From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 17 Apr 2019 14:32:58 +0000 (+0100)
Subject: Merge branch 'documentation/JAL-3111_release_211' into develop
X-Git-Tag: Release_2_11_0~17^2~16
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5ccaaa04373a6f6ae265c43c579adb58421efba0;hp=1497b61431f9ef98f8d2f18c6d2347d28477af08;p=jalview.git

Merge branch 'documentation/JAL-3111_release_211' into develop
---

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 5b76d10..3529cae 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -78,8 +78,10 @@
     within the similarity space, as points in a rotateable 3D
     scatterplot. The colour of each sequence point is the same as the
     sequence group colours, white if no colour has been defined for the
-    sequence, and green if the sequence is part of a the currently
-    selected group.</p>
+    sequence, and grey if the sequence is part of the currently selected
+    group. The viewer also employs depth cueing, so points appear darker
+    the farther away they are, and become brighter as they are rotated
+    towards the front of the view.</p>
   <p>
     The 3d view can be rotated by dragging the mouse with the <strong>left
       mouse button</strong> pressed. The view can also be zoomed in and out with
diff --git a/help/html/releases.html b/help/html/releases.html
index 0fba08a..91ba69c 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,10 +71,46 @@ li:before {
       <td width="60" nowrap>
         <div align="center">
           <strong><a name="Jalview.2.11.0">2.11.0</a><br />
-            <em>29/01/2019</em></strong>
+            <em>14/05/2019 (final due date !)</em></strong>
         </div>
       </td>
     <td><div align="left">
+        <ul>
+          <li>
+            <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
+            Viewer state is saved in Jalview Project<br />The 'Change
+            parameters' option has also been removed from the PCA
+            viewer.
+          </li>
+          <li>
+            <!-- JAL-3198 -->More efficient creation of selections and
+            multiple groups when working with large alignments
+          </li>
+          <li>
+            <!-- JAL-3200 -->Speedier import of annotation rows when
+            parsing stockholm files
+          </li>
+          <li>
+            <!-- JAL-3018 -->Update of Ensembl Rest Client to API v9.0
+          </li>
+          <li>
+            <!-- JAL-3... -->Sequence features can be filtered and
+            shaded according to any associated attributes (e.g. variant
+            attributes from VCF file, or key-value pairs imported from
+            column 9 of GFF file)
+          </li>
+          <li>
+            <!-- JAL-3139, -->More efficient sequence feature render
+            algorithm (Z-sort/transparency and filter aware)
+          </li>
+          <li>
+            <!-- JAL-2527 -->Alignment Overview now by default shows
+            only visible region of alignment (this can be changed in
+            user preferences)
+          </li>
+          <li><!--  -->
+          </li>
+        </ul>
         <em>Deprecations</em>
         <ul>
           <li>
@@ -84,14 +120,50 @@ li:before {
         </ul>
         <em>Release Processes</em>
         <ul>
-        <li>Atlassian Bamboo continuous integration server for unattended Test Suite execution</li>
-        <li><!-- JAL-2864 -->Memory test suite to detect leaks in common operations</li> 
+          <li>Atlassian Bamboo continuous integration server for
+            unattended Test Suite execution</li>
+          <li>
+            <!-- JAL-2864 -->Memory test suite to detect leaks in common
+            operations
+          </li>
+          <li>
+            <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
+            implementation) used for Sequence Feature collections
+          </li>
+          <li>
+            <!-- JAL-3063 -->Castor library for XML marshalling and
+            unmarshalling has been replaced by JAXB for Jalview projects
+            and XML based data retrieval clients
+          </li>
+          <li>
+          <!-- JAL -->
+
         </ul>
       </div></td>
     <td><div align="left">
         <em></em>
         <ul>
           <li>
+            <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
+            Jalview project involving multiple views
+          </li>
+          <li>
+            <!-- JAL-3164 -->Overview for complementary view in a linked
+            CDS/Protein alignment is not updated when Hide Columns by
+            Annotation dialog hides columns
+          </li>
+          <li>
+            <!-- JAL-3158 -->Selection highlighting in the complement of
+            a CDS/Protein alignment stops working after making a
+            selection in one view, then making another selection in the
+            other view.
+          </li>
+          <li><!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
+          <li>
+            <!-- JAL-3154 -->Table Columns could be re-ordered in
+            Feature Settings and Jalview Preferences panels
+          </li>
+          <li>
             <!-- JAL-2865 -->Jalview hangs when closing windows
             or the overview updates with large alignments.
           </li>
@@ -127,6 +199,7 @@ li:before {
             <!-- JAL-3178 -->Nonpositional features lose feature group
             on export as jalview features file
           </li>
+          <li><!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li> 
         </ul>
       </div></td>
     </tr>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 13fe656..3538ff4 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,49 +24,47 @@
 </head>
 <body>
   <p>
-    <strong>What's new in Jalview 2.10.5 ?</strong>
+    <strong>Jalview 2.11 - major and minor new features</strong>
   </p>
-  <p>Jalview 2.10.5 is a minor release that includes critical
-    patches for users working with Ensembl, RNA secondary structure
-    annotation, and those running Jalview on OSX with Java 10.</p>
+  <p>Jalview 2.11 introduces support for loading VCF files, and new
+    filters and shading models for sequence features. Under the hood,
+    we've addressed many bugs, and also made some important changes in
+    the way the Jalview desktop is installed and launched.</p>
   <ul>
-    <li>Jalview's default memory limit increased to 1G. <br/>If you have
-      problems starting Jalview 2.10.5 and you have 1G or less
-      physical memory on your machine, you will need to <a
-      href="memory.html#memsetting">reduce the memory</a> allocated to
-      Jalview.
-    </li>
-    <li>EPS, PNG and SVG export now includes hidden sequence
-      markers, and representative sequences are marked in bold.</li>
-    <li>Ensembl Client updated for Ensembl Rest API v7.<br />The
-      latest Ensembl API is not backwards compatible with earlier
-      versions of Jalview, so if you require Ensembl functionality you
-      will need to install this release.
-    </li>
-    <li>Improved support for VIENNA extended dot-bracket notation
-      for RNA secondary structure.</li>
-    <li>Positional and selected region highlighting in VARNA
-      'trimmed sequence' view made more reliable.</li>
+    <li><em>VCF Support</em>. Proteins and genomic contigs with
+      chromosomal location annotation (such as protein coding genes
+      retrieved from Ensembl) can be annotated with variants imported
+      from a local VCF file.</li>
+    <li><em>The Jalview Launcher and Update System</em><br />
+      Jalview's new installation model means you'll only need to
+      download and install Jalview once. After installation, Jalview
+      will automatically keep itself up to date. The launcher also sets
+      Jalview's memory automatically, so you'll never again have to
+      manually configure Java's memory settings.<br />We are grateful to
+      Install4J who provided us with a free license for their
+      installation system, and Jalview's over the air update system is
+      via Getdown.</li>
   </ul>
   <p>
     The full list of bugs fixed in this release can be found in the <a
-      href="releases.html#Jalview.2.10.5">2.10.5 Release Notes</a>. The
-    majority of bug fixes and improvements in 2.10.5 are due to Jalview users
-    contacting us via the jalview-discuss email list. Thanks to everyone
-    who took the time to help make Jalview better !
+      href="releases.html#Jalview.2.11">2.11 Release Notes</a>.
   </p>
   <p>
-    <strong>Jalview and Java 10</strong>
+    <strong>Jalview and Java 11, 13, and onwards</strong>
   </p>
-  <p>This release addresses a critical bug for OSX users who are
-    running Jalview with Java 10 which can prevent files being saved
-    correctly through the 'Save As' dialog box.</p>
-    <em>Known Issues</em>
+  <p>Java 11 provides improved performance and better OS
+    integration, so we now recommend users select our Java 11 Jalview
+    distribution rather than the legacy Java 8 build.</p>
+  <em>Known Issues - update for 211 </em>
   <ul>
     <li>OSX: The 'Open File' dialog for Jalview's Groovy Console
-      appears with the title 'Save As', and attempting to select a file to load yields a FileNotFound exception.</br>The workaround is to first clear the 'Untitled' filename before selecting the file you wish to load.
-      </li>
-    <li>OSX: Links don't open when clicked on or via the Sequence or Alignment window popup menu.</li>
+      appears with the title 'Save As', and attempting to select a file
+      to load yields a FileNotFound exception.</br>The workaround is to first
+      clear the 'Untitled' filename before selecting the file you wish
+      to load.
+    </li>
+    <li>OSX: Links don't open when clicked on or via the Sequence
+      or Alignment window popup menu.</li>
     <li>OSX (Webstart): Jalview only displays old news feed items</li>
   </ul>
 </body>