- <li><strong>Save Project</strong><br>\r
- <em>Saves all currently open alignment windows with their current visible \r
- settings as a Jalview File, with the .jar extension. Each alignment will \r
- also save the currently active tree associated with the window, if one \r
- exists. </em></li>\r
- <li><strong>Load Project</strong><br>\r
- <em>Loads Jalview file formatted alignments only. </em></li>\r
- <li><strong>Quit</strong><br>\r
- <em>Close Jalview. Warning - any annotations you have made on alignments \r
- will be lost unless you Save your work before quitting.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Tools </strong> \r
- <ul>\r
- <li><strong><a href="../features/preferences.html">Preferences<br>\r
- </a></strong><em>Change the default visual settings for opening new alignment \r
- windows.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Help </strong> \r
- <ul>\r
- <li><strong>About<br>\r
- </strong><em>Displays the version and creation date of the application, \r
- as well as acknowledgements and a citation reference. </em></li>\r
- <li><strong>Documentation<br>\r
- </strong><em>Displays help files as a browseable, searchable set of pages \r
- with a table of contents. </em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Window<br>\r
- </strong><em>Each time a new window is added to the Jalview Desktop a new \r
- menu item will be added to the "Window" menu. If you are working \r
- with several alignments, trees or other types of windows use the "Window" \r
- menu to bring your window of choice to the top of the pile if it has been \r
- hidden by other windows. </em></li>\r
-</ul>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Tools </strong>\r
+ <ul>\r
+ <li><strong><a href="../features/preferences.html">Preferences<br>\r
+ </a></strong><em>Change the default visual settings for opening new alignment\r
+ windows.</em><strong><br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Help </strong>\r
+ <ul>\r
+ <li><strong>About<br>\r
+ </strong><em>Displays the version and creation date of the application, as\r
+ well as acknowledgements and a citation reference. </em></li>\r
+ <li><strong>Documentation<br>\r
+ </strong><em>Displays help files as a browseable, searchable set of pages\r
+ with a table of contents. </em><strong><br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Window</strong><br>\r
+ <em>Each time a new window is added to the Jalview Desktop a\r
+ corresponding menu item will be added to the "Window" menu\r
+ that will bring the window to the top of the pile when it is selected.\r
+ <ul>\r
+ <li><strong>Close All</strong><br>\r
+ Close all alignment and analysis windows.<br><strong>Note: This will erase all alignments from memory, and cannot be undone!</strong></li>\r
+ <li><strong>Raise Associated Windows</strong><br>\r
+ Bring all windows associated with the current alignment to the top of the pile. \r
+ </li>\r
+ <li><strong>Minimise Associated Windows</strong><br>\r
+ Hide all windows related to the current alignment behind icons on the Jalview Desktop.\r
+ </ul>\r
+ </em></li>\r
+ </ul>\r