JAL-2590 release notes

[jalview.git] / help / html / releases.html

diff --git a/help/html/releases.html b/help/html/releases.html
index 673faee..5c8da91 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -81,7 +81,17 @@ li:before {
           <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><!--  --></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>
           </ul>
           <em>Application</em>
           <ul>
@@ -108,7 +118,7 @@ li:before {
           <li><!--  --></li>
           </ul>
           <em>Test Suite</em>
-          <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>
@@ -118,7 +128,7 @@ li:before {
             <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
+              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
@@ -151,7 +161,9 @@ li:before {
           <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-2547 -->Sequence features shown in tooltip for gaps before start of features</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-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
           </ul>
           <em>Application</em>
           <ul>
@@ -166,17 +178,26 @@ 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><!--  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>  
           </ul>
           
           </div>