From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 4 Oct 2016 09:46:33 +0000 (+0100)
Subject: JAL-2189 release notes
X-Git-Tag: Release_2_10_0~21^2~3
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=71a996fbcf51882725dd0e22a8fd986e1c5cd97a

JAL-2189 release notes
---

diff --git a/help/html/releases.html b/help/html/releases.html
index cc4942f..f35494d 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -63,7 +63,6 @@
             
         </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>          
@@ -71,7 +70,7 @@
             <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>
@@ -79,6 +78,7 @@
             <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>
@@ -86,6 +86,21 @@
             <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>
+              <!-- -->   
+            </li>
+            <li>
+              <!-- JAL- -->  
+            </li>
+            <li>
+              <!-- JAL- -->  
+            </li>
+            <li>
+              <!-- JAL- -->  
+            </li>
                     
              
         </ul> <em>Applet</em>
@@ -132,10 +147,10 @@
               columns
             </li>
             <li>
-              <!-- JAL- -->
+              <!-- 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- -->
+              <!-- JAL-2065 -->Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
             </li>
             <li>
               <!-- JAL- -->
@@ -180,6 +195,30 @@
             <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>
@@ -196,6 +235,8 @@
             <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>