X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6eb42bc7d90a51d5a90ec2ac2a6fc7dcd20f919e;hb=e5ff0544866ec954e311b7401f5c3989c0016a5e;hp=94323f2494576f57dad24efa3e9db63a96aa6f42;hpb=812ca2d3e6a71824c891b42b59c93fe2d5bc7400;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 94323f2..6eb42bc 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,17 +47,66 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
         </div>
       </td>
       <td><em>General</em>
         <ul>
-            <li><!-- JAL---></li>
+            <li><!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
+            <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+            <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
+            <li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
+            <li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
+            <li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
+            <li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
+            <li><!-- JAL-2236 -->Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
+            
         </ul> <em>Application</em>
         <ul>
-            <li><!-- JAL---></li>
+            <li><!-- JAL-2050-->Automatically hide introns when opening a gene/transcript view</li>
+            <li><!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search dialog</li>
+            <li><!--  JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>          
+            <li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
+            <li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
+            <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
             <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
-            <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
+            <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API</li>
+            <li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
+            <li><!--  JAL-1812 -->Update to groovy-2.4.6-indy - for faster groovy script execution</li>
+            <li><!--  JAL-1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
+            <li><!--  JAL-1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+            <li><!--  JAL-2068 -->Support for creating new alignment calculation workers from groovy scripts</li>
+            <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
+            <li><!-- JAL-1803 -->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+            <li><!-- JAL-1993 -->Database selection dialog always shown before sequence fetcher is opened</li>
+            <li><!-- JAL-2183 -->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
+            <li><!-- JAL-1563 -->Free-text search client for UniProt using the UniProt REST API</li>
+            <li><!-- JAL-2168 -->-nonews command line parameter to prevent the news reader opening</li>
+            <li><!-- JAL-2028 -->Displayed columns for PDBe and Uniprot querying stored in preferences</li>
+            <li><!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot search results</li>
+            <li><!-- JAL-1977-->Tooltips shown on database chooser</li>
+            <li><!--  JAL-391 -->Reverse complement function in calculate menu for nucleotide sequences</li>
+            <li>
+              <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).  
+            </li>
+            <li>
+              <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10   
+            </li>
+            <li>
+              <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API   
+            </li>
+            <li>
+              <!-- JAL-2049 -->Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)   
+            </li>
+            <li><!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot sequences</li>
+            <li>
+              <!-- JAL- -->  
+            </li>
+            <li>
+              <!-- JAL- -->  
+            </li>
+                    
+             
         </ul> <em>Applet</em>
         <ul>
             <li><!-- JAL---></li>
@@ -68,20 +117,131 @@
           <ul>
             <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
             <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
-            <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
-            <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
-            <li><!-- JAL-2067, JAL-  -->Tidied up links in help file table of contents</li>
+            <li><!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+            <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
+            <li><!-- JAL-2067 -->Tidied up links in help file table of contents</li>
+            <li><!-- JAL-2072  -->Feature based tree calculation not shown for DNA alignments</li>
+            <li><!-- JAL-2075  -->Hidden columns ignored during feature based tree calculation</li>
+            <li><!-- JAL-2065  -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
+            <li><!--  JAL-2086  -->Cannot insert gaps into sequence when set as reference</li>
+            <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as &quot;Sequence position&quot; when mousing over annotation</li>
+            <li><!--  JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
+            <li><!--  JAL-1577 -->Colour by RNA Helices not enabled when user created annotation added to alignment</li>
+            <li><!-- JAL-1841 -->RNA Structure consensus only computed for '()' base pair annotation</li>
+            <li><!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
+            <li><!-- JAL-2174-->Extend selection with columns containing feature not working</li>
+            <li><!-- JAL-2275 -->Pfam format writer puts extra space at beginning of sequence</li>            
+            <li><!-- JAL-1827 -->Incomplete sequence extracted from pdb entry 3a6s </li>
+            <li><!-- JAL-2238 -->Cannot create groups on an alignment from from a tree when t-coffee scores are shown</li>
+            <li><!-- JAL-1836,1967 -->Cannot import and view PDB structures with chains containing negative resnums (4q4h)</li>
+            <li><!--  JAL-1998 -->ArithmeticExceptions raised when parsing some structures</li>
+            <li><!--  JAL-1991, JAl-1952 -->'Empty' alignment blocks added to Clustal, PIR and PileUp output</li>
+            <li><!--  JAL-2008 -->Reordering sequence features that are not visible causes alignment window to repaint</li>
+            <li>
+              <!--  JAL-2006 -->Threshold sliders don't work in
+              graduated colour and colour by annotation row for e-value
+              scores associated with features and annotation rows
+            </li>
+            <li>
+              <!-- JAL-1797 -->amino acid physicochemical conservation
+              calculation should be case independent
+            </li>
+            <li>
+              <!-- JAL-2173 -->Remove annotation also updates hidden
+              columns
+            </li>
+            <li>
+              <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
+            </li>
+            <li>
+              <!-- JAL-2065 -->Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
+            </li>
+            <li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
+            <li>
+              <!--  -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
           </ul>
           <em>Application</em>
           <ul>
             <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
             <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
             <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
-            <li><!-- JAL-2030, JAL-1941-->InstallAnywhere distribution fails when launching Chimera or adding RNA 3D structure via DSSR service</li>
+            <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
+            <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
+            <li><!--  JAL-2085  -->Cannot save project when view has a reference sequence defined</li>
+            <li><!--  JAL-1011  -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
+            <li><!--  JAL-1989  -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
+            <li><!--  JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
+            <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
+            <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
+            <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>   
+            <li><!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type</li>
+            <li><!-- JAL-1975 -->Export complete shown after destination file chooser is cancelled during an image export </li>
+            <li><!-- JAL-2025 -->Error when querying PDB Service with sequence name containing special characters</li>
+            <li><!-- JAL-2024 -->Manual PDB structure querying should be case insensitive</li>
+            <li><!-- JAL-2104 -->Large tooltips with broken HTML formatting don't wrap</li>
+            <li><!-- JAL-1128 -->Figures exported from wrapped view are truncated so L looks like I in consensus annotation</li>
+            <li><!-- JAL-2003 -->Export features should only export the currently displayed features for the current selection or view</li>
+            <li><!-- JAL-2036 -->Enable 'Get Cross-References' in menu after fetching cross-references</li>
+            <li><!-- JAL-2032 -->Mouseover of a copy of a sequence is not followed in the structure viewer</li>
+            <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>            
+            <li>
+              <!-- JAL-2145 -->missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
+            </li>
+            <li>
+              <!-- JAL-1797 -->amino acid physicochemical conservation is case dependent
+            </li>
+            <li>
+              <!-- JAL-1448 -->RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
+            </li>
+            <li><!-- JAL-1960 -->Only offer PDB structures in structure viewer based on sequence name, PDB and Uniprot cross-references</li>
+            
+            <li>
+              <!-- JAL-1976 -->No progress bar shown during export of alignment as HTML
+            </li>
+            <li>
+              <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+            </li>
+            <li>
+              <!-- JAL-2213 -->Structures not always superimposed after multiple structures are shown for one or more sequences.
+            </li>
+            <li>
+              <!-- JAL-1370 -->Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+            </li>
+            <li>
+              <!-- JAL-1823 -->Cannot specify chain code when entering specific PDB id for sequence
+            </li>
+            <li>
+              <!-- JAL-1944 -->File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled. 
+            </li>
+            <li><!--JAL-2026-->Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence</li>
+            <li>
+              <!-- JAL-1887 -->Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+
+            <!--  may exclude, this is an external service stability issue  JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
           </ul>
           <em>Applet</em>
           <ul>
-            <li><!--  --></li>
+            <li><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
+            <li><!-- JAL-1986 -->Missing dependencies on applet pages (JSON jars)</li>
+            <li>
+              <!-- JAL-1947 -->Overview pixel size changes when sequences are hidden in applet
+            </li>
+            <li><!-- JAL-1996 -->Updated instructions for applet deployment on examples pages.
+            </li>
           </ul>
         </div>
       </td>
@@ -242,7 +402,7 @@
                 region export in flat file generation</li>
 
               <li>Export alignment views for display with the <a
-                href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+                href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
 
               <li>Export scrollable SVG in HTML page</li>
               <li>Optional embedding of BioJSON data when exporting
@@ -727,7 +887,7 @@
             <a href="https://www.certum.eu">Certum</a> to the Jalview
             open source project).
           </li>
-          <li>Jalview SRS links replaced by Uniprot and EBI-search
+          <li>Jalview SRS links replaced by UniProt and EBI-search
           </li>
           <li>Output in Stockholm format</li>
           <li>Allow import of data from gzipped files</li>
@@ -1082,8 +1242,8 @@
             current built in colourscheme is saved as new scheme</li>
           <li>AlignFrame-&gt;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
+          <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>
@@ -1658,7 +1818,7 @@
           <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
+          <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
@@ -1687,7 +1847,7 @@
             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
+          <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>
@@ -1831,7 +1991,7 @@
           <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
+          <li>UniProt ID discoverer uses any word separated by
             &#8739;
           <li>WsDbFetch query/result association resolved
           <li>Tree leaf to sequence mapping improved