From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 3 Aug 2017 13:04:43 +0000 (+0100)
Subject: JAL-2418 release notes
X-Git-Tag: Release_2_10_2~3^2~15^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4b037484ce621d0944589395653d46db274d63cd;p=jalview.git

JAL-2418 release notes
---

diff --git a/help/html/releases.html b/help/html/releases.html
index eff80b5..5376db8 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -77,7 +77,9 @@ li:before {
       <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>
@@ -119,9 +121,14 @@ 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>
@@ -171,6 +178,12 @@ li:before {
 	    <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>
@@ -195,9 +208,11 @@ li:before {
             <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>
@@ -208,7 +223,10 @@ li:before {
           <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>