--- /dev/null
+<?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>
--- /dev/null
+#!/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;
+}
git://source.jalview.org / jalview.git / commitdiff
