- </ul> See <a href="na/index.html">Nucleic Acid Support</a> for full
- details.</li>
- <li>Parse and display T-COFFEE alignment quality scores</li>
- <li>Shade individual sequence positions according to alignment
- annotation scores</li>
- <li>Enhanced PCA viewer: more export options, and switch between
- different PCA modes and residue score models</li>
- <li>New Jalview Desktop database fetcher GUI</li>
- <li>Support for DAS 1.6 and DAS 2.0 sources</li>
- <li>Export sequence database annotation as HTML report</li>
- <li>Normalised Sequence Logo Display</li>
- </ul>
- <p>
- <strong>Issues Resolved (a select list - see the <a
- href="releases.html#Jalview2.8">release history</a> for full details)
- </strong>
- </p>
- <p>
- <strong>Issues in the Jalview Desktop</strong>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] - -->
- <!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] - -->Stop
- windows being moved outside desktop on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] - -->Filetype
- associations not installed for webstart launch
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] - -->Jalview
- does not always retrieve progress of a JABAWS job execution in full
- once it is complete
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] - -->View
- all structures superposed fails with exception
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] - -->Jnet
- job queues forever if a very short sequence is submitted for
- prediction
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] - -->Structure
- view highlighting doesn't work on windows 7
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] - -->Jalview
- desktop fails to launch with exception when using proxy
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] - -->Tree
- calculation reports 'you must have 2 or more sequences
- selected' when selection is empty
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] - -->DAS
- Sequence retrieval with range qualification results in sequence xref
- which includes range qualification
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] - -->Cannot
- close news reader when JABAWS server warning dialog is shown
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] - -->Edited
- sequence not submitted to web service
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] - -->Jalview
- 2.7 Webstart and InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
- <ul>
- <li>The workaround for webstart is to go into the Security
- panel (gatekeeper symbol) under System settings, and select the
- 'allow any code to run' setting.</li>
- </ul>
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] - -->Annotation
- panel not given a scroll bar when sequences with alignment annotation
- are pasted into the alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] - -->Sequence
- associated annotation rows not associated when loaded from jalview
- project
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] - -->Exceptions
- when copy/paste sequences with grouped annotation rows to new window
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] - -->Browser
- launch fails with NPE on java 1.7
- </li>
-
- </ul>
-
- <strong>Issues specific to the JalviewLite Applet</strong>
- <ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-962'>JAL-962</a>] - -->Sequence
- features are momentarily displayed before they are hidden using
- hidefeaturegroups applet parameter
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-965'>JAL-965</a>] - -->loading
- features via javascript API automatically enables feature display
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1170'>JAL-1170</a>] - -->scrollToColumnIn
- javascript API method doesn't work
- </li>
- </ul>
- <strong>Issues affecting both applet and application</strong>
- <em>General</em>
- <ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] - -->Redundancy
- removal fails for rna alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1033'>JAL-1033</a>] - -->PCA
- window shows grey box when first opened on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1086'>JAL-1086</a>] - -->Letters
- coloured pink in sequence logo when alignment coloured with clustalx
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1099'>JAL-1099</a>] - -->Choosing
- fonts without letter symbols defined causes exceptions and redraw
- errors
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1123'>JAL-1123</a>] - -->Initial
- PCA plot view is not same as manually reconfigured view
- </li>
- </ul>
+ <li><em>Showing and hiding regions</em>
+ <ul>
+ <li><a href="menus/popupMenu.html#hideinserts">Hide
+ insertions</a> in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden columns.</li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the <strong>Tools→Enable
+ Experimental Features</strong> option, and then restart Jalview.
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>