From eef1420d2850900eb882afe7189cec3ad0fd9813 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 13 May 2024 14:33:12 +0100
Subject: [PATCH] JAL-4409 Fix some file extensions (including remove .txt)

---
 utils/install4j/auto_file_associations-i4j10.pl    |    6 +-
 .../file_associations_auto-Info_plist.xml          |   22 ++--
 .../file_associations_auto-install4j10.xml         |  138 ++++++++++----------
 utils/install4j/install4j10_template.install4j     |   12 ++
 4 files changed, 96 insertions(+), 82 deletions(-)

diff --git a/utils/install4j/auto_file_associations-i4j10.pl b/utils/install4j/auto_file_associations-i4j10.pl
index f7e17a1..96aee95 100755
--- a/utils/install4j/auto_file_associations-i4j10.pl
+++ b/utils/install4j/auto_file_associations-i4j10.pl
@@ -30,7 +30,9 @@ my $mimetypes = {
 };
 
 my @dontaddshortname = qw(features json);
-my @dontaddextension = qw(html xml json jar mfa fastq);
+# mfa and fastq not properly supported in Jalview (but enough to be in the application extensions)
+# ENA flatfile extension txt is too generic, as well as html xml json jar
+my @dontaddextension = qw(txt 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"]},
@@ -49,7 +51,7 @@ my $add_extensions = {
 my @put_first = qw(jalview jvl);
 my @owner = @put_first;
 
-my @non_primary = qw(mmcif mmcif2 pdb);
+my @non_primary = qw(mmcif mmcif2 pdb txt);
 
 my $v = ($i4jversion >= 8)?$i4jversion:"";
 my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
diff --git a/utils/install4j/file_associations_auto-Info_plist.xml b/utils/install4j/file_associations_auto-Info_plist.xml
index 2e23321..1a75139 100644
--- a/utils/install4j/file_associations_auto-Info_plist.xml
+++ b/utils/install4j/file_associations_auto-Info_plist.xml
@@ -217,10 +217,11 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>txt</string>
+<string>fa</string>
+<string>fasta</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>ENA Flatfile File</string>
+<string>Fasta File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
@@ -229,7 +230,7 @@
 <string>Default</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-embl+txt</string>
+<string>application/x-fasta+txt</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -238,11 +239,11 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>fa</string>
-<string>fasta</string>
+<string>features</string>
+<string>jvfeatures</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>Fasta File</string>
+<string>Jalview Features File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
@@ -251,7 +252,7 @@
 <string>Default</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-fasta+txt</string>
+<string>application/x-jalview-features+text</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
@@ -260,11 +261,10 @@
 <dict>
 <key>CFBundleTypeExtensions</key>
 <array>
-<string>features</string>
-<string>jvfeatures</string>
+<string>fc</string>
 </array>
 <key>CFBundleTypeName</key>
-<string>Jalview Features File</string>
+<string>Jalview Feature Settings File File</string>
 <key>CFBundleTypeIconFile</key>
 <string>Jalview-File.icns</string>
 <key>CFBundleTypeRole</key>
@@ -273,7 +273,7 @@
 <string>Default</string>
 <key>CFBundleTypeMIMETypes</key>
 <array>
-<string>application/x-jalview-features+text</string>
+<string>application/x-featuresettings+txt</string>
 </array>
 <key>LSIsAppleDefaultForType</key>
 <true/>
diff --git a/utils/install4j/file_associations_auto-install4j10.xml b/utils/install4j/file_associations_auto-install4j10.xml
index ee70251..4a87364 100644
--- a/utils/install4j/file_associations_auto-install4j10.xml
+++ b/utils/install4j/file_associations_auto-install4j10.xml
@@ -53,9 +53,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="Jalview Launch (.jvl) progress bar 4" id="10004" customizedId="Jalview Launch-jvl-10004-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Jalview Launch (.jvl) progress bar 3" id="10004" customizedId="Jalview Launch-jvl-10004-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="4" />
+                      <property name="percentValue" type="int" value="3" />
                     </serializedBean>
                   </action>
 
@@ -98,9 +98,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="CIF (.cif) progress bar 8" id="10007" customizedId="CIF-cif-10007-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="CIF (.cif) progress bar 7" id="10007" customizedId="CIF-cif-10007-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="8" />
+                      <property name="percentValue" type="int" value="7" />
                     </serializedBean>
                   </action>
 
@@ -143,9 +143,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="mmCIF (.mcif, .mmcif) progress bar 12" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="mmCIF (.mcif, .mmcif) progress bar 11" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="12" />
+                      <property name="percentValue" type="int" value="11" />
                     </serializedBean>
                   </action>
 
@@ -188,9 +188,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="PDB (.ent, .pdb) progress bar 16" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="PDB (.ent, .pdb) progress bar 15" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="16" />
+                      <property name="percentValue" type="int" value="15" />
                     </serializedBean>
                   </action>
 
@@ -233,9 +233,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="AMSA (.amsa) progress bar 20" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="AMSA (.amsa) progress bar 19" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="20" />
+                      <property name="percentValue" type="int" value="19" />
                     </serializedBean>
                   </action>
 
@@ -278,9 +278,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 24" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 23" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="24" />
+                      <property name="percentValue" type="int" value="23" />
                     </serializedBean>
                   </action>
 
@@ -323,9 +323,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="BioJSON (.biojson) progress bar 28" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="BioJSON (.biojson) progress bar 26" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="28" />
+                      <property name="percentValue" type="int" value="26" />
                     </serializedBean>
                   </action>
 
@@ -368,9 +368,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="BLC (.blc) progress bar 32" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="BLC (.blc) progress bar 30" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="32" />
+                      <property name="percentValue" type="int" value="30" />
                     </serializedBean>
                   </action>
 
@@ -413,9 +413,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="Clustal (.aln) progress bar 36" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Clustal (.aln) progress bar 34" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="36" />
+                      <property name="percentValue" type="int" value="34" />
                     </serializedBean>
                   </action>
 
@@ -448,26 +448,26 @@
                   </action>
 <!-- END -->
 
-<!-- ENA Flatfile (.txt) BEGIN -->
-                  <action name="ENA Flatfile (.txt) message" id="10030" customizedId="ENA Flatfile-txt-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+<!-- Fasta (.fa, .fasta) BEGIN -->
+                  <action name="Fasta (.fa, .fasta) message" id="10030" customizedId="Fasta-fa,fasta-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="detailMessage" type="string">ENA Flatfile (.txt)</property>
+                      <property name="detailMessage" type="string">Fasta (.fa, .fasta)</property>
                       <property name="statusMessage" type="string">Creating file associations...</property>
                       <property name="useDetail" type="boolean" value="true" />
                       <property name="useStatus" type="boolean" value="true" />
                     </serializedBean>
                   </action>
 
-                  <action name="ENA Flatfile (.txt) progress bar 40" id="10031" customizedId="ENA Flatfile-txt-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Fasta (.fa, .fasta) progress bar 38" id="10031" customizedId="Fasta-fa,fasta-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="40" />
+                      <property name="percentValue" type="int" value="38" />
                     </serializedBean>
                   </action>
 
-                  <action name="ENA Flatfile (.txt) file association" id="10032" customizedId="ENA Flatfile-txt-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .txt file association">
+                  <action name="Fasta (.fa, .fasta) file association" id="10032" customizedId="Fasta-fa,fasta-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
                     <serializedBean>
-                      <property name="description" type="string">ENA Flatfile File</property>
-                      <property name="extension" type="string">txt</property>
+                      <property name="description" type="string">Fasta File</property>
+                      <property name="extension" type="string">fa,fasta</property>
                       <property name="launcherId" type="string">JALVIEW</property>
                       <!--<property name="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
@@ -483,7 +483,7 @@
                           <string>Jalview-File.png</string>
                         </object>
                       </property>
-                      <property name="unixMimeType" type="string">application/x-embl+txt</property>
+                      <property name="unixMimeType" type="string">application/x-fasta+txt</property>
                       <property name="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
                           <string>Jalview-File.ico</string>
@@ -493,26 +493,26 @@
                   </action>
 <!-- END -->
 
-<!-- Fasta (.fa, .fasta) BEGIN -->
-                  <action name="Fasta (.fa, .fasta) message" id="10033" customizedId="Fasta-fa,fasta-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+<!-- Jalview Features (.features, .jvfeatures) BEGIN -->
+                  <action name="Jalview Features (.features, .jvfeatures) message" id="10033" customizedId="Jalview Features-features,jvfeatures-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="detailMessage" type="string">Fasta (.fa, .fasta)</property>
+                      <property name="detailMessage" type="string">Jalview Features (.features, .jvfeatures)</property>
                       <property name="statusMessage" type="string">Creating file associations...</property>
                       <property name="useDetail" type="boolean" value="true" />
                       <property name="useStatus" type="boolean" value="true" />
                     </serializedBean>
                   </action>
 
-                  <action name="Fasta (.fa, .fasta) progress bar 44" id="10034" customizedId="Fasta-fa,fasta-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Jalview Features (.features, .jvfeatures) progress bar 42" id="10034" customizedId="Jalview Features-features,jvfeatures-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="44" />
+                      <property name="percentValue" type="int" value="42" />
                     </serializedBean>
                   </action>
 
-                  <action name="Fasta (.fa, .fasta) file association" id="10035" customizedId="Fasta-fa,fasta-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
+                  <action name="Jalview Features (.features, .jvfeatures) file association" id="10035" customizedId="Jalview Features-features,jvfeatures-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
                     <serializedBean>
-                      <property name="description" type="string">Fasta File</property>
-                      <property name="extension" type="string">fa,fasta</property>
+                      <property name="description" type="string">Jalview Features File</property>
+                      <property name="extension" type="string">features,jvfeatures</property>
                       <property name="launcherId" type="string">JALVIEW</property>
                       <!--<property name="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
@@ -528,7 +528,7 @@
                           <string>Jalview-File.png</string>
                         </object>
                       </property>
-                      <property name="unixMimeType" type="string">application/x-fasta+txt</property>
+                      <property name="unixMimeType" type="string">application/x-jalview-features+text</property>
                       <property name="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
                           <string>Jalview-File.ico</string>
@@ -538,26 +538,26 @@
                   </action>
 <!-- END -->
 
-<!-- Jalview Features (.features, .jvfeatures) BEGIN -->
-                  <action name="Jalview Features (.features, .jvfeatures) message" id="10036" customizedId="Jalview Features-features,jvfeatures-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+<!-- Jalview Feature Settings File (.fc) BEGIN -->
+                  <action name="Jalview Feature Settings File (.fc) message" id="10036" customizedId="Jalview Feature Settings File-fc-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="detailMessage" type="string">Jalview Features (.features, .jvfeatures)</property>
+                      <property name="detailMessage" type="string">Jalview Feature Settings File (.fc)</property>
                       <property name="statusMessage" type="string">Creating file associations...</property>
                       <property name="useDetail" type="boolean" value="true" />
                       <property name="useStatus" type="boolean" value="true" />
                     </serializedBean>
                   </action>
 
-                  <action name="Jalview Features (.features, .jvfeatures) progress bar 48" id="10037" customizedId="Jalview Features-features,jvfeatures-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Jalview Feature Settings File (.fc) progress bar 46" id="10037" customizedId="Jalview Feature Settings File-fc-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="48" />
+                      <property name="percentValue" type="int" value="46" />
                     </serializedBean>
                   </action>
 
-                  <action name="Jalview Features (.features, .jvfeatures) file association" id="10038" customizedId="Jalview Features-features,jvfeatures-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
+                  <action name="Jalview Feature Settings File (.fc) file association" id="10038" customizedId="Jalview Feature Settings File-fc-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fc file association">
                     <serializedBean>
-                      <property name="description" type="string">Jalview Features File</property>
-                      <property name="extension" type="string">features,jvfeatures</property>
+                      <property name="description" type="string">Jalview Feature Settings File File</property>
+                      <property name="extension" type="string">fc</property>
                       <property name="launcherId" type="string">JALVIEW</property>
                       <!--<property name="macIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
@@ -573,7 +573,7 @@
                           <string>Jalview-File.png</string>
                         </object>
                       </property>
-                      <property name="unixMimeType" type="string">application/x-jalview-features+text</property>
+                      <property name="unixMimeType" type="string">application/x-featuresettings+txt</property>
                       <property name="windowsIconFile">
                         <object class="com.install4j.api.beans.ExternalFile">
                           <string>Jalview-File.ico</string>
@@ -593,9 +593,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="GenBank Flatfile (.gb, .gbk) progress bar 52" id="10040" customizedId="GenBank Flatfile-gb,gbk-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="GenBank Flatfile (.gb, .gbk) progress bar 50" id="10040" customizedId="GenBank Flatfile-gb,gbk-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="52" />
+                      <property name="percentValue" type="int" value="50" />
                     </serializedBean>
                   </action>
 
@@ -638,9 +638,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="Generic Features Format v2 (.gff2) progress bar 56" id="10043" customizedId="Generic Features Format v2-gff2-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Generic Features Format v2 (.gff2) progress bar 53" id="10043" customizedId="Generic Features Format v2-gff2-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="56" />
+                      <property name="percentValue" type="int" value="53" />
                     </serializedBean>
                   </action>
 
@@ -683,9 +683,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="Generic Features Format v3 (.gff3) progress bar 60" id="10046" customizedId="Generic Features Format v3-gff3-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Generic Features Format v3 (.gff3) progress bar 57" id="10046" customizedId="Generic Features Format v3-gff3-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="60" />
+                      <property name="percentValue" type="int" value="57" />
                     </serializedBean>
                   </action>
 
@@ -728,9 +728,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="JnetFile (.concise, .jnet) progress bar 64" id="10049" customizedId="JnetFile-concise,jnet-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="JnetFile (.concise, .jnet) progress bar 61" id="10049" customizedId="JnetFile-concise,jnet-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="64" />
+                      <property name="percentValue" type="int" value="61" />
                     </serializedBean>
                   </action>
 
@@ -773,9 +773,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="MSF (.msf) progress bar 68" id="10052" customizedId="MSF-msf-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="MSF (.msf) progress bar 65" id="10052" customizedId="MSF-msf-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="68" />
+                      <property name="percentValue" type="int" value="65" />
                     </serializedBean>
                   </action>
 
@@ -818,9 +818,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="PFAM (.pfam) progress bar 72" id="10055" customizedId="PFAM-pfam-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="PFAM (.pfam) progress bar 69" id="10055" customizedId="PFAM-pfam-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="72" />
+                      <property name="percentValue" type="int" value="69" />
                     </serializedBean>
                   </action>
 
@@ -863,9 +863,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="PHYLIP (.phy) progress bar 76" id="10058" customizedId="PHYLIP-phy-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="PHYLIP (.phy) progress bar 73" id="10058" customizedId="PHYLIP-phy-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="76" />
+                      <property name="percentValue" type="int" value="73" />
                     </serializedBean>
                   </action>
 
@@ -908,9 +908,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="PileUp (.pileup) progress bar 80" id="10061" customizedId="PileUp-pileup-10061-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="PileUp (.pileup) progress bar 76" id="10061" customizedId="PileUp-pileup-10061-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="80" />
+                      <property name="percentValue" type="int" value="76" />
                     </serializedBean>
                   </action>
 
@@ -953,9 +953,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="PIR (.pir) progress bar 84" id="10064" customizedId="PIR-pir-10064-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="PIR (.pir) progress bar 80" id="10064" customizedId="PIR-pir-10064-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="84" />
+                      <property name="percentValue" type="int" value="80" />
                     </serializedBean>
                   </action>
 
@@ -998,9 +998,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="RNAML (.rnaml) progress bar 88" id="10067" customizedId="RNAML-rnaml-10067-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="RNAML (.rnaml) progress bar 84" id="10067" customizedId="RNAML-rnaml-10067-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="88" />
+                      <property name="percentValue" type="int" value="84" />
                     </serializedBean>
                   </action>
 
@@ -1043,9 +1043,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="Substitution Matrix (.mat) progress bar 92" id="10070" customizedId="Substitution Matrix-mat-10070-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Substitution Matrix (.mat) progress bar 88" id="10070" customizedId="Substitution Matrix-mat-10070-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="92" />
+                      <property name="percentValue" type="int" value="88" />
                     </serializedBean>
                   </action>
 
@@ -1088,9 +1088,9 @@
                     </serializedBean>
                   </action>
 
-                  <action name="Stockholm (.stk, .sto) progress bar 96" id="10073" customizedId="Stockholm-stk,sto-10073-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+                  <action name="Stockholm (.stk, .sto) progress bar 92" id="10073" customizedId="Stockholm-stk,sto-10073-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
                     <serializedBean>
-                      <property name="percentValue" type="int" value="96" />
+                      <property name="percentValue" type="int" value="92" />
                     </serializedBean>
                   </action>
 
diff --git a/utils/install4j/install4j10_template.install4j b/utils/install4j/install4j10_template.install4j
index bf57307..53b5b27 100644
--- a/utils/install4j/install4j10_template.install4j
+++ b/utils/install4j/install4j10_template.install4j
@@ -62,6 +62,8 @@
       <variable name="BACKGROUND" value="utils/channels/release/images/jalview_logo_background_fade-640x480.png" />
       <variable name="BATCH_WRAPPER_SCRIPT" value="jalview.bat" />
       <variable name="POWERSHELL_WRAPPER_SCRIPT" value="jalview.ps1" />
+      <variable name="WIZARD_WIDTH" value="640" description="Default/initial width of installer wizard window.  Linux media types adapt this.&#xA;NOT USED" />
+      <variable name="WIZARD_HEIGHT" value="480" description="Default/initial width of installer wizard window.  Linux media types adapt this.&#xA;NOT USED" />
     </variables>
     <codeSigning macEnabled="true" macPkcs12File="${compiler:OSX_KEYSTORE}" macNotarize="true" appleId="${compiler:OSX_APPLEID}">
       <macAdditionalBinaries>
@@ -162,6 +164,8 @@
     <applications>
       <application id="installer" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" styleId="35" customIcnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customIcoFile="${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}">
         <serializedBean>
+          <property name="frameHeight" type="int" value="480" />
+          <property name="frameWidth" type="int" value="640" />
           <property name="useCustomIcon" type="boolean" value="true" />
         </serializedBean>
         <styleOverrides>
@@ -1534,6 +1538,10 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.</property>
         <entry filesetId="2801" />
         <entry filesetId="2803" />
       </exclude>
+      <variables>
+        <variable name="variable" value="720" />
+        <variable name="WIZARD_HEIGHT" value="540" />
+      </variables>
       <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
     </unixInstaller>
     <unixInstaller name="Linux aarch64 Shell Installer" id="2782" customizedId="LINUX-AARCH64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-aarch64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
@@ -1545,6 +1553,10 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.</property>
         <entry filesetId="2801" />
         <entry filesetId="2803" />
       </exclude>
+      <variables>
+        <variable name="variable" value="720" />
+        <variable name="WIZARD_HEIGHT" value="540" />
+      </variables>
       <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_AARCH64_JAVA_VM_TGZ}" manualJreEntry="true" />
     </unixInstaller>
     <unixArchive name="Unix .tar.gz Archive" id="1596" customizedId="UNIX--TGZ" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}">
-- 
1.7.10.2