<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
-<tr>
-<td><div align="center"><strong><a name="Jalview2.8">2.8</a></strong><br/> <em>08/11/2012</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>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>08/11/2012</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<!--[<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>
+ <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>
-</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>
-</ul>
-
-</tr>
- <tr>
- <td>
- <div align="center">
- <strong><a name="Jalview2.7">2.7</a>
- </strong><br> <em>27/09/2011</em>
- </div></td>
- <td><em>Application</em>
- <ul>
- <li>Jalview Desktop News Reader</li>
- <li>Tweaked default layout of web services menu</li>
- <li>View/alignment association menu to enable user to easily
- specify which alignment a multi-structure view takes its
- colours/correspondences from</li>
- <li>Allow properties file location to be specified as URL </li>
- <li>Extend jalview project to preserve associations between
- many alignment views and a single Jmol display</li>
- <li>Store annotation row height in jalview project file</li>
- <li>Annotation row column label formatting attributes stored
- in project file</li>
- <li>Annotation row order for auto-calculated annotation rows
- preserved in jalview project file</li>
- <li>Visual progress indication when Jalview state is saved
- using Desktop window menu</li>
- <li>Visual indication that command line arguments are still
- being processed</li>
- <li>Groovy script execution from URL</li>
- <li>Colour by annotation default min and max colours in
- preferences</li>
- <li>Automatically associate PDB files dragged onto an
- alignment with sequences that have high similarity and matching
- IDs</li>
- <li>Update JGoogleAnalytics to latest release (0.3)</li>
- <li>'view structures' option to open many structures
- in same window</li>
- <li>Sort associated views menu option for tree panel</li>
- <li>Group all JABA and non-JABA services for a particular
- analysis function in its own submenu</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Userdefined and autogenerated annotation rows for groups</li>
- <li>Adjustment of alignment annotation pane height</li>
- <li>Annotation scrollbar for annotation panel</li>
- <li>Drag to reorder annotation rows in annotation panel</li>
- <li>'automaticScrolling' parameter</li>
- <li>Allow sequences with partial ID string matches to be
- annotated from GFF/jalview features files</li>
- <li>Sequence logo annotation row in applet</li>
- <li>Absolute paths relative to host server in applet
- parameters are treated as such</li>
- <li>New in the JalviewLite javascript API:
- <ul>
- <li>JalviewLite.js javascript library</li>
- <li>Javascript callbacks for
- <ul>
- <li>Applet initialisation</li>
- <li>Sequence/alignment mouse-overs and selections</li>
- </ul>
- </li>
- <li>scrollTo row and column alignment scrolling functions</li>
- <li>Select sequence/alignment regions from javascript</li>
- <li>javascript structure viewer harness to pass messages
- between Jmol and Jalview when running as distinct applets</li>
- <li>sortBy method</li>
- <li>Set of applet and application examples shipped with
- documentation</li>
- <li>New example to demonstrate jalviewLite and Jmol
- javascript message exchange</li>
- </ul>
- </ul> <em>General</em>
- <ul>
- <li>Enable Jmol displays to be associated with multiple
- multiple alignments</li>
- <li>Option to automatically sort alignment with new tree</li>
- <li>User configurable link to enable redirects to a
- www.jalview.org mirror</li>
- <li>Jmol colours option for Jmol displays</li>
- <li>Configurable newline string when writing alignment and
- other flat files</li>
- <li>Allow alignment annotation description lines to contain
- html tags</li>
- </ul> <em>Documentation and Development</em>
- <ul>
- <li>Add groovy test harness for bulk load testing to examples
- </li>
- <li>Groovy script to load and align a set of sequences using a
- web service before displaying the result in the Jalview desktop</li>
- <li>Restructured javascript and applet api documentation</li>
- <li>Ant target to publish example html files with applet archive</li>
- <li>Netbeans project for building jalview from source</li>
- <li>ant task to create online javadoc for jalview source</li>
- </ul></td>
- <td><em>Application</em>
- <ul>
- <li>User defined colourscheme throws exception when current
- built in colourscheme is saved as new scheme</li>
- <li>AlignFrame->Save in application pops up save dialog for
- valid filename/format</li>
- <li>Cannot view associated structure for Uniprot sequence</li>
- <li>PDB file association breaks for Uniprot sequence P37173</li>
- <li>Associate PDB from file dialog does not tell you which
- sequence is to be associated with the file</li>
- <li>Find All raises null pointer exception when query only
- matches sequence IDs</li>
- <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
- <li>Jalview project with Jmol views created with Jalview 2.4
- cannot be loaded</li>
- <li>Filetype associations not installed for webstart launch</li>
- <li>Two or more chains in a single PDB file associated with
- sequences in different alignments do not get coloured by their
- associated sequence</li>
- <li>Visibility status of autocalculated annotation row not
- preserved when project is loaded</li>
- <li>Annotation row height and visibility attributes not stored
- in jalview project</li>
- <li>Tree bootstraps are not preserved when saved as a jalview
- project</li>
- <li>Envision2 workflow tooltips are corrupted</li>
- <li>Enabling show group conservation also enables colour by
- conservation</li>
- <li>Duplicate group associated conservation or consensus
- created on new view</li>
- <li>Annotation scrollbar not displayed after 'show all
- hidden annotation rows' option selected</li>
- <li>Alignment quality not updated after alignment annotation
- row is hidden then shown</li>
- <li>Preserve colouring of structures coloured by sequences in pre
- jalview 2.7 projects</li>
- <li>Web service job parameter dialog is not laid out properly
- </li>
- <li>Web services menu not refreshed after 'reset
- services' button is pressed in preferences</li>
- <li>Annotation off by one in jalview v2_3 example project</li>
- <li>Structures imported from file and saved in project get
- name like jalview_pdb1234.txt when reloaded</li>
- <li>Jalview does not always retrieve progress of a JABAWS job
- execution in full once it is complete</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Alignment height set incorrectly when lots of annotation
- rows are displayed</li>
- <li>Relative URLs in feature HTML text not resolved to
- codebase</li>
- <li>View follows highlighting does not work for positions in
- sequences</li>
- <li><= shown as = in tooltip</li>
- <li>Export features raises exception when no features exist</li>
- <li>Separator string used for serialising lists of IDs for
- javascript api is modified when separator string provided as
- parameter</li>
- <li>Null pointer exception when selecting tree leaves for
- alignment with no existing selection</li>
- <li>Relative URLs for datasources assumed to be relative to
- applet's codebase</li>
- <li>Status bar not updated after finished searching and search
- wraps around to first result</li>
- <li>StructureSelectionManager instance shared between several
- jalview applets causes race conditions and memory leaks</li>
- <li>Hover tooltip and mouseover of position on structure not
- sent from Jmol in applet</li>
- <li>Certain sequences of javascript method calls to applet API
- fatally hang browser</li>
- </ul> <em>General</em>
- <ul>
- <li>View follows structure mouseover scrolls beyond position
- with wrapped view and hidden regions</li>
- <li>Find sequence position moves to wrong residue with/without
- hidden columns</li>
- <li>Sequence length given in alignment properties window is
- off by 1</li>
- <li>InvalidNumberFormat exceptions thrown when trying to
- import PDB like structure files</li>
- <li>Positional search results are only highlighted between
- user-supplied sequence start/end bounds</li>
- <li>End attribute of sequence is not validated</li>
- <li>Find dialog only finds first sequence containing a given
- sequence position</li>
- <li>Sequence numbering not preserved in MSF alignment output</li>
- <li>Jalview PDB file reader does not extract sequence from
- nucleotide chains correctly</li>
- <li>Structure colours not updated when tree partition changed
- in alignment</li>
- <li>Sequence associated secondary structure not correctly
- parsed in interleaved stockholm</li>
- <li>Colour by annotation dialog does not restore current state
- </li>
- <li>Hiding (nearly) all sequences doesn't work properly</li>
- <li>Sequences containing lowercase letters are not properly
- associated with their pdb files</li>
- </ul> <em>Documentation and Development</em>
- <ul>
- <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
- tool</li>
- </ul></td>
- </tr>
- <tr>
+ </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>
+ </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>
+ </ul>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>Jalview Desktop News Reader</li>
+ <li>Tweaked default layout of web services menu</li>
+ <li>View/alignment association menu to enable user to easily
+ specify which alignment a multi-structure view takes its
+ colours/correspondences from</li>
+ <li>Allow properties file location to be specified as URL</li>
+ <li>Extend jalview project to preserve associations between
+ many alignment views and a single Jmol display</li>
+ <li>Store annotation row height in jalview project file</li>
+ <li>Annotation row column label formatting attributes stored
+ in project file</li>
+ <li>Annotation row order for auto-calculated annotation rows
+ preserved in jalview project file</li>
+ <li>Visual progress indication when Jalview state is saved
+ using Desktop window menu</li>
+ <li>Visual indication that command line arguments are still
+ being processed</li>
+ <li>Groovy script execution from URL</li>
+ <li>Colour by annotation default min and max colours in
+ preferences</li>
+ <li>Automatically associate PDB files dragged onto an
+ alignment with sequences that have high similarity and matching
+ IDs</li>
+ <li>Update JGoogleAnalytics to latest release (0.3)</li>
+ <li>'view structures' option to open many structures
+ in same window</li>
+ <li>Sort associated views menu option for tree panel</li>
+ <li>Group all JABA and non-JABA services for a particular
+ analysis function in its own submenu</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Userdefined and autogenerated annotation rows for groups</li>
+ <li>Adjustment of alignment annotation pane height</li>
+ <li>Annotation scrollbar for annotation panel</li>
+ <li>Drag to reorder annotation rows in annotation panel</li>
+ <li>'automaticScrolling' parameter</li>
+ <li>Allow sequences with partial ID string matches to be
+ annotated from GFF/jalview features files</li>
+ <li>Sequence logo annotation row in applet</li>
+ <li>Absolute paths relative to host server in applet
+ parameters are treated as such</li>
+ <li>New in the JalviewLite javascript API:
+ <ul>
+ <li>JalviewLite.js javascript library</li>
+ <li>Javascript callbacks for
+ <ul>
+ <li>Applet initialisation</li>
+ <li>Sequence/alignment mouse-overs and selections</li>
+ </ul>
+ </li>
+ <li>scrollTo row and column alignment scrolling functions</li>
+ <li>Select sequence/alignment regions from javascript</li>
+ <li>javascript structure viewer harness to pass messages
+ between Jmol and Jalview when running as distinct applets</li>
+ <li>sortBy method</li>
+ <li>Set of applet and application examples shipped with
+ documentation</li>
+ <li>New example to demonstrate jalviewLite and Jmol
+ javascript message exchange</li>
+ </ul>
+ </ul> <em>General</em>
+ <ul>
+ <li>Enable Jmol displays to be associated with multiple
+ multiple alignments</li>
+ <li>Option to automatically sort alignment with new tree</li>
+ <li>User configurable link to enable redirects to a
+ www.jalview.org mirror</li>
+ <li>Jmol colours option for Jmol displays</li>
+ <li>Configurable newline string when writing alignment and
+ other flat files</li>
+ <li>Allow alignment annotation description lines to contain
+ html tags</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>Add groovy test harness for bulk load testing to examples
+ </li>
+ <li>Groovy script to load and align a set of sequences using a
+ web service before displaying the result in the Jalview desktop</li>
+ <li>Restructured javascript and applet api documentation</li>
+ <li>Ant target to publish example html files with applet
+ archive</li>
+ <li>Netbeans project for building jalview from source</li>
+ <li>ant task to create online javadoc for jalview source</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>User defined colourscheme throws exception when current
+ built in colourscheme is saved as new scheme</li>
+ <li>AlignFrame->Save in application pops up save dialog for
+ valid filename/format</li>
+ <li>Cannot view associated structure for Uniprot sequence</li>
+ <li>PDB file association breaks for Uniprot sequence P37173</li>
+ <li>Associate PDB from file dialog does not tell you which
+ sequence is to be associated with the file</li>
+ <li>Find All raises null pointer exception when query only
+ matches sequence IDs</li>
+ <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
+ <li>Jalview project with Jmol views created with Jalview 2.4
+ cannot be loaded</li>
+ <li>Filetype associations not installed for webstart launch</li>
+ <li>Two or more chains in a single PDB file associated with
+ sequences in different alignments do not get coloured by their
+ associated sequence</li>
+ <li>Visibility status of autocalculated annotation row not
+ preserved when project is loaded</li>
+ <li>Annotation row height and visibility attributes not stored
+ in jalview project</li>
+ <li>Tree bootstraps are not preserved when saved as a jalview
+ project</li>
+ <li>Envision2 workflow tooltips are corrupted</li>
+ <li>Enabling show group conservation also enables colour by
+ conservation</li>
+ <li>Duplicate group associated conservation or consensus
+ created on new view</li>
+ <li>Annotation scrollbar not displayed after 'show all
+ hidden annotation rows' option selected</li>
+ <li>Alignment quality not updated after alignment annotation
+ row is hidden then shown</li>
+ <li>Preserve colouring of structures coloured by sequences in
+ pre jalview 2.7 projects</li>
+ <li>Web service job parameter dialog is not laid out properly
+ </li>
+ <li>Web services menu not refreshed after 'reset
+ services' button is pressed in preferences</li>
+ <li>Annotation off by one in jalview v2_3 example project</li>
+ <li>Structures imported from file and saved in project get
+ name like jalview_pdb1234.txt when reloaded</li>
+ <li>Jalview does not always retrieve progress of a JABAWS job
+ execution in full once it is complete</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Alignment height set incorrectly when lots of annotation
+ rows are displayed</li>
+ <li>Relative URLs in feature HTML text not resolved to
+ codebase</li>
+ <li>View follows highlighting does not work for positions in
+ sequences</li>
+ <li><= shown as = in tooltip</li>
+ <li>Export features raises exception when no features exist</li>
+ <li>Separator string used for serialising lists of IDs for
+ javascript api is modified when separator string provided as
+ parameter</li>
+ <li>Null pointer exception when selecting tree leaves for
+ alignment with no existing selection</li>
+ <li>Relative URLs for datasources assumed to be relative to
+ applet's codebase</li>
+ <li>Status bar not updated after finished searching and search
+ wraps around to first result</li>
+ <li>StructureSelectionManager instance shared between several
+ jalview applets causes race conditions and memory leaks</li>
+ <li>Hover tooltip and mouseover of position on structure not
+ sent from Jmol in applet</li>
+ <li>Certain sequences of javascript method calls to applet API
+ fatally hang browser</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>View follows structure mouseover scrolls beyond position
+ with wrapped view and hidden regions</li>
+ <li>Find sequence position moves to wrong residue with/without
+ hidden columns</li>
+ <li>Sequence length given in alignment properties window is
+ off by 1</li>
+ <li>InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files</li>
+ <li>Positional search results are only highlighted between
+ user-supplied sequence start/end bounds</li>
+ <li>End attribute of sequence is not validated</li>
+ <li>Find dialog only finds first sequence containing a given
+ sequence position</li>
+ <li>Sequence numbering not preserved in MSF alignment output</li>
+ <li>Jalview PDB file reader does not extract sequence from
+ nucleotide chains correctly</li>
+ <li>Structure colours not updated when tree partition changed
+ in alignment</li>
+ <li>Sequence associated secondary structure not correctly
+ parsed in interleaved stockholm</li>
+ <li>Colour by annotation dialog does not restore current state
+ </li>
+ <li>Hiding (nearly) all sequences doesn't work properly</li>
+ <li>Sequences containing lowercase letters are not properly
+ associated with their pdb files</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
+ tool</li>
+ </ul></td>
+ </tr>
+ <tr>
<td>
<div align="center">
<strong><a name="Jalview2.6.1">2.6.1</a>
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong>
- </p>
- <p>
- Jalview 2.8 includes a brand new logo, which you'll see in file browsers, splash screens, and also on the new look Jalview site.
- </p>
- <p>
- In addition to our new look, Jalview 2.8 includes a number of new
- features.. some of which have been in development since July 2010. The
- highlights are below, and - as usual, for a comprehensive list, take a
- look at the <a href="releases.html#Jalview2.8">Jalview 2.8 Release
- Notes</a>.
- </p>
- <p>
- <strong>Highlights in Jalview Desktop Version 2.8</strong>
- </p>
- <ul>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>Jalview 2.8 includes a brand new logo, which you'll see in file
+ browsers, splash screens, and also on the new look Jalview site.</p>
+ <p>
+ In addition to our new look, Jalview 2.8 includes a number of new
+ features.. some of which have been in development since July 2010. The
+ highlights are below, and - as usual, for a comprehensive list, take a
+ look at the <a href="releases.html#Jalview2.8">Jalview 2.8 Release
+ Notes</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview Version 2.8</strong>
+ </p>
+ <ul>
+ <li>Improved JABA client and new JABAWS 2.0 Services
+ <ul>
+ <li>AACon alignment conservation</li>
+ <li>Protein disorder - DisEMBL, RONN, GlobPlot and IUPred</li>
+ <li>Clustal Omega - huge protein alignments</li>
+ </ul>
+ </li>
+ <li><strong>Support for RNA</strong>
+ <ul>
+ <li>Import sequence and alignment associated WUSS or VIENNA
+ secondary structure notation from stockholm and clustalW files or
+ as jalview annotation.</li>
+ <li>Interactive editing of RNA secondary structure annotation</li>
+ <li>Colour scheme for purine/pyrimidine and to highlight RNA
+ helices</li>
+ <li>RNA canonical base pair consensus score and sequence logo</li>
+ <li>Embedded <a href="http://varna.lri.fr/">VARNA</a> RNA
+ secondary structure viewer in the Desktop
+ </li>
+ </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>
- <li>New Purine/Pyrimidine colour scheme</li>
- <li>Colouring of RNA secondary structure by helices. See <a href="na/index.html">Nucleic Acid Support</a></li>
- <li>Embedded <a href="http://www.varna.fr/">VARNA</a> RNA secondary structure viewer.
- </ul>
+ </ul>
- <p>
- <strong>Issues Resolved (a select list - see the <a
- href="releases.html#Jalview2.7.1">release history</a> for full details)
- </strong>
- </p>
- <p>
- <strong>Issues in the Jalview Desktop</strong>
- <ul>
- </ul>
- <strong>Issues specific to the JalviewLite Applet</strong>
- <ul>
- </ul>
- <strong>Issues affecting both applet and application</strong>
- <ul>
- </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>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff