X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=877a3b1ed341682a04c3c39893c7d4278d2e56cb;hb=713db61b4724485414159cfc145f9ffa4a24bb6d;hp=e3dc703467bb3fe00acb5d698eb4d253637e5e03;hpb=72f4770815185305bd18aeeb74f829b1f9ed55c8;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index e3dc703..877a3b1 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -4,8 +4,22 @@
Preferences
-The "Visual" tab on the preferences window allows you to configure - the default display for a new alignment window.
+There are three tabs in the Preferences dialog box: +
Visual Preferences tab
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 @@ -18,12 +32,63 @@
Font - The default font name, size and style can be set for a new alignment window.
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.
-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.
+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.
+ +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.
EPS Rendering Style
+This is a selection box which allows the
+ user to set a default rendering 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:
+
+ >ID//1-10 + AACDEAAFEA ++
+