jalview 2.5.1 release notes
authorjprocter <Jim Procter>
Fri, 11 Jun 2010 14:39:02 +0000 (14:39 +0000)
committerjprocter <Jim Procter>
Fri, 11 Jun 2010 14:39:02 +0000 (14:39 +0000)
help/html/releases.html
help/html/whatsNew.html

index 4c2d98c..3dd6fda 100755 (executable)
                </td>
        </tr>
        <tr>
+               <td>
+               <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
+               <em>14/6/2010</em></div>
+               </td>
+               <td></td>
+               <td>
+               <ul>
+                       <li>Alignment prettyprinter doesn't cope with long sequence IDs
+                       </li>
+                       <li>clustalx colourscheme colours Ds preferentially when both
+                       D+E are present in over 50% of the column</li>
+                       <li>nucleic acid structures retrieved from PDB do not import
+                       correctly</li>
+                       <li>More columns get selected than were clicked on when a number
+                       of columns are hidden</li>
+                       <li>annotation label popup menu not providing correct
+                       add/hide/show options when rows are hidden or none are present</li>
+               </ul>
+               <em>Applet</em>
+               <ul>
+                       <li>annotation panel disappears when annotation is
+                       hidden/removed</li>
+               </ul>
+               <em>Application</em>
+               <ul>
+                       <li>Alignment view not redrawn properly when new alignment
+                       opened where annotation panel is visible but no annotations are
+                       present on alignment</li>
+                       <li>pasted region containing hidden columns is incorrectly
+                       displayed in new alignment window</li>
+                       <li>Jalview slow to complete operations when stdout is flooded
+                       (fix is to close the Jalview console)</li>
+                       <li>CSV output of consensus only includes the percentage of all
+                       symbols if sequence logo display is enabled</li>
+                       <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
+                       selected Rregions menu item.</li>
+                       <li>inconsistent group submenu and Format submenu entry 'Un' or
+                       'Non'conserved</li>
+                       <li>Sequence feature settings are being shared by multiple
+                       distinct alignments</li>
+                       <li>group annotation not recreated when tree partition is
+                       changed</li>
+                       <li>double click on group annotation to select sequences does
+                       not propagate to associated trees</li>
+                       <li>Mac OSX specific issues:
+                       <ul>
+                               <li>exception raised when mouse clicked on desktop window
+                               background</li>
+                               <li>Desktop menu placed on menu bar and application name set
+                               correctly</li>
+                               <li>sequence feature settings not wide enough for the save
+                               feature colourscheme button</li>
+                       </ul>
+                       </li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
 
                <td>
                <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
                <em>30/4/2010</em></div>
                </td>
-               <td>
-               <em>New Capabilities</em>
+               <td><em>New Capabilities</em>
                <ul>
                        <li>URL links generated from description line for
                        regular-expression based URL links (applet and application)
                        <li>Linked viewing of nucleic acid sequences and structures</li>
                        <li>Automatic Scrolling option in View menu to display the
                        currently highlighted region of an alignment.</li>
-                       <li>Order an alignment by sequence length, or using the average score or total feature count for each sequence.</li>
+                       <li>Order an alignment by sequence length, or using the average
+                       score or total feature count for each sequence.</li>
                        <li>Shading features by score or associated description</li>
-                       <li>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
-                       <li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</li>
+                       <li>Subdivide alignment and groups based on identity of selected
+                       subsequence (Make Groups from Selection).</li>
+                       <li>New hide/show options including Shift+Control+H to hide
+                       everything but the currently selected region.</li>
                        <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
-</ul>
-<em>Application</em>
-<ul>
-       <li>Fetch DB References capabilities and UI expanded to support
-       retrieval from DAS sequence sources</li>
-       <li>Local DAS Sequence sources can be added via the command line
-       or via the Add local source dialog box.</li>
-       <li>DAS Dbref and DbxRef feature types are parsed as database
-       references and protein_name is parsed as description line (BioSapiens
-       terms).</li>
-       <li>Enable or disable non-positional feature and database
-       references in sequence ID tooltip from View menu in application.</li>
-       <!--                    <li>New hidden columns and rows and representatives capabilities
+               </ul>
+               <em>Application</em>
+               <ul>
+                       <li>Fetch DB References capabilities and UI expanded to support
+                       retrieval from DAS sequence sources</li>
+                       <li>Local DAS Sequence sources can be added via the command line
+                       or via the Add local source dialog box.</li>
+                       <li>DAS Dbref and DbxRef feature types are parsed as database
+                       references and protein_name is parsed as description line (BioSapiens
+                       terms).</li>
+                       <li>Enable or disable non-positional feature and database
+                       references in sequence ID tooltip from View menu in application.</li>
+                       <!--                    <li>New hidden columns and rows and representatives capabilities
                        in annotations file (in progress - not yet fully implemented)</li> -->
-       <li>Group-associated consensus, sequence logos and conservation
-       plots</li>
-       <li>Symbol distributions for each column can be exported and
-       visualized as sequence logos</li>
-       <li>Optionally scale multi-character column labels to fit within
-       each column of annotation row<!-- todo for applet --></li>
-       <li>Optional automatic sort of associated alignment view when a
-       new tree is opened.</li>
-       <li>Jalview Java Console</li>
-       <li>Better placement of desktop window when moving between different screens.</li>
-       <li>New preference items for sequence ID tooltip and consensus
-       annotation</li>
-       <li>Client to submit sequences and IDs to <a
-               href="webServices/index.html#envision2">Envision2</a> Workflows</li>
-       <li><em>Vamsas Capabilities</em>
-       <ul>
-               <li>Improved VAMSAS synchronization (jalview archive used to
-               preserve views, structures, and tree display settings)</li>
-               <li>Import of vamsas documents from disk or URL via command line</li>
-               <li>Sharing of selected regions between views and with other
-               VAMSAS applications (Experimental feature!)</li>
-               <li>Updated API to VAMSAS version 0.2</li>
-       </ul>
-       </li>
-</ul>
-<em>Applet</em>
-<ul>
-       <li>Middle button resizes annotation row height</li>
-       <li>New Parameters
-       <ul>
-               <li>sortByTree (true/false) - automatically sort the associated
-               alignment view by the tree when a new tree is opened.</li>
-               <li>showTreeBootstraps (true/false) - show or hide branch
-               bootstraps (default is to show them if available)</li>
-               <li>showTreeDistances (true/false) - show or hide branch lengths
-               (default is to show them if available)</li>
-               <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated
-               nodes should be highlighted in the tree view</li>
-               <li>heightScale and widthScale (1.0 or more) - increase the
-               height or width of a cell in the alignment grid relative to the
-               current font size.</li>
-       </ul>
-       </li>
-       <li>Non-positional features displayed in sequence ID tooltip</li>
-</ul>
-<em>Other</em>
-<ul>
-       <li>Features format: graduated colour definitions and
-       specification of feature scores</li>
-       <li>Alignment Annotations format: new keywords for group
-       associated annotation (GROUP_REF) and annotation row display properties
-       (ROW_PROPERTIES)</li>
-       <li>XML formats extended to support graduated feature
-       colourschemes, group associated annotation, and profile visualization
-       settings.</li>
-       </td>
-       <td>
-       <ul>
-               <li>Source field in GFF files parsed as feature source rather
-               than description</li>
-               <li>Non-positional features are now included in sequence feature
-               and gff files (controlled via non-positional feature visibility in
-               tooltip).</li>
-               <li>URL links generated for all feature links (bugfix)</li>
-               <li>Added URL embedding instructions to features file
-               documentation.</li>
-               <li>Codons containing ambiguous nucleotides translated as 'X' in
-               peptide product</li>
-               <li>Match case switch in find dialog box works for both sequence
-               ID and sequence string and query strings do not have to be in upper
-               case to match case-insensitively.</li>
-               <li>AMSA files only contain first column of multi-character
-               column annotation labels</li>
-               <li>Jalview Annotation File generation/parsing consistent with
-               documentation (e.g. Stockholm annotation can be exported and
-               re-imported)</li>
-               <li>PDB files without embedded PDB IDs given a friendly name</li>
-               <li>Find incrementally searches ID string matches as well as
-               subsequence matches, and correctly reports total number of both.</li>
-               <li>Application:
-               <ul>
-                       <li>Better handling of exceptions during sequence retrieval</li>
-                       <li>Dasobert generated non-positional feature URL link text
-                       excludes the start_end suffix</li>
-                       <li>DAS feature and source retrieval buttons disabled when fetch
-                       or registry operations in progress.</li>
-                       <li>PDB files retrieved from URLs are cached properly</li>
-                       <li>Sequence description lines properly shared via VAMSAS</li>
-                       <li>Sequence fetcher fetches multiple records for all data
-                       sources</li>
-                       <li>Ensured that command line das feature retrieval completes
-                       before alignment figures are generated.</li>
-                       <li>Reduced time taken when opening file browser for first time.</li>
-                       <li>isAligned check prior to calculating tree, PCA or submitting
-                       an MSA to JNet now excludes hidden sequences.</li>
-                       <li>User defined group colours properly recovered from Jalview projects.</li>
-               </ul>
-               </li>
-       </ul>
-       </td>
+                       <li>Group-associated consensus, sequence logos and conservation
+                       plots</li>
+                       <li>Symbol distributions for each column can be exported and
+                       visualized as sequence logos</li>
+                       <li>Optionally scale multi-character column labels to fit within
+                       each column of annotation row<!-- todo for applet --></li>
+                       <li>Optional automatic sort of associated alignment view when a
+                       new tree is opened.</li>
+                       <li>Jalview Java Console</li>
+                       <li>Better placement of desktop window when moving between
+                       different screens.</li>
+                       <li>New preference items for sequence ID tooltip and consensus
+                       annotation</li>
+                       <li>Client to submit sequences and IDs to <a
+                               href="webServices/index.html#envision2">Envision2</a> Workflows</li>
+                       <li><em>Vamsas Capabilities</em>
+                       <ul>
+                               <li>Improved VAMSAS synchronization (jalview archive used to
+                               preserve views, structures, and tree display settings)</li>
+                               <li>Import of vamsas documents from disk or URL via command
+                               line</li>
+                               <li>Sharing of selected regions between views and with other
+                               VAMSAS applications (Experimental feature!)</li>
+                               <li>Updated API to VAMSAS version 0.2</li>
+                       </ul>
+                       </li>
+               </ul>
+               <em>Applet</em>
+               <ul>
+                       <li>Middle button resizes annotation row height</li>
+                       <li>New Parameters
+                       <ul>
+                               <li>sortByTree (true/false) - automatically sort the associated
+                               alignment view by the tree when a new tree is opened.</li>
+                               <li>showTreeBootstraps (true/false) - show or hide branch
+                               bootstraps (default is to show them if available)</li>
+                               <li>showTreeDistances (true/false) - show or hide branch
+                               lengths (default is to show them if available)</li>
+                               <li>showUnlinkedTreeNodes (true/false) - indicate if
+                               unassociated nodes should be highlighted in the tree view</li>
+                               <li>heightScale and widthScale (1.0 or more) - increase the
+                               height or width of a cell in the alignment grid relative to the
+                               current font size.</li>
+                       </ul>
+                       </li>
+                       <li>Non-positional features displayed in sequence ID tooltip</li>
+               </ul>
+               <em>Other</em>
+               <ul>
+                       <li>Features format: graduated colour definitions and
+                       specification of feature scores</li>
+                       <li>Alignment Annotations format: new keywords for group
+                       associated annotation (GROUP_REF) and annotation row display
+                       properties (ROW_PROPERTIES)</li>
+                       <li>XML formats extended to support graduated feature
+                       colourschemes, group associated annotation, and profile visualization
+                       settings.</li>
+               </td>
+               <td>
+               <ul>
+                       <li>Source field in GFF files parsed as feature source rather
+                       than description</li>
+                       <li>Non-positional features are now included in sequence feature
+                       and gff files (controlled via non-positional feature visibility in
+                       tooltip).</li>
+                       <li>URL links generated for all feature links (bugfix)</li>
+                       <li>Added URL embedding instructions to features file
+                       documentation.</li>
+                       <li>Codons containing ambiguous nucleotides translated as 'X' in
+                       peptide product</li>
+                       <li>Match case switch in find dialog box works for both sequence
+                       ID and sequence string and query strings do not have to be in upper
+                       case to match case-insensitively.</li>
+                       <li>AMSA files only contain first column of multi-character
+                       column annotation labels</li>
+                       <li>Jalview Annotation File generation/parsing consistent with
+                       documentation (e.g. Stockholm annotation can be exported and
+                       re-imported)</li>
+                       <li>PDB files without embedded PDB IDs given a friendly name</li>
+                       <li>Find incrementally searches ID string matches as well as
+                       subsequence matches, and correctly reports total number of both.</li>
+                       <li>Application:
+                       <ul>
+                               <li>Better handling of exceptions during sequence retrieval</li>
+                               <li>Dasobert generated non-positional feature URL link text
+                               excludes the start_end suffix</li>
+                               <li>DAS feature and source retrieval buttons disabled when
+                               fetch or registry operations in progress.</li>
+                               <li>PDB files retrieved from URLs are cached properly</li>
+                               <li>Sequence description lines properly shared via VAMSAS</li>
+                               <li>Sequence fetcher fetches multiple records for all data
+                               sources</li>
+                               <li>Ensured that command line das feature retrieval completes
+                               before alignment figures are generated.</li>
+                               <li>Reduced time taken when opening file browser for first
+                               time.</li>
+                               <li>isAligned check prior to calculating tree, PCA or
+                               submitting an MSA to JNet now excludes hidden sequences.</li>
+                               <li>User defined group colours properly recovered from Jalview
+                               projects.</li>
+                       </ul>
+                       </li>
+               </ul>
+               </td>
 
        </tr>
        <tr>
                <li>Sequence Group colour can be specified in Annotation File</li>
                <li>Ad-hoc colouring of group in Annotation File using RGB
                triplet as name of colourscheme</li>
-</ul>
-<em>VAMSAS Client capabilities (Experimental)</em>
-<ul>
-       <li>treenode binding for VAMSAS tree exchange</li>
-       <li>local editing and update of sequences in VAMSAS alignments
-       (experimental)</li>
-       <li>Create new or select existing session to join</li>
-       <li>load and save of vamsas documents</li>
-</ul>
-<em>Application command line</em>
-<ul>
-       <li>-tree parameter to open trees (introduced for passing from
-       applet)</li>
-       <li>-fetchfrom command line argument to specify nicknames of DAS
-       servers to query for alignment features</li>
-       <li>-dasserver command line argument to add new servers that are
-       also automatically queried for features</li>
-       <li>-groovy command line argument executes a given groovy script
-       after all input data has been loaded and parsed</li>
-</ul>
-<em>Applet-Application data exchange</em>
-<ul>
-       <li>Trees passed as applet parameters can be passed to application
-       (when using &quot;View in full application&quot;)</li>
-</ul>
-<em>Applet Parameters</em>
-<ul>
-       <li>feature group display control parameter</li>
-       <li>debug parameter</li>
-       <li>showbutton parameter</li>
-</ul>
-<em>Applet API methods</em>
-<ul>
-       <li>newView public method</li>
-       <li>Window (current view) specific get/set public methods</li>
-       <li>Feature display control methods</li>
-       <li>get list of currently selected sequences</li>
-</ul>
-<em>New Jalview distribution features</em>
-<ul>
-       <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
-       <li>RELEASE file gives build properties for the latest Jalview
-       release.</li>
-       <li>Java 1.1 Applet build made easier and donotobfuscate property
-       controls execution of obfuscator</li>
-       <li>Build target for generating source distribution</li>
-       <li>Debug flag for javacc</li>
-       <li>.jalview_properties file is documented (slightly) in
-       jalview.bin.Cache</li>
-       <li>Continuous Build Integration for stable and development
-       version of Application, Applet and source distribution</li>
-</ul>
+               </ul>
+               <em>VAMSAS Client capabilities (Experimental)</em>
+               <ul>
+                       <li>treenode binding for VAMSAS tree exchange</li>
+                       <li>local editing and update of sequences in VAMSAS alignments
+                       (experimental)</li>
+                       <li>Create new or select existing session to join</li>
+                       <li>load and save of vamsas documents</li>
+               </ul>
+               <em>Application command line</em>
+               <ul>
+                       <li>-tree parameter to open trees (introduced for passing from
+                       applet)</li>
+                       <li>-fetchfrom command line argument to specify nicknames of DAS
+                       servers to query for alignment features</li>
+                       <li>-dasserver command line argument to add new servers that are
+                       also automatically queried for features</li>
+                       <li>-groovy command line argument executes a given groovy script
+                       after all input data has been loaded and parsed</li>
+               </ul>
+               <em>Applet-Application data exchange</em>
+               <ul>
+                       <li>Trees passed as applet parameters can be passed to
+                       application (when using &quot;View in full application&quot;)</li>
+               </ul>
+               <em>Applet Parameters</em>
+               <ul>
+                       <li>feature group display control parameter</li>
+                       <li>debug parameter</li>
+                       <li>showbutton parameter</li>
+               </ul>
+               <em>Applet API methods</em>
+               <ul>
+                       <li>newView public method</li>
+                       <li>Window (current view) specific get/set public methods</li>
+                       <li>Feature display control methods</li>
+                       <li>get list of currently selected sequences</li>
+               </ul>
+               <em>New Jalview distribution features</em>
+               <ul>
+                       <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+                       <li>RELEASE file gives build properties for the latest Jalview
+                       release.</li>
+                       <li>Java 1.1 Applet build made easier and donotobfuscate
+                       property controls execution of obfuscator</li>
+                       <li>Build target for generating source distribution</li>
+                       <li>Debug flag for javacc</li>
+                       <li>.jalview_properties file is documented (slightly) in
+                       jalview.bin.Cache</li>
+                       <li>Continuous Build Integration for stable and development
+                       version of Application, Applet and source distribution</li>
+               </ul>
 
-</td>
-<td>
-<ul>
-       <li>selected region output includes visible annotations (for
-       certain formats)</li>
-       <li>edit label/displaychar contains existing label/char for
-       editing</li>
-       <li>update PDBEntries when DBRefEntries change (vamsas)</li>
-       <li>shorter peptide product names from EMBL records</li>
-       <li>Newick string generator makes compact representations</li>
-       <li>bootstrap values parsed correctly for tree files with comments</li>
-       <li>pathological filechooser bug avoided by not allowing filenames
-       containing a ':'</li>
-       <li>Fixed exception when parsing GFF files containing global
-       sequence features</li>
-       <li>Alignment datasets are finalized only when number of
-       references from alignment sequences goes to zero</li>
-       <li>Close of tree branch colour box without colour selection
-       causes cascading exceptions</li>
-       <li>occasional negative imgwidth exceptions</li>
-       <li>better reporting of non-fatal warnings to user when file
-       parsing fails.</li>
-       <li>Save works when Jalview project is default format</li>
-       <li>Save as dialog opened if current alignment format is not a
-       valid output format</li>
-       <li>Uniprot canonical names introduced for both das and vamsas</li>
-       <li>Histidine should be midblue (not pink!) in Zappo</li>
-       <li>error messages passed up and output when data read fails</li>
-       <li>edit undo recovers previous dataset sequence when sequence is
-       edited</li>
-       <li>allow PDB files without pdb ID HEADER lines (like those
-       generated by MODELLER) to be read in properly</li>
-       <li>allow reading of JPred concise files as a normal filetype</li>
-       <li>Stockholm annotation parsing and alignment properties import
-       fixed for PFAM records</li>
-       <li>Structure view windows have correct name in Desktop window
-       list</li>
-       <li>annotation consisting of sequence associated scores can be
-       read and written correctly to annotation file</li>
-       <li>Aligned cDNA translation to aligned peptide works correctly</li>
-       <li>Fixed display of hidden sequence markers and non-italic font
-       for representatives in Applet</li>
-       <li>Applet Menus are always embedded in applet window on Macs.</li>
-       <li>Newly shown features appear at top of stack (in Applet)</li>
-       <li>Annotations added via parameter not drawn properly due to null
-       pointer exceptions</li>
-       <li>Secondary structure lines are drawn starting from first column
-       of alignment</li>
-       <li>Uniprot XML import updated for new schema release in July 2008</li>
-       <li>Sequence feature to sequence ID match for Features file is
-       case-insensitive</li>
-       <li>Sequence features read from Features file appended to all
-       sequences with matching IDs</li>
-       <li>PDB structure coloured correctly for associated views
-       containing a sub-sequence</li>
-       <li>PDB files can be retrieved by applet from Jar files</li>
-       <li>feature and annotation file applet parameters referring to
-       different directories are retrieved correctly</li>
-       <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
-       <li>Fixed application hang whilst waiting for splash-screen
-       version check to complete</li>
-       <li>Applet properly URLencodes input parameter values when passing
-       them to the launchApp service</li>
-       <li>display name and local features preserved in results retrieved
-       from web service</li>
-       <li>Visual delay indication for sequence retrieval and sequence
-       fetcher initialisation</li>
-       <li>updated Application to use DAS 1.53e version of dasobert DAS
-       client</li>
-       <li>Re-instated Full AMSA support and .amsa file association</li>
-       <li>Fixed parsing of JNet Concise annotation <em>sans</em>
-       sequences</li>
-</ul>
-</td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.3</strong><br>
-       9/5/07</div>
-       </td>
-       <td>
-       <ul>
-               <li>Jmol 11.0.2 integration</li>
-               <li>PDB views stored in Jalview XML files</li>
-               <li>Slide sequences</li>
-               <li>Edit sequence in place</li>
-               <li>EMBL CDS features</li>
-               <li>DAS Feature mapping</li>
-               <li>Feature ordering</li>
-               <li>Alignment Properties</li>
-               <li>Annotation Scores</li>
-               <li>Sort by scores</li>
-               <li>Feature/annotation editing in applet</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Headless state operation in 2.2.1</li>
-               <li>Incorrect and unstable DNA pairwise alignment</li>
-               <li>Cut and paste of sequences with annotation</li>
-               <li>Feature group display state in XML</li>
-               <li>Feature ordering in XML</li>
-               <li>blc file iteration selection using filename # suffix</li>
-               <li>Stockholm alignment properties</li>
-               <li>Stockhom alignment secondary structure annotation</li>
-               <li>2.2.1 applet had no feature transparency</li>
-               <li>Number pad keys can be used in cursor mode</li>
-               <li>Structure Viewer mirror image resolved</li>
-       </ul>
-       </td>
+               </td>
+               <td>
+               <ul>
+                       <li>selected region output includes visible annotations (for
+                       certain formats)</li>
+                       <li>edit label/displaychar contains existing label/char for
+                       editing</li>
+                       <li>update PDBEntries when DBRefEntries change (vamsas)</li>
+                       <li>shorter peptide product names from EMBL records</li>
+                       <li>Newick string generator makes compact representations</li>
+                       <li>bootstrap values parsed correctly for tree files with
+                       comments</li>
+                       <li>pathological filechooser bug avoided by not allowing
+                       filenames containing a ':'</li>
+                       <li>Fixed exception when parsing GFF files containing global
+                       sequence features</li>
+                       <li>Alignment datasets are finalized only when number of
+                       references from alignment sequences goes to zero</li>
+                       <li>Close of tree branch colour box without colour selection
+                       causes cascading exceptions</li>
+                       <li>occasional negative imgwidth exceptions</li>
+                       <li>better reporting of non-fatal warnings to user when file
+                       parsing fails.</li>
+                       <li>Save works when Jalview project is default format</li>
+                       <li>Save as dialog opened if current alignment format is not a
+                       valid output format</li>
+                       <li>Uniprot canonical names introduced for both das and vamsas</li>
+                       <li>Histidine should be midblue (not pink!) in Zappo</li>
+                       <li>error messages passed up and output when data read fails</li>
+                       <li>edit undo recovers previous dataset sequence when sequence
+                       is edited</li>
+                       <li>allow PDB files without pdb ID HEADER lines (like those
+                       generated by MODELLER) to be read in properly</li>
+                       <li>allow reading of JPred concise files as a normal filetype</li>
+                       <li>Stockholm annotation parsing and alignment properties import
+                       fixed for PFAM records</li>
+                       <li>Structure view windows have correct name in Desktop window
+                       list</li>
+                       <li>annotation consisting of sequence associated scores can be
+                       read and written correctly to annotation file</li>
+                       <li>Aligned cDNA translation to aligned peptide works correctly</li>
+                       <li>Fixed display of hidden sequence markers and non-italic font
+                       for representatives in Applet</li>
+                       <li>Applet Menus are always embedded in applet window on Macs.</li>
+                       <li>Newly shown features appear at top of stack (in Applet)</li>
+                       <li>Annotations added via parameter not drawn properly due to
+                       null pointer exceptions</li>
+                       <li>Secondary structure lines are drawn starting from first
+                       column of alignment</li>
+                       <li>Uniprot XML import updated for new schema release in July
+                       2008</li>
+                       <li>Sequence feature to sequence ID match for Features file is
+                       case-insensitive</li>
+                       <li>Sequence features read from Features file appended to all
+                       sequences with matching IDs</li>
+                       <li>PDB structure coloured correctly for associated views
+                       containing a sub-sequence</li>
+                       <li>PDB files can be retrieved by applet from Jar files</li>
+                       <li>feature and annotation file applet parameters referring to
+                       different directories are retrieved correctly</li>
+                       <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
+                       <li>Fixed application hang whilst waiting for splash-screen
+                       version check to complete</li>
+                       <li>Applet properly URLencodes input parameter values when
+                       passing them to the launchApp service</li>
+                       <li>display name and local features preserved in results
+                       retrieved from web service</li>
+                       <li>Visual delay indication for sequence retrieval and sequence
+                       fetcher initialisation</li>
+                       <li>updated Application to use DAS 1.53e version of dasobert DAS
+                       client</li>
+                       <li>Re-instated Full AMSA support and .amsa file association</li>
+                       <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+                       sequences</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.3</strong><br>
+               9/5/07</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Jmol 11.0.2 integration</li>
+                       <li>PDB views stored in Jalview XML files</li>
+                       <li>Slide sequences</li>
+                       <li>Edit sequence in place</li>
+                       <li>EMBL CDS features</li>
+                       <li>DAS Feature mapping</li>
+                       <li>Feature ordering</li>
+                       <li>Alignment Properties</li>
+                       <li>Annotation Scores</li>
+                       <li>Sort by scores</li>
+                       <li>Feature/annotation editing in applet</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Headless state operation in 2.2.1</li>
+                       <li>Incorrect and unstable DNA pairwise alignment</li>
+                       <li>Cut and paste of sequences with annotation</li>
+                       <li>Feature group display state in XML</li>
+                       <li>Feature ordering in XML</li>
+                       <li>blc file iteration selection using filename # suffix</li>
+                       <li>Stockholm alignment properties</li>
+                       <li>Stockhom alignment secondary structure annotation</li>
+                       <li>2.2.1 applet had no feature transparency</li>
+                       <li>Number pad keys can be used in cursor mode</li>
+                       <li>Structure Viewer mirror image resolved</li>
+               </ul>
+               </td>
 
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.2.1</strong><br>
-       12/2/07</div>
-       </td>
-       <td>
-       <ul>
-               <li>Non standard characters can be read and displayed
-               <li>Annotations/Features can be imported/exported to the applet
-               via textbox
-               <li>Applet allows editing of sequence/annotation/group name &amp;
-               description
-               <li>Preference setting to display sequence name in italics
-               <li>Annotation file format extended to allow Sequence_groups to
-               be defined
-               <li>Default opening of alignment overview panel can be specified
-               in preferences
-               <li>PDB residue numbering annotation added to associated
-               sequences
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Applet crash under certain Linux OS with Java 1.6 installed
-               <li>Annotation file export / import bugs fixed
-               <li>PNG / EPS image output bugs fixed
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.2</strong><br>
-       27/11/06</div>
-       </td>
-       <td>
-       <ul>
-               <li>Multiple views on alignment
-               <li>Sequence feature editing
-               <li>&quot;Reload&quot; alignment
-               <li>&quot;Save&quot; to current filename
-               <li>Background dependent text colour
-               <li>Right align sequence ids
-               <li>User-defined lower case residue colours
-               <li>Format Menu
-               <li>Select Menu
-               <li>Menu item accelerator keys
-               <li>Control-V pastes to current alignment
-               <li>Cancel button for DAS Feature Fetching
-               <li>PCA and PDB Viewers zoom via mouse roller
-               <li>User-defined sub-tree colours and sub-tree selection
-               <li>'New Window' button on the 'Output to Text box'
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>New memory efficient Undo/Redo System
-               <li>Optimised symbol lookups and conservation/consensus
-               calculations
-               <li>Region Conservation/Consensus recalculated after edits
-               <li>Fixed Remove Empty Columns Bug (empty columns at end of
-               alignment)
-               <li>Slowed DAS Feature Fetching for increased robustness.
-               <li>Made angle brackets in ASCII feature descriptions display
-               correctly
-               <li>Re-instated Zoom function for PCA
-               <li>Sequence descriptions conserved in web service analysis
-               results
-               <li>Uniprot ID discoverer uses any word separated by &#8739;
-               <li>WsDbFetch query/result association resolved
-               <li>Tree leaf to sequence mapping improved
-               <li>Smooth fonts switch moved to FontChooser dialog box.
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.1.1</strong><br>
-       12/9/06</div>
-       </td>
-       <td>
-       <ul>
-               <li>Copy consensus sequence to clipboard</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Image output - rightmost residues are rendered if sequence id
-               panel has been resized</li>
-               <li>Image output - all offscreen group boundaries are rendered</li>
-               <li>Annotation files with sequence references - all elements in
-               file are relative to sequence position</li>
-               <li>Mac Applet users can use Alt key for group editing</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.1</strong><br>
-       22/8/06</div>
-       </td>
-       <td>
-       <ul>
-               <li>MAFFT Multiple Alignment in default Web Service list</li>
-               <li>DAS Feature fetching</li>
-               <li>Hide sequences and columns</li>
-               <li>Export Annotations and Features</li>
-               <li>GFF file reading / writing</li>
-               <li>Associate structures with sequences from local PDB files</li>
-               <li>Add sequences to exisiting alignment</li>
-               <li>Recently opened files / URL lists</li>
-               <li>Applet can launch the full application</li>
-               <li>Applet has transparency for features (Java 1.2 required)</li>
-               <li>Applet has user defined colours parameter</li>
-               <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Redundancy Panel reinstalled in the Applet</li>
-               <li>Monospaced font - EPS / rescaling bug fixed</li>
-               <li>Annotation files with sequence references bug fixed</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.08.1</strong><br>
-       2/5/06</div>
-       </td>
-       <td>
-       <ul>
-               <li>Change case of selected region from Popup menu</li>
-               <li>Choose to match case when searching</li>
-               <li>Middle mouse button and mouse movement can compress / expand
-               the visible width and height of the alignment</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Annotation Panel displays complete JNet results</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.08b</strong><br>
-       18/4/06</div>
-       </td>
-       <td>&nbsp;</td>
-       <td>
-       <ul>
-               <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
-               <li>Righthand label on wrapped alignments shows correct value</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.08</strong><br>
-       10/4/06</div>
-       </td>
-       <td>
-       <ul>
-               <li>Editing can be locked to the selection area</li>
-               <li>Keyboard editing</li>
-               <li>Create sequence features from searches</li>
-               <li>Precalculated annotations can be loaded onto alignments</li>
-               <li>Features file allows grouping of features</li>
-               <li>Annotation Colouring scheme added</li>
-               <li>Smooth fonts off by default - Faster rendering</li>
-               <li>Choose to toggle Autocalculate Consensus On/Off</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Drag &amp; Drop fixed on Linux</li>
-               <li>Jalview Archive file faster to load/save, sequence
-               descriptions saved.</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.07</strong><br>
-       12/12/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>PDB Structure Viewer enhanced</li>
-               <li>Sequence Feature retrieval and display enhanced</li>
-               <li>Choose to output sequence start-end after sequence name for
-               file output</li>
-               <li>Sequence Fetcher WSDBFetch@EBI</li>
-               <li>Applet can read feature files, PDB files and can be used for
-               HTML form input</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>HTML output writes groups and features</li>
-               <li>Group editing is Control and mouse click</li>
-               <li>File IO bugs</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.06</strong><br>
-       28/9/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>View annotations in wrapped mode</li>
-               <li>More options for PCA viewer</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>GUI bugs resolved</li>
-               <li>Runs with -nodisplay from command line</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td height="63">
-       <div align="center"><strong>2.05b</strong><br>
-       15/9/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>Choose EPS export as lineart or text</li>
-               <li>Jar files are executable</li>
-               <li>Can read in Uracil - maps to unknown residue</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Known OutOfMemory errors give warning message</li>
-               <li>Overview window calculated more efficiently</li>
-               <li>Several GUI bugs resolved</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.05</strong><br>
-       30/8/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>Edit and annotate in &quot;Wrapped&quot; view</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Several GUI bugs resolved</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.04</strong><br>
-       24/8/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>Hold down mouse wheel &amp; scroll to change font size</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Improved JPred client reliability</li>
-               <li>Improved loading of Jalview files</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.03</strong><br>
-       18/8/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>Set Proxy server name and port in preferences</li>
-               <li>Multiple URL links from sequence ids</li>
-               <li>User Defined Colours can have a scheme name and added to
-               Colour Menu</li>
-               <li>Choose to ignore gaps in consensus calculation</li>
-               <li>Unix users can set default web browser</li>
-               <li>Runs without GUI for batch processing</li>
-               <li>Dynamically generated Web Service Menus</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>InstallAnywhere download for Sparc Solaris</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.02</strong><br>
-       18/7/05</div>
-       </td>
-       <td>&nbsp;</td>
-       <td>
-       <ul>
-               <li>Copy &amp; Paste order of sequences maintains alignment
-               order.</li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.01</strong><br>
-       12/7/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>Use delete key for deleting selection.</li>
-               <li>Use Mouse wheel to scroll sequences.</li>
-               <li>Help file updated to describe how to add alignment
-               annotations.</li>
-               <li>Version and build date written to build properties file.</li>
-               <li>InstallAnywhere installation will check for updates at launch
-               of Jalview.</li>
-       </ul>
-       </td>
-       <td>
-       <ul>
-               <li>Delete gaps bug fixed.</li>
-               <li>FileChooser sorts columns.</li>
-               <li>Can remove groups one by one.</li>
-               <li>Filechooser icons installed.</li>
-               <li>Finder ignores return character when searching. Return key
-               will initiate a search.<br>
-               </li>
-       </ul>
-       </td>
-</tr>
-<tr>
-       <td>
-       <div align="center"><strong>2.0</strong><br>
-       20/6/05</div>
-       </td>
-       <td>
-       <ul>
-               <li>New codebase</li>
-       </ul>
-       </td>
-       <td>&nbsp;</td>
-</tr>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.2.1</strong><br>
+               12/2/07</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Non standard characters can be read and displayed
+                       <li>Annotations/Features can be imported/exported to the applet
+                       via textbox
+                       <li>Applet allows editing of sequence/annotation/group name
+                       &amp; description
+                       <li>Preference setting to display sequence name in italics
+                       <li>Annotation file format extended to allow Sequence_groups to
+                       be defined
+                       <li>Default opening of alignment overview panel can be specified
+                       in preferences
+                       <li>PDB residue numbering annotation added to associated
+                       sequences
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Applet crash under certain Linux OS with Java 1.6 installed
+                       <li>Annotation file export / import bugs fixed
+                       <li>PNG / EPS image output bugs fixed
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.2</strong><br>
+               27/11/06</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Multiple views on alignment
+                       <li>Sequence feature editing
+                       <li>&quot;Reload&quot; alignment
+                       <li>&quot;Save&quot; to current filename
+                       <li>Background dependent text colour
+                       <li>Right align sequence ids
+                       <li>User-defined lower case residue colours
+                       <li>Format Menu
+                       <li>Select Menu
+                       <li>Menu item accelerator keys
+                       <li>Control-V pastes to current alignment
+                       <li>Cancel button for DAS Feature Fetching
+                       <li>PCA and PDB Viewers zoom via mouse roller
+                       <li>User-defined sub-tree colours and sub-tree selection
+                       <li>'New Window' button on the 'Output to Text box'
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>New memory efficient Undo/Redo System
+                       <li>Optimised symbol lookups and conservation/consensus
+                       calculations
+                       <li>Region Conservation/Consensus recalculated after edits
+                       <li>Fixed Remove Empty Columns Bug (empty columns at end of
+                       alignment)
+                       <li>Slowed DAS Feature Fetching for increased robustness.
+                       <li>Made angle brackets in ASCII feature descriptions display
+                       correctly
+                       <li>Re-instated Zoom function for PCA
+                       <li>Sequence descriptions conserved in web service analysis
+                       results
+                       <li>Uniprot ID discoverer uses any word separated by &#8739;
+                       <li>WsDbFetch query/result association resolved
+                       <li>Tree leaf to sequence mapping improved
+                       <li>Smooth fonts switch moved to FontChooser dialog box.
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.1.1</strong><br>
+               12/9/06</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Copy consensus sequence to clipboard</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Image output - rightmost residues are rendered if sequence
+                       id panel has been resized</li>
+                       <li>Image output - all offscreen group boundaries are rendered</li>
+                       <li>Annotation files with sequence references - all elements in
+                       file are relative to sequence position</li>
+                       <li>Mac Applet users can use Alt key for group editing</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.1</strong><br>
+               22/8/06</div>
+               </td>
+               <td>
+               <ul>
+                       <li>MAFFT Multiple Alignment in default Web Service list</li>
+                       <li>DAS Feature fetching</li>
+                       <li>Hide sequences and columns</li>
+                       <li>Export Annotations and Features</li>
+                       <li>GFF file reading / writing</li>
+                       <li>Associate structures with sequences from local PDB files</li>
+                       <li>Add sequences to exisiting alignment</li>
+                       <li>Recently opened files / URL lists</li>
+                       <li>Applet can launch the full application</li>
+                       <li>Applet has transparency for features (Java 1.2 required)</li>
+                       <li>Applet has user defined colours parameter</li>
+                       <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Redundancy Panel reinstalled in the Applet</li>
+                       <li>Monospaced font - EPS / rescaling bug fixed</li>
+                       <li>Annotation files with sequence references bug fixed</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.08.1</strong><br>
+               2/5/06</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Change case of selected region from Popup menu</li>
+                       <li>Choose to match case when searching</li>
+                       <li>Middle mouse button and mouse movement can compress / expand
+                       the visible width and height of the alignment</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Annotation Panel displays complete JNet results</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.08b</strong><br>
+               18/4/06</div>
+               </td>
+               <td>&nbsp;</td>
+               <td>
+               <ul>
+                       <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+                       <li>Righthand label on wrapped alignments shows correct value</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.08</strong><br>
+               10/4/06</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Editing can be locked to the selection area</li>
+                       <li>Keyboard editing</li>
+                       <li>Create sequence features from searches</li>
+                       <li>Precalculated annotations can be loaded onto alignments</li>
+                       <li>Features file allows grouping of features</li>
+                       <li>Annotation Colouring scheme added</li>
+                       <li>Smooth fonts off by default - Faster rendering</li>
+                       <li>Choose to toggle Autocalculate Consensus On/Off</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Drag &amp; Drop fixed on Linux</li>
+                       <li>Jalview Archive file faster to load/save, sequence
+                       descriptions saved.</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.07</strong><br>
+               12/12/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>PDB Structure Viewer enhanced</li>
+                       <li>Sequence Feature retrieval and display enhanced</li>
+                       <li>Choose to output sequence start-end after sequence name for
+                       file output</li>
+                       <li>Sequence Fetcher WSDBFetch@EBI</li>
+                       <li>Applet can read feature files, PDB files and can be used for
+                       HTML form input</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>HTML output writes groups and features</li>
+                       <li>Group editing is Control and mouse click</li>
+                       <li>File IO bugs</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.06</strong><br>
+               28/9/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>View annotations in wrapped mode</li>
+                       <li>More options for PCA viewer</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>GUI bugs resolved</li>
+                       <li>Runs with -nodisplay from command line</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td height="63">
+               <div align="center"><strong>2.05b</strong><br>
+               15/9/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Choose EPS export as lineart or text</li>
+                       <li>Jar files are executable</li>
+                       <li>Can read in Uracil - maps to unknown residue</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Known OutOfMemory errors give warning message</li>
+                       <li>Overview window calculated more efficiently</li>
+                       <li>Several GUI bugs resolved</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.05</strong><br>
+               30/8/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Edit and annotate in &quot;Wrapped&quot; view</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Several GUI bugs resolved</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.04</strong><br>
+               24/8/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Hold down mouse wheel &amp; scroll to change font size</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Improved JPred client reliability</li>
+                       <li>Improved loading of Jalview files</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.03</strong><br>
+               18/8/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Set Proxy server name and port in preferences</li>
+                       <li>Multiple URL links from sequence ids</li>
+                       <li>User Defined Colours can have a scheme name and added to
+                       Colour Menu</li>
+                       <li>Choose to ignore gaps in consensus calculation</li>
+                       <li>Unix users can set default web browser</li>
+                       <li>Runs without GUI for batch processing</li>
+                       <li>Dynamically generated Web Service Menus</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>InstallAnywhere download for Sparc Solaris</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.02</strong><br>
+               18/7/05</div>
+               </td>
+               <td>&nbsp;</td>
+               <td>
+               <ul>
+                       <li>Copy &amp; Paste order of sequences maintains alignment
+                       order.</li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.01</strong><br>
+               12/7/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>Use delete key for deleting selection.</li>
+                       <li>Use Mouse wheel to scroll sequences.</li>
+                       <li>Help file updated to describe how to add alignment
+                       annotations.</li>
+                       <li>Version and build date written to build properties file.</li>
+                       <li>InstallAnywhere installation will check for updates at
+                       launch of Jalview.</li>
+               </ul>
+               </td>
+               <td>
+               <ul>
+                       <li>Delete gaps bug fixed.</li>
+                       <li>FileChooser sorts columns.</li>
+                       <li>Can remove groups one by one.</li>
+                       <li>Filechooser icons installed.</li>
+                       <li>Finder ignores return character when searching. Return key
+                       will initiate a search.<br>
+                       </li>
+               </ul>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center"><strong>2.0</strong><br>
+               20/6/05</div>
+               </td>
+               <td>
+               <ul>
+                       <li>New codebase</li>
+               </ul>
+               </td>
+               <td>&nbsp;</td>
+       </tr>
 </table>
 <p>&nbsp;</p>
 </body>
index 4723a9a..1173c61 100755 (executable)
 </head>
 <body>
 <p><strong>What's new ?</strong></p>
+<p>Jalview 2.5.1 is a bug fix release for the 2.5 version of
+Jalview. See the <a href="releases.html#Jalview2.5.1">release
+history</a> for the bugs that this release resolves.</p>
 <p><strong>Highlights in Jalview Version 2.5</strong></p>
 <ul>
-                       Linked viewing of nucleic acid sequences and structures<br/>
-                       Automatic Scrolling option in View menu to display the
-                       currently highlighted region of an alignment.<br/>
-                       Order an alignment by sequence length, or using the average score or total feature count for each sequence.<br/>
-                       Shading features by score or associated description<br/>
-                       Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).<br/>
-                       New hide/show options including Shift+Control+H to hide everything but the currently selected region.<br/>
+       Linked viewing of nucleic acid sequences and structures
+       <br />
+       Automatic Scrolling option in View menu to display the currently
+       highlighted region of an alignment.
+       <br />
+       Order an alignment by sequence length, or using the average score or
+       total feature count for each sequence.
+       <br />
+       Shading features by score or associated description
+       <br />
+       Subdivide alignment and groups based on identity of selected
+       subsequence (Make Groups from Selection).
+       <br />
+       New hide/show options including Shift+Control+H to hide everything but
+       the currently selected region.
+       <br />
 </ul>
 <em>Jalview Desktop:</em>
 <ul>
-       Fetch DB References capabilities and UI expanded to support
-       retrieval from DAS sequence sources<br/>
-       Enable or disable non-positional feature and database
-       references in sequence ID tooltip from View menu in application.<br/>
-       Group-associated consensus, sequence logos and conservation
-       plots<br/>
-       Symbol distributions for each column can be exported and
-       visualized as sequence logos<br/>
-       Jalview Java Console<br/>
-       New webservice for submitting sequences and IDs to <a
-               href="webServices/index.html#envision2">Envision2</a> Workflows<br/>
-       Improved VAMSAS synchronization and sharing of selections.<br/>
+       Fetch DB References capabilities and UI expanded to support retrieval
+       from DAS sequence sources
+       <br />
+       Enable or disable non-positional feature and database references in
+       sequence ID tooltip from View menu in application.
+       <br />
+       Group-associated consensus, sequence logos and conservation plots
+       <br />
+       Symbol distributions for each column can be exported and visualized as
+       sequence logos
+       <br />
+       Jalview Java Console
+       <br />
+       New webservice for submitting sequences and IDs to
+       <a href="webServices/index.html#envision2">Envision2</a>
+       Workflows
+       <br />
+       Improved VAMSAS synchronization and sharing of selections.
+       <br />
 </ul>
 <em>JalviewLite:</em>
 <ul>
-       Middle button resizes annotation row height<br/>
-       New Parameters  - including default tree display settings.<br/>
-       Non-positional features displayed in ID tooltip<br/>
+       Middle button resizes annotation row height
+       <br />
+       New Parameters - including default tree display settings.
+       <br />
+       Non-positional features displayed in ID tooltip
+       <br />
 </ul>
 <p><strong>Issues Resolved (a select list)</strong></p>
 <ul>
        <ul>
-               Source field in GFF files parsed as feature source rather
-               than description<br/>
-               Non-positional features are now included in sequence feature
-               and gff files (controlled via non-positional feature visibility in
-               tooltip).<br/>
-               URL links generated for all feature links (bugfix)<br/>
-               Codons containing ambiguous nucleotides translated as 'X' in
-               peptide product<br/>
-               Match case switch in find dialog box works for both sequence
-               ID and sequence string and query strings do not have to be in upper
-               case to match case-insensitively.<br/>
+               Source field in GFF files parsed as feature source rather than
+               description
+               <br />
+               Non-positional features are now included in sequence feature and gff
+               files (controlled via non-positional feature visibility in tooltip).
+               <br />
+               URL links generated for all feature links (bugfix)
+               <br />
+               Codons containing ambiguous nucleotides translated as 'X' in peptide
+               product
+               <br />
+               Match case switch in find dialog box works for both sequence ID and
+               sequence string and query strings do not have to be in upper case to
+               match case-insensitively.
+               <br />
                Jalview Annotation File generation/parsing consistent with
                documentation (e.g. Stockholm annotation can be exported and
-               re-imported)<br/>
-               Find incrementally searches ID string matches as well as
-               subsequence matches, and correctly reports total number of both.<br/>
+               re-imported)
+               <br />
+               Find incrementally searches ID string matches as well as subsequence
+               matches, and correctly reports total number of both.
+               <br />
        </ul>
        <em>Desktop Issues</em>
        <ul>
-                       Better handling of exceptions during sequence retrieval<br/>
-                       PDB files retrieved from URLs are cached properly<br/>
-                       Sequence description lines properly shared via VAMSAS<br/>
-                       Sequence fetcher fetches multiple records for all data
-                       sources<br/>
-                       Ensured that command line das feature retrieval completes
-                       before alignment figures are generated.<br/>
-                       Reduced time taken when opening file browser for first time.<br/>
-                       User defined group colours properly recovered from Jalview projects.<br/>
-               </ul>
+               Better handling of exceptions during sequence retrieval
+               <br />
+               PDB files retrieved from URLs are cached properly
+               <br />
+               Sequence description lines properly shared via VAMSAS
+               <br />
+               Sequence fetcher fetches multiple records for all data sources
+               <br />
+               Ensured that command line das feature retrieval completes before
+               alignment figures are generated.
+               <br />
+               Reduced time taken when opening file browser for first time.
+               <br />
+               User defined group colours properly recovered from Jalview projects.
+               <br />
+       </ul>
 </ul>
 
 <p>&nbsp;</p>