The Java Console, Logging and Reporting Bugs

Using Groovy to add new Alignment Calculations

-       /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
       \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa
 # Jalview Launch File
 # Please install the Jalview Desktop from 
-# http://www.jalview.org/getdown/release
+# https://www.jalview.org/getdown/release
 # and then try to open this file again
 jalview.apparg=-open
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta
 jalview.apparg=-annotations
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
 jalview.apparg=-colour
 jalview.apparg=Clustal
 
/*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)

diff --git a/help/help/html/index.html b/help/help/html/index.html
index 442c508..a6bb1b6 100755
--- a/help/help/html/index.html
+++ b/help/help/html/index.html
@@ -45,7 +45,7 @@
   
     For more information, you might also want to take a look at the
     documentation section of the Jalview website (http://www.jalview.org/about/documentation).
+      href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation).
   
   
     If you are using the Jalview Desktop application and are looking for
@@ -54,9 +54,14 @@
     google the online version of these pages. If you don't find what you
     are looking for, or want to report a bug or make a feature request,
     then get in contact over at http://www.jalview.org/community
+      href="https://www.jalview.org/community">https://www.jalview.org/community
+  
+  
+    Logging, troubleshooting and reporting bugs
If
+    something seems to be wrong with your Jalview installation, or you
+    think you've found a problem, take a look at Jalview's
+      logging and bug reporting documentation.
   
-
   
     Citing Jalview
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
new file mode 100644
index 0000000..0975a47
--- /dev/null
+++ b/help/help/html/logging.html
@@ -0,0 +1,212 @@
+
+
+
+The Java Console, Logging and Reporting Bugs
+
+
+  

+    The Java Console, Logging and Reporting Bugs

+  
+  
+    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 reporting bugs, since they help the
+    Jalview developers diagnose and find a workaround for specific
+    problems that you might encounter.
+  
+  
+    The primary place to look for logs is in the Java
+      Console which you can open from within Jalview by going to the Tools
+    menu and checking the box next to Show Java Console. This
+    option is stored in your Jalview preferences file and so is
+    remembered across Jalview sessions.
+  
+  The Java Console will show you information about what the
+    Jalview application is doing (often in the background) whilst it is
+    running.
+  However, when tracking down problems preventing Jalview from
+    starting up properly, you need to look at the startup logs - which
+    are not shown in the Jalview Console. The location of these depends
+    on how you launched Jalview:
+  
+    Jalview Desktop Installation Launch Logs
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
+  
JALVIEW_APP_DIR/launcher.log
+  where
+  JALVIEW_APP_DIR is the directory that Jalview's application
+  was installed into.
+  
 For Jalview 2.11.0 onwards:
+  
+    In Windows this is %APPDATA%\Local\Jalview by
+      default
+    
+    In macOS this is /Applications/Jalview.app/Contents/Resources/app
+      by default
+    
+    In Linux and other Unix OSes this is ~/opt/jalview
+      by default
+    
+  
+  Jalview Executable Jar Launch Logs
If you are using the Jalview executable jar file (also
+  used by bioconda and OSX homebrew installations) then the default run class (
+  jalview.bin.Launcher -- a minimised launcher that will set
+  memory and linux dpi settings before re-launching
+  jalview.bin.Jalview), will output logging information to
+  STDOUT and STDERR.
+  
+
+  
+    Java Console and Log Level
+  
+  
+    The Java Console is opened by selecting Tools
+      → Show Java Console. The visibility of the console is stored
+    in your preferences, so if you quit Jalview with the console open,
+    it will be shown the next time you start Jalview. You can close the
+    console by selecting the same menu option again, or just closing the
+    console window.
+  
+  The Java Console's text display always shows information about
+    your system and Jalview installation details. The rest are the most
+    recent messages output during your Jalview session. Some messages
+    are only captured by the console when it is open, so to get a full
+    log for debugging a problem, enable the console and then restart
+    Jalview.
+
+  
+    You can temporarily control the detail of what appears as output by
+    selecting a Log level using the drop-down list at the
+    bottom left of the console. There are several levels to choose from:
+    The most verbose is TRACE, followed by DEBUG, INFO, WARN. When the
+    Console is opened, the default level will be chosen (INFO).
+  
+  
+    Note! If you change the log level in the Java
+      Console, this change will only persist for as long as the console
+      is open. Once you close the console the log level will revert back
+      to what it had been when you opened the console (usually INFO).
+  
+  Permanently changing Jalview's default log level

+    You can change the default log level by editing the Jalview
+    preferences file, .jalview_properties, found in your home
+    directory (on Windows: %HOMEPATH%, or the folder above 'My
+    Documents'; on macOS: ~ or /Users/username; on linux/unix:
+    ~ or /home/username), and setting the property logs.Jalview.level
+    to the log level you prefer, e.g.
+  
+  logs.Jalview.level=DEBUG
+  
+  You can also set the property
+  +  logs.Axis.level=DEBUG
+  
+  to get debug information for Jalview's JPred service. The Axis log
+  level cannot be set from within the Java Console.
+  
+  
+    You can also set the logs.jalview.level property to a log level
+    not usually presented in the Java Console (though restricted to log
+    levels used by Apache Log4j -- see Log4j
+      Custom Log Levels for details of the standard log levels
+    available). Jalview does not currently define any custom log levels.
+    If you do set the property with a log level that is normally not
+    visible in the Java Console this should be respected and visibly
+    selected when you open the console.
+  
+  
+    The Clear button at the bottom of the console will clear
+    all logging messages except for the initial system information which
+    is rewritten to the console.
+  
+  
+    The Copy to clipboard button at the bottom right of the
+    console will copy all of the text in the console to your system
+    clipboard, ready to paste into another application (e.g. email
+    composer or issue tracker).
+  
+
+  Reporting Bugs
+
+  
+    If you come across a problem in Jalview where something is not
+    working as described, or how you think it should, you should first
+    check the Jalview FAQ to
+    see if this is a known problem and if there is a suggested
+    workaround.
+  
+  
+    If there is no FAQ answer covering your problem then you can submit
+    a bug report on the Jalview
+      Issue Tracker. It is good practice to search the issue tracker
+    first to see if the issue has already been reported. If an issue
+    already exists please continue to add your own comments to the issue
+    which may well help narrow down the problem, if not then you can
+    create an account and submit a new bug report:
+  
+  
+    Make sure that you set Project to Jalview (JAL), and Issue
+    Type to Bug or New Feature or Improvement
+    appropriately.
 Give a one line summary of the issue in the Summary.
+    
 In the Environment text box you can describe the
+    system you are using. This is usually most easily done by opening
+    the Java Console, clicking the Clear button, and then
+    immediately on the Copy to clipboard button, and then
+    pasting the clipboard into the text box.
+  
+  
+    You can then give more detailed information about how to recreate
+    the problem in the Description text box. If you want to
+    attach any screenshots or example alignment files that demonstrate
+    the problem then you can drag them to the Create Issue dialog in
+    your browser, or use the Attachment browse facility to
+    locate them on your computer.
+  
+
+  
+    To help the Jalview team with diagnosing a particular issue, it is
+    really helpful if you can also add more detailed logs output whilst
+    re-creating the problem. To do this, open the Java Console, click
+    the Clear button and select TRACE in the Log level
+    drop down list. 
 Whilst leaving the console open, perform the
+    task in Jalview that re-creates the problem. 
 Then you can
+    copy the debug information in the Java Console by clicking on the Copy
+      to clipboard button and then paste that into the Description, or a
+    Comment of your issue.
+  
+
+  
+    For other queries or comments about Jalview, remember you can
+    contact the Jalview team using email via the
+    Jalview
+      discussion list, on Twitter @Jalview, or for technical
+    discussions, via the Jalview developer's chatroom at
+    https://gitter.im/jalview/developers.
+  
+
+
+
diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 0374dcb..7d6fb85 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -80,7 +80,7 @@
       arguments, but you must put the jvl file first, e.g.        /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa Alternatively, you can use the standard Jalview command line
       arguments with or without the jvl file (first), e.g. -       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal You can use command line arguments to control memory
+       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
       \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 6820883..dd7a3f8 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -58,10 +58,9 @@ li:before {
     
       2.11.1.1

-          13/07/2020
+          17/09/2020
       
         
-          
           
             Shift+arrow keys navigate to next gap or
             residue in cursor mode
@@ -91,23 +90,53 @@ li:before {
             ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
             EMBL flat file
           
+          
+            Improved warning messages, debug logging
+            and fixed Retry action when Jalview encounters errors when
+            saving or making backup files.
+          
+          
+            Enhanced Jalview Java Console:
+            
+              Jalview's logging level can be configured
+              Copy to Clipboard Buttion
+            
+          
+          
+            Improved support for Hi-DPI (4K) screens
+            when running on Linux (Requires Java 11+)
+          
         
 Launching Jalview
         
           
             Configure Jalview Desktop's look and feel
             through a system property
           
+          
+            Improved built-in documentation and command
+            line help for configuring Jalview's memory
+                             
         
       
       
         
           
+            Conservation and Quality tracks are shown
+            but not calculated and no protein or DNA score models are
+            available for tree/PCA calculation when launched with
+            Turkish language locale
+          
+          
             Escape does not clear highlights on the
             alignment (Since Jalview 2.10.3)
           
           
             Alt+Left or Right arrow in cursor mode
-            doesn't slide selected sequences
+            doesn't slide selected sequences, just sequence under cursor
+          
+          
+            Alt+Up/Down in cursor mode doesn't move
+            sequence under the cursor
           
           
             Peptide-to-CDS tracking broken when
@@ -124,13 +153,81 @@ li:before {
             to the position under the cursor
           
           
+            Sequence ID for reference sequence is
+            clipped when Right align Sequence IDs enabled
+          
+          
             Slider with negative range values not
             rendered correctly in VAqua4 (Since 2.10.4)
           
-        
-        New Known defects
+          
+            Single quotes not displayed correctly in
+            internationalised text for some messages and log output
+          
+          
+            Find doesn't report matches that span
+            hidden gapped columns
+          
+          
+            Resolved memory leaks in Tree and PCA
+            panels, Alignment viewport and annotation renderer.
+          
+          
+            Jalview ignores file format parameter
+            specifying output format when exporting an alignment via the
+            command line
+          
+          
+            Windows 10: For a minority of users, if
+            backups are not enabled, Jalview sometimes fails to
+            overwrite an existing file and raises a warning dialog. (in
+            2.11.0, and 2.11.1.0, the workaround is to try to save the
+            file again, and if that fails, delete the original file and
+            save in place.)
+          
+         Launching Jalview
+        
+          
+            Jalview application fails when launched the
+            first time for a version that has different jars to the
+            previous launched version.
+          
+        
 Developing Jalview
+        
+          
+            Fixed issue with cleaning up old coverage
+            data, causing cloverReport gradle task to fail with an
+            OutOfMemory error.
+          
+          
+            Migrated the Jalview Version Checker to
+            monitor the release channel
+          
+        
 New Known defects
         
-          Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
+          

+            CDS shown in result of submitting proteins
+            in a CDS/Protein alignment to a web service is wrong when
+            proteins share a common transcript sequence (e.g.
+            genome of RNA viruses)
+          
+          
+            Co-located features exported and re-imported
+            are ordered differently when shown on alignment and in
+            tooltips. (Also affects v2.11.1.0)
+          
+          
+            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
+          
+          
+            Stale build data in jalview standalone jar
+            builds (only affects 2.11.1.1 branch)
+          
+          
+            Sequence ID colourscheme not re-applied
+            when alignment view restored from project (since Jalview 2.11.0)
           
         
       
diff --git a/help/help/html/webServices/newsreader.html b/help/help/html/webServices/newsreader.html
index c3c1d3f..2e8b69a 100644
--- a/help/help/html/webServices/newsreader.html
+++ b/help/help/html/webServices/newsreader.html
@@ -25,7 +25,7 @@
   
     The Jalview Desktop RSS News Reader
 The
     Jalview Desktop includes a built in news reader for the Jalview
+      href="https://www.jalview.org/feeds/desktop/rss">Jalview
       Desktop News Channel.
   
 
@@ -48,9 +48,9 @@
   

   
     The Jalview news reader was introduced in Jalview
+      href="https://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
       version 2.7. Its implementation is based on JSwingReader.
+      href="https://jswingreader.sourceforge.net/">JSwingReader.
   
   

   If you need to prevent the news-reader opening, then add the
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 0f0c7f1..2e18bae 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -24,58 +24,62 @@
 
 
   
-    Jalview 2.11.1.0
-  
-  
-    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 four
-    number versioning scheme, which will allow us to keep track of
-    patches and bug fixes.
+    Jalview 2.11.1.1
   
+  Jalview 2.11.1.1 is the first patch release for Jalview version
+    2.11.1. In addition to fixes for some critical bugs, it also
+    contains a handful of new features suggested by the Jalview
+    community.
+  
+    Shift+arrow keys navigate to next gap or residue in cursor
+      mode (enable with F2)
+    Support import of VCF 4.3 by updating HTSJDK from 2.12 to
+      2.23
+    Improved recognition of GZipped files from local disk or
+      retrieved via the web
+    EMBL and EMBL CDS database records retrieved from the
+      European Nucleotide Archive's Data API as 'EMBL Flatfile' records
+    Improved Java Console and
+        logging to help track down problems
+    
+    Improved support for Hi-DPI (4K) screens when running on
+      Linux (Requires Java 11+)
+  
+  Critical bug fixes include
   
-    Virtual Features
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
-      Sequence
-        Features dialog. This allows more analyses of nucleotide and
-      peptide sequence features on alignments in a more flexible and
-      memory efficient way than in earlier versions.

-    Note: Virtual features work best when variants are
-        annotated with CSQ fields. Please see this
-          Groovy script workaround if you are working with VCF files
-        without CSQ fields.
-    
-    Improved VCF data import
 Standard attributes for
-        filtering variants (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.
-    Extended feature attributes are exported
-        in GFF3
Complex attributes from VCF files can be exported
-      and imported via GFF3
-    Updated Jalview Installer and Launcher
Jalview's
-      installation packages are now built with Install4j 8, which brings
-      better support for Linux and improved control of file
-      associations. New parameters on the
-        Jalview launcher allow an upper memory limit to be specified via
-      a Jalview launch file, to prevent it from hogging your system.
+    Jalview runs correctly when launched with Turkish language
+      settings
+    Peptide-to-CDS tracking broken when multiple EMBL gene
+      products shown for a single contig (such as viral genomes)
+    Errors encountered when processing variants from VCF files
+      yield "Error processing VCF: Format specifier '%s'" on the console
+    Count of features not shown can be wrong when there are
+      both DNA and Protein features mapped to the position under
+      the cursor
+    Sequence ID for reference sequence is clipped when Right
+      align Sequence IDs enabled
+    Find doesn't report matches that span hidden gapped columns
+    Jalview ignores file format parameter specifying output
+      format when exporting an alignment via the command line
   
   
-    See the 2.11.1.0
-      release notes for full details of bugs fixed and new known issues.
+    For the full release notes, see the
+      Jalview 2.11.1.1 release notes.
   
   
-    JalviewJS News
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 http://www.jalview.org/jalview-js/
-    and follow updates on our new JalviewJS
-      Releases github repository.
+    Known Issues
   
+  
+    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!
+    Co-located features exported and re-imported are ordered
+      differently when shown on alignment and in tooltips. (Also affects
+      v2.11.1.0)
+    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
+  
 
 
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 216b498..29f0d84 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -182,8 +182,8 @@ import jalview.ws.sifts.SiftsSettings;
  * when shading by annotation
  * ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
  * when shading by annotation
- * www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org
+ * www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org
  * FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
  * alignment figure to accommodate even the longest sequence ID or annotation
  * label.
@@ -523,7 +523,7 @@ public class Cache
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4c21624..0b5fafa 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -453,7 +453,7 @@ public class Jalview
               // String defurl =
               // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
               // //
-              String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+              String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
               Cache.log.debug(
                       "Starting questionnaire with default url: " + defurl);
               desktop.checkForQuestionnaire(defurl);
@@ -782,14 +782,18 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      file = Cache.getDefault("STARTUP_FILE",
-              Cache.getDefault("www.jalview.org", "http://www.jalview.org")
-                      + "/examples/exampleFile_2_7.jar");
+      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+              jalview.bin.Cache.getDefault("www.jalview.org",
+                      "https://www.jalview.org")
+                      + "/examples/exampleFile_2_7.jvp");
       if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+                      "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
+        file.replace("http:", "https:");
         // hardwire upgrade of the startup file
-        file.replace("_2_3.jar", "_2_7.jar");
+        file.replace("_2_3", "_2_7");
+        file.replace("2_7.jar", "2_7.jvp");
         // and remove the stale setting
         Cache.removeProperty("STARTUP_FILE");
       }
@@ -1085,7 +1089,7 @@ public class Jalview
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                     + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
                     + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
-                    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+                    + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
   }
 
   private static void startUsageStats(final Desktop desktop)
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 757bb01..8ba3dce 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -256,7 +256,7 @@ public class BlogReader extends JPanel
     chan.setURL(
             jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
                     jalview.bin.Cache.getDefault("www.jalview.org",
-                            "http://www.jalview.org")
+                            "https://www.jalview.org")
                             + "/feeds/desktop/rss"));
     loadLastM();
     _channelModel.addChannel(chan);
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 67ef952..e214816 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -850,8 +850,13 @@ public class Desktop extends jalview.jbgui.GDesktop
     } catch (java.beans.PropertyVetoException ve) {
     } catch (java.lang.ClassCastException cex) {
       Cache.log.warn(
+<<<<<<< HEAD
           "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
           cex);
+=======
+              "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
+              cex);
+>>>>>>> 48040645e (JAL-3741 http to https (and jar to jvp for exampleFile defaults!))
     }
   }
 
@@ -1016,6 +1021,15 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     JPanel panel = new JPanel(new GridLayout(2, 1));
     panel.add(label);
+<<<<<<< HEAD
+=======
+    panel.add(history);
+    history.setPreferredSize(new Dimension(400, 20));
+    history.setEditable(true);
+    history.addItem("https://www.");
+
+    String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+>>>>>>> 48040645e (JAL-3741 http to https (and jar to jvp for exampleFile defaults!))
 
     /*
      * the URL to fetch is input in Java: an editable combobox with history JS:
@@ -1188,6 +1202,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         message.append("");
       }
 
+<<<<<<< HEAD
       message.append("
!! Version ").append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
           .append(" is available for download from ")
           .append(Cache.getDefault("www.jalview.org", "https://www.jalview.org")).append(" !!");
@@ -1202,6 +1217,31 @@ public class Desktop extends jalview.jbgui.GDesktop
     message.append("");
 
     return message.toString();
+=======
+      message.append("
!! Version "
+              + jalview.bin.Cache.getDefault("LATEST_VERSION",
+                      "..Checking..")
+              + " is available for download from "
+              + jalview.bin.Cache.getDefault("www.jalview.org",
+                      "https://www.jalview.org")
+              + " !!");
+      if (red)
+      {
+        message.append("