X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=5376db890f5370ecb6e8f134817a632089e3f818;hb=cfa90577b4ddcb2e163a9bac0b2786d45de57933;hp=330105383188fb25083a8910b4d3542b7c063c6c;hpb=6bfa5b3f409851b020aacf1f5c033842c4b1fde8;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 3301053..5376db8 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,13 +71,15 @@ 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">
           <em>General</em>
           <ul>
-          <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
+        	  <li><!-- JAL-2379 -->Revised implementation of PCA for speed and memory efficiency (~30x faster)</li>
+        	  <li><!-- JAL-2500 -->Trees computed on Sequence Feature Similarity may have different topology due to increased precision</li>
+        	  <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>
@@ -91,6 +93,8 @@ li:before {
               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>
@@ -117,17 +121,22 @@ li:before {
           <li><!--  --></li>
           </ul>
           <em>Test Suite</em>
+          <ul>
           <li><!--  JAL-2474 -->Added PrivilegedAccessor to test suite</li>
           <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
           <li><!--  -->  
+          <em>Scripting</em>
+          <ul>
+        		<li><!-- JAL-2344 -->FileFormatI interface for describing and identifying file formats (instead of String constants)</li>
+          </ul>
           </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
+              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
@@ -135,7 +144,7 @@ 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
@@ -161,7 +170,20 @@ li:before {
           <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-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
-          <li><!-- JAL-2563 -->Sequence position for ambiguous codon not shown in status bar</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>
+	    <li><!-- JAL-2602 -->Copy consensus sequence failed if alignment included gapped columns</li>
+	    <li><!-- JAL-2589 -->User defined gap colour not shown in overview when features overlaid on alignment</li>
+	    </ul>
+	      <strong>Documentation</strong>
+	      <ul>
+	        <li><!-- JAL-2339 -->Release notes reformatted for readibility with the built-in Java help viewer</li>
           </ul>
           <em>Application</em>
           <ul>
@@ -182,9 +204,15 @@ li:before {
               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>
+	  <li><!-- JAL-2582 -->Cannot retrieve protein products from Ensembl by Peptide ID</li>
+	  <li><!-- JAL-2431 -->cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins</li>
           </ul>
           <em>Applet</em>
           <ul>
+          <li><!-- JAL-2468 -->Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot</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>
           <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
@@ -192,10 +220,13 @@ li:before {
           <em>New Known Issues</em>
           <ul>
           <li><!--  JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
-          <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</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>
+          <em>Test Suite</em>
+          <ul><li><!-- JAL-2314 -->Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails</li>
+          <li><!-- JAL- --></li>
           </ul>
-          
           </div>
     <tr>
       <td width="60" nowrap>