From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 5 Feb 2021 17:24:58 +0000 (+0000)
Subject: Merge branch 'releases/Release_2_11_1_4_debianpatches' into task/JAL-3521_Slimmed_dow... 
X-Git-Tag: Release_2_11_1_4~9^2~9^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=92e5bdb7399d549344f32bd16d87ab489ce19712;hp=3d08653a0dec6b8ce7adb3308cb58faa73c0f466

Merge branch 'releases/Release_2_11_1_4_debianpatches' into task/JAL-3521_Slimmed_down_build.gradle_for_debian
---

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 600d19c..579b490 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -167,6 +167,8 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</li>
  * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
  * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
  * warning dialog box is displayed.</li>
@@ -194,7 +196,13 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
  * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
  * </li>
- * 
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
  * </ul>
  * Deprecated settings:
  * <ul>
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3a238bb..19de95e 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -375,12 +375,17 @@ public class Jalview
         System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
 
-      if (!aparser.contains("nonews"))
+      if (!aparser.contains("nonews")
+              || Cache.getProperty("NONEWS") == null)
       {
         desktop.checkForNews();
       }
 
-      BioJsHTMLOutput.updateBioJS();
+      if (!aparser.contains("nohtmltemplates")
+              || Cache.getProperty("NOHTMLTEMPLATES") == null)
+      {
+        BioJsHTMLOutput.updateBioJS();
+      }
     }
 
     // Move any new getdown-launcher-new.jar into place over old
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b1efed6..9013416 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4174,9 +4174,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   webService.add(me.webServiceNoServices);
                 }
                 // TODO: move into separate menu builder class.
-                boolean new_sspred = false;
-                if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
+                  // logic for 2.11.1.4 is
+                  // always look to see if there is a discover. if there isn't
+                  // we can't show any Jws2 services
+                  // if there are services available, show them - regardless of
+                  // the 'show JWS2 preference'
+                  // if the discoverer is running then say so
+                  // otherwise offer to trigger discovery if 'show JWS2' is not
+                  // enabled
                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
                   if (jws2servs != null)
                   {
@@ -4193,8 +4199,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           }
                         }
                       }
-
                     }
+
                     if (jws2servs.isRunning())
                     {
                       JMenuItem tm = new JMenuItem(
@@ -4202,6 +4208,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       tm.setEnabled(false);
                       webService.add(tm);
                     }
+                    else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
+                    {
+                      JMenuItem enableJws2 = new JMenuItem(
+                              "Discover Web Services");
+                      enableJws2.setToolTipText(
+                              "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
+                      enableJws2.setEnabled(true);
+                      enableJws2.addActionListener(new ActionListener()
+                      {
+
+                        @Override
+                        public void actionPerformed(ActionEvent e)
+                        {
+                          // start service discoverer, but ignore preference
+                          Desktop.instance.startServiceDiscovery(false,
+                                  true);
+                        }
+                      });
+                      webService.add(enableJws2);
+                    }
                   }
                 }
                 build_urlServiceMenu(me.webService);
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index c43c699..1807764 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -272,13 +272,16 @@ public class BlogReader extends JPanel
 
     initItems(chan);
     updating = false;
-    boolean setvisible = checkForNew(chan, true);
-
-    if (setvisible)
+    if (!Cache.getDefault("NONEWS", false))
     {
+      boolean setvisible = checkForNew(chan, true);
+
+      if (setvisible)
+      {
 
-      Cache.log.debug("Will show jalview news automatically");
-      showNews();
+        Cache.log.debug("Will show jalview news automatically");
+        showNews();
+      }
     }
     Cache.log.debug("Completed construction of reader.");
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 0441e5e..21a0e37 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -559,26 +559,27 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public void getIdentifiersOrgData()
   {
-    // Thread off the identifiers fetcher
-    new Thread(new Runnable()
-    {
-      @Override
-      public void run()
+    if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+    {// Thread off the identifiers fetcher
+      new Thread(new Runnable()
       {
-        Cache.log.debug("Downloading data from identifiers.org");
-        UrlDownloadClient client = new UrlDownloadClient();
-        try
-        {
-          client.download(IdOrgSettings.getUrl(),
-                  IdOrgSettings.getDownloadLocation());
-        } catch (IOException e)
+        @Override
+        public void run()
         {
-          Cache.log.debug("Exception downloading identifiers.org data"
-                  + e.getMessage());
+          Cache.log.debug("Downloading data from identifiers.org");
+          try
+          {
+            UrlDownloadClient.download(IdOrgSettings.getUrl(),
+                    IdOrgSettings.getDownloadLocation());
+          } catch (IOException e)
+          {
+            Cache.log.debug("Exception downloading identifiers.org data"
+                    + e.getMessage());
+          }
         }
-      }
-    }).start();
-    ;
+      }).start();
+      ;
+    }
   }
 
   @Override
@@ -2571,13 +2572,36 @@ public class Desktop extends jalview.jbgui.GDesktop
     this.inBatchMode = inBatchMode;
   }
 
+  /**
+   * start service discovery and wait till it is done
+   */
   public void startServiceDiscovery()
   {
     startServiceDiscovery(false);
   }
 
+  /**
+   * start service discovery threads - blocking or non-blocking
+   * 
+   * @param blocking
+   */
   public void startServiceDiscovery(boolean blocking)
   {
+    startServiceDiscovery(blocking,false);
+  }
+
+  /**
+   * start service discovery threads
+   * 
+   * @param blocking
+   *          - false means call returns immediately
+   * @param ignore_SHOW_JWS2_SERVICES_preference
+   *          - when true JABA services are discovered regardless of user's JWS2
+   *          discovery preference setting
+   */
+  public void startServiceDiscovery(boolean blocking,
+          boolean ignore_SHOW_JWS2_SERVICES_preference)
+  {
     boolean alive = true;
     Thread t0 = null, t1 = null, t2 = null;
     // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
@@ -2595,7 +2619,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       (t0 = new Thread(discoverer)).start();
     }
 
-    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    if (ignore_SHOW_JWS2_SERVICES_preference
+            || Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
               .startDiscoverer(changeSupport);
diff --git a/src/jalview/ws/utils/UrlDownloadClient.java b/src/jalview/ws/utils/UrlDownloadClient.java
index 448edd9..e42c21e 100644
--- a/src/jalview/ws/utils/UrlDownloadClient.java
+++ b/src/jalview/ws/utils/UrlDownloadClient.java
@@ -33,11 +33,6 @@ import java.nio.file.StandardCopyOption;
 
 public class UrlDownloadClient
 {
-  public UrlDownloadClient()
-  {
-
-  }
-
   /**
    * Download and save a file from a URL
    * 
diff --git a/utils/debian/debian/jalview-file.png b/utils/debian/debian/jalview-file.png
new file mode 100644
index 0000000..1d98699
Binary files /dev/null and b/utils/debian/debian/jalview-file.png differ
diff --git a/utils/debian/debian/jalview-icon.png b/utils/debian/debian/jalview-icon.png
new file mode 100644
index 0000000..340f8e5
Binary files /dev/null and b/utils/debian/debian/jalview-icon.png differ
diff --git a/utils/debian/debian/jalview-mailcap b/utils/debian/debian/jalview-mailcap
new file mode 100644
index 0000000..5be7ab9
--- /dev/null
+++ b/utils/debian/debian/jalview-mailcap
@@ -0,0 +1,22 @@
+application/x-jalview+xml+zip; jalview -open '%s'; description="Jalview File"; nametemplate=%s.jvp; test=test -n "$DISPLAY"; priority=10
+chemical/x-cif; jalview -open '%s'; description="CIF File"; nametemplate=%s.cif; test=test -n "$DISPLAY"; priority=4
+chemical/x-mmcif; jalview -open '%s'; description="mmCIF File"; nametemplate=%s.mcif; test=test -n "$DISPLAY"; priority=4
+chemical/x-pdb; jalview -open '%s'; description="PDB File"; nametemplate=%s.pdb; test=test -n "$DISPLAY"; priority=4
+application/x-amsa+txt; jalview -open '%s'; description="AMSA File"; nametemplate=%s.amsa; test=test -n "$DISPLAY"; priority=9
+application/x-jalview-annotations+text; jalview -open '%s'; description="Jalview Annotations File"; nametemplate=%s.annotations; test=test -n "$DISPLAY"; priority=10
+application/x-jalview-biojson+json; jalview -open '%s'; description="BioJSON File"; nametemplate=%s.biojson; test=test -n "$DISPLAY"; priority=10
+application/x-blc+txt; jalview -open '%s'; description="BLC File"; nametemplate=%s.blc; test=test -n "$DISPLAY"; priority=9
+application/x-clustal+txt; jalview -open '%s'; description="Clustal File"; nametemplate=%s.aln; test=test -n "$DISPLAY"; priority=9
+application/x-fasta+txt; jalview -open '%s'; description="Fasta File"; nametemplate=%s.fa; test=test -n "$DISPLAY"; priority=9
+application/x-jalview-features+text; jalview -open '%s'; description="Jalview Features File"; nametemplate=%s.features; test=test -n "$DISPLAY"; priority=10
+application/x-gff2+txt; jalview -open '%s'; description="Generic Features Format v2 File"; nametemplate=%s.gff2; test=test -n "$DISPLAY"; priority=9
+application/x-gff3+txt; jalview -open '%s'; description="Generic Features Format v3 File"; nametemplate=%s.gff3; test=test -n "$DISPLAY"; priority=9
+application/x-jalview-jnet+text; jalview -open '%s'; description="JnetFile File"; nametemplate=%s.concise; test=test -n "$DISPLAY"; priority=10
+application/x-msf+txt; jalview -open '%s'; description="MSF File"; nametemplate=%s.msf; test=test -n "$DISPLAY"; priority=9
+application/x-pfam+txt; jalview -open '%s'; description="PFAM File"; nametemplate=%s.pfam; test=test -n "$DISPLAY"; priority=9
+application/x-phylip+txt; jalview -open '%s'; description="PHYLIP File"; nametemplate=%s.phy; test=test -n "$DISPLAY"; priority=9
+application/x-pileup+txt; jalview -open '%s'; description="PileUp File"; nametemplate=%s.pileup; test=test -n "$DISPLAY"; priority=9
+application/x-pir+txt; jalview -open '%s'; description="PIR File"; nametemplate=%s.pir; test=test -n "$DISPLAY"; priority=9
+application/rnaml+xml; jalview -open '%s'; description="RNAML File"; nametemplate=%s.rnaml; test=test -n "$DISPLAY"; priority=9
+application/x-jalview-scorematrix+text; jalview -open '%s'; description="Substitution Matrix File"; nametemplate=%s.mat; test=test -n "$DISPLAY"; priority=10
+application/x-stockholm+txt; jalview -open '%s'; description="Stockholm File"; nametemplate=%s.sto; test=test -n "$DISPLAY"; priority=9
diff --git a/utils/debian/debian/jalview-mime.xml b/utils/debian/debian/jalview-mime.xml
new file mode 100644
index 0000000..181fbed
--- /dev/null
+++ b/utils/debian/debian/jalview-mime.xml
@@ -0,0 +1,143 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
+
+  <mime-type type="application/x-jalview+xml+zip">
+    <comment>Jalview File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.jvp" weight="100"/>
+  </mime-type>
+
+  <mime-type type="chemical/x-cif">
+    <comment>CIF File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.cif" weight="40"/>
+  </mime-type>
+
+  <mime-type type="chemical/x-mmcif">
+    <comment>mmCIF File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.mcif" weight="40"/>
+    <glob pattern="*.mmcif" weight="40"/>
+  </mime-type>
+
+  <mime-type type="chemical/x-pdb">
+    <comment>PDB File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.pdb" weight="40"/>
+    <glob pattern="*.ent" weight="40"/>
+  </mime-type>
+
+  <mime-type type="application/x-amsa+txt">
+    <comment>AMSA File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.amsa" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-jalview-annotations+text">
+    <comment>Jalview Annotations File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.annotations" weight="100"/>
+    <glob pattern="*.jvannotations" weight="100"/>
+  </mime-type>
+
+  <mime-type type="application/x-jalview-biojson+json">
+    <comment>BioJSON File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.biojson" weight="100"/>
+  </mime-type>
+
+  <mime-type type="application/x-blc+txt">
+    <comment>BLC File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.blc" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-clustal+txt">
+    <comment>Clustal File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.aln" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-fasta+txt">
+    <comment>Fasta File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.fa" weight="90"/>
+    <glob pattern="*.fasta" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-jalview-features+text">
+    <comment>Jalview Features File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.features" weight="100"/>
+    <glob pattern="*.jvfeatures" weight="100"/>
+  </mime-type>
+
+  <mime-type type="application/x-gff2+txt">
+    <comment>Generic Features Format v2 File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.gff2" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-gff3+txt">
+    <comment>Generic Features Format v3 File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.gff3" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-jalview-jnet+text">
+    <comment>JnetFile File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.concise" weight="100"/>
+    <glob pattern="*.jnet" weight="100"/>
+  </mime-type>
+
+  <mime-type type="application/x-msf+txt">
+    <comment>MSF File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.msf" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-pfam+txt">
+    <comment>PFAM File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.pfam" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-phylip+txt">
+    <comment>PHYLIP File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.phy" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-pileup+txt">
+    <comment>PileUp File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.pileup" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-pir+txt">
+    <comment>PIR File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.pir" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/rnaml+xml">
+    <comment>RNAML File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.rnaml" weight="90"/>
+  </mime-type>
+
+  <mime-type type="application/x-jalview-scorematrix+text">
+    <comment>Substitution Matrix File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.mat" weight="100"/>
+  </mime-type>
+
+  <mime-type type="application/x-stockholm+txt">
+    <comment>Stockholm File</comment>
+    <icon name="jalview-file"/>
+    <glob pattern="*.sto" weight="90"/>
+    <glob pattern="*.stk" weight="90"/>
+  </mime-type>
+
+</mime-info>
diff --git a/utils/debian/debian/jalview.desktop b/utils/debian/debian/jalview.desktop
new file mode 100644
index 0000000..d4cc896
--- /dev/null
+++ b/utils/debian/debian/jalview.desktop
@@ -0,0 +1,13 @@
+[Desktop Entry]
+Version=1.1
+Type=Application
+Name=Jalview
+Comment=Multiple Sequence Alignment Editor
+Icon=jalview-icon
+Type=Application
+TryExec=jalview
+Exec=jalview -open %u
+Terminal=false
+Categories=Science;Biology;
+Keywords=alignment;sequence;
+MimeType=application/x-jalview+xml+zip;chemical/x-cif;chemical/x-mmcif;chemical/x-pdb;application/x-amsa+txt;application/x-jalview-annotations+text;application/x-jalview-biojson+json;application/x-blc+txt;application/x-clustal+txt;application/x-fasta+txt;application/x-jalview-features+text;application/x-gff2+txt;application/x-gff3+txt;application/x-jalview-jnet+text;application/x-msf+txt;application/x-pfam+txt;application/x-phylip+txt;application/x-pileup+txt;application/x-pir+txt;application/rnaml+xml;application/x-jalview-scorematrix+text;application/x-stockholm+txt
diff --git a/utils/debian/file_associations_template-mailcap.txt b/utils/debian/file_associations_template-mailcap.txt
new file mode 100644
index 0000000..9a96e97
--- /dev/null
+++ b/utils/debian/file_associations_template-mailcap.txt
@@ -0,0 +1 @@
+$$MIMETYPE$$; jalview -open '%s'; description="$$NAME$$ File"; nametemplate=%s.$$EXTENSION$$; test=test -n "$DISPLAY"; priority=$$PRIORITY$$
diff --git a/utils/debian/file_associations_template-shared-mime-info.xml b/utils/debian/file_associations_template-shared-mime-info.xml
new file mode 100644
index 0000000..5136d0b
--- /dev/null
+++ b/utils/debian/file_associations_template-shared-mime-info.xml
@@ -0,0 +1,6 @@
+  <mime-type type="$$MIMETYPE$$">
+    <comment>$$NAME$$ File</comment>
+    <icon name="$$ICONFILE$$"/>
+$$    <glob pattern="*.EXTENSIONS" weight="$$PRIORITY$$0"/>
+$$  </mime-type>
+
diff --git a/utils/debian/mime_types_for_debian.pl b/utils/debian/mime_types_for_debian.pl
new file mode 100755
index 0000000..56fc037
--- /dev/null
+++ b/utils/debian/mime_types_for_debian.pl
@@ -0,0 +1,249 @@
+#!/usr/bin/env perl
+
+use strict;
+
+my $fileformats = $ARGV[0];
+$fileformats = "../../src/jalview/io/FileFormat.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-mmcif",
+  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"]},
+  mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
+  mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
+  #jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jalview-launch"},
+  jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
+  scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
+};
+my $add_extensions = {
+  blc => ["blc"],
+};
+my @put_first = qw(jalview jvl);
+
+my @non_primary = qw(mmcif mmcif2 pdb);
+
+my $mailcaptemplatefile = "file_associations_template-mailcap.txt";
+my $mailcaptemplate;
+my $sharedmimeinfotemplatefile = "file_associations_template-shared-mime-info.xml";
+my $sharedmimeinfotemplate;
+
+open(SMT,"<$sharedmimeinfotemplatefile") or die("Could not open '$sharedmimeinfotemplatefile' for reading");
+while(<SMT>){
+  $sharedmimeinfotemplate .= $_;
+}
+close(SMT);
+open(MCT,"<$mailcaptemplatefile") or die("Could not open '$mailcaptemplatefile' for reading");
+while(<MCT>){
+  $mailcaptemplate .= $_;
+}
+close(MCT);
+my $sharedmimeinfoauto;
+my $mailcapauto;
+
+# this file should go in /usr/share/mime/packages
+my $sharedmimeinfoautofile = "debian/jalview-mime.xml";
+
+# this file should go in /usr/lib/mime/packages
+my $mailcapautofile = "debian/jalview-mailcap";
+
+# this should be part of the jalview.desktop file that goes in /usr/shares/applications
+my $desktopfile = "debian/jalview.desktop";
+
+my $MimeType = "";
+
+for my $key (sort keys %$add_associations) {
+  my $a = $add_associations->{$key};
+  warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
+}
+
+open(SMI,">$sharedmimeinfoautofile") or die ("Could not open '$sharedmimeinfoautofile' for writing");
+
+open(MCA,">$mailcapautofile") or die ("Could not open '$mailcapautofile' 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;
+    $extensions =~ s/\s+//g;
+    my @possextensions = map(lc($_),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);
+    }
+    next unless scalar(@extensions);
+    $file_associations->{$shortname} = {
+      shortname => $shortname,
+      name => $name,
+      extensions => \@extensions
+    };
+    warn("Reading file association for $shortname (".join(",",@extensions).")\n");
+  }
+}
+close(IN);
+
+my %all_associations = (%$file_associations, %$add_associations);
+
+my @ordered = (@put_first, @non_primary);
+for my $key (sort keys %all_associations) {
+  next if grep($_ eq $key, @ordered);
+  push(@ordered, $key);
+}
+my $num = $#ordered + 1;
+
+warn("--\n");
+print SMI qq(<?xml version="1.0" encoding="UTF-8"?>\n<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">\n\n);
+
+my $mailcapcount = 0;
+for my $shortname (@ordered) {
+  my $a = $all_associations{$shortname};
+  next if (ref($a) ne "HASH");
+
+  my $name = $a->{name};
+  my $extensions = $a->{extensions};
+  my $mimetype = $mimetypes->{$shortname};
+  $mimetype = "application/x-$shortname+txt" unless $mimetype;
+
+  $MimeType .= $MimeType?";":"";
+  $MimeType .= $mimetype;
+
+  my $iconfile = $a->{iconfile};
+  $iconfile = "jalview-file" unless $iconfile;
+
+  my $primary = (! grep($_ eq $shortname, @non_primary));
+  my $primarystring = $primary?"true":"false";
+  my $role = $primary?"Editor":"Viewer";
+  my $priority = $primary?9:4;
+  $priority = 10 if $mimetype =~ m/\bjalview\b/;
+
+  my @extensions = @$extensions;
+  my $extension0 = $extensions[0];
+
+  my $xname = xml_escape($name);
+  my $xmimetype = xml_escape($mimetype);
+  my $xshortname = xml_escape($shortname);
+  my $xiconfile = xml_escape($iconfile);
+  my $xrole = xml_escape($role);
+  my $xROLE = xml_escape(uc($role));
+  my $xprimarystring = xml_escape($primarystring);
+
+  my $sharedmimeinfoentry = $sharedmimeinfotemplate;
+  $sharedmimeinfoentry =~ s/\$\$NAME\$\$/$xname/g;
+  $sharedmimeinfoentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
+  $sharedmimeinfoentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
+  $sharedmimeinfoentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
+  $sharedmimeinfoentry =~ s/\$\$ROLE\$\$/$xrole/g;
+  $sharedmimeinfoentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+  $sharedmimeinfoentry =~ s/\$\$PRIORITY\$\$/$priority/g;
+  while ($sharedmimeinfoentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
+    my $pre = $1;
+    my $post = $2;
+    my $sharedmimeinfoextensions;
+    for my $ext (@extensions) {
+      my $xext = xml_escape($ext);
+      $sharedmimeinfoextensions .= $pre.$xext.$post;
+    }
+    my $prere = $pre;
+    $prere =~ s/([\*\.])/\\\1/g;
+    my $postre = $post;
+    $postre =~ s/([\*\.])/\\\1/g;
+    $sharedmimeinfoentry =~ s/\$\$${prere}EXTENSIONS${postre}\$\$/$sharedmimeinfoextensions/gs;
+  }
+  print SMI $sharedmimeinfoentry;
+
+  my $mailcapentry = $mailcaptemplate;
+  $mailcapentry =~ s/\$\$NAME\$\$/$xname/g;
+  $mailcapentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
+  $mailcapentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
+  $mailcapentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
+  $mailcapentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+  $mailcapentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
+  $mailcapentry =~ s/\$\$EXTENSION\$\$/$extension0/g;
+  $mailcapentry =~ s/\$\$PRIORITY\$\$/$priority/g;
+
+  my $ext = join(",",sort(@extensions));
+  my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
+  my $progresspercent = int(($mailcapcount/$num)*100);
+  $progresspercent = 100 if $progresspercent > 100;
+  $mailcapcount++;
+  my $xext = xml_escape($ext);
+  my $addunixextension = "true";
+
+  $mailcapentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
+  $mailcapentry =~ s/\$\$EXTENSION\$\$/$xext/g;
+  $mailcapentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
+  $mailcapentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
+  $mailcapentry =~ s/\$\$ID\$\$/$id/g;
+  $id++;
+  $mailcapentry =~ s/\$\$ID1\$\$/$id/g;
+  $id++;
+  $mailcapentry =~ s/\$\$ID2\$\$/$id/g;
+  $id++;
+
+  print MCA $mailcapentry;
+
+  delete $all_associations{$shortname};
+  warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
+}
+
+print SMI "</mime-info>\n";
+
+close(MCA);
+close(SMI);
+
+open(D,">$desktopfile") or die ("Could not open '$desktopfile' for writing");
+print D qq([Desktop Entry]
+Version=1.1
+Type=Application
+Name=Jalview
+Comment=Multiple Sequence Alignment Editor
+Icon=jalview-icon
+Type=Application
+TryExec=jalview
+Exec=jalview -open %u
+Terminal=false
+Categories=Science;Biology;
+Keywords=alignment;sequence;
+MimeType=${MimeType}
+);
+close(D);
+
+sub xml_escape {
+  my $x = shift;
+  # stolen from Pod::Simple::XMLOutStream in base distro
+  $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;
+  return $x;
+}