From: Ben Soares <bsoares@dundee.ac.uk>
Date: Wed, 8 May 2019 16:17:05 +0000 (+0100)
Subject: JAL-3247 JAL-3254 Automatically creating correct file association inserts for Info... 
X-Git-Tag: Release_2_11_0~12^2^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dc6ceea570e7a937da802708ab4d94f998e4760d;p=jalview.git

JAL-3247 JAL-3254 Automatically creating correct file association inserts for Info.plist and install4j installer
---

diff --git a/utils/install4j/auto_file_associations.pl b/utils/install4j/auto_file_associations.pl
index b46e274..69c07bf 100755
--- a/utils/install4j/auto_file_associations.pl
+++ b/utils/install4j/auto_file_associations.pl
@@ -5,6 +5,40 @@ use strict;
 my $fileformats = $ARGV[0];
 $fileformats = "./src/jalview/io/FileFormats.java" unless $fileformats;
 
+# default mimetype will be text/x-$shortname
+# TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
+# TODO: look up standard mime type used for BLASTfmt matrices, etc
+my $mimetypes = {
+  rnaml => "application/rnaml+xml",
+  biojson => "application/x-jalview-biojson+json",
+  jnet => "application/x-jalview-jnet+text",
+  features => "application/x-jalview-features+text",
+  scorematrix => "application/x-jalview-scorematrix+text",
+  pdb => "chemical/x-pdb",
+  mmcif => "chemical/x-cif",
+  mmcif2 => "chemical/x-mcif",
+  jalview => "application/x-jalview+xml+zip",
+  jvl => "application/x-jalview-jvl+text",
+  annotations => "application/x-jalview-annotations+text",
+};
+
+my @dontaddshortname = qw(features json);
+my @dontaddextension = qw(html xml json jar mfa fastq);
+my $add_associations = {
+  biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
+  gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
+  gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
+  features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
+  annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
+  mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
+  jvl => {shortname=>"jvl",name=>"Jalview Version Locator",extensions=>["jvl"],iconfile=>"Jalview-Version-Locator"},
+  jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
+  scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
+};
+my $add_extensions = {
+  blc => ["blc"],
+};
+
 my $mactemplatefile = "file_associations_template-Info_plist.xml";
 my $i4jtemplatefile = "file_associations_template-install4j.xml";
 my $mactemplate;
@@ -33,49 +67,87 @@ open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
 
 open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
 my $id = 10000;
+my $file_associations = {};
 while(my $line = <IN>) {
   $line =~ s/\s+/ /g;
   $line =~ s/(^ | $)//g;
   if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
     my $shortname = lc($1);
+    next if (grep($_ eq $shortname, @dontaddshortname));
     my $name = $2;
     my $extensions = $3;
     $extensions =~ s/\s+//g;
-    my @extensions = split(m/,/,$extensions);
-    #warn("LINE: $line\nFound extensions '".join("', '", @extensions)."' for $name Files ($shortname)'n");
-
-    my $macentry = $mactemplate;
-    my $i4jentry = $i4jtemplate;
-
-    $macentry =~ s/\$\$NAME\$\$/$name/g;
-    $macentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
-
-    $i4jentry =~ s/\$\$NAME\$\$/$name/g;
-    $i4jentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
-
-    while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
-      my $pre = $1;
-      my $post = $2;
-      my $macextensions;
-      for my $ext (@extensions) {
-        $macextensions .= $pre.$ext.$post;
-      }
-      $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
+    my @possextensions = split(m/,/,$extensions);
+    my @extensions;
+    my $addext = $add_extensions->{$shortname};
+    if (ref($addext) eq "ARRAY") {
+      push(@possextensions, @$addext);
+    }
+    for my $possext (@possextensions) {
+      next if grep($_ eq $possext, @extensions);
+      next if grep($_ eq $possext, @dontaddextension);
+      push(@extensions,$possext);
     }
-    print MA $macentry;
+    next unless scalar(@extensions);
+    $file_associations->{$shortname} = {
+      shortname => $shortname,
+      name => $name,
+      extensions => \@extensions
+    };
+  }
+}
+close(IN);
 
-    for my $ext (@extensions) {
-      my $i4jextentry = $i4jentry;
-      $i4jextentry =~ s/\$\$EXTENSION\$\$/$ext/g;
-      $i4jextentry =~ s/\$\$ID\$\$/$id/g;
-      $id++;
+my %all_associations = (%$file_associations, %$add_associations);
+
+for my $fa (sort keys %all_associations) {
+  my $shortname = $fa;
+  my $a = $all_associations{$fa};
+  my $name = $a->{name};
+  my $extensions = $a->{extensions};
+  my $mimetype = $mimetypes->{$shortname};
+  $mimetype = "text/x-$shortname" unless $mimetype;
+
+  my $iconfile = $a->{iconfile};
+  $iconfile = "Jalview-File" unless $iconfile;
 
-      print IA $i4jextentry;
+  my @extensions = @$extensions;
+  #warn("LINE: $line\nFound extensions '".join("', '", @extensions)."' for $name Files ($shortname)'n");
+
+  my $macentry = $mactemplate;
+  my $i4jentry = $i4jtemplate;
+
+  $macentry =~ s/\$\$NAME\$\$/$name/g;
+  $macentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
+  $macentry =~ s/\$\$MIMETYPE\$\$/$mimetype/g;
+  $macentry =~ s/\$\$ICONFILE\$\$/$iconfile/g;
+
+  $i4jentry =~ s/\$\$NAME\$\$/$name/g;
+  $i4jentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
+  $i4jentry =~ s/\$\$MIMETYPE\$\$/$mimetype/g;
+  $i4jentry =~ s/\$\$ICONFILE\$\$/$iconfile/g;
+
+  while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
+    my $pre = $1;
+    my $post = $2;
+    my $macextensions;
+    for my $ext (@extensions) {
+      $macextensions .= $pre.$ext.$post;
     }
+    $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
+  }
+  print MA $macentry;
+
+  for my $ext (@extensions) {
+    my $i4jextentry = $i4jentry;
+    $i4jextentry =~ s/\$\$EXTENSION\$\$/$ext/g;
+    $i4jextentry =~ s/\$\$ID\$\$/$id/g;
+    $id++;
 
+    print IA $i4jextentry;
   }
 }
-close(IN);
+
 close(IA);
 print MA "</array>\n";
 close(MA);
diff --git a/utils/install4j/file_associations_auto-Info_plist.xml b/utils/install4j/file_associations_auto-Info_plist.xml
index f799885..8be95e6 100644
--- a/utils/install4j/file_associations_auto-Info_plist.xml
+++ b/utils/install4j/file_associations_auto-Info_plist.xml
@@ -4,20 +4,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>fa</string>
-<string>fasta</string>
-<string>mfa</string>
-<string>fastq</string>
+<string>amsa</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>Fasta File</string>
+<string>AMSA File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-fasta</string>
+<string>text/x-amsa</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -26,17 +23,18 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>pfam</string>
+<string>annotations</string>
+<string>jvannotations</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>PFAM File</string>
+<string>Jalview Annotations File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-pfam</string>
+<string>application/x-jalview-annotations+text</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -45,18 +43,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>sto</string>
-<string>stk</string>
+<string>biojson</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>Stockholm File</string>
+<string>BioJSON File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-stockholm</string>
+<string>application/x-jalview-biojson+json</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -65,17 +62,18 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>pir</string>
+<string>BLC</string>
+<string>blc</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>PIR File</string>
+<string>BLC File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-pir</string>
+<string>text/x-blc</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -84,17 +82,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>BLC</string>
+<string>aln</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>BLC File</string>
+<string>Clustal File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-blc</string>
+<string>text/x-clustal</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -103,17 +101,18 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>amsa</string>
+<string>fa</string>
+<string>fasta</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>AMSA File</string>
+<string>Fasta File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-amsa</string>
+<string>text/x-fasta</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -122,17 +121,18 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>html</string>
+<string>features</string>
+<string>jvfeatures</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>HTML File</string>
+<string>Jalview Features File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-html</string>
+<string>application/x-jalview-features+text</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -141,18 +141,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>xml</string>
-<string>rnaml</string>
+<string>gff2</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>RNAML File</string>
+<string>Generic Features Format v2 File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-rnaml</string>
+<string>text/x-gff2</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -161,17 +160,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>json</string>
+<string>gff3</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>JSON File</string>
+<string>Generic Features Format v3 File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-json</string>
+<string>text/x-gff3</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -180,17 +179,95 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>pileup</string>
+<string>jvp</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>PileUp File</string>
+<string>Jalview File</string>
+<key>CFBundleTypeIconFile</key>
+<string>Jalview-File.icns</string>
+<key>CFBundleTypeRole</key>
+<string>Editor</string>
+<key>CFBundleTypeMIMETypes</key>
+<array>
+<string>application/x-jalview+xml+zip</string>
+</array>
+<key>LSIsAppleDefaultForType</key>
+<true/>
+</dict>
+
+<dict>
+<key>CFBundleTypeExtensions</key>
+<array>
+<string>concise</string>
+<string>jnet</string>
+</array>
+<key>CFBundleTypeName</key>
+<string>JnetFile File</string>
+<key>CFBundleTypeIconFile</key>
+<string>Jalview-File.icns</string>
+<key>CFBundleTypeRole</key>
+<string>Editor</string>
+<key>CFBundleTypeMIMETypes</key>
+<array>
+<string>application/x-jalview-jnet+text</string>
+</array>
+<key>LSIsAppleDefaultForType</key>
+<true/>
+</dict>
+
+<dict>
+<key>CFBundleTypeExtensions</key>
+<array>
+<string>jvl</string>
+</array>
+<key>CFBundleTypeName</key>
+<string>Jalview Version Locator File</string>
+<key>CFBundleTypeIconFile</key>
+<string>Jalview-Version-Locator.icns</string>
+<key>CFBundleTypeRole</key>
+<string>Editor</string>
+<key>CFBundleTypeMIMETypes</key>
+<array>
+<string>application/x-jalview-jvl+text</string>
+</array>
+<key>LSIsAppleDefaultForType</key>
+<true/>
+</dict>
+
+<dict>
+<key>CFBundleTypeExtensions</key>
+<array>
+<string>cif</string>
+</array>
+<key>CFBundleTypeName</key>
+<string>mmCIF File</string>
+<key>CFBundleTypeIconFile</key>
+<string>Jalview-File.icns</string>
+<key>CFBundleTypeRole</key>
+<string>Editor</string>
+<key>CFBundleTypeMIMETypes</key>
+<array>
+<string>chemical/x-cif</string>
+</array>
+<key>LSIsAppleDefaultForType</key>
+<true/>
+</dict>
+
+<dict>
+<key>CFBundleTypeExtensions</key>
+<array>
+<string>mcif</string>
+<string>mmcif</string>
+</array>
+<key>CFBundleTypeName</key>
+<string>mmCIF File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-pileup</string>
+<string>chemical/x-mcif</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -209,7 +286,7 @@
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-msf</string>
+<string>text/x-msf</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -218,17 +295,18 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>aln</string>
+<string>pdb</string>
+<string>ent</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>Clustal File</string>
+<string>PDB File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-clustal</string>
+<string>chemical/x-pdb</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -237,17 +315,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>phy</string>
+<string>pfam</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>PHYLIP File</string>
+<string>PFAM File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-phylip</string>
+<string>text/x-pfam</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -256,16 +334,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
+<string>phy</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>JnetFile File</string>
+<string>PHYLIP File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-jnet</string>
+<string>text/x-phylip</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -274,18 +353,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>gff2</string>
-<string>gff3</string>
+<string>pileup</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>GFF or Jalview features File</string>
+<string>PileUp File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-features</string>
+<string>text/x-pileup</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -294,16 +372,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
+<string>pir</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>Substitution matrix File</string>
+<string>PIR File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-scorematrix</string>
+<string>text/x-pir</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -312,18 +391,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>pdb</string>
-<string>ent</string>
+<string>rnaml</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>PDB File</string>
+<string>RNAML File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-pdb</string>
+<string>application/rnaml+xml</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -332,17 +410,17 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>cif</string>
+<string>mat</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>mmCIF File</string>
+<string>Substitution Matrix File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-mmcif</string>
+<string>application/x-jalview-scorematrix+text</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -351,18 +429,18 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>jvp</string>
-<string>jar</string>
+<string>sto</string>
+<string>stk</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>Jalview File</string>
+<string>Stockholm File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-jalview</string>
+<string>text/x-stockholm</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
diff --git a/utils/install4j/file_associations_auto-install4j.xml b/utils/install4j/file_associations_auto-install4j.xml
index d82eff3..c7b07ee 100644
--- a/utils/install4j/file_associations_auto-install4j.xml
+++ b/utils/install4j/file_associations_auto-install4j.xml
@@ -1,19 +1,19 @@
-              <action name="" id="10000" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .fa file association">
+              <action name="" id="10000" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .amsa file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Fasta File</string>
+                        <string>AMSA File</string>
                       </void>
                       <void property="extension">
-                        <string>fa</string>
+                        <string>amsa</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -24,7 +24,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -33,22 +33,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10001" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .fasta file association">
+              <action name="" id="10001" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .annotations file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Fasta File</string>
+                        <string>Jalview Annotations File</string>
                       </void>
                       <void property="extension">
-                        <string>fasta</string>
+                        <string>annotations</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -59,7 +59,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -68,22 +68,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10002" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .mfa file association">
+              <action name="" id="10002" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .jvannotations file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Fasta File</string>
+                        <string>Jalview Annotations File</string>
                       </void>
                       <void property="extension">
-                        <string>mfa</string>
+                        <string>jvannotations</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -94,7 +94,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -103,22 +103,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10003" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .fastq file association">
+              <action name="" id="10003" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .biojson file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Fasta File</string>
+                        <string>BioJSON File</string>
                       </void>
                       <void property="extension">
-                        <string>fastq</string>
+                        <string>biojson</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -129,7 +129,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -138,22 +138,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10004" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pfam file association">
+              <action name="" id="10004" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .BLC file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>PFAM File</string>
+                        <string>BLC File</string>
                       </void>
                       <void property="extension">
-                        <string>pfam</string>
+                        <string>BLC</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -164,7 +164,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -173,22 +173,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10005" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .sto file association">
+              <action name="" id="10005" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .blc file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Stockholm File</string>
+                        <string>BLC File</string>
                       </void>
                       <void property="extension">
-                        <string>sto</string>
+                        <string>blc</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -199,7 +199,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -208,22 +208,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10006" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .stk file association">
+              <action name="" id="10006" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .aln file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Stockholm File</string>
+                        <string>Clustal File</string>
                       </void>
                       <void property="extension">
-                        <string>stk</string>
+                        <string>aln</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -234,7 +234,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -243,22 +243,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10007" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pir file association">
+              <action name="" id="10007" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .fa file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>PIR File</string>
+                        <string>Fasta File</string>
                       </void>
                       <void property="extension">
-                        <string>pir</string>
+                        <string>fa</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -269,7 +269,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -278,22 +278,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10008" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .BLC file association">
+              <action name="" id="10008" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .fasta file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>BLC File</string>
+                        <string>Fasta File</string>
                       </void>
                       <void property="extension">
-                        <string>BLC</string>
+                        <string>fasta</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -304,7 +304,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -313,22 +313,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10009" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .amsa file association">
+              <action name="" id="10009" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .features file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>AMSA File</string>
+                        <string>Jalview Features File</string>
                       </void>
                       <void property="extension">
-                        <string>amsa</string>
+                        <string>features</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -339,7 +339,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -348,22 +348,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10010" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .html file association">
+              <action name="" id="10010" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .jvfeatures file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>HTML File</string>
+                        <string>Jalview Features File</string>
                       </void>
                       <void property="extension">
-                        <string>html</string>
+                        <string>jvfeatures</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -374,7 +374,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -383,22 +383,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10011" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .xml file association">
+              <action name="" id="10011" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .gff2 file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>RNAML File</string>
+                        <string>Generic Features Format v2 File</string>
                       </void>
                       <void property="extension">
-                        <string>xml</string>
+                        <string>gff2</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -409,7 +409,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -418,22 +418,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10012" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .rnaml file association">
+              <action name="" id="10012" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .gff3 file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>RNAML File</string>
+                        <string>Generic Features Format v3 File</string>
                       </void>
                       <void property="extension">
-                        <string>rnaml</string>
+                        <string>gff3</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -444,7 +444,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -453,22 +453,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10013" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .json file association">
+              <action name="" id="10013" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .jvp file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>JSON File</string>
+                        <string>Jalview File</string>
                       </void>
                       <void property="extension">
-                        <string>json</string>
+                        <string>jvp</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -479,7 +479,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -488,22 +488,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10014" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pileup file association">
+              <action name="" id="10014" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .concise file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>PileUp File</string>
+                        <string>JnetFile File</string>
                       </void>
                       <void property="extension">
-                        <string>pileup</string>
+                        <string>concise</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -514,7 +514,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -523,22 +523,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10015" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .msf file association">
+              <action name="" id="10015" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .jnet file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>MSF File</string>
+                        <string>JnetFile File</string>
                       </void>
                       <void property="extension">
-                        <string>msf</string>
+                        <string>jnet</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -549,7 +549,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -558,22 +558,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10016" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .aln file association">
+              <action name="" id="10016" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .jvl file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Clustal File</string>
+                        <string>Jalview Version Locator File</string>
                       </void>
                       <void property="extension">
-                        <string>aln</string>
+                        <string>jvl</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-Version-Locator.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -584,7 +584,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-Version-Locator.ico</string>
                         </object>
                       </void>
                     </object>
@@ -593,22 +593,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10017" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .phy file association">
+              <action name="" id="10017" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .cif file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>PHYLIP File</string>
+                        <string>mmCIF File</string>
                       </void>
                       <void property="extension">
-                        <string>phy</string>
+                        <string>cif</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -619,7 +619,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -628,22 +628,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10018" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .gff2 file association">
+              <action name="" id="10018" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .mcif file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>GFF or Jalview features File</string>
+                        <string>mmCIF File</string>
                       </void>
                       <void property="extension">
-                        <string>gff2</string>
+                        <string>mcif</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -654,7 +654,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -663,22 +663,57 @@
                 <condition />
               </action>
 
-              <action name="" id="10019" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .gff3 file association">
+              <action name="" id="10019" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .mmcif file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>GFF or Jalview features File</string>
+                        <string>mmCIF File</string>
                       </void>
                       <void property="extension">
-                        <string>gff3</string>
+                        <string>mmcif</string>
+                      </void>
+                      <void property="launcherId">
+                        <string>737</string>
+                      </void>
+                      <void property="macIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.icns</string>
+                        </object>
+                      </void>
+                      <void property="macRole">
+                        <object class="java.lang.Enum" method="valueOf">
+                          <class>com.install4j.runtime.beans.actions.desktop.MacAssociationRole</class>
+                          <string>EDITOR</string>
+                        </object>
+                      </void>
+                      <void property="windowsIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.ico</string>
+                        </object>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition />
+              </action>
+
+              <action name="" id="10020" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .msf file association">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
+                      <void property="description">
+                        <string>MSF File</string>
+                      </void>
+                      <void property="extension">
+                        <string>msf</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -689,7 +724,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -698,7 +733,7 @@
                 <condition />
               </action>
 
-              <action name="" id="10020" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pdb file association">
+              <action name="" id="10021" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pdb file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
@@ -713,7 +748,7 @@
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -724,7 +759,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -733,7 +768,7 @@
                 <condition />
               </action>
 
-              <action name="" id="10021" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .ent file association">
+              <action name="" id="10022" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .ent file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
@@ -748,7 +783,7 @@
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -759,7 +794,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -768,22 +803,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10022" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .cif file association">
+              <action name="" id="10023" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pfam file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>mmCIF File</string>
+                        <string>PFAM File</string>
                       </void>
                       <void property="extension">
-                        <string>cif</string>
+                        <string>pfam</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -794,7 +829,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -803,22 +838,22 @@
                 <condition />
               </action>
 
-              <action name="" id="10023" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .jvp file association">
+              <action name="" id="10024" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .phy file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Jalview File</string>
+                        <string>PHYLIP File</string>
                       </void>
                       <void property="extension">
-                        <string>jvp</string>
+                        <string>phy</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -829,7 +864,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
@@ -838,22 +873,197 @@
                 <condition />
               </action>
 
-              <action name="" id="10024" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .jar file association">
+              <action name="" id="10025" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pileup file association">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
                     <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
                       <void property="description">
-                        <string>Jalview File</string>
+                        <string>PileUp File</string>
                       </void>
                       <void property="extension">
-                        <string>jar</string>
+                        <string>pileup</string>
+                      </void>
+                      <void property="launcherId">
+                        <string>737</string>
+                      </void>
+                      <void property="macIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.icns</string>
+                        </object>
+                      </void>
+                      <void property="macRole">
+                        <object class="java.lang.Enum" method="valueOf">
+                          <class>com.install4j.runtime.beans.actions.desktop.MacAssociationRole</class>
+                          <string>EDITOR</string>
+                        </object>
+                      </void>
+                      <void property="windowsIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.ico</string>
+                        </object>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition />
+              </action>
+
+              <action name="" id="10026" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .pir file association">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
+                      <void property="description">
+                        <string>PIR File</string>
+                      </void>
+                      <void property="extension">
+                        <string>pir</string>
+                      </void>
+                      <void property="launcherId">
+                        <string>737</string>
+                      </void>
+                      <void property="macIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.icns</string>
+                        </object>
+                      </void>
+                      <void property="macRole">
+                        <object class="java.lang.Enum" method="valueOf">
+                          <class>com.install4j.runtime.beans.actions.desktop.MacAssociationRole</class>
+                          <string>EDITOR</string>
+                        </object>
+                      </void>
+                      <void property="windowsIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.ico</string>
+                        </object>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition />
+              </action>
+
+              <action name="" id="10027" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .rnaml file association">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
+                      <void property="description">
+                        <string>RNAML File</string>
+                      </void>
+                      <void property="extension">
+                        <string>rnaml</string>
+                      </void>
+                      <void property="launcherId">
+                        <string>737</string>
+                      </void>
+                      <void property="macIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.icns</string>
+                        </object>
+                      </void>
+                      <void property="macRole">
+                        <object class="java.lang.Enum" method="valueOf">
+                          <class>com.install4j.runtime.beans.actions.desktop.MacAssociationRole</class>
+                          <string>EDITOR</string>
+                        </object>
+                      </void>
+                      <void property="windowsIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.ico</string>
+                        </object>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition />
+              </action>
+
+              <action name="" id="10028" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .mat file association">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
+                      <void property="description">
+                        <string>Substitution Matrix File</string>
+                      </void>
+                      <void property="extension">
+                        <string>mat</string>
+                      </void>
+                      <void property="launcherId">
+                        <string>737</string>
+                      </void>
+                      <void property="macIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.icns</string>
+                        </object>
+                      </void>
+                      <void property="macRole">
+                        <object class="java.lang.Enum" method="valueOf">
+                          <class>com.install4j.runtime.beans.actions.desktop.MacAssociationRole</class>
+                          <string>EDITOR</string>
+                        </object>
+                      </void>
+                      <void property="windowsIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.ico</string>
+                        </object>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition />
+              </action>
+
+              <action name="" id="10029" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .sto file association">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
+                      <void property="description">
+                        <string>Stockholm File</string>
+                      </void>
+                      <void property="extension">
+                        <string>sto</string>
+                      </void>
+                      <void property="launcherId">
+                        <string>737</string>
+                      </void>
+                      <void property="macIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.icns</string>
+                        </object>
+                      </void>
+                      <void property="macRole">
+                        <object class="java.lang.Enum" method="valueOf">
+                          <class>com.install4j.runtime.beans.actions.desktop.MacAssociationRole</class>
+                          <string>EDITOR</string>
+                        </object>
+                      </void>
+                      <void property="windowsIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>Jalview-File.ico</string>
+                        </object>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition />
+              </action>
+
+              <action name="" id="10030" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make .stk file association">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction">
+                      <void property="description">
+                        <string>Stockholm File</string>
+                      </void>
+                      <void property="extension">
+                        <string>stk</string>
                       </void>
                       <void property="launcherId">
                         <string>737</string>
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>Jalview-File.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -864,7 +1074,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>Jalview-File.ico</string>
                         </object>
                       </void>
                     </object>
diff --git a/utils/install4j/file_associations_template-Info_plist.xml b/utils/install4j/file_associations_template-Info_plist.xml
index 66720a1..7fa4fed 100644
--- a/utils/install4j/file_associations_template-Info_plist.xml
+++ b/utils/install4j/file_associations_template-Info_plist.xml
@@ -6,12 +6,12 @@ $$</array>
 <key>CFBundleTypeName</key>
 <string>$$NAME$$ File</string>
 <key>CFBundleTypeIconFile</key>
-<string>Jalview-File.icns</string>
+<string>$$ICONFILE$$.icns</string>
 <key>CFBundleTypeRole</key>
 <string>Editor</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-$$SHORTNAME$$</string>
+<string>$$MIMETYPE$$</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
diff --git a/utils/install4j/file_associations_template-install4j.xml b/utils/install4j/file_associations_template-install4j.xml
index 96eff1e..697029a 100644
--- a/utils/install4j/file_associations_template-install4j.xml
+++ b/utils/install4j/file_associations_template-install4j.xml
@@ -13,7 +13,7 @@
                       </void>
                       <void property="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.icns</string>
+                          <string>$$ICONFILE$$.icns</string>
                         </object>
                       </void>
                       <void property="macRole">
@@ -24,7 +24,7 @@
                       </void>
                       <void property="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>./Jalview-File.ico</string>
+                          <string>$$ICONFILE$$.ico</string>
                         </object>
                       </void>
                     </object>