-<html>\r
-<head><title>What's new</title></head>\r
-<body>\r
-<p><strong>What's new</strong> </p>\r
-<p>If you can read this then you'll already have seen some of the recent changes\r
- made to Jalview.<br>\r
- Jalview takes advantage of some of the more recent user interface developments\r
- in the Java programming language. For instance Jalview is now a multi windowed\r
- application, this keeps all your Jalview windows neatly together in one main\r
- application window. </p>\r
-<p>If you were familiar with the original Jalview, here is a list of important\r
- features you should know about the current development:</p>\r
-<ul>\r
- <li>Editing sequences is no longer the default when mouse clicking the alignment.\r
- Instead, mouse clicking on the alignment will create a "selection region"\r
- which may be full sequences or groups of residues.</li>\r
- <li>To edit a sequence, the "Shift" key must be held down</li>\r
- <li>To edit groups, either the "Alt" key or the "Control"\r
- key must be held down.</li>\r
- <li>Colours maybe applied to the background, ie the whole alignment, or to selected\r
- regions. If the tickbox "Apply colour to all groups" is ticked (this\r
- is the default), then the colour will be applied to all groups.</li>\r
- <li>Use the right mouse button (apple and click on the mac) to define a selected\r
- region on the alignment as a new group. </li>\r
- <li>Conservation is automatically updated whenever the alignment is edited</li>\r
- <li>There is no "quick draw" option</li>\r
- <li>Edits can be undone! (and redone)</li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>What's new ?</title>
+</head>
+<body>
+<p><strong>What's new ?</strong></p>
+
+<p><strong>Jalview Version 2.2</strong></p>
+<p>Multiple views with different styles, colours, hidden regions for
+one alignment</p>
+<p>Easily add, amend and delete sequence features</p>
+<p>"Reload" alignment from File or URL to revert to
+original</p>
+<p>"Save" to current filename or "Save As" to
+new filename</p>
+<p>New <strong>"New Window"</strong> button on the
+"Output To Textbox" opens output window for quick 'sequence
+editing'.</p>
+<p>Set different text colour for dark or light background</p>
+<p>Right align sequence ids</p>
+<p>Set colour of lower case residues in a user defined colour scheme
+</p>
+<p>Menu Rearrangements: New <strong>Format</strong> for alignment
+layout and <strong>Select</strong> for region selection.</p>
+</p>
+<p>Menu item accelerator keys added</p>
+<p>Control-V pastes sequences to active window, Control-Shift-V
+pastes to a new window.</p>
+<p>Raise/Minimise alignment and all associated windows from desktop
+window's <strong>window</strong> menu</p>
+<p>Select and colour whole branches of a tree</p>
+<p>'New Window' button on the 'Output to Text box' alignment output
+option to open a new alignment window after editing.</p>
+<p><strong>Issues Resolved</strong></p>
+</p>
+<p>Optimisations for large alignments: faster multithreaded
+calculations and Undo/Redo system.</p>
+<p>Remove empty columns - if empty columns exist at the end of the
+alignment bug fixed.</p>
+<p>DAS feature fetching slowed down, doesn't overload DAS servers</p>
+<p>DAS feature fetching can be cancelled</p>
+<p>Correct display of > and < symbols for feature descriptions
+without explicit <html> tags.</p>
+<p>Zoom working in PCA viewer</p>
+<p>Sequence Descriptions retained after running a web service</p>
+<p> </p>
+<p>See the <a href="releases.html">Release History</a> page for
+details of all new features and resolved issues.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff