From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 18 Aug 2017 13:14:17 +0000 (+0100)
Subject: Merge branch 'develop' into releases/Release_2_10_2_Branch
X-Git-Tag: Release_2_10_2b1~11^2~14
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=e114d4676469632ad07f356c1ee0ee63c3e418e9;hp=ff044a6dc70d85fcef18cac3129386c98d7edda3

Merge branch 'develop' into releases/Release_2_10_2_Branch
---

diff --git a/help/help.jhm b/help/help.jhm
index cb0c4c4..c12436f 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -22,7 +22,7 @@
    <mapID target="home" url="html/index.html" />
    
    <mapID target="new" url="html/whatsNew.html"/>
-   <mapID target="release" url="html/releases.html#Jalview.2.10.2"/>
+   <mapID target="release" url="html/releases.html#Jalview.2.10.2b1"/>
    <mapID target="alannotation" url="html/features/annotation.html"/>
    <mapID target="keys" url="html/keys.html"/>
    <mapID target="newkeys" url="html/features/newkeystrokes.html"/>
diff --git a/help/html/releases.html b/help/html/releases.html
index 471e12a..c331ae1 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,6 +70,24 @@ 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>
+          </ul>
+        </div></td>
+      <td><div align="left">
+          <em></em>
+          <ul>
+          </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>
@@ -210,7 +228,9 @@ 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
@@ -272,25 +292,23 @@ 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><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 />
+            <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>
+                calculations (not recommended)</em></li>
             <li>
               <!-- JAL-2424 -->Fixed off-by-one bug that affected
               scaling of branch lengths for trees computed using
@@ -643,7 +661,8 @@ 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>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 90f6832..ff0fe35 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,15 +24,23 @@
 </head>
 <body>
   <p>
+  <strong>Jalview 2.10.2b1 bugfix release</strong>
+  </p>
+  <p>
+    This is patch release for 2.10.2. See the <a
+      href="releases.html#Jalview2.10.2b1">release notes</a>.
+  </p>
+  <p>
     <strong>What's new in Jalview 2.10.2 ?</strong>
   </p>
   <p>
-    This August 2017 release of Jalview introduces new user interface
-    features, improved and more extensible tree and PCA analysis, more
-    robust 3D structure viewing with UCSF Chimera and an updated service
-    client for JABAWS. The full list of bug fixes and new features can
-    be found in the <a href="releases.html#Jalview.2.10.2"> 2.10.2
-      Release Notes</a>, but the highlights are below.
+    Version 2.10.2 was released in August 2017, and introduced new user
+    interface features, improved and more extensible tree and PCA
+    analysis, more robust 3D structure viewing with UCSF Chimera and an
+    updated service client for JABAWS. The full list of bug fixes and
+    new features can be found in the <a
+      href="releases.html#Jalview.2.10.2"> 2.10.2 Release Notes</a>, but
+    the highlights are below.
   </p>
   <ul>
     <li><strong>New dialog and faster and more