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 @@ -18,12 +18,52 @@
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.
+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.
The "Output" tab has a selection box allowing the
+ user to set a default rendering style for EPS export. "Lineart" will
+ produce an accurate representation of the visible alignment in Jalview, all
+ the characters will be graphics objects. "Text" will produce a much
+ smaller file and will rely on the software you use to view the EPS file, such
+ as Adobe Illustrator, having the same font as the file was created with. You
+ will only be able to edit text in an EPS file if you select the "Text"
+ option.
+ Choose "Prompt each time" to select between Lineart and Text each
+ time you make an EPS file.
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. If the boxes are left unchecked for a paritcular + format, the sequence limits will not be appended to the sequence id.
++