From 0df0212d23b9c373d042c56213c06bde16b62b1c Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 3 Sep 2020 11:42:43 +0100
Subject: [PATCH] JAL-3675 whats new, logging and release notes tidying for
 2.11.1.1.

---
 help/help/helpTOC.xml        |    2 +-
 help/help/html/index.html    |    7 +++-
 help/help/html/logging.html  |   19 +++++----
 help/help/html/whatsNew.html |   95 ++++++++++++++++++++++--------------------
 4 files changed, 68 insertions(+), 55 deletions(-)

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index c5660fe..a72f5ac 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -27,7 +27,7 @@
         <tocitem text="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
 				<tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
 				<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-				
+        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
diff --git a/help/help/html/index.html b/help/help/html/index.html
index 442c508..8adbdb8 100755
--- a/help/help/html/index.html
+++ b/help/help/html/index.html
@@ -56,7 +56,12 @@
     then get in contact over at <a
       href="http://www.jalview.org/community">http://www.jalview.org/community</a>
   </p>
-
+  <p>
+    <strong>Logging, troubleshooting and reporting bugs</strong><br />If
+    something seems to be wrong with your Jalview installation, or you
+    think you've found a problem, take a look at <a href="logging.html">Jalview's
+      logging and bug reporting</a> documentation.
+  </p>
   <p>
     <strong>Citing Jalview</strong><br />If you use Jalview in your
     work, please cite the Jalview 2 paper in Bioinformatics:
diff --git a/help/help/html/logging.html b/help/help/html/logging.html
index dce1c7b..0975a47 100644
--- a/help/help/html/logging.html
+++ b/help/help/html/logging.html
@@ -26,10 +26,15 @@
   <p>
     <strong>The Java Console, Logging and Reporting Bugs<br /></strong>
   </p>
-  <p>Like most programs, Jalview produces a series of messages
-    during its operation, often referred to as 'logs'. These logs can be
-    extremely useful for diagnosing and helping the Jalview developers
-    find a workaround for specific problems that you might encounter.</p>
+  <p>
+    Like most programs, Jalview contains bugs, despite our best efforts.
+    However, Jalview also produces a series of messages during its
+    operation, often referred to as 'logs'. These logs provide a record
+    of Jalview's operation. They can also be extremely useful when <a
+      href="#reportingbugs">reporting bugs</a>, since they help the
+    Jalview developers diagnose and find a workaround for specific
+    problems that you might encounter.
+  </p>
   <p>
     The primary place to look for logs is in the <a href="#java_console">Java
       Console</a> which you can open from within Jalview by going to the <em>Tools</em>
@@ -45,7 +50,7 @@
     are not shown in the Jalview Console. The location of these depends
     on how you launched Jalview:</p>
   <p>
-    <strong>Jalview Desktop Installations</strong><br />If you are using
+    <strong>Jalview Desktop Installation Launch Logs</strong><br />If you are using
     a standard desktop version of Jalview installed from one of our
     install4j installers, then messages about Jalview's initial launch
     can be found in
@@ -65,7 +70,7 @@
       by default
     </li>
   </ul>
-  <p><strong>Jalview Executable Jar</strong><br/>If you are using the Jalview executable jar file (also
+  <p><strong>Jalview Executable Jar Launch Logs</strong><br/>If you are using the Jalview executable jar file (also
   used by bioconda and OSX homebrew installations) then the default run class (
   <em>jalview.bin.Launcher</em> -- a minimised launcher that will set
   memory and linux dpi settings before re-launching
@@ -144,7 +149,7 @@
     composer or issue tracker).
   </p>
 
-  <h3>Reporting Bugs</h3>
+  <p><strong><a name="reportingbugs">Reporting Bugs</a></strong></p>
 
   <p>
     If you come across a problem in Jalview where something is not
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 0f0c7f1..a62e71d 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -24,58 +24,61 @@
 </head>
 <body>
   <p>
-    <strong>Jalview 2.11.1.0</strong>
-  </p>
-  <p>
-    Jalview 2.11.1.0 is the first minor release for the 2.11 series.
-    Along with a number of critical bug fixes and improvements it brings
-    new functionality for mapping sequence features between CDS and
-    Protein alignments. It is also the first release made under a new <em>four</em>
-    number versioning scheme, which will allow us to keep track of
-    patches and bug fixes.
+    <strong>Jalview 2.11.1.1</strong>
   </p>
+  <p>Jalview 2.11.1.1 is the first patch release for Jalview version
+    2.11.1. In addition to fixes for some critical it also contains a
+    handful of new features suggested by the Jalview community.</p>
+  <ul>
+    <li>Shift+arrow keys navigate to next gap or residue in cursor
+      mode (enable with F2)</li>
+    <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
+      2.23</li>
+    <li>Improved recognition of GZipped files from local disk or
+      retrieved via the web</li>
+    <li>EMBL and EMBL CDS database records retrieved from the
+      European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
+    <li>Improved <a href="logging.html">Java Console and
+        logging</a> to help track down problems
+    </li>
+    <li>Improved support for Hi-DPI (4K) screens when running on
+      Linux (Requires Java 11+)</li>
+  </ul>
+  <p>Critical bug fixes include</p>
   <ul>
-    <li><strong>Virtual Features</strong><br />In previous
-      versions of Jalview, specific nucleotide sequence features such as
-      genomic variants and exons were transferred to protein products on
-      import. Jalview 2.11.1 instead provides 'virtual features' that
-      can be enabled and overlaid on linked CDS/Protein views via their
-      <a href="features/splitView.html#virtualfeats">Sequence
-        Features dialog</a>. This allows more analyses of nucleotide and
-      peptide sequence features on alignments in a more flexible and
-      memory efficient way than in earlier versions.<br />
-    <em>Note: Virtual features work best when variants are
-        annotated with CSQ fields. Please <a
-        href="features/importvcf.html#computepepvariants">see this
-          Groovy script workaround</a> if you are working with VCF files
-        without CSQ fields.
-    </em></li>
-    <li><strong>Improved VCF data import</strong><br /> <a
-      href="features/importvcf.html#attribs">Standard attributes for
-        filtering variants</a> (e.g. position, QUAL field etc) are now
-      extracted from VCF files. This new feature was suggested by a user
-      at the Jalview booth during ISMB 2019.</li>
-    <li><strong>Extended feature attributes are exported
-        in GFF3</strong><br />Complex attributes from VCF files can be exported
-      and imported via GFF3</li>
-    <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
-      installation packages are now built with Install4j 8, which brings
-      better support for Linux and improved control of file
-      associations. New <a href="memory.html#jvm">parameters on the
-        Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
-      a Jalview launch file, to prevent it from hogging your system.</li>
+    <li>Jalview runs correctly when launched with Turkish language
+      settings</li>
+    <li>Peptide-to-CDS tracking broken when multiple EMBL gene
+      products shown for a single contig (such as viral genomes)</li>
+    <li>Errors encountered when processing variants from VCF files
+      yield "Error processing VCF: Format specifier '%s'" on the console</li>
+    <li>Count of features not shown can be wrong when there are
+      both DNA and Protein features mapped to the position under
+      the cursor</li>
+    <li>Sequence ID for reference sequence is clipped when Right
+      align Sequence IDs enabled</li>
+    <li>Find doesn't report matches that span hidden gapped columns</li>
+    <li>Jalview ignores file format parameter specifying output
+      format when exporting an alignment via the command line</li>
   </ul>
   <p>
-    See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
-      release notes</a> for full details of bugs fixed and new known issues.
+    For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
+      Jalview 2.11.1.1 release notes</a>.
   </p>
   <p>
-    <em>JalviewJS News</em><br />With the release of Jalview 2.11.1.0,
-    the team are now focused on bringing JalviewJS to full production.
-    To follow our progress take a look at <em>http://www.jalview.org/jalview-js/</em>
-    and follow updates on our new <a
-      href="https://github.com/jalview/jalview-js/">JalviewJS
-      Releases github repository</a>.
+    <strong>Known Issues</strong>
   </p>
+  <ul>
+    <li>We've had reports from a small number of windows 10 users
+      who see a warning dialog pop up when Jalview tries to save a new
+      version of an existing file. If you are affected by this bug and
+      this latest version of Jalview doesn't fix it, please let us know!</li>
+    <li>Co-located features exported and re-imported are ordered
+      differently when shown on alignment and in tooltips. (Also affects
+      v2.11.1.0)</li>
+    <li>Drag and drop of alignment file onto alignment window when
+      in a HiDPI scaled mode in Linux only works for the top left
+      quadrant of the alignment window</li>
+  </ul>
 </body>
 </html>
-- 
1.7.10.2