--- /dev/null
+<html>\r
+\r
+<head><title>Preferences</title></head>\r
+\r
+<body>\r
+<p><strong>Preferences</strong></p>\r
+<p>The "Visual" tab on the preferences window allows you to configure \r
+ the default display for a new alignment window. </p>\r
+<p>Maximise Window - If this is selected, a new alignment window will stretch \r
+ to fit the available space.</p>\r
+<p>Show Annotations - If this is selected the new window will display an annotation \r
+ panel below the sequences. This annotation panel may have several rows describing \r
+ the whole alignment. The 3 standard annotations Conservation, Quality and Consensus \r
+ may be shown or hidden by default.</p>\r
+<p>Full Sequence ID - If selected the ID panel will display the name of a sequence \r
+ plus the start and end residues in the format name/start-end. If not selected, \r
+ the displayed ID will be the name of the sequence.</p>\r
+<p>Font - The default font name, size and style can be set for a new alignment \r
+ window. </p>\r
+<p>Gap Symbol - The default gap symbol may be set to either "-" or "."</p>\r
+<p>Colour - The default colour scheme for a new alignment window. If the chosen \r
+ option is "User Defined" then the last User Defined Colour loaded \r
+ or saved via the User Defined Colours panel will be loaded. </p>\r
+<p>Open file - If this is selected then the default alignment file will be opened \r
+ when Jalview is started. You can change the default file by clicking on file \r
+ name and either typing in the file path or selecting it from the file chooser \r
+ window. </p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff
