<body>\r
<p><strong>What's new ?</strong> </p>\r
<p>Jalview Version 2.08</p>\r
-<p> <a href="editing/index.html">Editing</a> can be locked to the selection area. \r
- Any edits made within the locked area do not affect the rest of the alignment.</p>\r
-<p> Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list \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 results from searches were added as alignment positions, which was \r
- wrong. Now the search results are saved as sequence features and their visibility \r
- and colour can be modified using the <a href="features/seqfeatures.html">Sequence \r
- Feature Settings</a> window.</p>\r
-<p> Precalculated annotations can be loaded onto alignments. The <a href="features/annotationsFormat.html">Annotation \r
- File</a> format is a tab delimited set of values.</p>\r
-<p> <a href="features/featuresFormat.html">Features file</a> allows grouping of \r
- features. The <a href="features/seqfeatures.html">Sequence Feature Settings</a> \r
- window then makes it very easy to set the visibility of groups of features. \r
-</p>\r
-<p> <a href="colourSchemes/annotationColouring.html">Annotation Colouring</a> \r
- scheme added. A new colour scheme which colours columns on a per-column value.</p>\r
-<p> Smooth fonts off by default - faster rendering. Toggle on / off from the View \r
- menu, or can be set in Preferences.</p>\r
-<p> Choose to toggle Autocalculate Consensus On/Off from the Calculate menu.<br>\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
-<p> Drag & Drop fixed on Linux</p>\r
-<p> Jalview Archive file faster to load/save, sequence descriptions saved.<br>\r
-</p>\r
+<ul>\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
<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
git://source.jalview.org / jalview.git / blobdiff