<head><title>What's new ?</title></head>\r
<body>\r
<p><strong>What's new ?</strong> </p>\r
-<p>If you are reading this then you will 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 creates a "selection region"\r
- which may be full sequences or groups of residues.</li>\r
- <li>To insert or edit the gaps in one sequence in alignment, the "Shift"\r
- key must be held down when dragging the mouse.</li>\r
- <li>To insert or edit gaps for a group of sequences, the "Alt" key\r
- (or in X windows the "Control" key) must be held down.</li>\r
- <li>Selecting colour schemes in the colour menu either sets just the "background"\r
- colourscheme for the alignment, or - when the tickbox "Apply colour to\r
- all groups" is ticked, applies the scheme to the background and all groups\r
- defined on the alignment.</li>\r
- <li>Use the right mouse button (apple and click on the Mac) whilst the pointer\r
- is within the selection area to access the "define" region menu\r
- to define a new region, give it a name, and change its colourscheme and display\r
- properties.</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
-<table border="1">\r
- <tr> \r
- <td><div align="center"><em><strong>Release</strong></em></div></td>\r
- <td><div align="center"><em><strong>New Features</strong></em></div></td>\r
- <td><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.07</strong><br>\r
- 7 /12/05</div></td>\r
- <td><ul>\r
- <li>PDB Structure Viewer enhanced</li>\r
- <li>Sequence Feature retrieval and display enhanced</li>\r
- <li>Choose to output sequence start-end after sequence name for file output</li>\r
- <li>Sequence Fetcher WSDBFetch@EBI</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>HTML output writes groups and features</li>\r
- <li>Group editing is Control and mouse click</li>\r
- <li>Applet can read feature files, PDB files and can be used for HTML \r
- form input</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.06</strong><br>\r
- 28/9/05</div></td>\r
- <td><ul>\r
- <li>View annotations in wrapped mode</li>\r
- <li>More options for PCA viewer</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>GUI bugs resolved</li>\r
- <li>Runs with -nodisplay from command line</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.05b</strong><br>\r
- 15/9/05</div></td>\r
- <td><ul>\r
- <li>Choose EPS export as lineart or text</li>\r
- <li>Jar files are executable</li>\r
- <li>Can read in Uracil - maps to unknown residue</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Known OutOfMemory errors give warning message</li>\r
- <li>Overview window calculated more efficiently</li>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.05</strong><br>\r
- 30/8/05</div></td>\r
- <td><ul>\r
- <li>Edit and annotate in "Wrapped" view</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.04</strong><br>\r
- 24/8/05</div></td>\r
- <td><ul>\r
- <li>Hold down mouse wheel & scroll to change font size</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Improved JPred client reliability</li>\r
- <li>Improved loading of Jalview files</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.03</strong><br>\r
- 18/8/05</div></td>\r
- <td><ul>\r
- <li>Set Proxy server name and port in preferences</li>\r
- <li>Multiple URL links from sequence ids</li>\r
- <li>User Defined Colours can have a scheme name and added to Colour Menu</li>\r
- <li>Choose to ignore gaps in consensus calculation</li>\r
- <li>Unix users can set default web browser</li>\r
- <li>Runs without GUI for batch processing</li>\r
- <li>Dynamically generated Web Service Menus</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>InstallAnywhere download for Sparc Solaris</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.02</strong><br>\r
- 18/7/05</div></td>\r
- <td> </td>\r
- <td><ul>\r
- <li>Copy & Paste order of sequences maintains alignment order.</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.01</strong><br>\r
- 12/7/05</div></td>\r
- <td><ul>\r
- <li>Use delete key for deleting selection.</li>\r
- <li>Use Mouse wheel to scroll sequences.</li>\r
- <li>Help file updated to describe how to add alignment annotations.</li>\r
- <li>Version and build date written to build properties file.</li>\r
- <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Delete gaps bug fixed.</li>\r
- <li>FileChooser sorts columns.</li>\r
- <li>Can remove groups one by one.</li>\r
- <li>Filechooser icons installed.</li>\r
- <li>Finder ignores return character when searching. Return key will initiate \r
- a search.<br>\r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.0</strong><br>\r
- 20/6/05</div></td>\r
- <td ><ul>\r
- <li> New codebase</li>\r
- </ul></td>\r
- <td > </td>\r
- </tr>\r
-</table>\r
+<p>Jalview Version 2.07 </p>\r
+<p><a href="features/seqfetch.html">Sequence Fetcher</a> has been added to quickly \r
+ retrieve sequences with known ids from several databases.</p>\r
+<p><a href="features/seqfeatures.html">Sequence Features enhanced</a> to allow \r
+ the user to display all features of a Uniprot file on the alignment and subsequently \r
+ colour, hide or show overlapping features. </p>\r
+<p><a href="io/fileformats.html">Choose to omit /start-end from sequences when \r
+ saving files.</a> This is important for saving files to be used by some programs \r
+ which cannot read the original Jalview sequence output with the appended /start-end.</p>\r
+<p><a href="features/pdbviewer.html">PDB structure viewer enhanced</a>. Mapping \r
+ between sequence and structure has been enhanced, colours on the alignment are \r
+ reflected in the structure viewer.</p>\r
+<p><a href="http://www.jalview.org/examples/applet.html">Jalview Applet can read \r
+ in feature files, PDB files be used as input to HTML form</a> See the website \r
+ to find out the new parameters available for the Applet Version of Jalview.</p>\r
<p> </p>\r
+<p><strong>Issues Resolved</strong></p>\r
+<p>Group Editing is possible with Control and mouse click. Alt key and mouse press \r
+ does not work as this translates as the middle mouse button, which since 2.04 \r
+ is now used to scroll the alignment and change the font size. </p>\r
+<p>HTML export now writes groups and features which were previously missing.</p>\r
+<p> </p>\r
+<p>See the <a href="releases.html">Release History</a> page for details of all \r
+ new features and resolved issues. </p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff