Merge branch 'develop' into releases/Release_2_10_2_Branch

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

diff --git a/help/html/releases.html b/help/html/releases.html
index 89a39a3..471e12a 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -122,10 +122,6 @@ li:before {
               with alignment and overview windows
             </li>
             <li>
-              <!--  JAL-2491 -->Linked scrolling of CDS/Protein views
-              via Overview or sequence motif search operations
-            </li>
-            <li>
               <!-- JAL-2514 -->Scrolling of wrapped alignment views via
               overview
             </li>
@@ -167,6 +163,10 @@ li:before {
               the application.
             </li>
             <li>
+              <!--  JAL-2491 -->Linked scrolling of CDS/Protein views
+              via Overview or sequence motif search operations
+            </li>
+            <li>
               <!-- JAL-2547 -->Amend sequence features dialog box can be
               opened by double clicking gaps within sequence feature
               extent
@@ -180,6 +180,10 @@ li:before {
           <em>3D Structure</em>
           <ul>
             <li>
+              <!-- JAL-2430 -->Hidden regions in alignment views are not
+              coloured in linked structure views
+            </li>
+            <li>
               <!-- JAL-1596 -->Faster Chimera/Jalview communication by
               file-based command exchange
             </li>
@@ -197,7 +201,7 @@ li:before {
               <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
               to transfer Chimera's structure attributes as Jalview
               features, and vice-versa (<strong>Experimental
-                Feauture</strong>)
+                Feature</strong>)
             </li>
           </ul>
           <em>Web Services</em>
@@ -237,7 +241,7 @@ li:before {
           <em>Documentation</em>
           <ul>
             <li>
-              <!-- JAL-2339 -->Release notes reformatted for readibility
+              <!-- JAL-2339 -->Release notes reformatted for readability
               with the built-in Java help viewer
             </li>
             <li>
@@ -268,21 +272,24 @@ li:before {
               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>
+            <li><a name="2102scoremodelbugs"/>
               <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
-              and substitution matrix based Tree calculations.<br />In
+              and substitution matrix based Tree calculations.<br /> <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 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
-              behaviour<br />
-              jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
-              2.10.1 mode<br />
-              jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
-              restore 2.10.2 mode
+              SeqSpace (ie it scores them as 0). <br /> <br />Enter
+              the following in the Groovy console to restore pre-2.10.2
+              behaviour:<br />
+              jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+              // for 2.10.1 mode <br />
+              jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
+              // to restore 2.10.2 mode <br /> <br /> <em>Note:
+                these settings will affect all subsequent tree and PCA
+                calculations (not recommended)</em>
             </li>
             <li>
               <!-- JAL-2424 -->Fixed off-by-one bug that affected
@@ -415,10 +422,6 @@ li:before {
           <em>Rendering</em>
           <ul>
             <li>
-              <!-- JAL-2430 -->Hidden regions in alignment views are not
-              coloured in linked structure views
-            </li>
-            <li>
               <!-- JAL-2421 -->Overview window visible region moves
               erratically when hidden rows or columns are present
             </li>
@@ -624,11 +627,11 @@ 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
+              interpreted as WUSS RNA secondary structure symbols
             </li>
             <li>
-              <!-- JAL-2590 -->Cannot load Newick trees from eggnog
-              ortholog database
+              <!-- JAL-2590 -->Cannot load and display Newick trees
+              reliably from eggnog Ortholog database
             </li>
             <li>
               <!-- JAL-2468 -->Status bar shows 'Marked x columns