X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=1fe2602739f69f4c26454d0fcdaef9400f61bf69;hb=79501a7433d7fd26f958b8574e2147e011433224;hp=aa589e9e7a2de0c06048ac0ef0b44c730146c4c5;hpb=d8bf5506216e7a0726a1fa5baa6b4d244f035741;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index aa589e9..1fe2602 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,6 +70,114 @@ li:before {
     <tr>
       <td width="60" nowrap>
         <div align="center">
+          <strong><a name="Jalview.2.10.2">2.10.2</a><br />
+            <em>30/5/2017</em></strong>
+        </div>
+      </td>
+      <td><div align="left">
+          <em>General</em>
+          <ul>
+          <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
+          <li><!--  JAL-384 -->Custom shading schemes created via groovy scripts</li>
+          </ul>
+          <em>Application</em>
+          <ul>
+            <li>
+              <!-- JAL-2447 -->
+              Experimental Features Checkbox in Desktop's Tools
+              menu to hide or show untested features in the application.
+            </li>
+            <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</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>Experimental features</em>
+          <ul>
+            <li>
+              <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
+              to transfer Chimera's structure attributes as Jalview
+              features, and vice-versa.
+            </li>
+          </ul>
+          <em>Applet</em>
+          <ul>
+          <li><!--  --></li>
+          </ul>
+          <em>Test Suite</em>
+          <li><!--  JAL-2474 -->Added PrivelegedAccessor to test suite</li>
+          <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
+          <li><!--  -->  
+          </ul>
+          </div></td><td><div align="left">
+          <em>General</em>
+          <ul>
+            <li>
+              <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
+              matrix - C->R should be '3'<br />Old matrix restored with
+              this one-line groovy script:<br />jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
+            </li>
+            <li>
+              <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
+              and substitution matrix based Tree calculations.<br />In
+              earlier versions of Jalview, gaps matching gaps were
+              penalised, and gaps matching non-gaps penalised even more.
+              In the PCA calculation, gaps were actually treated as
+              non-gaps - so different costs were applied, which mean't
+              Jalview's PCAs were different to those produced by
+              SeqSpace.<br />Jalview now treats gaps in the same way as
+              SeqSpace (ie it scores them as 0). To restore pre-2.10.2
+              behaviour<br />
+              jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
+              2.10.1 mode<br />
+              jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
+              restore 2.10.2 mode
+            </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>
+          <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
+          <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
+          <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li> 
+          </ul>
+          <em>Application</em>
+          <ul>
+          <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>
+          <li><!--  JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li> 
+          
+          </ul>
+          <em>Applet</em>
+          <ul>
+          <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>
+          <li></li>
+          </ul>
+          
+          </div>
+    <tr>
+      <td width="60" nowrap>
+        <div align="center">
           <strong><a name="Jalview.2.10.1">2.10.1</a><br />
             <em>29/11/2016</em></strong>
         </div>
@@ -211,6 +319,9 @@ 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>