X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6eb42bc7d90a51d5a90ec2ac2a6fc7dcd20f919e;hb=e5ff0544866ec954e311b7401f5c3989c0016a5e;hp=b8854f37748eb6cbd05100265d8a5d2e88334794;hpb=739e52dd5387687cce4831eaafa24116dcaddcb9;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index b8854f3..6eb42bc 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -60,17 +60,17 @@
             <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---></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>
@@ -78,12 +78,33 @@
             <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>
@@ -96,9 +117,9 @@
           <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-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, JAL-  -->Tidied up links in help file table of contents</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>
@@ -115,7 +136,36 @@
             <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>
@@ -137,13 +187,61 @@
             <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><!-- 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>