+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
+ </div></td>
+ <td><em>Application</em>
+ <li>Support for JABAWS 2.0 Services (AACon alignment
+ conservation, protein disorder and Clustal Omega) <!--[<a href='http://issues.jalview.org/browse/JAL-976'>JAL-976</a>] - Enhance Jalview desktop to support to JABAWS v2.0 services -->
+ <!--[<a href='http://issues.jalview.org/browse/JAL-974'>JAL-974</a>]-->
+ <!--[<a href='http://issues.jalview.org/browse/JAL-975'>JAL-975</a>]-->
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1060'>JAL-1060</a>] - -->JABAWS
+ server status indicator in Web Services preferences
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-842'>JAL-842</a>] - -->VARNA
+ (http://varna.lri.fr) viewer for RNA structures in Jalview
+ alignment window
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1133'>JAL-1133</a>] - -->Updated
+ jalview build and deploy framework for OSX mountain lion, windows
+ 7, and 8
+ </li>
+ <li>Nucleotide substitution matrix for PCA that supports RNA
+ and ambiguity codes <!--[<a href='http://issues.jalview.org/browse/JAL-1027'>JAL-1027</a>] -->
+ </li>
+
+ <li>Improved sequence database retrieval GUI</li>
+ <li>Support fetching and database reference look up against
+ multiple DAS sources (Fetch all from in 'fetch db refs')<!--[<a href='http://issues.jalview.org/browse/JAL-1061'>JAL-1061</a>], [<a href='http://issues.jalview.org/browse/JAL-1075'>JAL-1075</a>] - GUI elements to select one or several DAS sources to query for sequences or database references-->
+ </li>
+ <li>Jalview project improvements
+ <ul>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1109'>JAL-1109</a>] -->Store
+ and retrieve the 'belowAlignment' flag for annotation
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1110'>JAL-1110</a>]-->calcId
+ attribute to group annotation rows on the alignment
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1136'>JAL-1136</a>] - -->Store
+ AACon calculation settings for a view in Jalview project
+ </li>
+
+ </ul>
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1160'>JAL-1160</a>] - -->horizontal
+ scrolling gesture support
+ </li>
+ <li>Visual progress indicator when PCA calculation is running<!--[<a href='http://issues.jalview.org/browse/JAL-1120'>JAL-1120</a>] - -->
+ </li>
+ <li>Simpler JABA web services menus<!--[<a href='http://issues.jalview.org/browse/JAL-1137'>JAL-1137</a>] - -->
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1165'>JAL-1165</a>] - -->visual
+ indication that web service results are still being retrieved from
+ server
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1183'>JAL-1183</a>] - -->Serialise
+ the dialogs that are shown when jalview starts up for first time
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1188'>JAL-1188</a>] - -->Jalview
+ user agent string for interacting with HTTP services
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-972'>JAL-972</a>] - -->DAS
+ 1.6 and DAS 2.0 source support using new JDAS client library
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1202'>JAL-1202</a>] - -->Examples
+ directory and Groovy library included in InstallAnywhere
+ distribution
+ </li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-963'>JAL-963</a>] - -->RNA
+ alignment and secondary structure annotation visualization applet
+ example
+ </li>
+ </ul> <em>General</em>
+ <ul>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-958'>JAL-958</a>] - -->Normalise
+ option for consensus sequence logo
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1121'>JAL-1121</a>] - -->Reset
+ button in PCA window to return dimensions to defaults
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1125'>JAL-1125</a>] - -->Allow
+ seqspace or Jalview variant of alignment PCA calculation
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1013'>JAL-1013</a>] -->PCA
+ with either nucleic acid and protein substitution matrices
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1157'>JAL-1157</a>] - -->Allow
+ windows containing HTML reports to be exported in HTML
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-970'>JAL-970</a>] - -->Interactive
+ display and editing of RNA secondary structure contacts
+ </li>
+ <li>RNA Helix Alignment Colouring</li>
+ <li>RNA base pair logo consensus</li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-878'>JAL-878</a>] - -->Parse
+ sequence associated secondary structure information in Stockholm
+ files
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1015'>JAL-1015</a>] - -->HTML
+ Export database accessions and annotation information presented in
+ tooltip for sequences
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1052'>JAL-1052</a>] - -->Import
+ secondary structure from LOCARNA clustalw style RNA alignment
+ files
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1065'>JAL-1065</a>] - [<a href='http://issues.jalview.org/browse/JAL-1078'>JAL-1078</a>]-->import
+ and visualise T-COFFEE quality scores for an alignment
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1066'>JAL-1066</a>] - -->'colour
+ by annotation' per sequence option to shade each sequence
+ according to its associated alignment annotation
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1130'>JAL-1130</a>] - -->New
+ Jalview Logo
+ </li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1167'>JAL-1167</a>] - -->documentation
+ for score matrices used in Jalview
+ </li>
+ <li>New Website!</li>
+ </ul></td>
+ <td><em>Application</em>
+ <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-979'>JAL-979</a>] - -->revise
+ SHMR RSBS definition to ensure alignment is uploaded via ali_file
+ parameter
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-980'>JAL-980</a>] - -->Jalview
+ 2.7 is incompatible with Jmol-12.2.2
+ </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-1004'>JAL-1004</a>] - -->Cut
+ and paste menu not opened when mouse clicked on desktop window
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1010'>JAL-1010</a>] - -->Putting
+ fractional value into integer text box in alignment parameter
+ dialog causes jalview to hang
+ </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-1023'>JAL-1023</a>] - -->View
+ all structures fails with exception shown in structure view
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1025'>JAL-1025</a>] - -->Characters
+ in filename associated with PDBEntry not escaped in a platform
+ independent way
+ </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-1040'>JAL-1040</a>] - -->Jalview
+ desktop fails to launch with jar signature failure when java web
+ start temporary file caching is disabled
+ </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-1087'>JAL-1087</a>] - -->Errors
+ during processing of command line arguments cause progress bar
+ (JAL-898) to be removed
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1097'>JAL-1097</a>] - -->Replace
+ comma for semi-colon option not disabled for DAS sources in
+ sequence fetcher
+ </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-1127'>JAL-1127</a>] - -->Option
+ widgets not updated to reflect user settings
+ </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 does not launch on mountain lion
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1135'>JAL-1135</a>] - -->InstallAnywhere
+ installer doesn't unpack and run on OSX Mountain Lion
+ </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-1149'>JAL-1149</a>] - -->Browser
+ launch fails with NPE on java 1.7
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1171'>JAL-1171</a>] - -->JABAWS
+ alignment marked as finished when job was cancelled or job failed
+ due to invalid input
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1185'>JAL-1185</a>] - -->NPE
+ with v2.7 example when clicking on Tree associated with all views
+ </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>
+ </ul> <em>Applet</em>
+ <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> <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-1032'>JAL-1032</a>] - -->PCA
+ calculation fails when sequence has been selected and then
+ deselected
+ </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>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1153'>JAL-1153</a>] - -->Grouped
+ annotation graph label has incorrect line colour
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1155'>JAL-1155</a>] - -->Grouped
+ annotation graph label display is corrupted for lots of labels
+ </li>