unix)
+ Its difficult in Java to detect the default web browser for Unix users. If Jalview + can't find your default web browser, enter the name or full path to your web + browser application.

Proxy Server
+ If you normally use a proxy server for using the internet, you must tick the + box "Use a Proxy Server" and enter the address and port details as + necessary. Web Services will not work if you are using a proxy server and do + not enter the settings here.

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