<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
+<p>Jalview Version 2.08</p>\r
+<p><a href="editing/index.html">Editing</a> can be <a href="editing/selectionAreas.html">locked to the\r
+ selection area</a> so that any edits made within the locked area do\r
+ not unexpectedly shift other parts of the alignment.</p>\r
+<p> Keyboard editing - press F2 to toggle <a href="features/cursorMode.html">cursor mode</a> On / Off. For a full list \r
+ of keyboard controls, look <a href="keys.html">here</a>.</p>\r
+<p> <a href="features/search.html">Create sequence features from searches</a>. \r
+ Previously, the regions of sequences highlighted as the result of\r
+ searches were added as new regions in the alignment. Now, the sequence region\r
+ selected by a search can be used to define named sequences features\r
+ attached to the sequence, rather than the alignment.\r
+ </p>\r
+<p>Sequence feature display and rendering has also been enhanced, with\r
+ the addition of sequence feature groups (which can be used to show\r
+ or hide a set of features <em>en masse</em>) and user defined\r
+ feature colours as well as transparency controls, using the <a\r
+ href="features/featuresettings.html">Sequence Feature Settings</a>\r
+ window. The <a href="features/featuresFormat.html">Features file</a>\r
+ has also been extended to accomodate these enhancements.</p>\r
+<p>Alignment annotation and colouring is also considerably\r
+ enhanced. Precalculated symbolic and quantitative annotations (text labels,\r
+ secondary structure symbols and multiple scalar graphs) can now be\r
+ loaded onto alignments via the <a\r
+ href="features/annotationsFormat.html">Annotation\r
+ File</a>. Additionally, the <a\r
+ href="colourSchemes/annotationColouring.html">Annotation\r
+ Colouring</a> dialog box allows an alignment to be coloured based on\r
+ any of the graphed quantities with which it is annotated.</p>\r
+<p>Rendering speed has been improved by disabling anti-aliasing via\r
+ the <strong>Smooth Fonts</strong>\r
+ option in the <strong>View \r
+ menu</strong> (its default set in <strong>Preferences</strong>). In addition, response\r
+ times when editing alignments can be reduced by turning off the automatic\r
+ calculation of amino acid property Consensus (which has been\r
+ reintroduced to the <strong>Calculate</strong> menu as <strong>Autocalculate Consensus</strong>).<br>\r
+</p>\r
+<p><strong>Issues Resolved</strong></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
+<li>Drag & Drop now works on common Linux desktops (at least KDE\r
+and Gnome)</li>\r
+<li>Jalview XML Archive Input/Output is now faster (using an\r
+internal Jalview schema), and sequence description strings are now\r
+preserved in the archive.</li>\r
+<li>Jalview can now correctly read and write <a\r
+href="io/modellerpir.html">MODELLER style\r
+PIR</a> files.\r
+</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>2.05b</strong><br>\r
- 30/8/05</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> </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