X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=86a1100c909cad066b4cef2378e6deb28cce5b4c;hb=51a7eedfc7d55c6f2dae8a75dcda6c4ccbe81893;hp=12b67064b510714aff95d5134b38ab3ea8198ce4;hpb=01dd726fbb6c68bd834304e49eef1d72cc9586f4;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 12b6706..86a1100 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,7 +71,7 @@ li:before {
       <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>
+            <em>8/8/2017</em></strong>
         </div>
       </td>
       <td><div align="left">
@@ -79,6 +79,20 @@ li:before {
           <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>
+          <li><!--  JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
+          <li><!--  JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
+          <li><!-- JAL-2388 -->Hidden columns and sequences can be omitted in Overview</li>
+            <li>
+              <!-- JAL-2535 -->Posterior probability annotation from
+              Stockholm files imported as sequence associated annotation
+            </li>
+            <li>
+              <!-- JAL-2533 -->Sequence names don't include file
+              extension when importing structure files without embedded
+              names or PDB accessions
+            </li>
+          <li><!-- JAL-2547 -->Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent</li>
+	  <li><!-- JAL-2631 -->Graduated feature colour style example included in the example feature file</li>
           </ul>
           <em>Application</em>
           <ul>
@@ -90,7 +104,7 @@ li:before {
             <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>
-          
+          <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
           </ul>
           <em>Experimental features</em>
           <ul>
@@ -105,8 +119,7 @@ li:before {
           <li><!--  --></li>
           </ul>
           <em>Test Suite</em>
-          <ul><li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)</li>
-          <li><!--  JAL-2474 -->Added PrivelegedAccessor to test suite</li>
+          <li><!--  JAL-2474 -->Added PrivilegedAccessor to test suite</li>
           <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
           <li><!--  -->  
           </ul>
@@ -115,8 +128,8 @@ li:before {
           <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
+              matrix - C->R should be '-3'<br />Old matrix restored with
+              this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
             </li>
             <li>
               <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
@@ -124,7 +137,7 @@ li:before {
               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
+              non-gaps - so different costs were applied, which meant
               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
@@ -148,7 +161,16 @@ li:before {
           <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> 
+          <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
+          <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
+          <li><!-- JAL-2576 -->Very large alignments take a long time to load</li>
+	    <li><!-- JAL-2623 -->Graduated feature colour threshold not restored to UI when feature colour is edited</li>
+	    <li><!-- JAL-2624 -->Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%</li>
+	    <li><!-- JAL-2630 -->Structure and alignment overview update as graduate feature colour settings are modified via the dialog box</li>
+	    <li><!-- JAL-147 -->Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.</li>
+	    <li><!-- JAL-2034 -->Overview window doesn't always update when a group defined on the alignment is resized</li>
+	    <li><!-- JAL-2605 -->Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
+	    <li><!-- JAL-2563 -->Status bar shows position for ambiguous amino acid and nucleotide symbols</li>
           </ul>
           <em>Application</em>
           <ul>
@@ -163,16 +185,27 @@ li:before {
           <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> 
-          
+          <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
+            <li>
+              <!-- JAL-2520 -->Structures loaded via URL are saved in
+              Jalview Projects rather than fetched via URL again when
+              the project is loaded and the structure viewed
+            </li>
+            <li><!-- JAL-1256 -->Trackpad horizontal scroll gesture adjusts start position in wrap mode</li>
+            <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
+            <li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</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>
+          <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
           </ul>
           <em>New Known Issues</em>
           <ul>
-          <li></li>
+          <li><!--  JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
+          <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>  
+            <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
           </ul>
           
           </div>