From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 16 May 2017 15:30:07 +0000 (+0100)
Subject: JAL-2418 release notes
X-Git-Tag: Release_2_10_2~3^2~83^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5dd91255a15114eacfaa0122c12462cde592ce86;hp=1aa769198666becd30648eed7f9037e9d0502ce9;p=jalview.git

JAL-2418 release notes
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 9018910..25fc04b 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -77,30 +77,56 @@ li:before {
       <td><div align="left">
           <em>General</em>
           <ul>
-          <li></li>
+          <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
+          <li><!--  JAL-384 -->Custom BLOSUM/Clustal type shading schemes can be created via groovy scripts</li>
+          
+          <li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
           </ul>
           <em>Application</em>
           <ul>
           <li><!--  --></li>
-  
+          <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>  
           <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
+          
           </ul>
           <em>Applet</em>
           <ul>
-          <li></li>
+          <li><!--  --></li>
           </ul>
           </div></td><td><div align="left">
           <em>General</em>
           <ul>
-          <li></li>
+          <li><!-- JAL-2346 -->Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view</li>
+          <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
+          <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
+          <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li> 
+          <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
+          <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
+          <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
+          <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
+          <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
+          <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>  
+          <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
+          <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
           </ul>
           <em>Application</em>
           <ul>
-          <li></li>
+          <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li> 
+          <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
+          <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li> 
+          <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
+          <li><!--  JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
+          <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
+          <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
+          <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
+          <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
+          <li><!--  JAL-2461 -->DAS registry not found exceptions removed from console output</li> 
+          
           </ul>
           <em>Applet</em>
           <ul>
-          <li></li>
+          <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li> 
+          <li><!--  JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
           </ul>
           <em>New Known Issues</em>
           <ul>
@@ -252,6 +278,9 @@ li:before {
               <!--JAL-2332 -->Attempting to view structure for Hen
               lysozyme results in a PDB Client error dialog box
             </li>
+            <li>
+            <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li> 
+            <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li> 
           </ul>
 <!--           <em>New Known Issues</em>
           <ul>