X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=53cac27ff9cd6e39b65c0689d8b9c09998eca873;hb=3936adfcc1bde0988719b6405d112ab43277ea76;hp=89a39a32698ac269d7fddac823fb99eef4d647bb;hpb=9414f9f58b1f9ea6027159d15a3d7b33d562b3e8;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 89a39a3..53cac27 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,6 +70,73 @@ li:before {
     <tr>
       <td width="60" nowrap>
         <div align="center">
+          <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
+            <em>TBA</em></strong>
+        </div>
+      </td>
+      <td><div align="left">
+          <em></em>
+          <ul>
+            <li>
+              <!-- JAL-2588 -->Show gaps in overview window by colouring
+              in grey (sequences used to be coloured grey, and gaps were
+              white)
+            </li>
+            <li>
+              <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
+              Preferences
+            </li>
+            <li>
+              <!-- JAL-2587 -->Overview updates immediately on increase
+              in size and progress bar shown as higher resolution
+              overview is recalculated
+            </li>
+
+          </ul>
+        </div></td>
+      <td><div align="left">
+          <em></em>
+          <ul>
+            <li>
+              <!-- JAL-2664 -->Overview window redraws every hidden
+              column region row by row
+            </li>
+            <li>
+              <!-- JAL-2681 -->duplicate protein sequences shown after
+              retrieving Ensembl crossrefs for sequences from Uniprot
+            </li>
+            <li>
+              <!-- JAL-2603 -->Overview window throws NPE if show boxes
+              format setting is unticked
+            </li>
+            <li>
+              <!-- JAL-2610 -->Groups are coloured wrongly in overview
+              if group has show boxes format setting unticked
+            </li>
+            <li>
+              <!-- JAL-2672,JAL-2665 -->Redraw problems when
+              autoscrolling whilst dragging current selection group to
+              include sequences and columns not currently displayed
+            </li>
+            <li>
+              <!-- JAL-2691 -->Not all chains are mapped when multimeric
+              assemblies are imported via CIF file
+            </li>
+            <li>
+              <!-- JAL-2704 -->Gap colour in custom colourscheme is not
+              displayed when threshold or conservation colouring is also
+              enabled.
+            </li>
+            <li>
+              <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
+              server version
+            </li>
+          </ul>
+        </div></td>
+    
+    <tr>
+      <td width="60" nowrap>
+        <div align="center">
           <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
         </div>
       </td>
@@ -122,10 +189,6 @@ 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 +230,10 @@ 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 +247,10 @@ 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 +268,7 @@ 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>
@@ -206,7 +277,9 @@ li:before {
               <!-- JAL-2549 -->Updated JABAWS client to v2.2
             </li>
             <li>
-              <!-- JAL-2335 -->Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
+              <!-- JAL-2335 -->Filter non-standard amino acids and
+              nucleotides when submitting to AACon and other MSA
+              Analysis services
             </li>
             <li>
               <!-- JAL-2316, -->URLs for viewing database
@@ -237,7 +310,7 @@ 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>
@@ -268,22 +341,23 @@ 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>
-              <!-- 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 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
-            </li>
+            <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
+              Jalview's treatment of gaps in PCA 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). <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
               scaling of branch lengths for trees computed using
@@ -415,10 +489,6 @@ 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 +694,11 @@ 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
@@ -640,7 +710,8 @@ li:before {
               doesn't always add secondary structure annotation.
             </li>
           </ul>
-        </div><tr>
+        </div>
+    <tr>
       <td width="60" nowrap>
         <div align="center">
           <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>