From 8ae11a7b547331602e2ccd6523d2663db29350a2 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 3 Oct 2016 15:06:34 +0100
Subject: [PATCH] JAL-2189 more release notes

---
 help/html/releases.html |   60 +++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 56 insertions(+), 4 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index b8854f3..cc4942f 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -60,10 +60,11 @@
             <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>
@@ -84,6 +85,7 @@
             <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>
                     
              
         </ul> <em>Applet</em>
@@ -115,7 +117,35 @@
             <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- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
           </ul>
           <em>Application</em>
           <ul>
@@ -137,13 +167,35 @@
             <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- -->
+            </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>
           </ul>
         </div>
       </td>
-- 
1.7.10.2