From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 16 May 2017 16:27:35 +0000 (+0100)
Subject: JAL-2418 release notes
X-Git-Tag: Release_2_10_2~3^2~83^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a299290c8f04a6bb68b18f8335b8f9f28486b54f;p=jalview.git

JAL-2418 release notes
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 25fc04b..2f983fa 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -78,8 +78,7 @@ li:before {
           <em>General</em>
           <ul>
           <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
-          <li><!--  JAL-384 -->Custom BLOSUM/Clustal type shading schemes can be created via groovy scripts</li>
-          
+          <li><!--  JAL-384 -->Custom shading schemes created via groovy scripts</li>
           <li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
           </ul>
           <em>Application</em>
@@ -96,7 +95,28 @@ li:before {
           </div></td><td><div align="left">
           <em>General</em>
           <ul>
-          <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-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> 
@@ -108,6 +128,9 @@ li:before {
           <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>
@@ -120,7 +143,8 @@ li:before {
           <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-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>